Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: A05

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: 100714657
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32

Warning! 3970000 characters in sequence are not A, C, G, or T


File 162 of 318

Found at i:51266190 original size:80 final size:80

Alignment explanation

Indices: 51266074--51266259 Score: 229 Period size: 80 Copynumber: 2.3 Consensus size: 80 51266064 AGTAACTCAT * * * 51266074 ACAATGCCTTCGGGACTTAACCCGGATTTTAAAACTCGCACGAATGCCTTCGGGA-CTTAACCCG 1 ACAAAGCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATGCCTTC-GGATCTTAACCCG * 51266138 GA-ATTAGT-A-TCTCGC 65 GATA-TAGTCACT-TAGC ** 51266153 ACAAAGGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACAAATGCCTTCGGATCTTAGTCC 1 ACAAA-GCCTTCGGGACTTAACCCGGATATTAA-AACTCGCACAAATGCCTTCGGATCTTAACCC 51266217 GGATATAGTCACTTAGC 64 GGATATAGTCACTTAGC * 51266234 ACAAAGCCTTCGGGACTTAGCCCGGA 1 ACAAAGCCTTCGGGACTTAACCCGGA 51266260 CAGCATTCAA Statistics Matches: 94, Mismatches: 7, Indels: 11 0.84 0.06 0.10 Matches are distributed among these distances: 79 11 0.12 80 72 0.77 81 10 0.11 82 1 0.01 ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24 Consensus pattern (80 bp): ACAAAGCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATGCCTTCGGATCTTAACCCGG ATATAGTCACTTAGC Found at i:51266219 original size:40 final size:40 Alignment explanation

Indices: 51266076--51266259 Score: 205 Period size: 40 Copynumber: 4.6 Consensus size: 40 51266066 TAACTCATAC * * 51266076 AATGCCTTCGGGACTTAACCCGGATTTTAA-AACTCGCACG 1 AATGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACA * * 51266116 AATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACA 1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA * 51266156 AAGGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA 1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA ** * * * 51266196 AATGCCTTC-GGATCTTAGTCCGG-ATATAGTCACTTAGCACA 1 AATGCCTTCGGGA-CTTAACCCGGAAT-TAATAAC-TCGCACA * 51266237 AA-GCCTTCGGGACTTAGCCCGGA 1 AATGCCTTCGGGACTTAACCCGGA 51266260 CAGCATTCAA Statistics Matches: 124, Mismatches: 14, Indels: 11 0.83 0.09 0.07 Matches are distributed among these distances: 39 8 0.06 40 105 0.85 41 11 0.09 ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24 Consensus pattern (40 bp): AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA Found at i:51272213 original size:40 final size:40 Alignment explanation

Indices: 51272154--51272257 Score: 172 Period size: 40 Copynumber: 2.6 Consensus size: 40 51272144 TGGATGATAA * * 51272154 CCGGGCTAAGTCCCAAAGGCATTTGTGCGAGCTACTATAT 1 CCGGGCTAAGTCCCGAAGGCATTGGTGCGAGCTACTATAT * 51272194 CCGGGCTAAGTCCCGAAGGCATTGGTGCGAGTTACTATAT 1 CCGGGCTAAGTCCCGAAGGCATTGGTGCGAGCTACTATAT * 51272234 CCGGGCTATGTCCCGAAGGCATTG 1 CCGGGCTAAGTCCCGAAGGCATTG 51272258 AGTGAGTAGC Statistics Matches: 60, Mismatches: 4, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 40 60 1.00 ACGTcount: A:0.22, C:0.25, G:0.29, T:0.24 Consensus pattern (40 bp): CCGGGCTAAGTCCCGAAGGCATTGGTGCGAGCTACTATAT Found at i:51279887 original size:40 final size:40 Alignment explanation

Indices: 51279792--51280009 Score: 232 Period size: 40 Copynumber: 5.5 Consensus size: 40 51279782 TGGATGATAA * * 51279792 CCGGGCTAAGTCCCGAAGGCATTT-TCCGCTAGTGACTAGT-T 1 CCGGGCTAAGTCCCGAAGGCATTTGT--GCGAGTTACTA-TAT * * 51279833 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTATTACAT 1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT * * * 51279873 CCGGGCCAAGTCCCGAAGGCATTTGTGCAAGCTACTATAT 1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT * 51279913 CTGGGCTAAGTCCCGAAGGCA-TTGATGCGAGTTACTATAT 1 CCGGGCTAAGTCCCGAAGGCATTTG-TGCGAGTTACTATAT * * * 51279953 CCGGTCTATGTCCCGAAGGCA-TTGAGCGAG-TAGCTATAT 1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT * * 51279992 CC-GGTTAAATCCCGAAGG 1 CCGGGCTAAGTCCCGAAGG 51280010 TACTTGGCTT Statistics Matches: 152, Mismatches: 21, Indels: 11 0.83 0.11 0.06 Matches are distributed among these distances: 38 14 0.09 39 16 0.11 40 97 0.64 41 24 0.16 42 1 0.01 ACGTcount: A:0.23, C:0.24, G:0.27, T:0.25 Consensus pattern (40 bp): CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT Found at i:51285999 original size:40 final size:40 Alignment explanation

Indices: 51285798--51285985 Score: 306 Period size: 40 Copynumber: 4.7 Consensus size: 40 51285788 ATTCGGATTG * 51285798 ATAACCAGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACT 1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT * * * 51285837 ATATCTGGGCTAAGTCTCGAAGGCATTTGTGCGAGTTACT 1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT * * 51285877 ATAACCGGGCCAAGTCCCGAAGGCAATTGTGCGAGTTACT 1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT * 51285917 ATAACCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTACT 1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT 51285957 ATAACCGGGCTAAGTCCCGAAGGCATTTG 1 ATAACCGGGCTAAGTCCCGAAGGCATTTG 51285986 AGCAAGAAGC Statistics Matches: 137, Mismatches: 11, Indels: 1 0.92 0.07 0.01 Matches are distributed among these distances: 39 11 0.08 40 126 0.92 ACGTcount: A:0.27, C:0.22, G:0.27, T:0.24 Consensus pattern (40 bp): ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT Found at i:51290404 original size:12 final size:12 Alignment explanation

Indices: 51290387--51290417 Score: 53 Period size: 12 Copynumber: 2.6 Consensus size: 12 51290377 TCGTGTCATG 51290387 CACATGGCCTAC 1 CACATGGCCTAC * 51290399 CACATGGCCTAG 1 CACATGGCCTAC 51290411 CACATGG 1 CACATGG 51290418 TTGTGTGGCC Statistics Matches: 18, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 12 18 1.00 ACGTcount: A:0.26, C:0.35, G:0.23, T:0.16 Consensus pattern (12 bp): CACATGGCCTAC Found at i:51293516 original size:45 final size:44 Alignment explanation

Indices: 51293431--51293516 Score: 109 Period size: 45 Copynumber: 1.9 Consensus size: 44 51293421 TATGTAATCT * * 51293431 GAACTCATTGAGTTGTGCCTGAGTTCATGATATATGTGACATCC 1 GAACTCACTGAGTTGTGCCTGAGTTCATGATATATATGACATCC * ** * 51293475 GAACTCACTGAGTTGTGGTCTGAGTTTGTGATATGTATGACA 1 GAACTCACTGAGTTGT-GCCTGAGTTCATGATATATATGACA 51293517 CATGTTTTGG Statistics Matches: 35, Mismatches: 6, Indels: 1 0.83 0.14 0.02 Matches are distributed among these distances: 44 15 0.43 45 20 0.57 ACGTcount: A:0.24, C:0.15, G:0.26, T:0.35 Consensus pattern (44 bp): GAACTCACTGAGTTGTGCCTGAGTTCATGATATATATGACATCC Found at i:51306456 original size:25 final size:25 Alignment explanation

Indices: 51306409--51306456 Score: 60 Period size: 25 Copynumber: 1.9 Consensus size: 25 51306399 TTATAGTATG * * * * 51306409 AAAATGACTGTTTTGCCCTTAGGTA 1 AAAATGACTATTATACCCCTAGGTA 51306434 AAAATGACTATTATACCCCTAGG 1 AAAATGACTATTATACCCCTAGG 51306457 GTTTAATTAT Statistics Matches: 19, Mismatches: 4, Indels: 0 0.83 0.17 0.00 Matches are distributed among these distances: 25 19 1.00 ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31 Consensus pattern (25 bp): AAAATGACTATTATACCCCTAGGTA Found at i:51306518 original size:11 final size:11 Alignment explanation

Indices: 51306504--51306559 Score: 66 Period size: 11 Copynumber: 5.5 Consensus size: 11 51306494 CAATATTGAT 51306504 ATGATATGCAC 1 ATGATATGCAC * 51306515 ATGATATG--T 1 ATGATATGCAC 51306524 ATGATATGCAC 1 ATGATATGCAC * 51306535 ATGATATG--T 1 ATGATATGCAC 51306544 ATGATATGCAC 1 ATGATATGCAC 51306555 ATGAT 1 ATGAT 51306560 GTGTATGACA Statistics Matches: 37, Mismatches: 4, Indels: 8 0.76 0.08 0.16 Matches are distributed among these distances: 9 16 0.43 11 21 0.57 ACGTcount: A:0.36, C:0.11, G:0.20, T:0.34 Consensus pattern (11 bp): ATGATATGCAC Found at i:51306581 original size:20 final size:20 Alignment explanation

Indices: 51306503--51306579 Score: 136 Period size: 20 Copynumber: 3.9 Consensus size: 20 51306493 ACAATATTGA 51306503 TATGATATGCACATGATATG 1 TATGATATGCACATGATATG 51306523 TATGATATGCACATGATATG 1 TATGATATGCACATGATATG * 51306543 TATGATATGCACATGATGTG 1 TATGATATGCACATGATATG * 51306563 TATGACATGCACATGAT 1 TATGATATGCACATGAT 51306580 GTATTCATAA Statistics Matches: 55, Mismatches: 2, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 20 55 1.00 ACGTcount: A:0.34, C:0.12, G:0.21, T:0.34 Consensus pattern (20 bp): TATGATATGCACATGATATG Found at i:51306639 original size:26 final size:26 Alignment explanation

Indices: 51306610--51306694 Score: 79 Period size: 25 Copynumber: 3.3 Consensus size: 26 51306600 TTGGGTATTT 51306610 GCCCCAGTTTATTGAAAAGGGCTTAG 1 GCCCCAGTTTATTGAAAAGGGCTTAG * ** ** 51306636 GCCCCAATTTACCG-AAAGGGCTTTT 1 GCCCCAGTTTATTGAAAAGGGCTTAG 51306661 GCCCCAG-TTATT-AAAAGAGGC-TAG 1 GCCCCAGTTTATTGAAAAG-GGCTTAG 51306685 GCCTCCAGTT 1 GCC-CCAGTT 51306695 ATATGATAAA Statistics Matches: 45, Mismatches: 10, Indels: 8 0.71 0.16 0.13 Matches are distributed among these distances: 24 11 0.24 25 22 0.49 26 12 0.27 ACGTcount: A:0.26, C:0.25, G:0.24, T:0.26 Consensus pattern (26 bp): GCCCCAGTTTATTGAAAAGGGCTTAG Found at i:51312698 original size:75 final size:74 Alignment explanation

Indices: 51312619--51312767 Score: 192 Period size: 75 Copynumber: 2.0 Consensus size: 74 51312609 GTAAAAGAAT * ** * * 51312619 TATTTTTTTATAATTTTATTATTTTTTATTACATTTAAATTATTTGTGATTTAATTGT-TACTTA 1 TATTTTTTAATAATTTTAAAATTTATTATTACATTTAAATTATTTGTGA-TTAATT-TCTACTCA * 51312683 ATGTTCAAATA 64 ATGTCCAAATA * * * 51312694 TATTTTTTAATAATTTTAAAATTTATTGTTATATTTTAATTATTTGTGATTAATTTCTACTCAAT 1 TATTTTTTAATAATTTTAAAATTTATTATTACATTTAAATTATTTGTGATTAATTTCTACTCAAT 51312759 GTCCAAATA 66 GTCCAAATA 51312768 AATTCATTTA Statistics Matches: 64, Mismatches: 9, Indels: 3 0.84 0.12 0.04 Matches are distributed among these distances: 73 1 0.02 74 21 0.33 75 42 0.66 ACGTcount: A:0.32, C:0.05, G:0.05, T:0.57 Consensus pattern (74 bp): TATTTTTTAATAATTTTAAAATTTATTATTACATTTAAATTATTTGTGATTAATTTCTACTCAAT GTCCAAATA Found at i:51318102 original size:27 final size:27 Alignment explanation

Indices: 51318072--51318211 Score: 131 Period size: 27 Copynumber: 5.1 Consensus size: 27 51318062 AAATGTCCTT * * * * 51318072 GATTTGTAGAATTGCCGCTTTACCTTC 1 GATTTATAGAATTACCGTTTTACCCTC * 51318099 GATTTATAGAATTACCATTTTACCCTC 1 GATTTATAGAATTACCGTTTTACCCTC * 51318126 GATTTACAGAATTACCGTTTTACCCTC 1 GATTTATAGAATTACCGTTTTACCCTC * * * * 51318153 GATTTACAAAATTACCATTTTACCTTC 1 GATTTATAGAATTACCGTTTTACCCTC * * 51318180 -AGTTTACA-AAGTTATTCGTTTTACCCTC 1 GA-TTTATAGAA-TTA-CCGTTTTACCCTC 51318208 GATT 1 GATT 51318212 GTGAAATTAC Statistics Matches: 96, Mismatches: 13, Indels: 7 0.83 0.11 0.06 Matches are distributed among these distances: 26 3 0.03 27 80 0.83 28 12 0.12 29 1 0.01 ACGTcount: A:0.26, C:0.22, G:0.11, T:0.41 Consensus pattern (27 bp): GATTTATAGAATTACCGTTTTACCCTC Found at i:51318221 original size:54 final size:53 Alignment explanation

Indices: 51318079--51318211 Score: 153 Period size: 54 Copynumber: 2.5 Consensus size: 53 51318069 CTTGATTTGT * * * * 51318079 AGAATTGCCGCTTTACCTTCGATTTATAGAATTACCATTTTACCCTCGATTTAC 1 AGAATTACCGTTTTACCCTCGATTTA-AAAATTACCATTTTACCCTCGATTTAC * 51318133 AGAATTACCGTTTTACCCTCGATTTACAAAATTACCATTTTACCTTC-AGTTTAC 1 AGAATTACCGTTTTACCCTCGATTTA-AAAATTACCATTTTACCCTCGA-TTTAC * 51318187 A-AAGTTATTCGTTTTACCCTCGATT 1 AGAA-TTA-CCGTTTTACCCTCGATT 51318212 GTGAAATTAC Statistics Matches: 69, Mismatches: 7, Indels: 5 0.85 0.09 0.06 Matches are distributed among these distances: 53 3 0.04 54 50 0.72 55 16 0.23 ACGTcount: A:0.27, C:0.23, G:0.10, T:0.40 Consensus pattern (53 bp): AGAATTACCGTTTTACCCTCGATTTAAAAATTACCATTTTACCCTCGATTTAC Found at i:51318273 original size:27 final size:27 Alignment explanation

Indices: 51318243--51318393 Score: 182 Period size: 27 Copynumber: 5.6 Consensus size: 27 51318233 TGTAGGATAG 51318243 AATTACCAAAATACCCCTAGTTTGTAA 1 AATTACCAAAATACCCCTAGTTTGTAA 51318270 AATTACCAAAATACCCCTAGTTTGTAA 1 AATTACCAAAATACCCCTAGTTTGTAA * * * * 51318297 AATTACCGAAATACCACTGGTTTGTGA 1 AATTACCAAAATACCCCTAGTTTGTAA * * 51318324 AATTACCGAAATA-CCCTCAATTTGTAA 1 AATTACCAAAATACCCCT-AGTTTGTAA ** 51318351 AATTACCAAAATACCCCT-GATTTACAA 1 AATTACCAAAATACCCCTAG-TTTGTAA 51318378 AATTA-CAGAAATACCC 1 AATTACCA-AAATACCC 51318394 TTGACTTTCT Statistics Matches: 108, Mismatches: 12, Indels: 8 0.84 0.09 0.06 Matches are distributed among these distances: 26 5 0.05 27 99 0.92 28 4 0.04 ACGTcount: A:0.41, C:0.23, G:0.09, T:0.28 Consensus pattern (27 bp): AATTACCAAAATACCCCTAGTTTGTAA Found at i:51318273 original size:54 final size:52 Alignment explanation

Indices: 51318210--51318393 Score: 188 Period size: 54 Copynumber: 3.4 Consensus size: 52 51318200 TTACCCTCGA * * ** * 51318210 TTGTGAAATTACTGAAATACCCCTGTAGGATAGAATTACCAAAATACCCCTAGT 1 TTGTAAAATTACCGAAATACCCCTGTTTG-TAAAATTACCAAAATACCCCT-GT * * * 51318264 TTGTAAAATTACCAAAATACCCCTAGTTTGTAAAATTACCGAAATACCACTGGT 1 TTGTAAAATTACCGAAATACCCCT-GTTTGTAAAATTACCAAAATACCCCT-GT * ** 51318318 TTGTGAAATTACCGAAATACCCTCAATTTGTAAAATTACCAAAATACCCCTGAT 1 TTGTAAAATTACCGAAATACCC-CTGTTTGTAAAATTACCAAAATACCCCTG-T ** * 51318372 TTACAAAATTACAGAAATACCC 1 TTGTAAAATTACCGAAATACCC 51318394 TTGACTTTCT Statistics Matches: 108, Mismatches: 19, Indels: 6 0.81 0.14 0.05 Matches are distributed among these distances: 53 1 0.01 54 103 0.95 55 4 0.04 ACGTcount: A:0.40, C:0.21, G:0.11, T:0.28 Consensus pattern (52 bp): TTGTAAAATTACCGAAATACCCCTGTTTGTAAAATTACCAAAATACCCCTGT Found at i:51318300 original size:81 final size:81 Alignment explanation

Indices: 51318210--51318393 Score: 214 Period size: 81 Copynumber: 2.3 Consensus size: 81 51318200 TTACCCTCGA * * * 51318210 TTGTGAAATTACTGAAATACCCCT-GTAGGAT-AGAATTACCAAAATACCC-CTAGTTTGTAAAA 1 TTGTAAAATTACAGAAATACCCCTGGTAGG-TGA-AATTACCAAAATACCCTC-AATTTGTAAAA 51318272 TTACCAAAATACCCCT-AGT 63 TTACCAAAATACCCCTGA-T * * ** * 51318291 TTGTAAAATTACCGAAATACCACTGGTTTGTGAAATTACCGAAATACCCTCAATTTGTAAAATTA 1 TTGTAAAATTACAGAAATACCCCTGGTAGGTGAAATTACCAAAATACCCTCAATTTGTAAAATTA 51318356 CCAAAATACCCCTGAT 66 CCAAAATACCCCTGAT ** 51318372 TTACAAAATTACAGAAATACCC 1 TTGTAAAATTACAGAAATACCC 51318394 TTGACTTTCT Statistics Matches: 88, Mismatches: 11, Indels: 8 0.82 0.10 0.07 Matches are distributed among these distances: 81 82 0.93 82 6 0.07 ACGTcount: A:0.40, C:0.21, G:0.11, T:0.28 Consensus pattern (81 bp): TTGTAAAATTACAGAAATACCCCTGGTAGGTGAAATTACCAAAATACCCTCAATTTGTAAAATTA CCAAAATACCCCTGAT Found at i:51318466 original size:27 final size:27 Alignment explanation

Indices: 51318371--51318456 Score: 86 Period size: 27 Copynumber: 3.1 Consensus size: 27 51318361 ATACCCCTGA * * * 51318371 TTTACAAAATTACAGAAATACCCTTGAC 1 TTTACAAAATTACTGAAATACCATTG-G * 51318399 TTT-CTAAAAACTA-TAGAAATACCATTGG 1 TTTAC--AAAATTACT-GAAATACCATTGG 51318427 TTTACAAAATTACTGAAATACCATTGG 1 TTTACAAAATTACTGAAATACCATTGG 51318454 TTT 1 TTT 51318457 GTAGATTTAC Statistics Matches: 48, Mismatches: 5, Indels: 11 0.75 0.08 0.17 Matches are distributed among these distances: 27 23 0.48 28 7 0.15 29 18 0.38 ACGTcount: A:0.41, C:0.16, G:0.09, T:0.34 Consensus pattern (27 bp): TTTACAAAATTACTGAAATACCATTGG Found at i:51318540 original size:27 final size:27 Alignment explanation

Indices: 51318510--51318570 Score: 70 Period size: 27 Copynumber: 2.3 Consensus size: 27 51318500 ACCCTTAATA 51318510 GGTAAAAAGACCGTAA-AGCCCCTGTAG 1 GGTAAAAAGACCGTAATA-CCCCTGTAG ** * * 51318537 GGTAAAGTGACCGTAATACCCTTGTAT 1 GGTAAAAAGACCGTAATACCCCTGTAG 51318564 GGTAAAA 1 GGTAAAA 51318571 TAACGAATAT Statistics Matches: 28, Mismatches: 5, Indels: 2 0.80 0.14 0.06 Matches are distributed among these distances: 27 27 0.96 28 1 0.04 ACGTcount: A:0.36, C:0.18, G:0.25, T:0.21 Consensus pattern (27 bp): GGTAAAAAGACCGTAATACCCCTGTAG Found at i:51319439 original size:25 final size:25 Alignment explanation

Indices: 51319384--51319453 Score: 88 Period size: 25 Copynumber: 2.8 Consensus size: 25 51319374 AGGAAGTACT * 51319384 AAAAGGGCTCTGCCCCAGTTTACCG 1 AAAAGGGCTCTGCCCCAGTTTACAG * 51319409 AAAAGGGCTTTGCCCCAGTTTATCAG 1 AAAAGGGCTCTGCCCCAGTTTA-CAG * * 51319435 -GAAGGGCTCTGCCCTAGTT 1 AAAAGGGCTCTGCCCCAGTT 51319454 ATTAAAAGAG Statistics Matches: 39, Mismatches: 5, Indels: 2 0.85 0.11 0.04 Matches are distributed among these distances: 25 37 0.95 26 2 0.05 ACGTcount: A:0.23, C:0.27, G:0.26, T:0.24 Consensus pattern (25 bp): AAAAGGGCTCTGCCCCAGTTTACAG Found at i:51320630 original size:68 final size:68 Alignment explanation

Indices: 51320521--51320652 Score: 248 Period size: 68 Copynumber: 1.9 Consensus size: 68 51320511 CACATATACA 51320521 TTACCATACCAATGCCATATCTCAGATATGGTCTTACATGGATCTCATATCGATGCCAATAGCCT 1 TTACCATACCAATGCCATATCTCAGATATGGTCTTACATGGATCTCATATCGATGCCAATAGCCT 51320586 ACG 66 ACG 51320589 TTACCATACCAATGCCATATC-CTAGATATGGTCTTACATGGATCTCATATCGATGCCAATAGCC 1 TTACCATACCAATGCCATATCTC-AGATATGGTCTTACATGGATCTCATATCGATGCCAATAGCC 51320653 CAGCTATGGT Statistics Matches: 63, Mismatches: 0, Indels: 2 0.97 0.00 0.03 Matches are distributed among these distances: 67 1 0.02 68 62 0.98 ACGTcount: A:0.30, C:0.27, G:0.14, T:0.30 Consensus pattern (68 bp): TTACCATACCAATGCCATATCTCAGATATGGTCTTACATGGATCTCATATCGATGCCAATAGCCT ACG Found at i:51320662 original size:42 final size:42 Alignment explanation

Indices: 51320600--51320720 Score: 129 Period size: 42 Copynumber: 2.9 Consensus size: 42 51320590 TACCATACCA * * * * * 51320600 ATGCCATATCCTAGATATGGTCTTACATGGA-TCTCATATCG 1 ATGCCATAGCCCAGATATGGTCTTACACGAAGTCTCACATCG * * * 51320641 ATGCCAATAGCCCAGCTATGGTCTTATACGAAGTCTCACATTG 1 ATGCC-ATAGCCCAGATATGGTCTTACACGAAGTCTCACATCG * 51320684 ATGCCATATCCCAGATATGGTCTTACACGTAA-TCTCA 1 ATGCCATAGCCCAGATATGGTCTTACACG-AAGTCTCA 51320721 AATAACCCTA Statistics Matches: 66, Mismatches: 11, Indels: 5 0.80 0.13 0.06 Matches are distributed among these distances: 41 5 0.08 42 46 0.70 43 15 0.23 ACGTcount: A:0.28, C:0.25, G:0.17, T:0.31 Consensus pattern (42 bp): ATGCCATAGCCCAGATATGGTCTTACACGAAGTCTCACATCG Found at i:51327118 original size:27 final size:27 Alignment explanation

Indices: 51326989--51327319 Score: 225 Period size: 27 Copynumber: 12.3 Consensus size: 27 51326979 TACCCTATAG * * * * 51326989 GGGTATGTCAGTCATTTTAC-ACTACAA 1 GGGTATTTCAGTAATTTTACAAAT-CGA * * * 51327016 GGGTATTTCAATAATTTTAC-ACTACAA 1 GGGTATTTCAGTAATTTTACAAAT-CGA * 51327043 GGGTATTTCAATAATTTTACAAATCGA 1 GGGTATTTCAGTAATTTTACAAATCGA 51327070 GGGTATTTCTA-TAATTTTACAAATCGA 1 GGGTATTTC-AGTAATTTTACAAATCGA * 51327097 GGGTATTTCAGTAATTTTACAAATTGA 1 GGGTATTTCAGTAATTTTACAAATCGA ** * * 51327124 GGGTGGTTCGGTAATTTTACAAATTGA 1 GGGTATTTCAGTAATTTTACAAATCGA * * 51327151 GGGTATTTTAGTAATTTTAC-AATTGA 1 GGGTATTTCAGTAATTTTACAAATCGA * * * * * 51327177 CGGTATTT-TGATAACTTTAGAAATTGA 1 GGGTATTTCAG-TAATTTTACAAATCGA * * 51327204 GGGTATTTTAGTAATTTTACAAAAT-AA 1 GGGTATTTCAGTAATTTTAC-AAATCGA * * * * 51327231 GGATATTTC-GATAATTTCAC-AAGCCA 1 GGGTATTTCAG-TAATTTTACAAATCGA * * 51327257 GGGGTATTTCGGTAATTTTTCAAATC-A 1 -GGGTATTTCAGTAATTTTACAAATCGA * * * 51327284 GGGGTACTTT-GGTAATTCTACAAACCG- 1 -GGGTA-TTTCAGTAATTTTACAAATCGA 51327311 GGGTATTTC 1 GGGTATTTC 51327320 GGTACAAATC Statistics Matches: 255, Mismatches: 34, Indels: 31 0.80 0.11 0.10 Matches are distributed among these distances: 25 6 0.02 26 28 0.11 27 206 0.81 28 15 0.06 ACGTcount: A:0.32, C:0.11, G:0.19, T:0.38 Consensus pattern (27 bp): GGGTATTTCAGTAATTTTACAAATCGA Found at i:51327126 original size:54 final size:54 Alignment explanation

Indices: 51327015--51327319 Score: 271 Period size: 54 Copynumber: 5.7 Consensus size: 54 51327005 TTACACTACA * * * * * 51327015 AGGGTATTTCAATAATTTTAC-ACTACAAGGGTATTTCAATAATTTTACAAATCG 1 AGGGTATTTCGATAATTTTACAAAT-CGAGGGTATTTCAGTAATTTTACAAATTG * 51327069 AGGGTATTTCTATAATTTTACAAATCGAGGGTATTTCAGTAATTTTACAAATTG 1 AGGGTATTTCGATAATTTTACAAATCGAGGGTATTTCAGTAATTTTACAAATTG ** * * * 51327123 AGGGTGGTTCGGTAATTTTACAAATTGAGGGTATTTTAGTAATTTTAC-AATTG 1 AGGGTATTTCGATAATTTTACAAATCGAGGGTATTTCAGTAATTTTACAAATTG * * * * * * * * 51327176 ACGGTATTTTGATAACTTTAGAAATTGAGGGTATTTTAGTAATTTTACAAAATA 1 AGGGTATTTCGATAATTTTACAAATCGAGGGTATTTCAGTAATTTTACAAATTG * * * * * * * 51327230 AGGATATTTCGATAATTTCAC-AAGCCAGGGGTATTTCGGTAATTTTTCAAA-TC 1 AGGGTATTTCGATAATTTTACAAATCGA-GGGTATTTCAGTAATTTTACAAATTG * * * 51327283 AGGGGTACTTT-GGTAATTCTACAAACCG-GGGTATTTC 1 A-GGGTA-TTTCGATAATTTTACAAATCGAGGGTATTTC 51327320 GGTACAAATC Statistics Matches: 206, Mismatches: 39, Indels: 13 0.80 0.15 0.05 Matches are distributed among these distances: 53 60 0.29 54 138 0.67 55 8 0.04 ACGTcount: A:0.32, C:0.10, G:0.19, T:0.38 Consensus pattern (54 bp): AGGGTATTTCGATAATTTTACAAATCGAGGGTATTTCAGTAATTTTACAAATTG Found at i:51327246 original size:80 final size:80 Alignment explanation

Indices: 51327042--51327252 Score: 230 Period size: 80 Copynumber: 2.6 Consensus size: 80 51327032 TTACACTACA * * 51327042 AGGGTATTTCAATAATTTTAC-AAATCGAGGGTATTTCTATAATTTTACAAATCGAGGGTATTTC 1 AGGGTATTTCAGTAATTTTACAAAAT-GAGGGTATTTCTATAATTTTAC-AATCGACGGTATTTC * 51327106 AGTAATTTTACAAATTG 64 AGTAACTTTACAAATTG ** * * * * 51327123 AGGGTGGTTCGGTAATTTTACAAATTGAGGGTATTT-TAGTAATTTTACAATTGACGGTATTT-T 1 AGGGTATTTCAGTAATTTTACAAAATGAGGGTATTTCTA-TAATTTTACAATCGACGGTATTTCA * 51327186 GATAACTTTAGAAATTG 65 G-TAACTTTACAAATTG * * * * * 51327203 AGGGTATTTTAGTAATTTTACAAAATAAGGATATTTCGATAATTTCACAA 1 AGGGTATTTCAGTAATTTTACAAAATGAGGGTATTTCTATAATTTTACAA 51327253 GCCAGGGGTA Statistics Matches: 107, Mismatches: 19, Indels: 9 0.79 0.14 0.07 Matches are distributed among these distances: 79 1 0.01 80 66 0.62 81 37 0.35 82 3 0.03 ACGTcount: A:0.34, C:0.08, G:0.18, T:0.40 Consensus pattern (80 bp): AGGGTATTTCAGTAATTTTACAAAATGAGGGTATTTCTATAATTTTACAATCGACGGTATTTCAG TAACTTTACAAATTG Found at i:51327262 original size:107 final size:108 Alignment explanation

Indices: 51326989--51327282 Score: 263 Period size: 107 Copynumber: 2.7 Consensus size: 108 51326979 TACCCTATAG * * ** * * * * * * 51326989 GGGTATGTCAGTCATTTTACACTACAAGGGTATTTCAATAATTTTACACTACA-AGGGTATTTCA 1 GGGTATTTCAGTAATTTTACAAAATAAGGATAGTTCGATAATTTCACA-AACAGAGGGTATTTCA * * * 51327053 ATAATTTTACAAATCGAGGGTATTTCTATAATTTTACAAATCGA 65 GTAATTTTACAAATCGACGGTATTTCTATAACTTTACAAATCGA * * * * * * ** * 51327097 GGGTATTTCAGTAATTTTACAAATTGAGGGTGGTTCGGTAATTTTACAAATTGAGGGTATTTTAG 1 GGGTATTTCAGTAATTTTACAAAATAAGGATAGTTCGATAATTTCACAAACAGAGGGTATTTCAG * * * 51327162 TAATTTTAC-AATTGACGGTATTT-TGATAACTTTAGAAATTGA 66 TAATTTTACAAATCGACGGTATTTCT-ATAACTTTACAAATCGA * * * * 51327204 GGGTATTTTAGTAATTTTACAAAATAAGGATATTTCGATAATTTCACAAGCCAG-GGGTATTTCG 1 GGGTATTTCAGTAATTTTACAAAATAAGGATAGTTCGATAATTTCACAA-ACAGAGGGTATTTCA * 51327268 GTAATTTTTCAAATC 65 GTAATTTTACAAATC 51327283 AGGGGTACTT Statistics Matches: 146, Mismatches: 36, Indels: 8 0.77 0.19 0.04 Matches are distributed among these distances: 106 1 0.01 107 85 0.58 108 60 0.41 ACGTcount: A:0.33, C:0.11, G:0.18, T:0.39 Consensus pattern (108 bp): GGGTATTTCAGTAATTTTACAAAATAAGGATAGTTCGATAATTTCACAAACAGAGGGTATTTCAG TAATTTTACAAATCGACGGTATTTCTATAACTTTACAAATCGA Found at i:51327327 original size:20 final size:21 Alignment explanation

Indices: 51327302--51327344 Score: 61 Period size: 21 Copynumber: 2.1 Consensus size: 21 51327292 TTGGTAATTC 51327302 TACAAACCG-GGGTATTTCGG 1 TACAAACCGAGGGTATTTCGG * * 51327322 TACAAATCGAGGGTATTTTGG 1 TACAAACCGAGGGTATTTCGG 51327343 TA 1 TA 51327345 ATTTCTCTTT Statistics Matches: 20, Mismatches: 2, Indels: 1 0.87 0.09 0.04 Matches are distributed among these distances: 20 8 0.40 21 12 0.60 ACGTcount: A:0.28, C:0.14, G:0.28, T:0.30 Consensus pattern (21 bp): TACAAACCGAGGGTATTTCGG Found at i:51333918 original size:27 final size:27 Alignment explanation

Indices: 51333875--51333968 Score: 107 Period size: 27 Copynumber: 3.5 Consensus size: 27 51333865 AAGGGCAAAA * * 51333875 CAGTCATTTTACCCTACAGGGGTATGT 1 CAGTCATTTTACACTACAAGGGTATGT * * 51333902 CGGTCATTTTACACTACAAGGGTATTT 1 CAGTCATTTTACACTACAAGGGTATGT * * * 51333929 CAATAATTTTACACTACAAGGGTATTT 1 CAGTCATTTTACACTACAAGGGTATGT * * 51333956 CAATAATTTTACA 1 CAGTCATTTTACA 51333969 AATCGAGGGT Statistics Matches: 60, Mismatches: 7, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 27 60 1.00 ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36 Consensus pattern (27 bp): CAGTCATTTTACACTACAAGGGTATGT Found at i:51333938 original size:54 final size:54 Alignment explanation

Indices: 51333880--51334156 Score: 161 Period size: 54 Copynumber: 5.1 Consensus size: 54 51333870 CAAAACAGTC * * ** * * 51333880 ATTTTACCCTACAGGGGTATGTCGGTCATTTTAC-ACTACAAGGGTATTTCAATA 1 ATTTTACACTACAAGGGTATGTCAATAATTTTACAAAT-CAAGGGTATTTCAATA * * * 51333934 ATTTTACACTACAAGGGTATTTCAATAATTTTACAAATCGAGGGTATTTCTATA 1 ATTTTACACTACAAGGGTATGTCAATAATTTTACAAATCAAGGGTATTTCAATA * * * * ** ** ** 51333988 ATTTTACA-AATCGAGGGTATTTCAGTAATTTTACAAATTGAGGGTGGTTCGGTA 1 ATTTTACACTA-CAAGGGTATGTCAATAATTTTACAAATCAAGGGTATTTCAATA * ** * * * * ** 51334042 ATTTTACA-AATTGAGGGTATTTCAGTAATTTTACAATTGATA--GTATTTCGGTA 1 ATTTTACACTA-CAAGGGTATGTCAATAATTTTACAAATCA-AGGGTATTTCAATA * * * * ** 51334095 ATTTTACGAAT-CAAGGGTATTTCAATAATTTTGCAAATCGAGGGTATTTCACGA 1 ATTTTAC-ACTACAAGGGTATGTCAATAATTTTACAAATCAAGGGTATTTCAATA 51334149 ATTTTACA 1 ATTTTACA 51334157 AATCAATGAT Statistics Matches: 182, Mismatches: 34, Indels: 15 0.79 0.15 0.06 Matches are distributed among these distances: 52 1 0.01 53 40 0.22 54 138 0.76 55 3 0.02 ACGTcount: A:0.32, C:0.12, G:0.18, T:0.38 Consensus pattern (54 bp): ATTTTACACTACAAGGGTATGTCAATAATTTTACAAATCAAGGGTATTTCAATA Found at i:51333977 original size:27 final size:27 Alignment explanation

Indices: 51333920--51334224 Score: 323 Period size: 27 Copynumber: 11.4 Consensus size: 27 51333910 TTACACTACA * * * 51333920 AGGGTATTTCAATAATTTTAC-ACTACA 1 AGGGTATTTCAGTAATTTTACAAAT-CG * 51333947 AGGGTATTTCAATAATTTTACAAATCG 1 AGGGTATTTCAGTAATTTTACAAATCG 51333974 AGGGTATTTCTA-TAATTTTACAAATCG 1 AGGGTATTTC-AGTAATTTTACAAATCG * 51334001 AGGGTATTTCAGTAATTTTACAAATTG 1 AGGGTATTTCAGTAATTTTACAAATCG ** * * 51334028 AGGGTGGTTCGGTAATTTTACAAATTG 1 AGGGTATTTCAGTAATTTTACAAATCG * 51334055 AGGGTATTTCAGTAATTTTAC-AATTG 1 AGGGTATTTCAGTAATTTTACAAATCG ** * * * 51334081 ATAGTATTTCGGTAATTTTACGAATCA 1 AGGGTATTTCAGTAATTTTACAAATCG * * 51334108 AGGGTATTTCAATAATTTTGCAAATCG 1 AGGGTATTTCAGTAATTTTACAAATCG * 51334135 AGGGTATTTCACG-AATTTTACAAATCA 1 AGGGTATTTCA-GTAATTTTACAAATCG * * * * 51334162 ATGATATTTCGGTAATTTTTCAAATCG 1 AGGGTATTTCAGTAATTTTACAAATCG * * * 51334189 GGGGTA-CTCGGTAATTTTACAAATCG 1 AGGGTATTTCAGTAATTTTACAAATCG 51334215 AGGGTATTTC 1 AGGGTATTTC 51334225 GGTACAAACC Statistics Matches: 235, Mismatches: 36, Indels: 14 0.82 0.13 0.05 Matches are distributed among these distances: 26 48 0.20 27 184 0.78 28 3 0.01 ACGTcount: A:0.32, C:0.11, G:0.18, T:0.38 Consensus pattern (27 bp): AGGGTATTTCAGTAATTTTACAAATCG Found at i:51334005 original size:81 final size:80 Alignment explanation

Indices: 51333920--51334224 Score: 285 Period size: 80 Copynumber: 3.8 Consensus size: 80 51333910 TTACACTACA * 51333920 AGGGTATTTCAATAATTTTACACTACAAGGGTATTTCAATAATTTTACAAATCGAGGGTATTTCT 1 AGGGTATTTCAGTAATTTTACA-TACAAGGGTATTTCAATAATTTTACAAATCGAGGGTATTTC- 51333985 A-TAATTTTACAAATCG 64 ACTAATTTTACAAATCG * ** ** ** * 51334001 AGGGTATTTCAGTAATTTTACAAATTGAGGGTGGTTCGGTAATTTTACAAATTGAGGGTATTTCA 1 AGGGTATTTCAGTAATTTTACATA-CAAGGGTATTTCAATAATTTTACAAATCGAGGGTATTTCA * * 51334066 GTAATTTTAC-AATTG 65 CTAATTTTACAAATCG ** * * 51334081 ATAGTATTTCGGTAATTTTACGA-ATCAAGGGTATTTCAATAATTTTGCAAATCGAGGGTATTTC 1 AGGGTATTTCAGTAATTTTAC-ATA-CAAGGGTATTTCAATAATTTTACAAATCGAGGGTATTTC * * 51334145 ACGAATTTTACAAATCA 64 ACTAATTTTACAAATCG * * * * * ** * ** 51334162 ATGATATTTCGGTAATTTTTCAAATCGGGGGTA-CTCGGTAATTTTACAAATCGAGGGTATTTC 1 AGGGTATTTCAGTAATTTTACATA-CAAGGGTATTTCAATAATTTTACAAATCGAGGGTATTTC 51334225 GGTACAAACC Statistics Matches: 185, Mismatches: 34, Indels: 11 0.80 0.15 0.05 Matches are distributed among these distances: 80 93 0.50 81 92 0.50 ACGTcount: A:0.32, C:0.11, G:0.18, T:0.38 Consensus pattern (80 bp): AGGGTATTTCAGTAATTTTACATACAAGGGTATTTCAATAATTTTACAAATCGAGGGTATTTCAC TAATTTTACAAATCG Found at i:51334170 original size:107 final size:108 Alignment explanation

Indices: 51333920--51334224 Score: 339 Period size: 107 Copynumber: 2.8 Consensus size: 108 51333910 TTACACTACA * * * 51333920 AGGGTATTTCAATAATTTTAC-ACTACAAGGGTATTTCAATAATTTTACAAATCGAGGGTATTTC 1 AGGGTATTTCAAGAATTTTACAAAT-CAAGGGTATTTCAGTAATTTTACAAATCGAGGGTATTTC ** * * 51333984 TATAATTTTACAAATCGAGGGTATTTCAGTAATTTTACAAATTG 65 GGTAATTTTACAAATCGAGGGTATTTCAATAATTTTACAAATCG ** * ** * ** 51334028 AGGGTGGTTC-GGTAATTTTACAAATTGAGGGTATTTCAGTAATTTTAC-AATTGATAGTATTTC 1 AGGGTATTTCAAG-AATTTTACAAATCAAGGGTATTTCAGTAATTTTACAAATCGAGGGTATTTC * * * 51334091 GGTAATTTTACGAATCAAGGGTATTTCAATAATTTTGCAAATCG 65 GGTAATTTTACAAATCGAGGGTATTTCAATAATTTTACAAATCG * * * * * * * 51334135 AGGGTATTTCACGAATTTTACAAATCAATGATATTTCGGTAATTTTTCAAATCGGGGGTA-CTCG 1 AGGGTATTTCAAGAATTTTACAAATCAAGGGTATTTCAGTAATTTTACAAATCGAGGGTATTTCG 51334199 GTAATTTTACAAATCGAGGGTATTTC 66 GTAATTTTACAAATCGAGGGTATTTC 51334225 GGTACAAACC Statistics Matches: 159, Mismatches: 34, Indels: 9 0.79 0.17 0.04 Matches are distributed among these distances: 107 113 0.71 108 44 0.28 109 2 0.01 ACGTcount: A:0.32, C:0.11, G:0.18, T:0.38 Consensus pattern (108 bp): AGGGTATTTCAAGAATTTTACAAATCAAGGGTATTTCAGTAATTTTACAAATCGAGGGTATTTCG GTAATTTTACAAATCGAGGGTATTTCAATAATTTTACAAATCG Found at i:51334602 original size:28 final size:28 Alignment explanation

Indices: 51334568--51334659 Score: 112 Period size: 28 Copynumber: 3.3 Consensus size: 28 51334558 TGGCCCGTTT * * 51334568 AGGCCCAATCTCTTTCATATGGCCCATC 1 AGGCCCAATCACATTCATATGGCCCATC * * * * 51334596 GGGCCCAATCACATTCATATGTCGCATT 1 AGGCCCAATCACATTCATATGGCCCATC * * 51334624 AGGCCCGATCACATTCATATGGACCATC 1 AGGCCCAATCACATTCATATGGCCCATC 51334652 AGGCCCAA 1 AGGCCCAA 51334660 CTACTTCCCA Statistics Matches: 51, Mismatches: 13, Indels: 0 0.80 0.20 0.00 Matches are distributed among these distances: 28 51 1.00 ACGTcount: A:0.26, C:0.33, G:0.17, T:0.24 Consensus pattern (28 bp): AGGCCCAATCACATTCATATGGCCCATC Found at i:51344716 original size:47 final size:47 Alignment explanation

Indices: 51344665--51344908 Score: 326 Period size: 47 Copynumber: 5.1 Consensus size: 47 51344655 TTAGGATTTT * 51344665 ATGTGATGGATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA 1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA 51344712 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA 1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA * *** * 51344759 CTGTGATGAATGTGAACCTGTATATATATATGCGTGATAAGGCCGAATGGCCA 1 ATGTGATGAATGTGAA-C-----ATGCGTATGTGTGATAAGGCCGAATGGCCA 51344812 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA 1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA ** ** * * 51344859 ATGTGATGAATGTGAACATGAATACATGTGGTAAGGCCGAATGGCTA 1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA 51344906 ATG 1 ATG 51344909 CGAAACGTGT Statistics Matches: 174, Mismatches: 17, Indels: 12 0.86 0.08 0.06 Matches are distributed among these distances: 47 131 0.75 48 1 0.01 52 1 0.01 53 41 0.24 ACGTcount: A:0.30, C:0.13, G:0.31, T:0.26 Consensus pattern (47 bp): ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA Found at i:51344811 original size:100 final size:100 Alignment explanation

Indices: 51344687--51344875 Score: 360 Period size: 100 Copynumber: 1.9 Consensus size: 100 51344677 TGAACATGCG * 51344687 TATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGA 1 TATGCGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGA * 51344752 ATGGCCACTGTGATGAATGTGAACCTGTATATATA 66 ATGGCCAATGTGATGAATGTGAACCTGTATATATA 51344787 TATGCGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGA 1 TATGCGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGA 51344852 ATGGCCAATGTGATGAATGTGAAC 66 ATGGCCAATGTGATGAATGTGAAC 51344876 ATGAATACAT Statistics Matches: 87, Mismatches: 2, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 100 87 1.00 ACGTcount: A:0.30, C:0.13, G:0.30, T:0.26 Consensus pattern (100 bp): TATGCGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGA ATGGCCAATGTGATGAATGTGAACCTGTATATATA Found at i:51344971 original size:46 final size:46 Alignment explanation

Indices: 51344884--51344972 Score: 115 Period size: 46 Copynumber: 1.9 Consensus size: 46 51344874 ACATGAATAC * * * * 51344884 ATGTGGTAAGGCCGAATGGCTAATGCGAAACGTGTATGAGATGGAT 1 ATGTGGTAAAGCCAAATGGCTAATGCGAAACATGTACGAGATGGAT * * * 51344930 ATGTGGTAAAGCCAAATGGCTAATGTGAGATATGTACGAGATG 1 ATGTGGTAAAGCCAAATGGCTAATGCGAAACATGTACGAGATG 51344973 TGTATATATA Statistics Matches: 36, Mismatches: 7, Indels: 0 0.84 0.16 0.00 Matches are distributed among these distances: 46 36 1.00 ACGTcount: A:0.33, C:0.10, G:0.33, T:0.25 Consensus pattern (46 bp): ATGTGGTAAAGCCAAATGGCTAATGCGAAACATGTACGAGATGGAT Found at i:51345338 original size:37 final size:37 Alignment explanation

Indices: 51345119--51345337 Score: 384 Period size: 37 Copynumber: 5.9 Consensus size: 37 51345109 GGAAATATAT 51345119 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG 1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG * 51345156 TCCGAGTAAGACCCGATGACTACGTGTGGAGATTATG 1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG * 51345193 TCTGGGTAAGACCCGATGACTACGTGTGGAGATTATG 1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG 51345230 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG 1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG * 51345267 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG 1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG * * * 51345304 TCCGGGTAAGACCCGATAACTTCATGTGGAGATT 1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATT 51345338 TCGTCTGAGC Statistics Matches: 174, Mismatches: 8, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 37 174 1.00 ACGTcount: A:0.25, C:0.19, G:0.31, T:0.26 Consensus pattern (37 bp): TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG Found at i:51346794 original size:46 final size:46 Alignment explanation

Indices: 51346727--51346901 Score: 194 Period size: 46 Copynumber: 3.8 Consensus size: 46 51346717 TGTAACCCGC * * 51346727 CCATAAGTGAACTCGGACTCAAATCAATGAGCTCAGGCGTTCGCAT 1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCAGGCGTTCGCAT * 51346773 CCATAAGTGAACTCGGACTCAACTCAACGAGCTC-GG-GTGC-CTAGTT 1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCAGGCGTTCGC-A--T * *** * * * 51346819 ACATCTCTCGAACTCGGACTCAACTCAACGAGTTCAGACATTCGCAT 1 CCATAAGT-GAACTCGGACTCAACTCAACGAGCTCAGGCGTTCGCAT * 51346866 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCAG 1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCAG 51346902 ATGCCCAAAT Statistics Matches: 107, Mismatches: 15, Indels: 14 0.79 0.11 0.10 Matches are distributed among these distances: 43 1 0.01 44 4 0.04 45 2 0.02 46 65 0.61 47 30 0.28 48 1 0.01 49 3 0.03 50 1 0.01 ACGTcount: A:0.30, C:0.29, G:0.20, T:0.22 Consensus pattern (46 bp): CCATAAGTGAACTCGGACTCAACTCAACGAGCTCAGGCGTTCGCAT Found at i:51351895 original size:39 final size:39 Alignment explanation

Indices: 51351852--51352016 Score: 285 Period size: 39 Copynumber: 4.2 Consensus size: 39 51351842 TCTTTAACCT ** * 51351852 GGATATTTTTCCAGCACGTAGCCTGCGGACCTCAAGTCC 1 GGATATTTTTCCAGCATATAGCCTGCGGACCTCATGTCC * * 51351891 GGATATATTTCTAGCATATAGCCTGCGGACCTCATGTCC 1 GGATATTTTTCCAGCATATAGCCTGCGGACCTCATGTCC 51351930 GGATATTTTTCCAGCATATAGCCTGCGGACCTCATGTCC 1 GGATATTTTTCCAGCATATAGCCTGCGGACCTCATGTCC 51351969 GGATATTTTTCCAGCATATAGCCTGCGGACCTCATGTCC 1 GGATATTTTTCCAGCATATAGCCTGCGGACCTCATGTCC 51352008 GGATATTTT 1 GGATATTTT 51352017 CAATCTCATA Statistics Matches: 119, Mismatches: 7, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 39 119 1.00 ACGTcount: A:0.21, C:0.27, G:0.21, T:0.31 Consensus pattern (39 bp): GGATATTTTTCCAGCATATAGCCTGCGGACCTCATGTCC Found at i:51353850 original size:40 final size:40 Alignment explanation

Indices: 51353799--51353977 Score: 263 Period size: 40 Copynumber: 4.5 Consensus size: 40 51353789 TGGATGATAA * 51353799 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA 1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT 51353839 CCGGGCTAAGTCCCCGAAGGCATTTGTGCGAGTTACTATAT 1 CCGGGCTAAGT-CCCGAAGGCATTTGTGCGAGTTACTATAT * 51353880 CCGGGCTAAGTCCCGAAGGCATTGGTGCGAGTTACTATAT 1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT * * * 51353920 CCGGGCTATGTCCCGAAGGCATTCGAGCGAG-TAGCTATAT 1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT * * 51353960 CC-GGTTAAATCCCGAAGG 1 CCGGGCTAAGTCCCGAAGG 51353978 TACTTGGCTT Statistics Matches: 129, Mismatches: 8, Indels: 5 0.91 0.06 0.04 Matches are distributed among these distances: 39 15 0.12 40 75 0.58 41 39 0.30 ACGTcount: A:0.23, C:0.24, G:0.28, T:0.24 Consensus pattern (40 bp): CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT Found at i:51364208 original size:132 final size:132 Alignment explanation

Indices: 51363971--51364233 Score: 429 Period size: 132 Copynumber: 2.0 Consensus size: 132 51363961 GTGCCCAGCC ** * * 51363971 CGTAGGCTAACATCCTCTTAGAACATACCAAGTGTTGGAATTCAGTAGAATCAGTGGATAGTAAC 1 CGTAGGCTAACATCCTCCGAGAACACACCAAGTGTTGGAATCCAGTAGAATCAGTGGATAGTAAC 51364036 AAGTCAGGAATCATCATCTCATCATAAGTCAATCCCATACAACGTGCAATATAACCTATTGGCAT 66 AAGTCAGGAATCATCATCTCATCATAAGTCAATCCCATACAACGTGCAATATAACCTATTGGCAT 51364101 GT 131 GT * * * * 51364103 CGTAGGCTAACATCCTCCCGA-AACACACCAAGTGTTGGACTCCGGTATAATCAGTGGATAGTAC 1 CGTAGGCTAACATCCT-CCGAGAACACACCAAGTGTTGGAATCCAGTAGAATCAGTGGATAGTAA * 51364167 CAAGTCAGGAATCATCATCTCATCATAAGTCAATCCCATACAGCGTGCAATATAACCTATTGGCA 65 CAAGTCAGGAATCATCATCTCATCATAAGTCAATCCCATACAACGTGCAATATAACCTATTGGCA 51364232 TG 130 TG 51364234 CCAATTGTAT Statistics Matches: 121, Mismatches: 9, Indels: 2 0.92 0.07 0.02 Matches are distributed among these distances: 132 119 0.98 133 2 0.02 ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25 Consensus pattern (132 bp): CGTAGGCTAACATCCTCCGAGAACACACCAAGTGTTGGAATCCAGTAGAATCAGTGGATAGTAAC AAGTCAGGAATCATCATCTCATCATAAGTCAATCCCATACAACGTGCAATATAACCTATTGGCAT GT Found at i:51373044 original size:29 final size:30 Alignment explanation

Indices: 51373001--51373091 Score: 139 Period size: 30 Copynumber: 3.1 Consensus size: 30 51372991 TCTCAGTCAC * 51373001 GTGCGGCACATGGCCTGGCCACATAG-CGT 1 GTGCGGCACATGGCCTGGCCACACAGCCGT * 51373030 GTGCGGCACACGGCCTGGCCACACAGCCGT 1 GTGCGGCACATGGCCTGGCCACACAGCCGT * * 51373060 GTGCGGCGCATGGCCTGGCCACACAGTCGT 1 GTGCGGCACATGGCCTGGCCACACAGCCGT 51373090 GT 1 GT 51373092 AACCCTTGTA Statistics Matches: 56, Mismatches: 5, Indels: 1 0.90 0.08 0.02 Matches are distributed among these distances: 29 24 0.43 30 32 0.57 ACGTcount: A:0.15, C:0.34, G:0.35, T:0.15 Consensus pattern (30 bp): GTGCGGCACATGGCCTGGCCACACAGCCGT Found at i:51380129 original size:15 final size:15 Alignment explanation

Indices: 51380109--51380139 Score: 53 Period size: 15 Copynumber: 2.1 Consensus size: 15 51380099 CTCCTCATAA * 51380109 TTCATACACATGCAT 1 TTCATACACAAGCAT 51380124 TTCATACACAAGCAT 1 TTCATACACAAGCAT 51380139 T 1 T 51380140 CAATCAATAC 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:0.26, G:0.06, T:0.32 Consensus pattern (15 bp): TTCATACACAAGCAT Found at i:51384072 original size:47 final size:47 Alignment explanation

Indices: 51384018--51384348 Score: 420 Period size: 47 Copynumber: 7.1 Consensus size: 47 51384008 TTAGGATTTT ** * * * 51384018 ATGTGATGAATGTGAATGTGTATATATGAGATAAGGCCGAATGGCAA 1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA * * 51384065 ATGTGATGAATGTGAACCTGTATATATATGCGTGATAAGGCCGAATGGCCA 1 ATGTGATGAATGTGAACATG--CATATAT--GTGATAAGGCCGAATGGCCA * * 51384116 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA 1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA * ** 51384163 ATGTGATGAATGTGAACATGCGTACGTGTGATAAGGCCGAATGGCCA 1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA ** * 51384210 ATGTGATGAA--T---CATGTGTATGTGTGATAAGGCCGAATGGCCA 1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA * 51384252 ATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCA 1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA * * * 51384299 ATGTGATGAATGTGAACATGTATATATGTGGTAAGGCCGAATGGCTA 1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA 51384346 ATG 1 ATG 51384349 CGAAACCTGT Statistics Matches: 256, Mismatches: 19, Indels: 18 0.87 0.06 0.06 Matches are distributed among these distances: 42 39 0.15 44 1 0.00 45 1 0.00 47 167 0.65 49 11 0.04 51 37 0.14 ACGTcount: A:0.32, C:0.11, G:0.30, T:0.27 Consensus pattern (47 bp): ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA Found at i:51384167 original size:89 final size:91 Alignment explanation

Indices: 51384090--51384348 Score: 339 Period size: 89 Copynumber: 2.8 Consensus size: 91 51384080 ACCTGTATAT * * 51384090 ATATGCGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCG 1 ATATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGTGTATGTGTGATAAGGCCG 51384155 AATGGCCAATGTGATGAATGTGAACATGC 66 AATGGCCAATGTGA-GAATGT-AACAT-C * * 51384184 GTACGTGTGATAAGGCCGAATGGCCAATGTGATGAA--T---CATGTGTATGTGTGATAAGGCCG 1 ATATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGTGTATGTGTGATAAGGCCG 51384244 AATGGCCAATGTGATGAATGTGAACATGC 66 AATGGCCAATGTGA-GAATGT-AACAT-C * * * * * 51384273 ATATATGAGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGTATATATGTGGTAAGGCCG 1 ATATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGTGTATGTGTGATAAGGCCG * 51384338 AATGGCTAATG 66 AATGGCCAATG 51384349 CGAAACCTGT Statistics Matches: 148, Mismatches: 12, Indels: 10 0.87 0.07 0.06 Matches are distributed among these distances: 89 83 0.56 91 1 0.01 92 1 0.01 94 63 0.43 ACGTcount: A:0.31, C:0.13, G:0.31, T:0.25 Consensus pattern (91 bp): ATATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGTGTATGTGTGATAAGGCCG AATGGCCAATGTGAGAATGTAACATC Found at i:51384270 original size:136 final size:136 Alignment explanation

Indices: 51384091--51384348 Score: 426 Period size: 136 Copynumber: 1.9 Consensus size: 136 51384081 CCTGTATATA * * * 51384091 TATGCGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGA 1 TATGCGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGA * * 51384156 ATGGCCAATGTGATGAATGTGAACATGCGTACGTGTGATAAGGCCGAATGGCCAATGTGATGAAT 66 ATGGCCAATGTGATGAATGTGAACATGCATACATGTGATAAGGCCGAATGGCCAATGTGATGAAT 51384221 CATGTG 131 CATGTG * 51384227 TATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGA 1 TATGCGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGA * * * * 51384292 ATGGCCAATGTGATGAATGTGAACATGTATATATGTGGTAAGGCCGAATGGCTAATG 66 ATGGCCAATGTGATGAATGTGAACATGCATACATGTGATAAGGCCGAATGGCCAATG 51384349 CGAAACCTGT Statistics Matches: 112, Mismatches: 10, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 136 112 1.00 ACGTcount: A:0.31, C:0.13, G:0.31, T:0.26 Consensus pattern (136 bp): TATGCGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGA ATGGCCAATGTGATGAATGTGAACATGCATACATGTGATAAGGCCGAATGGCCAATGTGATGAAT CATGTG Found at i:51384452 original size:46 final size:46 Alignment explanation

Indices: 51384322--51384458 Score: 193 Period size: 46 Copynumber: 3.0 Consensus size: 46 51384312 GAACATGTAT * * * 51384322 ATATGTGGTAAGGCCGAATGGCTAATGCGAAACCTGTATGAGATAG 1 ATATGTGGTAAAGCCGAATGGCTAATGCGAAACATGTATGAGATGG * * 51384368 ATATGAGGTAAAGCCGAATGGCTAATGCGAAACGTGTATGAGATGG 1 ATATGTGGTAAAGCCGAATGGCTAATGCGAAACATGTATGAGATGG * * * * 51384414 ATATGTGGTAAAGCCAAATGGCTAATGTGAGATATGTATGAGATG 1 ATATGTGGTAAAGCCGAATGGCTAATGCGAAACATGTATGAGATG 51384459 TGTATATATA Statistics Matches: 81, Mismatches: 10, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 46 81 1.00 ACGTcount: A:0.34, C:0.10, G:0.31, T:0.25 Consensus pattern (46 bp): ATATGTGGTAAAGCCGAATGGCTAATGCGAAACATGTATGAGATGG Found at i:51389898 original size:21 final size:20 Alignment explanation

Indices: 51389874--51389912 Score: 51 Period size: 21 Copynumber: 1.9 Consensus size: 20 51389864 GGACTAATCT * 51389874 GAAACAAAACAGAAAAATATG 1 GAAAAAAAAC-GAAAAATATG * 51389895 GAAAAAAAACTAAAAATA 1 GAAAAAAAACGAAAAATA 51389913 GGGGTCATAC Statistics Matches: 16, Mismatches: 2, Indels: 1 0.84 0.11 0.05 Matches are distributed among these distances: 20 7 0.44 21 9 0.56 ACGTcount: A:0.72, C:0.08, G:0.10, T:0.10 Consensus pattern (20 bp): GAAAAAAAACGAAAAATATG Found at i:51396199 original size:28 final size:28 Alignment explanation

Indices: 51396162--51396236 Score: 105 Period size: 28 Copynumber: 2.7 Consensus size: 28 51396152 TGTTCCCTTT * 51396162 AGGCCCAATCTCATTCATATGGCCCATC 1 AGGCCCAATCACATTCATATGGCCCATC * * * 51396190 AGGCCTAATCACTTTCATATGGCCTATC 1 AGGCCCAATCACATTCATATGGCCCATC * 51396218 AGGCCCAATCACACTCATA 1 AGGCCCAATCACATTCATA 51396237 GTCATGCAAT Statistics Matches: 40, Mismatches: 7, Indels: 0 0.85 0.15 0.00 Matches are distributed among these distances: 28 40 1.00 ACGTcount: A:0.28, C:0.33, G:0.13, T:0.25 Consensus pattern (28 bp): AGGCCCAATCACATTCATATGGCCCATC Found at i:51401569 original size:29 final size:29 Alignment explanation

Indices: 51401483--51401589 Score: 110 Period size: 29 Copynumber: 3.7 Consensus size: 29 51401473 TACATACATG 51401483 CATATGGCCCACTAGGCCCAA-TCTTATT 1 CATATGGCCCACTAGGCCCAATTCTTATT * * * * 51401511 CAAATGGCCCATTTGGCCCAGTT-TATATT 1 CATATGGCCCACTAGGCCCAATTCT-TATT * * 51401540 CTTATGGCCCACTAGGCCCAATTCTCATT 1 CATATGGCCCACTAGGCCCAATTCTTATT * * * 51401569 CATCTAGCCCATTAGGCCCAA 1 CATATGGCCCACTAGGCCCAA 51401590 ATCATATTAT Statistics Matches: 62, Mismatches: 14, Indels: 5 0.77 0.17 0.06 Matches are distributed among these distances: 28 18 0.29 29 43 0.69 30 1 0.02 ACGTcount: A:0.24, C:0.32, G:0.15, T:0.29 Consensus pattern (29 bp): CATATGGCCCACTAGGCCCAATTCTTATT Found at i:51401597 original size:58 final size:57 Alignment explanation

Indices: 51401485--51401597 Score: 145 Period size: 58 Copynumber: 2.0 Consensus size: 57 51401475 CATACATGCA * * * ** * 51401485 TATGGCCCACTAGGCCCAATCTTATTCAAATGGCCCATTTGGCCCAGTTTATATTCT 1 TATGGCCCACTAGGCCCAATCTCATTCAAATAGCCCATTAGGCCCAAATCATATTCT ** 51401542 TATGGCCCACTAGGCCCAATTCTCATTCATCTAGCCCATTAGGCCCAAATCATATT 1 TATGGCCCACTAGGCCCAA-TCTCATTCAAATAGCCCATTAGGCCCAAATCATATT 51401598 ATATTCATGC Statistics Matches: 47, Mismatches: 8, Indels: 1 0.84 0.14 0.02 Matches are distributed among these distances: 57 19 0.40 58 28 0.60 ACGTcount: A:0.25, C:0.30, G:0.14, T:0.31 Consensus pattern (57 bp): TATGGCCCACTAGGCCCAATCTCATTCAAATAGCCCATTAGGCCCAAATCATATTCT Found at i:51401715 original size:19 final size:19 Alignment explanation

Indices: 51401679--51401715 Score: 56 Period size: 19 Copynumber: 1.9 Consensus size: 19 51401669 CAGCCCATCA * 51401679 GGCCCATTTAGCCTATTCC 1 GGCCCATTTAGCCAATTCC * 51401698 GGCCCATTTGGCCAATTC 1 GGCCCATTTAGCCAATTC 51401716 TCAACCCAAG Statistics Matches: 16, Mismatches: 2, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 19 16 1.00 ACGTcount: A:0.16, C:0.35, G:0.19, T:0.30 Consensus pattern (19 bp): GGCCCATTTAGCCAATTCC Found at i:51410280 original size:16 final size:16 Alignment explanation

Indices: 51410259--51410291 Score: 66 Period size: 16 Copynumber: 2.1 Consensus size: 16 51410249 AATAAGAAGA 51410259 AGAGAAGAAGGAATCG 1 AGAGAAGAAGGAATCG 51410275 AGAGAAGAAGGAATCG 1 AGAGAAGAAGGAATCG 51410291 A 1 A 51410292 CTAAAACCAA Statistics Matches: 17, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 16 17 1.00 ACGTcount: A:0.52, C:0.06, G:0.36, T:0.06 Consensus pattern (16 bp): AGAGAAGAAGGAATCG Found at i:51428576 original size:30 final size:31 Alignment explanation

Indices: 51428465--51428578 Score: 178 Period size: 31 Copynumber: 3.7 Consensus size: 31 51428455 TTAGTCTTGA * * 51428465 CATAT-ACTGGGCCGAGGCCTTTCCATAAAT 1 CATATCACTGGGCCGAAGCCTTTTCATAAAT 51428495 CATATCACTGGGCCGAAGCCTTTTCATAAAT 1 CATATCACTGGGCCGAAGCCTTTTCATAAAT * 51428526 CATATCACTGGGCTGAAGCCTTTTCATAAAT 1 CATATCACTGGGCCGAAGCCTTTTCATAAAT * 51428557 CATTTCAC-GGGCCGAAGCCTTT 1 CATATCACTGGGCCGAAGCCTTT 51428579 ATTGCAAACG Statistics Matches: 78, Mismatches: 5, Indels: 2 0.92 0.06 0.02 Matches are distributed among these distances: 30 18 0.23 31 60 0.77 ACGTcount: A:0.26, C:0.26, G:0.18, T:0.29 Consensus pattern (31 bp): CATATCACTGGGCCGAAGCCTTTTCATAAAT Found at i:51431399 original size:47 final size:47 Alignment explanation

Indices: 51431338--51431635 Score: 452 Period size: 47 Copynumber: 6.3 Consensus size: 47 51431328 CAGCCAAGAC * 51431338 AGTGTATATGTGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA 1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA * 51431385 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA 1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA 51431432 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA 1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA * * 51431479 AGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA 1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA * * * 51431526 AGTGTATATATGTAATAAGGCCTAATGGCTGATGTGAGGAATGTGAA 1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA * * * * * * * 51431573 AGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAA 1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA * * 51431620 AGTGCATAAATGTGAT 1 AGTGTATATATGTGAT 51431636 CAGTCCCGAA Statistics Matches: 228, Mismatches: 23, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 47 228 1.00 ACGTcount: A:0.32, C:0.09, G:0.31, T:0.29 Consensus pattern (47 bp): AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA Found at i:51431813 original size:37 final size:37 Alignment explanation

Indices: 51431757--51431835 Score: 115 Period size: 37 Copynumber: 2.1 Consensus size: 37 51431747 CCGAGCTCTA * * 51431757 AAGACCCGATGACTACGTGTGG-GAATTTTGTCCGGGT 1 AAGACCCGATAACTACGTGTGGAG-ATTATGTCCGGGT * 51431794 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT 1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT 51431831 AAGAC 1 AAGAC 51431836 TTCGTAATAA Statistics Matches: 38, Mismatches: 3, Indels: 2 0.88 0.07 0.05 Matches are distributed among these distances: 37 37 0.97 38 1 0.03 ACGTcount: A:0.25, C:0.19, G:0.30, T:0.25 Consensus pattern (37 bp): AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT Found at i:51434002 original size:27 final size:27 Alignment explanation

Indices: 51433972--51434036 Score: 78 Period size: 27 Copynumber: 2.4 Consensus size: 27 51433962 GGGCATATTC 51433972 GTCATTTTACCATACAAGGG-TATTACG 1 GTCATTTTACCATACAAGGGCT-TTACG * * * 51433999 GTCACTTTACCCTACAGGGGCTTTACG 1 GTCATTTTACCATACAAGGGCTTTACG * 51434026 GTCTTTTTACC 1 GTCATTTTACC 51434037 TATTAGGGGT Statistics Matches: 32, Mismatches: 5, Indels: 2 0.82 0.13 0.05 Matches are distributed among these distances: 27 31 0.97 28 1 0.03 ACGTcount: A:0.22, C:0.25, G:0.18, T:0.35 Consensus pattern (27 bp): GTCATTTTACCATACAAGGGCTTTACG Found at i:51434120 original size:27 final size:27 Alignment explanation

Indices: 51434090--51434141 Score: 88 Period size: 27 Copynumber: 1.9 Consensus size: 27 51434080 GTAAATCTAC 51434090 AAACCAATGGTATTTC-AGTAATTTTGT 1 AAACCAATGGTATTTCTA-TAATTTTGT 51434117 AAACCAATGGTATTTCTATAATTTT 1 AAACCAATGGTATTTCTATAATTTT 51434142 TAGAAAGTTA Statistics Matches: 24, Mismatches: 0, Indels: 2 0.92 0.00 0.08 Matches are distributed among these distances: 27 23 0.96 28 1 0.04 ACGTcount: A:0.35, C:0.12, G:0.12, T:0.42 Consensus pattern (27 bp): AAACCAATGGTATTTCTATAATTTTGT Found at i:51434193 original size:27 final size:27 Alignment explanation

Indices: 51434150--51434276 Score: 175 Period size: 27 Copynumber: 4.7 Consensus size: 27 51434140 TTTAGAAAGT ** * 51434150 TAAGGGTATTTAT-GTAATTTTGTAAAT 1 TAAGGGTATTT-TGGTAATTTTACAAAC * * 51434177 TAGGGGTATTTTGGTAATTTTACAAAT 1 TAAGGGTATTTTGGTAATTTTACAAAC * 51434204 TAAGGGTATTTCGGTAATTTTACAAAC 1 TAAGGGTATTTTGGTAATTTTACAAAC * 51434231 TAGGGGTATTTTGGTAATTTTACAAAC 1 TAAGGGTATTTTGGTAATTTTACAAAC 51434258 TAAGGGTATTTTGGTAATT 1 TAAGGGTATTTTGGTAATT 51434277 CTATCCTATA Statistics Matches: 90, Mismatches: 9, Indels: 2 0.89 0.09 0.02 Matches are distributed among these distances: 26 1 0.01 27 89 0.99 ACGTcount: A:0.31, C:0.05, G:0.21, T:0.43 Consensus pattern (27 bp): TAAGGGTATTTTGGTAATTTTACAAAC Found at i:51434235 original size:54 final size:54 Alignment explanation

Indices: 51434139--51434276 Score: 195 Period size: 54 Copynumber: 2.5 Consensus size: 54 51434129 TTTCTATAAT * * ** * 51434139 TTTTAGAAAGTTAAGGGTATTTATGTAATTTTGTAAATTAGGGGTATTTTGGTAA 1 TTTTACAAA-TTAAGGGTATTTAGGTAATTTTACAAACTAGGGGTATTTTGGTAA * 51434194 TTTTACAAATTAAGGGTATTTCGGTAATTTTACAAACTAGGGGTATTTTGGTAA 1 TTTTACAAATTAAGGGTATTTAGGTAATTTTACAAACTAGGGGTATTTTGGTAA * * 51434248 TTTTACAAACTAAGGGTATTTTGGTAATT 1 TTTTACAAATTAAGGGTATTTAGGTAATT 51434277 CTATCCTATA Statistics Matches: 75, Mismatches: 8, Indels: 1 0.89 0.10 0.01 Matches are distributed among these distances: 54 67 0.89 55 8 0.11 ACGTcount: A:0.31, C:0.04, G:0.21, T:0.43 Consensus pattern (54 bp): TTTTACAAATTAAGGGTATTTAGGTAATTTTACAAACTAGGGGTATTTTGGTAA Found at i:51434343 original size:27 final size:27 Alignment explanation

Indices: 51434307--51434587 Score: 285 Period size: 27 Copynumber: 10.4 Consensus size: 27 51434297 GTAATTTCAC * * * * 51434307 AATCGAGGGTAAAACGATAATTTTGTA 1 AATCGAGGGTAAAATGGTAATTCTATA * * 51434334 AA-CTGAGGGTAAAATGGTAATTTTGTA 1 AATC-GAGGGTAAAATGGTAATTCTATA * ** 51434361 AATTGAGGGTAAAACAGTAATTCTATA 1 AATCGAGGGTAAAATGGTAATTCTATA *** 51434388 AATCGAGGGTACTTTGGTAATTCTATA 1 AATCGAGGGTAAAATGGTAATTCTATA * 51434415 AATCGAGGGTAAAATGGTAATTCTGTA 1 AATCGAGGGTAAAATGGTAATTCTATA * 51434442 AATCAAGGGTAAAATGGTAATTCTATA 1 AATCGAGGGTAAAATGGTAATTCTATA * * * * 51434469 AATTGAGGGTGAAATAGTAATTCTACA 1 AATCGAGGGTAAAATGGTAATTCTATA * * 51434496 AATCAAGGGTAAAATGGTAATTTTATA 1 AATCGAGGGTAAAATGGTAATTCTATA * * * 51434523 AATCGAAGGTAAAACGGTAATTTTATA 1 AATCGAGGGTAAAATGGTAATTCTATA * * * * * 51434550 AATAGAGGGTAAAACGATAATTTTGTA 1 AATCGAGGGTAAAATGGTAATTCTATA * 51434577 AATCAAGGGTA 1 AATCGAGGGTA 51434588 CTTTGGTAAT Statistics Matches: 213, Mismatches: 39, Indels: 4 0.83 0.15 0.02 Matches are distributed among these distances: 26 1 0.00 27 212 1.00 ACGTcount: A:0.41, C:0.07, G:0.22, T:0.31 Consensus pattern (27 bp): AATCGAGGGTAAAATGGTAATTCTATA Found at i:51436208 original size:21 final size:20 Alignment explanation

Indices: 51436165--51436209 Score: 63 Period size: 21 Copynumber: 2.2 Consensus size: 20 51436155 CTATCATTAT * 51436165 TAAGTCTCTATTTATGTGGC 1 TAAGTCTCTATTTATGTAGC * 51436185 TAAGTACTCTATTTATGTATC 1 TAAGT-CTCTATTTATGTAGC 51436206 TAAG 1 TAAG 51436210 ATTGGAGGTT Statistics Matches: 22, Mismatches: 2, Indels: 1 0.88 0.08 0.04 Matches are distributed among these distances: 20 5 0.23 21 17 0.77 ACGTcount: A:0.27, C:0.13, G:0.16, T:0.44 Consensus pattern (20 bp): TAAGTCTCTATTTATGTAGC Found at i:51440853 original size:122 final size:122 Alignment explanation

Indices: 51440703--51440948 Score: 492 Period size: 122 Copynumber: 2.0 Consensus size: 122 51440693 ATAACTATAA 51440703 ACCTATACCAATGCCATAAGATTCATAAATCTATATAACCATCAACTCATTAATGAGTAAGTTTA 1 ACCTATACCAATGCCATAAGATTCATAAATCTATATAACCATCAACTCATTAATGAGTAAGTTTA 51440768 TTAGTGTCACATATATTTATCATTCATAACATAATAGGATCTTAGAAGACATAATAT 66 TTAGTGTCACATATATTTATCATTCATAACATAATAGGATCTTAGAAGACATAATAT 51440825 ACCTATACCAATGCCATAAGATTCATAAATCTATATAACCATCAACTCATTAATGAGTAAGTTTA 1 ACCTATACCAATGCCATAAGATTCATAAATCTATATAACCATCAACTCATTAATGAGTAAGTTTA 51440890 TTAGTGTCACATATATTTATCATTCATAACATAATAGGATCTTAGAAGACATAATAT 66 TTAGTGTCACATATATTTATCATTCATAACATAATAGGATCTTAGAAGACATAATAT 51440947 AC 1 AC 51440949 AATCATCAAC Statistics Matches: 124, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 122 124 1.00 ACGTcount: A:0.41, C:0.17, G:0.09, T:0.33 Consensus pattern (122 bp): ACCTATACCAATGCCATAAGATTCATAAATCTATATAACCATCAACTCATTAATGAGTAAGTTTA TTAGTGTCACATATATTTATCATTCATAACATAATAGGATCTTAGAAGACATAATAT Found at i:51446766 original size:64 final size:63 Alignment explanation

Indices: 51446697--51446903 Score: 161 Period size: 68 Copynumber: 3.1 Consensus size: 63 51446687 ATCATACATA 51446697 AATGTGATTCCTATGATTATGGATATTATGGGAAATTGTAAGTTCATATGATTTTTAATAAAGC 1 AATGTGATT-CTATGATTATGGATATTATGGGAAATTGTAAGTTCATATGATTTTTAATAAAGC *** * 51446761 AATGTGTAATT-TAATG-TTATTGCCTTGATATTAAATGACA-TGTAAG-TCTATATGCATTGAA 1 AATGTG--ATTCT-ATGATTA-TG----GATATTATGGGAAATTGTAAGTTC-ATATG-ATT--- * * ** 51446822 TTATCATACATA 53 TT-TAATAAAGC * 51446834 AATGTGATTTCTATGATTATGGATATTATGGGAAATTGTAAGTTCATATGATTTTTAATAAGGC 1 AATGTGA-TTCTATGATTATGGATATTATGGGAAATTGTAAGTTCATATGATTTTTAATAAAGC 51446898 AATGTG 1 AATGTG 51446904 TAATTTAATG Statistics Matches: 107, Mismatches: 17, Indels: 38 0.66 0.10 0.23 Matches are distributed among these distances: 64 20 0.19 65 7 0.07 66 3 0.03 67 2 0.02 68 24 0.22 69 24 0.22 70 2 0.02 71 1 0.01 72 9 0.08 73 15 0.14 ACGTcount: A:0.34, C:0.07, G:0.18, T:0.41 Consensus pattern (63 bp): AATGTGATTCTATGATTATGGATATTATGGGAAATTGTAAGTTCATATGATTTTTAATAAAGC Found at i:51446814 original size:68 final size:67 Alignment explanation

Indices: 51446728--51446944 Score: 178 Period size: 68 Copynumber: 3.2 Consensus size: 67 51446718 GATATTATGG 51446728 GAAATTGTAAGTTCATATGATTTTTAATAAAGCAATGTGTAATTTAATGTTATTGCCTTGATATT 1 GAAA-TGTAAGTTCATATGATTTTTAATAAAGCAATGTGTAATTTAATGTTA-TGCCTTGATATT 51446793 AAAT 64 AAAT * * * ** * 51446797 GACATGTAAG-TCTATATGCATTGAATTATCATACATAAATGTG--ATTTCTATGATTATG---- 1 GAAATGTAAGTTC-ATATG-ATT---TT-TAATAAAGCAATGTGTAATTT-AATG-TTATGCCTT *** 51446855 GATATTATGG 58 GATATTAAAT * 51446865 GAAATTGTAAGTTCATATGATTTTTAATAAGGCAATGTGTAATTTAATGTTACTGCCTTGATATT 1 GAAA-TGTAAGTTCATATGATTTTTAATAAAGCAATGTGTAATTTAATGTTA-TGCCTTGATATT 51446930 AAAT 64 AAAT * 51446934 GAGATGTAAGT 1 GAAATGTAAGT 51446945 CTATATGTAA Statistics Matches: 111, Mismatches: 20, Indels: 35 0.67 0.12 0.21 Matches are distributed among these distances: 64 13 0.12 65 7 0.06 66 4 0.04 67 2 0.02 68 31 0.28 69 27 0.24 70 2 0.02 71 4 0.04 72 7 0.06 73 14 0.13 ACGTcount: A:0.35, C:0.07, G:0.17, T:0.41 Consensus pattern (67 bp): GAAATGTAAGTTCATATGATTTTTAATAAAGCAATGTGTAATTTAATGTTATGCCTTGATATTAA AT Found at i:51446922 original size:137 final size:137 Alignment explanation

Indices: 51446676--51446951 Score: 516 Period size: 137 Copynumber: 2.0 Consensus size: 137 51446666 GTACATGAAG 51446676 TGCATTGAATTATCATACATAAATGTGATTCCTATGATTATGGATATTATGGGAAATTGTAAGTT 1 TGCATTGAATTATCATACATAAATGTGATTCCTATGATTATGGATATTATGGGAAATTGTAAGTT * 51446741 CATATGATTTTTAATAAAGCAATGTGTAATTTAATGTTATTGCCTTGATATTAAATGACATGTAA 66 CATATGATTTTTAATAAAGCAATGTGTAATTTAATGTTACTGCCTTGATATTAAATGACATGTAA 51446806 GTCTATA 131 GTCTATA * 51446813 TGCATTGAATTATCATACATAAATGTGATTTCTATGATTATGGATATTATGGGAAATTGTAAGTT 1 TGCATTGAATTATCATACATAAATGTGATTCCTATGATTATGGATATTATGGGAAATTGTAAGTT * * 51446878 CATATGATTTTTAATAAGGCAATGTGTAATTTAATGTTACTGCCTTGATATTAAATGAGATGTAA 66 CATATGATTTTTAATAAAGCAATGTGTAATTTAATGTTACTGCCTTGATATTAAATGACATGTAA 51446943 GTCTATA 131 GTCTATA 51446950 TG 1 TG 51446952 TAAGTAATAC Statistics Matches: 135, Mismatches: 4, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 137 135 1.00 ACGTcount: A:0.34, C:0.08, G:0.17, T:0.41 Consensus pattern (137 bp): TGCATTGAATTATCATACATAAATGTGATTCCTATGATTATGGATATTATGGGAAATTGTAAGTT CATATGATTTTTAATAAAGCAATGTGTAATTTAATGTTACTGCCTTGATATTAAATGACATGTAA GTCTATA Found at i:51447249 original size:64 final size:64 Alignment explanation

Indices: 51447168--51447350 Score: 176 Period size: 67 Copynumber: 2.8 Consensus size: 64 51447158 AGACATTATG * * 51447168 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT 1 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA * * * * * * 51447232 ATGTAGCTAGGTCGCATGCGTGGCT-CCAGGTGAAGGATACCATGTAGACAAGAGAGCTACGAGA 1 ATGTAGCTAGGTCGCATGGGT-GATACTA--TG-TGTACACCATGTAGACAAGAGAGCTACGAGA 51447296 TAA 62 TAA * * * * * 51447299 AT-TGGCTAGGTCACATGGGTGGTACTGA-GTGTTCACCATGTTG-CAAGAGAGC 1 ATGTAGCTAGGTCGCATGGGTGATACT-ATGTGTACACCATGTAGACAAGAGAGC 51447351 CGAACTCTAT Statistics Matches: 95, Mismatches: 18, Indels: 14 0.75 0.14 0.11 Matches are distributed among these distances: 62 9 0.09 63 9 0.09 64 23 0.24 65 4 0.04 66 18 0.19 67 32 0.34 ACGTcount: A:0.28, C:0.17, G:0.31, T:0.23 Consensus pattern (64 bp): ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA Found at i:51449501 original size:35 final size:36 Alignment explanation

Indices: 51449433--51449522 Score: 155 Period size: 35 Copynumber: 2.5 Consensus size: 36 51449423 AGTACATCGA * 51449433 TAATCCAGCCAAAACACACCAGATGCTTATAAGAGC 1 TAATCCATCCAAAACACACCAGATGCTTATAAGAGC * 51449469 TAATCCATCCGAAACACACCA-ATGCTTATAAGAGC 1 TAATCCATCCAAAACACACCAGATGCTTATAAGAGC 51449504 TAATCCATCCAAAACACAC 1 TAATCCATCCAAAACACAC 51449523 AAAAATAGAG Statistics Matches: 51, Mismatches: 3, Indels: 1 0.93 0.05 0.02 Matches are distributed among these distances: 35 32 0.63 36 19 0.37 ACGTcount: A:0.42, C:0.30, G:0.10, T:0.18 Consensus pattern (36 bp): TAATCCATCCAAAACACACCAGATGCTTATAAGAGC Found at i:51456571 original size:30 final size:30 Alignment explanation

Indices: 51456514--51456572 Score: 73 Period size: 30 Copynumber: 2.0 Consensus size: 30 51456504 TCCCGAGCCT * * 51456514 AGGGGCAAAAGTGTAAATATGCTAAAGTTC 1 AGGGGCAAAAGTGTAAATATACCAAAGTTC * * * 51456544 AGGGGCAAAATTGTAATTTTACCAAAGTT 1 AGGGGCAAAAGTGTAAATATACCAAAGTT 51456573 TGAGTTAAGG Statistics Matches: 24, Mismatches: 5, Indels: 0 0.83 0.17 0.00 Matches are distributed among these distances: 30 24 1.00 ACGTcount: A:0.39, C:0.10, G:0.24, T:0.27 Consensus pattern (30 bp): AGGGGCAAAAGTGTAAATATACCAAAGTTC Found at i:51461024 original size:30 final size:30 Alignment explanation

Indices: 51460990--51461050 Score: 104 Period size: 30 Copynumber: 2.0 Consensus size: 30 51460980 TTCCCGAGCC 51460990 TAGGGGTAAAAGTGTAAATTTGCAAAAGTT 1 TAGGGGTAAAAGTGTAAATTTGCAAAAGTT * * 51461020 TAGGGGTAAAATTGTAATTTTGCAAAAGTT 1 TAGGGGTAAAAGTGTAAATTTGCAAAAGTT 51461050 T 1 T 51461051 GAGTTAAGGA Statistics Matches: 29, Mismatches: 2, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 30 29 1.00 ACGTcount: A:0.38, C:0.03, G:0.25, T:0.34 Consensus pattern (30 bp): TAGGGGTAAAAGTGTAAATTTGCAAAAGTT Found at i:51475451 original size:40 final size:40 Alignment explanation

Indices: 51475399--51475752 Score: 541 Period size: 40 Copynumber: 8.9 Consensus size: 40 51475389 GTTATATATG 51475399 ATCCGGGCTAAGTCCCGAAGAGCATACGTGCTGGTGTTAT 1 ATCCGGGCTAAGTCCCGAAGAGCATACGTGCTGGTGTTAT * * 51475439 ATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGAGTTAT 1 ATCCGGGCTAAGTCCCGAAGAGCATACGTGCTGGTGTTAT * 51475479 ATCCGGGCTAAGTCCCGAAGAGCATACGTGCTGGAG-T-T 1 ATCCGGGCTAAGTCCCGAAGAGCATACGTGCTGGTGTTAT * * * 51475517 ATCCGGGCTAAGTCCCGATGAGCATATGTGCTGGAGTTAT 1 ATCCGGGCTAAGTCCCGAAGAGCATACGTGCTGGTGTTAT * 51475557 ATCCGAGCTAAGTCCCGAAGAGCATACGTGCTGGTGTTAT 1 ATCCGGGCTAAGTCCCGAAGAGCATACGTGCTGGTGTTAT 51475597 ATCCGGGCTAAGTCCCGAAGAGCATACGTGCTGGTGTTAT 1 ATCCGGGCTAAGTCCCGAAGAGCATACGTGCTGGTGTTAT * * * 51475637 ATCCGGGCTAAGTCTCGAAGAGCATTCGTGCTGGAGTTAT 1 ATCCGGGCTAAGTCCCGAAGAGCATACGTGCTGGTGTTAT ** * * * 51475677 ATCAAGGTTAAGTCCCGAAGAGCATTCGTACTGGTGTTAT 1 ATCCGGGCTAAGTCCCGAAGAGCATACGTGCTGGTGTTAT * * 51475717 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTGGTG 1 ATCCGGGCTAAGTCCCGAAGAGCATACGTGCTGGTG 51475753 ATGTGTATTC Statistics Matches: 288, Mismatches: 24, Indels: 4 0.91 0.08 0.01 Matches are distributed among these distances: 38 35 0.12 39 2 0.01 40 251 0.87 ACGTcount: A:0.23, C:0.22, G:0.29, T:0.25 Consensus pattern (40 bp): ATCCGGGCTAAGTCCCGAAGAGCATACGTGCTGGTGTTAT Found at i:51475667 original size:158 final size:160 Alignment explanation

Indices: 51475399--51475752 Score: 561 Period size: 158 Copynumber: 2.2 Consensus size: 160 51475389 GTTATATATG 51475399 ATCCGGGCTAAGTCCCGAAGAGCATACGTGCTGGTGTTATATCCGGGCTAAGTCCCGAAGAGCAT 1 ATCCGGGCTAAGTCCCGAAGAGCATACGTGCTGGTGTTATATCCGGGCTAAGTCCCGAAGAGCAT * ** 51475464 TCGTGCTGGAGTTATATCCGGGCTAAGTCCCGAAGAGCATACGTGCTGGAG-T-TATCCGGGCTA 66 ACGTGCTGGAGTTATATCCGGGCTAAGTCCCGAAGAGCATACGTGCTGGAGTTATATCAAGGCTA * * 51475527 AGTCCCGATGAGCATAT-GTGCTGGAGTTAT 131 AGTCCCGAAGAGCAT-TCGTACTGGAGTTAT * 51475557 ATCCGAGCTAAGTCCCGAAGAGCATACGTGCTGGTGTTATATCCGGGCTAAGTCCCGAAGAGCAT 1 ATCCGGGCTAAGTCCCGAAGAGCATACGTGCTGGTGTTATATCCGGGCTAAGTCCCGAAGAGCAT * * * * 51475622 ACGTGCTGGTGTTATATCCGGGCTAAGTCTCGAAGAGCATTCGTGCTGGAGTTATATCAAGGTTA 66 ACGTGCTGGAGTTATATCCGGGCTAAGTCCCGAAGAGCATACGTGCTGGAGTTATATCAAGGCTA * 51475687 AGTCCCGAAGAGCATTCGTACTGGTGTTAT 131 AGTCCCGAAGAGCATTCGTACTGGAGTTAT * * 51475717 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTGGTG 1 ATCCGGGCTAAGTCCCGAAGAGCATACGTGCTGGTG 51475753 ATGTGTATTC Statistics Matches: 179, Mismatches: 14, Indels: 4 0.91 0.07 0.02 Matches are distributed among these distances: 158 111 0.62 159 2 0.01 160 66 0.37 ACGTcount: A:0.23, C:0.22, G:0.29, T:0.25 Consensus pattern (160 bp): ATCCGGGCTAAGTCCCGAAGAGCATACGTGCTGGTGTTATATCCGGGCTAAGTCCCGAAGAGCAT ACGTGCTGGAGTTATATCCGGGCTAAGTCCCGAAGAGCATACGTGCTGGAGTTATATCAAGGCTA AGTCCCGAAGAGCATTCGTACTGGAGTTAT Found at i:51475966 original size:25 final size:25 Alignment explanation

Indices: 51475916--51475968 Score: 63 Period size: 25 Copynumber: 2.1 Consensus size: 25 51475906 TGTGTAACAA * * 51475916 CAAATGAATAGGGGCACTATGTGTG 1 CAAATGAATAGAGGCACTATGAGTG * 51475941 CAAATGATTAGAGGCACTGA-GAGTG 1 CAAATGAATAGAGGCACT-ATGAGTG 51475966 CAA 1 CAA 51475969 GTTCTTCAAC Statistics Matches: 24, Mismatches: 3, Indels: 2 0.83 0.10 0.07 Matches are distributed among these distances: 25 23 0.96 26 1 0.04 ACGTcount: A:0.36, C:0.13, G:0.30, T:0.21 Consensus pattern (25 bp): CAAATGAATAGAGGCACTATGAGTG Found at i:51489306 original size:30 final size:28 Alignment explanation

Indices: 51489272--51489335 Score: 96 Period size: 26 Copynumber: 2.3 Consensus size: 28 51489262 AAATTAATAC 51489272 TTAAAGTACAATCACTTCTTAATTTGATAT 1 TTAAAGT--AATCACTTCTTAATTTGATAT 51489302 TTAAAG--ATCACTTCTTAATTTGATAT 1 TTAAAGTAATCACTTCTTAATTTGATAT 51489328 TTAAAGTA 1 TTAAAGTA 51489336 TGTCTCTATT Statistics Matches: 32, Mismatches: 0, Indels: 6 0.84 0.00 0.16 Matches are distributed among these distances: 26 26 0.81 30 6 0.19 ACGTcount: A:0.38, C:0.11, G:0.08, T:0.44 Consensus pattern (28 bp): TTAAAGTAATCACTTCTTAATTTGATAT Found at i:51489312 original size:26 final size:26 Alignment explanation

Indices: 51489282--51489333 Score: 104 Period size: 26 Copynumber: 2.0 Consensus size: 26 51489272 TTAAAGTACA 51489282 ATCACTTCTTAATTTGATATTTAAAG 1 ATCACTTCTTAATTTGATATTTAAAG 51489308 ATCACTTCTTAATTTGATATTTAAAG 1 ATCACTTCTTAATTTGATATTTAAAG 51489334 TATGTCTCTA Statistics Matches: 26, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 26 26 1.00 ACGTcount: A:0.35, C:0.12, G:0.08, T:0.46 Consensus pattern (26 bp): ATCACTTCTTAATTTGATATTTAAAG Found at i:51489482 original size:23 final size:23 Alignment explanation

Indices: 51489454--51489501 Score: 71 Period size: 23 Copynumber: 2.0 Consensus size: 23 51489444 ATACATAATA 51489454 AAATATATATAAAAATT-AGAAAT 1 AAATATATA-AAAAATTAAGAAAT 51489477 AAATATATAAAAAATTCAAGAAAT 1 AAATATATAAAAAATT-AAGAAAT 51489501 A 1 A 51489502 TATAAAATCT Statistics Matches: 23, Mismatches: 0, Indels: 3 0.88 0.00 0.12 Matches are distributed among these distances: 22 7 0.30 23 9 0.39 24 7 0.30 ACGTcount: A:0.67, C:0.02, G:0.04, T:0.27 Consensus pattern (23 bp): AAATATATAAAAAATTAAGAAAT Found at i:51489484 original size:21 final size:20 Alignment explanation

Indices: 51489453--51489529 Score: 79 Period size: 20 Copynumber: 3.9 Consensus size: 20 51489443 TATACATAAT * 51489453 AAAATATATATAAAAATTAG 1 AAAAAATATATAAAAATTAG * 51489473 AAATAAATATATAAAAAATT-C 1 AAA-AAATATAT-AAAAATTAG * 51489494 AAGAAATATAT-AAAATCTAG 1 AAAAAATATATAAAAAT-TAG 51489514 AAAAAA-ATATAAAAAT 1 AAAAAATATATAAAAAT 51489530 AAAATTTACA Statistics Matches: 47, Mismatches: 5, Indels: 10 0.76 0.08 0.16 Matches are distributed among these distances: 18 5 0.11 19 5 0.11 20 21 0.45 21 9 0.19 22 7 0.15 ACGTcount: A:0.68, C:0.03, G:0.04, T:0.26 Consensus pattern (20 bp): AAAAAATATATAAAAATTAG Found at i:51489613 original size:10 final size:11 Alignment explanation

Indices: 51489584--51489611 Score: 56 Period size: 11 Copynumber: 2.5 Consensus size: 11 51489574 TTAATAATAT 51489584 TATTTTTAAAA 1 TATTTTTAAAA 51489595 TATTTTTAAAA 1 TATTTTTAAAA 51489606 TATTTT 1 TATTTT 51489612 AATTTTTTTA 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:0.39, C:0.00, G:0.00, T:0.61 Consensus pattern (11 bp): TATTTTTAAAA Found at i:51489841 original size:26 final size:26 Alignment explanation

Indices: 51489785--51489842 Score: 64 Period size: 26 Copynumber: 2.2 Consensus size: 26 51489775 ATTAAAAATT * * 51489785 AAAAAATTATTTTAATACCTAATTGA 1 AAAAAATTATTTTAATACCAAAATGA * * 51489811 GAAAAATT-TTTATAATACGAAAATGA 1 AAAAAATTATTT-TAATACCAAAATGA 51489837 AAAAAA 1 AAAAAA 51489843 AATATTTCAA Statistics Matches: 26, Mismatches: 5, Indels: 2 0.79 0.15 0.06 Matches are distributed among these distances: 25 3 0.12 26 23 0.88 ACGTcount: A:0.57, C:0.05, G:0.07, T:0.31 Consensus pattern (26 bp): AAAAAATTATTTTAATACCAAAATGA Found at i:51490814 original size:54 final size:53 Alignment explanation

Indices: 51490695--51490827 Score: 166 Period size: 54 Copynumber: 2.5 Consensus size: 53 51490685 ATGGTAAGGG * * * * 51490695 TTAATTTTAAATTTAGAATATTATTTA-ATTTTTTTAATTTATGTAATTTTAA 1 TTAATTTTAATTTTATAATATTATTTATATTCTTTTAATTTATGTAATTTAAA * * 51490747 TTAATTTTAATTTTTTAATATTATTTATTATTCTTTTCATTTATGTAATTTAAA 1 TTAATTTTAATTTTATAATATTATTTA-TATTCTTTTAATTTATGTAATTTAAA 51490801 TTAATTTGT-ATTTTATAAT-TT-TTTATA 1 TTAATTT-TAATTTTATAATATTATTTATA 51490828 ACAATCTGTA Statistics Matches: 71, Mismatches: 7, Indels: 7 0.84 0.08 0.08 Matches are distributed among these distances: 51 2 0.03 52 28 0.39 53 2 0.03 54 38 0.54 55 1 0.01 ACGTcount: A:0.33, C:0.02, G:0.03, T:0.62 Consensus pattern (53 bp): TTAATTTTAATTTTATAATATTATTTATATTCTTTTAATTTATGTAATTTAAA Found at i:51492375 original size:18 final size:18 Alignment explanation

Indices: 51492352--51492394 Score: 68 Period size: 18 Copynumber: 2.4 Consensus size: 18 51492342 TGCCAAGTGG * 51492352 GTATCCTAGCCCTTATAT 1 GTATCCTAACCCTTATAT 51492370 GTATCCTAACCCTTATAT 1 GTATCCTAACCCTTATAT * 51492388 GTTTCCT 1 GTATCCT 51492395 TTTTCCAGTC Statistics Matches: 23, Mismatches: 2, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 18 23 1.00 ACGTcount: A:0.21, C:0.28, G:0.09, T:0.42 Consensus pattern (18 bp): GTATCCTAACCCTTATAT Found at i:51496140 original size:126 final size:126 Alignment explanation

Indices: 51495907--51496175 Score: 358 Period size: 126 Copynumber: 2.1 Consensus size: 126 51495897 GGCCAAGCAT * * * * * * * * 51495907 GAACTACTGTAGAAAAATAGCGTCCACATGAGAGCTTTTTTTAGAACTTTTGTTGATATTGCATC 1 GAACTACTGTAGAAAAAGAACGTCCACATGAGAGCTTTTTTAAAAAATTTTGCTGACATTACATC * * * * 51495972 ATGCTTGAAGCGTTTTTGACACTATTTGTTTAGAAATATCTTCTCAAATTTATTTTTTCAG 66 ATACTTGAAGCGTTTTTGACACTATTTGTTTAGAAACATCTTCTCAAAATTATTTTTTCAA * * * * 51496033 GAACTACTATAGAAAAAGAACGTCCACGTGGGAGCTTTTTTAAAAAATTTTGCTGACATTACGTC 1 GAACTACTGTAGAAAAAGAACGTCCACATGAGAGCTTTTTTAAAAAATTTTGCTGACATTACATC * * * 51496098 ATACTTGAAGCGTTTTTGACACTATTTGTTTGGAAACGTCTTCTTAAAATTATTTTTTCAA 66 ATACTTGAAGCGTTTTTGACACTATTTGTTTAGAAACATCTTCTCAAAATTATTTTTTCAA * 51496159 GAACTATTGTAGAAAAA 1 GAACTACTGTAGAAAAA 51496176 CCATAAACCC Statistics Matches: 122, Mismatches: 21, Indels: 0 0.85 0.15 0.00 Matches are distributed among these distances: 126 122 1.00 ACGTcount: A:0.32, C:0.14, G:0.16, T:0.38 Consensus pattern (126 bp): GAACTACTGTAGAAAAAGAACGTCCACATGAGAGCTTTTTTAAAAAATTTTGCTGACATTACATC ATACTTGAAGCGTTTTTGACACTATTTGTTTAGAAACATCTTCTCAAAATTATTTTTTCAA Found at i:51496333 original size:42 final size:43 Alignment explanation

Indices: 51496242--51496339 Score: 110 Period size: 42 Copynumber: 2.3 Consensus size: 43 51496232 TTAAAATCTA * * * 51496242 CTAAAATCCTAAACCCTAACTTATTCTAACAAAAACTTAAAAC 1 CTAAAAACCTAAACCCTAAATTATTCTAACAAAAACCTAAAAC * * * * 51496285 CT-AAAACCTAAACCCTAAATTATTTTAGCAAAACCCT-AACC 1 CTAAAAACCTAAACCCTAAATTATTCTAACAAAAACCTAAAAC 51496326 CTAAAAACCCTAAA 1 CTAAAAA-CCTAAA 51496340 AAACCCTAGG Statistics Matches: 46, Mismatches: 7, Indels: 4 0.81 0.12 0.07 Matches are distributed among these distances: 41 5 0.11 42 33 0.72 43 8 0.17 ACGTcount: A:0.48, C:0.28, G:0.01, T:0.23 Consensus pattern (43 bp): CTAAAAACCTAAACCCTAAATTATTCTAACAAAAACCTAAAAC Found at i:51505691 original size:51 final size:49 Alignment explanation

Indices: 51505573--51505712 Score: 199 Period size: 51 Copynumber: 2.8 Consensus size: 49 51505563 AGGCTATCTA * * 51505573 GTACGCATAGTAGCCTGCACTTAGTACTATACATGCGACCAATTATCCG 1 GTACGCATAGTAGCCTGCACTTAGTACTACACATGTGACCAATTATCCG * * * * * 51505622 GTACACGTAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGTTATCGG 1 GTACGCATAGTAGCCTGCACTTAGTACTACACATGTGA-CCAA-TTATCCG 51505673 GTACGCATAGTAGCCTGCACTTAGTACTACACATGTGACC 1 GTACGCATAGTAGCCTGCACTTAGTACTACACATGTGACC 51505713 TCACAATAGA Statistics Matches: 78, Mismatches: 11, Indels: 3 0.85 0.12 0.03 Matches are distributed among these distances: 49 33 0.42 50 4 0.05 51 41 0.53 ACGTcount: A:0.28, C:0.26, G:0.21, T:0.26 Consensus pattern (49 bp): GTACGCATAGTAGCCTGCACTTAGTACTACACATGTGACCAATTATCCG Found at i:51505989 original size:27 final size:27 Alignment explanation

Indices: 51505959--51506012 Score: 72 Period size: 27 Copynumber: 2.0 Consensus size: 27 51505949 TCATACAACC * * 51505959 CATGTAATAGTAATTTAACATTCAATT 1 CATGTAACAATAATTTAACATTCAATT ** 51505986 CATGTAACAATAATTTGCCATTCAATT 1 CATGTAACAATAATTTAACATTCAATT 51506013 TCACGTGACA Statistics Matches: 23, Mismatches: 4, Indels: 0 0.85 0.15 0.00 Matches are distributed among these distances: 27 23 1.00 ACGTcount: A:0.39, C:0.15, G:0.07, T:0.39 Consensus pattern (27 bp): CATGTAACAATAATTTAACATTCAATT Found at i:51512268 original size:22 final size:22 Alignment explanation

Indices: 51512243--51512292 Score: 91 Period size: 22 Copynumber: 2.3 Consensus size: 22 51512233 TTAAGATACA * 51512243 ATGTGACATTTCACTAGGAACT 1 ATGTGACATGTCACTAGGAACT 51512265 ATGTGACATGTCACTAGGAACT 1 ATGTGACATGTCACTAGGAACT 51512287 ATGTGA 1 ATGTGA 51512293 ATATGAGCTC Statistics Matches: 27, Mismatches: 1, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 22 27 1.00 ACGTcount: A:0.32, C:0.16, G:0.22, T:0.30 Consensus pattern (22 bp): ATGTGACATGTCACTAGGAACT Found at i:51513533 original size:42 final size:42 Alignment explanation

Indices: 51513474--51513554 Score: 103 Period size: 42 Copynumber: 1.9 Consensus size: 42 51513464 AGAAATTGTC * * 51513474 CACACGGTTAGACACACGGGCATGTGTCT-AGGCCGTGTGTGA 1 CACACGGTTAGACACACGGCCATATGTCTCA-GCCGTGTGTGA * 51513516 CACACGAG-TAGAGACACGGCCATATGTCTCAGCCGTGTG 1 CACACG-GTTAGACACACGGCCATATGTCTCAGCCGTGTG 51513555 AAGGACACGG Statistics Matches: 34, Mismatches: 3, Indels: 4 0.83 0.07 0.10 Matches are distributed among these distances: 42 32 0.94 43 2 0.06 ACGTcount: A:0.23, C:0.26, G:0.31, T:0.20 Consensus pattern (42 bp): CACACGGTTAGACACACGGCCATATGTCTCAGCCGTGTGTGA Found at i:51516686 original size:49 final size:49 Alignment explanation

Indices: 51516619--51516798 Score: 188 Period size: 49 Copynumber: 3.7 Consensus size: 49 51516609 TGTTGCGTGT * 51516619 CAGTGTAAGACCTGTCTGGGACATGGCATCGACACCGATAGATGAGAGC 1 CAGTGTAAGACCTGTCTGGGACATGGCATCGACACCGATAGATGAAAGC * * * * 51516668 CAGTGTAAGACCTGTCTGGAACACGGCATC-A-ACCTTGATATATGAAAGT 1 CAGTGTAAGACCTGTCTGGGACATGGCATCGACACC--GATAGATGAAAGC * *** ** 51516717 TAGTGTAAGACCTGTCTGGGACATGGCATCGACTTTGAT-G-TGCTAGC 1 CAGTGTAAGACCTGTCTGGGACATGGCATCGACACCGATAGATGAAAGC * * 51516764 CAGTGTAAGACCATGTCTAGGACATGGCGTCGACA 1 CAGTGTAAGACC-TGTCTGGGACATGGCATCGACA 51516799 TCTTATCCCA Statistics Matches: 107, Mismatches: 19, Indels: 11 0.78 0.14 0.08 Matches are distributed among these distances: 47 18 0.17 48 20 0.19 49 68 0.64 50 1 0.01 ACGTcount: A:0.28, C:0.21, G:0.28, T:0.23 Consensus pattern (49 bp): CAGTGTAAGACCTGTCTGGGACATGGCATCGACACCGATAGATGAAAGC Found at i:51522575 original size:63 final size:64 Alignment explanation

Indices: 51522395--51522646 Score: 199 Period size: 63 Copynumber: 3.9 Consensus size: 64 51522385 ATATAGTTCG * * * * * 51522395 GCTCTCTTGTAC-ACATGGTGAACACTTAGTACCACCCATGTGACCTAGC--CAGTTTATCTCGT 1 GCTCTCTTGT-CTACATGGTGTACACTTAGTACCACCCATGCGACCTAGCTACA-TATATCCCAT 51522457 A 64 A * * * * 51522458 GCTCTCTTGTCTACATGGTGTCCTTCACTTGGAACCACGCATGCGACCTAGCTACATATATCCCA 1 GCTCTCTTGTCTACATGGTG---TACACTTAGTACCACCCATGCGACCTAGCTACATATATCCCA 51522523 TA 63 TA * * * 51522525 GCTCTCTT-TCTACATGGTGTACACATAGTATCACCCATGCGACCTAGCTACATCATAATGTCTC 1 GCTCTCTTGTCTACATGGTGTACACTTAGTACCACCCATGCGACCTAGCTACAT-AT-A--TCCC * 51522589 GTA 62 ATA * * * * ** * 51522592 GCTCTCTTGTAC-ACATGATGTGCACTCAGCACCATACATGTGACCTAGCTACATA 1 GCTCTCTTGT-CTACATGGTGTACACTTAGTACCACCCATGCGACCTAGCTACATA 51522647 CCATCTGTAT Statistics Matches: 151, Mismatches: 26, Indels: 20 0.77 0.13 0.10 Matches are distributed among these distances: 62 1 0.01 63 46 0.30 64 2 0.01 65 1 0.01 66 34 0.23 67 30 0.20 68 36 0.24 69 1 0.01 ACGTcount: A:0.25, C:0.29, G:0.16, T:0.30 Consensus pattern (64 bp): GCTCTCTTGTCTACATGGTGTACACTTAGTACCACCCATGCGACCTAGCTACATATATCCCATA Found at i:51523346 original size:30 final size:30 Alignment explanation

Indices: 51523312--51523372 Score: 77 Period size: 30 Copynumber: 2.0 Consensus size: 30 51523302 TCCTTAACTC 51523312 AAACTTTGGAAAAATTACAATTTTGCCCCT 1 AAACTTTGGAAAAATTACAATTTTGCCCCT * * * * * 51523342 AAACTTTTGCATATTTACACTTTTGCCCCT 1 AAACTTTGGAAAAATTACAATTTTGCCCCT 51523372 A 1 A 51523373 GGCTCGGGAA Statistics Matches: 26, Mismatches: 5, Indels: 0 0.84 0.16 0.00 Matches are distributed among these distances: 30 26 1.00 ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38 Consensus pattern (30 bp): AAACTTTGGAAAAATTACAATTTTGCCCCT Found at i:51524262 original size:45 final size:45 Alignment explanation

Indices: 51524211--51524386 Score: 174 Period size: 50 Copynumber: 3.7 Consensus size: 45 51524201 TACGAGAGCT * 51524211 AGTGTAAGACCATGTCTGGGACATGGCATCGGCTTGATATGTGTC 1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCTTGATATGTGCC * * 51524256 AGTGTAAGACCATGTCTGGGACATGGCATTGGCACTAATAGATGA-GAGCC 1 AGTGTAAGACCATGTCTGGGACATGGCATCGG--CT--T-GAT-ATGTGCC * * * * * 51524306 AATGTAAGACCATGCCTGGGACATGACATCGACTTTGATGTGTGAGCC 1 AGTGTAAGACCATGTCTGGGACATGGCATCGGC-TTGATATGT--GCC * * 51524354 AGTGTAAGACCATGTCCGGGACATGGTATCGGC 1 AGTGTAAGACCATGTCTGGGACATGGCATCGGC 51524387 ACCTTACCCT Statistics Matches: 105, Mismatches: 16, Indels: 17 0.76 0.12 0.12 Matches are distributed among these distances: 45 31 0.30 46 4 0.04 47 3 0.03 48 31 0.30 49 2 0.02 50 33 0.31 51 1 0.01 ACGTcount: A:0.26, C:0.19, G:0.30, T:0.24 Consensus pattern (45 bp): AGTGTAAGACCATGTCTGGGACATGGCATCGGCTTGATATGTGCC Found at i:51526510 original size:77 final size:78 Alignment explanation

Indices: 51526383--51526538 Score: 269 Period size: 77 Copynumber: 2.0 Consensus size: 78 51526373 GCGTGTTACA 51526383 AAAATATCATCGATGAAAACAACCACGAACCTGTCCAGGTATGGCCTGAAAATTCTGTTCACTAA 1 AAAATATCATCGATGAAAACAACCACGAACCTGTCCAGGTATGGCCTGAAAATTCTGTTCACTAA 51526448 ATCCATAAA-ACC 66 ATCCATAAATACC * * * * 51526460 AAAATATCATCGATGAAAACAACCACGAATCTGTCTAGGTTTGGTCTGAAAATTCTGTTCACTAA 1 AAAATATCATCGATGAAAACAACCACGAACCTGTCCAGGTATGGCCTGAAAATTCTGTTCACTAA 51526525 ATCCATAAATACC 66 ATCCATAAATACC 51526538 A 1 A 51526539 TCGGGGCATT Statistics Matches: 74, Mismatches: 4, Indels: 1 0.94 0.05 0.01 Matches are distributed among these distances: 77 70 0.95 78 4 0.05 ACGTcount: A:0.40, C:0.22, G:0.13, T:0.25 Consensus pattern (78 bp): AAAATATCATCGATGAAAACAACCACGAACCTGTCCAGGTATGGCCTGAAAATTCTGTTCACTAA ATCCATAAATACC Found at i:51528896 original size:43 final size:44 Alignment explanation

Indices: 51528837--51528997 Score: 168 Period size: 43 Copynumber: 3.7 Consensus size: 44 51528827 CACAATGCCC * * * 51528837 TATCCTAGATATGGTCTTACATGCT-ATCACATAT-CGATGCCAC 1 TATCCCAGACATGGTCTTACATG-TAATCACATATACGATGCCAA * * * * 51528880 TATCCCAGACAAGGTCTTACACGAAATCATA-ATACGATGCCAA 1 TATCCCAGACATGGTCTTACATGTAATCACATATACGATGCCAA * * * * 51528923 TGTCCCAGACATGGTCTTTCATGTAATCA-AAATACAATGCCAA 1 TATCCCAGACATGGTCTTACATGTAATCACATATACGATGCCAA * * 51528966 TGTCCCAAACATGGTCTTACATGTAATCACAT 1 TATCCCAGACATGGTCTTACATGTAATCACAT 51528998 CTTGATAACC Statistics Matches: 98, Mismatches: 16, Indels: 7 0.81 0.13 0.06 Matches are distributed among these distances: 42 3 0.03 43 94 0.96 44 1 0.01 ACGTcount: A:0.34, C:0.25, G:0.14, T:0.28 Consensus pattern (44 bp): TATCCCAGACATGGTCTTACATGTAATCACATATACGATGCCAA Found at i:51533694 original size:57 final size:57 Alignment explanation

Indices: 51533598--51533736 Score: 144 Period size: 57 Copynumber: 2.4 Consensus size: 57 51533588 GCTATATTAT * * * * 51533598 AGGATTACCAGTCTAGGCTAAATCCTTTTCATATCATATACTCTGAAG-AGCTTA-AT- 1 AGGATTACCCGTCTGGGCTAAATCCCTCTCATATCATATACTC--AAGCAGCTTACATC * 51533654 ATGGATTACCCGTCTGGGCTAAATCCACTCT-ATAGT-ATATACTCAAGCGGCTTACATC 1 A-GGATTACCCGTCTGGGCTAAATCC-CTCTCATA-TCATATACTCAAGCAGCTTACATC * 51533712 AGGATTACCCGTCTGAGCTAAATCC 1 AGGATTACCCGTCTGGGCTAAATCC 51533737 TTTATACAAC Statistics Matches: 71, Mismatches: 6, Indels: 11 0.81 0.07 0.12 Matches are distributed among these distances: 55 3 0.04 56 6 0.08 57 58 0.82 58 4 0.06 ACGTcount: A:0.29, C:0.24, G:0.17, T:0.30 Consensus pattern (57 bp): AGGATTACCCGTCTGGGCTAAATCCCTCTCATATCATATACTCAAGCAGCTTACATC Found at i:51538753 original size:23 final size:22 Alignment explanation

Indices: 51538727--51538776 Score: 57 Period size: 23 Copynumber: 2.2 Consensus size: 22 51538717 CTTCCTTTTG * * 51538727 TTTTCTTTTTCTTC-CTTTCGCT 1 TTTTCCTTTGCTTCTCTTTC-CT 51538749 CTTTTCCTTTGCTTCTCTTTCCT 1 -TTTTCCTTTGCTTCTCTTTCCT 51538772 TTTTC 1 TTTTC 51538777 GCTTGGTTAC Statistics Matches: 24, Mismatches: 2, Indels: 3 0.83 0.07 0.10 Matches are distributed among these distances: 22 5 0.21 23 14 0.58 24 5 0.21 ACGTcount: A:0.00, C:0.30, G:0.04, T:0.66 Consensus pattern (22 bp): TTTTCCTTTGCTTCTCTTTCCT Found at i:51541222 original size:43 final size:44 Alignment explanation

Indices: 51541127--51541281 Score: 140 Period size: 43 Copynumber: 3.6 Consensus size: 44 51541117 ATCGAGATGT * * * * * 51541127 GATTACATGTAAGACCATGTTTGGGACATTGACAT-TGTATTGA 1 GATTACGTGTAAGACCATGTCTGGGACATTGGCATCTGTAATCA 51541170 GATTACGTGTAAGACCATGTCTGGGACATTGGCATCAT-TAATCA 1 GATTACGTGTAAGACCATGTCTGGGACATTGGCATC-TGTAATCA * * * * * 51541214 -ATTTCGTGTAAGACCCTGTCTGAGACAGTGGCATC-G-ATATGA 1 GATTACGTGTAAGACCATGTCTGGGACATTGGCATCTGTA-ATCA * * * 51541256 GATAACATGTAAGACCATATCTGGGA 1 GATTACGTGTAAGACCATGTCTGGGA 51541282 TATCGCATTG Statistics Matches: 91, Mismatches: 16, Indels: 10 0.78 0.14 0.09 Matches are distributed among these distances: 41 1 0.01 42 3 0.03 43 82 0.90 44 4 0.04 45 1 0.01 ACGTcount: A:0.30, C:0.16, G:0.24, T:0.30 Consensus pattern (44 bp): GATTACGTGTAAGACCATGTCTGGGACATTGGCATCTGTAATCA Found at i:51542143 original size:24 final size:23 Alignment explanation

Indices: 51542086--51542144 Score: 57 Period size: 24 Copynumber: 2.5 Consensus size: 23 51542076 TGGTATGTTT * 51542086 TGATTATGGAATTGAGTGGTTGAA 1 TGATTAT-GAATAGAGTGGTTGAA * * 51542110 TGGTTGTGAATAGA-TGGTGTGATA 1 TGATTATGAATAGAGTGGT-TGA-A 51542134 TGATTATGAAT 1 TGATTATGAAT 51542145 TGGCATGTTT Statistics Matches: 28, Mismatches: 5, Indels: 4 0.76 0.14 0.11 Matches are distributed among these distances: 22 4 0.14 23 9 0.32 24 15 0.54 ACGTcount: A:0.29, C:0.00, G:0.32, T:0.39 Consensus pattern (23 bp): TGATTATGAATAGAGTGGTTGAA Found at i:51546833 original size:50 final size:50 Alignment explanation

Indices: 51546709--51546992 Score: 248 Period size: 50 Copynumber: 5.6 Consensus size: 50 51546699 AGCTAACTGG * * * * * 51546709 TACACATAGTAGCCTGCACTTAGTACTACACATGCGACC-AACAATC-CA 1 TACACATAGTAGCCTACACTTAGTACTACACACGTGACCTAACCATCTGA * * 51546757 GTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAACCATCTGA 1 -TACACATAGTAGCCTACACTTAGTACTACACACGTGACCTAACCATCTGA * *** *** * * 51546808 TACACGTAGTAGCCTACACTTAGTACTACACACGTGATAGAAGTTGTCGGG 1 TACACATAGTAGCCTACACTTAGTACTACACACGTGACCTAA-CCATCTGA * * * * * * * 51546859 TACGCATAGGAGCCTACACTTAGTACTACACATGCGACATAACTATCTGG 1 TACACATAGTAGCCTACACTTAGTACTACACACGTGACCTAACCATCTGA ** * * 51546909 TACATGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAAAACCATCTTA 1 TACACATAGTAGCCTACACTTAGTACTACACACGTGACCT--AACCATCTGA * * * 51546961 AACACATAGTAGCCTATACATAGTACTACACA 1 TACACATAGTAGCCTACACTTAGTACTACACA 51546993 TGTGTTCTCA Statistics Matches: 189, Mismatches: 41, Indels: 7 0.80 0.17 0.03 Matches are distributed among these distances: 49 36 0.19 50 81 0.43 51 39 0.21 52 33 0.17 ACGTcount: A:0.33, C:0.27, G:0.16, T:0.24 Consensus pattern (50 bp): TACACATAGTAGCCTACACTTAGTACTACACACGTGACCTAACCATCTGA Found at i:51549400 original size:28 final size:29 Alignment explanation

Indices: 51549360--51549471 Score: 147 Period size: 29 Copynumber: 3.9 Consensus size: 29 51549350 TGGGAAGTAG * 51549360 TTGGGCCTGATGGGCTATATGAATGTGA- 1 TTGGGCCTGATGGGCCATATGAATGTGAT 51549388 TTGGGCCTGATGGGCCATATGAATGTGAT 1 TTGGGCCTGATGGGCCATATGAATGTGAT * ** * 51549417 TTGGGCCTAATGGGCCATACAAATGTAAT 1 TTGGGCCTGATGGGCCATATGAATGTGAT * 51549446 TTGGGCCT-AGTGGGCCATATGCATGT 1 TTGGGCCTGA-TGGGCCATATGAATGT 51549472 ATGTATACTT Statistics Matches: 74, Mismatches: 8, Indels: 3 0.87 0.09 0.04 Matches are distributed among these distances: 28 28 0.38 29 46 0.62 ACGTcount: A:0.22, C:0.15, G:0.32, T:0.30 Consensus pattern (29 bp): TTGGGCCTGATGGGCCATATGAATGTGAT Found at i:51549466 original size:58 final size:57 Alignment explanation

Indices: 51549360--51549471 Score: 145 Period size: 57 Copynumber: 1.9 Consensus size: 57 51549350 TGGGAAGTAG * * ** * 51549360 TTGGGCCTGATGGGCTATATGAATGTGATTGGGCCTGATGGGCCATATGAATGTGAT 1 TTGGGCCTAATGGGCCATACAAATGTAATTGGGCCTGATGGGCCATATGAATGTGAT * 51549417 TTGGGCCTAATGGGCCATACAAATGTAATTTGGGCCT-AGTGGGCCATATGCATGT 1 TTGGGCCTAATGGGCCATACAAATGTAA-TTGGGCCTGA-TGGGCCATATGAATGT 51549472 ATGTATACTT Statistics Matches: 47, Mismatches: 6, Indels: 3 0.84 0.11 0.05 Matches are distributed among these distances: 57 24 0.51 58 23 0.49 ACGTcount: A:0.22, C:0.15, G:0.32, T:0.30 Consensus pattern (57 bp): TTGGGCCTAATGGGCCATACAAATGTAATTGGGCCTGATGGGCCATATGAATGTGAT Found at i:51549922 original size:24 final size:24 Alignment explanation

Indices: 51549890--51549946 Score: 114 Period size: 24 Copynumber: 2.4 Consensus size: 24 51549880 TTTGAAATTT 51549890 TTATTATTAGATATATTTATAAAA 1 TTATTATTAGATATATTTATAAAA 51549914 TTATTATTAGATATATTTATAAAA 1 TTATTATTAGATATATTTATAAAA 51549938 TTATTATTA 1 TTATTATTA 51549947 TTATAATTAT Statistics Matches: 33, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 24 33 1.00 ACGTcount: A:0.44, C:0.00, G:0.04, T:0.53 Consensus pattern (24 bp): TTATTATTAGATATATTTATAAAA Found at i:51549954 original size:15 final size:15 Alignment explanation

Indices: 51549936--51549964 Score: 58 Period size: 15 Copynumber: 1.9 Consensus size: 15 51549926 ATATTTATAA 51549936 AATTATTATTATTAT 1 AATTATTATTATTAT 51549951 AATTATTATTATTA 1 AATTATTATTATTA 51549965 GATAGAAAAT Statistics Matches: 14, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 15 14 1.00 ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59 Consensus pattern (15 bp): AATTATTATTATTAT Found at i:51549957 original size:27 final size:26 Alignment explanation

Indices: 51549884--51549957 Score: 89 Period size: 24 Copynumber: 2.8 Consensus size: 26 51549874 TTGATATTTG * * 51549884 AAATTTTTATTATTAGATATATTTATA 1 AAATTATTATTATTATAT-TATTTATA * 51549911 AAATTATTATTA-GATA-TATTTATA 1 AAATTATTATTATTATATTATTTATA 51549935 AAATTATTATTATTATAATTATT 1 AAATTATTATTATTAT-ATTATT 51549958 ATTATTAGAT Statistics Matches: 40, Mismatches: 4, Indels: 6 0.80 0.08 0.12 Matches are distributed among these distances: 24 20 0.50 25 2 0.05 26 3 0.08 27 15 0.38 ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54 Consensus pattern (26 bp): AAATTATTATTATTATATTATTTATA Found at i:51556138 original size:16 final size:17 Alignment explanation

Indices: 51556106--51556138 Score: 50 Period size: 18 Copynumber: 1.9 Consensus size: 17 51556096 CATCAAGAAG 51556106 GGTTTTCAATGAAAACAT 1 GGTTTTCAA-GAAAACAT 51556124 GGTTTTCAA-AAAACA 1 GGTTTTCAAGAAAACA 51556139 CTTCAATGTG Statistics Matches: 15, Mismatches: 0, Indels: 2 0.88 0.00 0.12 Matches are distributed among these distances: 16 6 0.40 18 9 0.60 ACGTcount: A:0.42, C:0.12, G:0.15, T:0.30 Consensus pattern (17 bp): GGTTTTCAAGAAAACAT Found at i:51556407 original size:27 final size:27 Alignment explanation

Indices: 51556377--51556662 Score: 262 Period size: 27 Copynumber: 10.7 Consensus size: 27 51556367 TAATAAAGAG * * 51556377 AAATTACTAAAATACCCTCAATTTGTA 1 AAATTACTGAAATACCCTCGATTTGTA ** 51556404 AAATTACCAAAATACCCTCGATTTGTA 1 AAATTACTGAAATACCCTCGATTTGTA * * * 51556431 AAATTACCGAAACACCCTCGA-TTGTG 1 AAATTACTGAAATACCCTCGATTTGTA * * 51556457 AAATTA-TCGAAATACCCTTGATTTATA 1 AAATTACT-GAAATACCCTCGATTTGTA * * 51556484 AAATTACTGAAATACCCCCGATTTGTG 1 AAATTACTGAAATACCCTCGATTTGTA * * * 51556511 AAATTACCGAAACA-CCTTGATTTGTA 1 AAATTACTGAAATACCCTCGATTTGTA * * 51556537 AAATTA-TCAAAATATCCTCGATTTGTA 1 AAATTACT-GAAATACCCTCGATTTGTA * ** 51556564 AAATTA-TCAAAATACCCTTAATTTGTA 1 AAATTACT-GAAATACCCTCGATTTGTA * 51556591 AAATTACTGAAATACCCCCGATTTGTA 1 AAATTACTGAAATACCCTCGATTTGTA * * * * 51556618 AACTTA-TCAAAATACCCTTG-TAGTGTA 1 AAATTACT-GAAATACCCTCGAT-TTGTA 51556645 AAATTACTGAAATACCCT 1 AAATTACTGAAATACCCT 51556663 TGTAGTGTAA Statistics Matches: 213, Mismatches: 37, Indels: 18 0.79 0.14 0.07 Matches are distributed among these distances: 26 42 0.20 27 168 0.79 28 3 0.01 ACGTcount: A:0.40, C:0.20, G:0.09, T:0.32 Consensus pattern (27 bp): AAATTACTGAAATACCCTCGATTTGTA Found at i:51556509 original size:80 final size:80 Alignment explanation

Indices: 51556376--51556662 Score: 314 Period size: 80 Copynumber: 3.6 Consensus size: 80 51556366 ATAATAAAGA * * 51556376 GAAATTA-CTAAAATACCCTCAATTTGTAAAATTACCAAAATACCCTCGATTTGTAAAATTACCG 1 GAAATTATC-AAAATACCCTCGATTTGTAAAATTACTAAAATACCCTCGATTTGTAAAATTACCG 51556440 AAACACCCTCGATTGT 65 AAACACCCTCGATTGT * * * * * * 51556456 GAAATTATCGAAATACCCTTGATTTATAAAATTACTGAAATACCCCCGATTTGTGAAATTACCGA 1 GAAATTATCAAAATACCCTCGATTTGTAAAATTACTAAAATACCCTCGATTTGTAAAATTACCGA * 51556521 AACA-CCTTGATTTGT 66 AACACCCTCGA-TTGT * * ** * 51556536 AAAATTATCAAAATATCCTCGATTTGTAAAATTA-TCAAAATACCCTTAATTTGTAAAATTACTG 1 GAAATTATCAAAATACCCTCGATTTGTAAAATTACT-AAAATACCCTCGATTTGTAAAATTACCG * * 51556600 AAATACCCCCGATT-T 65 AAACACCCTCGATTGT * * * 51556615 GTAAACTTATCAAAATACCCTTG-TAGTGTAAAATTACTGAAATACCCT 1 G-AAA-TTATCAAAATACCCTCGAT-TTGTAAAATTACTAAAATACCCT 51556663 TGTAGTGTAA Statistics Matches: 171, Mismatches: 28, Indels: 15 0.80 0.13 0.07 Matches are distributed among these distances: 79 7 0.04 80 124 0.73 81 39 0.23 82 1 0.01 ACGTcount: A:0.39, C:0.20, G:0.09, T:0.32 Consensus pattern (80 bp): GAAATTATCAAAATACCCTCGATTTGTAAAATTACTAAAATACCCTCGATTTGTAAAATTACCGA AACACCCTCGATTGT Found at i:51556568 original size:107 final size:107 Alignment explanation

Indices: 51556377--51556635 Score: 340 Period size: 107 Copynumber: 2.4 Consensus size: 107 51556367 TAATAAAGAG * * * * * 51556377 AAATTACTAAAATACCCTCAATTTGTAAAATTACCAAAATACCCTCGATTTGTAAAATTACCGAA 1 AAATTACTGAAATACCCCCGATTTGTAAAATTACCAAAACACCCTCGATTTGTAAAATTACCAAA * * * 51556442 ACACCCTCGATTGTGAAATTATCGAAATACCCTTGATTTATA 66 ACACCCTCGATTGTAAAATTATCAAAATACCCTTAATTTATA * * * * 51556484 AAATTACTGAAATACCCCCGATTTGTGAAATTACCGAAACA-CCTTGATTTGTAAAATTATCAAA 1 AAATTACTGAAATACCCCCGATTTGTAAAATTACCAAAACACCCTCGATTTGTAAAATTACCAAA * * * 51556548 ATATCCTCGATTTGTAAAATTATCAAAATACCCTTAATTTGTA 66 ACACCCTCGA-TTGTAAAATTATCAAAATACCCTTAATTTATA * * * 51556591 AAATTACTGAAATACCCCCGATTTGTAAACTTATCAAAATACCCT 1 AAATTACTGAAATACCCCCGATTTGTAAAATTACCAAAACACCCT 51556636 TGTAGTGTAA Statistics Matches: 130, Mismatches: 20, Indels: 3 0.85 0.13 0.02 Matches are distributed among these distances: 106 28 0.22 107 99 0.76 108 3 0.02 ACGTcount: A:0.40, C:0.20, G:0.08, T:0.32 Consensus pattern (107 bp): AAATTACTGAAATACCCCCGATTTGTAAAATTACCAAAACACCCTCGATTTGTAAAATTACCAAA ACACCCTCGATTGTAAAATTATCAAAATACCCTTAATTTATA Found at i:51556604 original size:54 final size:54 Alignment explanation

Indices: 51556377--51556662 Score: 346 Period size: 54 Copynumber: 5.3 Consensus size: 54 51556367 TAATAAAGAG * * * * 51556377 AAATTACTAAAATACCCTCAATTTGTAAAATTACCAAAATACCCTCGATTTGTA 1 AAATTACTGAAATACCCTCGATTTGTAAAATTATCAAAATACCCTTGATTTGTA * * * * * 51556431 AAATTACCGAAACACCCTCGA-TTGTGAAATTATCGAAATACCCTTGATTTATA 1 AAATTACTGAAATACCCTCGATTTGTAAAATTATCAAAATACCCTTGATTTGTA * * * * * 51556484 AAATTACTGAAATACCCCCGATTTGTGAAATTACCGAAACA-CCTTGATTTGTA 1 AAATTACTGAAATACCCTCGATTTGTAAAATTATCAAAATACCCTTGATTTGTA * * * 51556537 AAATTA-TCAAAATATCCTCGATTTGTAAAATTATCAAAATACCCTTAATTTGTA 1 AAATTACT-GAAATACCCTCGATTTGTAAAATTATCAAAATACCCTTGATTTGTA * * * 51556591 AAATTACTGAAATACCCCCGATTTGTAAACTTATCAAAATACCCTTG-TAGTGTA 1 AAATTACTGAAATACCCTCGATTTGTAAAATTATCAAAATACCCTTGAT-TTGTA 51556645 AAATTACTGAAATACCCT 1 AAATTACTGAAATACCCT 51556663 TGTAGTGTAA Statistics Matches: 197, Mismatches: 30, Indels: 10 0.83 0.13 0.04 Matches are distributed among these distances: 52 1 0.01 53 89 0.45 54 106 0.54 55 1 0.01 ACGTcount: A:0.40, C:0.20, G:0.09, T:0.32 Consensus pattern (54 bp): AAATTACTGAAATACCCTCGATTTGTAAAATTATCAAAATACCCTTGATTTGTA Found at i:51556663 original size:27 final size:27 Alignment explanation

Indices: 51556587--51556675 Score: 101 Period size: 27 Copynumber: 3.3 Consensus size: 27 51556577 ACCCTTAATT ** * 51556587 TGTAAAATTACTGAAATACCCCCG-ATT 1 TGTAAAATTACTGAAATACCCTTGTA-G * * 51556614 TGTAAACTTA-TCAAAATACCCTTGTAG 1 TGTAAAATTACT-GAAATACCCTTGTAG 51556641 TGTAAAATTACTGAAATACCCTTGTAG 1 TGTAAAATTACTGAAATACCCTTGTAG 51556668 TGTAAAAT 1 TGTAAAAT 51556676 GACCGACATA Statistics Matches: 52, Mismatches: 7, Indels: 6 0.80 0.11 0.09 Matches are distributed among these distances: 26 1 0.02 27 49 0.94 28 2 0.04 ACGTcount: A:0.38, C:0.17, G:0.12, T:0.33 Consensus pattern (27 bp): TGTAAAATTACTGAAATACCCTTGTAG Found at i:51556686 original size:27 final size:27 Alignment explanation

Indices: 51556627--51556688 Score: 97 Period size: 27 Copynumber: 2.3 Consensus size: 27 51556617 AAACTTATCA * * 51556627 AAATACCCTTGTAGTGTAAAATTACTG 1 AAATACCCTTGTAGTGTAAAATGACCG 51556654 AAATACCCTTGTAGTGTAAAATGACCG 1 AAATACCCTTGTAGTGTAAAATGACCG * 51556681 ACATACCC 1 AAATACCC 51556689 CTATAGGGTA Statistics Matches: 32, Mismatches: 3, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 27 32 1.00 ACGTcount: A:0.37, C:0.21, G:0.15, T:0.27 Consensus pattern (27 bp): AAATACCCTTGTAGTGTAAAATGACCG Found at i:51556699 original size:27 final size:27 Alignment explanation

Indices: 51556627--51556701 Score: 69 Period size: 27 Copynumber: 2.8 Consensus size: 27 51556617 AAACTTATCA * * * * * 51556627 AAATACCCTTGTAGTGTAAAATTACTG 1 AAATACCCCTATAGGGTAAAATGACCG * * * 51556654 AAATACCCTTGTAGTGTAAAATGACCG 1 AAATACCCCTATAGGGTAAAATGACCG * 51556681 ACATACCCCTATAGGGTAAAA 1 AAATACCCCTATAGGGTAAAA 51556702 GGATTATTTT Statistics Matches: 42, Mismatches: 6, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 27 42 1.00 ACGTcount: A:0.39, C:0.19, G:0.16, T:0.27 Consensus pattern (27 bp): AAATACCCCTATAGGGTAAAATGACCG Found at i:51558286 original size:21 final size:21 Alignment explanation

Indices: 51558260--51558311 Score: 86 Period size: 21 Copynumber: 2.5 Consensus size: 21 51558250 GGGGTTACAT 51558260 GCCCGTGTGGCTTTGGAACAC 1 GCCCGTGTGGCTTTGGAACAC * 51558281 GCCCGTGTGGCTTTGGGACAC 1 GCCCGTGTGGCTTTGGAACAC * 51558302 GCCTGTGTGG 1 GCCCGTGTGG 51558312 GTAGGCTGTA Statistics Matches: 29, Mismatches: 2, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 21 29 1.00 ACGTcount: A:0.10, C:0.27, G:0.38, T:0.25 Consensus pattern (21 bp): GCCCGTGTGGCTTTGGAACAC Found at i:51562031 original size:41 final size:40 Alignment explanation

Indices: 51561978--51562147 Score: 161 Period size: 41 Copynumber: 4.2 Consensus size: 40 51561968 AGTCTGACTC * 51561978 TTAG-CACCGGCTCAAAAGCCCTTCGAGACCAAGCTCGGA 1 TTAGACACTGGCTCAAAAGCCCTTCGAGACCAAGCTCGGA * * * 51562017 TTAGACTACTGGCTCGAAGGCCCTTCG-GAACTAAG-TCCGG- 1 TTAGAC-ACTGGCTCAAAAGCCCTTCGAG-ACCAAGCT-CGGA * * * 51562057 TTATGACACTGGCTCTAAAAAGCCCTTCGAAACTAAGTTCGGTTA 1 TTA-GACACTGGCTC--AAAAGCCCTTCGAGACCAAGCTCGG--A 51562102 TTAG-CACTGGCTCAAAAGCCCTTCGAGACCAAGCTCGGA 1 TTAGACACTGGCTCAAAAGCCCTTCGAGACCAAGCTCGGA 51562141 TTTAGAC 1 -TTAGAC 51562148 CCCGATTAGC Statistics Matches: 107, Mismatches: 10, Indels: 26 0.75 0.07 0.18 Matches are distributed among these distances: 39 5 0.05 40 18 0.17 41 51 0.48 42 19 0.18 43 10 0.09 44 1 0.01 45 3 0.03 ACGTcount: A:0.28, C:0.28, G:0.22, T:0.22 Consensus pattern (40 bp): TTAGACACTGGCTCAAAAGCCCTTCGAGACCAAGCTCGGA Found at i:51574242 original size:118 final size:120 Alignment explanation

Indices: 51574059--51574282 Score: 287 Period size: 118 Copynumber: 1.9 Consensus size: 120 51574049 GCTCCTCGTT * ** 51574059 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG 1 CAAATGCCTTCGGGACATAGCCAGAATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG * 51574124 AT-TTAGTAAC-TCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA 66 ATATT-GTAACTTAGCACAAA-GCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA * * ** 51574179 CAAATGCCTTCGGG-CTTAGCCAGAAT-TAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCCG 1 CAAATGCCTTCGGGACATAGCCAGAATATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCG * * * 51574241 GATATTGTCACTTAGCCCAAAGCCTTCGGGACTTAGCCCGGA 65 GATATTGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGA 51574283 CATCATTCAA Statistics Matches: 90, Mismatches: 11, Indels: 8 0.83 0.10 0.07 Matches are distributed among these distances: 117 3 0.03 118 56 0.62 119 17 0.19 120 14 0.16 ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25 Consensus pattern (120 bp): CAAATGCCTTCGGGACATAGCCAGAATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG ATATTGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA Found at i:51574282 original size:40 final size:41 Alignment explanation

Indices: 51574059--51574282 Score: 277 Period size: 40 Copynumber: 5.6 Consensus size: 41 51574049 GCTCCTCGTT * * 51574059 CAAATGCCTTCGGGACATAGCCCGGTTA-TAGTAACTCGCA 1 CAAATGCCTTCGGGACTTAGCCCGGATATTAGTAACTCGCA * 51574099 CAAATGCCTTCGGGACTTAACCCGGAT-TTAGTAACTCGCA 1 CAAATGCCTTCGGGACTTAGCCCGGATATTAGTAACTCGCA * 51574139 CAAATGCCTTCGGGACTTAACCCGGAT-TTAGTAACTCGCA 1 CAAATGCCTTCGGGACTTAGCCCGGATATTAGTAACTCGCA * * 51574179 CAAATGCCTTCGGG-CTTAG-CCAGA-ATTAGTATCTCGCA 1 CAAATGCCTTCGGGACTTAGCCCGGATATTAGTAACTCGCA * * * * 51574217 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCACTTAGCC 1 CAAATGCCTTCGGGA-CTTAGCCCGGATATTAGTAAC-TCGCA 51574258 CAAA-GCCTTCGGGACTTAGCCCGGA 1 CAAATGCCTTCGGGACTTAGCCCGGA 51574283 CATCATTCAA Statistics Matches: 164, Mismatches: 12, Indels: 16 0.85 0.06 0.08 Matches are distributed among these distances: 37 2 0.01 38 27 0.16 39 9 0.05 40 113 0.69 41 13 0.08 ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25 Consensus pattern (41 bp): CAAATGCCTTCGGGACTTAGCCCGGATATTAGTAACTCGCA Found at i:51582413 original size:39 final size:40 Alignment explanation

Indices: 51582256--51582427 Score: 276 Period size: 40 Copynumber: 4.3 Consensus size: 40 51582246 GCTCCTCGTT * * 51582256 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA 1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA 51582296 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA 1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA 51582336 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA 1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA * * * 51582376 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA 1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA 51582415 CAAATGCCTTCGG 1 CAAATGCCTTCGG 51582428 ATCTTAGTCC Statistics Matches: 126, Mismatches: 5, Indels: 3 0.94 0.04 0.02 Matches are distributed among these distances: 39 35 0.28 40 89 0.71 41 2 0.02 ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24 Consensus pattern (40 bp): CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA Found at i:51582464 original size:79 final size:80 Alignment explanation

Indices: 51582256--51582480 Score: 262 Period size: 80 Copynumber: 2.8 Consensus size: 80 51582246 GCTCCTCGTT * * * * * 51582256 CAAATGCCTTCGGGACATAGCCCG-GTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCG 1 CAAATGCCTTCGGGACTTAACCCGAATT-TAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCG * 51582320 GATTTAGTAACTCGCA 65 GAATTAGTAACTCGCA * * 51582336 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGCCCGG 1 CAAATGCCTTCGGGACTTAACCCGAATTTAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGG * 51582400 AATTAGTATCTCGCA 66 AATTAGTAACTCGCA ** * * 51582415 CAAATGCCTTC-GGATCTTAGTCCGAATATT-GTCACTTAGCCCAAA-GCCTTCGGGACTTAGCC 1 CAAATGCCTTCGGGA-CTTAACCCGAAT-TTAGTAAC-TAGCACAAATGCCTTCGGGACTTAGCC 51582477 CGGA 63 CGGA 51582481 CATCATTCAA Statistics Matches: 128, Mismatches: 12, Indels: 10 0.85 0.08 0.07 Matches are distributed among these distances: 78 3 0.02 79 55 0.43 80 68 0.53 81 2 0.02 ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25 Consensus pattern (80 bp): CAAATGCCTTCGGGACTTAACCCGAATTTAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGG AATTAGTAACTCGCA Found at i:51582464 original size:119 final size:120 Alignment explanation

Indices: 51582256--51582480 Score: 289 Period size: 119 Copynumber: 1.9 Consensus size: 120 51582246 GCTCCTCGTT * * 51582256 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG 1 CAAATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGA * 51582321 ATTTAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA 66 ATTTAGTAACTAGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA * * ** 51582376 CAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCC 1 CAAATGCCTTCGGGACATAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC * * * 51582438 GAATATT-GTCACTTAGCCCAAA-GCCTTCGGGACTTAGCCCGGA 64 GAAT-TTAGTAAC-TAGCACAAATGCCTTCGGGACTTAACCCGGA 51582481 CATCATTCAA Statistics Matches: 91, Mismatches: 10, Indels: 9 0.83 0.09 0.08 Matches are distributed among these distances: 118 4 0.04 119 64 0.70 120 23 0.25 ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25 Consensus pattern (120 bp): CAAATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGA ATTTAGTAACTAGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA Found at i:51591950 original size:41 final size:40 Alignment explanation

Indices: 51591900--51592068 Score: 170 Period size: 41 Copynumber: 4.2 Consensus size: 40 51591890 AGTCCGACTC 51591900 TTAG-CACTGGCTCAAAAGCCCTTCGAGACCAAGCTCGGA 1 TTAGACACTGGCTCAAAAGCCCTTCGAGACCAAGCTCGGA * * 51591939 TTAGACTACTGGCTC-AAGGCCCTTCG-GAACTAAG-TCCGG- 1 TTAGAC-ACTGGCTCAAAAGCCCTTCGAG-ACCAAGCT-CGGA * * * 51591978 TTATGACACTGGCTCTAAAAAGCCCTTCGAAACTAAGTTCGGTTA 1 TTA-GACACTGGCTC--AAAAGCCCTTCGAGACCAAGCTCGG--A 51592023 TTAG-CACTGGCTCAAAAGCCCTTCGAGACCAAGCTCGGA 1 TTAGACACTGGCTCAAAAGCCCTTCGAGACCAAGCTCGGA 51592062 TTTAGAC 1 -TTAGAC 51592069 CCCGATTAGC Statistics Matches: 108, Mismatches: 7, Indels: 28 0.76 0.05 0.20 Matches are distributed among these distances: 39 18 0.17 40 26 0.24 41 31 0.29 42 19 0.18 43 10 0.09 44 1 0.01 45 3 0.03 ACGTcount: A:0.28, C:0.27, G:0.22, T:0.23 Consensus pattern (40 bp): TTAGACACTGGCTCAAAAGCCCTTCGAGACCAAGCTCGGA Found at i:51592006 original size:42 final size:41 Alignment explanation

Indices: 51591902--51592048 Score: 160 Period size: 42 Copynumber: 3.6 Consensus size: 41 51591892 TCCGACTCTT * * 51591902 AGCACTGGCTCAAAAGCCCTTCGAGACCAAG-CTCGGATTA-G 1 AGCACTGGCTCAAAAGCCCTTCGAAACTAAGTC-CGG-TTATG * * 51591943 A-CTACTGGCTC-AAGGCCCTTCGGAACTAAGTCCGGTTATG 1 AGC-ACTGGCTCAAAAGCCCTTCGAAACTAAGTCCGGTTATG * * 51591983 A-CACTGGCTCTAAAAAGCCCTTCGAAACTAAGTTCGGTTATT 1 AGCACTGGCTC--AAAAGCCCTTCGAAACTAAGTCCGGTTATG 51592025 AGCACTGGCTCAAAAGCCCTTCGA 1 AGCACTGGCTCAAAAGCCCTTCGA 51592049 GACCAAGCTC Statistics Matches: 91, Mismatches: 8, Indels: 14 0.81 0.07 0.12 Matches are distributed among these distances: 39 11 0.12 40 22 0.24 41 23 0.25 42 26 0.29 43 9 0.10 ACGTcount: A:0.28, C:0.28, G:0.22, T:0.22 Consensus pattern (41 bp): AGCACTGGCTCAAAAGCCCTTCGAAACTAAGTCCGGTTATG Done.