Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Gbar_A13

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: 109233746
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32

Warning! 2708888 characters in sequence are not A, C, G, or T


File 62 of 332

Found at i:18429645 original size:40 final size:40

Alignment explanation

Indices: 18429444--18429631 Score: 290 Period size: 40 Copynumber: 4.7 Consensus size: 40 18429434 TATTTGGATG * * 18429444 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT 1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT ** * * 18429484 A-ATTTCGGGCTAAG-CCCGAAGGCATTTTTGCGAGCTACT 1 ATA-ACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT * 18429523 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT 1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT 18429563 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT 1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT 18429603 ATAACCGGGCTAAGTCCCGAAGGCATTTG 1 ATAACCGGGCTAAGTCCCGAAGGCATTTG 18429632 AGCAAGTAGC Statistics Matches: 135, Mismatches: 10, Indels: 6 0.89 0.07 0.04 Matches are distributed among these distances: 39 33 0.24 40 102 0.76 ACGTcount: A:0.24, C:0.23, G:0.27, T:0.26 Consensus pattern (40 bp): ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT Found at i:18429662 original size:119 final size:119 Alignment explanation

Indices: 18429444--18429664 Score: 304 Period size: 119 Copynumber: 1.9 Consensus size: 119 18429434 TATTTGGATG * ** 18429444 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATTTCGGGCTAAGCCCGAAGGCAT 1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAATACCGGGCTAAGCCCGAAGGCAT ** * * 18429509 TTTTGCGAGCTACTATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT 66 TTGAGCAAGCTACTATATCCGGGCTAAATCCCGAAGGCATTTGTGCGAGTTACT * 18429563 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTAAGTCCCGAAGGC 1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAAT-ACCGGGCTAAG-CCCGAAGGC * * 18429627 ATTTGAGCAAG-TAGCTATAT-CTGGCTAAATTCCGAAGG 64 ATTTGAGCAAGCTA-CTATATCCGGGCTAAATCCCGAAGG 18429665 TACTCGGTTT Statistics Matches: 89, Mismatches: 10, Indels: 6 0.85 0.10 0.06 Matches are distributed among these distances: 118 2 0.02 119 64 0.72 120 23 0.26 ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25 Consensus pattern (119 bp): ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAATACCGGGCTAAGCCCGAAGGCAT TTGAGCAAGCTACTATATCCGGGCTAAATCCCGAAGGCATTTGTGCGAGTTACT Found at i:18434710 original size:40 final size:40 Alignment explanation

Indices: 18434654--18434878 Score: 357 Period size: 40 Copynumber: 5.6 Consensus size: 40 18434644 CGGATGATAA * * 18434654 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATT 1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-T * 18434694 CCGGGCTAAG-CTCCGAAGGCATTTGTGCAAGTTACTATAT 1 CCGGGCTAAGTC-CCGAAGGCATTTGTGCGAGTTACTATAT * 18434734 CCGGGCTAAGTCCCGAAGGCATTTGTGTGAGTTACTATAT 1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT 18434774 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT 1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT * 18434814 CTGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATCA- 1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAT-AT 18434854 CCGGGCTAAGTCCCGAAGGCATTTG 1 CCGGGCTAAGTCCCGAAGGCATTTG 18434879 AGCAAGTAGT Statistics Matches: 174, Mismatches: 7, Indels: 8 0.92 0.04 0.04 Matches are distributed among these distances: 39 1 0.01 40 170 0.98 41 3 0.02 ACGTcount: A:0.23, C:0.23, G:0.28, T:0.27 Consensus pattern (40 bp): CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT Found at i:18441024 original size:19 final size:19 Alignment explanation

Indices: 18441000--18441039 Score: 80 Period size: 19 Copynumber: 2.1 Consensus size: 19 18440990 TACTGAGTTT 18441000 GTATGTGCTAGTTGATAAA 1 GTATGTGCTAGTTGATAAA 18441019 GTATGTGCTAGTTGATAAA 1 GTATGTGCTAGTTGATAAA 18441038 GT 1 GT 18441040 TTACAAGAAT Statistics Matches: 21, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 19 21 1.00 ACGTcount: A:0.30, C:0.05, G:0.28, T:0.38 Consensus pattern (19 bp): GTATGTGCTAGTTGATAAA Found at i:18441051 original size:27 final size:27 Alignment explanation

Indices: 18441021--18441076 Score: 112 Period size: 27 Copynumber: 2.1 Consensus size: 27 18441011 TTGATAAAGT 18441021 ATGTGCTAGTTGATAAAGTTTACAAGA 1 ATGTGCTAGTTGATAAAGTTTACAAGA 18441048 ATGTGCTAGTTGATAAAGTTTACAAGA 1 ATGTGCTAGTTGATAAAGTTTACAAGA 18441075 AT 1 AT 18441077 TGTCCTTTGA Statistics Matches: 29, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 27 29 1.00 ACGTcount: A:0.38, C:0.07, G:0.21, T:0.34 Consensus pattern (27 bp): ATGTGCTAGTTGATAAAGTTTACAAGA Found at i:18441495 original size:9 final size:9 Alignment explanation

Indices: 18441476--18441512 Score: 65 Period size: 9 Copynumber: 4.0 Consensus size: 9 18441466 TTTAGTACCT 18441476 AGAACTTGAA 1 AGAA-TTGAA 18441486 AGAATTGAA 1 AGAATTGAA 18441495 AGAATTGAA 1 AGAATTGAA 18441504 AGAATTGAA 1 AGAATTGAA 18441513 TGCTCAGTTT Statistics Matches: 27, Mismatches: 0, Indels: 1 0.96 0.00 0.04 Matches are distributed among these distances: 9 23 0.85 10 4 0.15 ACGTcount: A:0.54, C:0.03, G:0.22, T:0.22 Consensus pattern (9 bp): AGAATTGAA Found at i:18445159 original size:39 final size:39 Alignment explanation

Indices: 18445105--18445183 Score: 149 Period size: 39 Copynumber: 2.0 Consensus size: 39 18445095 ACACTATGTA 18445105 TGATTATGCTAAACCTAATTTAATAGGAACTGAGTCAAG 1 TGATTATGCTAAACCTAATTTAATAGGAACTGAGTCAAG * 18445144 TGATTATTCTAAACCTAATTTAATAGGAACTGAGTCAAG 1 TGATTATGCTAAACCTAATTTAATAGGAACTGAGTCAAG 18445183 T 1 T 18445184 ATAGTTAGAC Statistics Matches: 39, Mismatches: 1, Indels: 0 0.98 0.03 0.00 Matches are distributed among these distances: 39 39 1.00 ACGTcount: A:0.38, C:0.13, G:0.16, T:0.33 Consensus pattern (39 bp): TGATTATGCTAAACCTAATTTAATAGGAACTGAGTCAAG Found at i:18458082 original size:13 final size:13 Alignment explanation

Indices: 18458064--18458088 Score: 50 Period size: 13 Copynumber: 1.9 Consensus size: 13 18458054 TTTTACGCGG 18458064 CCGTGTAACACGA 1 CCGTGTAACACGA 18458077 CCGTGTAACACG 1 CCGTGTAACACG 18458089 TCCATGTTCA Statistics Matches: 12, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 12 1.00 ACGTcount: A:0.28, C:0.32, G:0.24, T:0.16 Consensus pattern (13 bp): CCGTGTAACACGA Found at i:18463465 original size:41 final size:40 Alignment explanation

Indices: 18463303--18463528 Score: 264 Period size: 40 Copynumber: 5.6 Consensus size: 40 18463293 GCTACTCGTT * * 18463303 CAAATGCCTTCGGGACATAGCCCGGTTA-TAGTAACTCGCA 1 CAAATGCCTTC-GGACTTAGCCCGGATATTAGTAACTCGCA * 18463343 CAAATGCCTTCGGGACTTAACCCGGAT-TTAGTAACTCGCA 1 CAAATGCCTTC-GGACTTAGCCCGGATATTAGTAACTCGCA * * 18463383 CAAATGCCTTCGGGCTTAGCCCGGA-ATTAGTATCTCGCA 1 CAAATGCCTTCGGACTTAGCCCGGATATTAGTAACTCGCA * * 18463422 CAAATGCCTTCGGATCTTAGTCCGGATATTAGTATCTCGCA 1 CAAATGCCTTCGGA-CTTAGCCCGGATATTAGTAACTCGCA * * * * 18463463 CAAATGCCTTCGGATCTTAGTCCGGATA-TGGTCACTTAGCA 1 CAAATGCCTTCGGA-CTTAGCCCGGATATTAGTAAC-TCGCA 18463504 CAAA-GCCTTCGGGACTTAGCCCGGA 1 CAAATGCCTTC-GGACTTAGCCCGGA 18463529 CATCATTCAA Statistics Matches: 167, Mismatches: 13, Indels: 12 0.87 0.07 0.06 Matches are distributed among these distances: 39 37 0.22 40 77 0.46 41 53 0.32 ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26 Consensus pattern (40 bp): CAAATGCCTTCGGACTTAGCCCGGATATTAGTAACTCGCA Found at i:18463465 original size:80 final size:80 Alignment explanation

Indices: 18463303--18463528 Score: 264 Period size: 79 Copynumber: 2.8 Consensus size: 80 18463293 GCTACTCGTT * 18463303 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG 1 CAAATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG 18463368 ATTTAGTAACTCGCA 66 ATTTAGTAACTCGCA * * ** 18463383 CAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCC 1 CAAATGCCTTCGGGACATAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC * 18463445 GGATATTAGTATCTCGCA 64 GGAT-TTAGTAACTCGCA * * * * * * 18463463 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGCCC 1 CAAATGCCTTCGGGA-CATAGCCCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAACCC 18463526 GGA 64 GGA 18463529 CATCATTCAA Statistics Matches: 126, Mismatches: 12, Indels: 15 0.82 0.08 0.10 Matches are distributed among these distances: 78 4 0.03 79 43 0.34 80 37 0.29 81 30 0.24 82 12 0.10 ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26 Consensus pattern (80 bp): CAAATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG ATTTAGTAACTCGCA Found at i:18463488 original size:120 final size:120 Alignment explanation

Indices: 18463303--18463528 Score: 298 Period size: 120 Copynumber: 1.9 Consensus size: 120 18463293 GCTACTCGTT * 18463303 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG 1 CAAATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG * * 18463368 ATTTAGTAAC-TCGCACAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA 66 ATATAGTAACTTAGCACAAA-GCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA * * * ** 18463422 CAAATGCCTTC-GGATCTTAGTCCGGATATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGTC 1 CAAATGCCTTCGGGA-CATAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAACC * * 18463485 CGGATATGGTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA 63 CGGATATAGTAACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA 18463529 CATCATTCAA Statistics Matches: 92, Mismatches: 10, Indels: 8 0.84 0.09 0.07 Matches are distributed among these distances: 118 3 0.03 119 24 0.26 120 46 0.50 121 19 0.21 ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26 Consensus pattern (120 bp): CAAATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG ATATAGTAACTTAGCACAAAGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA Found at i:18467667 original size:3 final size:3 Alignment explanation

Indices: 18467659--18467683 Score: 50 Period size: 3 Copynumber: 8.3 Consensus size: 3 18467649 AGATATTTAC 18467659 TTA TTA TTA TTA TTA TTA TTA TTA T 1 TTA TTA TTA TTA TTA TTA TTA TTA T 18467684 AATATTTTAT Statistics Matches: 22, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 3 22 1.00 ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68 Consensus pattern (3 bp): TTA Found at i:18467938 original size:26 final size:25 Alignment explanation

Indices: 18467857--18467939 Score: 73 Period size: 26 Copynumber: 3.2 Consensus size: 25 18467847 AATAAATAAA 18467857 AGAAAGAA-AAAA-AAGAAGAAAAAG 1 AGAAAGAAGAAAAGAA-AAGAAAAAG * * 18467881 AAACAGAGAAGAAACGAAATAGAAATAA- 1 AGA-A-AGAAGAAAAGAAA-AGAAA-AAG 18467909 AGAAAGAAGAAAAGAAAAGAAAAAGG 1 AGAAAGAAGAAAAGAAAAGAAAAA-G 18467935 AGAAA 1 AGAAA 18467940 TTAGGGTTTG Statistics Matches: 47, Mismatches: 4, Indels: 14 0.72 0.06 0.22 Matches are distributed among these distances: 24 4 0.09 25 6 0.13 26 21 0.45 27 5 0.11 28 9 0.19 29 2 0.04 ACGTcount: A:0.73, C:0.02, G:0.22, T:0.02 Consensus pattern (25 bp): AGAAAGAAGAAAAGAAAAGAAAAAG Found at i:18471230 original size:6 final size:6 Alignment explanation

Indices: 18471221--18471283 Score: 56 Period size: 6 Copynumber: 10.5 Consensus size: 6 18471211 AATAAAATTG * * * * * 18471221 AAATGA AAATCA AAATCA AAAGAA ATATAA AAAT-A AAATAA AAATAA 1 AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA * 18471268 GAATAA ATAATAA AAA 1 AAATAA A-AATAA AAA 18471284 AATAGGAGGA Statistics Matches: 47, Mismatches: 8, Indels: 4 0.80 0.14 0.07 Matches are distributed among these distances: 5 5 0.11 6 36 0.77 7 6 0.13 ACGTcount: A:0.75, C:0.03, G:0.05, T:0.17 Consensus pattern (6 bp): AAATAA Found at i:18471258 original size:17 final size:17 Alignment explanation

Indices: 18471226--18471274 Score: 53 Period size: 17 Copynumber: 2.8 Consensus size: 17 18471216 AATTGAAATG * 18471226 AAAATCAAAATCAAAAGA 1 AAAATAAAAAT-AAAAGA * * 18471244 AATATAAAAATAAAATA 1 AAAATAAAAATAAAAGA * 18471261 AAAATAAGAATAAA 1 AAAATAAAAATAAA 18471275 TAATAAAAAA Statistics Matches: 26, Mismatches: 5, Indels: 1 0.81 0.16 0.03 Matches are distributed among these distances: 17 17 0.65 18 9 0.35 ACGTcount: A:0.76, C:0.04, G:0.04, T:0.16 Consensus pattern (17 bp): AAAATAAAAATAAAAGA Found at i:18471264 original size:29 final size:31 Alignment explanation

Indices: 18471221--18471283 Score: 78 Period size: 29 Copynumber: 2.1 Consensus size: 31 18471211 AATAAAATTG * 18471221 AAATGAAAATCAAAATCAA-AAGAAAT-ATAA 1 AAATGAAAATAAAAAT-AAGAAGAAATAATAA * 18471251 AAAT-AAAATAAAAATAAGAATAAATAATAA 1 AAATGAAAATAAAAATAAGAAGAAATAATAA 18471281 AAA 1 AAA 18471284 AATAGGAGGA Statistics Matches: 29, Mismatches: 2, Indels: 4 0.83 0.06 0.11 Matches are distributed among these distances: 28 2 0.07 29 16 0.55 30 11 0.38 ACGTcount: A:0.75, C:0.03, G:0.05, T:0.17 Consensus pattern (31 bp): AAATGAAAATAAAAATAAGAAGAAATAATAA Found at i:18482135 original size:27 final size:28 Alignment explanation

Indices: 18482051--18482148 Score: 135 Period size: 27 Copynumber: 3.5 Consensus size: 28 18482041 CATGAGATTG * * * * 18482051 GCACTAAGTGTGCGGGTTTAAATTGTACA 1 GCACTAAGTGTGCGAGTTT-GATTATATA 18482080 GCACTAAGTGTGCGAGTTTGATTATATA 1 GCACTAAGTGTGCGAGTTTGATTATATA 18482108 GCACTAAGTGTGCGAG-TTGATTATATA 1 GCACTAAGTGTGCGAGTTTGATTATATA * 18482135 GCACTGAGTGTGCG 1 GCACTAAGTGTGCG 18482149 GACTTAATAT Statistics Matches: 64, Mismatches: 5, Indels: 2 0.90 0.07 0.03 Matches are distributed among these distances: 27 24 0.38 28 22 0.34 29 18 0.28 ACGTcount: A:0.27, C:0.13, G:0.29, T:0.32 Consensus pattern (28 bp): GCACTAAGTGTGCGAGTTTGATTATATA Found at i:18482159 original size:27 final size:27 Alignment explanation

Indices: 18482079--18482161 Score: 96 Period size: 27 Copynumber: 3.0 Consensus size: 27 18482069 TAAATTGTAC * * 18482079 AGCACTAAGTGTGCGAGTTTGATTATAT 1 AGCACTAAGTGTGCGA-CTTGAATATAT * * 18482107 AGCACTAAGTGTGCGAGTTGATTATAT 1 AGCACTAAGTGTGCGACTTGAATATAT * 18482134 AGCACTGAGTGTGCGGACTT-AATATAT 1 AGCACTAAGTGTGC-GACTTGAATATAT 18482161 A 1 A 18482162 TTTTTGAATC Statistics Matches: 50, Mismatches: 4, Indels: 3 0.88 0.07 0.05 Matches are distributed among these distances: 27 30 0.60 28 20 0.40 ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33 Consensus pattern (27 bp): AGCACTAAGTGTGCGACTTGAATATAT Found at i:18482162 original size:29 final size:27 Alignment explanation

Indices: 18482051--18482162 Score: 98 Period size: 28 Copynumber: 4.0 Consensus size: 27 18482041 CATGAGATTG ** * * 18482051 GCACTAAGTGTGCGGGTTTAAATTGTACA 1 GCACTAAGTGTGC-GACTT-AATTATATA * * 18482080 GCACTAAGTGTGCGAGTTTGATTATATA 1 GCACTAAGTGTGCGA-CTTAATTATATA * * 18482108 GCACTAAGTGTGCGAGTTGATTATATA 1 GCACTAAGTGTGCGACTTAATTATATA * 18482135 GCACTGAGTGTGCGGACTTAATATATAT 1 GCACTAAGTGTGC-GACTTAAT-TATAT 18482163 TTTTGAATCA Statistics Matches: 72, Mismatches: 8, Indels: 6 0.84 0.09 0.07 Matches are distributed among these distances: 27 23 0.32 28 28 0.39 29 21 0.29 ACGTcount: A:0.29, C:0.12, G:0.26, T:0.33 Consensus pattern (27 bp): GCACTAAGTGTGCGACTTAATTATATA Found at i:18486744 original size:12 final size:11 Alignment explanation

Indices: 18486726--18486759 Score: 50 Period size: 12 Copynumber: 3.0 Consensus size: 11 18486716 GATTTCATCG 18486726 TTTGTTTATTT 1 TTTGTTTATTT 18486737 TATTGTTTATTT 1 T-TTGTTTATTT * 18486749 TTTATTTATTT 1 TTTGTTTATTT 18486760 AATTTCTATT Statistics Matches: 21, Mismatches: 1, Indels: 2 0.88 0.04 0.08 Matches are distributed among these distances: 11 10 0.48 12 11 0.52 ACGTcount: A:0.15, C:0.00, G:0.06, T:0.79 Consensus pattern (11 bp): TTTGTTTATTT Found at i:18505797 original size:21 final size:21 Alignment explanation

Indices: 18505773--18505815 Score: 68 Period size: 21 Copynumber: 2.0 Consensus size: 21 18505763 TTGTATTACT * 18505773 TATATTTCATTGTATATTATA 1 TATATTTCATTATATATTATA * 18505794 TATATTTTATTATATATTATA 1 TATATTTCATTATATATTATA 18505815 T 1 T 18505816 TTTATTATAT Statistics Matches: 20, Mismatches: 2, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 21 20 1.00 ACGTcount: A:0.35, C:0.02, G:0.02, T:0.60 Consensus pattern (21 bp): TATATTTCATTATATATTATA Found at i:18505806 original size:14 final size:14 Alignment explanation

Indices: 18505787--18505892 Score: 63 Period size: 15 Copynumber: 6.9 Consensus size: 14 18505777 TTTCATTGTA 18505787 TATTATATATATTT 1 TATTATATATATTT 18505801 TATTATATATTATATTT 1 TA-T-TATA-TATATTT 18505818 TATTATATAT-TGTT 1 TATTATATATAT-TT * * 18505832 CTCTATATTATCTTCATTT 1 -TAT-TA-TAT-AT-ATTT 18505851 TATTATATATTATTT 1 TATTATATA-TATTT * 18505866 TATTATTTAT-TATT 1 TATTATATATAT-TT 18505880 TATTAGTATATAT 1 TATTA-TATATAT 18505893 ATAATCAAAA Statistics Matches: 72, Mismatches: 6, Indels: 26 0.69 0.06 0.25 Matches are distributed among these distances: 13 2 0.03 14 15 0.21 15 23 0.32 16 12 0.17 17 14 0.19 18 3 0.04 19 2 0.03 20 1 0.01 ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63 Consensus pattern (14 bp): TATTATATATATTT Found at i:18505807 original size:12 final size:12 Alignment explanation

Indices: 18505785--18505894 Score: 56 Period size: 12 Copynumber: 9.4 Consensus size: 12 18505775 TATTTCATTG 18505785 TATATTATA-TA 1 TATATTATATTA 18505796 TAT-TT-TATTA 1 TATATTATATTA * 18505806 TATATTATATTT 1 TATATTATATTA * 18505818 TAT-TATATATTG 1 TATAT-TATATTA * 18505830 T-TCTCTATATTA 1 TATAT-TATATTA * * 18505842 TCTTCATTTTATTA 1 T-AT-ATTATATTA * 18505856 TATATTATTTTA 1 TATATTATATTA 18505868 T-TATT-TATTA 1 TATATTATATTA * 18505878 TTTATTAGTA-TA 1 TATATTA-TATTA 18505890 TATAT 1 TATAT 18505895 AATCAAAATT Statistics Matches: 77, Mismatches: 11, Indels: 21 0.71 0.10 0.19 Matches are distributed among these distances: 9 2 0.03 10 12 0.16 11 15 0.19 12 36 0.47 13 3 0.04 14 8 0.10 15 1 0.01 ACGTcount: A:0.32, C:0.04, G:0.02, T:0.63 Consensus pattern (12 bp): TATATTATATTA Found at i:18505810 original size:33 final size:31 Alignment explanation

Indices: 18505773--18505892 Score: 106 Period size: 33 Copynumber: 3.8 Consensus size: 31 18505763 TTGTATTACT 18505773 TATATTTCATTGTATATTATATATATTTTATTA 1 TATATTTCATT-T-TATTATATATATTTTATTA * * 18505806 TATATTAT-ATTTTATTATATAT-TGTTCTCTA 1 TATATT-TCATTTTATTATATATATTTTAT-TA 18505837 TATTATCTTCATTTTATTATATATTATTTTATTA 1 TA-TAT-TTCATTTTATTATATA-TATTTTATTA * 18505871 TTTA-TT-A-TTTATTAGTATATAT 1 TATATTTCATTTTATTA-TATATAT 18505893 ATAATCAAAA Statistics Matches: 74, Mismatches: 5, Indels: 20 0.75 0.05 0.20 Matches are distributed among these distances: 29 10 0.14 30 9 0.12 31 16 0.22 32 5 0.07 33 25 0.34 34 5 0.07 35 4 0.05 ACGTcount: A:0.31, C:0.04, G:0.03, T:0.62 Consensus pattern (31 bp): TATATTTCATTTTATTATATATATTTTATTA Found at i:18517992 original size:44 final size:44 Alignment explanation

Indices: 18517929--18518278 Score: 436 Period size: 44 Copynumber: 7.9 Consensus size: 44 18517919 TGGAGATAGT * * * 18517929 AGATTTGGCGCCTCTGTATTGACAGAGAGCAAATCAAATATGAC 1 AGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCAAAGATGAC * * * 18517973 AGATTTGGAGTCTCTGTATTGTCAGAGAGCAGATCGAAGAT-AGC 1 AGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCAAAGATGA-C * 18518017 ATATTTGGCGTCTCTGTATTGACAGAGAGCAGATCAAAGAT-AGC 1 AGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCAAAGATGA-C * * * * * * * 18518061 AGATTTGACGTCTCTGTATCGACGGGGAGCAGATAAAAAATAAC 1 AGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCAAAGATGAC ** 18518105 AGATTTGGCGTCTCTGTATTGACAGAGAGCAGATTGAAGATAGA- 1 AGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCAAAGAT-GAC * * 18518149 AGATTTGGTGTCTCTGTATTGACAGAGAGCAGATCGAAGATGAC 1 AGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCAAAGATGAC * * 18518193 AGATTTGGCGTCTCTGTGTTGACAGAGAGCAGATCGAAGATGAC 1 AGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCAAAGATGAC * * * 18518237 AGATTTGGCGTCTCTGTATTAGCCAAAGAGCAGATCGAAGAT 1 AGATTTGGCGTCTCTGTATT-GACAGAGAGCAGATCAAAGAT 18518279 AGCAGATCTG Statistics Matches: 269, Mismatches: 32, Indels: 9 0.87 0.10 0.03 Matches are distributed among these distances: 43 3 0.01 44 245 0.91 45 21 0.08 ACGTcount: A:0.31, C:0.15, G:0.27, T:0.26 Consensus pattern (44 bp): AGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCAAAGATGAC Found at i:18518162 original size:132 final size:132 Alignment explanation

Indices: 18517922--18518285 Score: 505 Period size: 132 Copynumber: 2.8 Consensus size: 132 18517912 TATAGATTGG * * * * * 18517922 AGATAGTAGATTTGGCGCCTCTGTATTGACAGAGAGCAAATCAAATATGACAGATTTGGAGTCTC 1 AGATAGCAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCAAAAATGACAGATTTGGCGTCTC * * 18517987 TGTATTGTCAGAGAGCAGATCGAAGATAGCATATTTGGCGTCTCTGTATTGACAGAGAGCAGATC 66 TGTATTGACAGAGAGCAGATCGAAGATAGCAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATC 18518052 AA 131 AA * * * * * * 18518054 AGATAGCAGATTTGACGTCTCTGTATCGACGGGGAGCAGATAAAAAATAACAGATTTGGCGTCTC 1 AGATAGCAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCAAAAATGACAGATTTGGCGTCTC * * * 18518119 TGTATTGACAGAGAGCAGATTGAAGATAGAAGATTTGGTGTCTCTGTATTGACAGAGAGCAGATC 66 TGTATTGACAGAGAGCAGATCGAAGATAGCAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATC * 18518184 GA 131 AA * * * 18518186 AGAT-GACAGATTTGGCGTCTCTGTGTTGACAGAGAGCAGATCGAAGATGACAGATTTGGCGTCT 1 AGATAG-CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCAAAAATGACAGATTTGGCGTCT * * 18518250 CTGTATTAGCCAAAGAGCAGATCGAAGATAGCAGAT 65 CTGTATT-GACAGAGAGCAGATCGAAGATAGCAGAT 18518286 CTGACATTCG Statistics Matches: 200, Mismatches: 30, Indels: 3 0.86 0.13 0.01 Matches are distributed among these distances: 131 1 0.00 132 175 0.88 133 24 0.12 ACGTcount: A:0.32, C:0.15, G:0.27, T:0.26 Consensus pattern (132 bp): AGATAGCAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCAAAAATGACAGATTTGGCGTCTC TGTATTGACAGAGAGCAGATCGAAGATAGCAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATC AA Found at i:18518334 original size:90 final size:90 Alignment explanation

Indices: 18518132--18518458 Score: 292 Period size: 90 Copynumber: 3.7 Consensus size: 90 18518122 ATTGACAGAG * ** 18518132 AGCAGATTGAAGATAGA-AGATTTGGTGTCTCTGTATT-GAC-AGAGAGCAGATCGAAGAT-GAC 1 AGCAGATCGAAGAT-GACAGATTTGGCATCTCTGTATTAGACAAG-GAGCAGATCGAAGATAG-C * * * * * 18518193 AGATTTGGCGTCTC-TGTGTTGACA--GA 63 AGATCTGACAT-TCGTATGTTCACATCGA * * * 18518219 GAGCAGATCGAAGATGACAGATTTGGCGTCTCTGTATTAGCCAAAGAGCAGATCGAAGATAGCAG 1 -AGCAGATCGAAGATGACAGATTTGGCATCTCTGTATTAGACAAGGAGCAGATCGAAGATAGCAG * 18518284 ATCTGACATTCGTATGTTCGCATCGA 65 ATCTGACATTCGTATGTTCACATCGA * * * ** * * 18518310 AGTAGATCGAAAATGACAGATTTGGCATCTCTGTGTTAGACGGGGAACAGATCGAAGATAGTAGA 1 AGCAGATCGAAGATGACAGATTTGGCATCTCTGTATTAGACAAGGAGCAGATCGAAGATAGCAGA * * * 18518375 TCTGACATTTGTATGTTTATATCGA 66 TCTGACATTCGTATGTTCACATCGA * * * * * * 18518400 AGCAGA-CTGAAGATGACATATTTGGCCTCTCTGTTTTAGGCAAGGAGTAGATCAAAGAT 1 AGCAGATC-GAAGATGACAGATTTGGCATCTCTGTATTAGACAAGGAGCAGATCGAAGAT 18518459 TTCAGCATGG Statistics Matches: 196, Mismatches: 35, Indels: 14 0.80 0.14 0.06 Matches are distributed among these distances: 87 2 0.01 88 34 0.17 89 34 0.17 90 124 0.63 91 2 0.01 ACGTcount: A:0.31, C:0.15, G:0.27, T:0.27 Consensus pattern (90 bp): AGCAGATCGAAGATGACAGATTTGGCATCTCTGTATTAGACAAGGAGCAGATCGAAGATAGCAGA TCTGACATTCGTATGTTCACATCGA Found at i:18520043 original size:20 final size:22 Alignment explanation

Indices: 18519994--18520043 Score: 54 Period size: 20 Copynumber: 2.5 Consensus size: 22 18519984 TCCTTTTATA * 18519994 TATATACATTTTACATATAATT 1 TATATATATTTTACATATAATT * 18520016 TAT-T-TATTTTA-A-ATATTT 1 TATATATATTTTACATATAATT 18520034 TATATATATT 1 TATATATATT 18520044 ATTTATACAT Statistics Matches: 24, Mismatches: 2, Indels: 6 0.75 0.06 0.19 Matches are distributed among these distances: 18 8 0.33 19 2 0.08 20 10 0.42 21 1 0.04 22 3 0.12 ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58 Consensus pattern (22 bp): TATATATATTTTACATATAATT Found at i:18520154 original size:17 final size:17 Alignment explanation

Indices: 18520122--18520166 Score: 81 Period size: 17 Copynumber: 2.6 Consensus size: 17 18520112 TTCATTGTAC 18520122 ATTATATATATATATTTT 1 ATTATATAT-TATATTTT 18520140 ATTATATATTATATTTT 1 ATTATATATTATATTTT 18520157 ATTATATATT 1 ATTATATATT 18520167 GTTCTCTATA Statistics Matches: 27, Mismatches: 0, Indels: 1 0.96 0.00 0.04 Matches are distributed among these distances: 17 18 0.67 18 9 0.33 ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62 Consensus pattern (17 bp): ATTATATATTATATTTT Found at i:18520166 original size:12 final size:12 Alignment explanation

Indices: 18520122--18520163 Score: 52 Period size: 12 Copynumber: 3.6 Consensus size: 12 18520112 TTCATTGTAC 18520122 ATTATATATATAT 1 ATTATAT-TATAT * 18520135 ATTTTATTATAT 1 ATTATATTATAT 18520147 ATTATATT-T-T 1 ATTATATTATAT 18520157 ATTATAT 1 ATTATAT 18520164 ATTGTTCTCT Statistics Matches: 27, Mismatches: 2, Indels: 3 0.84 0.06 0.09 Matches are distributed among these distances: 10 8 0.30 11 1 0.04 12 12 0.44 13 6 0.22 ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62 Consensus pattern (12 bp): ATTATATTATAT Found at i:18522884 original size:13 final size:14 Alignment explanation

Indices: 18522866--18522897 Score: 57 Period size: 14 Copynumber: 2.4 Consensus size: 14 18522856 TATTTGGTAA 18522866 ATTTTTT-AAAATT 1 ATTTTTTAAAAATT 18522879 ATTTTTTAAAAATT 1 ATTTTTTAAAAATT 18522893 ATTTT 1 ATTTT 18522898 CAGTGAAACA Statistics Matches: 18, Mismatches: 0, Indels: 1 0.95 0.00 0.05 Matches are distributed among these distances: 13 7 0.39 14 11 0.61 ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62 Consensus pattern (14 bp): ATTTTTTAAAAATT Found at i:18524014 original size:20 final size:20 Alignment explanation

Indices: 18523974--18524014 Score: 57 Period size: 20 Copynumber: 2.0 Consensus size: 20 18523964 CTTCTAATTG * 18523974 TATTTATATATATTATTATA 1 TATTTATATATAATATTATA 18523994 TATTTATATA-AATATTGATA 1 TATTTATATATAATATT-ATA 18524014 T 1 T 18524015 GCTAATCTTA Statistics Matches: 19, Mismatches: 1, Indels: 2 0.86 0.05 0.09 Matches are distributed among these distances: 19 5 0.26 20 14 0.74 ACGTcount: A:0.41, C:0.00, G:0.02, T:0.56 Consensus pattern (20 bp): TATTTATATATAATATTATA Found at i:18527156 original size:46 final size:45 Alignment explanation

Indices: 18527010--18527216 Score: 213 Period size: 46 Copynumber: 4.4 Consensus size: 45 18527000 TTTGTGTGTT * * 18527010 AGTGTAAGACATGTCTGGGACATGCATTGGCCAT-ATTATGAGAGCC 1 AGTGTAAGACATGTCTGGGACATGCATTGGCCTTGA-GATGA-AGCC * * * * 18527056 AGTGTAAGACCAAGTCTGGGACATGGCATTGGCATTGAGACGAAAGCT 1 AGTGTAAGA-CATGTCTGGGACAT-GCATTGGCCTTGAGATG-AAGCC * * 18527104 AGTGTAAGACATGTCTGGGACATGCATTAGCCTCGAGATGTAAGCC 1 AGTGTAAGACATGTCTGGGACATGCATTGGCCTTGAGATG-AAGCC * * 18527150 AGTGTAAGACATGTCTGGGACATGTCA-TCGACTTGATAGATG-AGCC 1 AGTGTAAGACATGTCTGGGACATG-CATTGGCCTTG--AGATGAAGCC 18527196 AGTGTAAGACCATGTCTGGGA 1 AGTGTAAGA-CATGTCTGGGA 18527217 TATGGCATCG Statistics Matches: 137, Mismatches: 16, Indels: 15 0.82 0.10 0.09 Matches are distributed among these distances: 46 68 0.50 47 39 0.28 48 28 0.20 49 2 0.01 ACGTcount: A:0.29, C:0.17, G:0.29, T:0.24 Consensus pattern (45 bp): AGTGTAAGACATGTCTGGGACATGCATTGGCCTTGAGATGAAGCC Found at i:18528939 original size:46 final size:43 Alignment explanation

Indices: 18528854--18528978 Score: 135 Period size: 46 Copynumber: 2.7 Consensus size: 43 18528844 GTCAGGTGCT 18528854 GATGCAATGTCCCAGACATGGTCTTACACTGGCACATCTCGTA-GCC 1 GATGC-ATGTCCCAGACAT-GTC-TACACTGGCACATCTCG-AGGCC * * 18528900 GATGCATGTTCCAGACATGTCTACCACTGGCTTATATCTCGAGGCC 1 GATGCATGTCCCAGACATGTCTA-CACTGGC--ACATCTCGAGGCC * * 18528946 AATGCATGTCCCAGACATGTCTTACACTAGCAC 1 GATGCATGTCCCAGACATGTC-TACACTGGCAC 18528979 TCGTCTCAAT Statistics Matches: 68, Mismatches: 6, Indels: 12 0.79 0.07 0.14 Matches are distributed among these distances: 43 2 0.03 44 11 0.16 45 13 0.19 46 40 0.59 47 2 0.03 ACGTcount: A:0.25, C:0.30, G:0.20, T:0.26 Consensus pattern (43 bp): GATGCATGTCCCAGACATGTCTACACTGGCACATCTCGAGGCC Found at i:18534687 original size:56 final size:56 Alignment explanation

Indices: 18534601--18534720 Score: 222 Period size: 56 Copynumber: 2.1 Consensus size: 56 18534591 ACAAGGGATG 18534601 ATGGGCAAAACATGTCATGAAACATGTTGTGTCAATGGAAAAATAAAATAAGAAGC 1 ATGGGCAAAACATGTCATGAAACATGTTGTGTCAATGGAAAAATAAAATAAGAAGC * * 18534657 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC 1 ATGGGCAAAACATGTCATGAAACATGTTGTGTCAATGGAAAAATAAAATAAGAAGC 18534713 ATGGGCAA 1 ATGGGCAA 18534721 TAAACTAATA Statistics Matches: 62, Mismatches: 2, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 56 62 1.00 ACGTcount: A:0.45, C:0.10, G:0.23, T:0.22 Consensus pattern (56 bp): ATGGGCAAAACATGTCATGAAACATGTTGTGTCAATGGAAAAATAAAATAAGAAGC Found at i:18536552 original size:49 final size:49 Alignment explanation

Indices: 18536483--18537033 Score: 928 Period size: 49 Copynumber: 11.5 Consensus size: 49 18536473 ATTCAGCCAA 18536483 GAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT 1 GAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT * 18536530 GAAAGTGTATATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGT 1 GAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT 18536579 GAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT 1 GAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT 18536626 GAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT 1 GAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT 18536675 GAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT 1 GAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT 18536722 GAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT 1 GAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT * 18536771 GAAAGTG--TATATATGTGATAAGGCATAATGGCCGATGTGATGAATGT 1 GAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT 18536818 GAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT 1 GAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT * * 18536867 GAAAGTGTATATATATGTGATAAGTCCTAATGGCCAATGTGATGAATGT 1 GAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT 18536916 GAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT 1 GAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT * * * * * * 18536965 GAAAGTG--TATATATGTGATAGGGCCGAGTGGCCAACGTGATGGATGT 1 GAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT 18537012 GAAAGTGTATA-A-ATGTGATAAG 1 GAAAGTGTATATATATGTGATAAG 18537034 TCCCGAAGGG Statistics Matches: 479, Mismatches: 15, Indels: 20 0.93 0.03 0.04 Matches are distributed among these distances: 47 196 0.41 48 1 0.00 49 282 0.59 ACGTcount: A:0.33, C:0.08, G:0.29, T:0.30 Consensus pattern (49 bp): GAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT Found at i:18536647 original size:96 final size:96 Alignment explanation

Indices: 18536483--18537033 Score: 980 Period size: 96 Copynumber: 5.7 Consensus size: 96 18536473 ATTCAGCCAA 18536483 GAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGT 1 GAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGT * 18536548 GATAAGGCCTAATGGCCAATGTGATGAATGT 66 GATAAGGCCTAATGGCCGATGTGATGAATGT 18536579 GAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGT 1 GAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGT 18536644 GATAAGGCCTAATGGCCGATGTGATGAATGT 66 GATAAGGCCTAATGGCCGATGTGATGAATGT 18536675 GAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGT 1 GAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGT 18536740 GATAAGGCCTAATGGCCGATGTGATGAATGT 66 GATAAGGCCTAATGGCCGATGTGATGAATGT * 18536771 GAAAGTGTATATATGTGATAAGGCATAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGT 1 GAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGT 18536836 GATAAGGCCTAATGGCCGATGTGATGAATGT 66 GATAAGGCCTAATGGCCGATGTGATGAATGT * * 18536867 GAAAGTGTATATATATGTGATAAGTCCTAATGGCCAATGTGATGAATGTGAAAGTGTATATATAT 1 GAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATAT 18536932 GTGATAAGGCCTAATGGCCGATGTGATGAATGT 64 GTGATAAGGCCTAATGGCCGATGTGATGAATGT * * * * * * 18536965 GAAAGTGTATATATGTGATAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGTATA-A-ATGT 1 GAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGT 18537028 GATAAG 66 GATAAG 18537034 TCCCGAAGGG Statistics Matches: 442, Mismatches: 11, Indels: 6 0.96 0.02 0.01 Matches are distributed among these distances: 94 10 0.02 95 1 0.00 96 338 0.76 98 93 0.21 ACGTcount: A:0.33, C:0.08, G:0.29, T:0.30 Consensus pattern (96 bp): GAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGT GATAAGGCCTAATGGCCGATGTGATGAATGT Found at i:18536744 original size:145 final size:144 Alignment explanation

Indices: 18536483--18537033 Score: 916 Period size: 145 Copynumber: 3.8 Consensus size: 144 18536473 ATTCAGCCAA 18536483 GAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGT 1 GAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG-ATATATATGT 18536548 GATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGC 65 GATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGC 18536611 CGATGTGATGAATGT 130 CGATGTGATGAATGT 18536626 GAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG-TATATATG 1 GAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGATATATATG * 18536690 TGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGG 64 TGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGG 18536755 CCGATGTGATGAATGT 129 CCGATGTGATGAATGT * 18536771 GAAAGTGTATATATGTGATAAGGCATAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGT 1 GAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG-ATATATATGT * * 18536836 GATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGTCCTAATGGC 65 GATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGC * 18536901 CAATGTGATGAATGT 130 CGATGTGATGAATGT 18536916 GAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG-TATATATG 1 GAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGATATATATG * * * * * 18536980 TGATAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGTATA-A-ATGTGATAAG 64 TGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATATATATGTGATAAG 18537034 TCCCGAAGGG Statistics Matches: 389, Mismatches: 11, Indels: 16 0.94 0.03 0.04 Matches are distributed among these distances: 143 109 0.28 144 1 0.00 145 233 0.60 147 46 0.12 ACGTcount: A:0.33, C:0.08, G:0.29, T:0.30 Consensus pattern (144 bp): GAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGATATATATGTG ATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCC GATGTGATGAATGT Found at i:18537202 original size:37 final size:37 Alignment explanation

Indices: 18537152--18537267 Score: 187 Period size: 37 Copynumber: 3.1 Consensus size: 37 18537142 CCGAGCTCTA 18537152 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT 1 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT 18537189 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT 1 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT * * * * * 18537226 AAGACCCGATAACTTCTTGTGGAGATTATGTCCGGGT 1 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT 18537263 AAGAC 1 AAGAC 18537268 TTCGTAATAA Statistics Matches: 74, Mismatches: 5, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 37 74 1.00 ACGTcount: A:0.22, C:0.19, G:0.32, T:0.27 Consensus pattern (37 bp): AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT Found at i:18539270 original size:40 final size:40 Alignment explanation

Indices: 18539124--18539345 Score: 206 Period size: 40 Copynumber: 5.6 Consensus size: 40 18539114 TCGAATGATG * * * * 18539124 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA 1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA * * 18539164 TCCGGACTAAGAT-CCGAAGGCATTTG-GCGAGTTACTAAT 1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA * * 18539203 TCTGGGCTAAG--CCGAAGGCATTGGTGCGAGTTACTAAA 1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA * 18539241 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA 1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA ** * * ** 18539282 -CCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGA-TGTA 1 TCCGGGCTAAGTCCCGAAG-GCATTTGTGCGAGTTACTAAA * 18539321 TCCGGGCTAAGTTCCGAAGAGCATT 1 TCCGGGCTAAGTCCCGAAG-GCATT 18539346 CATGCTAGTG Statistics Matches: 153, Mismatches: 21, Indels: 16 0.81 0.11 0.08 Matches are distributed among these distances: 37 12 0.08 38 21 0.14 39 16 0.10 40 85 0.56 41 19 0.12 ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25 Consensus pattern (40 bp): TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA Found at i:18539338 original size:80 final size:80 Alignment explanation

Indices: 18539124--18539397 Score: 238 Period size: 80 Copynumber: 3.5 Consensus size: 80 18539114 TCGAATGATG ** * * * 18539124 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT 1 TCCGGGCTAAGTCCCGAAGGCATTCATGCT-AGTGACTATATCCGGGCTAAGTTCCGAAGGCATT 18539188 TG-GCGAGTTACTA-A 65 TGTGCGAGTTACTATA * ** * * * * * 18539202 TTCTGGGCTAAG--CCGAAGGCATTGGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATT 1 -TCCGGGCTAAGTCCCGAAGGCATTCATGCTAGTGACTATATCCGGGCTAAGTTCCGAAGGCATT 18539265 TGTGCGAGTTACTATA 65 TGTGCGAGTTACTATA * * 18539281 ACCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGA-TGTATCCGGGCTAAGTTCCGAAGAGCAT 1 TCCGGGCTAAGTCCCGAAG-GCATTCATGCTAGTGACTATATCCGGGCTAAGTTCCGAAG-GCAT ** * * * 18539345 TCATGCTAGTGA-TGTA 64 TTGTGCGAGTTACTATA * * * * 18539361 TCCGGGCTAGGTCTCGAAGAGCAATCATGCTGGTGAC 1 TCCGGGCTAAGTCCCGAAG-GCATTCATGCTAGTGAC 18539398 GTGTATTCGG Statistics Matches: 157, Mismatches: 30, Indels: 14 0.78 0.15 0.07 Matches are distributed among these distances: 77 37 0.24 78 26 0.17 79 11 0.07 80 59 0.38 81 24 0.15 ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25 Consensus pattern (80 bp): TCCGGGCTAAGTCCCGAAGGCATTCATGCTAGTGACTATATCCGGGCTAAGTTCCGAAGGCATTT GTGCGAGTTACTATA Found at i:18539346 original size:40 final size:40 Alignment explanation

Indices: 18539282--18539396 Score: 178 Period size: 40 Copynumber: 2.9 Consensus size: 40 18539272 GTTACTATAA * 18539282 CCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTAT 1 CCGGGCTAAGTTCCGAAGAGCATTCATGCTAGTGATGTAT 18539322 CCGGGCTAAGTTCCGAAGAGCATTCATGCTAGTGATGTAT 1 CCGGGCTAAGTTCCGAAGAGCATTCATGCTAGTGATGTAT * * * 18539362 CCGGGCT-AGGTCTCGAAGAGCAATCATGCTGGTGA 1 CCGGGCTAAGTTC-CGAAGAGCATTCATGCTAGTGA 18539397 CGTGTATTCG Statistics Matches: 70, Mismatches: 4, Indels: 2 0.92 0.05 0.03 Matches are distributed among these distances: 39 4 0.06 40 66 0.94 ACGTcount: A:0.24, C:0.22, G:0.30, T:0.24 Consensus pattern (40 bp): CCGGGCTAAGTTCCGAAGAGCATTCATGCTAGTGATGTAT Found at i:18540655 original size:56 final size:56 Alignment explanation

Indices: 18540569--18540688 Score: 222 Period size: 56 Copynumber: 2.1 Consensus size: 56 18540559 ACAAGGGATG 18540569 ATGGGCAAAACATGTCATGAAACATGTTGTGTCAATGGAAAAATAAAATAAGAAGC 1 ATGGGCAAAACATGTCATGAAACATGTTGTGTCAATGGAAAAATAAAATAAGAAGC * * 18540625 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC 1 ATGGGCAAAACATGTCATGAAACATGTTGTGTCAATGGAAAAATAAAATAAGAAGC 18540681 ATGGGCAA 1 ATGGGCAA 18540689 TAAACTAATA Statistics Matches: 62, Mismatches: 2, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 56 62 1.00 ACGTcount: A:0.45, C:0.10, G:0.23, T:0.22 Consensus pattern (56 bp): ATGGGCAAAACATGTCATGAAACATGTTGTGTCAATGGAAAAATAAAATAAGAAGC Found at i:18542560 original size:47 final size:47 Alignment explanation

Indices: 18542436--18543169 Score: 1267 Period size: 47 Copynumber: 15.5 Consensus size: 47 18542426 GATTCAGCAA 18542436 GAAAGTGTATATATGTGATAAGG-CTAATGGCCGATGTGATGAATGT 1 GAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT 18542482 GAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT 1 GAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT 18542531 GAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT 1 GAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT 18542578 GAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT 1 GAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT 18542625 GAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT 1 GAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT 18542672 GAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT 1 GAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT 18542721 GAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT 1 GAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT 18542770 GAAAGTGTATATATGTGATAAGG-CTAATGGCCGATGTGATGAATGT 1 GAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT 18542816 GAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT 1 GAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT 18542863 GAAAGTGTATATATATGTGATAAGGCCTAAT-GCCGATGTGATGAATGT 1 GAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT 18542911 GAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT 1 GAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT * 18542960 GAAAGTGTATATATGTGATAAGGCCTAATGGCCGTTGTGATGAATGT 1 GAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT 18543007 GAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT 1 GAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT * 18543054 GAAAGTGTATATATGTGAGAAGGCCTAATGGCCGATGTGATGAATGT 1 GAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT * * * * * * * 18543101 GAAAGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGT 1 GAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT * 18543148 GAAAGTGTATAAATGTGATAAG 1 GAAAGTGTATATATGTGATAAG 18543170 TCCCGAAGGG Statistics Matches: 666, Mismatches: 13, Indels: 17 0.96 0.02 0.02 Matches are distributed among these distances: 46 53 0.08 47 377 0.57 48 64 0.10 49 172 0.26 ACGTcount: A:0.32, C:0.08, G:0.30, T:0.30 Consensus pattern (47 bp): GAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT Found at i:18543347 original size:34 final size:35 Alignment explanation

Indices: 18543309--18543389 Score: 101 Period size: 37 Copynumber: 2.3 Consensus size: 35 18543299 ACTACGATTT * * * 18543309 CGGGTAAGACG-TGACTACGTGTGGGGATTTTGTC 1 CGGGTAAGACGATAACTACGTGTGGAGATTATGTC * 18543343 CGGGTAAGACCCGATAACTTCGTGTGGAGATTATGTC 1 CGGGTAAGA--CGATAACTACGTGTGGAGATTATGTC 18543380 CGGGTAAGAC 1 CGGGTAAGAC 18543390 TTCGTAATAA Statistics Matches: 40, Mismatches: 4, Indels: 5 0.82 0.08 0.10 Matches are distributed among these distances: 34 9 0.22 35 1 0.03 36 2 0.05 37 28 0.70 ACGTcount: A:0.22, C:0.17, G:0.35, T:0.26 Consensus pattern (35 bp): CGGGTAAGACGATAACTACGTGTGGAGATTATGTC Found at i:18545689 original size:46 final size:45 Alignment explanation

Indices: 18545588--18545800 Score: 180 Period size: 46 Copynumber: 4.6 Consensus size: 45 18545578 GTGCCTATGC * * * 18545588 CATGTCCCAGACATGGTCTTACACTGG-TACATCTC-ATAGCTGATG 1 CATGTCCCAGACAT-GTCTTACACTGGCTTCATCTCGA-GGCCGATG * * 18545633 CATGTTCCAGACATGTCTTACACTGGCTTACGTCTCGAGGCCGATG 1 CATGTCCCAGACATGTCTTACACTGGCTT-CATCTCGAGGCCGATG ** * * ** 18545679 CATGTCCCAGACATGTCTTACACTATCATTCGTCTCAACACCGATG 1 CATGTCCCAGACATGTCTTACACTGGC-TTCATCTCGAGGCCGATG * * * * * 18545725 ACATGTCCTAGACATGGTCTTACACCGACTCTCATAAT-GTGGCCGATG 1 -CATGTCCCAGACAT-GTCTTACACTGGCT-TCAT-CTCGAGGCCGATG * 18545773 CATGTCCCAGACTTGTCTTACACTGGCT 1 CATGTCCCAGACATGTCTTACACTGGCT 18545801 CACATAAGTG Statistics Matches: 135, Mismatches: 25, Indels: 15 0.77 0.14 0.09 Matches are distributed among these distances: 44 12 0.09 45 14 0.10 46 60 0.44 47 29 0.21 48 19 0.14 49 1 0.01 ACGTcount: A:0.23, C:0.29, G:0.19, T:0.29 Consensus pattern (45 bp): CATGTCCCAGACATGTCTTACACTGGCTTCATCTCGAGGCCGATG Found at i:18573388 original size:40 final size:39 Alignment explanation

Indices: 18573321--18573485 Score: 167 Period size: 40 Copynumber: 4.2 Consensus size: 39 18573311 GGACTAAGAT * * * 18573321 CCGAAGGCATTCGTGCGAGTTGCTATATCCGGGCTATATC 1 CCGAAGGCATTTGTGCTAGTTGTTATATCCGGGCTA-ATC * * * 18573361 CCAAAGGCATTTATGCTAG-TGATTATATCCGGGCTAAGAC 1 CCGAAGGCATTTGTGCTAGTTG-TTATATCCGGGCTAA-TC * 18573401 CCGAAGGCATTTGTG-TGAGTTGCTATATCCGGGCTGAGA-C 1 CCGAAGGCATTTGTGCT-AGTTGTTATATCCGGGCT-A-ATC * 18573441 CCGAAGGCATTTGTGCGAGTTGTTATATCC-GGCTAAATC 1 CCGAAGGCATTTGTGCTAGTTGTTATATCCGGGCT-AATC 18573480 CCGAAG 1 CCGAAG 18573486 ATACTTGGGT Statistics Matches: 105, Mismatches: 12, Indels: 17 0.78 0.09 0.13 Matches are distributed among these distances: 38 1 0.01 39 16 0.15 40 84 0.80 41 3 0.03 42 1 0.01 ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27 Consensus pattern (39 bp): CCGAAGGCATTTGTGCTAGTTGTTATATCCGGGCTAATC Found at i:18573448 original size:80 final size:80 Alignment explanation

Indices: 18573309--18573485 Score: 227 Period size: 80 Copynumber: 2.2 Consensus size: 80 18573299 CGGATGATAA * * * 18573309 CCGGACTAAGATCCGAAGGCATTCGTGCGAGTTGCTATATCCGGGCTATATCCCAAAGGCATTTA 1 CCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGCTATATCCGGGCTAGATCCCAAAGGCATTTA * 18573374 TGCTAG-TGATTATAT 66 TGCGAGTTG-TTATAT * * * 18573389 CCGGGCTAAGACCCGAAGGCATTTGTGTGAGTTGCTATATCCGGGCTGAGA-CCCGAAGGCATTT 1 CCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGCTATATCCGGGCT-AGATCCCAAAGGCATTT * 18573453 GTGCGAGTTGTTATAT 65 ATGCGAGTTGTTATAT 18573469 CC-GGCTAA-ATCCCGAAG 1 CCGGGCTAAGA-CCCGAAG 18573486 ATACTTGGGT Statistics Matches: 86, Mismatches: 8, Indels: 7 0.85 0.08 0.07 Matches are distributed among these distances: 78 1 0.01 79 13 0.15 80 68 0.79 81 4 0.05 ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27 Consensus pattern (80 bp): CCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGCTATATCCGGGCTAGATCCCAAAGGCATTTA TGCGAGTTGTTATAT Found at i:18580675 original size:40 final size:40 Alignment explanation

Indices: 18580556--18580723 Score: 205 Period size: 40 Copynumber: 4.2 Consensus size: 40 18580546 CGGATGATAA * * * 18580556 CCGGACTAAGATCCGAAGGCATTCGTGCGAGTTGCTATAT 1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT * * * * * * * 18580596 CCGAGCTATGTCCCAAAGGCATTTATGCTAG-TGATTATAT 1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CTATAT 18580636 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT 1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT * * 18580676 CCGGGCTGAGACCCGAAGGCATTTGTGCGAGTTGTTATAT 1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT 18580716 CC-GGCTAA 1 CCGGGCTAA 18580724 ATCTCGAAGA Statistics Matches: 106, Mismatches: 20, Indels: 5 0.81 0.15 0.04 Matches are distributed among these distances: 39 7 0.07 40 97 0.92 41 2 0.02 ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27 Consensus pattern (40 bp): CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT Found at i:18586444 original size:21 final size:21 Alignment explanation

Indices: 18586416--18586456 Score: 57 Period size: 22 Copynumber: 2.0 Consensus size: 21 18586406 CAAAACTTGT 18586416 ATAACTATCA-TCAAACATCC 1 ATAACTATCATTCAAACATCC * 18586436 ATAATCTATCATTTAAACATC 1 ATAA-CTATCATTCAAACATC 18586457 AAAATACTCA Statistics Matches: 18, Mismatches: 1, Indels: 2 0.86 0.05 0.10 Matches are distributed among these distances: 20 4 0.22 21 6 0.33 22 8 0.44 ACGTcount: A:0.44, C:0.24, G:0.00, T:0.32 Consensus pattern (21 bp): ATAACTATCATTCAAACATCC Found at i:18600810 original size:12 final size:12 Alignment explanation

Indices: 18600793--18600818 Score: 52 Period size: 12 Copynumber: 2.2 Consensus size: 12 18600783 AAAATATGGA 18600793 AATAAACAAAGT 1 AATAAACAAAGT 18600805 AATAAACAAAGT 1 AATAAACAAAGT 18600817 AA 1 AA 18600819 GCTTTATAGC 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:0.69, C:0.08, G:0.08, T:0.15 Consensus pattern (12 bp): AATAAACAAAGT Found at i:18605431 original size:18 final size:17 Alignment explanation

Indices: 18605404--18605444 Score: 55 Period size: 18 Copynumber: 2.3 Consensus size: 17 18605394 AGAAATAATC * 18605404 AAAATTAATAAAAATAAA 1 AAAATAAAT-AAAATAAA 18605422 AAAATAAATAAAATAAA 1 AAAATAAATAAAATAAA 18605439 ATAAAT 1 A-AAAT 18605445 TTTCTAAAAC Statistics Matches: 21, Mismatches: 1, Indels: 2 0.88 0.04 0.08 Matches are distributed among these distances: 17 9 0.43 18 12 0.57 ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22 Consensus pattern (17 bp): AAAATAAATAAAATAAA Found at i:18613143 original size:29 final size:28 Alignment explanation

Indices: 18613102--18613158 Score: 96 Period size: 29 Copynumber: 2.0 Consensus size: 28 18613092 GTCTGAACTA 18613102 CTGATATCATGGCCCGAAGCCAAATCAG 1 CTGATATCATGGCCCGAAGCCAAATCAG * 18613130 CTGATATTCATGGCCCGAATCCAAATCAG 1 CTGATA-TCATGGCCCGAAGCCAAATCAG 18613159 TATAACTCGC Statistics Matches: 27, Mismatches: 1, Indels: 1 0.93 0.03 0.03 Matches are distributed among these distances: 28 6 0.22 29 21 0.78 ACGTcount: A:0.32, C:0.28, G:0.19, T:0.21 Consensus pattern (28 bp): CTGATATCATGGCCCGAAGCCAAATCAG Found at i:18617476 original size:110 final size:112 Alignment explanation

Indices: 18617264--18617486 Score: 301 Period size: 110 Copynumber: 2.0 Consensus size: 112 18617254 TTTCTTAACG * * ** 18617264 AAATTTTCACACAATCATATTATCATGCTGTAGACATTAAAATAATAATAAAATAAAAATTTTGA 1 AAATTTTCACACAAACATATTATCATGCTATAGACATT-AAATAATAATAAAATAAAAATTTCAA * 18617329 CCTCGTATTTTTGGTTTCAAAACCACTATTCTAATTTGACTAAAAACA 65 CCTCGTATTTGTGGTTTCAAAACCACTATTCTAATTTGACTAAAAACA * 18617377 AAATTTTCACACAAACATATTATCATGTTATAGACATT-AA-AATAATAAAATAAATAA-TTCAA 1 AAATTTTCACACAAACATATTATCATGCTATAGACATTAAATAATAATAAAATAAA-AATTTCAA * * * * 18617439 CCTCGTATTTGTGG-TTCTAAAACCACTGTTTTGATTTGATTAAAAACA 65 CCTCGTATTTGTGGTTTC-AAAACCACTATTCTAATTTGACTAAAAACA 18617487 GGCTATTACA Statistics Matches: 98, Mismatches: 10, Indels: 7 0.85 0.09 0.06 Matches are distributed among these distances: 109 3 0.03 110 56 0.57 111 4 0.04 113 35 0.36 ACGTcount: A:0.43, C:0.14, G:0.08, T:0.35 Consensus pattern (112 bp): AAATTTTCACACAAACATATTATCATGCTATAGACATTAAATAATAATAAAATAAAAATTTCAAC CTCGTATTTGTGGTTTCAAAACCACTATTCTAATTTGACTAAAAACA Found at i:18618529 original size:61 final size:61 Alignment explanation

Indices: 18618445--18618599 Score: 231 Period size: 61 Copynumber: 2.5 Consensus size: 61 18618435 TAGGCTTAGA * * 18618445 GCAATAAGTGTGTTTTGATCATTACTTTAAAATAGTTCTAAAAATTACAAGGATTT-TTTCT 1 GCAATAAGTGTGTTTTGAACATTACTTTGAAATAGTTCTAAAAATTACAAGGATTTCTTT-T * * * * 18618506 GCAATAAGTGGGTTGTGAACATTACTTTGAAATAGTTTTAAAAATTACAGGGATTTCTTTT 1 GCAATAAGTGTGTTTTGAACATTACTTTGAAATAGTTCTAAAAATTACAAGGATTTCTTTT * 18618567 GCAGTAAGTGTGTTTTGAACATTACTTTGAAAT 1 GCAATAAGTGTGTTTTGAACATTACTTTGAAAT 18618600 GTCTGATAGG Statistics Matches: 84, Mismatches: 9, Indels: 2 0.88 0.09 0.02 Matches are distributed among these distances: 61 81 0.96 62 3 0.04 ACGTcount: A:0.33, C:0.09, G:0.17, T:0.41 Consensus pattern (61 bp): GCAATAAGTGTGTTTTGAACATTACTTTGAAATAGTTCTAAAAATTACAAGGATTTCTTTT Found at i:18620037 original size:27 final size:27 Alignment explanation

Indices: 18619989--18620041 Score: 72 Period size: 27 Copynumber: 2.0 Consensus size: 27 18619979 CAGTAACAAT * 18619989 TGGGCCTAGCCCATTAACAGAATCAAG 1 TGGGCCTAGCCCAATAACAGAATCAAG * 18620016 TGGGCCTAAGCCCAAT-ATAGAATCAA 1 TGGGCCT-AGCCCAATAACAGAATCAA 18620042 TATAAGATGC Statistics Matches: 23, Mismatches: 2, Indels: 2 0.85 0.07 0.07 Matches are distributed among these distances: 27 16 0.70 28 7 0.30 ACGTcount: A:0.36, C:0.25, G:0.21, T:0.19 Consensus pattern (27 bp): TGGGCCTAGCCCAATAACAGAATCAAG Found at i:18620875 original size:15 final size:15 Alignment explanation

Indices: 18620855--18620885 Score: 62 Period size: 15 Copynumber: 2.1 Consensus size: 15 18620845 ACAGTGAAGT 18620855 TTACACACATAGGCC 1 TTACACACATAGGCC 18620870 TTACACACATAGGCC 1 TTACACACATAGGCC 18620885 T 1 T 18620886 ACTCCCAGGC Statistics Matches: 16, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 15 16 1.00 ACGTcount: A:0.32, C:0.32, G:0.13, T:0.23 Consensus pattern (15 bp): TTACACACATAGGCC Found at i:18625772 original size:43 final size:42 Alignment explanation

Indices: 18625687--18625800 Score: 129 Period size: 43 Copynumber: 2.7 Consensus size: 42 18625677 GATGCTACTA * * * * 18625687 TCCCAGACAGGGTCTTACACGAATCATAATACGATGTCAATG 1 TCCCAGACATGGTCTTACACGAATCACAATACAATGCCAATG * * * 18625729 TCCCAGACATGGTCTTACGCATAATCACACTACAATGCCAATG 1 TCCCAGACATGGTCTTACAC-GAATCACAATACAATGCCAATG * * 18625772 TCCCAGACATGCTCTTACATGTAATCACA 1 TCCCAGACATGGTCTTACACG-AATCACA 18625801 TCTCAATAAC Statistics Matches: 59, Mismatches: 11, Indels: 3 0.81 0.15 0.04 Matches are distributed among these distances: 42 18 0.31 43 41 0.69 ACGTcount: A:0.32, C:0.28, G:0.15, T:0.25 Consensus pattern (42 bp): TCCCAGACATGGTCTTACACGAATCACAATACAATGCCAATG Found at i:18631307 original size:51 final size:51 Alignment explanation

Indices: 18631242--18631339 Score: 144 Period size: 51 Copynumber: 1.9 Consensus size: 51 18631232 GATATATGAG * 18631242 GCATCCGAGCTCGTTGA-ATGGTTCGAGTTCATAATGGATGTGATACATGTA 1 GCATCCGAGCTCGTTGAGA-GGTTCGAGTTCATAATAGATGTGATACATGTA * * * 18631293 GCATCCGAGCTCGTTGAGAGGTTCGAGTTTATTATAGATGTGTTACA 1 GCATCCGAGCTCGTTGAGAGGTTCGAGTTCATAATAGATGTGATACA 18631340 AGTTATAAGG Statistics Matches: 42, Mismatches: 4, Indels: 2 0.88 0.08 0.04 Matches are distributed among these distances: 51 41 0.98 52 1 0.02 ACGTcount: A:0.24, C:0.15, G:0.28, T:0.33 Consensus pattern (51 bp): GCATCCGAGCTCGTTGAGAGGTTCGAGTTCATAATAGATGTGATACATGTA Found at i:18639116 original size:32 final size:32 Alignment explanation

Indices: 18639075--18639138 Score: 128 Period size: 32 Copynumber: 2.0 Consensus size: 32 18639065 TCGTTCTAAG 18639075 ATGTGAAGGGTCATTTGTTGAGTAGAGACAAA 1 ATGTGAAGGGTCATTTGTTGAGTAGAGACAAA 18639107 ATGTGAAGGGTCATTTGTTGAGTAGAGACAAA 1 ATGTGAAGGGTCATTTGTTGAGTAGAGACAAA 18639139 CTCGACAATG Statistics Matches: 32, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 32 32 1.00 ACGTcount: A:0.34, C:0.06, G:0.31, T:0.28 Consensus pattern (32 bp): ATGTGAAGGGTCATTTGTTGAGTAGAGACAAA Found at i:18645018 original size:10 final size:9 Alignment explanation

Indices: 18644996--18645029 Score: 50 Period size: 9 Copynumber: 3.7 Consensus size: 9 18644986 TTCTAAAAAG 18644996 GTTAGACTA 1 GTTAGACTA 18645005 GTTAGACATA 1 GTTAGAC-TA 18645015 GTTAGACTA 1 GTTAGACTA * 18645024 GATAGA 1 GTTAGA 18645030 TATTTGTAGT Statistics Matches: 23, Mismatches: 1, Indels: 2 0.88 0.04 0.08 Matches are distributed among these distances: 9 14 0.61 10 9 0.39 ACGTcount: A:0.38, C:0.09, G:0.24, T:0.29 Consensus pattern (9 bp): GTTAGACTA Found at i:18653357 original size:27 final size:27 Alignment explanation

Indices: 18653320--18653524 Score: 216 Period size: 27 Copynumber: 7.6 Consensus size: 27 18653310 TAAATTGTAC * 18653320 AGCACTAAGTGTGCGATTTGGCTATGT 1 AGCACTAAGTGTGCGATTTGACTATGT * 18653347 AGCACTAAGTGTGCGATTTGACCATGT 1 AGCACTAAGTGTGCGATTTGACTATGT * ** ** 18653374 TGCACTAAGTGTGCGAAATGAAAATG- 1 AGCACTAAGTGTGCGATTTGACTATGT * * 18653400 ATGCACTAAGTGTGCGAATTGACCATG- 1 A-GCACTAAGTGTGCGATTTGACTATGT * * 18653427 CGACACTAAGTGTGCGAGTTGACTATGT 1 AG-CACTAAGTGTGCGATTTGACTATGT * 18653455 AGCACTAAGTGTGCGAGTTTGATTATGT 1 AGCACTAAGTGTGCGA-TTTGACTATGT * * * * 18653483 GGCACTAAGTGTGCGAGTTGATTATAT 1 AGCACTAAGTGTGCGATTTGACTATGT * 18653510 AGCACTGAGTGTGCG 1 AGCACTAAGTGTGCG 18653525 GACTTAATAT Statistics Matches: 152, Mismatches: 22, Indels: 8 0.84 0.12 0.04 Matches are distributed among these distances: 26 1 0.01 27 126 0.83 28 25 0.16 ACGTcount: A:0.27, C:0.15, G:0.29, T:0.29 Consensus pattern (27 bp): AGCACTAAGTGTGCGATTTGACTATGT Found at i:18653381 original size:54 final size:54 Alignment explanation

Indices: 18653321--18653524 Score: 241 Period size: 54 Copynumber: 3.8 Consensus size: 54 18653311 AAATTGTACA * * * 18653321 GCACTAAGTGTGCGATTTGGCTATGTAGCACTAAGTGTGCGATTTGACCATGTT 1 GCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGATTTGACCATGTC ** ** * 18653375 GCACTAAGTGTGCGAAATGAAAATG-ATGCACTAAGTGTGCGAATTGACCATG-C 1 GCACTAAGTGTGCGAGTTGACTATGTA-GCACTAAGTGTGCGATTTGACCATGTC ** * 18653428 GACACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGATTATGTG 1 G-CACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGA-TTTGACCATGTC * * * 18653484 GCACTAAGTGTGCGAGTTGATTATATAGCACTGAGTGTGCG 1 GCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCG 18653525 GACTTAATAT Statistics Matches: 127, Mismatches: 18, Indels: 9 0.82 0.12 0.06 Matches are distributed among these distances: 53 2 0.02 54 79 0.62 55 45 0.35 56 1 0.01 ACGTcount: A:0.26, C:0.15, G:0.29, T:0.29 Consensus pattern (54 bp): GCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGATTTGACCATGTC Found at i:18661418 original size:27 final size:27 Alignment explanation

Indices: 18661381--18661585 Score: 223 Period size: 27 Copynumber: 7.6 Consensus size: 27 18661371 TAAATTGTAC * 18661381 AGCACTAAGTGTGCGATTTGGCTATGT 1 AGCACTAAGTGTGCGATTTGACTATGT * 18661408 AGCACTAAGTGTGCGATTTGACCATGT 1 AGCACTAAGTGTGCGATTTGACTATGT * ** ** 18661435 TGCACTAAGTGTGCGAAATGAAAATG- 1 AGCACTAAGTGTGCGATTTGACTATGT * * * 18661461 ATGCACTAAGTGTGCGAATTGACCATGC 1 A-GCACTAAGTGTGCGATTTGACTATGT * * 18661489 GGCACTAAGTGTGCGAGTTGACTATGT 1 AGCACTAAGTGTGCGATTTGACTATGT * 18661516 AGCACTAAGTGTGCGAGTTTGATTATGT 1 AGCACTAAGTGTGCGA-TTTGACTATGT * * * * 18661544 GGCACTAAGTGTGCGAGTTGATTATAT 1 AGCACTAAGTGTGCGATTTGACTATGT * 18661571 AGCACTGAGTGTGCG 1 AGCACTAAGTGTGCG 18661586 GACTTAATAT Statistics Matches: 152, Mismatches: 23, Indels: 6 0.84 0.13 0.03 Matches are distributed among these distances: 27 128 0.84 28 24 0.16 ACGTcount: A:0.26, C:0.15, G:0.29, T:0.29 Consensus pattern (27 bp): AGCACTAAGTGTGCGATTTGACTATGT Found at i:18661442 original size:54 final size:54 Alignment explanation

Indices: 18661382--18661585 Score: 257 Period size: 54 Copynumber: 3.8 Consensus size: 54 18661372 AAATTGTACA * * * 18661382 GCACTAAGTGTGCGATTTGGCTATGTAGCACTAAGTGTGCGATTTGACCATGTT 1 GCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGATTTGACCATGTG ** ** * * 18661436 GCACTAAGTGTGCGAAATGAAAATG-ATGCACTAAGTGTGCGAATTGACCATGCG 1 GCACTAAGTGTGCGAGTTGACTATGTA-GCACTAAGTGTGCGATTTGACCATGTG ** 18661490 GCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGATTATGTG 1 GCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGA-TTTGACCATGTG * * * 18661545 GCACTAAGTGTGCGAGTTGATTATATAGCACTGAGTGTGCG 1 GCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCG 18661586 GACTTAATAT Statistics Matches: 128, Mismatches: 19, Indels: 5 0.84 0.12 0.03 Matches are distributed among these distances: 53 1 0.01 54 80 0.62 55 47 0.37 ACGTcount: A:0.26, C:0.15, G:0.29, T:0.29 Consensus pattern (54 bp): GCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGATTTGACCATGTG Found at i:18664288 original size:20 final size:18 Alignment explanation

Indices: 18664265--18664301 Score: 56 Period size: 20 Copynumber: 1.9 Consensus size: 18 18664255 ACCTAACATG 18664265 AATTAAATCTAAATCATATT 1 AATTAAAT-TAAA-CATATT 18664285 AATTAAATTAAACATAT 1 AATTAAATTAAACATAT 18664302 CAACATAAAA Statistics Matches: 17, Mismatches: 0, Indels: 2 0.89 0.00 0.11 Matches are distributed among these distances: 18 5 0.29 19 4 0.24 20 8 0.47 ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38 Consensus pattern (18 bp): AATTAAATTAAACATATT Found at i:18667895 original size:16 final size:15 Alignment explanation

Indices: 18667869--18667898 Score: 51 Period size: 16 Copynumber: 1.9 Consensus size: 15 18667859 AACTATTTTA 18667869 TTACAAATTTCACTC 1 TTACAAATTTCACTC 18667884 TTACATAATTTCACT 1 TTACA-AATTTCACT 18667899 TACTCCATTC Statistics Matches: 14, Mismatches: 0, Indels: 1 0.93 0.00 0.07 Matches are distributed among these distances: 15 5 0.36 16 9 0.64 ACGTcount: A:0.33, C:0.23, G:0.00, T:0.43 Consensus pattern (15 bp): TTACAAATTTCACTC Found at i:18668210 original size:50 final size:50 Alignment explanation

Indices: 18668112--18668382 Score: 206 Period size: 50 Copynumber: 5.4 Consensus size: 50 18668102 GTACGCATAG * * * ** 18668112 CTGCACTTAGTACTACACATGCGACC-AACAATCTGGTACATGTAGTAGC 1 CTGCACTTAGTACTACACACGTGACCTAACCATCTGGTACACATAGTAGC * * * ** 18668161 CTGCACTTAGTATTACACACGTGACCTGACCATCTGATACATGTAGTAGC 1 CTGCACTTAGTACTACACACGTGACCTAACCATCTGGTACACATAGTAGC * * * ** * * * * 18668211 CTGCACTTACTATTACACAAGTGATCGGAACTATCAGCTACGCATAGTAGC 1 CTGCACTTAGTACTACACACGTGA-CCTAACCATCTGGTACACATAGTAGC * * * 18668262 CTGCACCTAGTAC-A-ACGCGTGCGACCTAACCATCTGGTACACATAGTAGT 1 CTGCACTTAGTACTACACACGT--GACCTAACCATCTGGTACACATAGTAGC * * *** * 18668312 CTGCACTTAGTACTACACAGGTGACCTAAAACCATTTTAAACACACAGTAGC 1 CTGCACTTAGTACTACACACGTGACCT--AACCATCTGGTACACATAGTAGC * * 18668364 CTGTACATAGTACTACACA 1 CTGCACTTAGTACTACACA 18668383 TGTGGTCTCA Statistics Matches: 174, Mismatches: 40, Indels: 13 0.77 0.18 0.06 Matches are distributed among these distances: 49 27 0.16 50 79 0.45 51 30 0.17 52 38 0.22 ACGTcount: A:0.31, C:0.27, G:0.17, T:0.25 Consensus pattern (50 bp): CTGCACTTAGTACTACACACGTGACCTAACCATCTGGTACACATAGTAGC Found at i:18670425 original size:340 final size:341 Alignment explanation

Indices: 18669803--18670489 Score: 1162 Period size: 340 Copynumber: 2.0 Consensus size: 341 18669793 CCATAAAAAT * * * * * 18669803 ATAATAAAAATAAATTTTAATGTGTCGAATTTGTGGTCCCAAAACCACTGTTCCGACTAGGTCAT 1 ATAATAAAAACAAATTTTAATGTGTCAAATTTGAGATCCCAAAACCACTGTTCCGACTAGGCCAT * * 18669868 AATTCGGGATGTTACAACTCTCCCCCTTTTAGGGATTTTCGTCCTTGAAAATCTTACCAGAAGAG 66 AATTCGGGATGTTACAACTCTCCCCCCTTTAAGGATTTTCGTCCTTGAAAATCTTACCAGAAGAG * 18669933 TGGTTCGATTTTCAAATAAACTCCACTATCTCATAATCATTGTTGAATAACTTTTACTCAGGCTA 131 TGGTTCGATTTTCAAATAAACTCCACTATCTCATAATCATTGCTGAATAACTTTTACTCAGGCTA * * 18669998 TGTTTAATACTTAGCTCTTTAATTTCTCATACTAAAGTCATGAACAATTCCGTGTTATACGACGC 196 TGTTTAATACTTAGCTCTTTAATTTCTCATACTAAAGACATGAACAATTCCGTGTTATAAGACGC * * * 18670063 ATCAATTGAATCTTGACTTCTATCAGAGAACTCATGTATACAAGGGTCAAACCCATACCGTCGGA 261 ATCAATCGAATCTTGACTTCTATCAGAGAACTCATGTATACAAGGGTCAAACCCATACCATCAGA 18670128 GAATAAGTATTTACAC 326 GAATAAGTATTTACAC * ** * * 18670144 ATAATAAAAACAAATTTTACTGTGTCAAATTTGAGATCCTGAAACCACTGTTCTGACTAGGCCCT 1 ATAATAAAAACAAATTTTAATGTGTCAAATTTGAGATCCCAAAACCACTGTTCCGACTAGGCCAT 18670209 AATTCGGGATGTTA-AACTCTCCCCCCTTTAAGGATTTTCGTCCTTGAAAATCTTACCAGAAGAG 66 AATTCGGGATGTTACAACTCTCCCCCCTTTAAGGATTTTCGTCCTTGAAAATCTTACCAGAAGAG * * 18670273 TGGTTCGATTTTCACATAAACTCCACTATCTCATAATCATTGCTGAATAACTTTTACTCGGGCTA 131 TGGTTCGATTTTCAAATAAACTCCACTATCTCATAATCATTGCTGAATAACTTTTACTCAGGCTA * 18670338 TGTTTAATACTTAGCTCTTTAATTTCTCATGCTAAAGACATGAACAATTCCGTGTTATAAGACGC 196 TGTTTAATACTTAGCTCTTTAATTTCTCATACTAAAGACATGAACAATTCCGTGTTATAAGACGC 18670403 ATCAATCGAATCTT-AGCTTCTATCAGAGAACTCATGTATACAAGGGTCAAACCCATACCATCAG 261 ATCAATCGAATCTTGA-CTTCTATCAGAGAACTCATGTATACAAGGGTCAAACCCATACCATCAG 18670467 AGAATAAGTATTTACAC 325 AGAATAAGTATTTACAC 18670484 ATAATA 1 ATAATA 18670490 CTTGAATCCT Statistics Matches: 324, Mismatches: 21, Indels: 3 0.93 0.06 0.01 Matches are distributed among these distances: 339 1 0.00 340 254 0.78 341 69 0.21 ACGTcount: A:0.32, C:0.21, G:0.14, T:0.33 Consensus pattern (341 bp): ATAATAAAAACAAATTTTAATGTGTCAAATTTGAGATCCCAAAACCACTGTTCCGACTAGGCCAT AATTCGGGATGTTACAACTCTCCCCCCTTTAAGGATTTTCGTCCTTGAAAATCTTACCAGAAGAG TGGTTCGATTTTCAAATAAACTCCACTATCTCATAATCATTGCTGAATAACTTTTACTCAGGCTA TGTTTAATACTTAGCTCTTTAATTTCTCATACTAAAGACATGAACAATTCCGTGTTATAAGACGC ATCAATCGAATCTTGACTTCTATCAGAGAACTCATGTATACAAGGGTCAAACCCATACCATCAGA GAATAAGTATTTACAC Found at i:18671728 original size:15 final size:15 Alignment explanation

Indices: 18671694--18671753 Score: 75 Period size: 15 Copynumber: 4.0 Consensus size: 15 18671684 TATAGATAAC * * * 18671694 AAGAAAACCAGGATT 1 AAGAAATCCAAGATA * 18671709 AAGAAGTCCAAGATA 1 AAGAAATCCAAGATA * 18671724 GAGAAATCCAAGATA 1 AAGAAATCCAAGATA 18671739 AAGAAATCCAAGATA 1 AAGAAATCCAAGATA 18671754 CAATATCATA Statistics Matches: 38, Mismatches: 7, Indels: 0 0.84 0.16 0.00 Matches are distributed among these distances: 15 38 1.00 ACGTcount: A:0.55, C:0.13, G:0.18, T:0.13 Consensus pattern (15 bp): AAGAAATCCAAGATA Found at i:18675632 original size:50 final size:50 Alignment explanation

Indices: 18675513--18675790 Score: 256 Period size: 50 Copynumber: 5.5 Consensus size: 50 18675503 CTGGTATGCA * * * 18675513 TAGTAGCCTGCACTTAGTACTACACATGTGACC-AACAATC-CAGTACACG 1 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAACCATCTGA-TACACG * * * * 18675562 TATTAGACTGCACCTAGTACTACACGCGTGACCTAACCATCTGATACACG 1 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAACCATCTGATACACG * * * ** * * ** * 18675612 TAATAGCCTACACTTAGTACTACACACGTGA-TTGAAAATATCAGGTATGCA 1 TAGTAGCCTGCACTTAGTACTACACACGTGACCT--AACCATCTGATACACG * * * 18675663 TAGTAGCCTGCACTTAGTACTACACATGCGACCTAACCATCTGGTACACG 1 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAACCATCTGATACACG * * * * * 18675713 TAGTAGCCTGCACTTAGTACTACACAGGTGACCTAAAACCATTTTAAACACA 1 TAGTAGCCTGCACTTAGTACTACACACGTGACCT--AACCATCTGATACACG * 18675765 TAGTAGCCTGCACATAGTACTACACA 1 TAGTAGCCTGCACTTAGTACTACACA 18675791 TGTGTTCTCA Statistics Matches: 183, Mismatches: 39, Indels: 11 0.79 0.17 0.05 Matches are distributed among these distances: 49 29 0.16 50 80 0.44 51 37 0.20 52 37 0.20 ACGTcount: A:0.33, C:0.27, G:0.16, T:0.24 Consensus pattern (50 bp): TAGTAGCCTGCACTTAGTACTACACACGTGACCTAACCATCTGATACACG Found at i:18681601 original size:14 final size:14 Alignment explanation

Indices: 18681582--18681612 Score: 62 Period size: 14 Copynumber: 2.2 Consensus size: 14 18681572 CAAATCACCA 18681582 GGCCAGTTTGGTTG 1 GGCCAGTTTGGTTG 18681596 GGCCAGTTTGGTTG 1 GGCCAGTTTGGTTG 18681610 GGC 1 GGC 18681613 TAAATGACCT Statistics Matches: 17, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 14 17 1.00 ACGTcount: A:0.06, C:0.16, G:0.45, T:0.32 Consensus pattern (14 bp): GGCCAGTTTGGTTG Found at i:18686620 original size:14 final size:14 Alignment explanation

Indices: 18686601--18686632 Score: 64 Period size: 14 Copynumber: 2.3 Consensus size: 14 18686591 TCAAATCACC 18686601 GGGCCAGTTTGGTT 1 GGGCCAGTTTGGTT 18686615 GGGCCAGTTTGGTT 1 GGGCCAGTTTGGTT 18686629 GGGC 1 GGGC 18686633 TAAATGACCT Statistics Matches: 18, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 14 18 1.00 ACGTcount: A:0.06, C:0.16, G:0.47, T:0.31 Consensus pattern (14 bp): GGGCCAGTTTGGTT Found at i:18687355 original size:23 final size:21 Alignment explanation

Indices: 18687302--18687353 Score: 95 Period size: 21 Copynumber: 2.5 Consensus size: 21 18687292 TTTGTTGGTC * 18687302 AAATTTTATACTTTTGTATAT 1 AAATTTTATACTTTGGTATAT 18687323 AAATTTTATACTTTGGTATAT 1 AAATTTTATACTTTGGTATAT 18687344 AAATTTTATA 1 AAATTTTATA 18687354 TATTTTCGCA Statistics Matches: 30, Mismatches: 1, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 21 30 1.00 ACGTcount: A:0.37, C:0.04, G:0.06, T:0.54 Consensus pattern (21 bp): AAATTTTATACTTTGGTATAT Found at i:18687408 original size:17 final size:16 Alignment explanation

Indices: 18687386--18687439 Score: 58 Period size: 14 Copynumber: 3.4 Consensus size: 16 18687376 AAAATGTACA * 18687386 TATTTTCTTATATTAT 1 TATTTTTTTATATTAT * 18687402 TATTTTTGTA-A-TAT 1 TATTTTTTTATATTAT * 18687416 TATTTGTTTATATTAT 1 TATTTTTTTATATTAT 18687432 ATATTTTT 1 -TATTTTT 18687440 GACTCAATAT Statistics Matches: 30, Mismatches: 5, Indels: 5 0.75 0.12 0.12 Matches are distributed among these distances: 14 11 0.37 15 2 0.07 16 11 0.37 17 6 0.20 ACGTcount: A:0.26, C:0.02, G:0.04, T:0.69 Consensus pattern (16 bp): TATTTTTTTATATTAT Found at i:18688741 original size:10 final size:10 Alignment explanation

Indices: 18688726--18688772 Score: 60 Period size: 10 Copynumber: 4.6 Consensus size: 10 18688716 CTAGGATGTG 18688726 AATTGAATTA 1 AATTGAATTA 18688736 AATTGAATTA 1 AATTGAATTA 18688746 AATTGAATATGA 1 AATTGAAT-T-A * 18688758 AA-TGGATTA 1 AATTGAATTA 18688767 AATTGA 1 AATTGA 18688773 CATCAAATTC Statistics Matches: 32, Mismatches: 2, Indels: 6 0.80 0.05 0.15 Matches are distributed among these distances: 9 3 0.09 10 21 0.66 11 5 0.16 12 3 0.09 ACGTcount: A:0.49, C:0.00, G:0.15, T:0.36 Consensus pattern (10 bp): AATTGAATTA Found at i:18701760 original size:18 final size:18 Alignment explanation

Indices: 18701737--18701773 Score: 74 Period size: 18 Copynumber: 2.1 Consensus size: 18 18701727 CGAGGACGAA 18701737 AATTCTTTAAGGCGGGAG 1 AATTCTTTAAGGCGGGAG 18701755 AATTCTTTAAGGCGGGAG 1 AATTCTTTAAGGCGGGAG 18701773 A 1 A 18701774 GTTGTAACAA Statistics Matches: 19, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 18 19 1.00 ACGTcount: A:0.30, C:0.11, G:0.32, T:0.27 Consensus pattern (18 bp): AATTCTTTAAGGCGGGAG Found at i:18702228 original size:24 final size:24 Alignment explanation

Indices: 18702196--18702245 Score: 91 Period size: 24 Copynumber: 2.1 Consensus size: 24 18702186 AACCCTAGGA 18702196 AAGAGAAAGAAAATTAAGCAAGCC 1 AAGAGAAAGAAAATTAAGCAAGCC * 18702220 AAGAGAAAGAAAATTAAGCATGCC 1 AAGAGAAAGAAAATTAAGCAAGCC 18702244 AA 1 AA 18702246 ATTGGGTAAG Statistics Matches: 25, Mismatches: 1, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 24 25 1.00 ACGTcount: A:0.58, C:0.12, G:0.20, T:0.10 Consensus pattern (24 bp): AAGAGAAAGAAAATTAAGCAAGCC Found at i:18702695 original size:21 final size:20 Alignment explanation

Indices: 18702671--18702709 Score: 60 Period size: 21 Copynumber: 1.9 Consensus size: 20 18702661 TGTGAATTGA 18702671 ATTAAATTGAATATGAAATGG 1 ATTAAATTG-ATATGAAATGG * 18702692 ATTAAATTGATATTAAAT 1 ATTAAATTGATATGAAAT 18702710 TCATTTATAT Statistics Matches: 17, Mismatches: 1, Indels: 1 0.89 0.05 0.05 Matches are distributed among these distances: 20 8 0.47 21 9 0.53 ACGTcount: A:0.49, C:0.00, G:0.13, T:0.38 Consensus pattern (20 bp): ATTAAATTGATATGAAATGG Found at i:18709040 original size:47 final size:47 Alignment explanation

Indices: 18708986--18709389 Score: 657 Period size: 47 Copynumber: 8.6 Consensus size: 47 18708976 TATTTGAATA * 18708986 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG 1 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCGATGTGATG * * 18709033 AATGTGAAAGTGTATATATGTGATAAGGTCGAATGGCCAATGTGATG 1 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCGATGTGATG * * 18709080 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATAGCCGATGTGATG 1 AATGTGAAAGTG--TATATATGTGATAAGGCCGAATGGCCGATGTGATG * 18709129 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG 1 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCGATGTGATG * 18709176 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG 1 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCGATGTGATG * 18709223 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG 1 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCGATGTGATG 18709270 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCC-ATGTGATG 1 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCGATGTGATG * * * * 18709316 AATGTGAAAGTGTATATATGTGATAGGGCCGAGTGGCCAACGTGATG 1 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCGATGTGATG * * 18709363 GATGTGAAAGTGTATAAATGTGATAAG 1 AATGTGAAAGTGTATATATGTGATAAG 18709390 TCCCGAAGGG Statistics Matches: 335, Mismatches: 19, Indels: 6 0.93 0.05 0.02 Matches are distributed among these distances: 46 44 0.13 47 248 0.74 49 43 0.13 ACGTcount: A:0.33, C:0.08, G:0.30, T:0.29 Consensus pattern (47 bp): AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCGATGTGATG Found at i:18709145 original size:143 final size:143 Alignment explanation

Indices: 18708986--18709389 Score: 710 Period size: 143 Copynumber: 2.9 Consensus size: 143 18708976 TATTTGAATA 18708986 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA 1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA * 18709051 TGTGATAAGGTCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAAT 66 TGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAAT 18709116 AGCCGATGTGATG 131 AGCCGATGTGATG 18709129 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA 1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA 18709194 TGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAAT 66 TGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAAT * 18709257 GGCCGATGTGATG 131 AGCCGATGTGATG * 18709270 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCC-ATGTGATGAATGTGAAAGTGTATATA 1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA * * * * 18709334 TGTGATAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGTATA-A-ATGTGATAAG 66 TGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATATGTGATAAG 18709390 TCCCGAAGGG Statistics Matches: 252, Mismatches: 7, Indels: 7 0.95 0.03 0.03 Matches are distributed among these distances: 140 73 0.29 141 72 0.29 142 2 0.01 143 105 0.42 ACGTcount: A:0.33, C:0.08, G:0.30, T:0.29 Consensus pattern (143 bp): AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA TGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAAT AGCCGATGTGATG Found at i:18716114 original size:5 final size:5 Alignment explanation

Indices: 18716104--18716141 Score: 58 Period size: 5 Copynumber: 7.2 Consensus size: 5 18716094 TTGTGTGTTC 18716104 TTTAT TTTATT TTATAT TTTAT TTTAT TTTAT TTTAT T 1 TTTAT TTTA-T TT-TAT TTTAT TTTAT TTTAT TTTAT T 18716142 CACAAATTGG Statistics Matches: 31, Mismatches: 0, Indels: 4 0.89 0.00 0.11 Matches are distributed among these distances: 5 23 0.74 6 6 0.19 7 2 0.06 ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79 Consensus pattern (5 bp): TTTAT Found at i:18720550 original size:5 final size:6 Alignment explanation

Indices: 18720531--18720567 Score: 60 Period size: 6 Copynumber: 6.5 Consensus size: 6 18720521 TTGTGTGTTC 18720531 TTTATT TTTATT TTTATT TTTA-T TTTA-T TTTATT TTT 1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTT 18720568 CTCAGTGTTG Statistics Matches: 30, Mismatches: 0, Indels: 2 0.94 0.00 0.06 Matches are distributed among these distances: 5 10 0.33 6 20 0.67 ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84 Consensus pattern (6 bp): TTTATT Found at i:18723742 original size:21 final size:21 Alignment explanation

Indices: 18723713--18723755 Score: 77 Period size: 21 Copynumber: 2.0 Consensus size: 21 18723703 AGAACATGCC * 18723713 AACAGAAGCTCGTGAGAGCTG 1 AACAAAAGCTCGTGAGAGCTG 18723734 AACAAAAGCTCGTGAGAGCTG 1 AACAAAAGCTCGTGAGAGCTG 18723755 A 1 A 18723756 TCCACCCAAA Statistics Matches: 21, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 21 21 1.00 ACGTcount: A:0.37, C:0.19, G:0.30, T:0.14 Consensus pattern (21 bp): AACAAAAGCTCGTGAGAGCTG Found at i:18735051 original size:46 final size:46 Alignment explanation

Indices: 18734981--18735208 Score: 332 Period size: 46 Copynumber: 5.0 Consensus size: 46 18734971 TTTGACATGA * * * * * * * 18734981 TGCCATAGTGTCTTTCAACTATGGTTTTACTCATTTTC-TGTCATGT 1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGT *** * 18735027 TGCCATGGTATCTTTCAACCATGGTCTTGTTCATTTCATATCACGT 1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT * 18735073 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGC 1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT 18735119 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT 1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT 18735165 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG 1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG 18735209 AGAGCACACT Statistics Matches: 167, Mismatches: 14, Indels: 2 0.91 0.08 0.01 Matches are distributed among these distances: 45 4 0.02 46 163 0.98 ACGTcount: A:0.22, C:0.24, G:0.15, T:0.39 Consensus pattern (46 bp): TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT Found at i:18737977 original size:46 final size:44 Alignment explanation

Indices: 18737866--18737981 Score: 126 Period size: 46 Copynumber: 2.6 Consensus size: 44 18737856 TTACAGATAT 18737866 CATGTCCCAGACATGGTCTTACACTAACACAGCTCGTAGCCGATG 1 CATGTCCCAGACAT-GTCTTACACTAACACAGCTCGTAGCCGATG * * * * ** * 18737911 CATGTCCCAAACAAGCCTTACATTGGCTTACATCTCG-AGCCTGATG 1 CATGTCCCAGACATGTCTTACACTAAC--ACAGCTCGTAGCC-GATG 18737957 CATGTCCCAGACATGTCTTACACTA 1 CATGTCCCAGACATGTCTTACACTA 18737982 GCATACGAAA Statistics Matches: 56, Mismatches: 12, Indels: 5 0.77 0.16 0.07 Matches are distributed among these distances: 44 9 0.16 45 16 0.29 46 31 0.55 ACGTcount: A:0.27, C:0.31, G:0.17, T:0.25 Consensus pattern (44 bp): CATGTCCCAGACATGTCTTACACTAACACAGCTCGTAGCCGATG Found at i:18740006 original size:47 final size:46 Alignment explanation

Indices: 18739936--18740291 Score: 214 Period size: 47 Copynumber: 7.7 Consensus size: 46 18739926 TTTGTGCGCT * * * * 18739936 AGTGTAAG-GCATGTCTCGGACATGCTTCGGCCACATTTTGAGAGCC 1 AGTGTAAGACCATGTCTAGGACATGCATCGGCCACA-TATGAGAGCC * * * * * 18739982 AGTGTAAGACCATGTCTAGTACATGGCATCGG-CATCCAGACGAGGGCT 1 AGTGTAAGACCATGTCTAGGACAT-GCATCGGCCA--CATATGAGAGCC * * * 18740030 AGTGTAAGA-CATGTCTAGGACATGCATCAGCCATACTATGATAGCC 1 AGTGTAAGACCATGTCTAGGACATGCATCGGCCACA-TATGAGAGCC * * * * 18740076 AGTGTAAGACCATGTCTGGGACATGGCATTGG--A-AAATGAGTGCC 1 AGTGTAAGACCATGTCTAGGACAT-GCATCGGCCACATATGAGAGCC * * * 18740120 AGTGTAAGA-CATGTCTGGGACATGCATCGGCCTCGACAGA-GATAGCC 1 AGTGTAAGACCATGTCTAGGACATGCATCGG-C-C-ACATATGAGAGCC * * * * * * * * 18740167 AGTGTAAGA-CGTGTTTGGGACACGCATCGGCTA-AGA-GATGTGCT 1 AGTGTAAGACCATGTCTAGGACATGCATCGGCCACATATGA-GAGCC * * ** * 18740211 AGTGTAAGA-CATGTTTGGGACATGCATTAGCACGCGTATATGAGAGCC 1 AGTGTAAGACCATGTCTAGGACATGCATCGGC-CAC--ATATGAGAGCC 18740259 AGTGTAAGACCATGTCTAGGACATGGCATCGGC 1 AGTGTAAGACCATGTCTAGGACAT-GCATCGGC 18740292 AATATAACCC Statistics Matches: 241, Mismatches: 47, Indels: 40 0.73 0.14 0.12 Matches are distributed among these distances: 42 6 0.02 43 19 0.08 44 46 0.19 45 2 0.01 46 30 0.12 47 75 0.31 48 41 0.17 49 16 0.07 50 6 0.02 ACGTcount: A:0.28, C:0.20, G:0.29, T:0.23 Consensus pattern (46 bp): AGTGTAAGACCATGTCTAGGACATGCATCGGCCACATATGAGAGCC Found at i:18740100 original size:94 final size:91 Alignment explanation

Indices: 18739933--18740292 Score: 333 Period size: 94 Copynumber: 3.9 Consensus size: 91 18739923 TGATTTGTGC * * * * * * * 18739933 GCTAGTGTAAGGCATGTCTCGGACATGCTTCGGCCACATTTTGAGAGCCAGTGTAAGACCATGTC 1 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCCATACTATGAGAGCCAGTGTAAGACCATGTC * * 18739998 TAGTACATGGCATCGGCATCCAGACGAGG 66 TAGGACATGGCATCGGCAT--AGA-GAGT * * 18740027 GCTAGTGTAAGACATGTCTAGGACATGCATCAGCCATACTATGATAGCCAGTGTAAGACCATGTC 1 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCCATACTATGAGAGCCAGTGTAAGACCATGTC * * * 18740092 TGGGACATGGCATTGG-A-AAATGAGT 66 TAGGACATGGCATCGGCATAGA-GAGT * * * 18740117 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCC-TCGAC-A-GAGATAGCCAGTGTAAGA-CG 1 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCCAT--ACTATGAG--AGCCAGTGTAAGACCA * * * 18740178 TGTTTGGGACA-CGCATCGGC-TAAGAGATGT 62 TGTCTAGGACATGGCATCGGCAT-AGAGA-GT * * * 18740208 GCTAGTGTAAGACATGTTTGGGACATGCATTAGCACGCGTA-TATGAGAGCCAGTGTAAGACCAT 1 GCTAGTGTAAGACATGTCTGGGACATGCATCAG--C-CATACTATGAGAGCCAGTGTAAGACCAT 18740272 GTCTAGGACATGGCATCGGCA 63 GTCTAGGACATGGCATCGGCA 18740293 ATATAACCCA Statistics Matches: 218, Mismatches: 31, Indels: 33 0.77 0.11 0.12 Matches are distributed among these distances: 89 9 0.04 90 51 0.23 91 48 0.22 92 13 0.06 93 14 0.06 94 82 0.38 95 1 0.00 ACGTcount: A:0.28, C:0.20, G:0.29, T:0.23 Consensus pattern (91 bp): GCTAGTGTAAGACATGTCTGGGACATGCATCAGCCATACTATGAGAGCCAGTGTAAGACCATGTC TAGGACATGGCATCGGCATAGAGAGT Found at i:18747213 original size:30 final size:30 Alignment explanation

Indices: 18747156--18747213 Score: 98 Period size: 30 Copynumber: 1.9 Consensus size: 30 18747146 TTTTCGAGTA ** 18747156 TAGGGGCAAAATGGTCATTTTGTCAAAGTC 1 TAGGGGCAAAATGGTCATTTTACCAAAGTC 18747186 TAGGGGCAAAATGGTCATTTTACCAAAG 1 TAGGGGCAAAATGGTCATTTTACCAAAG 18747214 ATGTGAATTT Statistics Matches: 26, Mismatches: 2, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 30 26 1.00 ACGTcount: A:0.33, C:0.14, G:0.26, T:0.28 Consensus pattern (30 bp): TAGGGGCAAAATGGTCATTTTACCAAAGTC Found at i:18747624 original size:47 final size:45 Alignment explanation

Indices: 18747556--18747820 Score: 194 Period size: 46 Copynumber: 5.7 Consensus size: 45 18747546 TTTGTGCGCT * * * * 18747556 AGTGTAAGACATGTCTAGGACATGCTTTGGCCACATTATGAGAGCC 1 AGTGTAAGACATGTTTGGGACATGCATCGGCCACA-TATGAGAGCC * * * * 18747602 AGTGTAAGACCATGTTTGGGACATGGCATCGG-CATCCAGACGAGGGCT 1 AGTGTAAGA-CATGTTTGGGACAT-GCATCGGCCA--CATATGAGAGCC * * * 18747650 AGTGTAAGACATGTTTGGGACATGCATCAGCCATACTATGATAGCC 1 AGTGTAAGACATGTTTGGGACATGCATCGGCCACA-TATGAGAGCC * * * * * * * 18747696 AGTGTAAGACGTGTCTGGGACACGCATCGGCTA-AGA-GATGTGCT 1 AGTGTAAGACATGTTTGGGACATGCATCGGCCACATATGA-GAGCC * * * * 18747740 AGTGTAAGACATATCTGGGACATGCATCAGCACGCGTATATGAGAGCC 1 AGTGTAAGACATGTTTGGGACATGCATCGGC-CAC--ATATGAGAGCC * 18747788 AGTGTAAGACCATGTCTGGGACATGGCATCGGC 1 AGTGTAAGA-CATGTTTGGGACAT-GCATCGGC 18747821 AATATAACCC Statistics Matches: 170, Mismatches: 35, Indels: 24 0.74 0.15 0.10 Matches are distributed among these distances: 43 2 0.01 44 30 0.18 45 2 0.01 46 48 0.28 47 30 0.18 48 34 0.20 49 17 0.10 50 7 0.04 ACGTcount: A:0.28, C:0.20, G:0.29, T:0.23 Consensus pattern (45 bp): AGTGTAAGACATGTTTGGGACATGCATCGGCCACATATGAGAGCC Found at i:18752420 original size:15 final size:15 Alignment explanation

Indices: 18752395--18752437 Score: 50 Period size: 15 Copynumber: 2.9 Consensus size: 15 18752385 TTTTCTTTAA * 18752395 AAAATTCTAAAATTT 1 AAAATTTTAAAATTT * * 18752410 ATAATTTTAAATTTT 1 AAAATTTTAAAATTT * 18752425 AAAATTTCAAAAT 1 AAAATTTTAAAAT 18752438 AATATATAAA Statistics Matches: 22, Mismatches: 6, Indels: 0 0.79 0.21 0.00 Matches are distributed among these distances: 15 22 1.00 ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44 Consensus pattern (15 bp): AAAATTTTAAAATTT Found at i:18752590 original size:17 final size:17 Alignment explanation

Indices: 18752564--18752597 Score: 50 Period size: 17 Copynumber: 2.0 Consensus size: 17 18752554 TTTTTTCTAA 18752564 ATATTCTTTACAATTTT 1 ATATTCTTTACAATTTT * * 18752581 ATATTTTTTACAGTTTT 1 ATATTCTTTACAATTTT 18752598 TAGTAATATT Statistics Matches: 15, Mismatches: 2, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 17 15 1.00 ACGTcount: A:0.26, C:0.09, G:0.03, T:0.62 Consensus pattern (17 bp): ATATTCTTTACAATTTT Found at i:18769696 original size:11 final size:11 Alignment explanation

Indices: 18769664--18769697 Score: 50 Period size: 11 Copynumber: 3.1 Consensus size: 11 18769654 CAACAACTGA * 18769664 AAAAAGAAAAA 1 AAAAAGAAAAG 18769675 AAAAAGAAAAG 1 AAAAAGAAAAG * 18769686 AAAGAGAAAAG 1 AAAAAGAAAAG 18769697 A 1 A 18769698 GATAGTGTAT Statistics Matches: 21, Mismatches: 2, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 11 21 1.00 ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00 Consensus pattern (11 bp): AAAAAGAAAAG Found at i:18774547 original size:10 final size:9 Alignment explanation

Indices: 18774534--18774577 Score: 52 Period size: 10 Copynumber: 4.4 Consensus size: 9 18774524 GGAAATTTAT 18774534 AAAAATGATA 1 AAAAAT-ATA 18774544 AAAAGATATA 1 AAAA-ATATA 18774554 GAAAAATAATA 1 -AAAAAT-ATA 18774565 AAAAATATA 1 AAAAATATA 18774574 AAAA 1 AAAA 18774578 TTCTATAACA Statistics Matches: 31, Mismatches: 0, Indels: 7 0.82 0.00 0.18 Matches are distributed among these distances: 9 7 0.23 10 15 0.48 11 9 0.29 ACGTcount: A:0.75, C:0.00, G:0.07, T:0.18 Consensus pattern (9 bp): AAAAATATA Found at i:18774558 original size:21 final size:19 Alignment explanation

Indices: 18774534--18774577 Score: 61 Period size: 21 Copynumber: 2.2 Consensus size: 19 18774524 GGAAATTTAT * 18774534 AAAAATGATAAAAAGATATA 1 AAAAATAATAAAAA-ATATA 18774554 GAAAAATAATAAAAAATATA 1 -AAAAATAATAAAAAATATA 18774574 AAAA 1 AAAA 18774578 TTCTATAACA Statistics Matches: 22, Mismatches: 1, Indels: 2 0.88 0.04 0.08 Matches are distributed among these distances: 19 4 0.18 20 5 0.23 21 13 0.59 ACGTcount: A:0.75, C:0.00, G:0.07, T:0.18 Consensus pattern (19 bp): AAAAATAATAAAAAATATA Found at i:18778063 original size:30 final size:30 Alignment explanation

Indices: 18778029--18778091 Score: 108 Period size: 30 Copynumber: 2.1 Consensus size: 30 18778019 ACTTAACAAG * 18778029 CAAATGTCTCTAAAATAATAACAAAATTAA 1 CAAATGACTCTAAAATAATAACAAAATTAA * 18778059 CAAATGACTTTAAAATAATAACAAAATTAA 1 CAAATGACTCTAAAATAATAACAAAATTAA 18778089 CAA 1 CAA 18778092 TAAAATAAGT Statistics Matches: 31, Mismatches: 2, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 30 31 1.00 ACGTcount: A:0.59, C:0.13, G:0.03, T:0.25 Consensus pattern (30 bp): CAAATGACTCTAAAATAATAACAAAATTAA Found at i:18780477 original size:21 final size:22 Alignment explanation

Indices: 18780444--18780484 Score: 57 Period size: 21 Copynumber: 1.9 Consensus size: 22 18780434 TTCCTTTATG * 18780444 TTTCATTGGCACATA-ATCATA 1 TTTCATTGCCACATACATCATA * 18780465 TTTCATTTCCACATACATCA 1 TTTCATTGCCACATACATCA 18780485 CAATACATTC Statistics Matches: 17, Mismatches: 2, Indels: 1 0.85 0.10 0.05 Matches are distributed among these distances: 21 13 0.76 22 4 0.24 ACGTcount: A:0.32, C:0.24, G:0.05, T:0.39 Consensus pattern (22 bp): TTTCATTGCCACATACATCATA Found at i:18786282 original size:26 final size:26 Alignment explanation

Indices: 18786252--18786305 Score: 108 Period size: 26 Copynumber: 2.1 Consensus size: 26 18786242 ATGGGAATAG 18786252 TTCAAATTTAGAATATTGATGTTAGA 1 TTCAAATTTAGAATATTGATGTTAGA 18786278 TTCAAATTTAGAATATTGATGTTAGA 1 TTCAAATTTAGAATATTGATGTTAGA 18786304 TT 1 TT 18786306 TACAAAAGTT Statistics Matches: 28, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 26 28 1.00 ACGTcount: A:0.37, C:0.04, G:0.15, T:0.44 Consensus pattern (26 bp): TTCAAATTTAGAATATTGATGTTAGA Found at i:18790226 original size:45 final size:45 Alignment explanation

Indices: 18790143--18790228 Score: 111 Period size: 45 Copynumber: 1.9 Consensus size: 45 18790133 TTTCAATTCT * * * 18790143 TAATTTAACAATATTCCATTTCTCAACAATATATTAAATACTTAA 1 TAATTTAACAACATACCATTTCTCAACAATATACTAAATACTTAA * * 18790188 TAATTTAACAACATACTATTTTTCAACAA-AGTACTAAATAC 1 TAATTTAACAACATACCATTTCTCAACAATA-TACTAAATAC 18790229 ATATTAACAT Statistics Matches: 35, Mismatches: 5, Indels: 2 0.83 0.12 0.05 Matches are distributed among these distances: 44 1 0.03 45 34 0.97 ACGTcount: A:0.45, C:0.16, G:0.01, T:0.37 Consensus pattern (45 bp): TAATTTAACAACATACCATTTCTCAACAATATACTAAATACTTAA Found at i:18797828 original size:25 final size:26 Alignment explanation

Indices: 18797800--18797864 Score: 66 Period size: 25 Copynumber: 2.6 Consensus size: 26 18797790 CAATTTATAG 18797800 CTCGTGAGAGCATACT-GA-TCTACAA 1 CTCGTGAGAGCATACTCGATTC-ACAA * * 18797825 CTCGAGTGAGCATA-TCGATTCACAA 1 CTCGTGAGAGCATACTCGATTCACAA 18797850 CTCGT-ATGAGCATAC 1 CTCGTGA-GAGCATAC 18797865 ATGTACATGA Statistics Matches: 32, Mismatches: 4, Indels: 7 0.74 0.09 0.16 Matches are distributed among these distances: 24 1 0.03 25 29 0.91 26 2 0.06 ACGTcount: A:0.31, C:0.25, G:0.20, T:0.25 Consensus pattern (26 bp): CTCGTGAGAGCATACTCGATTCACAA Found at i:18801545 original size:3 final size:3 Alignment explanation

Indices: 18801531--18801599 Score: 52 Period size: 3 Copynumber: 22.7 Consensus size: 3 18801521 AAATAAATGA * * * 18801531 AAT AAT AGT AAT AAT AAT AAT AAT AAT ACA- AGT AAA AAT AAAT AAT 1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT -AAT AAT * * 18801577 -TT AAT TAT AAT AAT AAAT AAT AA 1 AAT AAT AAT AAT AAT -AAT AAT AA 18801600 ATGAATTATG Statistics Matches: 51, Mismatches: 10, Indels: 10 0.72 0.14 0.14 Matches are distributed among these distances: 2 1 0.02 3 43 0.84 4 7 0.14 ACGTcount: A:0.64, C:0.01, G:0.03, T:0.32 Consensus pattern (3 bp): AAT Found at i:18801608 original size:24 final size:23 Alignment explanation

Indices: 18801508--18801601 Score: 72 Period size: 25 Copynumber: 4.0 Consensus size: 23 18801498 GTACAATTTG * 18801508 TAATAAAATATATAAATAAATGAAA 1 TAATATAATA-ATAAATAAAT-AAA 18801533 TAATAGTAATAAT-AAT-AAT-AA 1 TAATA-TAATAATAAATAAATAAA * * 18801554 TAATACAAGTAA-AAATAAATAATT 1 TAATATAA-TAATAAATAAATAA-A 18801578 TAATTATAATAATAAAT-AATAAA 1 TAA-TATAATAATAAATAAATAAA 18801601 T 1 T 18801602 GAATTATGCT Statistics Matches: 56, Mismatches: 5, Indels: 18 0.71 0.06 0.23 Matches are distributed among these distances: 20 2 0.04 21 13 0.23 22 3 0.05 23 5 0.09 24 14 0.25 25 15 0.27 26 4 0.07 ACGTcount: A:0.64, C:0.01, G:0.03, T:0.32 Consensus pattern (23 bp): TAATATAATAATAAATAAATAAA Found at i:18802397 original size:22 final size:22 Alignment explanation

Indices: 18802367--18802408 Score: 59 Period size: 22 Copynumber: 1.9 Consensus size: 22 18802357 CGCTCTGATT 18802367 ATTAACACAT-TAGTGCTCTCCA 1 ATTAACACATGT-GTGCTCTCCA * 18802389 ATTAGCACATGTGTGCTCTC 1 ATTAACACATGTGTGCTCTC 18802409 TGTTTATCTG Statistics Matches: 18, Mismatches: 1, Indels: 2 0.86 0.05 0.10 Matches are distributed among these distances: 22 17 0.94 23 1 0.06 ACGTcount: A:0.26, C:0.26, G:0.14, T:0.33 Consensus pattern (22 bp): ATTAACACATGTGTGCTCTCCA Found at i:18807516 original size:13 final size:13 Alignment explanation

Indices: 18807478--18807516 Score: 51 Period size: 13 Copynumber: 3.0 Consensus size: 13 18807468 AACTTTGTAA 18807478 AAAATATTTTAAT 1 AAAATATTTTAAT * * * 18807491 ACAATAATATAAT 1 AAAATATTTTAAT 18807504 AAAATATTTTAAT 1 AAAATATTTTAAT 18807517 TTTATGAAAT Statistics Matches: 20, Mismatches: 6, Indels: 0 0.77 0.23 0.00 Matches are distributed among these distances: 13 20 1.00 ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41 Consensus pattern (13 bp): AAAATATTTTAAT Found at i:18807888 original size:61 final size:61 Alignment explanation

Indices: 18807818--18807941 Score: 212 Period size: 61 Copynumber: 2.0 Consensus size: 61 18807808 GGTCAGATTG * * * 18807818 TGGTAACATGTTGTGTACTTCATAGCTTCACTTGTTAGTAGAATTGGGATGACCCATACTT 1 TGGTAACATGTTGTATACTTCATAGCGTCACTTGTTAGTAGAATTGGAATGACCCATACTT * 18807879 TGGTAACATGTTGTATACTTCATAGCGTCACTTGTTAGTAGAATTGGAATGACCTATACTT 1 TGGTAACATGTTGTATACTTCATAGCGTCACTTGTTAGTAGAATTGGAATGACCCATACTT 18807940 TG 1 TG 18807942 AAGAGTACAA Statistics Matches: 59, Mismatches: 4, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 61 59 1.00 ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38 Consensus pattern (61 bp): TGGTAACATGTTGTATACTTCATAGCGTCACTTGTTAGTAGAATTGGAATGACCCATACTT Found at i:18809244 original size:28 final size:28 Alignment explanation

Indices: 18809200--18809254 Score: 76 Period size: 28 Copynumber: 2.0 Consensus size: 28 18809190 CCAAACAATA * 18809200 TTTTCTTTTAATTTTTTTATTCTTTTAC 1 TTTTCTTTTAATCTTTTTATTCTTTTAC * 18809228 TTTTACTTTTAA-CTTTTTATTTTTTTA 1 TTTT-CTTTTAATCTTTTTATTCTTTTA 18809255 TTTAATTTTA Statistics Matches: 24, Mismatches: 2, Indels: 2 0.86 0.07 0.07 Matches are distributed among these distances: 28 17 0.71 29 7 0.29 ACGTcount: A:0.16, C:0.09, G:0.00, T:0.75 Consensus pattern (28 bp): TTTTCTTTTAATCTTTTTATTCTTTTAC Found at i:18822234 original size:11 final size:11 Alignment explanation

Indices: 18822206--18822242 Score: 58 Period size: 11 Copynumber: 3.4 Consensus size: 11 18822196 ATAGAAAGTC 18822206 TTATTTT-ATT 1 TTATTTTGATT 18822216 TTATTTTTGATT 1 TTA-TTTTGATT 18822228 TTATTTTGATT 1 TTATTTTGATT 18822239 TTAT 1 TTAT 18822243 GTTAAATTAG Statistics Matches: 25, Mismatches: 0, Indels: 3 0.89 0.00 0.11 Matches are distributed among these distances: 10 3 0.12 11 16 0.64 12 6 0.24 ACGTcount: A:0.19, C:0.00, G:0.05, T:0.76 Consensus pattern (11 bp): TTATTTTGATT Found at i:18823096 original size:17 final size:18 Alignment explanation

Indices: 18823074--18823108 Score: 54 Period size: 17 Copynumber: 2.0 Consensus size: 18 18823064 AAAATTCTGA 18823074 ATTTATTTCCAAT-TTAC 1 ATTTATTTCCAATATTAC * 18823091 ATTTATTTTCAATATTAC 1 ATTTATTTCCAATATTAC 18823109 TCAATTGTTT Statistics Matches: 16, Mismatches: 1, Indels: 1 0.89 0.06 0.06 Matches are distributed among these distances: 17 12 0.75 18 4 0.25 ACGTcount: A:0.31, C:0.14, G:0.00, T:0.54 Consensus pattern (18 bp): ATTTATTTCCAATATTAC Found at i:18824900 original size:18 final size:18 Alignment explanation

Indices: 18824877--18824912 Score: 63 Period size: 18 Copynumber: 2.0 Consensus size: 18 18824867 ATTTTACTTT * 18824877 TATTTTATTTTACCAATG 1 TATTTTATTTTAACAATG 18824895 TATTTTATTTTAACAATG 1 TATTTTATTTTAACAATG 18824913 ATTCGAGTTA Statistics Matches: 17, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 18 17 1.00 ACGTcount: A:0.31, C:0.08, G:0.06, T:0.56 Consensus pattern (18 bp): TATTTTATTTTAACAATG Found at i:18836001 original size:16 final size:16 Alignment explanation

Indices: 18835982--18836014 Score: 66 Period size: 16 Copynumber: 2.1 Consensus size: 16 18835972 GGCCCGTGTC 18835982 CTTCACACGGCGATGA 1 CTTCACACGGCGATGA 18835998 CTTCACACGGCGATGA 1 CTTCACACGGCGATGA 18836014 C 1 C 18836015 ACGTCCTTGT 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:0.24, C:0.33, G:0.24, T:0.18 Consensus pattern (16 bp): CTTCACACGGCGATGA Found at i:18837213 original size:46 final size:45 Alignment explanation

Indices: 18837114--18837236 Score: 149 Period size: 46 Copynumber: 2.7 Consensus size: 45 18837104 ATATCCCGAG * * * 18837114 GCCGATGCATGTCCCAGACATGTCTTACATTAGCTCTCATCTCAAT 1 GCCGATGCATGTCCCAGACATGTCTTACACTAGCACTCATAT-AAT * 18837160 GCCGATGCATGTCCCAGACATGTCTTACACTAGCACTCATGAT-GT 1 GCCGATGCATGTCCCAGACATGTCTTACACTAGCACTCAT-ATAAT * * * 18837205 GGCTGATGCATGTCTCAGGCATGTCTTACACT 1 -GCCGATGCATGTCCCAGACATGTCTTACACT 18837237 GGCTCACATA Statistics Matches: 68, Mismatches: 7, Indels: 4 0.86 0.09 0.05 Matches are distributed among these distances: 45 1 0.01 46 66 0.97 47 1 0.01 ACGTcount: A:0.23, C:0.28, G:0.20, T:0.29 Consensus pattern (45 bp): GCCGATGCATGTCCCAGACATGTCTTACACTAGCACTCATATAAT Found at i:18839059 original size:20 final size:20 Alignment explanation

Indices: 18839034--18839074 Score: 57 Period size: 20 Copynumber: 2.0 Consensus size: 20 18839024 TAACGATTGA * 18839034 TATC-AAGATTTTGACAAGAT 1 TATCAAAGATTTAGA-AAGAT 18839054 TATCAAAGATTTAGAAAGAT 1 TATCAAAGATTTAGAAAGAT 18839074 T 1 T 18839075 TGAAGAAATT Statistics Matches: 19, Mismatches: 1, Indels: 2 0.86 0.05 0.09 Matches are distributed among these distances: 20 10 0.53 21 9 0.47 ACGTcount: A:0.44, C:0.07, G:0.15, T:0.34 Consensus pattern (20 bp): TATCAAAGATTTAGAAAGAT Found at i:18840455 original size:14 final size:14 Alignment explanation

Indices: 18840429--18840456 Score: 56 Period size: 14 Copynumber: 2.0 Consensus size: 14 18840419 TTAATTTTAC 18840429 TTTGGATTTTTTTT 1 TTTGGATTTTTTTT 18840443 TTTGGATTTTTTTT 1 TTTGGATTTTTTTT 18840457 GTTCTTAAAC Statistics Matches: 14, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 14 14 1.00 ACGTcount: A:0.07, C:0.00, G:0.14, T:0.79 Consensus pattern (14 bp): TTTGGATTTTTTTT Found at i:18847439 original size:40 final size:40 Alignment explanation

Indices: 18847376--18847468 Score: 127 Period size: 40 Copynumber: 2.4 Consensus size: 40 18847366 ATCTCTGTCT * * * 18847376 AACCCAACACACC-A-TGTGAGGATAAAATCGACCCACCC 1 AACCCTACACACCAAGTATGAGGATAAAATCAACCCACCC * * 18847414 AGCCCTACACACCAAGTATGAGGATAAAATCAACCCATCC 1 AACCCTACACACCAAGTATGAGGATAAAATCAACCCACCC 18847454 AACCCTACACACCAA 1 AACCCTACACACCAA 18847469 ATGGTACCGT Statistics Matches: 47, Mismatches: 6, Indels: 2 0.85 0.11 0.04 Matches are distributed among these distances: 38 11 0.23 39 1 0.02 40 35 0.74 ACGTcount: A:0.41, C:0.37, G:0.11, T:0.12 Consensus pattern (40 bp): AACCCTACACACCAAGTATGAGGATAAAATCAACCCACCC Found at i:18860382 original size:17 final size:16 Alignment explanation

Indices: 18860363--18860412 Score: 55 Period size: 18 Copynumber: 2.9 Consensus size: 16 18860353 TTTTTTTATT 18860363 TTTTATATTTAATTAC 1 TTTTATATTTAATTAC * 18860379 TTTTATTGTTTAATTAC 1 TTTTA-TATTTAATTAC * 18860396 ATTTAATGATTTAATTA 1 -TTTTAT-ATTTAATTA 18860413 ATTATCGCTT Statistics Matches: 28, Mismatches: 3, Indels: 4 0.80 0.09 0.11 Matches are distributed among these distances: 16 5 0.18 17 11 0.39 18 12 0.43 ACGTcount: A:0.32, C:0.04, G:0.04, T:0.60 Consensus pattern (16 bp): TTTTATATTTAATTAC Found at i:18860410 original size:18 final size:18 Alignment explanation

Indices: 18860369--18860412 Score: 63 Period size: 17 Copynumber: 2.5 Consensus size: 18 18860359 TATTTTTTAT * * 18860369 ATTTAATTACTTTTATTG 1 ATTTAATTACATTTAATG 18860387 -TTTAATTACATTTAATG 1 ATTTAATTACATTTAATG 18860404 ATTTAATTA 1 ATTTAATTA 18860413 ATTATCGCTT Statistics Matches: 23, Mismatches: 2, Indels: 2 0.85 0.07 0.07 Matches are distributed among these distances: 17 15 0.65 18 8 0.35 ACGTcount: A:0.34, C:0.05, G:0.05, T:0.57 Consensus pattern (18 bp): ATTTAATTACATTTAATG Found at i:18861445 original size:17 final size:16 Alignment explanation

Indices: 18861425--18861498 Score: 55 Period size: 17 Copynumber: 4.6 Consensus size: 16 18861415 ATAGATTAAT 18861425 TTATATTTTATGTATCA 1 TTATATTTTAT-TATCA ** 18861442 TTATATTAAATTAT-- 1 TTATATTTTATTATCA * * * 18861456 TTAAACTTTATTTATTA 1 TTATATTTTA-TTATCA 18861473 TTATATTTTATATATCA 1 TTATATTTTAT-TATCA 18861490 TTA-ATTTTA 1 TTATATTTTA 18861499 CAAATGATTT Statistics Matches: 44, Mismatches: 9, Indels: 9 0.71 0.15 0.15 Matches are distributed among these distances: 14 6 0.14 15 4 0.09 16 10 0.23 17 24 0.55 ACGTcount: A:0.35, C:0.04, G:0.01, T:0.59 Consensus pattern (16 bp): TTATATTTTATTATCA Found at i:18875200 original size:24 final size:25 Alignment explanation

Indices: 18875173--18875221 Score: 64 Period size: 25 Copynumber: 2.0 Consensus size: 25 18875163 TTTTTTTTAT * 18875173 TAAATAAAAAAC-TTTAAAATATAA 1 TAAATAAAAAACATTTAAAACATAA * * 18875197 TAAATCAAATACATTTAAAACATAA 1 TAAATAAAAAACATTTAAAACATAA 18875222 AAACAAATAT Statistics Matches: 21, Mismatches: 3, Indels: 1 0.84 0.12 0.04 Matches are distributed among these distances: 24 10 0.48 25 11 0.52 ACGTcount: A:0.63, C:0.08, G:0.00, T:0.29 Consensus pattern (25 bp): TAAATAAAAAACATTTAAAACATAA Found at i:18875214 original size:25 final size:23 Alignment explanation

Indices: 18875185--18875249 Score: 75 Period size: 25 Copynumber: 2.9 Consensus size: 23 18875175 AATAAAAAAC * 18875185 TTTAAAATATAATAAATCAAATACA 1 TTTAAAACATAA-AAA-CAAATACA 18875210 TTTAAAACATAAAAACAAAT--A 1 TTTAAAACATAAAAACAAATACA 18875231 -TTAAAACA-AAAAACAAATA 1 TTTAAAACATAAAAACAAATA 18875250 AGAAATAAGA Statistics Matches: 38, Mismatches: 1, Indels: 7 0.83 0.02 0.15 Matches are distributed among these distances: 19 10 0.26 20 8 0.21 21 1 0.03 23 5 0.13 24 3 0.08 25 11 0.29 ACGTcount: A:0.66, C:0.09, G:0.00, T:0.25 Consensus pattern (23 bp): TTTAAAACATAAAAACAAATACA Found at i:18875244 original size:19 final size:20 Alignment explanation

Indices: 18875211--18875249 Score: 71 Period size: 19 Copynumber: 2.0 Consensus size: 20 18875201 TCAAATACAT 18875211 TTAAAACATAAAAACAAATA 1 TTAAAACATAAAAACAAATA 18875231 TTAAAACA-AAAAACAAATA 1 TTAAAACATAAAAACAAATA 18875250 AGAAATAAGA Statistics Matches: 19, Mismatches: 0, Indels: 1 0.95 0.00 0.05 Matches are distributed among these distances: 19 11 0.58 20 8 0.42 ACGTcount: A:0.72, C:0.10, G:0.00, T:0.18 Consensus pattern (20 bp): TTAAAACATAAAAACAAATA Done.