Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.04

Sequence: scaffold867

Parameters: 2 7 7 80 10 50 500

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500

Length: 1160077
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.29

Warning! 150854 characters in sequence are not A, C, G, or T


File 2 of 4

Found at i:2738 original size:13 final size:13

Alignment explanation

Indices: 2720--2749 Score: 53 Period size: 13 Copynumber: 2.4 Consensus size: 13 2710 TTTTAAGGAG 2720 ACATTTAAGTGTT 1 ACATTTAAGTGTT 2733 ACATTTAAGTGTT 1 ACATTTAAGTGTT 2746 -CATT 1 ACATT 2750 GATTTACAAA Statistics Matches: 17, Mismatches: 0, Indels: 1 0.94 0.00 0.06 Matches are distributed among these distances: 12 4 0.24 13 13 0.76 ACGTcount: A:0.30, C:0.10, G:0.13, T:0.47 Consensus pattern (13 bp): ACATTTAAGTGTT Found at i:6789 original size:167 final size:166 Alignment explanation

Indices: 6485--6791 Score: 386 Period size: 167 Copynumber: 1.8 Consensus size: 166 6475 GGCGTGTGTC * 6485 TTTAAAAATCTTCTCAAGAACCACTGCACCAGAAATGCCAAAATTTACACAAAAGCTTGGACATG 1 TTTAAAAATCTTCTCAAGAACAACTGCACCAGAAATGCCAAAATTTACACAAAA----GGACATG * * * * * 6550 TATATAAAGTGAAGATTCTAAATTGTAAAAATCGTGACTCTCGGACCAAAACTGGGGTCCCAGGC 62 TATATAAAGTGAAGATTCTAAATTGTAAAAATCGTGACCCCCGGACAAAAACTGGAGCCCCAGGC 6615 AGGGTTCAAAGTTTAACATAGAAATGCATATGAAACATTA 127 AGGGTTCAAAGTTTAACATAGAAATGCATATGAAACATTA * * * * 6655 TTTAAAAATCTTCTTTCCAAGAACAACTGCACCAGAAATGCCAATATTTATATAAAA-GA-TTGT 1 TTTAAAAATCTTC--T-CAAGAACAACTGCACCAGAAATGCCAAAATTTACACAAAAGGACATGT * * * * * 6718 ATATATAGTGAAGATTCTAAATTGTTAAAATTGTGACCCCCGGACAAAAAGTGTAGCCCCAGG-A 63 ATATAAAGTGAAGATTCTAAATTGTAAAAATCGTGACCCCCGGACAAAAACTGGAGCCCCAGGCA 6782 GGGGTTCAAA 128 -GGGTTCAAA 6792 AATTAACACA Statistics Matches: 118, Mismatches: 15, Indels: 11 0.82 0.10 0.08 Matches are distributed among these distances: 166 1 0.01 167 65 0.55 168 2 0.02 170 13 0.11 172 1 0.01 173 36 0.31 ACGTcount: A:0.39, C:0.18, G:0.17, T:0.26 Consensus pattern (166 bp): TTTAAAAATCTTCTCAAGAACAACTGCACCAGAAATGCCAAAATTTACACAAAAGGACATGTATA TAAAGTGAAGATTCTAAATTGTAAAAATCGTGACCCCCGGACAAAAACTGGAGCCCCAGGCAGGG TTCAAAGTTTAACATAGAAATGCATATGAAACATTA Found at i:12174 original size:63 final size:63 Alignment explanation

Indices: 12098--12221 Score: 198 Period size: 63 Copynumber: 2.0 Consensus size: 63 12088 CCAACAATGG * 12098 TTCAAATGTTATTCCTCCACGCA-TCGTTCCAAAGAAACAGCATACTTTTGAT-TCAAAGGTTTT 1 TTCAAATGTTATTCCTCCACGCATTC-TTCCAAAGAAACAACATACTTTTGATAT-AAAGGTTTT * 12161 TTCAAATGTTATTCCTCCACGCATTCTTCCAAAGAAGCAACATACTTTTGATATAAAGGTT 1 TTCAAATGTTATTCCTCCACGCATTCTTCCAAAGAAACAACATACTTTTGATATAAAGGTT 12222 GCTAACAGAT Statistics Matches: 57, Mismatches: 2, Indels: 4 0.90 0.03 0.06 Matches are distributed among these distances: 63 54 0.95 64 3 0.05 ACGTcount: A:0.31, C:0.22, G:0.12, T:0.35 Consensus pattern (63 bp): TTCAAATGTTATTCCTCCACGCATTCTTCCAAAGAAACAACATACTTTTGATATAAAGGTTTT Found at i:19501 original size:2 final size:2 Alignment explanation

Indices: 19473--19537 Score: 100 Period size: 2 Copynumber: 34.0 Consensus size: 2 19463 CAGGTCATAT * 19473 GA GA GA AA GA GA -A GA GA -A GA G- GA GA GA GA GA GA GA GA GA 1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 19512 GA GA GA GA GA GA GA GA GA GA GA GA GA 1 GA GA GA GA GA GA GA GA GA GA GA GA GA 19538 ATATGAAATT Statistics Matches: 58, Mismatches: 2, Indels: 6 0.88 0.03 0.09 Matches are distributed among these distances: 1 3 0.05 2 55 0.95 ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00 Consensus pattern (2 bp): GA Found at i:19627 original size:15 final size:16 Alignment explanation

Indices: 19599--19679 Score: 87 Period size: 15 Copynumber: 5.1 Consensus size: 16 19589 AGGTCAAATG 19599 AGAGAAAGAGAAGAGA 1 AGAGAAAGAGAAGAGA 19615 AGAGAAA-AGAAGAGA 1 AGAGAAAGAGAAGAGA * 19630 AGAGAGAGAG-AGAG- 1 AGAGAAAGAGAAGAGA * 19644 AGAGAGAGAGAGAGAGA 1 AGAGAAAGAGA-AGAGA * 19661 GAGAGAGAGAGAGAGAGA 1 -AGAGAAAGAGA-AGAGA 19679 A 1 A 19680 TATGAAATTC Statistics Matches: 59, Mismatches: 1, Indels: 9 0.86 0.01 0.13 Matches are distributed among these distances: 14 10 0.17 15 18 0.31 16 13 0.22 17 1 0.02 18 17 0.29 ACGTcount: A:0.57, C:0.00, G:0.43, T:0.00 Consensus pattern (16 bp): AGAGAAAGAGAAGAGA Found at i:19637 original size:2 final size:2 Alignment explanation

Indices: 19598--19678 Score: 109 Period size: 2 Copynumber: 43.0 Consensus size: 2 19588 CAGGTCAAAT * * 19598 GA GA GA AA GA GA -A GA GA -A GA GA -A AA GA -A GA GA -A GA GA 1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 19635 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 19677 GA 1 GA 19679 ATATGAAATT Statistics Matches: 71, Mismatches: 3, Indels: 10 0.85 0.04 0.12 Matches are distributed among these distances: 1 5 0.07 2 66 0.93 ACGTcount: A:0.56, C:0.00, G:0.44, T:0.00 Consensus pattern (2 bp): GA Found at i:22393 original size:18 final size:18 Alignment explanation

Indices: 22370--22424 Score: 60 Period size: 16 Copynumber: 3.1 Consensus size: 18 22360 ACCCCCCCCC 22370 CCCAAAAAAAAAAAACAA 1 CCCAAAAAAAAAAAACAA * 22388 CCC--AAAAAACAAACAA 1 CCCAAAAAAAAAAAACAA * * 22404 ACCAAAAAAAACAAAAAAA 1 CCCAAAAAAAA-AAAACAA 22423 CC 1 CC 22425 TCAAGAGTTA Statistics Matches: 29, Mismatches: 5, Indels: 5 0.74 0.13 0.13 Matches are distributed among these distances: 16 14 0.48 18 9 0.31 19 6 0.21 ACGTcount: A:0.75, C:0.25, G:0.00, T:0.00 Consensus pattern (18 bp): CCCAAAAAAAAAAAACAA Found at i:22396 original size:16 final size:16 Alignment explanation

Indices: 22375--22414 Score: 62 Period size: 16 Copynumber: 2.5 Consensus size: 16 22365 CCCCCCCCAA * 22375 AAAAAAAAAACAACCC 1 AAAAAAAAAACAAACC * 22391 AAAAAACAAACAAACC 1 AAAAAAAAAACAAACC 22407 AAAAAAAA 1 AAAAAAAA 22415 CAAAAAAACC Statistics Matches: 21, Mismatches: 3, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 16 21 1.00 ACGTcount: A:0.80, C:0.20, G:0.00, T:0.00 Consensus pattern (16 bp): AAAAAAAAAACAAACC Found at i:23395 original size:16 final size:15 Alignment explanation

Indices: 23370--23404 Score: 52 Period size: 16 Copynumber: 2.3 Consensus size: 15 23360 CCCCCCCCCC 23370 CAAAAAAAAAAAAAA 1 CAAAAAAAAAAAAAA * 23385 CAAAAACAAAAACAAA 1 CAAAAA-AAAAAAAAA 23401 CAAA 1 CAAA 23405 CCAAGAGATG Statistics Matches: 18, Mismatches: 1, Indels: 1 0.90 0.05 0.05 Matches are distributed among these distances: 15 6 0.33 16 12 0.67 ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00 Consensus pattern (15 bp): CAAAAAAAAAAAAAA Found at i:23788 original size:162 final size:157 Alignment explanation

Indices: 23450--23864 Score: 543 Period size: 162 Copynumber: 2.6 Consensus size: 157 23440 CTTGAAAACA * * * * 23450 TCTGCAAAGAAAATGAACGGAAACTACAAATAATAGAAAATTTTCTAAGTCCAAGGGGCATAAGT 1 TCTGCAAAGAAAATGAACGGAAACTGCAAATAATTGAAATTTTTCTACGTCCAAGGGGCATAAGT * * * * * 23515 CGAAAATTGCTCGAACGTACCCAAAATCAACTTTAACCTAGATATTATTATGATTAAGCTGTATA 66 CGAAAATTGCTAGAACGTACCCAAAATCAAATTTAACCTAGATATTATTATAATAAACCTGTATA * 23580 CCAAATTTCATTTCAATATGCACATCC 131 CCAAATTTCAATTCAATATGCACATCC * 23607 TCTGCAAAGAAAATGAACGGAAACTGCAAATAATTGGAATTTTTCTACGTCCAAGGGGCATAAGT 1 TCTGCAAAGAAAATGAACGGAAACTGCAAATAATTGAAATTTTTCTACGTCCAAGGGGCATAA-- * * * 23672 CTGTCGAAAATTGCTAGATCGTACCCAGAATCAAATTTGACCTAGATATTATTATAATAAAACCT 64 --GTCGAAAATTGCTAGAACGTACCCAAAATCAAATTTAACCTAGATATTATTATAAT-AAACCT * 23737 GTATACCAAATTTCAATTCAATATGCGCATCC 126 GTATACCAAATTTCAATTCAATATGCACATCC ** * * * 23769 TCTGCAAAGAAAATGAACGGAAACTGCAAATAATTTTAATTTTTCTACCTCTAA--GTC-T--GT 1 TCTGCAAAGAAAATGAACGGAAACTGCAAATAATTGAAATTTTTCTACGTCCAAGGGGCATAAGT * * * 23829 CGAAAATTGCTCGAACGTACCCAAACTCAAACTTAA 66 CGAAAATTGCTAGAACGTACCCAAAATCAAATTTAA 23865 GGTAGTCCTA Statistics Matches: 227, Mismatches: 26, Indels: 14 0.85 0.10 0.05 Matches are distributed among these distances: 153 32 0.14 157 58 0.26 159 1 0.00 160 2 0.01 161 50 0.22 162 84 0.37 ACGTcount: A:0.39, C:0.19, G:0.14, T:0.28 Consensus pattern (157 bp): TCTGCAAAGAAAATGAACGGAAACTGCAAATAATTGAAATTTTTCTACGTCCAAGGGGCATAAGT CGAAAATTGCTAGAACGTACCCAAAATCAAATTTAACCTAGATATTATTATAATAAACCTGTATA CCAAATTTCAATTCAATATGCACATCC Found at i:25095 original size:16 final size:16 Alignment explanation

Indices: 25074--25105 Score: 64 Period size: 16 Copynumber: 2.0 Consensus size: 16 25064 GTTGGTGAAA 25074 CGACCGACCGACAGAC 1 CGACCGACCGACAGAC 25090 CGACCGACCGACAGAC 1 CGACCGACCGACAGAC 25106 AGCAGCAAAG Statistics Matches: 16, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 16 16 1.00 ACGTcount: A:0.31, C:0.44, G:0.25, T:0.00 Consensus pattern (16 bp): CGACCGACCGACAGAC Found at i:33399 original size:18 final size:18 Alignment explanation

Indices: 33376--33417 Score: 66 Period size: 18 Copynumber: 2.3 Consensus size: 18 33366 CCAACTGATG * 33376 TATTATTACTATCACTAT 1 TATTATTAATATCACTAT * 33394 TATTATTAATATTACTAT 1 TATTATTAATATCACTAT 33412 TATTAT 1 TATTAT 33418 CATTATTATC Statistics Matches: 22, Mismatches: 2, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 18 22 1.00 ACGTcount: A:0.36, C:0.10, G:0.00, T:0.55 Consensus pattern (18 bp): TATTATTAATATCACTAT Found at i:33400 original size:6 final size:6 Alignment explanation

Indices: 33376--33435 Score: 57 Period size: 6 Copynumber: 10.0 Consensus size: 6 33366 CCAACTGATG * * * * * * 33376 TATTAT TACTAT CACTAT TATTAT TAATAT TACTAT TATTAT CATTAT 1 TATTAT TATTAT TATTAT TATTAT TATTAT TATTAT TATTAT TATTAT * 33424 TATCAT TATTAT 1 TATTAT TATTAT 33436 AATCATTTGA Statistics Matches: 43, Mismatches: 11, Indels: 0 0.80 0.20 0.00 Matches are distributed among these distances: 6 43 1.00 ACGTcount: A:0.35, C:0.10, G:0.00, T:0.55 Consensus pattern (6 bp): TATTAT Found at i:44738 original size:14 final size:14 Alignment explanation

Indices: 44719--44747 Score: 58 Period size: 14 Copynumber: 2.1 Consensus size: 14 44709 TTTATGCAAT 44719 GTGCACAAAGAACA 1 GTGCACAAAGAACA 44733 GTGCACAAAGAACA 1 GTGCACAAAGAACA 44747 G 1 G 44748 AACAATCTAA Statistics Matches: 15, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 14 15 1.00 ACGTcount: A:0.48, C:0.21, G:0.24, T:0.07 Consensus pattern (14 bp): GTGCACAAAGAACA Found at i:55105 original size:396 final size:398 Alignment explanation

Indices: 54415--55204 Score: 1110 Period size: 396 Copynumber: 2.0 Consensus size: 398 54405 GTCTAAACTC * * * 54415 TTTTATTTTGTAGATCTTTGCTGAGGGGTATTTTGTAATAGGTTATAGAAGCGGAAATGTTTATC 1 TTTTATTTTGTAGATCATTACTGAGGGGTATTTTGTAATAGGTTATAGAAGCGAAAATGTTTATC * * * * 54480 TAATAGTTATGTACCCATACAATATAACGACTCTCTCATGTGTGGCGTATTTCGGGGTTTTAAGG 66 TAATAGTTATGTACCCATACAATATAAAGACTCTCTCATGTGTGACGTATTTAGAGGTTTTAAGG * ** * 54545 GGCCAGAAGTTCAAAACTTTAATCATATATATCTAGTAAAGGAAAAATATTTTGATGAGCATTTA 131 GGCCAGAAATTCAAAACTTTAATCATATATATCTAGTAAAGGAAAAATATTTTGACAAGCATATA * 54610 AGAAAAAAAAAGATGCTCAAAATGATGTACTCAACAATATTCAACCCTAAAATTTCATTAAAGGG 196 AGAAAAAAAAAGATGCTCAAAATGATGTACTCAACAATATTCAACCCTAAAATTTCATTAAACGG * * * * ** 54675 TCCCGATAAGGAGATAAGGTGGCGGCCCCTAAAATCTTCTTTCTTGGATATCTTAAAAACGATTA 261 CCCCAATAAGGAGATAAGGTGGCGGCCCCTAAAATCGTCTTTCTTGGATATCTCAAAAACGAAAA 54740 CAAATTTGTAAACACTTGTTGTAA-AAAATGTGTGTAGTTCAAAGTCACCTTTCATTTAATACCA 326 CAAATTTGTAAACACTTGTTG-AACAAAATGTGTGTAGTTCAAAGTCACCTTTCATTTAATACCA 54804 AGAAAAGTA 390 AGAAAAGTA * 54813 TTTTA-TTTGTAGCTCATTACTGAGGGGTATTTTGTAATAGGTTATAGAAGC-AAAATGTTTATC 1 TTTTATTTTGTAGATCATTACTGAGGGGTATTTTGTAATAGGTTATAGAAGCGAAAATGTTTATC * * * * 54876 TAATAGTTATGTACCCATATAATTTAAAGACTTTCTCATGTGTGACGTATTTAGAGGTTTTTAGG 66 TAATAGTTATGTACCCATACAATATAAAGACTCTCTCATGTGTGACGTATTTAGAGGTTTTAAGG * * * * * 54941 GGGCAGAAAATAT-AAAATTTTAATCATCTTTATCTAGTAAAGGAAAACTATTTTGACAAGCAGT 131 GGCCAG-AAAT-TCAAAACTTTAATCATATATATCTAGTAAAGGAAAAATATTTTGACAAGCA-T * * * * * 55005 AT-AG-AAGAAAAA-ATGCTCTAAATGATGTACTCAACAATATTTATCCCTCAAAATTTCATTGA 193 ATAAGAAAAAAAAAGATGCTCAAAATGATGTACTCAACAATATTCAACCCT-AAAATTTCATTAA * * 55067 ACGGCCCCAATAAGGAGATAAGG-GGTTGGCCGCTAAAATCGTCTTTCTTGGATATCTCAAAAAC 257 ACGGCCCCAATAAGGAGATAAGGTGG-CGGCCCCTAAAATCGTCTTTCTTGGATATCTCAAAAAC * ** * * 55131 GAAAACAAATTTTTAAACACTTGTTGAACAAAATGTGTGTAGTTTTAGGTCACCTTTCATTTTAT 321 GAAAACAAATTTGTAAACACTTGTTGAACAAAATGTGTGTAGTTCAAAGTCACCTTTCATTTAAT 55196 ACCAAGAAA 386 ACCAAGAAA 55205 TAGGGAATGG Statistics Matches: 346, Mismatches: 40, Indels: 14 0.87 0.10 0.04 Matches are distributed among these distances: 395 37 0.11 396 210 0.61 397 91 0.26 398 8 0.02 ACGTcount: A:0.35, C:0.14, G:0.17, T:0.34 Consensus pattern (398 bp): TTTTATTTTGTAGATCATTACTGAGGGGTATTTTGTAATAGGTTATAGAAGCGAAAATGTTTATC TAATAGTTATGTACCCATACAATATAAAGACTCTCTCATGTGTGACGTATTTAGAGGTTTTAAGG GGCCAGAAATTCAAAACTTTAATCATATATATCTAGTAAAGGAAAAATATTTTGACAAGCATATA AGAAAAAAAAAGATGCTCAAAATGATGTACTCAACAATATTCAACCCTAAAATTTCATTAAACGG CCCCAATAAGGAGATAAGGTGGCGGCCCCTAAAATCGTCTTTCTTGGATATCTCAAAAACGAAAA CAAATTTGTAAACACTTGTTGAACAAAATGTGTGTAGTTCAAAGTCACCTTTCATTTAATACCAA GAAAAGTA Found at i:55859 original size:38 final size:38 Alignment explanation

Indices: 55817--55895 Score: 149 Period size: 38 Copynumber: 2.1 Consensus size: 38 55807 GGAGATTTTT * 55817 TTTGTTGCATGCATTTGTAACTAATAATAGGTACAGTA 1 TTTGTTGCATGCATTTGTAACTAATAATAGGCACAGTA 55855 TTTGTTGCATGCATTTGTAACTAATAATAGGCACAGTA 1 TTTGTTGCATGCATTTGTAACTAATAATAGGCACAGTA 55893 TTT 1 TTT 55896 AACAATAATA Statistics Matches: 40, Mismatches: 1, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 38 40 1.00 ACGTcount: A:0.30, C:0.11, G:0.18, T:0.41 Consensus pattern (38 bp): TTTGTTGCATGCATTTGTAACTAATAATAGGCACAGTA Found at i:58069 original size:17 final size:18 Alignment explanation

Indices: 58020--58063 Score: 56 Period size: 17 Copynumber: 2.5 Consensus size: 18 58010 GATTTTACGT * 58020 CAACAATTTTGAG-CAGGC 1 CAAC-ATTTGGAGCCAGGC 58038 CAACATTTGGAGCCAGGC 1 CAACATTTGGAGCCAGGC 58056 CAA-ATTTG 1 CAACATTTG 58064 AGGCCAAAAG Statistics Matches: 24, Mismatches: 1, Indels: 3 0.86 0.04 0.11 Matches are distributed among these distances: 17 12 0.50 18 12 0.50 ACGTcount: A:0.32, C:0.23, G:0.23, T:0.23 Consensus pattern (18 bp): CAACATTTGGAGCCAGGC Found at i:61738 original size:8 final size:8 Alignment explanation

Indices: 61725--61774 Score: 57 Period size: 8 Copynumber: 6.4 Consensus size: 8 61715 TGAAAAGTGT 61725 ACAGACGG 1 ACAGACGG * 61733 ACAGACAG 1 ACAGACGG * * 61741 ACGGACAG 1 ACAGACGG * 61749 ACGGACGG 1 ACAGACGG 61757 ACAGACGG 1 ACAGACGG 61765 AC-GACGG 1 ACAGACGG 61772 ACA 1 ACA 61775 AAATGTGATC Statistics Matches: 37, Mismatches: 4, Indels: 2 0.86 0.09 0.05 Matches are distributed among these distances: 7 7 0.19 8 30 0.81 ACGTcount: A:0.38, C:0.26, G:0.36, T:0.00 Consensus pattern (8 bp): ACAGACGG Found at i:61742 original size:12 final size:12 Alignment explanation

Indices: 61725--61767 Score: 68 Period size: 12 Copynumber: 3.6 Consensus size: 12 61715 TGAAAAGTGT 61725 ACAGACGGACAG 1 ACAGACGGACAG 61737 ACAGACGGACAG 1 ACAGACGGACAG * 61749 ACGGACGGACAG 1 ACAGACGGACAG * 61761 ACGGACG 1 ACAGACG 61768 ACGGACAAAA Statistics Matches: 30, Mismatches: 1, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 12 30 1.00 ACGTcount: A:0.37, C:0.26, G:0.37, T:0.00 Consensus pattern (12 bp): ACAGACGGACAG Found at i:64274 original size:2 final size:2 Alignment explanation

Indices: 64267--64293 Score: 54 Period size: 2 Copynumber: 13.5 Consensus size: 2 64257 TGTTAAATAG 64267 TA TA TA TA TA TA TA TA TA TA TA TA TA T 1 TA TA TA TA TA TA TA TA TA TA TA TA TA T 64294 TAGAGAGAGA Statistics Matches: 25, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 25 1.00 ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52 Consensus pattern (2 bp): TA Found at i:64300 original size:2 final size:2 Alignment explanation

Indices: 64295--64334 Score: 80 Period size: 2 Copynumber: 20.0 Consensus size: 2 64285 TATATATATT 64295 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG 1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG 64335 TCGGATTACA Statistics Matches: 38, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 38 1.00 ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00 Consensus pattern (2 bp): AG Found at i:66123 original size:2 final size:2 Alignment explanation

Indices: 66098--66162 Score: 85 Period size: 2 Copynumber: 32.5 Consensus size: 2 66088 TTACTTATTT * * * * 66098 TC TC TC TT TC TC CC TG TC TG TC TC TC TC TC TC TC TC TC TC TC 1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC * 66140 TC TC TC TC TC TA TC TC TC TC TC T 1 TC TC TC TC TC TC TC TC TC TC TC T 66163 TGTATATTAA Statistics Matches: 53, Mismatches: 10, Indels: 0 0.84 0.16 0.00 Matches are distributed among these distances: 2 53 1.00 ACGTcount: A:0.02, C:0.45, G:0.03, T:0.51 Consensus pattern (2 bp): TC Found at i:76726 original size:31 final size:32 Alignment explanation

Indices: 76666--76726 Score: 79 Period size: 31 Copynumber: 1.9 Consensus size: 32 76656 ATCAGGAAGG * * 76666 TTTTGGTTAAGTCGTACTAAAAATCATTCGGA 1 TTTTGGTTAAGTCGTACCAAAAATAATTCGGA ** 76698 TTTT-GTTAAGTCGTACCAGGAATAATTCG 1 TTTTGGTTAAGTCGTACCAAAAATAATTCG 76727 ATTATTTTTA Statistics Matches: 25, Mismatches: 4, Indels: 1 0.83 0.13 0.03 Matches are distributed among these distances: 31 21 0.84 32 4 0.16 ACGTcount: A:0.30, C:0.13, G:0.20, T:0.38 Consensus pattern (32 bp): TTTTGGTTAAGTCGTACCAAAAATAATTCGGA Found at i:76855 original size:17 final size:17 Alignment explanation

Indices: 76833--76873 Score: 82 Period size: 17 Copynumber: 2.4 Consensus size: 17 76823 GACCCACTCG 76833 TTGCTCTGCAACGAGCT 1 TTGCTCTGCAACGAGCT 76850 TTGCTCTGCAACGAGCT 1 TTGCTCTGCAACGAGCT 76867 TTGCTCT 1 TTGCTCT 76874 AGTTTCTATT Statistics Matches: 24, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 17 24 1.00 ACGTcount: A:0.15, C:0.29, G:0.22, T:0.34 Consensus pattern (17 bp): TTGCTCTGCAACGAGCT Found at i:78952 original size:2 final size:2 Alignment explanation

Indices: 78945--79013 Score: 120 Period size: 2 Copynumber: 34.5 Consensus size: 2 78935 ATCCCAATAT * * 78945 GA GA GA GA GA GA GA GA GA GA GA AA GA AA GA GA GA GA GA GA GA 1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 78987 GA GA GA GA GA GA GA GA GA GA GA GA GA G 1 GA GA GA GA GA GA GA GA GA GA GA GA GA G 79014 CACCTTGCAA Statistics Matches: 63, Mismatches: 4, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 2 63 1.00 ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00 Consensus pattern (2 bp): GA Found at i:80523 original size:2 final size:2 Alignment explanation

Indices: 80516--80553 Score: 76 Period size: 2 Copynumber: 19.0 Consensus size: 2 80506 GTTAAAACAA 80516 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT 1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT 80554 NNNNNNNNNN Statistics Matches: 36, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 36 1.00 ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50 Consensus pattern (2 bp): AT Found at i:80742 original size:2 final size:2 Alignment explanation

Indices: 80735--80768 Score: 68 Period size: 2 Copynumber: 17.0 Consensus size: 2 80725 NNNNNNNNNN 80735 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA 1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA 80769 CACACAATAA Statistics Matches: 32, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 32 1.00 ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50 Consensus pattern (2 bp): TA Found at i:84017 original size:207 final size:209 Alignment explanation

Indices: 83675--84196 Score: 832 Period size: 207 Copynumber: 2.5 Consensus size: 209 83665 AAAATGATTT * * * 83675 TGATTCCATTACTTAGTAATAAAAGAACCATTACTTGGGAATAAAACAAGGAACTTTTATCTTCC 1 TGATTCCATTTCTTAGTAATAAAAAAAACATTACTTGGGAATAAAACAAGGAACTTTTATCTTCC 83740 TTATTTATATAGTATTATATCATACAACTATTGTAAGGTCGCCTGAGGTTTAATGATAGTAAAAT 66 TTATTTATATAGTATTATATCATACAACTATTGTAAGGTCGCCTGAGGTTTAATGATAGTAAAAT * * 83805 GTATTTTCTTGTACATTTGTAGTTTGTTAAACTTATAGAAAATTCAGT-GG-TTTTTTTTCGATT 131 GTATTTTCTTGTACATTTGTAGTTTGTTAAACTTAAAGAAAATTCAATGGGTTTTTTTTTCGATT 83868 TTGAAAAATA-ACTA 196 TTGAAAAA-AGACTA 83882 TGATTCCATTTCTTAGTAATAAAAAAAACATTACTTGGGAATAAAACAAGGAACTTTTATCTTCC 1 TGATTCCATTTCTTAGTAATAAAAAAAACATTACTTGGGAATAAAACAAGGAACTTTTATCTTCC * 83947 TTATTTATATCGTATTATATCATACAACTATTGTAAGGTCGCCTGAGGTTTAATGATAGTAAAAT 66 TTATTTATATAGTATTATATCATACAACTATTGTAAGGTCGCCTGAGGTTTAATGATAGTAAAAT 84012 GTATTTTCTTGTACATTTGTAGTTTGTTAAACTTAAAGAAAATTCAATGGGTTTTTTTTTTCGAT 131 GTATTTTCTTGTACATTTGTAGTTTGTTAAACTTAAAGAAAATTCAATGGG-TTTTTTTTTCGAT * 84077 TTTGAAAAAAGACTT 195 TTTGAAAAAAGACTA * * * * 84092 TGATTCCATTTCTTATTAAT-AAAAAAACATCACTTGGAAATAATACAAAGG-------ATCTTC 1 TGATTCCATTTCTTAGTAATAAAAAAAACATTACTTGGGAATAAAAC-AAGGAACTTTTATCTTC * 84149 CTTATTTATATAGTAATATATCATACAACTATTGTAAGGTCGCCTGAG 65 CTTATTTATATAGTATTATATCATACAACTATTGTAAGGTCGCCTGAG 84197 ATCGATTAAA Statistics Matches: 297, Mismatches: 13, Indels: 14 0.92 0.04 0.04 Matches are distributed among these distances: 203 52 0.18 207 172 0.58 208 2 0.01 209 24 0.08 210 47 0.16 ACGTcount: A:0.35, C:0.12, G:0.13, T:0.40 Consensus pattern (209 bp): TGATTCCATTTCTTAGTAATAAAAAAAACATTACTTGGGAATAAAACAAGGAACTTTTATCTTCC TTATTTATATAGTATTATATCATACAACTATTGTAAGGTCGCCTGAGGTTTAATGATAGTAAAAT GTATTTTCTTGTACATTTGTAGTTTGTTAAACTTAAAGAAAATTCAATGGGTTTTTTTTTCGATT TTGAAAAAAGACTA Found at i:87467 original size:35 final size:35 Alignment explanation

Indices: 87421--87687 Score: 369 Period size: 35 Copynumber: 7.6 Consensus size: 35 87411 ACTGTCCATA * * * 87421 AAATTAAACTGTATTTATACTATAAATTATACATG 1 AAATTCAACTGTATATATACTATAAATTCTACATG * 87456 AAATTCAACTGTATATATAC-AGTAAATTCTGCATG 1 AAATTCAACTGTATATATACTA-TAAATTCTACATG 87491 AAATTCAACTGTATATATAC-AGTAAATTCTACATG 1 AAATTCAACTGTATATATACTA-TAAATTCTACATG 87526 AAATTCAACTGTATATATACTATAAATTCTACATG 1 AAATTCAACTGTATATATACTATAAATTCTACATG * * * 87561 AAATTCAATTGTATACATACAATAAACTT-TACATG 1 AAATTCAACTGTATATATACTATAAA-TTCTACATG * 87596 AAATTCAACTGTATATATACTATAAATTCTATATG 1 AAATTCAACTGTATATATACTATAAATTCTACATG * * * * 87631 AAATTCAATTGTATACATACAATAAATTTTACATG 1 AAATTCAACTGTATATATACTATAAATTCTACATG * 87666 AAATTCAACTGTATTTATACTA 1 AAATTCAACTGTATATATACTA 87688 AAACTTTAAT Statistics Matches: 207, Mismatches: 21, Indels: 8 0.88 0.09 0.03 Matches are distributed among these distances: 34 3 0.01 35 201 0.97 36 3 0.01 ACGTcount: A:0.43, C:0.13, G:0.07, T:0.37 Consensus pattern (35 bp): AAATTCAACTGTATATATACTATAAATTCTACATG Found at i:90532 original size:11 final size:11 Alignment explanation

Indices: 90502--90533 Score: 55 Period size: 11 Copynumber: 2.9 Consensus size: 11 90492 TAAAGACGAT * 90502 CTTTAAGCCAC 1 CTTTAAGCTAC 90513 CTTTAAGCTAC 1 CTTTAAGCTAC 90524 CTTTAAGCTA 1 CTTTAAGCTA 90534 TAAGTATTGC Statistics Matches: 20, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 11 20 1.00 ACGTcount: A:0.28, C:0.28, G:0.09, T:0.34 Consensus pattern (11 bp): CTTTAAGCTAC Found at i:90592 original size:22 final size:22 Alignment explanation

Indices: 90542--90594 Score: 70 Period size: 22 Copynumber: 2.4 Consensus size: 22 90532 TATAAGTATT * 90542 GCTTAAAGGTGGCTTAAAGAAA 1 GCTTAAAGATGGCTTAAAGAAA * ** 90564 GCGTAAAGATGGCTTAAAGGCA 1 GCTTAAAGATGGCTTAAAGAAA 90586 GCTTAAAGA 1 GCTTAAAGA 90595 CTATCTTTAA Statistics Matches: 26, Mismatches: 5, Indels: 0 0.84 0.16 0.00 Matches are distributed among these distances: 22 26 1.00 ACGTcount: A:0.40, C:0.11, G:0.28, T:0.21 Consensus pattern (22 bp): GCTTAAAGATGGCTTAAAGAAA Found at i:90615 original size:11 final size:11 Alignment explanation

Indices: 90599--90627 Score: 58 Period size: 11 Copynumber: 2.6 Consensus size: 11 90589 TAAAGACTAT 90599 CTTTAAGCCAC 1 CTTTAAGCCAC 90610 CTTTAAGCCAC 1 CTTTAAGCCAC 90621 CTTTAAG 1 CTTTAAG 90628 GACAACTTAT Statistics Matches: 18, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 11 18 1.00 ACGTcount: A:0.28, C:0.31, G:0.10, T:0.31 Consensus pattern (11 bp): CTTTAAGCCAC Found at i:90707 original size:10 final size:11 Alignment explanation

Indices: 90659--90708 Score: 84 Period size: 11 Copynumber: 4.6 Consensus size: 11 90649 GTCCAAACTT 90659 CTTTAAGCCAC 1 CTTTAAGCCAC 90670 CTTTAAGCCAC 1 CTTTAAGCCAC 90681 CTTTAAGCCAC 1 CTTTAAGCCAC * 90692 CTTTAAG-CAT 1 CTTTAAGCCAC 90702 CTTTAAG 1 CTTTAAG 90709 TGGCATTTAC Statistics Matches: 38, Mismatches: 1, Indels: 1 0.95 0.03 0.03 Matches are distributed among these distances: 10 9 0.24 11 29 0.76 ACGTcount: A:0.28, C:0.30, G:0.10, T:0.32 Consensus pattern (11 bp): CTTTAAGCCAC Found at i:90758 original size:22 final size:22 Alignment explanation

Indices: 90701--90761 Score: 70 Period size: 22 Copynumber: 2.8 Consensus size: 22 90691 CCTTTAAGCA * * 90701 TCTTTAAGTGGCATTTACGCTC 1 TCTTTAAGTGGCCTTTACACTC * * 90723 TCTTTACACT-GCCTTTACACTG 1 TCTTTA-AGTGGCCTTTACACTC 90745 TCTTTAAGTGGCCTTTA 1 TCTTTAAGTGGCCTTTA 90762 AGTCAATATT Statistics Matches: 32, Mismatches: 5, Indels: 4 0.78 0.12 0.10 Matches are distributed among these distances: 21 2 0.06 22 28 0.88 23 2 0.06 ACGTcount: A:0.18, C:0.25, G:0.15, T:0.43 Consensus pattern (22 bp): TCTTTAAGTGGCCTTTACACTC Found at i:91093 original size:2 final size:2 Alignment explanation

Indices: 91088--91117 Score: 60 Period size: 2 Copynumber: 15.0 Consensus size: 2 91078 GTGAAAAAAA 91088 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 91118 AGTTCATCCG Statistics Matches: 28, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 28 1.00 ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50 Consensus pattern (2 bp): TC Found at i:91529 original size:112 final size:112 Alignment explanation

Indices: 91332--91554 Score: 419 Period size: 112 Copynumber: 2.0 Consensus size: 112 91322 AGTTTTGTTC * 91332 GTTTGTGTATATCTAATTAGAGTCTATTGTTTGTACAACTTAAGAAAACCCCTGGAACTAACACA 1 GTTTGTGTATATCTAATTAAAGTCTATTGTTTGTACAACTTAAGAAAACCCCTGGAACTAACACA * 91397 GAATATACAAGATATACACAACAGTTGTGTCGTGTGCCCAGGTGCAT 66 GAATATACAAGATATACACAACAGGTGTGTCGTGTGCCCAGGTGCAT * 91444 GTTTGTGTATATCTAATTAAAGTCTATTGTTTGTCCAACTTAAGAAAACCCCTGGAACTAACACA 1 GTTTGTGTATATCTAATTAAAGTCTATTGTTTGTACAACTTAAGAAAACCCCTGGAACTAACACA 91509 GAATATACAAGATATACACAACAGGTGTGTCGTGTGCCCAGGTGCA 66 GAATATACAAGATATACACAACAGGTGTGTCGTGTGCCCAGGTGCA 91555 CGTCAGGGTT Statistics Matches: 108, Mismatches: 3, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 112 108 1.00 ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30 Consensus pattern (112 bp): GTTTGTGTATATCTAATTAAAGTCTATTGTTTGTACAACTTAAGAAAACCCCTGGAACTAACACA GAATATACAAGATATACACAACAGGTGTGTCGTGTGCCCAGGTGCAT Found at i:98533 original size:30 final size:30 Alignment explanation

Indices: 98499--99053 Score: 770 Period size: 30 Copynumber: 18.8 Consensus size: 30 98489 TTTTTCAAGT ** * 98499 GAACCTCTGAACATTTACAATTATCAAAGA 1 GAACCTCTGAACACCTACCATTATCAAAGA * ** 98529 GAACCTCTGAACACTTACCATTATTTAAGA 1 GAACCTCTGAACACCTACCATTATCAAAGA * 98559 GAACCTCTGAACACCTACCATTATCTAAGA 1 GAACCTCTGAACACCTACCATTATCAAAGA * 98589 GAACCTCTGAGCACCTACCATTATCAAAGA 1 GAACCTCTGAACACCTACCATTATCAAAGA * * 98619 GAACCTCTGAGCACCTACCATTATCTAAGA 1 GAACCTCTGAACACCTACCATTATCAAAGA * 98649 GAACCTCTGAACACCTACCATTATCTAAGA 1 GAACCTCTGAACACCTACCATTATCAAAGA * 98679 GAACTTCTGAACACCTACCATTATCAAAGA 1 GAACCTCTGAACACCTACCATTATCAAAGA 98709 GAACCTCTGAACACCTACCATTATCAAAGA 1 GAACCTCTGAACACCTACCATTATCAAAGA * * * 98739 GAACCTCTGAACACTTATCATTATCAGAGA 1 GAACCTCTGAACACCTACCATTATCAAAGA * 98769 GAACCTCTGAACACTTACCATTATCAAAGA 1 GAACCTCTGAACACCTACCATTATCAAAGA * 98799 GAACCTCTGAACACTTACCATTAT------ 1 GAACCTCTGAACACCTACCATTATCAAAGA * * 98823 ----CTCTGAGCACCTACCATTATCTAAGA 1 GAACCTCTGAACACCTACCATTATCAAAGA * 98849 GAACCTCTGAACACCTACCATTATCTAAGA 1 GAACCTCTGAACACCTACCATTATCAAAGA * 98879 GAACTTCTGAACACCTACCATTATCAAAGA 1 GAACCTCTGAACACCTACCATTATCAAAGA 98909 GAACCTCTGAACACCTACCATTATCAAAGA 1 GAACCTCTGAACACCTACCATTATCAAAGA * * * 98939 GAACCTCTGAACACTTATCATTATCAGAGA 1 GAACCTCTGAACACCTACCATTATCAAAGA * 98969 GAACCTCTGAACACTTACCATTATCAAAGA 1 GAACCTCTGAACACCTACCATTATCAAAGA * ** 98999 GAACCTCTGAACACTTACCATTATTTAAGA 1 GAACCTCTGAACACCTACCATTATCAAAGA * * 99029 GAACCTCTGAACACTTACCTTTATC 1 GAACCTCTGAACACCTACCATTATC 99054 TATGTGAACT Statistics Matches: 482, Mismatches: 33, Indels: 20 0.90 0.06 0.04 Matches are distributed among these distances: 20 18 0.04 30 464 0.96 ACGTcount: A:0.37, C:0.27, G:0.11, T:0.25 Consensus pattern (30 bp): GAACCTCTGAACACCTACCATTATCAAAGA Found at i:98828 original size:20 final size:20 Alignment explanation

Indices: 98803--98844 Score: 66 Period size: 20 Copynumber: 2.1 Consensus size: 20 98793 CAAAGAGAAC * 98803 CTCTGAACACTTACCATTAT 1 CTCTGAACACCTACCATTAT * 98823 CTCTGAGCACCTACCATTAT 1 CTCTGAACACCTACCATTAT 98843 CT 1 CT 98845 AAGAGAACCT Statistics Matches: 20, Mismatches: 2, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 20 20 1.00 ACGTcount: A:0.26, C:0.33, G:0.07, T:0.33 Consensus pattern (20 bp): CTCTGAACACCTACCATTAT Found at i:98854 original size:20 final size:20 Alignment explanation

Indices: 98814--98854 Score: 55 Period size: 20 Copynumber: 2.0 Consensus size: 20 98804 TCTGAACACT ** * 98814 TACCATTATCTCTGAGCACC 1 TACCATTATCTAAGAGAACC 98834 TACCATTATCTAAGAGAACC 1 TACCATTATCTAAGAGAACC 98854 T 1 T 98855 CTGAACACCT Statistics Matches: 18, Mismatches: 3, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 20 18 1.00 ACGTcount: A:0.32, C:0.29, G:0.10, T:0.29 Consensus pattern (20 bp): TACCATTATCTAAGAGAACC Found at i:98942 original size:170 final size:170 Alignment explanation

Indices: 98653--98993 Score: 601 Period size: 170 Copynumber: 2.0 Consensus size: 170 98643 CTAAGAGAAC * 98653 CTCTGAACACCTACCATTATCTAAGAGAACTTCTGAACACCTACCATTATCAAAGAGAACCTCTG 1 CTCTGAACACCTACCATTATCTAAGAGAACCTCTGAACACCTACCATTATCAAAGAGAACCTCTG * * * 98718 AACACCTACCATTATCAAAGAGAACCTCTGAACACTTATCATTATCAGAGAGAACCTCTGAACAC 66 AACACCTACCATTATCAAAGAGAACCTCTGAACACCTACCATTATCAAAGAGAACCTCTGAACAC 98783 TTACCATTATCAAAGAGAACCTCTGAACACTTACCATTAT 131 TTACCATTATCAAAGAGAACCTCTGAACACTTACCATTAT * * * 98823 CTCTGAGCACCTACCATTATCTAAGAGAACCTCTGAACACCTACCATTATCTAAGAGAACTTCTG 1 CTCTGAACACCTACCATTATCTAAGAGAACCTCTGAACACCTACCATTATCAAAGAGAACCTCTG 98888 AACACCTACCATTATCAAAGAGAACCTCTGAACACCTACCATTATCAAAGAGAACCTCTGAACAC 66 AACACCTACCATTATCAAAGAGAACCTCTGAACACCTACCATTATCAAAGAGAACCTCTGAACAC * * 98953 TTATCATTATCAGAGAGAACCTCTGAACACTTACCATTAT 131 TTACCATTATCAAAGAGAACCTCTGAACACTTACCATTAT 98993 C 1 C 98994 AAAGAGAACC Statistics Matches: 162, Mismatches: 9, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 170 162 1.00 ACGTcount: A:0.37, C:0.28, G:0.10, T:0.25 Consensus pattern (170 bp): CTCTGAACACCTACCATTATCTAAGAGAACCTCTGAACACCTACCATTATCAAAGAGAACCTCTG AACACCTACCATTATCAAAGAGAACCTCTGAACACCTACCATTATCAAAGAGAACCTCTGAACAC TTACCATTATCAAAGAGAACCTCTGAACACTTACCATTAT Found at i:102505 original size:22 final size:23 Alignment explanation

Indices: 102480--102524 Score: 65 Period size: 24 Copynumber: 2.0 Consensus size: 23 102470 TGAAAGCTAA * 102480 TTTTTGG-TGGGATCGAGATTTT 1 TTTTTGGTTGGGATCAAGATTTT 102502 TTTTTGGTTTGGGATCAAGATTT 1 TTTTTGG-TTGGGATCAAGATTT 102525 CATCGGGATC Statistics Matches: 20, Mismatches: 1, Indels: 2 0.87 0.04 0.09 Matches are distributed among these distances: 22 7 0.35 24 13 0.65 ACGTcount: A:0.16, C:0.04, G:0.29, T:0.51 Consensus pattern (23 bp): TTTTTGGTTGGGATCAAGATTTT Found at i:102940 original size:30 final size:30 Alignment explanation

Indices: 102906--102967 Score: 124 Period size: 30 Copynumber: 2.1 Consensus size: 30 102896 CATATGAAAC 102906 TTTGTTTCCTTGGTATTAACTAAGATTAAA 1 TTTGTTTCCTTGGTATTAACTAAGATTAAA 102936 TTTGTTTCCTTGGTATTAACTAAGATTAAA 1 TTTGTTTCCTTGGTATTAACTAAGATTAAA 102966 TT 1 TT 102968 ATAAAAAGTT Statistics Matches: 32, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 30 32 1.00 ACGTcount: A:0.29, C:0.10, G:0.13, T:0.48 Consensus pattern (30 bp): TTTGTTTCCTTGGTATTAACTAAGATTAAA Found at i:104151 original size:208 final size:207 Alignment explanation

Indices: 103793--104208 Score: 814 Period size: 208 Copynumber: 2.0 Consensus size: 207 103783 GGTTGACTAT 103793 TGGACCTTCGATTTAATGAACCTTCTGGTTACTGGGCAGACCCCTTGTTCATCATTACGAAACAG 1 TGGACCTTCGATTTAATGAACCTTCTGGTTACTGGGCAGACCCCTTGTTCATCATTACGAAACAG * 103858 AAACGCGGAAGAAAAAATCTTGGATTTCTTGACCATAGTTGTTTTGCAGATATAATGTACTGATG 66 AAACGCGGAAGAAAAAATCGTGGATTTCTTGACCATAGTTGTTTTGCAGATATAATGTACTGATG 103923 TGTGTGAATCTAGACATCATGGAAAGTGAACCCCCAATAAACATGATAAACCTTTTATGCTCGGC 131 TGTGTGAATCTAGACATCATGGAAAGTGAACCCCCAATAAACATGATAAACCTTTTATGCTCGGC 103988 TTAAATTTTAGA 196 TTAAATTTTAGA 104000 NTGGACCTTCGATTTAATGAACCTTCTGGTTACTGGGCAGACCCCTTGTTCATCATTACGAAACA 1 -TGGACCTTCGATTTAATGAACCTTCTGGTTACTGGGCAGACCCCTTGTTCATCATTACGAAACA 104065 GAAACGCGGAAGAAAAAATCGTGGATTTCTTGACCATAGTTGTTTTGCAGATATAATGTACTGAT 65 GAAACGCGGAAGAAAAAATCGTGGATTTCTTGACCATAGTTGTTTTGCAGATATAATGTACTGAT 104130 GTGTGTGAATCTAGACATCATGGAAAGTGAACCCCCAATAAACATGATAAACCTTTTATGCTCGG 130 GTGTGTGAATCTAGACATCATGGAAAGTGAACCCCCAATAAACATGATAAACCTTTTATGCTCGG 104195 CTTAAATTTTAGA 195 CTTAAATTTTAGA 104208 T 1 T 104209 AAAAGCCTTC Statistics Matches: 207, Mismatches: 1, Indels: 1 0.99 0.00 0.00 Matches are distributed among these distances: 207 1 0.00 208 206 1.00 ACGTcount: A:0.31, C:0.18, G:0.19, T:0.31 Consensus pattern (207 bp): TGGACCTTCGATTTAATGAACCTTCTGGTTACTGGGCAGACCCCTTGTTCATCATTACGAAACAG AAACGCGGAAGAAAAAATCGTGGATTTCTTGACCATAGTTGTTTTGCAGATATAATGTACTGATG TGTGTGAATCTAGACATCATGGAAAGTGAACCCCCAATAAACATGATAAACCTTTTATGCTCGGC TTAAATTTTAGA Found at i:107344 original size:32 final size:31 Alignment explanation

Indices: 107273--107383 Score: 141 Period size: 31 Copynumber: 3.5 Consensus size: 31 107263 TTCAGGCAAA * 107273 GGGGTCATTTTTCTACGAAGAATAATGACCG 1 GGGGTCATTTTTCTACGTAGAATAATGACCG * 107304 GGGGTCATTTTTCTGCGTAGAATAATGACCGG 1 GGGGTCATTTTTCTACGTAGAATAATGACC-G * * * 107336 GGGGTCATTATTCTACGTAGAAAAATGACCC 1 GGGGTCATTTTTCTACGTAGAATAATGACCG ** * 107367 CCGGTCATTATTCTACG 1 GGGGTCATTTTTCTACG 107384 GGGGTCATTA Statistics Matches: 71, Mismatches: 8, Indels: 2 0.88 0.10 0.02 Matches are distributed among these distances: 31 43 0.61 32 28 0.39 ACGTcount: A:0.26, C:0.19, G:0.25, T:0.30 Consensus pattern (31 bp): GGGGTCATTTTTCTACGTAGAATAATGACCG Found at i:108189 original size:2 final size:2 Alignment explanation

Indices: 108182--108210 Score: 58 Period size: 2 Copynumber: 14.5 Consensus size: 2 108172 GCTAGGTGAT 108182 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G 1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G 108211 CCGATGTAAA Statistics Matches: 27, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 27 1.00 ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00 Consensus pattern (2 bp): GA Found at i:108406 original size:4 final size:4 Alignment explanation

Indices: 108399--108435 Score: 56 Period size: 4 Copynumber: 9.2 Consensus size: 4 108389 ACTCTCTCTG * * 108399 TGTC TGTC TGGC TGTC TGTC TGTC TGTC TCTC TGTC T 1 TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC T 108436 CTCTCTCTCT Statistics Matches: 29, Mismatches: 4, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 4 29 1.00 ACGTcount: A:0.00, C:0.27, G:0.24, T:0.49 Consensus pattern (4 bp): TGTC Found at i:108433 original size:12 final size:12 Alignment explanation

Indices: 108391--108457 Score: 57 Period size: 12 Copynumber: 5.6 Consensus size: 12 108381 ACTACAAAAC 108391 TCTCTCTG--TG 1 TCTCTCTGTCTG * * 108401 TCTGTCTGGCTG 1 TCTCTCTGTCTG * 108413 TCTGTCTGTCTG 1 TCTCTCTGTCTG * 108425 TCTCTCTGTCTCTC 1 TCTCTCTG--TCTG * 108439 TCTCTCTCTCTG 1 TCTCTCTGTCTG 108451 TCTCTCT 1 TCTCTCT 108458 CTCTCTCTCA Statistics Matches: 47, Mismatches: 6, Indels: 6 0.80 0.10 0.10 Matches are distributed among these distances: 10 7 0.15 12 30 0.64 14 10 0.21 ACGTcount: A:0.00, C:0.34, G:0.16, T:0.49 Consensus pattern (12 bp): TCTCTCTGTCTG Found at i:108436 original size:8 final size:8 Alignment explanation

Indices: 108393--108465 Score: 65 Period size: 8 Copynumber: 8.9 Consensus size: 8 108383 TACAAAACTC * 108393 TCTCTGTG 1 TCTCTCTG * 108401 TCTGTCTG 1 TCTCTCTG * * 108409 GCTGTCTG 1 TCTCTCTG * 108417 TCTGTCTG 1 TCTCTCTG 108425 TCTCTCTG 1 TCTCTCTG * 108433 TCTCTCTCTC 1 --TCTCTCTG 108443 TCTCTCTG 1 TCTCTCTG * 108451 TCTCTCTC 1 TCTCTCTG 108459 TCTCTCT 1 TCTCTCT 108466 CATATCGACA Statistics Matches: 55, Mismatches: 8, Indels: 4 0.82 0.12 0.06 Matches are distributed among these distances: 8 48 0.87 10 7 0.13 ACGTcount: A:0.00, C:0.36, G:0.15, T:0.49 Consensus pattern (8 bp): TCTCTCTG Found at i:108438 original size:2 final size:2 Alignment explanation

Indices: 108425--108466 Score: 66 Period size: 2 Copynumber: 21.0 Consensus size: 2 108415 TGTCTGTCTG * * 108425 TC TC TC TG TC TC TC TC TC TC TC TC TG TC TC TC TC TC TC TC TC 1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 108467 ATATCGACAA Statistics Matches: 36, Mismatches: 4, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 2 36 1.00 ACGTcount: A:0.00, C:0.45, G:0.05, T:0.50 Consensus pattern (2 bp): TC Found at i:108976 original size:7 final size:7 Alignment explanation

Indices: 108961--109027 Score: 64 Period size: 7 Copynumber: 9.6 Consensus size: 7 108951 TTTAGATATG 108961 GAATCTC 1 GAATCTC * 108968 GAATTTC 1 GAATCTC 108975 GAATCTC 1 GAATCTC 108982 GAATCTC 1 GAATCTC * 108989 -ATATTTC 1 GA-ATCTC 108996 GAATCTC 1 GAATCTC * * * 109003 GTATTTT 1 GAATCTC 109010 GAATCTC 1 GAATCTC * 109017 GAATCTT 1 GAATCTC 109024 GAAT 1 GAAT 109028 GATCCTTCTC Statistics Matches: 47, Mismatches: 11, Indels: 4 0.76 0.18 0.06 Matches are distributed among these distances: 6 1 0.02 7 45 0.96 8 1 0.02 ACGTcount: A:0.28, C:0.19, G:0.13, T:0.39 Consensus pattern (7 bp): GAATCTC Found at i:108986 original size:21 final size:21 Alignment explanation

Indices: 108961--109027 Score: 73 Period size: 21 Copynumber: 3.2 Consensus size: 21 108951 TTTAGATATG 108961 GAATCTCGAATTTCGAATCTC 1 GAATCTCGAATTTCGAATCTC 108982 GAATCTC-ATATTTCGAATCTC 1 GAATCTCGA-ATTTCGAATCTC * * * * * 109003 GTATTTTGAATCTCGAATCTT 1 GAATCTCGAATTTCGAATCTC 109024 GAAT 1 GAAT 109028 GATCCTTCTC Statistics Matches: 38, Mismatches: 6, Indels: 4 0.79 0.12 0.08 Matches are distributed among these distances: 20 1 0.03 21 36 0.95 22 1 0.03 ACGTcount: A:0.28, C:0.19, G:0.13, T:0.39 Consensus pattern (21 bp): GAATCTCGAATTTCGAATCTC Found at i:117510 original size:13 final size:13 Alignment explanation

Indices: 117492--117517 Score: 52 Period size: 13 Copynumber: 2.0 Consensus size: 13 117482 GACAGTTTTA 117492 AATAAAGTACCCG 1 AATAAAGTACCCG 117505 AATAAAGTACCCG 1 AATAAAGTACCCG 117518 TCAATATTTT Statistics Matches: 13, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 13 1.00 ACGTcount: A:0.46, C:0.23, G:0.15, T:0.15 Consensus pattern (13 bp): AATAAAGTACCCG Found at i:119457 original size:12 final size:12 Alignment explanation

Indices: 119430--119489 Score: 66 Period size: 12 Copynumber: 5.0 Consensus size: 12 119420 CCTCATCGGG * * 119430 TGTTGTTTTTTG 1 TGTTGTTCTTTC * * 119442 TGTTATTCTATC 1 TGTTGTTCTTTC * 119454 TGTTGTTTTTTC 1 TGTTGTTCTTTC 119466 TGTTGTTCTTTC 1 TGTTGTTCTTTC * 119478 TGTTGTTTTTTC 1 TGTTGTTCTTTC 119490 CGAAACTACA Statistics Matches: 39, Mismatches: 9, Indels: 0 0.81 0.19 0.00 Matches are distributed among these distances: 12 39 1.00 ACGTcount: A:0.03, C:0.10, G:0.17, T:0.70 Consensus pattern (12 bp): TGTTGTTCTTTC Found at i:119462 original size:24 final size:24 Alignment explanation

Indices: 119430--119489 Score: 93 Period size: 24 Copynumber: 2.5 Consensus size: 24 119420 CCTCATCGGG * 119430 TGTTGTTTTTTGTGTTATTCTATC 1 TGTTGTTTTTTCTGTTATTCTATC * * 119454 TGTTGTTTTTTCTGTTGTTCTTTC 1 TGTTGTTTTTTCTGTTATTCTATC 119478 TGTTGTTTTTTC 1 TGTTGTTTTTTC 119490 CGAAACTACA Statistics Matches: 33, Mismatches: 3, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 24 33 1.00 ACGTcount: A:0.03, C:0.10, G:0.17, T:0.70 Consensus pattern (24 bp): TGTTGTTTTTTCTGTTATTCTATC Found at i:119584 original size:2 final size:2 Alignment explanation

Indices: 119579--119612 Score: 68 Period size: 2 Copynumber: 17.0 Consensus size: 2 119569 AGAGAGAAAG 119579 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA 1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA 119613 GAGAGAGAGA Statistics Matches: 32, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 32 1.00 ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50 Consensus pattern (2 bp): TA Found at i:119617 original size:2 final size:2 Alignment explanation

Indices: 119612--119691 Score: 115 Period size: 2 Copynumber: 40.0 Consensus size: 2 119602 ATATATATAT 119612 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG 1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG * * * * * 119654 AN AT AT AT AC AG AG AG AG AG AG AG AG AG AG AG AG AG AG 1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG 119692 GGGATACATG Statistics Matches: 74, Mismatches: 4, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 2 74 1.00 ACGTcount: A:0.50, C:0.01, G:0.44, T:0.04 Consensus pattern (2 bp): AG Found at i:123700 original size:15 final size:15 Alignment explanation

Indices: 123680--123710 Score: 53 Period size: 15 Copynumber: 2.1 Consensus size: 15 123670 TGTTTGGATG * 123680 TTATTTGGATGAAGA 1 TTATTTGAATGAAGA 123695 TTATTTGAATGAAGA 1 TTATTTGAATGAAGA 123710 T 1 T 123711 GATTAAGAAT Statistics Matches: 15, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 15 15 1.00 ACGTcount: A:0.35, C:0.00, G:0.23, T:0.42 Consensus pattern (15 bp): TTATTTGAATGAAGA Found at i:132766 original size:2 final size:2 Alignment explanation

Indices: 132759--132814 Score: 112 Period size: 2 Copynumber: 28.0 Consensus size: 2 132749 GATGAGTTGG 132759 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 132801 GA GA GA GA GA GA GA 1 GA GA GA GA GA GA GA 132815 TTATCAAAAA Statistics Matches: 54, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 54 1.00 ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00 Consensus pattern (2 bp): GA Found at i:139300 original size:8 final size:8 Alignment explanation

Indices: 139272--139368 Score: 64 Period size: 8 Copynumber: 12.8 Consensus size: 8 139262 ACATATTGAC 139272 CCTTATAAT 1 CCTTAT-AT 139281 CC-T-TAT 1 CCTTATAT 139287 CCTTATAT 1 CCTTATAT 139295 -CTT-TAT 1 CCTTATAT 139301 CCTTATAT 1 CCTTATAT * 139309 CCTTATAA 1 CCTTATAT * 139317 CCTTATAA 1 CCTTATAT * * 139325 ACAT-TAT 1 CCTTATAT * 139332 CCTTATAA 1 CCTTATAT * 139340 CCTTATAAA 1 CCTTAT-AT 139349 CC-T-TAT 1 CCTTATAT * 139355 CCTTATAA 1 CCTTATAT 139363 CCTTAT 1 CCTTAT 139369 CCTTATAGAT Statistics Matches: 71, Mismatches: 9, Indels: 17 0.73 0.09 0.18 Matches are distributed among these distances: 6 10 0.14 7 14 0.20 8 41 0.58 9 6 0.08 ACGTcount: A:0.31, C:0.25, G:0.00, T:0.44 Consensus pattern (8 bp): CCTTATAT Found at i:139302 original size:14 final size:14 Alignment explanation

Indices: 139272--139338 Score: 62 Period size: 15 Copynumber: 4.5 Consensus size: 14 139262 ACATATTGAC * 139272 CCTTATAATCCTTAT 1 CCTTAT-ATCTTTAT 139287 CCTTATATCTTTAT 1 CCTTATATCTTTAT * 139301 CCTTATATCCTTATAA 1 CCTTATAT-CTT-TAT * * 139317 CCTTATAAACATTAT 1 CCTTAT-ATCTTTAT 139332 CCTTATA 1 CCTTATA 139339 ACCTTATAAA Statistics Matches: 44, Mismatches: 5, Indels: 7 0.79 0.09 0.12 Matches are distributed among these distances: 14 16 0.36 15 17 0.39 16 10 0.23 17 1 0.02 ACGTcount: A:0.30, C:0.24, G:0.00, T:0.46 Consensus pattern (14 bp): CCTTATATCTTTAT Found at i:139336 original size:23 final size:23 Alignment explanation

Indices: 139306--139368 Score: 117 Period size: 23 Copynumber: 2.7 Consensus size: 23 139296 TTTATCCTTA 139306 TATCCTTATAACCTTATAAACAT 1 TATCCTTATAACCTTATAAACAT * 139329 TATCCTTATAACCTTATAAACCT 1 TATCCTTATAACCTTATAAACAT 139352 TATCCTTATAACCTTAT 1 TATCCTTATAACCTTAT 139369 CCTTATAGAT Statistics Matches: 39, Mismatches: 1, Indels: 0 0.98 0.03 0.00 Matches are distributed among these distances: 23 39 1.00 ACGTcount: A:0.35, C:0.24, G:0.00, T:0.41 Consensus pattern (23 bp): TATCCTTATAACCTTATAAACAT Found at i:139364 original size:14 final size:14 Alignment explanation

Indices: 139272--139375 Score: 101 Period size: 14 Copynumber: 7.5 Consensus size: 14 139262 ACATATTGAC 139272 CCTTATAATCCTTAT 1 CCTTATAA-CCTTAT * * 139287 CCTTATATCTTTAT 1 CCTTATAACCTTAT * 139301 CCTTATATCCTTAT 1 CCTTATAACCTTAT * 139315 AACCTTATAAACATTAT 1 --CCTTAT-AACCTTAT 139332 CCTTATAACCTTA- 1 CCTTATAACCTTAT 139345 ---TA-AACCTTAT 1 CCTTATAACCTTAT 139355 CCTTATAACCTTAT 1 CCTTATAACCTTAT 139369 CCTTATA 1 CCTTATA 139376 GATGTTTTAT Statistics Matches: 75, Mismatches: 6, Indels: 17 0.77 0.06 0.17 Matches are distributed among these distances: 9 7 0.09 10 2 0.03 13 2 0.03 14 39 0.52 15 13 0.17 16 6 0.08 17 6 0.08 ACGTcount: A:0.31, C:0.25, G:0.00, T:0.44 Consensus pattern (14 bp): CCTTATAACCTTAT Found at i:151301 original size:3 final size:3 Alignment explanation

Indices: 151293--151348 Score: 112 Period size: 3 Copynumber: 18.7 Consensus size: 3 151283 GTCAAAACCG 151293 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA 1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA 151341 GAA GAA GA 1 GAA GAA GA 151349 CGACACATGG Statistics Matches: 53, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 3 53 1.00 ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00 Consensus pattern (3 bp): GAA Found at i:151946 original size:11 final size:11 Alignment explanation

Indices: 151930--151957 Score: 56 Period size: 11 Copynumber: 2.5 Consensus size: 11 151920 ATGGATAAAA 151930 AAAACTGTTTG 1 AAAACTGTTTG 151941 AAAACTGTTTG 1 AAAACTGTTTG 151952 AAAACT 1 AAAACT 151958 TATCTTGATA Statistics Matches: 17, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 11 17 1.00 ACGTcount: A:0.43, C:0.11, G:0.14, T:0.32 Consensus pattern (11 bp): AAAACTGTTTG Found at i:152662 original size:11 final size:11 Alignment explanation

Indices: 152632--152663 Score: 55 Period size: 11 Copynumber: 2.9 Consensus size: 11 152622 TAAAGACGAT * 152632 CTTTAAGCCAC 1 CTTTAAGCTAC 152643 CTTTAAGCTAC 1 CTTTAAGCTAC 152654 CTTTAAGCTA 1 CTTTAAGCTA 152664 TATGTATTGC Statistics Matches: 20, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 11 20 1.00 ACGTcount: A:0.28, C:0.28, G:0.09, T:0.34 Consensus pattern (11 bp): CTTTAAGCTAC Found at i:152722 original size:22 final size:22 Alignment explanation

Indices: 152672--152724 Score: 70 Period size: 22 Copynumber: 2.4 Consensus size: 22 152662 TATATGTATT * 152672 GCTTAAAGGTGGCTTAAAGAAA 1 GCTTAAAGATGGCTTAAAGAAA * ** 152694 GCGTAAAGATGGCTTAAAGGCA 1 GCTTAAAGATGGCTTAAAGAAA 152716 GCTTAAAGA 1 GCTTAAAGA 152725 CTATCTTTAA Statistics Matches: 26, Mismatches: 5, Indels: 0 0.84 0.16 0.00 Matches are distributed among these distances: 22 26 1.00 ACGTcount: A:0.40, C:0.11, G:0.28, T:0.21 Consensus pattern (22 bp): GCTTAAAGATGGCTTAAAGAAA Found at i:152805 original size:11 final size:11 Alignment explanation

Indices: 152789--152842 Score: 90 Period size: 11 Copynumber: 4.9 Consensus size: 11 152779 GTCCAAACTT 152789 CTTTAAGCCAC 1 CTTTAAGCCAC 152800 CTTTAAGCCAC 1 CTTTAAGCCAC * * 152811 ATTTAAGCTAC 1 CTTTAAGCCAC 152822 CTTTAAGCCAC 1 CTTTAAGCCAC 152833 CTTTAAGCCA 1 CTTTAAGCCA 152843 TTAAAAAAAA Statistics Matches: 39, Mismatches: 4, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 11 39 1.00 ACGTcount: A:0.30, C:0.31, G:0.09, T:0.30 Consensus pattern (11 bp): CTTTAAGCCAC Found at i:159679 original size:19 final size:17 Alignment explanation

Indices: 159655--159696 Score: 57 Period size: 17 Copynumber: 2.4 Consensus size: 17 159645 CATAGTCTTA 159655 TTTAAAAGTTAATATAATG 1 TTTAAAAGTT--TATAATG * 159674 TTTAAATGTTTATAATG 1 TTTAAAAGTTTATAATG 159691 TTTAAA 1 TTTAAA 159697 TTTTAGCAAT Statistics Matches: 22, Mismatches: 1, Indels: 2 0.88 0.04 0.08 Matches are distributed among these distances: 17 13 0.59 19 9 0.41 ACGTcount: A:0.43, C:0.00, G:0.10, T:0.48 Consensus pattern (17 bp): TTTAAAAGTTTATAATG Found at i:159689 original size:17 final size:16 Alignment explanation

Indices: 159667--159701 Score: 61 Period size: 17 Copynumber: 2.1 Consensus size: 16 159657 TAAAAGTTAA 159667 TATAATGTTTAAATGTT 1 TATAATGTTTAAAT-TT 159684 TATAATGTTTAAATTT 1 TATAATGTTTAAATTT 159700 TA 1 TA 159702 GCAATGTTCA Statistics Matches: 18, Mismatches: 0, Indels: 1 0.95 0.00 0.05 Matches are distributed among these distances: 16 4 0.22 17 14 0.78 ACGTcount: A:0.37, C:0.00, G:0.09, T:0.54 Consensus pattern (16 bp): TATAATGTTTAAATTT Found at i:159707 original size:17 final size:17 Alignment explanation

Indices: 159670--159709 Score: 55 Period size: 17 Copynumber: 2.4 Consensus size: 17 159660 AAGTTAATAT * 159670 AATGTTTAAATGTTTAT 1 AATGTTTAAATGTTTAC 159687 AATGTTTAAAT-TTTAGC 1 AATGTTTAAATGTTTA-C 159704 AATGTT 1 AATGTT 159710 CAATTATTGT Statistics Matches: 21, Mismatches: 1, Indels: 2 0.88 0.04 0.08 Matches are distributed among these distances: 16 4 0.19 17 17 0.81 ACGTcount: A:0.35, C:0.03, G:0.12, T:0.50 Consensus pattern (17 bp): AATGTTTAAATGTTTAC Found at i:163733 original size:4 final size:4 Alignment explanation

Indices: 163724--163770 Score: 60 Period size: 4 Copynumber: 11.8 Consensus size: 4 163714 ACTGAAGTGG * * 163724 GACA GACA GACA GACA GACA GACG GACG GACA GACA GA-A GGACA GAC 1 GACA GACA GACA GACA GACA GACA GACA GACA GACA GACA -GACA GAC 163771 GGACTGACGG Statistics Matches: 39, Mismatches: 2, Indels: 4 0.87 0.04 0.09 Matches are distributed among these distances: 3 1 0.03 4 37 0.95 5 1 0.03 ACGTcount: A:0.45, C:0.23, G:0.32, T:0.00 Consensus pattern (4 bp): GACA Found at i:163774 original size:8 final size:8 Alignment explanation

Indices: 163723--163782 Score: 66 Period size: 8 Copynumber: 7.5 Consensus size: 8 163713 AACTGAAGTG 163723 GGACAGAC 1 GGACAGAC * 163731 AGACAGAC 1 GGACAGAC * 163739 AGACAGAC 1 GGACAGAC * 163747 GGACGGAC 1 GGACAGAC * * 163755 AGACAGAA 1 GGACAGAC 163763 GGACAGAC 1 GGACAGAC * 163771 GGACTGAC 1 GGACAGAC 163779 GGAC 1 GGAC 163783 GCAGAGGAAA Statistics Matches: 43, Mismatches: 9, Indels: 0 0.83 0.17 0.00 Matches are distributed among these distances: 8 43 1.00 ACGTcount: A:0.40, C:0.23, G:0.35, T:0.02 Consensus pattern (8 bp): GGACAGAC Found at i:170572 original size:140 final size:140 Alignment explanation

Indices: 170235--170630 Score: 621 Period size: 140 Copynumber: 2.8 Consensus size: 140 170225 ATCTTAGAAA * * * 170235 GAAGTATTTGGCGCATTCTGATATTCGTCAGCACCAATGTTTTCATACGTTTCATGACCTGTATA 1 GAAGTATTTGGCGCATTCTGGTATTCCTCAGCATCAATGTTTTCATACGTTTCATGACCTGTATA 170300 ACTAGTTCTCGAAGTTTTACGGTCACTGTGGCTTGTTATATATGAAGATTGTTGATTATCTTTTT 66 ACTAGTTCTCGAAGTTTTACGGTCACTGTGGCTTG-T-TATAT----A-TGTTGATTATCTTTTT * 170365 CTGTACGCTCTCTCATC 124 CTGTACACTCTCTCATC * * 170382 GAAATGTTTGGCGCATTCTGGTATTCCTCAGCATCAATGTTTTCATACGTTTCATGACCTGTATA 1 GAAGTATTTGGCGCATTCTGGTATTCCTCAGCATCAATGTTTTCATACGTTTCATGACCTGTATA 170447 ACTAGTTCTCGAAGTTTTACGGTCACTGTGGCTTGTTATATATGTTGATTATCTTTTTCTGTACA 66 ACTAGTTCTCGAAGTTTTACGGTCACTGTGGCTTGTTATATATGTTGATTATCTTTTTCTGTACA * 170512 CTCTCTCATT 131 CTCTCTCATC * * 170522 GAAGTATTTGGCGCATTCTGGTATTCCTCAGCATCAATGCTTTCATACGTTTCAAGACCTGTATA 1 GAAGTATTTGGCGCATTCTGGTATTCCTCAGCATCAATGTTTTCATACGTTTCATGACCTGTATA * * * 170587 ACTAGTTCTCGAAGTATTACGGTGACTTTGGCTTGTTATATATG 66 ACTAGTTCTCGAAGTTTTACGGTCACTGTGGCTTGTTATATATG 170631 AAGATTGTTG Statistics Matches: 235, Mismatches: 14, Indels: 7 0.92 0.05 0.03 Matches are distributed among these distances: 140 133 0.57 141 1 0.00 145 5 0.02 146 1 0.00 147 95 0.40 ACGTcount: A:0.22, C:0.19, G:0.18, T:0.41 Consensus pattern (140 bp): GAAGTATTTGGCGCATTCTGGTATTCCTCAGCATCAATGTTTTCATACGTTTCATGACCTGTATA ACTAGTTCTCGAAGTTTTACGGTCACTGTGGCTTGTTATATATGTTGATTATCTTTTTCTGTACA CTCTCTCATC Found at i:171129 original size:2 final size:2 Alignment explanation

Indices: 171122--171151 Score: 60 Period size: 2 Copynumber: 15.0 Consensus size: 2 171112 NNNNNNNNNN 171122 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA 1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA 171152 CACACACACA Statistics Matches: 28, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 28 1.00 ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50 Consensus pattern (2 bp): TA Found at i:173005 original size:11 final size:12 Alignment explanation

Indices: 172979--173005 Score: 54 Period size: 12 Copynumber: 2.2 Consensus size: 12 172969 GTTCATTGAC 172979 TTTTATCTTTAT 1 TTTTATCTTTAT 172991 TTTTATCTTTAT 1 TTTTATCTTTAT 173003 TTT 1 TTT 173006 GTTTGAGCCA Statistics Matches: 15, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 12 15 1.00 ACGTcount: A:0.15, C:0.07, G:0.00, T:0.78 Consensus pattern (12 bp): TTTTATCTTTAT Found at i:181982 original size:2 final size:2 Alignment explanation

Indices: 181975--182019 Score: 90 Period size: 2 Copynumber: 22.5 Consensus size: 2 181965 AAACTGGTAA 181975 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 182017 TC T 1 TC T 182020 NNNNNNNNNN Statistics Matches: 43, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 43 1.00 ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51 Consensus pattern (2 bp): TC Found at i:185379 original size:2 final size:2 Alignment explanation

Indices: 185372--185410 Score: 69 Period size: 2 Copynumber: 19.5 Consensus size: 2 185362 AAGGCATGAA * 185372 AG AG AG AG AG AG AG AG AG AG AG TG AG AG AG AG AG AG AG A 1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A 185411 TTAATTACCA Statistics Matches: 35, Mismatches: 2, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 2 35 1.00 ACGTcount: A:0.49, C:0.00, G:0.49, T:0.03 Consensus pattern (2 bp): AG Found at i:193708 original size:24 final size:24 Alignment explanation

Indices: 193676--193754 Score: 131 Period size: 24 Copynumber: 3.3 Consensus size: 24 193666 CCTCATCGGG * * 193676 TGTTGTTTTTTCTATTTTTCTTTC 1 TGTTGTTTTTTCTGTTGTTCTTTC * 193700 TGTTGTTTTTTCTGTCGTTCTTTC 1 TGTTGTTTTTTCTGTTGTTCTTTC 193724 TGTTGTTTTTTCTGTTGTTCTTTC 1 TGTTGTTTTTTCTGTTGTTCTTTC 193748 TGTTGTT 1 TGTTGTT 193755 CCTTCTGTAA Statistics Matches: 51, Mismatches: 4, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 24 51 1.00 ACGTcount: A:0.01, C:0.13, G:0.15, T:0.71 Consensus pattern (24 bp): TGTTGTTTTTTCTGTTGTTCTTTC Found at i:193755 original size:12 final size:12 Alignment explanation

Indices: 193676--193762 Score: 111 Period size: 12 Copynumber: 7.2 Consensus size: 12 193666 CCTCATCGGG * 193676 TGTTGTTTTTTC 1 TGTTGTTCTTTC * * 193688 TATTTTTCTTTC 1 TGTTGTTCTTTC * 193700 TGTTGTTTTTTC 1 TGTTGTTCTTTC * 193712 TGTCGTTCTTTC 1 TGTTGTTCTTTC * 193724 TGTTGTTTTTTC 1 TGTTGTTCTTTC 193736 TGTTGTTCTTTC 1 TGTTGTTCTTTC * 193748 TGTTGTTCCTTC 1 TGTTGTTCTTTC 193760 TGT 1 TGT 193763 AACGACATTT Statistics Matches: 63, Mismatches: 12, Indels: 0 0.84 0.16 0.00 Matches are distributed among these distances: 12 63 1.00 ACGTcount: A:0.01, C:0.15, G:0.15, T:0.69 Consensus pattern (12 bp): TGTTGTTCTTTC Found at i:194666 original size:433 final size:432 Alignment explanation

Indices: 193927--194764 Score: 1324 Period size: 433 Copynumber: 1.9 Consensus size: 432 193917 TCAAAGGGTG * * * * 193927 ATATTTTGAAATATCTTACGATGTCCTACTACATCCATGAAAAAGTTTTTCTCTACCATACTAAA 1 ATATTTTAAAATATCTTAAGATGCCCTACTACATCCATGAAAAAGTTTTTCTCTACCACACTAAA * * 193992 CAAAAGAGATACAAAAACCAATTAATTAAGAGATTTCCAGATGACCTTGACCTTTGACCTTTATG 66 CAAAAGAGATACAAAAACCAATTAATTAAGAGATTTCCAGATGACCTTGACCTTTGAACTATATG * 194057 TCATTTTGTGCGGCCAAGGTAGACGCTTCCATCCCAAGTGGTCCGAAGTCTCTATGATAAGTAAT 131 TCATTTTGTGCGGCCAAGGTAGACGCTTCCATCCCAAGTGGTCCGAAGTCTCTATGATAAATAAT * 194122 AAAAAAGTTGGAAGTGGTTTTATAGAAATGTAAATACTTTCAGGGGCAATAACTACTAGAAGGGG 196 AAAAAAGTTGGAAGTGATTTTATAGAAATGTAAATACTTTCAGGGGCAATAACTACTAGAAGGGG * 194187 GGCTCAGATCCTTTCGGTATGAATAGATTGAAGAACCCTCTAAGTGTACTGAAGACATTGGTAAA 261 GGCTCAGATCCTTTCGGTATGAATAAATTGAAGAACCCTCTAAGTGTACTGAAGACATTGGTAAA * * 194252 AGTTTCAAGTTTCTATCTCTTATGGTTTCAGAGGAGTAGCCATAACAAGCTTTTCGTACAAAAGG 326 AGTTCCAAGTCTCTATCTCTTATGGTTTCAGAGGAGTAGCCATAACAAGCTTTTCGTACAAAA-G 194317 GGCAATAACTCTGTAACTATTTAAAAGAAGGAGCCAAGGGGAT 390 GGCAATAACTCTGTAACTATTTAAAAGAAGGAGCCAAGGGGAT * * * * * 194360 ATATTTTAAAATGTCTTAAGATGCCCTATTGCATCCATGAAAAAGTTTTTCTTTACTACACTAAA 1 ATATTTTAAAATATCTTAAGATGCCCTACTACATCCATGAAAAAGTTTTTCTCTACCACACTAAA ** 194425 CAAAAGAGAT-CTAAAAACTC-ATTAATTAAGAGATTTTGAGATGACCTTGACCTTTGAACTATA 66 CAAAAGAGATAC-AAAAAC-CAATTAATTAAGAGATTTCCAGATGACCTTGACCTTTGAACTATA ** * 194488 TGTCATTTTGTTTGGCCAAGGTAGACGCTTCCATCCCAAGTGGTCCGAAGTCTTTATGATAAATA 129 TGTCATTTTGTGCGGCCAAGGTAGACGCTTCCATCCCAAGTGGTCCGAAGTCTCTATGATAAATA * 194553 ATAAAAAAGTTGGAAGTGATTTTATGGAAAT-TCAAATACTTTCAGGGGCAATAACTGA-TAGAA 194 ATAAAAAAGTTGGAAGTGATTTTATAGAAATGT-AAATACTTTCAGGGGCAATAACT-ACTAGAA * * * * * 194616 GGGGGTCTCGGATCCTTTCGGTATTAGTAAATTGAAGAACCCTCTAAGTGTACTGGAGACATTGG 257 GGGGGGCTCAGATCCTTTCGGTATGAATAAATTGAAGAACCCTCTAAGTGTACTGAAGACATTGG * * * 194681 TAAAAGTTCCAAGTCTCTATCTCTTATGGTTTCAGAGGAGTTGCGATAACAAGCTTTTCGTACAC 322 TAAAAGTTCCAAGTCTCTATCTCTTATGGTTTCAGAGGAGTAGCCATAACAAGCTTTTCGTACAA * 194746 AAGGGCAATAACTTTGTAA 387 AAGGGCAATAACTCTGTAA 194765 GTTCTGGGAG Statistics Matches: 370, Mismatches: 31, Indels: 9 0.90 0.08 0.02 Matches are distributed among these distances: 432 18 0.05 433 350 0.95 434 2 0.01 ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31 Consensus pattern (432 bp): ATATTTTAAAATATCTTAAGATGCCCTACTACATCCATGAAAAAGTTTTTCTCTACCACACTAAA CAAAAGAGATACAAAAACCAATTAATTAAGAGATTTCCAGATGACCTTGACCTTTGAACTATATG TCATTTTGTGCGGCCAAGGTAGACGCTTCCATCCCAAGTGGTCCGAAGTCTCTATGATAAATAAT AAAAAAGTTGGAAGTGATTTTATAGAAATGTAAATACTTTCAGGGGCAATAACTACTAGAAGGGG GGCTCAGATCCTTTCGGTATGAATAAATTGAAGAACCCTCTAAGTGTACTGAAGACATTGGTAAA AGTTCCAAGTCTCTATCTCTTATGGTTTCAGAGGAGTAGCCATAACAAGCTTTTCGTACAAAAGG GCAATAACTCTGTAACTATTTAAAAGAAGGAGCCAAGGGGAT Found at i:195823 original size:433 final size:432 Alignment explanation

Indices: 195225--196216 Score: 1408 Period size: 433 Copynumber: 2.3 Consensus size: 432 195215 TTGGACCCTG * * * * * 195225 TCGGTATGAATAGATTGAAGAAGCGTCTAAGTATACTGAATACATTAGTAAAAGTTTCAAGTCTC 1 TCGGTATGAATAGATTGAAGAACCATCTAAGTGTACTGAAGACATTGGTAAAAGTTTCAAGTCTC * * * * 195290 TATCTCTAACGG-TTAATGAGGAGTAGCGATAACAAGCATTTTGTACAATAGGGGCAATAACTCT 66 TATCTCTTATGGTTTCA-GAGGAGTAGCGATAACAAGC-TTTTGTACAAAAGGGGCAATAACTCT * * * 195354 ATAATTGTAACATGGTAAGGGTCAAAGGGTTATATTTTGAAATGTCTTAAGATGTCCTACTACAT 129 ATAATTGTAACATAGTAAGGGTCAAAGGGATATATTTTAAAATGTCTTAAGATGTCCTACTACAT * * * 195419 CCATGAAAAAGTTTTTCTCTACCATCCTAAACAAAAGAGATCTAAAAACTCATT-ATTTAACAGA 194 CCATGAAAAAGTTTTTCTCTACCACCCTAAACAAAAGAGATCCAAAAACCCATTAATTT-ACAGA 195483 TTTCCAAATGACCTTGACCTTTGACCTTTATGTCATTTTGTTCGGCAAA-AGTAAACGCTTCCAT 258 TTTCCAAATGACCTTGACCTTTGACCTTTATGTCATTTTGTTCGGCAAAGA-TAAACGCTTCCAT * * * * 195547 CCCAAGTGGTCCGAAGTCTCTATGATAAGTAATAAAAAAGTTGGATGTGATTTTATAGAAATGTA 322 CCCAAGTGGTCCGAAGTCTCTATGACAAATAATAAAAAAGTTGGAAGTGATTTTAAAGAAATGTA * * 195612 AATAATTTCAGGAGCAATAACTACTAGAAGGGGGGCTCAGATCCTT 387 AATAAGTTCAGGAGCAATAACTACTAGAAGGAGGGCTCAGATCCTT * * * 195658 TCGGTATGAATAGATTGAAGAACCCTCTAAGTGTACTGAAGACATTGGTAAAAGTTTCAAATTTC 1 TCGGTATGAATAGATTGAAGAACCATCTAAGTGTACTGAAGACATTGGTAAAAGTTTCAAGTCTC * * 195723 TATCTCTTGTGGTTTCAGAGGAGTAGCGATAACAAGCTTTTCAGT-CAAAAGGGGCAATTACTCT 66 TATCTCTTATGGTTTCAGAGGAGTAGCGATAACAAGCTTTT--GTACAAAAGGGGCAATAACTCT * * * * 195787 GTAACTATTTAA-A-AG-AAGGAG-CCAAGGTGATATATTTTAAAATGTCTTAAGATGTCCTATT 129 ATAA-T-TGTAACATAGTAAGG-GTCAAAGG-GATATATTTTAAAATGTCTTAAGATGTCCTACT * 195848 ACATCCATGAAAAAGTTTTTCTCTACCACCCTAAACAAAAGAGATCCAAAAACCCATTAATTTCC 190 ACATCCATGAAAAAGTTTTTCTCTACCACCCTAAACAAAAGAGATCCAAAAACCCATTAATTTAC * * * * * * 195913 AGATTTTCAGATGACCTTGGCCTTTGACCTTTATGTCATTTTGTTCGGCCAAGATAGACGCTTCT 255 AGATTTCCAAATGACCTTGACCTTTGACCTTTATGTCATTTTGTTCGGCAAAGATAAACGCTTCC * * 195978 ATCCCAAGTGGTCCGAAGTTTCTATGACAAATAATAAAAAAGTTGGAAGTGATTTTAAAGATATG 320 ATCCCAAGTGGTCCGAAGTCTCTATGACAAATAATAAAAAAGTTGGAAGTGATTTTAAAGAAATG * * * * 196043 TTAATACGTTCAGGGGCAATAACTACTTGAAGGAGGGCTCAGATCCTT 385 TAAATAAGTTCAGGAGCAATAACTACTAGAAGGAGGGCTCAGATCCTT * 196091 TCGGTATGAATAGATTGAAGAACCATCTAAGTGTACTGAAGACATTGGTAAAAGTTCCAAGTCTC 1 TCGGTATGAATAGATTGAAGAACCATCTAAGTGTACTGAAGACATTGGTAAAAGTTTCAAGTCTC * * 196156 TATCTCTTATGGTTTCAGAGGAGTAGTGATAACAAGCTTTTTGTACACAA-GGGCAATAACT 66 TATCTCTTATGGTTTCAGAGGAGTAGCGATAACAAGC-TTTTGTACAAAAGGGGCAATAACT 196217 TTGTAAGTTC Statistics Matches: 498, Mismatches: 50, Indels: 23 0.87 0.09 0.04 Matches are distributed among these distances: 432 25 0.05 433 453 0.91 434 16 0.03 435 4 0.01 ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31 Consensus pattern (432 bp): TCGGTATGAATAGATTGAAGAACCATCTAAGTGTACTGAAGACATTGGTAAAAGTTTCAAGTCTC TATCTCTTATGGTTTCAGAGGAGTAGCGATAACAAGCTTTTGTACAAAAGGGGCAATAACTCTAT AATTGTAACATAGTAAGGGTCAAAGGGATATATTTTAAAATGTCTTAAGATGTCCTACTACATCC ATGAAAAAGTTTTTCTCTACCACCCTAAACAAAAGAGATCCAAAAACCCATTAATTTACAGATTT CCAAATGACCTTGACCTTTGACCTTTATGTCATTTTGTTCGGCAAAGATAAACGCTTCCATCCCA AGTGGTCCGAAGTCTCTATGACAAATAATAAAAAAGTTGGAAGTGATTTTAAAGAAATGTAAATA AGTTCAGGAGCAATAACTACTAGAAGGAGGGCTCAGATCCTT Found at i:196418 original size:54 final size:54 Alignment explanation

Indices: 196354--196517 Score: 266 Period size: 54 Copynumber: 3.1 Consensus size: 54 196344 AGAAAAAAAA 196354 TAATAAAAAACATAAGAAATACAAAAGGTCTTTCACCTGAAAGGTGGAAAGACC 1 TAATAAAAAACATAAGAAATACAAAAGGTCTTTCACCTGAAAGGTGGAAAGACC * 196408 TAATAAAAAACATAAGAAATACAATAGGTCTTTCACCTGAAAGGTGGAAAGACC 1 TAATAAAAAACATAAGAAATACAAAAGGTCTTTCACCTGAAAGGTGGAAAGACC * 196462 ---T-AAAAACATAAAGAAA-ACAAGAGGTCTTTCACCTGAAAGGTGGAAAGACC 1 TAATAAAAAACAT-AAGAAATACAAAAGGTCTTTCACCTGAAAGGTGGAAAGACC 196512 TAATAA 1 TAATAA 196518 TGATTAAATC Statistics Matches: 103, Mismatches: 2, Indels: 10 0.90 0.02 0.09 Matches are distributed among these distances: 50 41 0.40 51 7 0.07 53 1 0.01 54 54 0.52 ACGTcount: A:0.49, C:0.15, G:0.17, T:0.19 Consensus pattern (54 bp): TAATAAAAAACATAAGAAATACAAAAGGTCTTTCACCTGAAAGGTGGAAAGACC Found at i:199266 original size:2 final size:2 Alignment explanation

Indices: 199259--199292 Score: 59 Period size: 2 Copynumber: 17.0 Consensus size: 2 199249 ATTAATATGC * 199259 GA GA GA GA GA GA GA GA GA GA GA GG GA GA GA GA GA 1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 199293 AAATAAGTAA Statistics Matches: 30, Mismatches: 2, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 2 30 1.00 ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00 Consensus pattern (2 bp): GA Found at i:203767 original size:182 final size:179 Alignment explanation

Indices: 203547--203880 Score: 503 Period size: 182 Copynumber: 1.8 Consensus size: 179 203537 AAGGTGTACC * 203547 CTATATGCAATATTTTGCCAAAAATGACTAAGTTCAAAAGCTGGTATTTTTTTCATAAATTATT- 1 CTATATGCAATATTTTGCCAAAAATGACTAAGTTCAAAAGCTGGTATTTTTTTCAAAAATT-TTC * 203611 GGAAATCAAAATCCTACCAATTATG-CACACCTCTGATATATGTACAATTGA-TCTGCAAAAGAA 65 GGAAATCAAAATCCTACCAA-TATGACACACCTCTGATATATGTACAA-TAATTCTGCAAAAGAA * * 203674 CAACTTCCTATCTTGAAAAATGTAGACGGAGTTATCCGTACAATGAGGGTATA 128 CAAATTCCTAACTT-AAAAATGTAGACGGAGTTATCCGTACAATGAGGGTATA * * * 203727 CTATATGCAATATTTTGCCCAAAAAATGACTTAGTTCAAAAGCTTGTGTTTTTTTCAAAAATTTT 1 CTATATGCAATATTTTG-CC-AAAAATGACTAAGTTCAAAAGCTGGTATTTTTTTCAAAAATTTT * 203792 CGGAAATCAAAATCCTAGCAATATGCACACACCTCTGATATATGTACAATAATTCTGCAAAAGAA 64 CGGAAATCAAAATCCTACCAATATG-ACACACCTCTGATATATGTACAATAATTCTGCAAAAGAA * 203857 CAAATTCCTAACTTAAAATTGTAG 128 CAAATTCCTAACTTAAAAATGTAG 203881 GAGGTACCCT Statistics Matches: 139, Mismatches: 9, Indels: 10 0.88 0.06 0.06 Matches are distributed among these distances: 180 17 0.12 181 8 0.06 182 68 0.49 183 46 0.33 ACGTcount: A:0.38, C:0.17, G:0.13, T:0.32 Consensus pattern (179 bp): CTATATGCAATATTTTGCCAAAAATGACTAAGTTCAAAAGCTGGTATTTTTTTCAAAAATTTTCG GAAATCAAAATCCTACCAATATGACACACCTCTGATATATGTACAATAATTCTGCAAAAGAACAA ATTCCTAACTTAAAAATGTAGACGGAGTTATCCGTACAATGAGGGTATA Found at i:206841 original size:24 final size:24 Alignment explanation

Indices: 206809--206856 Score: 78 Period size: 24 Copynumber: 2.0 Consensus size: 24 206799 TTAATGAAAT * 206809 TAATAATTTGTTATAGTATTAATG 1 TAATAATTTGTAATAGTATTAATG * 206833 TAATAATTTGTAATGGTATTAATG 1 TAATAATTTGTAATAGTATTAATG 206857 GTTTGGAAAG Statistics Matches: 22, Mismatches: 2, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 24 22 1.00 ACGTcount: A:0.38, C:0.00, G:0.15, T:0.48 Consensus pattern (24 bp): TAATAATTTGTAATAGTATTAATG Found at i:207168 original size:16 final size:16 Alignment explanation

Indices: 207132--207170 Score: 53 Period size: 16 Copynumber: 2.4 Consensus size: 16 207122 AAATGGAGTG 207132 CACACACATACATACA 1 CACACACATACATACA * 207148 TACACACATACGA-ACA 1 CACACACATAC-ATACA 207164 CACACAC 1 CACACAC 207171 GCACGGTAGT Statistics Matches: 20, Mismatches: 2, Indels: 2 0.83 0.08 0.08 Matches are distributed among these distances: 16 19 0.95 17 1 0.05 ACGTcount: A:0.49, C:0.38, G:0.03, T:0.10 Consensus pattern (16 bp): CACACACATACATACA Found at i:217826 original size:17 final size:17 Alignment explanation

Indices: 217804--217839 Score: 72 Period size: 17 Copynumber: 2.1 Consensus size: 17 217794 GTTCTGTTAA 217804 TGGTTTTTGGTCTAAGT 1 TGGTTTTTGGTCTAAGT 217821 TGGTTTTTGGTCTAAGT 1 TGGTTTTTGGTCTAAGT 217838 TG 1 TG 217840 CTTCTTGGTT Statistics Matches: 19, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 17 19 1.00 ACGTcount: A:0.11, C:0.06, G:0.31, T:0.53 Consensus pattern (17 bp): TGGTTTTTGGTCTAAGT Found at i:217847 original size:17 final size:17 Alignment explanation

Indices: 217810--217848 Score: 60 Period size: 17 Copynumber: 2.3 Consensus size: 17 217800 TTAATGGTTT * * 217810 TTGGTCTAAGTTGGTTT 1 TTGGTCTAAGTTGCTTC 217827 TTGGTCTAAGTTGCTTC 1 TTGGTCTAAGTTGCTTC 217844 TTGGT 1 TTGGT 217849 TACTGGTAGA Statistics Matches: 20, Mismatches: 2, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 17 20 1.00 ACGTcount: A:0.10, C:0.10, G:0.28, T:0.51 Consensus pattern (17 bp): TTGGTCTAAGTTGCTTC Found at i:232207 original size:261 final size:261 Alignment explanation

Indices: 231743--232265 Score: 965 Period size: 261 Copynumber: 2.0 Consensus size: 261 231733 TTAAAAAGTG 231743 AATAAAGTGAAGCTGCATATTCATGATAATGACAAGCACTGTTTTTATTACGCAAATGTATCAAA 1 AATAAAGTGAAGCTGCATATTCATGATAATGACAAGCACTGTTTTTATTACGCAAATGTATCAAA * 231808 AATGATTCAAAATAGTTTTATATGTTTAAAGACCTTATCTTCATTCTTGCAAAGGGGTTTGGAGA 66 AATGATTCAAAATAGTTTTATATGTTTAAAGACCTTATCTTCATTCTTGCAAAGGGATTTGGAGA 231873 GTTGCAGAGTGGGTTTACAAATATGAAGGGTAACAGACAAGTTAGTTTAACAAACGGATAATAAG 131 GTTGCAGAGTGGGTTTACAAATATGAAGGGTAACAGACAAGTTAGTTTAACAAACGGATAATAAG * * 231938 ATTAAACTAGACAGGATCTCGTTGCAAGCAACGAAGAGGTCTTCCGTCTGATTTAGAATTTGAGA 196 ATTAAACTAGACACGATCTCGTTGCAAGCAACGAAGAGGCCTTCCGTCTGATTTAGAATTTGAGA 232003 T 261 T * * * 232004 AATAAAGTGAAGCTGCATATTCATGTTAATGACAAGCACTGTTTTTTTTACGCAAATGTGTCAAA 1 AATAAAGTGAAGCTGCATATTCATGATAATGACAAGCACTGTTTTTATTACGCAAATGTATCAAA * 232069 AATGATTCAAAATAGTTTTATATGTTTAAAGACTTTATCTTCATTCTTGCAAAGGGATTTGGAGA 66 AATGATTCAAAATAGTTTTATATGTTTAAAGACCTTATCTTCATTCTTGCAAAGGGATTTGGAGA 232134 GTTGCAGAGTGGGTTTACAAATATGAAGGGTAACAGACAAGTTAGTTTAACAAACGGATAATAAG 131 GTTGCAGAGTGGGTTTACAAATATGAAGGGTAACAGACAAGTTAGTTTAACAAACGGATAATAAG * * 232199 ATTAAACTAGACACGATCTCGTTGCGAGCAACGAGGAGGCCTTCCGTCTGATTTAGAATTTGAGA 196 ATTAAACTAGACACGATCTCGTTGCAAGCAACGAAGAGGCCTTCCGTCTGATTTAGAATTTGAGA 232264 T 261 T 232265 A 1 A 232266 TATGTTCGAT Statistics Matches: 253, Mismatches: 9, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 261 253 1.00 ACGTcount: A:0.35, C:0.13, G:0.21, T:0.31 Consensus pattern (261 bp): AATAAAGTGAAGCTGCATATTCATGATAATGACAAGCACTGTTTTTATTACGCAAATGTATCAAA AATGATTCAAAATAGTTTTATATGTTTAAAGACCTTATCTTCATTCTTGCAAAGGGATTTGGAGA GTTGCAGAGTGGGTTTACAAATATGAAGGGTAACAGACAAGTTAGTTTAACAAACGGATAATAAG ATTAAACTAGACACGATCTCGTTGCAAGCAACGAAGAGGCCTTCCGTCTGATTTAGAATTTGAGA T Found at i:250139 original size:18 final size:18 Alignment explanation

Indices: 250087--250139 Score: 61 Period size: 18 Copynumber: 2.9 Consensus size: 18 250077 TATTATGGTT * * 250087 AGAGCTATTCATTTTCTT 1 AGAGCTATTCATTTGCTG * * 250105 AAAGCTATTCATATGCTG 1 AGAGCTATTCATTTGCTG * 250123 AGAGCTATTCGTTTGCT 1 AGAGCTATTCATTTGCT 250140 TAAAAGTTCT Statistics Matches: 28, Mismatches: 7, Indels: 0 0.80 0.20 0.00 Matches are distributed among these distances: 18 28 1.00 ACGTcount: A:0.25, C:0.17, G:0.17, T:0.42 Consensus pattern (18 bp): AGAGCTATTCATTTGCTG Found at i:252795 original size:8 final size:8 Alignment explanation

Indices: 252784--252841 Score: 73 Period size: 8 Copynumber: 7.4 Consensus size: 8 252774 TAAAAAGTTT 252784 ACAGACGG 1 ACAGACGG * 252792 ACAGACAG 1 ACAGACGG * * 252800 ACGGACAG 1 ACAGACGG 252808 ACAGACGG 1 ACAGACGG * 252816 ACGGACGG 1 ACAGACGG 252824 ACAGACGG 1 ACAGACGG 252832 AC-GACGG 1 ACAGACGG 252839 ACA 1 ACA 252842 AAATGTGATC Statistics Matches: 43, Mismatches: 6, Indels: 2 0.84 0.12 0.04 Matches are distributed among these distances: 7 7 0.16 8 36 0.84 ACGTcount: A:0.38, C:0.26, G:0.36, T:0.00 Consensus pattern (8 bp): ACAGACGG Found at i:252801 original size:12 final size:12 Alignment explanation

Indices: 252784--252841 Score: 73 Period size: 12 Copynumber: 4.9 Consensus size: 12 252774 TAAAAAGTTT 252784 ACAGACGGACAG 1 ACAGACGGACAG 252796 ACAGACGGACAG 1 ACAGACGGACAG * 252808 ACAGACGGACGG 1 ACAGACGGACAG * * * 252820 ACGGACAGACGG 1 ACAGACGGACAG 252832 AC-GACGGACA 1 ACAGACGGACA 252842 AAATGTGATC Statistics Matches: 41, Mismatches: 5, Indels: 1 0.87 0.11 0.02 Matches are distributed among these distances: 11 6 0.15 12 35 0.85 ACGTcount: A:0.38, C:0.26, G:0.36, T:0.00 Consensus pattern (12 bp): ACAGACGGACAG Found at i:252834 original size:4 final size:4 Alignment explanation

Indices: 252787--252840 Score: 56 Period size: 4 Copynumber: 13.8 Consensus size: 4 252777 AAAGTTTACA * * * * * 252787 GACG GACA GACA GACG GACA GACA GACG GACG GACG GACA GACG GAC- 1 GACG GACG GACG GACG GACG GACG GACG GACG GACG GACG GACG GACG 252834 GACG GAC 1 GACG GAC 252841 AAAATGTGAT Statistics Matches: 43, Mismatches: 6, Indels: 2 0.84 0.12 0.04 Matches are distributed among these distances: 3 3 0.07 4 40 0.93 ACGTcount: A:0.35, C:0.26, G:0.39, T:0.00 Consensus pattern (4 bp): GACG Found at i:260043 original size:20 final size:20 Alignment explanation

Indices: 260020--260069 Score: 66 Period size: 20 Copynumber: 2.5 Consensus size: 20 260010 TATATGAAAT 260020 AATACTGTATCATATGC-TAC 1 AATACTGTATCATAT-CATAC * 260040 AATAGTGTATCATATCATAC 1 AATACTGTATCATATCATAC * 260060 AATACCGTAT 1 AATACTGTAT 260070 TATAAAAACA Statistics Matches: 26, Mismatches: 3, Indels: 2 0.84 0.10 0.06 Matches are distributed among these distances: 19 1 0.04 20 25 0.96 ACGTcount: A:0.38, C:0.18, G:0.10, T:0.34 Consensus pattern (20 bp): AATACTGTATCATATCATAC Found at i:261402 original size:165 final size:165 Alignment explanation

Indices: 260940--261967 Score: 977 Period size: 166 Copynumber: 6.1 Consensus size: 165 260930 ATTTGAAAGA ** 260940 TATATATTCCTATGTAAAAAGTT-GACCCCCCATTGTGGCCCCATCGAACCCCCAAGGGTCATGA 1 TATATATTCCTATGTAAAAA-TTGGACCCCCCATTGTGGCCCCATCCTA-CCCCAAGGGTCATGA * * * * * * * 261004 TTTTCACAACTTTGAATTCTCACTACCTGAGGATGCTTCTATACAAGTTTCCGA-TTTCCTGG-C 64 TTTTCACAACCTTGAATTCACACTACCTAAGGATGCTTCCACATAAGTTT-CAACTTTCCTGGCC * * * 261067 ATAATGGTT-TCTGAGAAGAAGATCTTTAAAAATATACTC 128 A-AATGGTTCT-TGAGAAGAAGATTTTTAAAGATTTACTC * * * * * ** * * 261106 TGTATATTTCTATGTAAAAATTCGTCCCACTTTTATGGACCCATCCTACCCCTAAGGGTCATGAT 1 TATATATTCCTATGTAAAAATTGGACCCCCCATTGTGGCCCCATCCTACCCC-AAGGGTCATGAT * * * * * 261171 TTTCACAACTTTGAA-TCTACACTACCTGAGGATGTTTCCACACAAGTTTCCGA-TTTCCTGGCC 65 TTTCACAACCTTGAATTC-ACACTACCTAAGGATGCTTCCACATAAGTTT-CAACTTTCCTGGCC * 261234 AAATGGTTCTTGAGAAGATGATTTTTAAAGATTTACTC 128 AAATGGTTCTTGAGAAGAAGATTTTTAAAGATTTACTC * ** * 261272 GATATATTTATATGTAAAAATTGGA-CCCCCATTGTGGCCCCAACCTACCCTCAAGGGTCAT-AG 1 TATATATTCCTATGTAAAAATTGGACCCCCCATTGTGGCCCCATCCTACCC-CAAGGGTCATGA- * * * * 261335 TTTTCACAACCTTGAATTCACGCCAGCTAAGGATGCTTCCACATAAGTTTCAACTTTCCTTGCCA 64 TTTTCACAACCTTGAATTCACACTACCTAAGGATGCTTCCACATAAGTTTCAACTTTCCTGGCCA 261400 AATGGTTCTTGAGAAGAAGATTTTTAAAGATTTACTC 129 AATGGTTCTTGAGAAGAAGATTTTTAAAGATTTACTC * * * *** 261437 TATATTTTCCTATGTAAAAA-TGAAACCCCCCATTGTGGCCTCATCCTACCCTTGGGGTTCATGA 1 TATATATTCCTATGTAAAAATTG-GACCCCCCATTGTGGCCCCATCCTACCCCAAGGG-TCATGA * ** * ** * * * 261501 TTTTCACAACTTTGAATTTTCACTACCCAAGGATGCTTTAACAAAAGTTTCAGCCTTT-CTGGCT 64 TTTTCACAACCTTGAATTCACACTACCTAAGGATGCTTCCACATAAGTTTCA-ACTTTCCTGGCC * * * 261565 GATTGCTT-TCTGAGAAGAA-ATTTTTTTTTTAAAGATTTACTC 128 AAATGGTTCT-TGAGAAGAAGA-----TTTTTAAAGATTTACTC * * * * * * 261607 TATATATTCCTATGTAAAAAGTCGACCCCCAAATGTGGCCCCACCCTACCCCCAAGGGTCTTGAT 1 TATATATTCCTATGTAAAAATTGGACCCCCCATTGTGGCCCCATCCTA-CCCCAAGGGTCATGAT * * * * * * * 261672 TTTCACAACCTTAAATTAACACTACCTGAGGGTGCTTCCATACT-AGTTTCAGCTTTCCTGGCCT 65 TTTCACAACCTTGAATTCACACTACCTAAGGATGCTTCCACA-TAAGTTTCAACTTTCCTGGCCA * * * 261736 CATGGTTCTTGAGAAGAAGATTTTTTAAAAATTTATTC 129 AATGGTTCTTGAGAAGAAGA-TTTTTAAAGATTTACTC * * * * 261774 TATATATTCCTCTGTAAAAATTTGACCATCCCCCCCCCATTGTGGCCTCA-CCGTAACCCCGAGG 1 TATATATTCCTATGTAAAAA-TTG--GA----CCCCCCATTGTGGCCCCATCC-T-ACCCCAAGG * * * * 261838 GTCATAATTTTCACAACCTTGAAATCACACCAACTAAGGATGCTTCCACATAAGTTTCAACTTTC 57 GTCATGATTTTCACAACCTTGAATTCACACTACCTAAGGATGCTTCCACATAAGTTTCAACTTTC * 261903 CAGGCCAAATGGTTCTTGAGAAGAAGATTTTTAAAGATTTACTC 122 CTGGCCAAATGGTTCTTGAGAAGAAGATTTTTAAAGATTTACTC 261947 TATATATTCCTATGTAAAAAT 1 TATATATTCCTATGTAAAAAT 261968 NAAAAGGTGT Statistics Matches: 706, Mismatches: 120, Indels: 66 0.79 0.13 0.07 Matches are distributed among these distances: 164 5 0.01 165 144 0.20 166 242 0.34 167 43 0.06 168 1 0.00 169 4 0.01 170 120 0.17 171 9 0.01 172 1 0.00 173 37 0.05 174 99 0.14 175 1 0.00 ACGTcount: A:0.29, C:0.23, G:0.15, T:0.33 Consensus pattern (165 bp): TATATATTCCTATGTAAAAATTGGACCCCCCATTGTGGCCCCATCCTACCCCAAGGGTCATGATT TTCACAACCTTGAATTCACACTACCTAAGGATGCTTCCACATAAGTTTCAACTTTCCTGGCCAAA TGGTTCTTGAGAAGAAGATTTTTAAAGATTTACTC Found at i:261581 original size:331 final size:332 Alignment explanation

Indices: 260941--261967 Score: 951 Period size: 331 Copynumber: 3.1 Consensus size: 332 260931 TTTGAAAGAT * * ** 260941 ATATATTCCTATGTAAAAAGTTGACCCCCCATTGTGGCCCCATCGAACCCCCAAGGGTCATGATT 1 ATATATTCATATGTAAAAA-TTGA-CCCCCATTGTGGCCCCAACCTACCCCCAAGGGTCATGATT * * * * * * 261006 TTCACAACTTTGAATTCTCACTACCTGAGGATGCTTCTATACAAGTTTCCGA-TTTCC-TGGCAT 64 TTCACAACCTTGAATTCACACTACCTGAGGATGCTTCCATATAAGTTT-CAACTTTCCTTGCCA- * * * **** 261069 AATGGTT-TCTGAGAAGAAGATCTTTAAAAATATACTCTGTATATTT-CTATGTAAAAATTCGTC 127 AATGGTTCT-TGAGAAGAAGATTTTTAAAAATTTACTCTATAT-TTTCCTATGTAAAAATGAAAC ** 261132 CCACTTTTATGGACCCATCCTACCCCTAAGGGTCATGATTTTCACAACTTTGAATCTACACTACC 190 CCACCATTATGGACCCATCCTACCCCTAAGGGTCATGATTTTCACAACTTTGAATCTACACTACC ** * * * 261197 TGAGGATGTTTCCACACAAGTTTCCGATTTCCTGGCCAAATGGTTCTTGAGAAG-A-TGATTTTT 255 CAAGGATGTTTCAACAAAAGTTTCAGATTTCCTGGCCAAATGGTTCTTGAGAAGAATTGATTTTT 261260 AAAGATTTACTCG 320 AAAGATTTACTCG * * 261273 ATATATTTATATGTAAAAATTGGACCCCCATTGTGGCCCCAACCTACCCTCAAGGGTCAT-AGTT 1 ATATATTCATATGTAAAAATT-GACCCCCATTGTGGCCCCAACCTACCCCCAAGGGTCATGA-TT * * * * * 261337 TTCACAACCTTGAATTCACGCCAGCTAAGGATGCTTCCACATAAGTTTCAACTTTCCTTGCCAAA 64 TTCACAACCTTGAATTCACACTACCTGAGGATGCTTCCATATAAGTTTCAACTTTCCTTGCCAAA * * 261402 TGGTTCTTGAGAAGAAGATTTTTAAAGATTTACTCTATATTTTCCTATGTAAAAATGAAACCCCC 129 TGGTTCTTGAGAAGAAGATTTTTAAAAATTTACTCTATATTTTCCTATGTAAAAATGAAACCCAC * ** * * 261467 CATTGTGG-CCTCATCCTA-CCCTTGGGGTTCATGATTTTCACAACTTTGAATTTTCACTACCCA 194 CATTATGGACC-CATCCTACCCCTAAGGG-TCATGATTTTCACAACTTTGAATCTACACTACCCA * ** * * ** 261530 AGGATGCTTT-AACAAAAGTTTCAGCCTTT-CTGGCTGATTGCTT-TCTGAGAAGAAATTTTTTT 257 AGGATG-TTTCAACAAAAGTTTCAG-ATTTCCTGGCCAAATGGTTCT-TGAGAAG-AA-TTGATT * 261592 TTTAAAGATTTACTCT 317 TTTAAAGATTTACTCG * * * * * 261608 ATATATTCCTATGTAAAAAGTCGACCCCCAAATGTGGCCCCACCCTACCCCCAAGGGTCTTGATT 1 ATATATTCATATGTAAAAA-TTGACCCCC-ATTGTGGCCCCAACCTACCCCCAAGGGTCATGATT * * * * * ** 261673 TTCACAACCTTAAATTAACACTACCTGAGGGTGCTTCCATACT-AGTTTCAGCTTTCCTGGCCTC 64 TTCACAACCTTGAATTCACACTACCTGAGGATGCTTCCATA-TAAGTTTCAACTTTCCTTGCCAA * * * 261737 ATGGTTCTTGAGAAGAAGATTTTTTAAAAATTTATTCTATATATTCCTCTGTAAAAATTTGACCA 128 ATGGTTCTTGAGAAGAAGA-TTTTTAAAAATTTACTCTATATTTTCCTATGTAAAAA--TGA--A * * * * * * 261802 TCCCCCCCCCATTGTGG-CCTCA-CCGTAACCCC-GAGGGTCATAATTTTCACAACCTTGAAATC 188 ---ACCCACCATTATGGACC-CATCC-T-ACCCCTAAGGGTCATGATTTTCACAACTTTG-AATC * * * * * * * 261864 -ACACCAACTAAGGATGCTTCCACATAAGTTTCA-ACTTTCCAGGCCAAATGGTTCTTGAGAAGA 246 TACACTACCCAAGGATGTTTCAACAAAAGTTTCAGA-TTTCCTGGCCAAATGGTTCTTGAGAAGA * 261927 A--GATTTTTAAAGATTTACTCT 310 ATTGATTTTTAAAGATTTACTCG * 261948 ATATATTCCTATGTAAAAAT 1 ATATATTCATATGTAAAAAT 261968 NAAAAGGTGT Statistics Matches: 570, Mismatches: 90, Indels: 63 0.79 0.12 0.09 Matches are distributed among these distances: 330 16 0.03 331 209 0.37 332 30 0.05 333 1 0.00 335 42 0.07 336 99 0.17 337 35 0.06 339 4 0.01 340 37 0.06 341 1 0.00 343 9 0.02 344 76 0.13 345 8 0.01 346 3 0.01 ACGTcount: A:0.29, C:0.23, G:0.15, T:0.33 Consensus pattern (332 bp): ATATATTCATATGTAAAAATTGACCCCCATTGTGGCCCCAACCTACCCCCAAGGGTCATGATTTT CACAACCTTGAATTCACACTACCTGAGGATGCTTCCATATAAGTTTCAACTTTCCTTGCCAAATG GTTCTTGAGAAGAAGATTTTTAAAAATTTACTCTATATTTTCCTATGTAAAAATGAAACCCACCA TTATGGACCCATCCTACCCCTAAGGGTCATGATTTTCACAACTTTGAATCTACACTACCCAAGGA TGTTTCAACAAAAGTTTCAGATTTCCTGGCCAAATGGTTCTTGAGAAGAATTGATTTTTAAAGAT TTACTCG Found at i:262632 original size:153 final size:152 Alignment explanation

Indices: 262318--262632 Score: 374 Period size: 153 Copynumber: 2.1 Consensus size: 152 262308 TTAGCCAGCT ** * * 262318 CAAAAACCTTAAGTTCATCCAGCATCTGAAACCTACGGCTCAGATTCAACATTTAAGCCTGTCAA 1 CAAAAACCTTAACCTCATCCAGCATCTGAAACCTACGGCTCAGATTCAACATTCAAACCTGTCAA * * * 262383 GTGCATCAGTATCATTATGCGCACCATCCATGCACGTTTTGTGAAGTTAGGACCAGTATAAGATA 66 GTGCATCAGTATCATTAAGCGCACCATCAATGCACGTTTGGTGAAGTTAGGACCAG-ATAAGATA * ** 262448 TAATTATCAGAGGGCATCTGCTC 130 TAATTATCAAAGGGCATCTGAAC * * * * 262471 CAAAAACCTTAACCTCATCCATCATCTTAAACCTATGGCTCAGATTCAGCATTCAAACCTGTCAA 1 CAAAAACCTTAACCTCATCCAGCATCTGAAACCTACGGCTCAGATTCAACATTCAAACCTGTCAA * * * 262536 GTTCATCAGTATTA-TAAGACGCACCATCAATGCAGGTTTGGTGAAGTTAGGACCAG-T-AG-TA 66 GTGCATCAGTATCATTAAG-CGCACCATCAATGCACGTTTGGTGAAGTTAGGACCAGATAAGATA * * 262597 -ACTTA-GAAAGGGCA-CATGAAC 130 TAATTATCAAAGGGCATC-TGAAC * 262618 CAAAAACTTTAACCT 1 CAAAAACCTTAACCT 262633 GCTCCAAAAA Statistics Matches: 140, Mismatches: 20, Indels: 10 0.82 0.12 0.06 Matches are distributed among these distances: 146 1 0.01 147 24 0.17 148 4 0.03 149 2 0.01 150 2 0.01 151 1 0.01 152 3 0.02 153 103 0.74 ACGTcount: A:0.34, C:0.23, G:0.17, T:0.26 Consensus pattern (152 bp): CAAAAACCTTAACCTCATCCAGCATCTGAAACCTACGGCTCAGATTCAACATTCAAACCTGTCAA GTGCATCAGTATCATTAAGCGCACCATCAATGCACGTTTGGTGAAGTTAGGACCAGATAAGATAT AATTATCAAAGGGCATCTGAAC Found at i:267048 original size:23 final size:22 Alignment explanation

Indices: 267022--267065 Score: 61 Period size: 22 Copynumber: 2.0 Consensus size: 22 267012 TCTAATTAAA 267022 TGATTAATAATAATTTAAAAAAT 1 TGATTAATAA-AATTTAAAAAAT ** 267045 TGATTTTTAAAATTTAAAAAA 1 TGATTAATAAAATTTAAAAAA 267066 AAAAAGTTGT Statistics Matches: 19, Mismatches: 2, Indels: 1 0.86 0.09 0.05 Matches are distributed among these distances: 22 11 0.58 23 8 0.42 ACGTcount: A:0.55, C:0.00, G:0.05, T:0.41 Consensus pattern (22 bp): TGATTAATAAAATTTAAAAAAT Found at i:270865 original size:2 final size:2 Alignment explanation

Indices: 270853--270912 Score: 104 Period size: 2 Copynumber: 30.5 Consensus size: 2 270843 TCTCAAGGGA 270853 AG AG A- AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG 1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG * 270894 AG AG AA AG AG AG AG AG AG A 1 AG AG AG AG AG AG AG AG AG A 270913 ACTAGAATTT Statistics Matches: 55, Mismatches: 2, Indels: 2 0.93 0.03 0.03 Matches are distributed among these distances: 1 1 0.02 2 54 0.98 ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00 Consensus pattern (2 bp): AG Found at i:271360 original size:20 final size:20 Alignment explanation

Indices: 271317--271364 Score: 62 Period size: 20 Copynumber: 2.4 Consensus size: 20 271307 CACTCCCCCC * * 271317 AACGAAACGAAATCTACATG 1 AACGAAACGAAACCTACACG 271337 AACGAAACGAAACCTAC-CG 1 AACGAAACGAAACCTACACG 271356 AAACGAAAC 1 -AACGAAAC 271365 TATCATAATA Statistics Matches: 25, Mismatches: 2, Indels: 2 0.86 0.07 0.07 Matches are distributed among these distances: 19 1 0.04 20 24 0.96 ACGTcount: A:0.52, C:0.25, G:0.15, T:0.08 Consensus pattern (20 bp): AACGAAACGAAACCTACACG Found at i:271816 original size:21 final size:21 Alignment explanation

Indices: 271809--271962 Score: 175 Period size: 21 Copynumber: 7.3 Consensus size: 21 271799 CAATAGTAGT 271809 ATCATTATATGCAGTGGTAAC 1 ATCATTATATGCAGTGGTAAC 271830 ATCATTATATGCAGTGGTAAC 1 ATCATTATATGCAGTGGTAAC * 271851 ATCATTACATGCAGTGGTAAC 1 ATCATTATATGCAGTGGTAAC * 271872 ATCATTATATGCAGTGCTAAC 1 ATCATTATATGCAGTGGTAAC * ** * 271893 ATCATTATATACTA-TTATATC 1 ATCATTATATGC-AGTGGTAAC * * * * 271914 ACCATTATATTCAGGGGTAAA 1 ATCATTATATGCAGTGGTAAC * * 271935 ATCTTTATATGAAGTGGTAAC 1 ATCATTATATGCAGTGGTAAC * 271956 ATTATTA 1 ATCATTA 271963 CGTTATGTCG Statistics Matches: 109, Mismatches: 22, Indels: 4 0.81 0.16 0.03 Matches are distributed among these distances: 20 1 0.01 21 107 0.98 22 1 0.01 ACGTcount: A:0.35, C:0.14, G:0.15, T:0.36 Consensus pattern (21 bp): ATCATTATATGCAGTGGTAAC Found at i:271838 original size:42 final size:42 Alignment explanation

Indices: 271792--271899 Score: 146 Period size: 42 Copynumber: 2.6 Consensus size: 42 271782 GGTATCTTAT ** * 271792 TTATATGCAATAGTAGTATCATTATATGCAGTGGTAACATCA 1 TTATATGCAATAGTAACATCATTACATGCAGTGGTAACATCA * * 271834 TTATATGCAGTGGTAACATCATTACATGCAGTGGTAACATCA 1 TTATATGCAATAGTAACATCATTACATGCAGTGGTAACATCA * 271876 TTATATGCAGT-GCTAACATCATTA 1 TTATATGCAATAG-TAACATCATTA 271900 TATACTATTA Statistics Matches: 60, Mismatches: 5, Indels: 2 0.90 0.07 0.03 Matches are distributed among these distances: 41 1 0.02 42 59 0.98 ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34 Consensus pattern (42 bp): TTATATGCAATAGTAACATCATTACATGCAGTGGTAACATCA Found at i:271848 original size:63 final size:63 Alignment explanation

Indices: 271770--271902 Score: 160 Period size: 63 Copynumber: 2.1 Consensus size: 63 271760 TCAATTTCAT * * * ** * 271770 ATTATATGAACTGGTATC-TTATTTATATGCAATAGTAGTATCATTATATGCAGTGGTAACATC 1 ATTATATGAACTGGTAACATCA-TTACATGCAATAGTAACATCATTATATGCAGTGCTAACATC * * * * 271833 ATTATATGCAGTGGTAACATCATTACATGCAGTGGTAACATCATTATATGCAGTGCTAACATC 1 ATTATATGAACTGGTAACATCATTACATGCAATAGTAACATCATTATATGCAGTGCTAACATC 271896 ATTATAT 1 ATTATAT 271903 ACTATTATAT Statistics Matches: 59, Mismatches: 10, Indels: 2 0.83 0.14 0.03 Matches are distributed among these distances: 63 57 0.97 64 2 0.03 ACGTcount: A:0.34, C:0.14, G:0.16, T:0.37 Consensus pattern (63 bp): ATTATATGAACTGGTAACATCATTACATGCAATAGTAACATCATTATATGCAGTGCTAACATC Found at i:272229 original size:21 final size:21 Alignment explanation

Indices: 272203--272245 Score: 61 Period size: 21 Copynumber: 2.0 Consensus size: 21 272193 TATGGTGTAT 272203 TAAAACCATT-ATGTATGGTGG 1 TAAAACC-TTAATGTATGGTGG * 272224 TAAAACCTTAATGTATTGTGG 1 TAAAACCTTAATGTATGGTGG 272245 T 1 T 272246 GAAAGCTTTA Statistics Matches: 20, Mismatches: 1, Indels: 2 0.87 0.04 0.09 Matches are distributed among these distances: 20 2 0.10 21 18 0.90 ACGTcount: A:0.33, C:0.09, G:0.21, T:0.37 Consensus pattern (21 bp): TAAAACCTTAATGTATGGTGG Found at i:281280 original size:165 final size:165 Alignment explanation

Indices: 281001--281335 Score: 570 Period size: 165 Copynumber: 2.0 Consensus size: 165 280991 NNNNNNNNNN 281001 ATTTACTCTATATATTCCTATGTAAAACTTCGAGCCCCCATTGTGGCCCCACCCTACCCCCGGGA 1 ATTTACTCTATATATTCCTATGTAAAACTTCGAGCCCCCATTGTGGCCCCACCCTACCCCCGGGA 281066 GTCATGAATTTCACAACTTTGAATCTACACTACCTGAGGATGCTTCCACACAAG-TTCAGCTTTC 66 GTCATGAATTTCACAACTTTGAATCTACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTC 281130 CTGGCTGATTAGT-TTC-TGAGAAGAAGATTTTT-AAA 131 CTGGCT--TT-GTGTTCTTGAGAAGAAGATTTTTGAAA * 281165 GATTTACTCTTTATATTCCTATGTAAAACTTCGAGCCCCCATTGTGGCCCCACCCTACCCCCGGG 1 -ATTTACTCTATATATTCCTATGTAAAACTTCGAGCCCCCATTGTGGCCCCACCCTACCCCCGGG * * 281230 TGTCATGAATTTCACAACTTTGAATCTACACTACCTGAGGATGTTTCCACACAAGTTTCAGCTTT 65 AGTCATGAATTTCACAACTTTGAATCTACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTT 281295 CCTGGCTTTGTGGTTCTTGAGAAGAAGATTTTTGAAA 130 CCTGGCTTTGT-GTTCTTGAGAAGAAGATTTTTGAAA 281332 ATTT 1 ATTT 281336 CTCGAAATTT Statistics Matches: 162, Mismatches: 3, Indels: 9 0.93 0.02 0.05 Matches are distributed among these distances: 163 2 0.01 164 2 0.01 165 119 0.73 166 36 0.22 167 3 0.02 ACGTcount: A:0.25, C:0.25, G:0.16, T:0.33 Consensus pattern (165 bp): ATTTACTCTATATATTCCTATGTAAAACTTCGAGCCCCCATTGTGGCCCCACCCTACCCCCGGGA GTCATGAATTTCACAACTTTGAATCTACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTC CTGGCTTTGTGTTCTTGAGAAGAAGATTTTTGAAA Found at i:281794 original size:31 final size:31 Alignment explanation

Indices: 281741--281889 Score: 120 Period size: 31 Copynumber: 4.7 Consensus size: 31 281731 GACACTCCTT * * * 281741 ATAAAGCCAGTCATCCGGGGGAAAGTTTCCCC 1 ATAAAGTCAGTCCT-CGGGGGAAAGTTTCCCA * * 281773 ATAAATTCAGTCCTCGGGGGAAAGCTTCCCA 1 ATAAAGTCAGTCCTCGGGGGAAAGTTTCCCA * * * * * 281804 ATAAAGTCAGTCCTTGGGGGTAAGTCTCACT 1 ATAAAGTCAGTCCTCGGGGGAAAGTTTCCCA * * * * 281835 ATATAGCCAGTTCTCTGGGGGAAAGTTTCACA 1 ATAAAGTCAGTCCTC-GGGGGAAAGTTTCCCA * * 281867 ATATAA-CCAGTCTTCGGGGGAAA 1 ATA-AAGTCAGTCCTCGGGGGAAA 281890 TTAAGTCTCA Statistics Matches: 93, Mismatches: 22, Indels: 5 0.77 0.18 0.04 Matches are distributed among these distances: 31 58 0.62 32 34 0.37 33 1 0.01 ACGTcount: A:0.29, C:0.22, G:0.25, T:0.24 Consensus pattern (31 bp): ATAAAGTCAGTCCTCGGGGGAAAGTTTCCCA Found at i:286334 original size:48 final size:46 Alignment explanation

Indices: 286202--286334 Score: 167 Period size: 46 Copynumber: 2.8 Consensus size: 46 286192 GGGGAAAGGA * * 286202 TTATCTGAGGCTGAGGTGCTGGCTATACTATGAGGGACATGCATGC 1 TTATCTGAGGCTGAGGTGCTGGCTTTACTATGAGGGACATGCATAC * * * * * 286248 TTATCTGGGGCTGAGGTGCTGCCTTTACTATAAAGGACATGCTTAC 1 TTATCTGAGGCTGAGGTGCTGGCTTTACTATGAGGGACATGCATAC * * 286294 TAGTATCTGAGGCTGAGGTGCAGGCTTTACTCTGAGGGACA 1 T--TATCTGAGGCTGAGGTGCTGGCTTTACTATGAGGGACA 286335 GGATTATCTG Statistics Matches: 72, Mismatches: 13, Indels: 2 0.83 0.15 0.02 Matches are distributed among these distances: 46 40 0.56 48 32 0.44 ACGTcount: A:0.22, C:0.18, G:0.31, T:0.29 Consensus pattern (46 bp): TTATCTGAGGCTGAGGTGCTGGCTTTACTATGAGGGACATGCATAC Found at i:289958 original size:3 final size:3 Alignment explanation

Indices: 289950--289994 Score: 90 Period size: 3 Copynumber: 15.0 Consensus size: 3 289940 CCATCAAAAA 289950 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT 1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT 289995 AGATATTCAT Statistics Matches: 42, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 3 42 1.00 ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67 Consensus pattern (3 bp): TCT Found at i:290775 original size:17 final size:17 Alignment explanation

Indices: 290724--290770 Score: 58 Period size: 18 Copynumber: 2.6 Consensus size: 17 290714 TTTGAAGGTG * * 290724 AATTTCAGGTCATTTGAA 1 AATTTCAGGTCAATT-CA 290742 AATTTCAGGTCAATTCA 1 AATTTCAGGTCAATTCA 290759 AATTCTCAGGTC 1 AATT-TCAGGTC 290771 TTTCACATTT Statistics Matches: 26, Mismatches: 2, Indels: 2 0.87 0.07 0.07 Matches are distributed among these distances: 17 5 0.19 18 21 0.81 ACGTcount: A:0.32, C:0.17, G:0.15, T:0.36 Consensus pattern (17 bp): AATTTCAGGTCAATTCA Found at i:290933 original size:16 final size:16 Alignment explanation

Indices: 290912--290944 Score: 57 Period size: 16 Copynumber: 2.1 Consensus size: 16 290902 ATTTCAGGTC 290912 TTTCAGGTCATTAGTA 1 TTTCAGGTCATTAGTA * 290928 TTTCAGGTCTTTAGTA 1 TTTCAGGTCATTAGTA 290944 T 1 T 290945 GTTCCAATAA Statistics Matches: 16, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 16 16 1.00 ACGTcount: A:0.21, C:0.12, G:0.18, T:0.48 Consensus pattern (16 bp): TTTCAGGTCATTAGTA Found at i:293658 original size:29 final size:29 Alignment explanation

Indices: 293633--293919 Score: 249 Period size: 29 Copynumber: 9.9 Consensus size: 29 293623 GGCAAAACAC * * * 293633 TCTCTTGTCATGATGTACCAGGAAAACTT 1 TCTCTAGTCAGGATGTACCAGCAAAACTT * ** * 293662 TCTCTTGTCACAATGTATCTA-CAAAACTT 1 TCTCTAGTCAGGATGTA-CCAGCAAAACTT * 293691 TCTCTAGTCAGGATATACCAGCAAAACTT 1 TCTCTAGTCAGGATGTACCAGCAAAACTT * 293720 TCTCTAGTCAGGATATACCAGCAAAACTT 1 TCTCTAGTCAGGATGTACCAGCAAAACTT * 293749 TCTCTAGTCAGGATATACCAGCAAAACTT 1 TCTCTAGTCAGGATGTACCAGCAAAACTT * * 293778 TCTCTAGTCAGGATGTA-CGGCAAAACGT 1 TCTCTAGTCAGGATGTACCAGCAAAACTT * * * 293806 TCTCTTGTCAGGATGT-CCAGCCATAACGT 1 TCTCTAGTCAGGATGTACCAG-CAAAACTT * * ** ** * * * 293835 TCTCTTGTAACAATGTGTCTGCAAAGCAT 1 TCTCTAGTCAGGATGTACCAGCAAAACTT * * * 293864 TCTCTAGTTAGGATGTCCCAGC-AAAGTGT 1 TCTCTAGTCAGGATGTACCAGCAAAACT-T * ** 293893 TCTCTTGTCAGGATGTACTGGCAAAAC 1 TCTCTAGTCAGGATGTACCAGCAAAAC 293920 GTTTTCTTGT Statistics Matches: 212, Mismatches: 39, Indels: 13 0.80 0.15 0.05 Matches are distributed among these distances: 28 30 0.14 29 175 0.83 30 7 0.03 ACGTcount: A:0.29, C:0.23, G:0.17, T:0.31 Consensus pattern (29 bp): TCTCTAGTCAGGATGTACCAGCAAAACTT Found at i:293921 original size:87 final size:86 Alignment explanation

Indices: 293633--293931 Score: 289 Period size: 87 Copynumber: 3.5 Consensus size: 86 293623 GGCAAAACAC * * * 293633 TCTCTTGTCATGATGTACCAGG-AAAACTTTCTCTTGTCACAATGTATCTACAAAACTTTCTCTA 1 TCTCTTGTCAGGATGTA-CAGGCAAAACGTTCTCTTGTCACAATGTATCTGCAAAACTTTCTCTA * 293697 GTCAGGATATACCAGCAAAACT-T 65 GTCAGGATGT-CCAGCAAAA-TGT * * * * ** * * * 293720 TCTCTAGTCAGGATATACCA-GCAAAACTTTCTCTAGTCAGGATATACCAGCAAAACTTTCTCTA 1 TCTCTTGTCAGGATGTA-CAGGCAAAACGTTCTCTTGTCACAATGTATCTGCAAAACTTTCTCTA * * * 293784 GTCAGGATGTACGGCAAAACGT 65 GTCAGGATGTCCAGCAAAATGT * * * * * * * 293806 TCTCTTGTCAGGATGTCCAGCCATAACGTTCTCTTGTAACAATGTGTCTGCAAAGCATTCTCTAG 1 TCTCTTGTCAGGATGTACAGGCAAAACGTTCTCTTGTCACAATGTATCTGCAAAACTTTCTCTAG * * 293871 TTAGGATGTCCCAGCAAAGTGT 66 TCAGGATGT-CCAGCAAAATGT * * 293893 TCTCTTGTCAGGATGTACTGGCAAAACGTTTTCTTGTCA 1 TCTCTTGTCAGGATGTACAGGCAAAACGTTCTCTTGTCA 293932 AGGTGTACTG Statistics Matches: 167, Mismatches: 41, Indels: 8 0.77 0.19 0.04 Matches are distributed among these distances: 85 2 0.01 86 63 0.38 87 102 0.61 ACGTcount: A:0.28, C:0.23, G:0.17, T:0.32 Consensus pattern (86 bp): TCTCTTGTCAGGATGTACAGGCAAAACGTTCTCTTGTCACAATGTATCTGCAAAACTTTCTCTAG TCAGGATGTCCAGCAAAATGT Found at i:305840 original size:2 final size:2 Alignment explanation

Indices: 305833--305893 Score: 122 Period size: 2 Copynumber: 30.5 Consensus size: 2 305823 TAATCACCTA 305833 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG 1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG 305875 AG AG AG AG AG AG AG AG AG A 1 AG AG AG AG AG AG AG AG AG A 305894 ATCTTTTTTC Statistics Matches: 59, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 59 1.00 ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00 Consensus pattern (2 bp): AG Found at i:312157 original size:21 final size:20 Alignment explanation

Indices: 312132--312531 Score: 363 Period size: 21 Copynumber: 19.0 Consensus size: 20 312122 TATTTTTTAT ** 312132 TAATTTGTTATAACGGATTA 1 TAATTTGTTATAACAAATTA * * 312152 GTAATTTGTTTTAACAAATCA 1 -TAATTTGTTATAACAAATTA * * 312173 TTAATTTGTTACAACAGATTA 1 -TAATTTGTTATAACAAATTA 312194 TCAATTTGTTATAACAAATTA 1 T-AATTTGTTATAACAAATTA * * 312215 TTAATTTGTTATAACAGATAA 1 -TAATTTGTTATAACAAATTA * 312236 GTAATTTGTTATAACAGATTA 1 -TAATTTGTTATAACAAATTA * 312257 TCAATTTGTTATATCAAATTA 1 T-AATTTGTTATAACAAATTA * * 312278 TTGATTTGTTATAACAGATTA 1 -TAATTTGTTATAACAAATTA * 312299 GTAATTTGTTATAACAGATTA 1 -TAATTTGTTATAACAAATTA * 312320 TCAATTTGGTATAACAAATTA 1 T-AATTTGTTATAACAAATTA * * ** * 312341 GTAGTCTGTTATAACAGGTAA 1 -TAATTTGTTATAACAAATTA 312362 TCAATTT-TTATAACAAATTA 1 T-AATTTGTTATAACAAATTA 312382 TCAATTTGTTATAACAAATTA 1 T-AATTTGTTATAACAAATTA * * 312403 CTAATCTGTTATAAAAAAAAATTA 1 -TAATTTGTTAT---AACAAATTA * 312427 GTAATTTGTTATAACAAATAA 1 -TAATTTGTTATAACAAATTA * 312448 TTAATTTGTTATAATAAATTA 1 -TAATTTGTTATAACAAATTA * 312469 TTAATTTGTTATAACAAGTTA 1 -TAATTTGTTATAACAAATTA * 312490 TCAATTTGTTATAACAGATTA 1 T-AATTTGTTATAACAAATTA 312511 TCAATTTGTT-TAAACAAATTA 1 T-AATTTGTTAT-AACAAATTA 312532 ATATTTACAA Statistics Matches: 316, Mismatches: 49, Indels: 28 0.80 0.12 0.07 Matches are distributed among these distances: 20 23 0.07 21 271 0.86 22 4 0.01 24 18 0.06 ACGTcount: A:0.41, C:0.07, G:0.09, T:0.43 Consensus pattern (20 bp): TAATTTGTTATAACAAATTA Found at i:312177 original size:42 final size:41 Alignment explanation

Indices: 312128--312520 Score: 403 Period size: 42 Copynumber: 9.3 Consensus size: 41 312118 GCAGTATTTT * * 312128 TTATTAATTTGTTATAACGGATTAGTAATTTGTTTTAACAAA 1 TTATTAATTTGTTATAACAGATTA-TAATTTGTTATAACAAA * * 312170 TCATTAATTTGTTACAACAGATTATCAATTTGTTATAACAAA 1 TTATTAATTTGTTATAACAGATTAT-AATTTGTTATAACAAA * * 312212 TTATTAATTTGTTATAACAGATAAGTAATTTGTTATAACAGA 1 TTATTAATTTGTTATAACAGATTA-TAATTTGTTATAACAAA * * * * * 312254 TTATCAATTTGTTATATCAAATTATTGATTTGTTATAACAGA 1 TTATTAATTTGTTATAACAGATTA-TAATTTGTTATAACAAA * * 312296 TTAGTAATTTGTTATAACAGATTATCAATTTGGTATAACAAA 1 TTATTAATTTGTTATAACAGATTAT-AATTTGTTATAACAAA * * * * * 312338 TTAGTAGTCTGTTATAACAGGTAATCAATTT-TTATAACAAA 1 TTATTAATTTGTTATAACAGATTAT-AATTTGTTATAACAAA * * * * 312379 TTATCAATTTGTTATAACAAATTACTAATCTGTTATAAAAAAAAA 1 TTATTAATTTGTTATAACAGATTA-TAATTTGTTAT---AACAAA * * * * 312424 TTAGTAATTTGTTATAACAAATAATTAATTTGTTATAATAAA 1 TTATTAATTTGTTATAACAGATTA-TAATTTGTTATAACAAA * 312466 TTATTAATTTGTTATAACA-AGTTATCAATTTGTTATAACAGA 1 TTATTAATTTGTTATAACAGA-TTAT-AATTTGTTATAACAAA * 312508 TTATCAATTTGTT 1 TTATTAATTTGTT 312521 TAAACAAATT Statistics Matches: 295, Mismatches: 46, Indels: 20 0.82 0.13 0.06 Matches are distributed among these distances: 41 34 0.12 42 224 0.76 43 1 0.00 45 36 0.12 ACGTcount: A:0.40, C:0.07, G:0.09, T:0.44 Consensus pattern (41 bp): TTATTAATTTGTTATAACAGATTATAATTTGTTATAACAAA Found at i:312241 original size:63 final size:63 Alignment explanation

Indices: 312128--312531 Score: 467 Period size: 63 Copynumber: 6.4 Consensus size: 63 312118 GCAGTATTTT * ** * * * * * * 312128 TTATTAATTTGTTATAACGGATTAGTAATTTGTTTTAACAAATCATTAATTTGTTACAACAGA 1 TTATCAATTTGTTATAACAAATTATTAATTTGTTATAACAGATTAGTAATTTGTTATAACAGA * 312191 TTATCAATTTGTTATAACAAATTATTAATTTGTTATAACAGATAAGTAATTTGTTATAACAGA 1 TTATCAATTTGTTATAACAAATTATTAATTTGTTATAACAGATTAGTAATTTGTTATAACAGA * * 312254 TTATCAATTTGTTATATCAAATTATTGATTTGTTATAACAGATTAGTAATTTGTTATAACAGA 1 TTATCAATTTGTTATAACAAATTATTAATTTGTTATAACAGATTAGTAATTTGTTATAACAGA * * * * * * * 312317 TTATCAATTTGGTATAACAAATTAGTAGTCTGTTATAACAG-GTAATCAATTT-TTATAACAAA 1 TTATCAATTTGTTATAACAAATTATTAATTTGTTATAACAGATTAGT-AATTTGTTATAACAGA * * * * * 312379 TTATCAATTTGTTATAACAAATTACTAATCTGTTATAAAAAAAAATTAGTAATTTGTTATAACAA 1 TTATCAATTTGTTATAACAAATTATTAATTTGTTAT---AACAGATTAGTAATTTGTTATAACAG 312444 A 63 A * * * 312445 TAATTAATTTGTTATAATAAATTATTAATTTGTTATAACA-AGTTA-TCAATTTGTTATAACAGA 1 TTATCAATTTGTTATAACAAATTATTAATTTGTTATAACAGA-TTAGT-AATTTGTTATAACAGA 312508 TTATCAATTTGTT-TAAACAAATTA 1 TTATCAATTTGTTAT-AACAAATTA 312532 ATATTTACAA Statistics Matches: 294, Mismatches: 38, Indels: 18 0.84 0.11 0.05 Matches are distributed among these distances: 62 48 0.16 63 194 0.66 65 8 0.03 66 44 0.15 ACGTcount: A:0.41, C:0.07, G:0.09, T:0.43 Consensus pattern (63 bp): TTATCAATTTGTTATAACAAATTATTAATTTGTTATAACAGATTAGTAATTTGTTATAACAGA Found at i:312431 original size:24 final size:24 Alignment explanation

Indices: 312397--312450 Score: 72 Period size: 24 Copynumber: 2.2 Consensus size: 24 312387 TTGTTATAAC 312397 AAATTACTAATCTGTTATAAAAAA 1 AAATTACTAATCTGTTATAAAAAA * * * 312421 AAATTAGTAATTTGTTATAACAAA 1 AAATTACTAATCTGTTATAAAAAA * 312445 TAATTA 1 AAATTA 312451 ATTTGTTATA Statistics Matches: 26, Mismatches: 4, Indels: 0 0.87 0.13 0.00 Matches are distributed among these distances: 24 26 1.00 ACGTcount: A:0.52, C:0.06, G:0.06, T:0.37 Consensus pattern (24 bp): AAATTACTAATCTGTTATAAAAAA Found at i:312568 original size:21 final size:21 Alignment explanation

Indices: 312544--312589 Score: 65 Period size: 21 Copynumber: 2.2 Consensus size: 21 312534 ATTTACAATA * 312544 GCATAGAGATATCATAGCATT 1 GCATAGAAATATCATAGCATT * * 312565 GCATAGAAATCTCATATCATT 1 GCATAGAAATATCATAGCATT 312586 GCAT 1 GCAT 312590 TTTTATACTT Statistics Matches: 22, Mismatches: 3, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 21 22 1.00 ACGTcount: A:0.37, C:0.17, G:0.15, T:0.30 Consensus pattern (21 bp): GCATAGAAATATCATAGCATT Found at i:315126 original size:21 final size:21 Alignment explanation

Indices: 315102--315173 Score: 110 Period size: 21 Copynumber: 3.4 Consensus size: 21 315092 GATAATTGAT * 315102 AATTGATAATCTGTTATAACA 1 AATTAATAATCTGTTATAACA * 315123 AATTAATAATTTGTTATAACA 1 AATTAATAATCTGTTATAACA 315144 AA-TAACTAATCTGTTATAACA 1 AATTAA-TAATCTGTTATAACA 315165 AATTAATAA 1 AATTAATAA 315174 AAAAAAAAAG Statistics Matches: 46, Mismatches: 3, Indels: 4 0.87 0.06 0.08 Matches are distributed among these distances: 20 3 0.07 21 40 0.87 22 3 0.07 ACGTcount: A:0.49, C:0.08, G:0.06, T:0.38 Consensus pattern (21 bp): AATTAATAATCTGTTATAACA Found at i:316218 original size:2 final size:2 Alignment explanation

Indices: 316213--316256 Score: 88 Period size: 2 Copynumber: 22.0 Consensus size: 2 316203 ACGATTTCGT 316213 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 316255 TC 1 TC 316257 ACACACACAC Statistics Matches: 42, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 42 1.00 ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50 Consensus pattern (2 bp): TC Done.