Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold765

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: 44580
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.32


Found at i:6352 original size:40 final size:40

Alignment explanation

Indices: 6322--6542 Score: 263 Period size: 40 Copynumber: 5.5 Consensus size: 40 6312 GCTACTCGTT * * 6322 CAAATGCCTTCGGGACATAGCCCGGTTATAGTGACTCGCA 1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA 6362 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA 1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA * 6402 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA 1 CAAATGCCTTCGGGACTTAGCCCGG-TTATAGTAACTCGCA * * * * 6442 CCAATGCCTTCGGG-CTTAGCCCAG-AATCAGTAACTTGCA 1 CAAATGCCTTCGGGACTTAGCCCGGTTAT-AGTAACTCGCA * * * * * 6481 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA 1 CAAATGCCTTCGGGA-CTTAGCCCGGTTATAGTAAC-TCGCA 6522 CAAA-GCCTTCGGGACTTAGCC 1 CAAATGCCTTCGGGACTTAGCC 6543 AGGACATCAT Statistics Matches: 157, Mismatches: 16, Indels: 16 0.83 0.08 0.08 Matches are distributed among these distances: 38 3 0.02 39 28 0.18 40 111 0.71 41 15 0.10 ACGTcount: A:0.25, C:0.28, G:0.22, T:0.24 Consensus pattern (40 bp): CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA Found at i:6500 original size:119 final size:120 Alignment explanation

Indices: 6324--6539 Score: 287 Period size: 119 Copynumber: 1.8 Consensus size: 120 6314 TACTCGTTCA * * * * 6324 AATGCCTTCGGGACATAGCCCGGTTATAGTGACTCGCACAAATGCCTTCGGGACTTAGCCCGGTT 1 AATGCCTTCGGGACATAGCCCAGTAATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGAT * 6389 ATAGTAAC-TCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC 66 ATAGTAACTTAGCACAAA-GCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC * * * 6444 AATGCCTTCGGG-CTTAGCCCAG-AATCAGTAACTTGCACAAATGCCTTC-GGATCTTAGTCCGG 1 AATGCCTTCGGGACATAGCCCAGTAAT-AGTAACTCGCACAAATGCCTTCGGGA-CTTAGCCCGG * * 6506 ATATGGTCACTTAGCACAAAGCCTTCGGGACTTA 64 ATATAGTAACTTAGCACAAAGCCTTCGGGACTTA 6540 GCCAGGACAT Statistics Matches: 83, Mismatches: 10, Indels: 7 0.83 0.10 0.07 Matches are distributed among these distances: 118 5 0.06 119 58 0.70 120 20 0.24 ACGTcount: A:0.25, C:0.27, G:0.22, T:0.25 Consensus pattern (120 bp): AATGCCTTCGGGACATAGCCCAGTAATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGAT ATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC Found at i:8888 original size:12 final size:12 Alignment explanation

Indices: 8871--8896 Score: 52 Period size: 12 Copynumber: 2.2 Consensus size: 12 8861 TGGAGGTGGG 8871 ACTAGCAGTAAA 1 ACTAGCAGTAAA 8883 ACTAGCAGTAAA 1 ACTAGCAGTAAA 8895 AC 1 AC 8897 ATTTTGGTTT Statistics Matches: 14, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 12 14 1.00 ACGTcount: A:0.50, C:0.19, G:0.15, T:0.15 Consensus pattern (12 bp): ACTAGCAGTAAA Found at i:9633 original size:27 final size:26 Alignment explanation

Indices: 9589--10036 Score: 186 Period size: 27 Copynumber: 16.7 Consensus size: 26 9579 TTAGTTTACC * 9589 AAATTACTGAAATA-CCCCCAGTTGTA 1 AAATTAC-GAAATACCCCCCACTTGTA * * * 9615 AAATTACCAAAGTACCCCCGACTTATA 1 AAATTACGAAA-TACCCCCCACTTGTA ** * * 9642 AAATTATCGAAATA-CCGTCAATTGTC 1 AAATTA-CGAAATACCCCCCACTTGTA * * * 9668 AAATTACTGAAATACCCTCAATTTGTA 1 AAATTAC-GAAATACCCCCCACTTGTA * * * 9695 AAATTACCGAAATA-CCCTCAGTTTGCA 1 AAATTA-CGAAATACCCCCCA-CTTGTA * * * 9722 AAATTACTGAAATACCCTCGATTTGTA 1 AAATTAC-GAAATACCCCCCACTTGTA * * 9749 AAATTACTGAAATACCCTCGACTTGTA 1 AAATTAC-GAAATACCCCCCACTTGTA * ** * * 9776 AAATTACCAAAGTACCCCTGATTTATA 1 AAATTACGAAA-TACCCCCCACTTGTA * * * * * 9803 AAATTACCCAAATATCCTCGATTTGTA 1 AAATTA-CGAAATACCCCCCACTTGTA ** ** * 9830 AAACCACGGAAATACCATCGA-TTGTA 1 AAATTAC-GAAATACCCCCCACTTGTA * ** * 9856 AAATTACTGACATACCTTCGACTTGTA 1 AAATTAC-GAAATACCCCCCACTTGTA * * 9883 AAATTACCGAAATA-CCCTCAGTTTGTA 1 AAATTA-CGAAATACCCCCCA-CTTGTA * * * * 9910 AAATTACTGAAATACCCTCAATTTGTG 1 AAATTAC-GAAATACCCCCCACTTGTA * * * * 9937 AAATTACTGAAATACCCTCGACCTATA 1 AAATTAC-GAAATACCCCCCACTTGTA * * * * 9964 AATTTACTGAAATACCCTCGACCTGTA 1 AAATTAC-GAAATACCCCCCACTTGTA * * * 9991 AATTTACTGAAATACCCTCGACTTGTA 1 AAATTAC-GAAATACCCCCCACTTGTA * 10018 AAATTACCAAAGTACCCCC 1 AAATTACGAAA-TACCCCC 10037 GATTTACAGA Statistics Matches: 339, Mismatches: 65, Indels: 35 0.77 0.15 0.08 Matches are distributed among these distances: 25 4 0.01 26 62 0.18 27 256 0.76 28 17 0.05 ACGTcount: A:0.38, C:0.23, G:0.10, T:0.29 Consensus pattern (26 bp): AAATTACGAAATACCCCCCACTTGTA Found at i:9857 original size:161 final size:161 Alignment explanation

Indices: 9589--9979 Score: 443 Period size: 161 Copynumber: 2.4 Consensus size: 161 9579 TTAGTTTACC * * * * 9589 AAATTACTGAAATACCC-CCAGTTGTAAAATTACCAAAGTACCCCCGACTTATAAAATTATCGAA 1 AAATTACTGAAATACCCTCAACTTGTAAAATTACCAAAGTACCCCCGACTTATAAAATTACCCAA * ** * * * 9653 ATACCGTCAATTGTCAAATTACTGAAATACCCTCAATTTGTAAAATTACCGAAATACCCTC-AGT 66 ATACCGTCAATTGTAAAACCACGGAAATACCATCAATTTGTAAAATTACCGAAATACCCTCGA-C * 9717 TTGCAAAATTACTGAAATACCCTC-GATTTGTA 130 TTGCAAAATTACCGAAATACCCTCAG-TTTGTA * * * 9749 AAATTACTGAAATACCCTCGACTTGTAAAATTACCAAAGTACCCCTGATTTATAAAATTACCCAA 1 AAATTACTGAAATACCCTCAACTTGTAAAATTACCAAAGTACCCCCGACTTATAAAATTACCCAA * * * * * 9814 ATATCC-TCGATTTGTAAAACCACGGAAATACCATCGA-TTGTAAAATTACTGACATACCTTCGA 66 ATA-CCGTC-AATTGTAAAACCACGGAAATACCATCAATTTGTAAAATTACCGAAATACCCTCGA * 9877 CTTGTAAAATTACCGAAATACCCTCAGTTTGTA 129 CTTGCAAAATTACCGAAATACCCTCAGTTTGTA * * * * * * ** 9910 AAATTACTGAAATACCCTCAATTTGTGAAATTACTGAAA-TACCCTCGACCTATAAATTTACTGA 1 AAATTACTGAAATACCCTCAACTTGTAAAATTAC-CAAAGTACCCCCGACTTATAAAATTACCCA 9974 AATACC 65 AATACC 9980 CTCGACCTGT Statistics Matches: 195, Mismatches: 30, Indels: 12 0.82 0.13 0.05 Matches are distributed among these distances: 160 19 0.10 161 148 0.76 162 28 0.14 ACGTcount: A:0.39, C:0.22, G:0.10, T:0.29 Consensus pattern (161 bp): AAATTACTGAAATACCCTCAACTTGTAAAATTACCAAAGTACCCCCGACTTATAAAATTACCCAA ATACCGTCAATTGTAAAACCACGGAAATACCATCAATTTGTAAAATTACCGAAATACCCTCGACT TGCAAAATTACCGAAATACCCTCAGTTTGTA Found at i:10034 original size:54 final size:54 Alignment explanation

Indices: 9589--10024 Score: 431 Period size: 54 Copynumber: 8.1 Consensus size: 54 9579 TTAGTTTACC * * * * * * 9589 AAATTACTGAAATACCC-CCAGTTGTAAAATTAC-CAAAGTACCCCCGACTTATA 1 AAATTACTGAAATACCCTCGACTTGTAAAATTACTGAAA-TACCCTCGATTTGTA * * * * 9642 AAATTA-TCGAAATACCGTC-AATTGTCAAATTACTGAAATACCCTCAATTTGTA 1 AAATTACT-GAAATACCCTCGACTTGTAAAATTACTGAAATACCCTCGATTTGTA * * * 9695 AAATTACCGAAATACCCTC-AGTTTGCAAAATTACTGAAATACCCTCGATTTGTA 1 AAATTACTGAAATACCCTCGA-CTTGTAAAATTACTGAAATACCCTCGATTTGTA * * 9749 AAATTACTGAAATACCCTCGACTTGTAAAATTAC-CAAAGTACCC-CTGATTTATA 1 AAATTACTGAAATACCCTCGACTTGTAAAATTACTGAAA-TACCCTC-GATTTGTA ** * * ** * * 9803 AAATTACCCAAATATCCTCGATTTGTAAAACCACGGAAATACCATCGA-TTGTA 1 AAATTACTGAAATACCCTCGACTTGTAAAATTACTGAAATACCCTCGATTTGTA * * * 9856 AAATTACTGACATACCTTCGACTTGTAAAATTACCGAAATACCCTC-AGTTTGTA 1 AAATTACTGAAATACCCTCGACTTGTAAAATTACTGAAATACCCTCGA-TTTGTA * * * ** * 9910 AAATTACTGAAATACCCTCAATTTGTGAAATTACTGAAATACCCTCGACCTATA 1 AAATTACTGAAATACCCTCGACTTGTAAAATTACTGAAATACCCTCGATTTGTA * * * * 9964 AATTTACTGAAATACCCTCGACCTGTAAATTTACTGAAATACCCTCGACTTGTA 1 AAATTACTGAAATACCCTCGACTTGTAAAATTACTGAAATACCCTCGATTTGTA 10018 AAATTAC 1 AAATTAC 10025 CAAAGTACCC Statistics Matches: 314, Mismatches: 56, Indels: 25 0.79 0.14 0.06 Matches are distributed among these distances: 52 2 0.01 53 98 0.31 54 208 0.66 55 6 0.02 ACGTcount: A:0.38, C:0.22, G:0.10, T:0.29 Consensus pattern (54 bp): AAATTACTGAAATACCCTCGACTTGTAAAATTACTGAAATACCCTCGATTTGTA Found at i:10049 original size:27 final size:27 Alignment explanation

Indices: 10017--10088 Score: 72 Period size: 27 Copynumber: 2.7 Consensus size: 27 10007 CTCGACTTGT * 10017 AAAATTACCAAAGTACCCCCGATTTAC 1 AAAATTACCAAAATACCCCCGATTTAC * **** * 10044 AGAATTACCGTTTTACCCTCGATTTAC 1 AAAATTACCAAAATACCCCCGATTTAC * 10071 AAAATTACAAAAATACCC 1 AAAATTACCAAAATACCC 10089 TTGTAACGTA Statistics Matches: 33, Mismatches: 12, Indels: 0 0.73 0.27 0.00 Matches are distributed among these distances: 27 33 1.00 ACGTcount: A:0.40, C:0.26, G:0.07, T:0.26 Consensus pattern (27 bp): AAAATTACCAAAATACCCCCGATTTAC Found at i:10061 original size:81 final size:80 Alignment explanation

Indices: 9589--10089 Score: 472 Period size: 81 Copynumber: 6.2 Consensus size: 80 9579 TTAGTTTACC * * * * 9589 AAATTACTGAAATACCC-CCAGTTGTAAAATTACCAAAGTACCCCCGACTTATAAAATTATCGAA 1 AAATTACTGAAATACCCTCGACTTGTAAAATTACCAAA-TACCCCCGATTTATAAAATTACCGAA * * * 9653 ATACCGTC-AATTGTC 65 ATACCCTCGATTTGTA * * * ** * 9668 AAATTACTGAAATACCCTCAATTTGTAAAATTACCGAAATACCCTC-AGTTTGCAAAATTACTGA 1 AAATTACTGAAATACCCTCGACTTGTAAAATTACC-AAATACCCCCGA-TTTATAAAATTACCGA 9732 AATACCCTCGATTTGTA 64 AATACCCTCGATTTGTA * * 9749 AAATTACTGAAATACCCTCGACTTGTAAAATTACCAAAGTACCCCTGATTTATAAAATTACCCAA 1 AAATTACTGAAATACCCTCGACTTGTAAAATTACCAAA-TACCCCCGATTTATAAAATTACCGAA * 9814 ATATCCTCGATTTGTA 65 ATACCCTCGATTTGTA ** * * * * ** * * 9830 AAACCACGGAAATACCATCGA-TTGTAAAATTACTGACATACCTTCGACTTGTAAAATTACCGAA 1 AAATTACTGAAATACCCTCGACTTGTAAAATTAC-CAAATACCCCCGATTTATAAAATTACCGAA 9894 ATACCCTC-AGTTTGTA 65 ATACCCTCGA-TTTGTA * * * * * ** * * 9910 AAATTACTGAAATACCCTCAATTTGTGAAATTACTGAAATACCCTCGACCTATAAATTTACTGAA 1 AAATTACTGAAATACCCTCGACTTGTAAAATTAC-CAAATACCCCCGATTTATAAAATTACCGAA ** 9975 ATACCCTCGACCTGTA 65 ATACCCTCGATTTGTA * * * ** 9991 AATTTACTGAAATACCCTCGACTTGTAAAATTACCAAAGTACCCCCGATTTACAGAATTACCGTT 1 AAATTACTGAAATACCCTCGACTTGTAAAATTACCAAA-TACCCCCGATTTATAAAATTACCGAA * ** 10056 TTACCCTCGATTTACA 65 ATACCCTCGATTTGTA ** 10072 AAATTACAAAAATACCCT 1 AAATTACTGAAATACCCT 10090 TGTAACGTAG Statistics Matches: 342, Mismatches: 69, Indels: 20 0.79 0.16 0.05 Matches are distributed among these distances: 79 19 0.06 80 107 0.31 81 214 0.63 82 2 0.01 ACGTcount: A:0.38, C:0.23, G:0.10, T:0.29 Consensus pattern (80 bp): AAATTACTGAAATACCCTCGACTTGTAAAATTACCAAATACCCCCGATTTATAAAATTACCGAAA TACCCTCGATTTGTA Found at i:10126 original size:27 final size:27 Alignment explanation

Indices: 10096--10214 Score: 121 Period size: 27 Copynumber: 4.4 Consensus size: 27 10086 CCCTTGTAAC 10096 GTAGAATTACCGAAATACCCCTATAGG 1 GTAGAATTACCGAAATACCCCTATAGG * ** * * 10123 GTAGAATTACTGAAATACCATTGTGGG 1 GTAGAATTACCGAAATACCCCTATAGG * * * 10150 GTAAAAATACCGAAATACCCCTGTAGG 1 GTAGAATTACCGAAATACCCCTATAGG * * * * 10177 ATAGAATTACCGAGATACCCTTATGGG 1 GTAGAATTACCGAAATACCCCTATAGG * 10204 GTAAAATTACC 1 GTAGAATTACC 10215 ATTTTGCCCT Statistics Matches: 72, Mismatches: 20, Indels: 0 0.78 0.22 0.00 Matches are distributed among these distances: 27 72 1.00 ACGTcount: A:0.37, C:0.18, G:0.20, T:0.24 Consensus pattern (27 bp): GTAGAATTACCGAAATACCCCTATAGG Found at i:10131 original size:54 final size:54 Alignment explanation

Indices: 10073--10186 Score: 138 Period size: 54 Copynumber: 2.1 Consensus size: 54 10063 CGATTTACAA * * * * 10073 AATTACAAAAATACCCTTGTAACGTAGAATTACCGAAATACCCCTATAGGGTAG 1 AATTACAAAAATACCATTGTAACGTAAAAATACCGAAATACCCCTATAGGATAG ** *** * 10127 AATTACTGAAATACCATTGTGGGGTAAAAATACCGAAATACCCCTGTAGGATAG 1 AATTACAAAAATACCATTGTAACGTAAAAATACCGAAATACCCCTATAGGATAG 10181 AATTAC 1 AATTAC 10187 CGAGATACCC Statistics Matches: 50, Mismatches: 10, Indels: 0 0.83 0.17 0.00 Matches are distributed among these distances: 54 50 1.00 ACGTcount: A:0.40, C:0.18, G:0.17, T:0.25 Consensus pattern (54 bp): AATTACAAAAATACCATTGTAACGTAAAAATACCGAAATACCCCTATAGGATAG Found at i:10195 original size:54 final size:54 Alignment explanation

Indices: 10103--10214 Score: 161 Period size: 54 Copynumber: 2.1 Consensus size: 54 10093 AACGTAGAAT * * * 10103 TACCGAAATACCCCTATAGGGTAGAATTACTGAAATACCATTGTGGGGTAAAAA 1 TACCGAAATACCCCTATAGGATAGAATTACCGAAATACCATTATGGGGTAAAAA * * * * 10157 TACCGAAATACCCCTGTAGGATAGAATTACCGAGATACCCTTATGGGGTAAAAT 1 TACCGAAATACCCCTATAGGATAGAATTACCGAAATACCATTATGGGGTAAAAA 10211 TACC 1 TACC 10215 ATTTTGCCCT Statistics Matches: 51, Mismatches: 7, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 54 51 1.00 ACGTcount: A:0.37, C:0.20, G:0.20, T:0.24 Consensus pattern (54 bp): TACCGAAATACCCCTATAGGATAGAATTACCGAAATACCATTATGGGGTAAAAA Found at i:10694 original size:22 final size:22 Alignment explanation

Indices: 10642--10706 Score: 78 Period size: 22 Copynumber: 3.0 Consensus size: 22 10632 TTAAAGTCTT * * 10642 CTGATTATGGCTTTGCGCCAAC 1 CTGATTATGGCTCTGTGCCAAC * 10664 CT-ACATATGGCTCTGTGCCAAC 1 CTGA-TTATGGCTCTGTGCCAAC * 10686 CTGATTATGGCTGTGTGCCAA 1 CTGATTATGGCTCTGTGCCAA 10707 ACGCATTTGC Statistics Matches: 36, Mismatches: 5, Indels: 4 0.80 0.11 0.09 Matches are distributed among these distances: 21 1 0.03 22 34 0.94 23 1 0.03 ACGTcount: A:0.20, C:0.26, G:0.23, T:0.31 Consensus pattern (22 bp): CTGATTATGGCTCTGTGCCAAC Found at i:10895 original size:27 final size:26 Alignment explanation

Indices: 10865--10971 Score: 108 Period size: 27 Copynumber: 4.0 Consensus size: 26 10855 ATTCTGTTAA * * 10865 GTGGCTTTGCCACATTATCTGTTTCTG 1 GTGGCTATGCCACAATATCTG-TTCTG 10892 GTGGCTATGCCACAAATATCTG-TCTG 1 GTGGCTATGCCAC-AATATCTGTTCTG * * 10918 GTGGCTCTGCCACAATATCTATATCTG 1 GTGGCTATGCCACAATATCTGT-TCTG * * * * 10945 GTGACTCTGTCACAATATCTATTCTG 1 GTGGCTATGCCACAATATCTGTTCTG 10971 G 1 G 10972 CAGCCATGCT Statistics Matches: 71, Mismatches: 6, Indels: 7 0.85 0.07 0.08 Matches are distributed among these distances: 25 7 0.10 26 21 0.30 27 36 0.51 28 7 0.10 ACGTcount: A:0.20, C:0.23, G:0.21, T:0.36 Consensus pattern (26 bp): GTGGCTATGCCACAATATCTGTTCTG Found at i:10971 original size:53 final size:53 Alignment explanation

Indices: 10865--10964 Score: 130 Period size: 53 Copynumber: 1.9 Consensus size: 53 10855 ATTCTGTTAA * * * * * 10865 GTGGCTTTGCCACATTATCTGTTTCTGGTGGCTATGCCACAAATATCTGTCTG 1 GTGGCTCTGCCACAATATCTATATCTGGTGACTATGCCACAAATATCTGTCTG * * 10918 GTGGCTCTGCCACAATATCTATATCTGGTGACTCTGTCAC-AATATCT 1 GTGGCTCTGCCACAATATCTATATCTGGTGACTATGCCACAAATATCT 10965 ATTCTGGCAG Statistics Matches: 40, Mismatches: 7, Indels: 1 0.83 0.15 0.02 Matches are distributed among these distances: 52 7 0.17 53 33 0.82 ACGTcount: A:0.20, C:0.24, G:0.20, T:0.36 Consensus pattern (53 bp): GTGGCTCTGCCACAATATCTATATCTGGTGACTATGCCACAAATATCTGTCTG Found at i:11098 original size:6 final size:6 Alignment explanation

Indices: 11089--11181 Score: 68 Period size: 6 Copynumber: 15.3 Consensus size: 6 11079 TTGCATTCCC * * 11089 ATTCTG ATTCTG ATTCTG ATTCTG -TTACCTG ATACTG GTTCTG ATTCT- 1 ATTCTG ATTCTG ATTCTG ATTCTG ATT--CTG ATTCTG ATTCTG ATTCTG * * * 11137 ATCACCTG ATTCTG ATTCTA ATTCTC ATT-TG ATTCT- AGTTCTG AT 1 AT--TCTG ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG A-TTCTG AT 11182 AATGTTTCTT Statistics Matches: 69, Mismatches: 9, Indels: 18 0.72 0.09 0.19 Matches are distributed among these distances: 5 9 0.13 6 51 0.74 7 6 0.09 8 3 0.04 ACGTcount: A:0.19, C:0.19, G:0.14, T:0.47 Consensus pattern (6 bp): ATTCTG Found at i:11120 original size:25 final size:25 Alignment explanation

Indices: 11092--11161 Score: 95 Period size: 25 Copynumber: 2.8 Consensus size: 25 11082 CATTCCCATT * * 11092 CTGATTCTGATTCTGATTCTGTTAC 1 CTGATTCTGATTCTGATTCTATCAC * * 11117 CTGATACTGGTTCTGATTCTATCAC 1 CTGATTCTGATTCTGATTCTATCAC * 11142 CTGATTCTGATTCTAATTCT 1 CTGATTCTGATTCTGATTCT 11162 CATTTGATTC Statistics Matches: 38, Mismatches: 7, Indels: 0 0.84 0.16 0.00 Matches are distributed among these distances: 25 38 1.00 ACGTcount: A:0.19, C:0.21, G:0.14, T:0.46 Consensus pattern (25 bp): CTGATTCTGATTCTGATTCTATCAC Found at i:14784 original size:30 final size:30 Alignment explanation

Indices: 14750--14810 Score: 77 Period size: 30 Copynumber: 2.0 Consensus size: 30 14740 TCCTTAACTC 14750 AAACTTTGGAAAAATTACAATTTTGCCCCT 1 AAACTTTGGAAAAATTACAATTTTGCCCCT * * * * * 14780 AAACTTTTGCATATTTACACTTTTGCCCCT 1 AAACTTTGGAAAAATTACAATTTTGCCCCT 14810 A 1 A 14811 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:25101 original size:85 final size:85 Alignment explanation

Indices: 24958--25192 Score: 296 Period size: 84 Copynumber: 2.8 Consensus size: 85 24948 ATCTGAGACA * * 24958 TCGTGTAAGACCGTGTCTGGGACACAGGCCTCGATTGAGATTTACGTATAAGACCATGTCTGGGA 1 TCGTGTAAGACCGTGTCTGGGACACAGGCCTCTATTGAGATTTACATATAAGACCATGTCTGGGA * 25023 CATCGGTATCGTATCTAATT 66 CATCGGCATCGTATCTAATT * * * * 25043 TCGTGTAAGACTGTGTTTGGGATACAGGCCTCTATTGAGATTTACATATAAGACCATGT-TTGGA 1 TCGTGTAAGACCGTGTCTGGGACACAGGCCTCTATTGAGATTTACATATAAGACCATGTCTGGGA * * 25107 CATCTGCATCGTATCTGATT 66 CATCGGCATCGTATCTAATT * * * * * * 25127 TCATGTAAGACCCTGTCTGGGACAGAGGCATCGATATTGA-A-TTACATGTAAGACCATGTCCGG 1 TCGTGTAAGACCGTGTCTGGGACACAGGCCTC--TATTGAGATTTACATATAAGACCATGTCTGG 25190 GAC 64 GAC 25193 GTTGATATTG Statistics Matches: 128, Mismatches: 19, Indels: 6 0.84 0.12 0.04 Matches are distributed among these distances: 84 63 0.49 85 59 0.46 86 6 0.05 ACGTcount: A:0.26, C:0.19, G:0.25, T:0.30 Consensus pattern (85 bp): TCGTGTAAGACCGTGTCTGGGACACAGGCCTCTATTGAGATTTACATATAAGACCATGTCTGGGA CATCGGCATCGTATCTAATT Found at i:25181 original size:43 final size:42 Alignment explanation

Indices: 24961--25192 Score: 163 Period size: 43 Copynumber: 5.5 Consensus size: 42 24951 TGAGACATCG * * * 24961 TGTAAGACCGTGTCTGGGACACAGGCCTCG-ATTGAGATTTACG 1 TGTAAGACCATGTCTGGGACACAGGCATCGTATTGA-A-TTACA * * * * 25004 TATAAGACCATGTCTGGGACATC-GGTATCGTATCT-AATTTCG 1 TGTAAGACCATGTCTGGGACA-CAGGCATCGTAT-TGAATTACA ** * * * 25046 TGTAAGACTGTGTTTGGGATACAGGCCTC-TATTGAGATTTACA 1 TGTAAGACCATGTCTGGGACACAGGCATCGTATTGA-A-TTACA * * * * 25089 TATAAGACCATGT-TTGGACATC-TGCATCGTATCTG-ATTTCA 1 TGTAAGACCATGTCTGGGACA-CAGGCATCGTAT-TGAATTACA * * 25130 TGTAAGACCCTGTCTGGGACAGAGGCATCGATATTGAATTACA 1 TGTAAGACCATGTCTGGGACACAGGCATCG-TATTGAATTACA * 25173 TGTAAGACCATGTCCGGGAC 1 TGTAAGACCATGTCTGGGAC 25193 GTTGATATTG Statistics Matches: 145, Mismatches: 30, Indels: 28 0.71 0.15 0.14 Matches are distributed among these distances: 40 1 0.01 41 20 0.14 42 49 0.34 43 68 0.47 44 6 0.04 45 1 0.01 ACGTcount: A:0.26, C:0.19, G:0.25, T:0.30 Consensus pattern (42 bp): TGTAAGACCATGTCTGGGACACAGGCATCGTATTGAATTACA Found at i:38843 original size:59 final size:59 Alignment explanation

Indices: 38780--38897 Score: 218 Period size: 59 Copynumber: 2.0 Consensus size: 59 38770 AGGGAAGATG * * 38780 AGTTTGTGCCAAAATAGGATTATTGCTTCTCAATTTCAGATTTGGTGGATATCCTCATT 1 AGTTTGTGCCAAAATAGGATTATTGCTTCTCAAGTTCAAATTTGGTGGATATCCTCATT 38839 AGTTTGTGCCAAAATAGGATTATTGCTTCTCAAGTTCAAATTTGGTGGATATCCTCATT 1 AGTTTGTGCCAAAATAGGATTATTGCTTCTCAAGTTCAAATTTGGTGGATATCCTCATT 38898 CCCTTTTCAG Statistics Matches: 57, Mismatches: 2, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 59 57 1.00 ACGTcount: A:0.26, C:0.15, G:0.19, T:0.40 Consensus pattern (59 bp): AGTTTGTGCCAAAATAGGATTATTGCTTCTCAAGTTCAAATTTGGTGGATATCCTCATT Found at i:40151 original size:26 final size:26 Alignment explanation

Indices: 40121--40178 Score: 71 Period size: 27 Copynumber: 2.2 Consensus size: 26 40111 GTATACCTAG * * 40121 ACCCTAAATTGATAAATGACTATTTT 1 ACCCTAAATGGAAAAATGACTATTTT * * 40147 TCCCTTATATGGAAAAATGACTATTTT 1 ACCC-TAAATGGAAAAATGACTATTTT 40174 ACCCT 1 ACCCT 40179 TATACGGTAA Statistics Matches: 26, Mismatches: 5, Indels: 2 0.79 0.15 0.06 Matches are distributed among these distances: 26 4 0.15 27 22 0.85 ACGTcount: A:0.34, C:0.19, G:0.09, T:0.38 Consensus pattern (26 bp): ACCCTAAATGGAAAAATGACTATTTT Found at i:40164 original size:27 final size:27 Alignment explanation

Indices: 40134--40205 Score: 90 Period size: 27 Copynumber: 2.7 Consensus size: 27 40124 CTAAATTGAT * * 40134 AAATGACTATTTTTCCCTTATATGGAA 1 AAATGACTATTTTACCCTTATACGGAA * 40161 AAATGACTATTTTACCCTTATACGGTA 1 AAATGACTATTTTACCCTTATACGGAA * * * 40188 AGATGACTGTTTTGCCCT 1 AAATGACTATTTTACCCT 40206 ATGTGATGTT Statistics Matches: 39, Mismatches: 6, Indels: 0 0.87 0.13 0.00 Matches are distributed among these distances: 27 39 1.00 ACGTcount: A:0.29, C:0.18, G:0.14, T:0.39 Consensus pattern (27 bp): AAATGACTATTTTACCCTTATACGGAA Found at i:40596 original size:18 final size:18 Alignment explanation

Indices: 40569--40618 Score: 64 Period size: 18 Copynumber: 2.8 Consensus size: 18 40559 GTTTAAACTG * 40569 TTACTACACTGATTACTA 1 TTACTGCACTGATTACTA * * 40587 TTACTGCACTGTTTACTG 1 TTACTGCACTGATTACTA * 40605 TTACTGCATTGATT 1 TTACTGCACTGATT 40619 GTTTGTAACA Statistics Matches: 27, Mismatches: 5, Indels: 0 0.84 0.16 0.00 Matches are distributed among these distances: 18 27 1.00 ACGTcount: A:0.24, C:0.20, G:0.12, T:0.44 Consensus pattern (18 bp): TTACTGCACTGATTACTA Found at i:41589 original size:28 final size:27 Alignment explanation

Indices: 41542--41646 Score: 106 Period size: 27 Copynumber: 3.8 Consensus size: 27 41532 TGCTAGAAAG * * * 41542 GATAATGTGACAGAGTCACCCGATACA 1 GATAATGTGGCAGAGCCACCAGATACA 41569 GATAATCGTGGCAGAGCCACCAGA-ACA 1 GATAAT-GTGGCAGAGCCACCAGATACA * 41596 GATATATGTGGTAGAGCCACCAGAT-CA 1 GATA-ATGTGGCAGAGCCACCAGATACA * * 41623 AATAATTTGTGGCATAGCCACCAG 1 GATAA--TGTGGCAGAGCCACCAG 41647 GACGCTTCCT Statistics Matches: 66, Mismatches: 7, Indels: 9 0.80 0.09 0.11 Matches are distributed among these distances: 26 1 0.02 27 34 0.52 28 31 0.47 ACGTcount: A:0.35, C:0.22, G:0.24, T:0.19 Consensus pattern (27 bp): GATAATGTGGCAGAGCCACCAGATACA Done.