Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: CP032253.1 Gossypioides kirkii chromosome KI_11

Parameters: 2 7 7 80 10 50 1000

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000

Length: 55708359
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33

Warning! 2600 characters in sequence are not A, C, G, or T


File 36 of 182

Found at i:13684873 original size:10 final size:10

Alignment explanation

Indices: 13684810--13684874 Score: 55 Period size: 10 Copynumber: 6.5 Consensus size: 10 13684800 TTTTAATTTT 13684810 TTTTAAAGTAA 1 TTTTAAA-TAA 13684821 -TTTATAATAA 1 TTTTA-AATAA * 13684831 TTTTAAA-AC 1 TTTTAAATAA * 13684840 TTTT-TATAA 1 TTTTAAATAA * 13684849 TTCTAAATAA 1 TTTTAAATAA 13684859 TTTTTAAATAA 1 -TTTTAAATAA 13684870 TTTTA 1 TTTTA 13684875 TCTTTTATAA Statistics Matches: 43, Mismatches: 6, Indels: 11 0.72 0.10 0.18 Matches are distributed among these distances: 8 1 0.02 9 9 0.21 10 18 0.42 11 15 0.35 ACGTcount: A:0.43, C:0.03, G:0.02, T:0.52 Consensus pattern (10 bp): TTTTAAATAA Found at i:13689387 original size:13 final size:13 Alignment explanation

Indices: 13689366--13689397 Score: 55 Period size: 13 Copynumber: 2.5 Consensus size: 13 13689356 CATATATAAG * 13689366 GGCACAAGATATA 1 GGCAAAAGATATA 13689379 GGCAAAAGATATA 1 GGCAAAAGATATA 13689392 GGCAAA 1 GGCAAA 13689398 GTCATGAAGA Statistics Matches: 18, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 13 18 1.00 ACGTcount: A:0.50, C:0.12, G:0.25, T:0.12 Consensus pattern (13 bp): GGCAAAAGATATA Found at i:13692160 original size:15 final size:15 Alignment explanation

Indices: 13692140--13692173 Score: 50 Period size: 15 Copynumber: 2.3 Consensus size: 15 13692130 ATGTAATTTT * 13692140 ATTTATCTGAGTTAA 1 ATTTATCTAAGTTAA * 13692155 ATTTATCTAATTTAA 1 ATTTATCTAAGTTAA 13692170 ATTT 1 ATTT 13692174 TAAAATCAAA Statistics Matches: 17, Mismatches: 2, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 15 17 1.00 ACGTcount: A:0.35, C:0.06, G:0.06, T:0.53 Consensus pattern (15 bp): ATTTATCTAAGTTAA Found at i:13693136 original size:25 final size:27 Alignment explanation

Indices: 13693108--13693158 Score: 70 Period size: 25 Copynumber: 2.0 Consensus size: 27 13693098 AATTTAGTAA * * 13693108 AATTATATTTTTATT-TTTT-AATTTT 1 AATTAAATTATTATTATTTTGAATTTT 13693133 AATTAAATTATTATTATTTTGAATTT 1 AATTAAATTATTATTATTTTGAATTT 13693159 AAAAAAACTT Statistics Matches: 22, Mismatches: 2, Indels: 2 0.85 0.08 0.08 Matches are distributed among these distances: 25 13 0.59 26 4 0.18 27 5 0.23 ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65 Consensus pattern (27 bp): AATTAAATTATTATTATTTTGAATTTT Found at i:13696460 original size:6 final size:6 Alignment explanation

Indices: 13696449--13696478 Score: 60 Period size: 6 Copynumber: 5.0 Consensus size: 6 13696439 ATGAAGATAA 13696449 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT 1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT 13696479 AAAAATATTA Statistics Matches: 24, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 6 24 1.00 ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83 Consensus pattern (6 bp): TTTTAT Found at i:13696807 original size:24 final size:25 Alignment explanation

Indices: 13696761--13696809 Score: 73 Period size: 25 Copynumber: 2.0 Consensus size: 25 13696751 TAAAAAAACA ** 13696761 TTTTATCATAAAAATTTTGGAAAAT 1 TTTTATCATAAAAAAATTGGAAAAT 13696786 TTTTATCATAAAAAAATT-GAAAAT 1 TTTTATCATAAAAAAATTGGAAAAT 13696810 GGGGGATTTT Statistics Matches: 22, Mismatches: 2, Indels: 1 0.88 0.08 0.04 Matches are distributed among these distances: 24 6 0.27 25 16 0.73 ACGTcount: A:0.49, C:0.04, G:0.06, T:0.41 Consensus pattern (25 bp): TTTTATCATAAAAAAATTGGAAAAT Found at i:13703488 original size:24 final size:24 Alignment explanation

Indices: 13703431--13703489 Score: 66 Period size: 24 Copynumber: 2.4 Consensus size: 24 13703421 AGATAATTAT * 13703431 ATAAAAAATTTCAATAAATATAAA 1 ATAAAAAAATTCAATAAATATAAA * * 13703455 ATATATAAAATT-ATTAAATATTAAA 1 ATA-AAAAAATTCAATAAATA-TAAA 13703480 ATAAAAAAAT 1 ATAAAAAAAT 13703490 ATTTTTTTAA Statistics Matches: 29, Mismatches: 4, Indels: 4 0.78 0.11 0.11 Matches are distributed among these distances: 24 16 0.55 25 13 0.45 ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32 Consensus pattern (24 bp): ATAAAAAAATTCAATAAATATAAA Found at i:13704776 original size:72 final size:72 Alignment explanation

Indices: 13704700--13704842 Score: 259 Period size: 72 Copynumber: 2.0 Consensus size: 72 13704690 ATGCCAAAAC * 13704700 AGCAAAGCAGAGCAGCAACAGACTGCATGCTCAAACCAGAAAACAAATCCCAGCTAACCAAGAAA 1 AGCAAAGCAGAGCAGCAACAGACTGCATGCTCAAACCAGAAAACAAATCCCAGCAAACCAAGAAA 13704765 CAACAGT 66 CAACAGT * * 13704772 AGCAAAGCAGAGCAGCAATAGACTGCATGCTCAAACCAGAAAACAAATCCCATCAAACCAAGAAA 1 AGCAAAGCAGAGCAGCAACAGACTGCATGCTCAAACCAGAAAACAAATCCCAGCAAACCAAGAAA 13704837 CAACAG 66 CAACAG 13704843 CCTGCACCAC Statistics Matches: 68, Mismatches: 3, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 72 68 1.00 ACGTcount: A:0.48, C:0.27, G:0.16, T:0.08 Consensus pattern (72 bp): AGCAAAGCAGAGCAGCAACAGACTGCATGCTCAAACCAGAAAACAAATCCCAGCAAACCAAGAAA CAACAGT Found at i:13725929 original size:232 final size:232 Alignment explanation

Indices: 13725523--13725990 Score: 927 Period size: 232 Copynumber: 2.0 Consensus size: 232 13725513 GCCCCCACTT 13725523 ACATATGTAAAATGCCATACTTAATACTGACCAACCTACTCAAACTAAATAAGGCAGTCTTGTTG 1 ACATATGTAAAATGCCATACTTAATACTGACCAACCTACTCAAACTAAATAAGGCAGTCTTGTTG 13725588 AGAATTTATACTGGTGCAAGTCAAGACAGGGAAACGGTGCAAGACTAGAAAGCAAGCAACTCCAT 66 AGAATTTATACTGGTGCAAGTCAAGACAGGGAAACGGTGCAAGACTAGAAAGCAAGCAACTCCAT 13725653 CTCATATTTCATGGTAATTGCTTTATAAATAATATTCCCATACGCACCTTGCATCTGTTAGCGAC 131 CTCATATTTCATGGTAATTGCTTTATAAATAATATTCCCATACGCACCTTGCATCTGTTAGCGAC 13725718 ATTTATGGCATCTGAGGGCCGTGCATCCACAATTATG 196 ATTTATGGCATCTGAGGGCCGTGCATCCACAATTATG 13725755 ACATATGTAAAATGCCATACTTAATACTGACCAACCTACTCAAACTAAATAAGGCAGTCTTGTTG 1 ACATATGTAAAATGCCATACTTAATACTGACCAACCTACTCAAACTAAATAAGGCAGTCTTGTTG * 13725820 AGATTTTATACTGGTGCAAGTCAAGACAGGGAAACGGTGCAAGACTAGAAAGCAAGCAACTCCAT 66 AGAATTTATACTGGTGCAAGTCAAGACAGGGAAACGGTGCAAGACTAGAAAGCAAGCAACTCCAT 13725885 CTCATATTTCATGGTAATTGCTTTATAAATAATATTCCCATACGCACCTTGCATCTGTTAGCGAC 131 CTCATATTTCATGGTAATTGCTTTATAAATAATATTCCCATACGCACCTTGCATCTGTTAGCGAC 13725950 ATTTATGGCATCTGAGGGCCGTGCATCCACAATTATG 196 ATTTATGGCATCTGAGGGCCGTGCATCCACAATTATG 13725987 ACAT 1 ACAT 13725991 CATTTTCCCC Statistics Matches: 235, Mismatches: 1, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 232 235 1.00 ACGTcount: A:0.34, C:0.21, G:0.18, T:0.28 Consensus pattern (232 bp): ACATATGTAAAATGCCATACTTAATACTGACCAACCTACTCAAACTAAATAAGGCAGTCTTGTTG AGAATTTATACTGGTGCAAGTCAAGACAGGGAAACGGTGCAAGACTAGAAAGCAAGCAACTCCAT CTCATATTTCATGGTAATTGCTTTATAAATAATATTCCCATACGCACCTTGCATCTGTTAGCGAC ATTTATGGCATCTGAGGGCCGTGCATCCACAATTATG Found at i:13727651 original size:20 final size:18 Alignment explanation

Indices: 13727610--13727654 Score: 54 Period size: 18 Copynumber: 2.3 Consensus size: 18 13727600 TATACACATT 13727610 AAAAAATATAAAAATTAA 1 AAAAAATATAAAAATTAA * 13727628 AAAATATATATAAAATCTAGA 1 AAAAAATATA-AAAAT-TA-A 13727649 AAAAAA 1 AAAAAA 13727655 ACATCATAAA Statistics Matches: 22, Mismatches: 2, Indels: 3 0.81 0.07 0.11 Matches are distributed among these distances: 18 9 0.41 19 5 0.23 20 2 0.09 21 6 0.27 ACGTcount: A:0.73, C:0.02, G:0.02, T:0.22 Consensus pattern (18 bp): AAAAAATATAAAAATTAA Found at i:13727801 original size:25 final size:27 Alignment explanation

Indices: 13727750--13727802 Score: 65 Period size: 25 Copynumber: 2.0 Consensus size: 27 13727740 GCAAAAAAAT * 13727750 AAAAATTATAAAAAATGTATTTCTAAA 1 AAAAATTATAAAAAATGTATTTATAAA * * 13727777 AAAAATTA-AAAATAT-TTTTTATAAA 1 AAAAATTATAAAAAATGTATTTATAAA 13727802 A 1 A 13727803 GTCAAAATAT Statistics Matches: 23, Mismatches: 3, Indels: 2 0.82 0.11 0.07 Matches are distributed among these distances: 25 9 0.39 26 6 0.26 27 8 0.35 ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36 Consensus pattern (27 bp): AAAAATTATAAAAAATGTATTTATAAA Found at i:13728358 original size:23 final size:21 Alignment explanation

Indices: 13728311--13728366 Score: 60 Period size: 22 Copynumber: 2.5 Consensus size: 21 13728301 ATATATAAAC * 13728311 AAATGTTTAAAATATTTTTTAT 1 AAAT-TTTAAAATATTATTTAT 13728333 AAAATTTTAAAATATATAATTT-T 1 -AAATTTTAAAATAT-T-ATTTAT 13728356 AAATTTTAAAA 1 AAATTTTAAAA 13728367 ATCTAAAATA Statistics Matches: 30, Mismatches: 1, Indels: 5 0.83 0.03 0.14 Matches are distributed among these distances: 22 21 0.70 23 6 0.20 24 3 0.10 ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48 Consensus pattern (21 bp): AAATTTTAAAATATTATTTAT Found at i:13728414 original size:19 final size:19 Alignment explanation

Indices: 13728356--13728414 Score: 59 Period size: 19 Copynumber: 3.2 Consensus size: 19 13728346 ATATAATTTT * 13728356 AAATTTTA-AAAATCTAAA 1 AAATTTTATAAAAACTAAA * * * 13728374 ATAA-TATATAAAAATTAGA 1 A-AATTTTATAAAAACTAAA 13728393 AAATTTTATAAAAACTAAA 1 AAATTTTATAAAAACTAAA 13728412 AAA 1 AAA 13728415 GTATTTAAAT Statistics Matches: 31, Mismatches: 7, Indels: 5 0.72 0.16 0.12 Matches are distributed among these distances: 18 6 0.19 19 25 0.81 ACGTcount: A:0.64, C:0.03, G:0.02, T:0.31 Consensus pattern (19 bp): AAATTTTATAAAAACTAAA Found at i:13728423 original size:19 final size:18 Alignment explanation

Indices: 13728356--13728423 Score: 57 Period size: 19 Copynumber: 3.6 Consensus size: 18 13728346 ATATAATTTT 13728356 AAAT-TTTAAAAATCTAAA 1 AAATATTTAAAAA-CTAAA * * * 13728374 ATAATATATAAAAATTAGA 1 A-AATATTTAAAAACTAAA * 13728393 AAATTTTATAAAAACTAAA 1 AAATATT-TAAAAACTAAA 13728412 AAAGTATTTAAA 1 AAA-TATTTAAA 13728424 TTTTAAGTAA Statistics Matches: 38, Mismatches: 8, Indels: 7 0.72 0.15 0.13 Matches are distributed among these distances: 18 5 0.13 19 23 0.61 20 10 0.26 ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32 Consensus pattern (18 bp): AAATATTTAAAAACTAAA Found at i:13729103 original size:21 final size:21 Alignment explanation

Indices: 13729079--13729119 Score: 55 Period size: 21 Copynumber: 2.0 Consensus size: 21 13729069 AGGGGAATTA * * 13729079 CTTGGATTTTTATAAAGAAAT 1 CTTGGAGTTTTACAAAGAAAT * 13729100 CTTGGGGTTTTACAAAGAAA 1 CTTGGAGTTTTACAAAGAAA 13729120 AATTATTTTA Statistics Matches: 17, Mismatches: 3, Indels: 0 0.85 0.15 0.00 Matches are distributed among these distances: 21 17 1.00 ACGTcount: A:0.37, C:0.07, G:0.20, T:0.37 Consensus pattern (21 bp): CTTGGAGTTTTACAAAGAAAT Found at i:13732418 original size:21 final size:21 Alignment explanation

Indices: 13732368--13732434 Score: 73 Period size: 21 Copynumber: 3.2 Consensus size: 21 13732358 GACTGCGGGT * 13732368 TGTAACTTGGAGAGGTAGGG-C 1 TGTAACTTGGTGAGGT-GGGAC * * * 13732389 TATAGCTTGGTGATGTGGGAC 1 TGTAACTTGGTGAGGTGGGAC * 13732410 TGTAACTTGGTGAGGTTGGAC 1 TGTAACTTGGTGAGGTGGGAC 13732431 TGTA 1 TGTA 13732435 CCCAGGAGAA Statistics Matches: 37, Mismatches: 8, Indels: 2 0.79 0.17 0.04 Matches are distributed among these distances: 20 3 0.08 21 34 0.92 ACGTcount: A:0.21, C:0.09, G:0.39, T:0.31 Consensus pattern (21 bp): TGTAACTTGGTGAGGTGGGAC Found at i:13732484 original size:42 final size:42 Alignment explanation

Indices: 13732438--13732644 Score: 168 Period size: 42 Copynumber: 4.9 Consensus size: 42 13732428 GACTGTACCC * * 13732438 AGGAGAAGTAGGGCTATAAGCGGGTGAAGTAGGGCTGTATGA 1 AGGAGATGTAGGGCTATAAGCAGGTGAAGTAGGGCTGTATGA * * * * 13732480 AGGAGATGTGGGGCTATAGGAAGGTGAAGTAGGGCTGTACGA 1 AGGAGATGTAGGGCTATAAGCAGGTGAAGTAGGGCTGTATGA * * * * * 13732522 AGGAGATGTTGGGCTGTATG-ACGGAGATGT-GGGACTGTATGA 1 AGGAGATGTAGGGCTATAAGCA-GGTGAAGTAGGG-CTGTATGA * * * * * * * 13732564 TGGAGAAGTGGGGCTATATGCAGGTGAAGTTGGGCTATATGC 1 AGGAGATGTAGGGCTATAAGCAGGTGAAGTAGGGCTGTATGA * * * * 13732606 TGGTGATGTAGGGCTATATA-CGGGTGAAGTGGGGCTGTA 1 AGGAGATGTAGGGCTATA-AGCAGGTGAAGTAGGGCTGTA 13732645 GCTAGGTGAA Statistics Matches: 133, Mismatches: 27, Indels: 10 0.78 0.16 0.06 Matches are distributed among these distances: 41 4 0.03 42 125 0.94 43 4 0.03 ACGTcount: A:0.26, C:0.08, G:0.43, T:0.24 Consensus pattern (42 bp): AGGAGATGTAGGGCTATAAGCAGGTGAAGTAGGGCTGTATGA Found at i:13732509 original size:63 final size:63 Alignment explanation

Indices: 13732438--13732623 Score: 192 Period size: 63 Copynumber: 3.0 Consensus size: 63 13732428 GACTGTACCC * * 13732438 AGGAGAAGTAGGGCTATAAGCGGGTGAAGTAGGGCTGTATGAAGGAGATGTGGGGCTATAGGA 1 AGGAGAAGTAGGGCTATAAGCAGGTGAAGTTGGGCTGTATGAAGGAGATGTGGGGCTATAGGA * * * * * * * * * * 13732501 AGGTGAAGTAGGGCTGTACGAAGGAGATGTTGGGCTGTATGACGGAGATGTGGGACTGTATGA 1 AGGAGAAGTAGGGCTATAAGCAGGTGAAGTTGGGCTGTATGAAGGAGATGTGGGGCTATAGGA * * * * ** * * 13732564 TGGAGAAGTGGGGCTATATGCAGGTGAAGTTGGGCTATATGCTGGTGATGTAGGGCTATA 1 AGGAGAAGTAGGGCTATAAGCAGGTGAAGTTGGGCTGTATGAAGGAGATGTGGGGCTATA 13732624 TACGGGTGAA Statistics Matches: 96, Mismatches: 27, Indels: 0 0.78 0.22 0.00 Matches are distributed among these distances: 63 96 1.00 ACGTcount: A:0.26, C:0.08, G:0.42, T:0.24 Consensus pattern (63 bp): AGGAGAAGTAGGGCTATAAGCAGGTGAAGTTGGGCTGTATGAAGGAGATGTGGGGCTATAGGA Found at i:13732592 original size:21 final size:21 Alignment explanation

Indices: 13732437--13732665 Score: 122 Period size: 21 Copynumber: 10.9 Consensus size: 21 13732427 GGACTGTACC * * * 13732437 CAGGAGAAGTAGGGCTATAAG 1 CAGGTGAAGTGGGGCTATATG * * * 13732458 CGGGTGAAGTAGGGCTGTATG 1 CAGGTGAAGTGGGGCTATATG * * * * 13732479 AAGGAGATGTGGGGCTATAGG 1 CAGGTGAAGTGGGGCTATATG * * * * 13732500 AAGGTGAAGTAGGGCTGTACG 1 CAGGTGAAGTGGGGCTATATG * * * * * 13732521 AAGGAGATGTTGGGCTGTATG 1 CAGGTGAAGTGGGGCTATATG * * * * 13732542 -ACGGAGATGTGGGACTGTATG 1 CA-GGTGAAGTGGGGCTATATG * 13732563 -ATGGAGAAGTGGGGCTATATG 1 CA-GGTGAAGTGGGGCTATATG * 13732584 CAGGTGAAGTTGGGCTATATG 1 CAGGTGAAGTGGGGCTATATG * * * * 13732605 CTGGTGATGTAGGGCTATATA 1 CAGGTGAAGTGGGGCTATATG * * 13732626 CGGGTGAAGTGGGGCTGTA-G 1 CAGGTGAAGTGGGGCTATATG * 13732646 CTAGGTGAAGTGGGACTATA 1 C-AGGTGAAGTGGGGCTATA 13732666 GCTGGGGGAT Statistics Matches: 165, Mismatches: 40, Indels: 6 0.78 0.19 0.03 Matches are distributed among these distances: 20 2 0.01 21 162 0.98 22 1 0.01 ACGTcount: A:0.26, C:0.08, G:0.42, T:0.24 Consensus pattern (21 bp): CAGGTGAAGTGGGGCTATATG Found at i:13732698 original size:63 final size:62 Alignment explanation

Indices: 13732505--13732707 Score: 157 Period size: 63 Copynumber: 3.2 Consensus size: 62 13732495 ATAGGAAGGT * * * * * * * 13732505 GAAGTAGGGCTGTACGAAGGAGATGTTGGGCTGTATGAC-GGAGATGTGGGACTGTATGA-TGGA 1 GAAGTGGGGCTGTATGCAGGTGAAGTTGGGCTATATG-CTGGGGATGTGGGACTGTA--ACTGGA * * * * * 13732568 GAAGTGGGGCTATATGCAGGTGAAGTTGGGCTATATGCTGGTGATGTAGGG-CTATATACGGGT 1 GAAGTGGGGCTGTATGCAGGTGAAGTTGGGCTATATGCTGGGGATGT-GGGACTGTA-ACTGGA 13732631 GAAGTGGGGCTGTA-GCTAGGTGAAG-TGGGACTATA-GCTGGGGGATGTGGGACTGTAACTTGG 1 GAAGTGGGGCTGTATGC-AGGTGAAGTTGGG-CTATATGCT-GGGGATGTGGGACTGTAAC-TGG 13732693 A 62 A * * 13732694 GAAGTAGGACTGTA 1 GAAGTGGGGCTGTA 13732708 ACTTGGAGAT Statistics Matches: 113, Mismatches: 19, Indels: 16 0.76 0.13 0.11 Matches are distributed among these distances: 62 16 0.14 63 94 0.83 64 3 0.03 ACGTcount: A:0.24, C:0.09, G:0.42, T:0.25 Consensus pattern (62 bp): GAAGTGGGGCTGTATGCAGGTGAAGTTGGGCTATATGCTGGGGATGTGGGACTGTAACTGGA Found at i:13732703 original size:21 final size:21 Alignment explanation

Indices: 13732679--13732761 Score: 103 Period size: 21 Copynumber: 4.0 Consensus size: 21 13732669 GGGGGATGTG 13732679 GGACTGTAACTTGGAGAAGTA 1 GGACTGTAACTTGGAGAAGTA * 13732700 GGACTGTAACTTGGAGATGTA 1 GGACTGTAACTTGGAGAAGTA * * 13732721 GGGCTGTAACTTGGAGAGGTA 1 GGACTGTAACTTGGAGAAGTA * * * * 13732742 GGGCTATAGCTTGGTGAAGT 1 GGACTGTAACTTGGAGAAGT 13732762 TGGAGAATAA Statistics Matches: 55, Mismatches: 7, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 21 55 1.00 ACGTcount: A:0.27, C:0.10, G:0.37, T:0.27 Consensus pattern (21 bp): GGACTGTAACTTGGAGAAGTA Found at i:13732755 original size:42 final size:42 Alignment explanation

Indices: 13732634--13732755 Score: 129 Period size: 42 Copynumber: 2.9 Consensus size: 42 13732624 TACGGGTGAA * * * * * * * 13732634 GTGGGGCTGTAGCTAGGTGAAGTGGGACTATAGCTGGGGGAT 1 GTGGGACTGTAACTTGGAGAAGTAGGACTATAGCTTGGAGAT * * 13732676 GTGGGACTGTAACTTGGAGAAGTAGGACTGTAACTTGGAGAT 1 GTGGGACTGTAACTTGGAGAAGTAGGACTATAGCTTGGAGAT * * 13732718 GTAGGG-CTGTAACTTGGAGAGGTAGGGCTATAGCTTGG 1 GT-GGGACTGTAACTTGGAGAAGTAGGACTATAGCTTGG 13732756 TGAAGTTGGA Statistics Matches: 66, Mismatches: 13, Indels: 2 0.81 0.16 0.02 Matches are distributed among these distances: 42 63 0.95 43 3 0.05 ACGTcount: A:0.23, C:0.10, G:0.42, T:0.25 Consensus pattern (42 bp): GTGGGACTGTAACTTGGAGAAGTAGGACTATAGCTTGGAGAT Found at i:13732872 original size:42 final size:41 Alignment explanation

Indices: 13732826--13732970 Score: 166 Period size: 42 Copynumber: 3.5 Consensus size: 41 13732816 TGGTGAGCTA ** * 13732826 GGACTGTAAGTAGGTGATGTGGGGCTGTAACCAGGAGAGGTG 1 GGACTGTAACCAGGTGATGT-GGACTGTAACCAGGAGAGGTG * * * 13732868 GGACTGTACCCAGGAGATGTAGGACTGTAACCAGGAGAGGTA 1 GGACTGTAACCAGGTGATGT-GGACTGTAACCAGGAGAGGTG * * 13732910 GGACTGTAACCAGGTGATGATGGACTGTATCCAGGAGATGATG 1 GGACTGTAACCAGGTGATG-TGGACTGTAACCAGGAGA-GGTG * 13732953 GG-CTGTAACCAGGGGATG 1 GGACTGTAACCAGGTGATG 13732971 ACGTAGGAGA Statistics Matches: 88, Mismatches: 13, Indels: 4 0.84 0.12 0.04 Matches are distributed among these distances: 42 83 0.94 43 5 0.06 ACGTcount: A:0.27, C:0.14, G:0.39, T:0.20 Consensus pattern (41 bp): GGACTGTAACCAGGTGATGTGGACTGTAACCAGGAGAGGTG Found at i:13732970 original size:21 final size:21 Alignment explanation

Indices: 13732850--13732971 Score: 133 Period size: 21 Copynumber: 5.8 Consensus size: 21 13732840 TGATGTGGGG * 13732850 CTGTAACCAGGAGA-GGTGGGA 1 CTGTAACCAGGAGATGAT-GGA * 13732871 CTGTACCCAGGAGATG-TAGGA 1 CTGTAACCAGGAGATGAT-GGA * 13732892 CTGTAACCAGGAGA-GGTAGGA 1 CTGTAACCAGGAGATGAT-GGA * 13732913 CTGTAACCAGGTGATGATGGA 1 CTGTAACCAGGAGATGATGGA * * 13732934 CTGTATCCAGGAGATGATGGG 1 CTGTAACCAGGAGATGATGGA * 13732955 CTGTAACCAGGGGATGA 1 CTGTAACCAGGAGATGA 13732972 CGTAGGAGAG Statistics Matches: 88, Mismatches: 10, Indels: 6 0.85 0.10 0.06 Matches are distributed among these distances: 20 1 0.01 21 84 0.95 22 3 0.03 ACGTcount: A:0.29, C:0.16, G:0.37, T:0.19 Consensus pattern (21 bp): CTGTAACCAGGAGATGATGGA Found at i:13739434 original size:16 final size:16 Alignment explanation

Indices: 13739413--13739445 Score: 57 Period size: 16 Copynumber: 2.1 Consensus size: 16 13739403 CTCAGGATCT 13739413 AATTTTGTCGGAAAGA 1 AATTTTGTCGGAAAGA * 13739429 AATTTTTTCGGAAAGA 1 AATTTTGTCGGAAAGA 13739445 A 1 A 13739446 GCCCTCCTCC 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:0.39, C:0.06, G:0.21, T:0.33 Consensus pattern (16 bp): AATTTTGTCGGAAAGA Found at i:13747387 original size:26 final size:27 Alignment explanation

Indices: 13747336--13747392 Score: 71 Period size: 26 Copynumber: 2.1 Consensus size: 27 13747326 GCCTAAGCCA * 13747336 CCACGTCAGCTACCATGTCAGCACGT- 1 CCACGTCAGCTACCACGTCAGCACGTG * ** 13747362 CCACGTCAGCTGCCACGTCATTACGTG 1 CCACGTCAGCTACCACGTCAGCACGTG 13747389 CCAC 1 CCAC 13747393 ATCATCACGT Statistics Matches: 26, Mismatches: 4, Indels: 1 0.84 0.13 0.03 Matches are distributed among these distances: 26 22 0.85 27 4 0.15 ACGTcount: A:0.21, C:0.40, G:0.19, T:0.19 Consensus pattern (27 bp): CCACGTCAGCTACCACGTCAGCACGTG Found at i:13747392 original size:15 final size:15 Alignment explanation

Indices: 13747372--13747439 Score: 61 Period size: 15 Copynumber: 4.7 Consensus size: 15 13747362 CCACGTCAGC * 13747372 TGCCACGTCATTACG 1 TGCCACGTCATCACG * 13747387 TGCCACATCATCACG 1 TGCCACGTCATCACG 13747402 T-CCACGTCAGT-AC- 1 TGCCACGTCA-TCACG * * * 13747415 TGCCACATCATCCCT 1 TGCCACGTCATCACG 13747430 TGCCACGTCA 1 TGCCACGTCA 13747440 GCCAGTGGTT Statistics Matches: 43, Mismatches: 6, Indels: 8 0.75 0.11 0.14 Matches are distributed among these distances: 13 2 0.05 14 17 0.40 15 24 0.56 ACGTcount: A:0.22, C:0.40, G:0.15, T:0.24 Consensus pattern (15 bp): TGCCACGTCATCACG Found at i:13747435 original size:29 final size:30 Alignment explanation

Indices: 13747372--13747440 Score: 97 Period size: 29 Copynumber: 2.4 Consensus size: 30 13747362 CCACGTCAGC * 13747372 TGCCACGTCATTACGTGCCACATCATCACG 1 TGCCACGTCAGTACGTGCCACATCATCACG * * 13747402 T-CCACGTCAGTAC-TGCCACATCATCCCT 1 TGCCACGTCAGTACGTGCCACATCATCACG 13747430 TGCCACGTCAG 1 TGCCACGTCAG 13747441 CCAGTGGTTG Statistics Matches: 35, Mismatches: 3, Indels: 3 0.85 0.07 0.07 Matches are distributed among these distances: 28 14 0.40 29 20 0.57 30 1 0.03 ACGTcount: A:0.22, C:0.39, G:0.16, T:0.23 Consensus pattern (30 bp): TGCCACGTCAGTACGTGCCACATCATCACG Found at i:13748749 original size:17 final size:15 Alignment explanation

Indices: 13748710--13748752 Score: 50 Period size: 17 Copynumber: 2.7 Consensus size: 15 13748700 ATCACCATTT 13748710 ATTTTTATTTTTAAA 1 ATTTTTATTTTTAAA * 13748725 ATGATTTATGTTTTATAA 1 AT-TTTTAT-TTTTA-AA 13748743 ATTTTTATTT 1 ATTTTTATTT 13748753 CCTTAAAGAC Statistics Matches: 23, Mismatches: 2, Indels: 5 0.77 0.07 0.17 Matches are distributed among these distances: 15 2 0.09 16 7 0.30 17 10 0.43 18 4 0.17 ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65 Consensus pattern (15 bp): ATTTTTATTTTTAAA Found at i:13749009 original size:121 final size:121 Alignment explanation

Indices: 13748857--13749076 Score: 302 Period size: 121 Copynumber: 1.8 Consensus size: 121 13748847 AAAAAAACAA * * * * 13748857 ACGTGGTTTCCCTTCTTAGCTCATAGCTTTTAAATCTCTTCAATT-TCCTTTTTTATTCCCTTAA 1 ACGTGGCTTCCCTTCTTAGCTCACAGCTTTTAAA-CCCTTCAATTGCCCTTTTTTATTCCCTTAA * * * 13748921 TAATAT-ATATTTTACTAATTTACTTTTAAAATCTTTTAAATTTAAATTGACATAGTT 65 TAAT-TGATATTTTACCAATTTACCTATAAAATCTTTTAAATTTAAATTGACATAGTT * * * 13748978 ACGTGGCTTCCCTTCTTAG-TCCACATCTTTTAAACCCTTTAATTGCCCTTTTTTATTCCTTTAA 1 ACGTGGCTTCCCTTCTTAGCT-CACAGCTTTTAAACCCTTCAATTGCCCTTTTTTATTCCCTTAA 13749042 TAATTGATATTTTACCAATTTACCTATAAAATCTT 65 TAATTGATATTTTACCAATTTACCTATAAAATCTT 13749077 AAATTCAAAT Statistics Matches: 86, Mismatches: 10, Indels: 6 0.84 0.10 0.06 Matches are distributed among these distances: 120 10 0.12 121 76 0.88 ACGTcount: A:0.27, C:0.20, G:0.06, T:0.48 Consensus pattern (121 bp): ACGTGGCTTCCCTTCTTAGCTCACAGCTTTTAAACCCTTCAATTGCCCTTTTTTATTCCCTTAAT AATTGATATTTTACCAATTTACCTATAAAATCTTTTAAATTTAAATTGACATAGTT Found at i:13750136 original size:20 final size:20 Alignment explanation

Indices: 13750098--13750136 Score: 51 Period size: 20 Copynumber: 1.9 Consensus size: 20 13750088 TCCTCACAAT ** * 13750098 TTTGTAAGAGTTTTGGTAAA 1 TTTGTAAGAAATTTAGTAAA 13750118 TTTGTAAGAAATTTAGTAA 1 TTTGTAAGAAATTTAGTAA 13750137 TATCGTAAAA Statistics Matches: 16, Mismatches: 3, Indels: 0 0.84 0.16 0.00 Matches are distributed among these distances: 20 16 1.00 ACGTcount: A:0.36, C:0.00, G:0.21, T:0.44 Consensus pattern (20 bp): TTTGTAAGAAATTTAGTAAA Found at i:13751309 original size:29 final size:28 Alignment explanation

Indices: 13751228--13751373 Score: 105 Period size: 29 Copynumber: 4.9 Consensus size: 28 13751218 AAATTGAATC * * * 13751228 TAAAAACAAGTTTAGGTGCCAAATTAGG 1 TAAAAAAAAGTTTAGGTACCAAATTGGG * * * 13751256 AAAAAAATGCCAAGTTCAAGTACCAAATTGGG 1 TAAAAAA----AAGTTTAGGTACCAAATTGGG ** 13751288 TTAAAAAAAAGTTTAGGTACCAAATTAAG 1 -TAAAAAAAAGTTTAGGTACCAAATTGGG * * 13751317 -AAAAAGTGTCAAGTTTAGTTACCAAATTGGG 1 TAAAAA----AAAGTTTAGGTACCAAATTGGG 13751348 TCAAAAAAAAGTTTAGGTACCAAATT 1 T-AAAAAAAAGTTTAGGTACCAAATT 13751374 AAGAAAAAGT Statistics Matches: 90, Mismatches: 17, Indels: 21 0.70 0.13 0.16 Matches are distributed among these distances: 27 5 0.06 28 5 0.06 29 34 0.38 31 18 0.20 32 17 0.19 33 11 0.12 ACGTcount: A:0.46, C:0.11, G:0.18, T:0.25 Consensus pattern (28 bp): TAAAAAAAAGTTTAGGTACCAAATTGGG Found at i:13751334 original size:31 final size:31 Alignment explanation

Indices: 13751296--13751391 Score: 110 Period size: 31 Copynumber: 3.2 Consensus size: 31 13751286 GGTTAAAAAA 13751296 AAGTTTAGGTACCAAATTAAGAAAAAGTGTC 1 AAGTTTAGGTACCAAATTAAGAAAAAGTGTC * ** * 13751327 AAGTTTAGTTACCAAATTGGGTCAAAAA----A 1 AAGTTTAGGTACCAAATTAAG--AAAAAGTGTC 13751356 AAGTTTAGGTACCAAATTAAGAAAAAGTGTC 1 AAGTTTAGGTACCAAATTAAGAAAAAGTGTC 13751387 AAGTT 1 AAGTT 13751392 CATATTAAGC Statistics Matches: 51, Mismatches: 8, Indels: 12 0.72 0.11 0.17 Matches are distributed among these distances: 27 5 0.10 29 18 0.35 31 23 0.45 33 5 0.10 ACGTcount: A:0.45, C:0.09, G:0.19, T:0.27 Consensus pattern (31 bp): AAGTTTAGGTACCAAATTAAGAAAAAGTGTC Found at i:13751354 original size:60 final size:60 Alignment explanation

Indices: 13751229--13751393 Score: 242 Period size: 60 Copynumber: 2.7 Consensus size: 60 13751219 AATTGAATCT * * * * * * 13751229 AAAAACAAGTTTAGGTGCCAAATTAGGAAAAAAATGCCAAGTTCAAGTACCAAATTGGGTT 1 AAAAAAAAGTTTAGGTACCAAATTAAG-AAAAAGTGTCAAGTTCAAGTACCAAATTGGGTC * 13751290 AAAAAAAAGTTTAGGTACCAAATTAAGAAAAAGTGTCAAGTT-TAGTTACCAAATTGGGTC 1 AAAAAAAAGTTTAGGTACCAAATTAAGAAAAAGTGTCAAGTTCAAG-TACCAAATTGGGTC 13751350 AAAAAAAAGTTTAGGTACCAAATTAAGAAAAAGTGTCAAGTTCA 1 AAAAAAAAGTTTAGGTACCAAATTAAGAAAAAGTGTCAAGTTCA 13751394 TATTAAGCCT Statistics Matches: 94, Mismatches: 8, Indels: 4 0.89 0.08 0.04 Matches are distributed among these distances: 59 2 0.02 60 68 0.72 61 24 0.26 ACGTcount: A:0.47, C:0.11, G:0.18, T:0.24 Consensus pattern (60 bp): AAAAAAAAGTTTAGGTACCAAATTAAGAAAAAGTGTCAAGTTCAAGTACCAAATTGGGTC Found at i:13752034 original size:20 final size:20 Alignment explanation

Indices: 13752011--13752057 Score: 78 Period size: 20 Copynumber: 2.4 Consensus size: 20 13752001 AATGGACTAA 13752011 TTTGTAAAAAAATC-AGTAAT 1 TTTGTAAAAAAATCGA-TAAT 13752031 TTTGTAAAAAAATCGATAAT 1 TTTGTAAAAAAATCGATAAT 13752051 TTTGTAA 1 TTTGTAA 13752058 GAAATATAAT Statistics Matches: 26, Mismatches: 0, Indels: 2 0.93 0.00 0.07 Matches are distributed among these distances: 20 25 0.96 21 1 0.04 ACGTcount: A:0.47, C:0.04, G:0.11, T:0.38 Consensus pattern (20 bp): TTTGTAAAAAAATCGATAAT Found at i:13753167 original size:21 final size:18 Alignment explanation

Indices: 13753107--13753160 Score: 65 Period size: 21 Copynumber: 2.9 Consensus size: 18 13753097 GTCTTTATAT 13753107 AATATC-CAAATACAAAA 1 AATATCTCAAATACAAAA * 13753124 AATATCTCAAATACATTATA 1 AATATCTCAAATACA--AAA 13753144 AATATCTTCAAATACAA 1 AATATC-TCAAATACAA 13753161 CACAAATGCA Statistics Matches: 32, Mismatches: 1, Indels: 6 0.82 0.03 0.15 Matches are distributed among these distances: 17 6 0.19 18 8 0.25 19 1 0.03 20 8 0.25 21 9 0.28 ACGTcount: A:0.56, C:0.17, G:0.00, T:0.28 Consensus pattern (18 bp): AATATCTCAAATACAAAA Found at i:13754471 original size:26 final size:26 Alignment explanation

Indices: 13754431--13754480 Score: 91 Period size: 26 Copynumber: 1.9 Consensus size: 26 13754421 AGTTCGTGTG 13754431 AGCTAGGTTCACGAGCTCCCCTTGCA 1 AGCTAGGTTCACGAGCTCCCCTTGCA * 13754457 AGCTAGGTTCCCGAGCTCCCCTTG 1 AGCTAGGTTCACGAGCTCCCCTTG 13754481 TTGTTTTTTC Statistics Matches: 23, Mismatches: 1, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 26 23 1.00 ACGTcount: A:0.16, C:0.36, G:0.24, T:0.24 Consensus pattern (26 bp): AGCTAGGTTCACGAGCTCCCCTTGCA Found at i:13756273 original size:2 final size:2 Alignment explanation

Indices: 13756266--13756305 Score: 80 Period size: 2 Copynumber: 20.0 Consensus size: 2 13756256 CAACAATTAC 13756266 AT 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 AT 13756306 TGGTGTTTTG 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:0.00, T:0.50 Consensus pattern (2 bp): AT Found at i:13758732 original size:25 final size:24 Alignment explanation

Indices: 13758679--13758733 Score: 58 Period size: 25 Copynumber: 2.2 Consensus size: 24 13758669 TTGTGTATTG * * 13758679 AATAGAATTTGAATTTTGAATTATT 1 AATATAATTTGAATTTTAAATTA-T 13758704 AATATAATTTGATATTTATAAATTA- 1 AATATAATTTGA-ATTT-TAAATTAT 13758729 AATAT 1 AATAT 13758734 GTAAGATATA Statistics Matches: 26, Mismatches: 2, Indels: 4 0.81 0.06 0.12 Matches are distributed among these distances: 25 16 0.62 26 4 0.15 27 6 0.23 ACGTcount: A:0.45, C:0.00, G:0.07, T:0.47 Consensus pattern (24 bp): AATATAATTTGAATTTTAAATTAT Found at i:13768642 original size:18 final size:19 Alignment explanation

Indices: 13768619--13768656 Score: 60 Period size: 19 Copynumber: 2.1 Consensus size: 19 13768609 TAAATAAATC 13768619 ATTAAAA-TATTTATAAAA 1 ATTAAAAGTATTTATAAAA * 13768637 ATTAAAAGTATTTTTAAAA 1 ATTAAAAGTATTTATAAAA 13768656 A 1 A 13768657 GTTCAACCAC Statistics Matches: 18, Mismatches: 1, Indels: 1 0.90 0.05 0.05 Matches are distributed among these distances: 18 7 0.39 19 11 0.61 ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39 Consensus pattern (19 bp): ATTAAAAGTATTTATAAAA Found at i:13774219 original size:6 final size:6 Alignment explanation

Indices: 13774205--13774237 Score: 57 Period size: 6 Copynumber: 5.5 Consensus size: 6 13774195 CACTAATCTC * 13774205 TCTCCT TCTCTT TCTCTT TCTCTT TCTCTT TCT 1 TCTCTT TCTCTT TCTCTT TCTCTT TCTCTT TCT 13774238 TTGGCTGCCT Statistics Matches: 26, Mismatches: 1, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 6 26 1.00 ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64 Consensus pattern (6 bp): TCTCTT Found at i:13781496 original size:56 final size:56 Alignment explanation

Indices: 13781430--13781551 Score: 226 Period size: 56 Copynumber: 2.2 Consensus size: 56 13781420 ACATACGACA * 13781430 CCTAATAGCAACTTACCACCTATTCTAAAGATCGTTGTTCATCATTATCATGACTC 1 CCTAAAAGCAACTTACCACCTATTCTAAAGATCGTTGTTCATCATTATCATGACTC * 13781486 CCTAAAAGCAACTTACCACCTATTCTAAAGATCGTTGTTTATCATTATCATGACTC 1 CCTAAAAGCAACTTACCACCTATTCTAAAGATCGTTGTTCATCATTATCATGACTC 13781542 CCTAAAAGCA 1 CCTAAAAGCA 13781552 CAATTCTCAA Statistics Matches: 64, Mismatches: 2, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 56 64 1.00 ACGTcount: A:0.33, C:0.26, G:0.09, T:0.32 Consensus pattern (56 bp): CCTAAAAGCAACTTACCACCTATTCTAAAGATCGTTGTTCATCATTATCATGACTC Found at i:13784898 original size:16 final size:17 Alignment explanation

Indices: 13784869--13784900 Score: 57 Period size: 17 Copynumber: 1.9 Consensus size: 17 13784859 ATATTTGTTA 13784869 TTTTAATTTGATATTTT 1 TTTTAATTTGATATTTT 13784886 TTTTAATTT-ATATTT 1 TTTTAATTTGATATTT 13784901 AAACTTTTTT Statistics Matches: 15, Mismatches: 0, Indels: 1 0.94 0.00 0.06 Matches are distributed among these distances: 16 6 0.40 17 9 0.60 ACGTcount: A:0.25, C:0.00, G:0.03, T:0.72 Consensus pattern (17 bp): TTTTAATTTGATATTTT Found at i:13784933 original size:27 final size:24 Alignment explanation

Indices: 13784882--13784933 Score: 59 Period size: 27 Copynumber: 2.0 Consensus size: 24 13784872 TAATTTGATA * 13784882 TTTTTTTTAATTTATATTTAAACT 1 TTTTTTTTAATTTATATCTAAACT * 13784906 TTTTTTATCTAATTTGATATCTGAACT 1 TTTTTT-T-TAATTT-ATATCTAAACT 13784933 T 1 T 13784934 GACATTTTTT Statistics Matches: 23, Mismatches: 2, Indels: 3 0.82 0.07 0.11 Matches are distributed among these distances: 24 6 0.26 25 1 0.04 26 6 0.26 27 10 0.43 ACGTcount: A:0.27, C:0.08, G:0.04, T:0.62 Consensus pattern (24 bp): TTTTTTTTAATTTATATCTAAACT Found at i:13784950 original size:31 final size:33 Alignment explanation

Indices: 13784905--13784975 Score: 85 Period size: 31 Copynumber: 2.2 Consensus size: 33 13784895 ATATTTAAAC 13784905 TTTTTTTATCTAATTTGATA-TCTGAACTTGACA 1 TTTTTTTATCTAATTTGATACT-TGAACTTGACA * * 13784938 TTTTTTT-T-TAATTTGGTACTTGAATTTGACA 1 TTTTTTTATCTAATTTGATACTTGAACTTGACA * 13784969 ATTTTTT 1 TTTTTTT 13784976 CCTAAGTTGG Statistics Matches: 34, Mismatches: 3, Indels: 4 0.83 0.07 0.10 Matches are distributed among these distances: 31 25 0.74 32 2 0.06 33 7 0.21 ACGTcount: A:0.24, C:0.08, G:0.10, T:0.58 Consensus pattern (33 bp): TTTTTTTATCTAATTTGATACTTGAACTTGACA Found at i:13784986 original size:32 final size:31 Alignment explanation

Indices: 13784927--13784988 Score: 79 Period size: 32 Copynumber: 2.0 Consensus size: 31 13784917 ATTTGATATC ** * 13784927 TGAACTTGACATTTTTTTTTAATTTGGTACT 1 TGAACTTGACATTTTTTCCTAAGTTGGTACT * 13784958 TGAATTTGACAATTTTTTCCTAAGTTGGTAC 1 TGAACTTGAC-ATTTTTTCCTAAGTTGGTAC 13784989 CTAAGCCTTT Statistics Matches: 26, Mismatches: 4, Indels: 1 0.84 0.13 0.03 Matches are distributed among these distances: 31 9 0.35 32 17 0.65 ACGTcount: A:0.24, C:0.11, G:0.15, T:0.50 Consensus pattern (31 bp): TGAACTTGACATTTTTTCCTAAGTTGGTACT Found at i:13795162 original size:21 final size:21 Alignment explanation

Indices: 13795124--13795163 Score: 55 Period size: 21 Copynumber: 2.0 Consensus size: 21 13795114 ATTTTAAAAG * 13795124 ATTTAAACTTTCTATTTTTTA 1 ATTTAAAATTTCTATTTTTTA * 13795145 ATTTAAAATTT-TAGTTTTT 1 ATTTAAAATTTCTATTTTTT 13795164 GTTATTAAAT Statistics Matches: 17, Mismatches: 2, Indels: 1 0.85 0.10 0.05 Matches are distributed among these distances: 20 7 0.41 21 10 0.59 ACGTcount: A:0.30, C:0.05, G:0.03, T:0.62 Consensus pattern (21 bp): ATTTAAAATTTCTATTTTTTA Found at i:13796457 original size:13 final size:13 Alignment explanation

Indices: 13796441--13796465 Score: 50 Period size: 13 Copynumber: 1.9 Consensus size: 13 13796431 AATTAAATTT 13796441 AAAATATTTTTTA 1 AAAATATTTTTTA 13796454 AAAATATTTTTT 1 AAAATATTTTTT 13796466 TGGTACAAAT Statistics Matches: 12, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 12 1.00 ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56 Consensus pattern (13 bp): AAAATATTTTTTA Found at i:13796500 original size:55 final size:53 Alignment explanation

Indices: 13796423--13796525 Score: 145 Period size: 55 Copynumber: 1.9 Consensus size: 53 13796413 AAATTAGTAA * * 13796423 AAATAAAAAATTAAATTTAAAATATTTTTTAAAA-ATATTTTTTTGGTACAAAT 1 AAATAAAAAATTAAATTTAAAATATATTTTAAAATA-AATTTTTTGGTACAAAT * 13796476 AAATAATAAAGTTAAAATTTAAAATATATTTTAAAATAAATTTTTTGGTA 1 AAATAA-AAAATT-AAATTTAAAATATATTTTAAAATAAATTTTTTGGTA 13796526 TCAGTTGGTA Statistics Matches: 44, Mismatches: 3, Indels: 4 0.86 0.06 0.08 Matches are distributed among these distances: 53 6 0.14 54 5 0.11 55 32 0.73 56 1 0.02 ACGTcount: A:0.51, C:0.01, G:0.05, T:0.43 Consensus pattern (53 bp): AAATAAAAAATTAAATTTAAAATATATTTTAAAATAAATTTTTTGGTACAAAT Found at i:13801336 original size:12 final size:13 Alignment explanation

Indices: 13801310--13801338 Score: 51 Period size: 12 Copynumber: 2.3 Consensus size: 13 13801300 ATTAATATAT 13801310 TAAAATTAGAAAG 1 TAAAATTAGAAAG 13801323 TAAAATTA-AAAG 1 TAAAATTAGAAAG 13801335 TAAA 1 TAAA 13801339 GCTTGAAACA Statistics Matches: 16, Mismatches: 0, Indels: 1 0.94 0.00 0.06 Matches are distributed among these distances: 12 8 0.50 13 8 0.50 ACGTcount: A:0.66, C:0.00, G:0.10, T:0.24 Consensus pattern (13 bp): TAAAATTAGAAAG Found at i:13806139 original size:14 final size:14 Alignment explanation

Indices: 13806120--13806146 Score: 54 Period size: 14 Copynumber: 1.9 Consensus size: 14 13806110 AGTGGTTCAA 13806120 GGAACAGCTGTGAC 1 GGAACAGCTGTGAC 13806134 GGAACAGCTGTGA 1 GGAACAGCTGTGA 13806147 GTGCTCGAAG Statistics Matches: 13, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 14 13 1.00 ACGTcount: A:0.30, C:0.19, G:0.37, T:0.15 Consensus pattern (14 bp): GGAACAGCTGTGAC Found at i:13811817 original size:24 final size:24 Alignment explanation

Indices: 13811790--13811845 Score: 103 Period size: 24 Copynumber: 2.3 Consensus size: 24 13811780 AGCCAACACA 13811790 AGCCCAGAATGATTAGCTCTTACG 1 AGCCCAGAATGATTAGCTCTTACG * 13811814 AGCCTAGAATGATTAGCTCTTACG 1 AGCCCAGAATGATTAGCTCTTACG 13811838 AGCCCAGA 1 AGCCCAGA 13811846 TAGAGTTTAA Statistics Matches: 30, Mismatches: 2, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 24 30 1.00 ACGTcount: A:0.30, C:0.25, G:0.21, T:0.23 Consensus pattern (24 bp): AGCCCAGAATGATTAGCTCTTACG Found at i:13814570 original size:15 final size:16 Alignment explanation

Indices: 13814550--13814589 Score: 55 Period size: 15 Copynumber: 2.6 Consensus size: 16 13814540 TTGTGTTGAG * 13814550 AAAATTATTTAA-TTA 1 AAAATTAATTAATTTA 13814565 AAAATTAATTAATTTA 1 AAAATTAATTAATTTA * 13814581 AAAAATAAT 1 AAAATTAAT 13814590 GTTCATTTTG Statistics Matches: 22, Mismatches: 2, Indels: 1 0.88 0.08 0.04 Matches are distributed among these distances: 15 11 0.50 16 11 0.50 ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40 Consensus pattern (16 bp): AAAATTAATTAATTTA Found at i:13818293 original size:4 final size:4 Alignment explanation

Indices: 13818286--13818315 Score: 60 Period size: 4 Copynumber: 7.5 Consensus size: 4 13818276 TATGTATGGA 13818286 TGGG TGGG TGGG TGGG TGGG TGGG TGGG TG 1 TGGG TGGG TGGG TGGG TGGG TGGG TGGG TG 13818316 AGTGAGAAGA Statistics Matches: 26, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 4 26 1.00 ACGTcount: A:0.00, C:0.00, G:0.73, T:0.27 Consensus pattern (4 bp): TGGG Found at i:13819484 original size:6 final size:6 Alignment explanation

Indices: 13819472--13819523 Score: 86 Period size: 6 Copynumber: 8.7 Consensus size: 6 13819462 TCCGTATACC * * 13819472 CCATTG GCATTG GCATTG CCATTG CCATTG CCATTG CCATTG CCATTG 1 CCATTG CCATTG CCATTG CCATTG CCATTG CCATTG CCATTG CCATTG 13819520 CCAT 1 CCAT 13819524 AGGCTTATTA Statistics Matches: 44, Mismatches: 2, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 6 44 1.00 ACGTcount: A:0.17, C:0.31, G:0.19, T:0.33 Consensus pattern (6 bp): CCATTG Found at i:13820068 original size:6 final size:6 Alignment explanation

Indices: 13820059--13820086 Score: 56 Period size: 6 Copynumber: 4.7 Consensus size: 6 13820049 ACTCTGGTTC 13820059 TGGCTG TGGCTG TGGCTG TGGCTG TGGC 1 TGGCTG TGGCTG TGGCTG TGGCTG TGGC 13820087 AGTGACCAAA Statistics Matches: 22, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 6 22 1.00 ACGTcount: A:0.00, C:0.18, G:0.50, T:0.32 Consensus pattern (6 bp): TGGCTG Found at i:13822943 original size:8 final size:8 Alignment explanation

Indices: 13822928--13822961 Score: 52 Period size: 8 Copynumber: 4.4 Consensus size: 8 13822918 TATTATTTCG 13822928 TAAT-TTT 1 TAATATTT 13822935 TAATATTT 1 TAATATTT 13822943 TAATATTT 1 TAATATTT * 13822951 TAATAATT 1 TAATATTT 13822959 TAA 1 TAA 13822962 CCATTATTTC Statistics Matches: 25, Mismatches: 1, Indels: 1 0.93 0.04 0.04 Matches are distributed among these distances: 7 4 0.16 8 21 0.84 ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59 Consensus pattern (8 bp): TAATATTT Found at i:13838762 original size:33 final size:33 Alignment explanation

Indices: 13838725--13838788 Score: 76 Period size: 33 Copynumber: 1.9 Consensus size: 33 13838715 GTTTTAAAAA * 13838725 TATAAATTCTAAAT-GATTTTATGGTTTTTTTTT 1 TATAAATTCTAAATAGATTTTA-GATTTTTTTTT * * * 13838758 TATAATTTTTAAATATATTTTAGATTTTTTT 1 TATAAATTCTAAATAGATTTTAGATTTTTTT 13838789 ATAAATTTCC Statistics Matches: 26, Mismatches: 4, Indels: 2 0.81 0.12 0.06 Matches are distributed among these distances: 33 20 0.77 34 6 0.23 ACGTcount: A:0.30, C:0.02, G:0.06, T:0.62 Consensus pattern (33 bp): TATAAATTCTAAATAGATTTTAGATTTTTTTTT Found at i:13838838 original size:20 final size:19 Alignment explanation

Indices: 13838754--13838841 Score: 79 Period size: 20 Copynumber: 4.5 Consensus size: 19 13838744 TATGGTTTTT * 13838754 TTTTTATAATTTTTAAATA 1 TTTTTATAATTTTTATATA * * * 13838773 TATTTTAGATTTTTTTATAAA 1 T-TTTTATA-ATTTTTATATA * * 13838794 TTTCCTATAACTTTTATAT- 1 TTT-TTATAATTTTTATATA 13838813 TTTTTATAATATTTTATATA 1 TTTTTATAAT-TTTTATATA 13838833 TTTTTATAA 1 TTTTTATAA 13838842 GGCTAATTTA Statistics Matches: 53, Mismatches: 11, Indels: 9 0.73 0.15 0.12 Matches are distributed among these distances: 18 5 0.09 19 12 0.23 20 24 0.45 21 12 0.23 ACGTcount: A:0.33, C:0.03, G:0.01, T:0.62 Consensus pattern (19 bp): TTTTTATAATTTTTATATA Found at i:13839594 original size:50 final size:51 Alignment explanation

Indices: 13839539--13839639 Score: 123 Period size: 50 Copynumber: 2.0 Consensus size: 51 13839529 TTGTTTTTAT * 13839539 AAATAAAAGAGTTATTAATTAAAAAGACGAATTAAAAA-TAAAAAACTTAA 1 AAATAAAAGAGTTATTAATTAAAAAGACGAATTAAAAACAAAAAAACTTAA * * * * * ** 13839589 AAATAATATATTTATTAATTATAAATATTAATTAAAAACAAAAAAACTTAA 1 AAATAAAAGAGTTATTAATTAAAAAGACGAATTAAAAACAAAAAAACTTAA 13839640 GAGCAAATAA Statistics Matches: 42, Mismatches: 8, Indels: 1 0.82 0.16 0.02 Matches are distributed among these distances: 50 31 0.74 51 11 0.26 ACGTcount: A:0.62, C:0.04, G:0.04, T:0.30 Consensus pattern (51 bp): AAATAAAAGAGTTATTAATTAAAAAGACGAATTAAAAACAAAAAAACTTAA Found at i:13840072 original size:25 final size:26 Alignment explanation

Indices: 13840043--13840096 Score: 65 Period size: 25 Copynumber: 2.1 Consensus size: 26 13840033 ATATTTTAAT * 13840043 TTTTACATTTTCAAAAT-TATATATA 1 TTTTACATTTTCAAAATATACATATA * * * 13840068 TTTTAGATTTTTAATATATACATATA 1 TTTTACATTTTCAAAATATACATATA 13840094 TTT 1 TTT 13840097 AAAATCTAGT Statistics Matches: 24, Mismatches: 4, Indels: 1 0.83 0.14 0.03 Matches are distributed among these distances: 25 14 0.58 26 10 0.42 ACGTcount: A:0.37, C:0.06, G:0.02, T:0.56 Consensus pattern (26 bp): TTTTACATTTTCAAAATATACATATA Found at i:13840512 original size:16 final size:16 Alignment explanation

Indices: 13840491--13840521 Score: 53 Period size: 16 Copynumber: 1.9 Consensus size: 16 13840481 TTAATTTTTA 13840491 TTTTAAAATTTTATTG 1 TTTTAAAATTTTATTG * 13840507 TTTTAAATTTTTATT 1 TTTTAAAATTTTATT 13840522 TAAAAATATA Statistics Matches: 14, Mismatches: 1, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 16 14 1.00 ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68 Consensus pattern (16 bp): TTTTAAAATTTTATTG Found at i:13859580 original size:27 final size:27 Alignment explanation

Indices: 13859509--13859582 Score: 103 Period size: 27 Copynumber: 2.7 Consensus size: 27 13859499 ACACGTCATG * * * * 13859509 AAAGAATAACCTTTGTGACGAACTTTG 1 AAAGAATAGCCTTTGTGGCGAACTCTA * 13859536 AAAGAAAAGCCTTTGTGGCGAACTCTA 1 AAAGAATAGCCTTTGTGGCGAACTCTA 13859563 AAAGAATAGCCTTTGTGGCG 1 AAAGAATAGCCTTTGTGGCG 13859583 TGTCTTAATA Statistics Matches: 41, Mismatches: 6, Indels: 0 0.87 0.13 0.00 Matches are distributed among these distances: 27 41 1.00 ACGTcount: A:0.35, C:0.16, G:0.23, T:0.26 Consensus pattern (27 bp): AAAGAATAGCCTTTGTGGCGAACTCTA Found at i:13860383 original size:2 final size:2 Alignment explanation

Indices: 13860376--13860400 Score: 50 Period size: 2 Copynumber: 12.5 Consensus size: 2 13860366 CTTACTTATT 13860376 TC TC TC TC TC TC TC TC TC TC TC TC T 1 TC TC TC TC TC TC TC TC TC TC TC TC T 13860401 ATATATATAT Statistics Matches: 23, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 23 1.00 ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52 Consensus pattern (2 bp): TC Found at i:13861252 original size:3 final size:3 Alignment explanation

Indices: 13861246--13861283 Score: 67 Period size: 3 Copynumber: 12.7 Consensus size: 3 13861236 ATAAGGTTTT * 13861246 TTG TTG TTG TTG TTT TTG TTG TTG TTG TTG TTG TTG TT 1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT 13861284 CAGGTTTTTG Statistics Matches: 33, Mismatches: 2, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 3 33 1.00 ACGTcount: A:0.00, C:0.00, G:0.29, T:0.71 Consensus pattern (3 bp): TTG Found at i:13865796 original size:184 final size:184 Alignment explanation

Indices: 13865487--13866410 Score: 1848 Period size: 184 Copynumber: 5.0 Consensus size: 184 13865477 CATCTCCACC 13865487 CTTGAAATATTAAGTTACTTAAGAAACTAAATTTGTTACCAACATCAGGCTCTAGGACTCAAAGA 1 CTTGAAATATTAAGTTACTTAAGAAACTAAATTTGTTACCAACATCAGGCTCTAGGACTCAAAGA 13865552 AAGAGTAATATCTTGGAAGACCTTAAGCCTCTTATCAGTTTTCTTTGGAAACATCCTTTGAGTCA 66 AAGAGTAATATCTTGGAAGACCTTAAGCCTCTTATCAGTTTTCTTTGGAAACATCCTTTGAGTCA 13865617 CTGCTTCGTTTGCTGGGCCTAGAACTGCTGCTGCAATGATAGCCTCATCAAAGT 131 CTGCTTCGTTTGCTGGGCCTAGAACTGCTGCTGCAATGATAGCCTCATCAAAGT 13865671 CTTGAAATATTAAGTTACTTAAGAAACTAAATTTGTTACCAACATCAGGCTCTAGGACTCAAAGA 1 CTTGAAATATTAAGTTACTTAAGAAACTAAATTTGTTACCAACATCAGGCTCTAGGACTCAAAGA 13865736 AAGAGTAATATCTTGGAAGACCTTAAGCCTCTTATCAGTTTTCTTTGGAAACATCCTTTGAGTCA 66 AAGAGTAATATCTTGGAAGACCTTAAGCCTCTTATCAGTTTTCTTTGGAAACATCCTTTGAGTCA 13865801 CTGCTTCGTTTGCTGGGCCTAGAACTGCTGCTGCAATGATAGCCTCATCAAAGT 131 CTGCTTCGTTTGCTGGGCCTAGAACTGCTGCTGCAATGATAGCCTCATCAAAGT 13865855 CTTGAAATATTAAGTTACTTAAGAAACTAAATTTGTTACCAACATCAGGCTCTAGGACTCAAAGA 1 CTTGAAATATTAAGTTACTTAAGAAACTAAATTTGTTACCAACATCAGGCTCTAGGACTCAAAGA 13865920 AAGAGTAATATCTTGGAAGACCTTAAGCCTCTTATCAGTTTTCTTTGGAAACATCCTTTGAGTCA 66 AAGAGTAATATCTTGGAAGACCTTAAGCCTCTTATCAGTTTTCTTTGGAAACATCCTTTGAGTCA 13865985 CTGCTTCGTTTGCTGGGCCTAGAACTGCTGCTGCAATGATAGCCTCATCAAAGT 131 CTGCTTCGTTTGCTGGGCCTAGAACTGCTGCTGCAATGATAGCCTCATCAAAGT 13866039 CTTGAAATATTAAGTTACTTAAGAAACTAAATTTGTTACCAACATCAGGCTCTAGGACTCAAAGA 1 CTTGAAATATTAAGTTACTTAAGAAACTAAATTTGTTACCAACATCAGGCTCTAGGACTCAAAGA 13866104 AAGAGTAATATCTTGGAAGACCTTAAGCCTCTTATCAGTTTTCTTTGGAAACATCCTTTGAGTCA 66 AAGAGTAATATCTTGGAAGACCTTAAGCCTCTTATCAGTTTTCTTTGGAAACATCCTTTGAGTCA 13866169 CTGCTTCGTTTGCTGGGCCTAGAACTGCTGCTGCAATGATAGCCTCATCAAAGT 131 CTGCTTCGTTTGCTGGGCCTAGAACTGCTGCTGCAATGATAGCCTCATCAAAGT 13866223 CTTGAAATATTAAGTTACTTAAGAAACTAAATTTGTTACCAACATCAGGCTCTAGGACTCAAAGA 1 CTTGAAATATTAAGTTACTTAAGAAACTAAATTTGTTACCAACATCAGGCTCTAGGACTCAAAGA 13866288 AAGAGTAATATCTTGGAAGACCTTAAGCCTCTTATCAGTTTTCTTTGGAAACATCCTTTGAGTCA 66 AAGAGTAATATCTTGGAAGACCTTAAGCCTCTTATCAGTTTTCTTTGGAAACATCCTTTGAGTCA 13866353 CTGCTTCGTTTGCTGGGCCTAGAACTGCTGCTGCAATGATAGCCTCATCAAAGT 131 CTGCTTCGTTTGCTGGGCCTAGAACTGCTGCTGCAATGATAGCCTCATCAAAGT 13866407 CTTG 1 CTTG 13866411 GCTATCTGGT Statistics Matches: 740, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 184 740 1.00 ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32 Consensus pattern (184 bp): CTTGAAATATTAAGTTACTTAAGAAACTAAATTTGTTACCAACATCAGGCTCTAGGACTCAAAGA AAGAGTAATATCTTGGAAGACCTTAAGCCTCTTATCAGTTTTCTTTGGAAACATCCTTTGAGTCA CTGCTTCGTTTGCTGGGCCTAGAACTGCTGCTGCAATGATAGCCTCATCAAAGT Found at i:13868411 original size:16 final size:16 Alignment explanation

Indices: 13868378--13868419 Score: 50 Period size: 16 Copynumber: 2.6 Consensus size: 16 13868368 AAATAATTTT * * 13868378 AATAAAAATATGGGAAA 1 AATAAAAA-ATAGCAAA 13868395 AATAAAAAATAGCAAA 1 AATAAAAAATAGCAAA 13868411 AA-AAAAAAT 1 AATAAAAAAT 13868420 TAAGAAAAAT Statistics Matches: 23, Mismatches: 2, Indels: 2 0.85 0.07 0.07 Matches are distributed among these distances: 15 7 0.30 16 8 0.35 17 8 0.35 ACGTcount: A:0.74, C:0.02, G:0.10, T:0.14 Consensus pattern (16 bp): AATAAAAAATAGCAAA Found at i:13874044 original size:31 final size:31 Alignment explanation

Indices: 13874004--13874074 Score: 79 Period size: 31 Copynumber: 2.3 Consensus size: 31 13873994 AAAATTTTAA * * * * 13874004 AATTAAAAAAATATAAAGATTAAAATTGACC 1 AATTTAAAAAATACAAAAACTAAAATTGACC * * 13874035 AATTTAAAAAGTACAAAAACTAAAATTGATC 1 AATTTAAAAAATACAAAAACTAAAATTGACC * 13874066 AAATTAAAA 1 AATTTAAAA 13874075 TAAAGGACTA Statistics Matches: 33, Mismatches: 7, Indels: 0 0.82 0.17 0.00 Matches are distributed among these distances: 31 33 1.00 ACGTcount: A:0.62, C:0.07, G:0.06, T:0.25 Consensus pattern (31 bp): AATTTAAAAAATACAAAAACTAAAATTGACC Found at i:13884316 original size:18 final size:18 Alignment explanation

Indices: 13884279--13884314 Score: 54 Period size: 19 Copynumber: 1.9 Consensus size: 18 13884269 TCATGTAAAA 13884279 AAATTAAAATAAAATTTT 1 AAATTAAAATAAAATTTT * 13884297 AAATATAAAATAATATTT 1 AAAT-TAAAATAAAATTT 13884315 AATTTTTTAT Statistics Matches: 16, Mismatches: 1, Indels: 1 0.89 0.06 0.06 Matches are distributed among these distances: 18 4 0.25 19 12 0.75 ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39 Consensus pattern (18 bp): AAATTAAAATAAAATTTT Found at i:13893041 original size:16 final size:16 Alignment explanation

Indices: 13893022--13893056 Score: 70 Period size: 16 Copynumber: 2.2 Consensus size: 16 13893012 TCATACATTC 13893022 ATACATACATATATAT 1 ATACATACATATATAT 13893038 ATACATACATATATAT 1 ATACATACATATATAT 13893054 ATA 1 ATA 13893057 TAAACGTAAA Statistics Matches: 19, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 16 19 1.00 ACGTcount: A:0.51, C:0.11, G:0.00, T:0.37 Consensus pattern (16 bp): ATACATACATATATAT Found at i:13893046 original size:20 final size:20 Alignment explanation

Indices: 13893021--13893058 Score: 67 Period size: 20 Copynumber: 1.9 Consensus size: 20 13893011 TTCATACATT 13893021 CATACATACATATATATATA 1 CATACATACATATATATATA * 13893041 CATACATATATATATATA 1 CATACATACATATATATA 13893059 AACGTAAAAA Statistics Matches: 17, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 20 17 1.00 ACGTcount: A:0.50, C:0.13, G:0.00, T:0.37 Consensus pattern (20 bp): CATACATACATATATATATA Found at i:13904470 original size:18 final size:18 Alignment explanation

Indices: 13904440--13904474 Score: 54 Period size: 18 Copynumber: 1.9 Consensus size: 18 13904430 AATAAAAAAT 13904440 ATCTCATTTTCATAATTA 1 ATCTCATTTTCATAATTA 13904458 ATCT-ATTTCTCATAATT 1 ATCTCATTT-TCATAATT 13904475 TTTTGTATTT Statistics Matches: 16, Mismatches: 0, Indels: 2 0.89 0.00 0.11 Matches are distributed among these distances: 17 4 0.25 18 12 0.75 ACGTcount: A:0.31, C:0.17, G:0.00, T:0.51 Consensus pattern (18 bp): ATCTCATTTTCATAATTA Found at i:13907380 original size:20 final size:21 Alignment explanation

Indices: 13907347--13907385 Score: 62 Period size: 20 Copynumber: 1.9 Consensus size: 21 13907337 TTGAATTAAT * 13907347 TTTTTATTTGAAAAAAAACAC 1 TTTTTATTTAAAAAAAAACAC 13907368 TTTTT-TTTAAAAAAAAAC 1 TTTTTATTTAAAAAAAAAC 13907386 TTGTATAAAA Statistics Matches: 17, Mismatches: 1, Indels: 1 0.89 0.05 0.05 Matches are distributed among these distances: 20 12 0.71 21 5 0.29 ACGTcount: A:0.49, C:0.08, G:0.03, T:0.41 Consensus pattern (21 bp): TTTTTATTTAAAAAAAAACAC Found at i:13913667 original size:35 final size:34 Alignment explanation

Indices: 13913628--13913706 Score: 88 Period size: 34 Copynumber: 2.3 Consensus size: 34 13913618 AATTTGATTA * * * 13913628 AATTTAATTTATGTATTTTTGA-ATTGATAAATTTT 1 AATTTTATTTATAT-TTTTTAAGATTGA-AAATTTT * * 13913663 AATTTTTTTTATATTTTTTAAGATTTAAAATTTT 1 AATTTTATTTATATTTTTTAAGATTGAAAATTTT 13913697 AATTTTATTT 1 AATTTTATTT 13913707 TAACTTAAGT Statistics Matches: 37, Mismatches: 6, Indels: 3 0.80 0.13 0.07 Matches are distributed among these distances: 34 22 0.59 35 15 0.41 ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62 Consensus pattern (34 bp): AATTTTATTTATATTTTTTAAGATTGAAAATTTT Found at i:13926317 original size:15 final size:16 Alignment explanation

Indices: 13926285--13926333 Score: 50 Period size: 15 Copynumber: 3.2 Consensus size: 16 13926275 AAATTTGGTG * * * 13926285 TTTTATTTTTCATAAT 1 TTTTATATTTAATTAT 13926301 TTTTATATTT-ATTAT 1 TTTTATATTTAATTAT 13926316 TTTTA-ATTTAATT-T 1 TTTTATATTTAATTAT 13926330 TTTT 1 TTTT 13926334 CTCATTTATA Statistics Matches: 30, Mismatches: 2, Indels: 4 0.83 0.06 0.11 Matches are distributed among these distances: 14 9 0.30 15 12 0.40 16 9 0.30 ACGTcount: A:0.24, C:0.02, G:0.00, T:0.73 Consensus pattern (16 bp): TTTTATATTTAATTAT Found at i:13926332 original size:14 final size:15 Alignment explanation

Indices: 13926285--13926351 Score: 50 Period size: 16 Copynumber: 4.4 Consensus size: 15 13926275 AAATTTGGTG * * 13926285 TTTTATTTTTCATAAT 1 TTTTATATTT-ATTAT 13926301 TTTTATATTTATTAT 1 TTTTATATTTATTAT 13926316 TTTTA-ATTTAATT-T 1 TTTTATATTT-ATTAT * 13926330 TTTTCTCATTTA-TACT 1 TTTTAT-ATTTATTA-T 13926346 TTTTAT 1 TTTTAT 13926352 TTAAATTATG Statistics Matches: 42, Mismatches: 4, Indels: 10 0.75 0.07 0.18 Matches are distributed among these distances: 14 10 0.24 15 13 0.31 16 19 0.45 ACGTcount: A:0.24, C:0.06, G:0.00, T:0.70 Consensus pattern (15 bp): TTTTATATTTATTAT Found at i:13936133 original size:99 final size:99 Alignment explanation

Indices: 13935958--13936155 Score: 342 Period size: 99 Copynumber: 2.0 Consensus size: 99 13935948 TTCCTAAGAA * * 13935958 ATGAGATTGAAATAGAGAACCTTGAAGGGTTTAGAGAGTGATGGAAGAAGAAGAAGTCATCGTTT 1 ATGAGATTAAAATAGAGAACCTTGAAGGGTTGAGAGAGTGATGGAAGAAGAAGAAGTCATCGTTT 13936023 GATTCAAAATCCAAGTGGAGAAGTAGCCATGGTT 66 GATTCAAAATCCAAGTGGAGAAGTAGCCATGGTT * * 13936057 ATGAGATTAAAATAGAGAACCTTGAAGGGTTGGGAGAGTGATGGAAGAAGAAGAAGTCATGGTTT 1 ATGAGATTAAAATAGAGAACCTTGAAGGGTTGAGAGAGTGATGGAAGAAGAAGAAGTCATCGTTT * * 13936122 GGTTCAGAATCCAAGTGGAGAAGTAGCCATGGTT 66 GATTCAAAATCCAAGTGGAGAAGTAGCCATGGTT 13936156 TGGTTCAAAA Statistics Matches: 93, Mismatches: 6, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 99 93 1.00 ACGTcount: A:0.36, C:0.09, G:0.31, T:0.24 Consensus pattern (99 bp): ATGAGATTAAAATAGAGAACCTTGAAGGGTTGAGAGAGTGATGGAAGAAGAAGAAGTCATCGTTT GATTCAAAATCCAAGTGGAGAAGTAGCCATGGTT Found at i:13936265 original size:17 final size:17 Alignment explanation

Indices: 13936240--13936293 Score: 53 Period size: 17 Copynumber: 3.3 Consensus size: 17 13936230 TTAGATGGAA * 13936240 AAATGGGGAAGAAGATG 1 AAATTGGGAAGAAGATG 13936257 AAATTGGGAAAGAA-AT- 1 AAATTGGG-AAGAAGATG 13936273 -AA-TGGAGAAGAAGATG 1 AAATTGG-GAAGAAGATG 13936289 AAATT 1 AAATT 13936294 AAAAATTAAA Statistics Matches: 30, Mismatches: 1, Indels: 11 0.71 0.02 0.26 Matches are distributed among these distances: 14 8 0.27 15 5 0.17 17 11 0.37 18 6 0.20 ACGTcount: A:0.52, C:0.00, G:0.31, T:0.17 Consensus pattern (17 bp): AAATTGGGAAGAAGATG Found at i:13936327 original size:19 final size:21 Alignment explanation

Indices: 13936299--13936391 Score: 72 Period size: 22 Copynumber: 4.6 Consensus size: 21 13936289 AAATTAAAAA 13936299 TTAAAATTA-TTT-AATAATT 1 TTAAAATTATTTTAAATAATT * 13936318 TTAAATTTATTTTAGAATAATT 1 TTAAAATTATTTTA-AATAATT * * * 13936340 TT--AATAATTTTATAT-TTT 1 TTAAAATTATTTTAAATAATT * 13936358 TTAAAAAATAATTTT-AATAATT 1 TT--AAAATTATTTTAAATAATT 13936380 TTAAAATTATTT 1 TTAAAATTATTT 13936392 GTTGATGTGG Statistics Matches: 58, Mismatches: 8, Indels: 15 0.72 0.10 0.19 Matches are distributed among these distances: 18 4 0.07 19 10 0.17 20 20 0.34 21 2 0.03 22 22 0.38 ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55 Consensus pattern (21 bp): TTAAAATTATTTTAAATAATT Found at i:13936343 original size:31 final size:32 Alignment explanation

Indices: 13936308--13936391 Score: 118 Period size: 31 Copynumber: 2.7 Consensus size: 32 13936298 ATTAAAATTA * * 13936308 TTTAATAATTTTAAATTTATTT-TAGAATAAT 1 TTTAATAATTTTAAATTTATTTAAAAAATAAT * 13936339 TTTAATAATTTTATATTT-TTTAAAAAATAAT 1 TTTAATAATTTTAAATTTATTTAAAAAATAAT * 13936370 TTTAATAATTTTAAAATTATTT 1 TTTAATAATTTTAAATTTATTT 13936392 GTTGATGTGG Statistics Matches: 46, Mismatches: 5, Indels: 3 0.85 0.09 0.06 Matches are distributed among these distances: 30 3 0.07 31 40 0.87 32 3 0.07 ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56 Consensus pattern (32 bp): TTTAATAATTTTAAATTTATTTAAAAAATAAT Found at i:13941395 original size:21 final size:21 Alignment explanation

Indices: 13941370--13941409 Score: 71 Period size: 21 Copynumber: 1.9 Consensus size: 21 13941360 TTGGAACCTA * 13941370 TGTTATTTTTTGGTCCAATCT 1 TGTTAGTTTTTGGTCCAATCT 13941391 TGTTAGTTTTTGGTCCAAT 1 TGTTAGTTTTTGGTCCAAT 13941410 ATGGTACTAT Statistics Matches: 18, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 21 18 1.00 ACGTcount: A:0.15, C:0.12, G:0.17, T:0.55 Consensus pattern (21 bp): TGTTAGTTTTTGGTCCAATCT Found at i:13943230 original size:21 final size:20 Alignment explanation

Indices: 13943206--13943265 Score: 57 Period size: 25 Copynumber: 2.7 Consensus size: 20 13943196 GAGTATACAT 13943206 ATTTTTTAAAATTTATTTTCA 1 ATTTTTTAAAATTTATTTT-A 13943227 ATTTTTTGAGAAATATTTATTTTA 1 ATTTTTT---AAA-ATTTATTTTA * 13943251 ATATTTTTAATATTT 1 AT-TTTTTAAAATTT 13943266 TTAATGTAAT Statistics Matches: 33, Mismatches: 1, Indels: 10 0.75 0.02 0.23 Matches are distributed among these distances: 21 11 0.33 22 2 0.06 24 6 0.18 25 14 0.42 ACGTcount: A:0.33, C:0.02, G:0.03, T:0.62 Consensus pattern (20 bp): ATTTTTTAAAATTTATTTTA Found at i:13943260 original size:9 final size:9 Alignment explanation

Indices: 13943246--13943270 Score: 50 Period size: 9 Copynumber: 2.8 Consensus size: 9 13943236 GAAATATTTA 13943246 TTTTAATAT 1 TTTTAATAT 13943255 TTTTAATAT 1 TTTTAATAT 13943264 TTTTAAT 1 TTTTAAT 13943271 GTAATATATA Statistics Matches: 16, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 9 16 1.00 ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68 Consensus pattern (9 bp): TTTTAATAT Found at i:13943301 original size:11 final size:11 Alignment explanation

Indices: 13943285--13943335 Score: 59 Period size: 11 Copynumber: 4.5 Consensus size: 11 13943275 TATATATATT 13943285 TAAAAATTATA 1 TAAAAATTATA * 13943296 TAAAAA-TATTT 1 TAAAAATTA-TA 13943307 TCAAAAATTATA 1 T-AAAAATTATA * 13943319 TAAAAATAATA 1 TAAAAATTATA 13943330 TAAAAA 1 TAAAAA 13943336 ATTTAATACG Statistics Matches: 34, Mismatches: 3, Indels: 6 0.79 0.07 0.14 Matches are distributed among these distances: 10 2 0.06 11 23 0.68 12 7 0.21 13 2 0.06 ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33 Consensus pattern (11 bp): TAAAAATTATA Found at i:13943312 original size:23 final size:23 Alignment explanation

Indices: 13943278--13943335 Score: 84 Period size: 23 Copynumber: 2.6 Consensus size: 23 13943268 AATGTAATAT 13943278 ATATATTTAAAAATTATATAAAA 1 ATATATTTAAAAATTATATAAAA 13943301 ATAT-TTTCAAAAATTATATAAAA 1 ATATATTT-AAAAATTATATAAAA * 13943324 ATA-ATATAAAAA 1 ATATATTTAAAAA 13943336 ATTTAATACG Statistics Matches: 32, Mismatches: 1, Indels: 5 0.84 0.03 0.13 Matches are distributed among these distances: 22 8 0.25 23 24 0.75 ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36 Consensus pattern (23 bp): ATATATTTAAAAATTATATAAAA Found at i:13951022 original size:2 final size:2 Alignment explanation

Indices: 13951015--13951042 Score: 56 Period size: 2 Copynumber: 14.0 Consensus size: 2 13951005 ATAATGATGA 13951015 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 13951043 GCATGTGTAG Statistics Matches: 26, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 26 1.00 ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50 Consensus pattern (2 bp): AT Found at i:13952500 original size:3 final size:3 Alignment explanation

Indices: 13952492--13952522 Score: 62 Period size: 3 Copynumber: 10.3 Consensus size: 3 13952482 GATCGATTGT 13952492 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T 1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T 13952523 GGGATATGGT Statistics Matches: 28, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 3 28 1.00 ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68 Consensus pattern (3 bp): TTA Found at i:13959248 original size:2 final size:2 Alignment explanation

Indices: 13959241--13959268 Score: 56 Period size: 2 Copynumber: 14.0 Consensus size: 2 13959231 CTTTAGTAGC 13959241 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 13959269 GAAGTGTGTG Statistics Matches: 26, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 26 1.00 ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50 Consensus pattern (2 bp): AT Found at i:13963672 original size:38 final size:40 Alignment explanation

Indices: 13963604--13963682 Score: 101 Period size: 38 Copynumber: 2.0 Consensus size: 40 13963594 AAATTTTAGG * 13963604 AGATTAAAATTAAATTATTTATACTCTTAAGA-ATTTAAA 1 AGATTAAAATTAAATTATTTATACTCTTAAGAGAATTAAA * * 13963643 AGATT-AAATTAAA-TATTTATTATTTTTAAGAGAATTAAA 1 AGATTAAAATTAAATTATTTA-TACTCTTAAGAGAATTAAA 13963682 A 1 A 13963683 TGTAATTTTA Statistics Matches: 35, Mismatches: 3, Indels: 4 0.83 0.07 0.10 Matches are distributed among these distances: 37 6 0.17 38 17 0.49 39 12 0.34 ACGTcount: A:0.49, C:0.03, G:0.06, T:0.42 Consensus pattern (40 bp): AGATTAAAATTAAATTATTTATACTCTTAAGAGAATTAAA Found at i:13975407 original size:26 final size:26 Alignment explanation

Indices: 13975371--13975435 Score: 112 Period size: 26 Copynumber: 2.4 Consensus size: 26 13975361 TGTTATCATC 13975371 AGAGAAAAGAAAGCAGAATAGAACAA 1 AGAGAAAAGAAAGCAGAATAGAACAA 13975397 AGAGAAAAGAAAGCAGAATAGAACAA 1 AGAGAAAAGAAAGCAGAATAGAACAA 13975423 AGAAGAAGAAGAA 1 AG-AGAA-AAGAA 13975436 GAAATGGACA Statistics Matches: 37, Mismatches: 0, Indels: 2 0.95 0.00 0.05 Matches are distributed among these distances: 26 28 0.76 27 4 0.11 28 5 0.14 ACGTcount: A:0.66, C:0.06, G:0.25, T:0.03 Consensus pattern (26 bp): AGAGAAAAGAAAGCAGAATAGAACAA Found at i:13981091 original size:5 final size:6 Alignment explanation

Indices: 13981073--13981098 Score: 52 Period size: 6 Copynumber: 4.3 Consensus size: 6 13981063 TAAAGATTTA 13981073 TTGTTT TTGTTT TTGTTT TTGTTT TT 1 TTGTTT TTGTTT TTGTTT TTGTTT TT 13981099 AACTCTAAAA Statistics Matches: 20, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 6 20 1.00 ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85 Consensus pattern (6 bp): TTGTTT Found at i:13982901 original size:21 final size:22 Alignment explanation

Indices: 13982867--13982918 Score: 65 Period size: 21 Copynumber: 2.5 Consensus size: 22 13982857 TAGTAATTGT * 13982867 TAAT-TTTTTGTTTTA-TTTAA 1 TAATATTTTTATTTTATTTTAA 13982887 TAATATTTTTATTTTATTTTAA 1 TAATATTTTTATTTTATTTTAA * 13982909 TTA-ATTTTTA 1 TAATATTTTTA 13982919 ACAGAGTTTT Statistics Matches: 28, Mismatches: 2, Indels: 3 0.85 0.06 0.09 Matches are distributed among these distances: 20 4 0.14 21 17 0.61 22 7 0.25 ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69 Consensus pattern (22 bp): TAATATTTTTATTTTATTTTAA Found at i:13985966 original size:52 final size:53 Alignment explanation

Indices: 13985885--13986014 Score: 183 Period size: 53 Copynumber: 2.5 Consensus size: 53 13985875 AAAGGGGTCT * * 13985885 GATGACTAAGTGTCATCGTGAGTAAATG-AATCCTTTACGGA-TTATGAGGCCC 1 GATGACTAAGTGTCATCGTGAGTATATGAAATCCTTTACGGATTTA-AAGGCCC * * 13985937 GATGACTAAGTGTCATCGTGAGTATATGAAATCCTTTATGGATTTAAAGGTCC 1 GATGACTAAGTGTCATCGTGAGTATATGAAATCCTTTACGGATTTAAAGGCCC ** 13985990 GATGACTCTGTGTCATCGTGAGTAT 1 GATGACTAAGTGTCATCGTGAGTAT 13986015 TAAATGAAAT Statistics Matches: 70, Mismatches: 6, Indels: 3 0.89 0.08 0.04 Matches are distributed among these distances: 52 27 0.39 53 40 0.57 54 3 0.04 ACGTcount: A:0.28, C:0.15, G:0.25, T:0.32 Consensus pattern (53 bp): GATGACTAAGTGTCATCGTGAGTATATGAAATCCTTTACGGATTTAAAGGCCC Found at i:13988013 original size:23 final size:23 Alignment explanation

Indices: 13987982--13988034 Score: 61 Period size: 23 Copynumber: 2.3 Consensus size: 23 13987972 AAAATAATTA * 13987982 TTAAACTATTCGAAAATTCTTAT 1 TTAAACTATTAGAAAATTCTTAT * * * 13988005 TTAAGCTATTAGAAAGTTTTTAT 1 TTAAACTATTAGAAAATTCTTAT * 13988028 TTTAACT 1 TTAAACT 13988035 CATTGGACTA Statistics Matches: 24, Mismatches: 6, Indels: 0 0.80 0.20 0.00 Matches are distributed among these distances: 23 24 1.00 ACGTcount: A:0.36, C:0.09, G:0.08, T:0.47 Consensus pattern (23 bp): TTAAACTATTAGAAAATTCTTAT Found at i:13988963 original size:22 final size:22 Alignment explanation

Indices: 13988935--13989038 Score: 64 Period size: 22 Copynumber: 5.0 Consensus size: 22 13988925 CAGCAAATGA 13988935 TTTTAAAATTATTAAAATTATT 1 TTTTAAAATTATTAAAATTATT 13988957 TTTTAAAA-TA-T-AAA--A-T 1 TTTTAAAATTATTAAAATTATT * * 13988973 TGTTAAAATTATTTTTAAA-T-TT 1 TTTTAAAATTA--TTAAAATTATT * * 13988995 ATTTAAAATTATTAAATTTATTT 1 TTTTAAAATTATTAAAATTA-TT * * 13989018 TTTTGAAA-TAATAAAATTATT 1 TTTTAAAATTATTAAAATTATT 13989039 AAATAATTTT Statistics Matches: 63, Mismatches: 9, Indels: 21 0.68 0.10 0.23 Matches are distributed among these distances: 16 8 0.13 17 3 0.05 19 3 0.05 20 6 0.10 21 8 0.13 22 27 0.43 23 8 0.13 ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53 Consensus pattern (22 bp): TTTTAAAATTATTAAAATTATT Found at i:13989026 original size:23 final size:23 Alignment explanation

Indices: 13988991--13989035 Score: 54 Period size: 23 Copynumber: 2.0 Consensus size: 23 13988981 TTATTTTTAA * * 13988991 ATTTATTTAAAATTATTAAATTT 1 ATTTATTTAAAATAATAAAATTT * * 13989014 ATTTTTTTGAAATAATAAAATT 1 ATTTATTTAAAATAATAAAATT 13989036 ATTAAATAAT Statistics Matches: 18, Mismatches: 4, Indels: 0 0.82 0.18 0.00 Matches are distributed among these distances: 23 18 1.00 ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53 Consensus pattern (23 bp): ATTTATTTAAAATAATAAAATTT Found at i:13989042 original size:31 final size:29 Alignment explanation

Indices: 13988938--13989041 Score: 113 Period size: 31 Copynumber: 3.4 Consensus size: 29 13988928 CAAATGATTT 13988938 TAAAATTATTAAAATTATTTTTTAAA-ATA 1 TAAAATTATTAAAATTATTTTTTAAATA-A * * 13988967 TAAAATTGTTAAAATTA-TTTTTAAATTTATT 1 TAAAATTATTAAAATTATTTTTTAAA--TA-A * 13988998 TAAAATTATTAAATTTATTTTTTTGAAATAA 1 TAAAATTATTAAAATTA-TTTTTT-AAATAA 13989029 TAAAATTATTAAA 1 TAAAATTATTAAA 13989042 TAATTTTAAT Statistics Matches: 64, Mismatches: 5, Indels: 10 0.81 0.06 0.13 Matches are distributed among these distances: 28 8 0.12 29 16 0.25 31 30 0.47 32 2 0.03 33 5 0.08 34 3 0.05 ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50 Consensus pattern (29 bp): TAAAATTATTAAAATTATTTTTTAAATAA Found at i:13989049 original size:60 final size:60 Alignment explanation

Indices: 13988936--13989050 Score: 162 Period size: 60 Copynumber: 1.9 Consensus size: 60 13988926 AGCAAATGAT * * 13988936 TTTAAAATTATTAAAATTATTTTTTAAAATATAAAATTGTTAAAATTATTTTTAAATTTA 1 TTTAAAATTATTAAAATTATTTTTTAAAATATAAAATTATTAAAATTAATTTTAAATTTA * * 13988996 TTTAAAATTATTAAATTTATTTTTTTGAAATAATAAAATTATT-AAA-TAATTTTAA 1 TTTAAAATTATTAAAATTA-TTTTTTAAAAT-ATAAAATTATTAAAATTAATTTTAA 13989051 TTTTCAATTT Statistics Matches: 49, Mismatches: 4, Indels: 4 0.86 0.07 0.07 Matches are distributed among these distances: 60 26 0.53 61 13 0.27 62 10 0.20 ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51 Consensus pattern (60 bp): TTTAAAATTATTAAAATTATTTTTTAAAATATAAAATTATTAAAATTAATTTTAAATTTA Found at i:13990128 original size:28 final size:30 Alignment explanation

Indices: 13990077--13990145 Score: 72 Period size: 28 Copynumber: 2.3 Consensus size: 30 13990067 ATTGGAAATT * 13990077 AAAATTATTTAATAATTTTATTAT-TTCAAAA 1 AAAATAATTTAATAA-TTTATTATATT-AAAA ** 13990108 AAAATAATTTAATAA-TT-TTATATTTTAA 1 AAAATAATTTAATAATTTATTATATTAAAA 13990136 AAAATAATTT 1 AAAATAATTT 13990146 TAAAATCATT Statistics Matches: 34, Mismatches: 3, Indels: 5 0.81 0.07 0.12 Matches are distributed among these distances: 28 16 0.47 29 4 0.12 31 14 0.41 ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48 Consensus pattern (30 bp): AAAATAATTTAATAATTTATTATATTAAAA Found at i:13990138 original size:30 final size:31 Alignment explanation

Indices: 13990077--13990139 Score: 101 Period size: 31 Copynumber: 2.1 Consensus size: 31 13990067 ATTGGAAATT * 13990077 AAAATTATTTAATAATTTTATTATTTCAAAA 1 AAAATAATTTAATAATTTTATTATTTCAAAA * 13990108 AAAATAATTTAATAATTTTA-TATTTTAAAA 1 AAAATAATTTAATAATTTTATTATTTCAAAA 13990138 AA 1 AA 13990140 TAATTTTAAA Statistics Matches: 30, Mismatches: 2, Indels: 1 0.91 0.06 0.03 Matches are distributed among these distances: 30 11 0.37 31 19 0.63 ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46 Consensus pattern (31 bp): AAAATAATTTAATAATTTTATTATTTCAAAA Found at i:13995620 original size:23 final size:23 Alignment explanation

Indices: 13995594--13995639 Score: 74 Period size: 23 Copynumber: 2.0 Consensus size: 23 13995584 CAAACACTTT * 13995594 TAAATAAACAATTAATAGAATCA 1 TAAAAAAACAATTAATAGAATCA * 13995617 TAAAAAAATAATTAATAGAATCA 1 TAAAAAAACAATTAATAGAATCA 13995640 GTTGGTCAAA Statistics Matches: 21, Mismatches: 2, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 23 21 1.00 ACGTcount: A:0.63, C:0.07, G:0.04, T:0.26 Consensus pattern (23 bp): TAAAAAAACAATTAATAGAATCA Found at i:13996727 original size:11 final size:11 Alignment explanation

Indices: 13996711--13996739 Score: 58 Period size: 11 Copynumber: 2.6 Consensus size: 11 13996701 GTTGGGTTGG 13996711 GTTTTGGATGA 1 GTTTTGGATGA 13996722 GTTTTGGATGA 1 GTTTTGGATGA 13996733 GTTTTGG 1 GTTTTGG 13996740 GTATTTATTA 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:0.14, C:0.00, G:0.38, T:0.48 Consensus pattern (11 bp): GTTTTGGATGA Found at i:13999510 original size:38 final size:37 Alignment explanation

Indices: 13999446--13999529 Score: 107 Period size: 38 Copynumber: 2.3 Consensus size: 37 13999436 TTTTTTATTT 13999446 TATATTA-TTTCAATTTTTTTATTTTTAATTAATAAA 1 TATATTATTTTCAATTTTTTTATTTTTAATTAATAAA * * * * 13999482 TATATTATTTTTAAGTTTTTTTATTTTTAGTTGATAAC 1 TATATTATTTTCAA-TTTTTTTATTTTTAATTAATAAA * 13999520 TTTATTATTT 1 TATATTATTT 13999530 ATAAAATCAA Statistics Matches: 41, Mismatches: 5, Indels: 2 0.85 0.10 0.04 Matches are distributed among these distances: 36 7 0.17 37 5 0.12 38 29 0.71 ACGTcount: A:0.30, C:0.02, G:0.04, T:0.64 Consensus pattern (37 bp): TATATTATTTTCAATTTTTTTATTTTTAATTAATAAA Found at i:14000591 original size:18 final size:19 Alignment explanation

Indices: 14000570--14000611 Score: 50 Period size: 18 Copynumber: 2.3 Consensus size: 19 14000560 TTTTTTCTAT 14000570 TTTTCCTATATTTT-TAAG 1 TTTTCCTATATTTTCTAAG ** * 14000588 TTTTTTTTTATTTTCTAAG 1 TTTTCCTATATTTTCTAAG 14000607 TTTTC 1 TTTTC 14000612 AACCAATCTC Statistics Matches: 19, Mismatches: 4, Indels: 1 0.79 0.17 0.04 Matches are distributed among these distances: 18 11 0.58 19 8 0.42 ACGTcount: A:0.17, C:0.10, G:0.05, T:0.69 Consensus pattern (19 bp): TTTTCCTATATTTTCTAAG Found at i:14000591 original size:19 final size:19 Alignment explanation

Indices: 14000569--14000610 Score: 50 Period size: 19 Copynumber: 2.2 Consensus size: 19 14000559 ATTTTTTCTA 14000569 TTTTTCCTATATTTT-TAAG 1 TTTTT-CTATATTTTCTAAG * * 14000588 TTTTTTTTTATTTTCTAAG 1 TTTTTCTATATTTTCTAAG 14000607 TTTT 1 TTTT 14000611 CAACCAATCT Statistics Matches: 20, Mismatches: 2, Indels: 2 0.83 0.08 0.08 Matches are distributed among these distances: 18 7 0.35 19 13 0.65 ACGTcount: A:0.17, C:0.07, G:0.05, T:0.71 Consensus pattern (19 bp): TTTTTCTATATTTTCTAAG Found at i:14004840 original size:26 final size:24 Alignment explanation

Indices: 14004789--14004848 Score: 59 Period size: 26 Copynumber: 2.3 Consensus size: 24 14004779 TTAGGTTGAA 14004789 TTATTTTAGATAAATTCAAATAATTT 1 TTATTTT--ATAAATTCAAATAATTT * 14004815 TAGTATTTTATAAATTATAAAT-ATTT 1 T--TATTTTATAAATT-CAAATAATTT 14004841 TTATTTTA 1 TTATTTTA 14004849 AACTTAATAA Statistics Matches: 30, Mismatches: 1, Indels: 8 0.77 0.03 0.21 Matches are distributed among these distances: 24 7 0.23 26 13 0.43 27 4 0.13 28 6 0.20 ACGTcount: A:0.40, C:0.02, G:0.03, T:0.55 Consensus pattern (24 bp): TTATTTTATAAATTCAAATAATTT Found at i:14005252 original size:91 final size:91 Alignment explanation

Indices: 14004945--14005220 Score: 552 Period size: 91 Copynumber: 3.0 Consensus size: 91 14004935 TACTAAAAAA 14004945 ATAATTTTTTAGTTGAATGTTGTAATTTTAATTTAAAAAACTATTTTGTCAAGATTCAATCTATT 1 ATAATTTTTTAGTTGAATGTTGTAATTTTAATTTAAAAAACTATTTTGTCAAGATTCAATCTATT 14005010 AGATTATTTACATTTTCCATTTAAAT 66 AGATTATTTACATTTTCCATTTAAAT 14005036 ATAATTTTTTAGTTGAATGTTGTAATTTTAATTTAAAAAACTATTTTGTCAAGATTCAATCTATT 1 ATAATTTTTTAGTTGAATGTTGTAATTTTAATTTAAAAAACTATTTTGTCAAGATTCAATCTATT 14005101 AGATTATTTACATTTTCCATTTAAAT 66 AGATTATTTACATTTTCCATTTAAAT 14005127 ATAATTTTTTAGTTGAATGTTGTAATTTTAATTTAAAAAACTATTTTGTCAAGATTCAATCTATT 1 ATAATTTTTTAGTTGAATGTTGTAATTTTAATTTAAAAAACTATTTTGTCAAGATTCAATCTATT 14005192 AGATTATTTACATTTTCCATTTAAAT 66 AGATTATTTACATTTTCCATTTAAAT 14005218 ATA 1 ATA 14005221 TATGATGAAT Statistics Matches: 185, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 91 185 1.00 ACGTcount: A:0.36, C:0.08, G:0.08, T:0.49 Consensus pattern (91 bp): ATAATTTTTTAGTTGAATGTTGTAATTTTAATTTAAAAAACTATTTTGTCAAGATTCAATCTATT AGATTATTTACATTTTCCATTTAAAT Found at i:14006621 original size:308 final size:308 Alignment explanation

Indices: 14006063--14006988 Score: 1825 Period size: 308 Copynumber: 3.0 Consensus size: 308 14006053 GTTCTGGTGA 14006063 GGCTTTGTTAAGGGGTCAAGTCAAGACTCTGTTGCAGAAGGTTGAAGAGGAGGCTGAGGTTTCAA 1 GGCTTTGTTAAGGGGTCAAGTCAAGACTCTGTTGCAGAAGGTTGAAGAGGAGGCTGAGGTTTCAA 14006128 AAGTTCCATTGGAGAGCCGTCCTTTTGTTCATCTTCAATCCCCAATGGCACTTGTGGCCCCCACT 66 AAGTTCCATTGGAGAGCCGTCCTTTTGTTCATCTTCAATCCCCAATGGCACTTGTGGCCCCCACT 14006193 CCTGCAAATACACCCGAGGTCTCTGATCTTTCTGAGGAGTTGACATTGGGTTCAATGTTGATGGA 131 CCTGCAAATACACCCGAGGTCTCTGATCTTTCTGAGGAGTTGACATTGGGTTCAATGTTGATGGA 14006258 TTTTCCTGTTGTCGAAGAAGAGTTGGACATATCTGAGGTTAGTTTTTTTACTCCCCCATTGCATG 196 TTTTCCTGTTGTCGAAGAAGAGTTGGACATATCTGAGGTTAGTTTTTTTACTCCCCCATTGCATG 14006323 ATGTCTTTTTTATTTCGTGATTGAATTACTGGACTTAACAAATACTTT 261 ATGTCTTTTTTATTTCGTGATTGAATTACTGGACTTAACAAATACTTT 14006371 GGCTTTGTTAAGGGGTCAAGTCAAGACTCTGTTGCAGAAGGTTGAAGAGGAGGCTGAGGTTTCAA 1 GGCTTTGTTAAGGGGTCAAGTCAAGACTCTGTTGCAGAAGGTTGAAGAGGAGGCTGAGGTTTCAA 14006436 AAGTTCCATTGGAGAGCCGTCCTTTTGTTCATCTTCAATCCCCAATGGCACTTGTGGCCCCCACT 66 AAGTTCCATTGGAGAGCCGTCCTTTTGTTCATCTTCAATCCCCAATGGCACTTGTGGCCCCCACT 14006501 CCTGCAAATACACCCGAGGTCTCTGATCTTTCTGAGGAGTTGACATTGGGTTCAATGTTGATGGA 131 CCTGCAAATACACCCGAGGTCTCTGATCTTTCTGAGGAGTTGACATTGGGTTCAATGTTGATGGA 14006566 TTTTCCTGTTGTCGAAGAAGAGTTGGACATATCTGAGGTTAGTTTTTTTACTCCCCCATTGCATG 196 TTTTCCTGTTGTCGAAGAAGAGTTGGACATATCTGAGGTTAGTTTTTTTACTCCCCCATTGCATG 14006631 ATGTCTTTTTTATTTCGTGATTGAATTACTGGACTTAACAAATACTTT 261 ATGTCTTTTTTATTTCGTGATTGAATTACTGGACTTAACAAATACTTT 14006679 GGCTTTGTTAAGGGGTCAAGTCAAGACTCTGTTGCAGAAGGTTGAAGAGGAGGCTGAGGTTTCAA 1 GGCTTTGTTAAGGGGTCAAGTCAAGACTCTGTTGCAGAAGGTTGAAGAGGAGGCTGAGGTTTCAA 14006744 AAGTTCCATTGGAGAGCCGTCCTTTTGTTCATCTTCAATCCCCAATGGCACTTGTGGCCCCCACT 66 AAGTTCCATTGGAGAGCCGTCCTTTTGTTCATCTTCAATCCCCAATGGCACTTGTGGCCCCCACT * 14006809 CCTGCAAATACACCCGAGGTCTCTGATCTTTCTGAGGAGTTAACATTGGGTTCAATGTTGATGGA 131 CCTGCAAATACACCCGAGGTCTCTGATCTTTCTGAGGAGTTGACATTGGGTTCAATGTTGATGGA * * 14006874 TTTTCCTGTTGTCGAAGAAGAGTTGAACATATCTGAGGTCAGTTTTTTTACTCCCCCATTGCATG 196 TTTTCCTGTTGTCGAAGAAGAGTTGGACATATCTGAGGTTAGTTTTTTTACTCCCCCATTGCATG 14006939 ATGTCTTTTTTATTTCGTGATTGAATTACTGGACTTAACAAATACTTT 261 ATGTCTTTTTTATTTCGTGATTGAATTACTGGACTTAACAAATACTTT 14006987 GG 1 GG 14006989 TATGTAATAC Statistics Matches: 615, Mismatches: 3, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 308 615 1.00 ACGTcount: A:0.23, C:0.20, G:0.23, T:0.34 Consensus pattern (308 bp): GGCTTTGTTAAGGGGTCAAGTCAAGACTCTGTTGCAGAAGGTTGAAGAGGAGGCTGAGGTTTCAA AAGTTCCATTGGAGAGCCGTCCTTTTGTTCATCTTCAATCCCCAATGGCACTTGTGGCCCCCACT CCTGCAAATACACCCGAGGTCTCTGATCTTTCTGAGGAGTTGACATTGGGTTCAATGTTGATGGA TTTTCCTGTTGTCGAAGAAGAGTTGGACATATCTGAGGTTAGTTTTTTTACTCCCCCATTGCATG ATGTCTTTTTTATTTCGTGATTGAATTACTGGACTTAACAAATACTTT Found at i:14009758 original size:27 final size:27 Alignment explanation

Indices: 14009711--14009774 Score: 85 Period size: 27 Copynumber: 2.4 Consensus size: 27 14009701 AAATATTCTC * * 14009711 TAAATTAAT-AAATATTAATTTTTCGA 1 TAAATTAATAAAATACTAATTTATCGA * 14009737 TAAATTAATAAAATACTCATTTATCGA 1 TAAATTAATAAAATACTAATTTATCGA * 14009764 TAAACTAATAA 1 TAAATTAATAA 14009775 CCTCGATAAA Statistics Matches: 33, Mismatches: 4, Indels: 1 0.87 0.11 0.03 Matches are distributed among these distances: 26 9 0.27 27 24 0.73 ACGTcount: A:0.50, C:0.08, G:0.03, T:0.39 Consensus pattern (27 bp): TAAATTAATAAAATACTAATTTATCGA Found at i:14011610 original size:13 final size:13 Alignment explanation

Indices: 14011592--14011697 Score: 56 Period size: 13 Copynumber: 8.1 Consensus size: 13 14011582 TCTATATCCT * 14011592 TATAAATATTTCA 1 TATAAACATTTCA 14011605 TATAAACATTTCA 1 TATAAACATTTCA * 14011618 -AGTAACCATTTCA 1 TA-TAAACATTTCA * * 14011631 TAT-ATCTATTCCCA 1 TATAAAC-ATT-TCA * * * 14011645 AATAAGCATTTCG 1 TATAAACATTTCA * * 14011658 TATAACCATTTCT 1 TATAAACATTTCA 14011671 TAT-AACATATTCA 1 TATAAACAT-TTCA * * 14011684 TTTAAATATTTCA 1 TATAAACATTTCA 14011697 T 1 T 14011698 TCTTACCATT Statistics Matches: 71, Mismatches: 15, Indels: 14 0.71 0.15 0.14 Matches are distributed among these distances: 12 7 0.10 13 50 0.70 14 12 0.17 15 2 0.03 ACGTcount: A:0.39, C:0.17, G:0.03, T:0.42 Consensus pattern (13 bp): TATAAACATTTCA Found at i:14012690 original size:19 final size:19 Alignment explanation

Indices: 14012667--14012712 Score: 58 Period size: 19 Copynumber: 2.5 Consensus size: 19 14012657 GTTCAATTTT 14012667 TTTTTTAATAA-ATAATTA 1 TTTTTTAATAAGATAATTA * * * 14012685 TATTTTAAAAAGATATTTA 1 TTTTTTAATAAGATAATTA 14012704 TTTTTTAAT 1 TTTTTTAAT 14012713 TGAATTAGGA Statistics Matches: 22, Mismatches: 5, Indels: 1 0.79 0.18 0.04 Matches are distributed among these distances: 18 9 0.41 19 13 0.59 ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57 Consensus pattern (19 bp): TTTTTTAATAAGATAATTA Found at i:14036731 original size:16 final size:16 Alignment explanation

Indices: 14036710--14036743 Score: 50 Period size: 16 Copynumber: 2.1 Consensus size: 16 14036700 AGCTAAATTT 14036710 TTTTTTTAAATATCTA 1 TTTTTTTAAATATCTA * * 14036726 TTTTTTTTAATATTTA 1 TTTTTTTAAATATCTA 14036742 TT 1 TT 14036744 ACTATACTTT Statistics Matches: 16, Mismatches: 2, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 16 16 1.00 ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71 Consensus pattern (16 bp): TTTTTTTAAATATCTA Found at i:14045691 original size:21 final size:20 Alignment explanation

Indices: 14045655--14045698 Score: 54 Period size: 21 Copynumber: 2.1 Consensus size: 20 14045645 GAAAAAAGTG 14045655 TTTTTAATATTATATTAATT 1 TTTTTAATATTATATTAATT * 14045675 TTTTTGAATGATT-TATTGATT 1 TTTTT-AAT-ATTATATTAATT 14045696 TTT 1 TTT 14045699 ATAAATAAAA Statistics Matches: 21, Mismatches: 1, Indels: 3 0.84 0.04 0.12 Matches are distributed among these distances: 20 5 0.24 21 13 0.62 22 3 0.14 ACGTcount: A:0.27, C:0.00, G:0.07, T:0.66 Consensus pattern (20 bp): TTTTTAATATTATATTAATT Found at i:14047602 original size:2 final size:2 Alignment explanation

Indices: 14047595--14047619 Score: 50 Period size: 2 Copynumber: 12.5 Consensus size: 2 14047585 TAAATTTAAA 14047595 AT AT AT AT AT AT AT AT AT AT AT AT A 1 AT AT AT AT AT AT AT AT AT AT AT AT A 14047620 CTTAAATAAC Statistics Matches: 23, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 23 1.00 ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48 Consensus pattern (2 bp): AT Found at i:14047784 original size:32 final size:32 Alignment explanation

Indices: 14047748--14047830 Score: 105 Period size: 32 Copynumber: 2.6 Consensus size: 32 14047738 CATAACAACG * * 14047748 AAATAGTAGCAAAATAGTGAAAAACAA-CAAGA 1 AAATAGTAACAAAATAGT-AAAAAAAATCAAGA * * 14047780 AAATAGTAACAAAACAATAAAAAAAATCAAGA 1 AAATAGTAACAAAATAGTAAAAAAAATCAAGA * 14047812 AAATAGTAAAAAAATAGTA 1 AAATAGTAACAAAATAGTA 14047831 GTCATTTTTT Statistics Matches: 43, Mismatches: 7, Indels: 2 0.83 0.13 0.04 Matches are distributed among these distances: 31 7 0.16 32 36 0.84 ACGTcount: A:0.67, C:0.07, G:0.11, T:0.14 Consensus pattern (32 bp): AAATAGTAACAAAATAGTAAAAAAAATCAAGA Found at i:14051409 original size:2 final size:2 Alignment explanation

Indices: 14051402--14051429 Score: 56 Period size: 2 Copynumber: 14.0 Consensus size: 2 14051392 TCCTCCACCC 14051402 CT CT CT CT CT CT CT CT CT CT CT CT CT CT 1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT 14051430 AGTGAGAGCT Statistics Matches: 26, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 26 1.00 ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50 Consensus pattern (2 bp): CT Found at i:14054541 original size:11 final size:11 Alignment explanation

Indices: 14054525--14054582 Score: 64 Period size: 11 Copynumber: 5.1 Consensus size: 11 14054515 GCCAAAACTC 14054525 ATTTTAAATTT 1 ATTTTAAATTT 14054536 ATTTTAAATTT 1 ATTTTAAATTT * 14054547 AAATTT-AATTT 1 -ATTTTAAATTT * 14054558 AAGTTTAAATTT 1 -ATTTTAAATTT 14054570 ATTTTCAAATTT 1 ATTTT-AAATTT 14054582 A 1 A 14054583 AAATAAATAA Statistics Matches: 41, Mismatches: 3, Indels: 5 0.84 0.06 0.10 Matches are distributed among these distances: 11 25 0.61 12 16 0.39 ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57 Consensus pattern (11 bp): ATTTTAAATTT Found at i:14054547 original size:6 final size:6 Alignment explanation

Indices: 14054527--14054584 Score: 59 Period size: 6 Copynumber: 10.0 Consensus size: 6 14054517 CAAAACTCAT * * * 14054527 TTTAAA TTT-AT TTTAAA TTTAAA TTT-AA TTTAAG TTTAAA TTT-AT 1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA 14054572 TTTCAAA TTTAAA 1 TTT-AAA TTTAAA 14054585 ATAAATAAAG Statistics Matches: 42, Mismatches: 6, Indels: 8 0.75 0.11 0.14 Matches are distributed among these distances: 5 13 0.31 6 25 0.60 7 4 0.10 ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55 Consensus pattern (6 bp): TTTAAA Found at i:14054549 original size:17 final size:17 Alignment explanation

Indices: 14054527--14054584 Score: 89 Period size: 17 Copynumber: 3.4 Consensus size: 17 14054517 CAAAACTCAT 14054527 TTTAAATTTATTTTAAA 1 TTTAAATTTATTTTAAA * * 14054544 TTTAAATTTAATTTAAG 1 TTTAAATTTATTTTAAA 14054561 TTTAAATTTATTTTCAAA 1 TTTAAATTTATTTT-AAA 14054579 TTTAAA 1 TTTAAA 14054585 ATAAATAAAG Statistics Matches: 36, Mismatches: 4, Indels: 1 0.88 0.10 0.02 Matches are distributed among these distances: 17 28 0.78 18 8 0.22 ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55 Consensus pattern (17 bp): TTTAAATTTATTTTAAA Found at i:14054596 original size:34 final size:34 Alignment explanation

Indices: 14054527--14054596 Score: 97 Period size: 34 Copynumber: 2.1 Consensus size: 34 14054517 CAAAACTCAT * * * 14054527 TTTAAATTTATTTTAAATTTAAATTTAATTTAAG 1 TTTAAATTTATTTTAAATTTAAATATAAATAAAG 14054561 TTTAAATTTATTTTCAAATTTAAA-ATAAATAAAG 1 TTTAAATTTATTTT-AAATTTAAATATAAATAAAG 14054595 TT 1 TT 14054597 CAATTACAAA Statistics Matches: 32, Mismatches: 3, Indels: 2 0.86 0.08 0.05 Matches are distributed among these distances: 34 23 0.72 35 9 0.28 ACGTcount: A:0.44, C:0.01, G:0.03, T:0.51 Consensus pattern (34 bp): TTTAAATTTATTTTAAATTTAAATATAAATAAAG Done.