Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Chr14

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: 244914714
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.31

Warning! 4503000 characters in sequence are not A, C, G, or T


File 646 of 770

Found at i:203039367 original size:40 final size:40

Alignment explanation

Indices: 203039282--203039432 Score: 134 Period size: 40 Copynumber: 3.8 Consensus size: 40 203039272 AATTGAATGA * * * 203039282 TATCCGGGCTAA-ATCCCGAAGACAATTATGCTG-GAAATTA- 1 TATCCGGGCTAAGA-CCCGAAGGCAATTGTGC-GAGACA-TAC * * * 203039322 TATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGC-TAC 1 TATCCGGGCTAAGACCCGAAGGCAATTGTGC--GAGACATAC * 203039363 -ATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGACATTC 1 TATCCGGGCTAAGACCCGAAGGCAATT-GTGCGAGACATAC * 203039402 TATCCGGGCTAAGACCCGAAGGCATTTGTGC 1 TATCCGGGCTAAGACCCGAAGGCAATTGTGC 203039433 ACATGGTTAT Statistics Matches: 92, Mismatches: 11, Indels: 16 0.77 0.09 0.13 Matches are distributed among these distances: 38 3 0.03 39 5 0.05 40 79 0.86 41 4 0.04 42 1 0.01 ACGTcount: A:0.27, C:0.24, G:0.26, T:0.23 Consensus pattern (40 bp): TATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGACATAC Found at i:203039446 original size:40 final size:40 Alignment explanation

Indices: 203039319--203039448 Score: 138 Period size: 40 Copynumber: 3.2 Consensus size: 40 203039309 ATGCTGGAAA * * * * 203039319 TTATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGG 1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATGG * * * ** 203039359 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGA-CA 1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-ATGG * 203039399 TTCTATCCGGGCTAAGACCCGAAGGCATTTGTGC-ACATGG 1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-ATGG 203039439 TTATATCCGG 1 TTATATCCGG 203039449 TTATATTCCG Statistics Matches: 71, Mismatches: 17, Indels: 4 0.77 0.18 0.04 Matches are distributed among these distances: 39 2 0.03 40 69 0.97 ACGTcount: A:0.25, C:0.24, G:0.28, T:0.24 Consensus pattern (40 bp): TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATGG Found at i:203045478 original size:28 final size:28 Alignment explanation

Indices: 203045413--203045513 Score: 114 Period size: 28 Copynumber: 3.5 Consensus size: 28 203045403 TATAGTGATC * 203045413 CGCACACTTAGTGCTATATGTATTC-AACT 1 CGCACACTTAGTGCTATA--TAATCAAACT 203045442 CGCACACTTAGTGCTATATAATCAAACT 1 CGCACACTTAGTGCTATATAATCAAACT * * * * 203045470 CGCACACTTAGTGCTGTACAATTTTAAACC 1 CGCACACTTAGTGCTATATAA--TCAAACT 203045500 CGCACACTTAGTGC 1 CGCACACTTAGTGC 203045514 CAATCTTGTC Statistics Matches: 64, Mismatches: 5, Indels: 5 0.86 0.07 0.07 Matches are distributed among these distances: 27 4 0.06 28 23 0.36 29 18 0.28 30 19 0.30 ACGTcount: A:0.30, C:0.27, G:0.14, T:0.30 Consensus pattern (28 bp): CGCACACTTAGTGCTATATAATCAAACT Found at i:203050240 original size:30 final size:30 Alignment explanation

Indices: 203050206--203050266 Score: 77 Period size: 30 Copynumber: 2.0 Consensus size: 30 203050196 TCCTTAACTC 203050206 AAACTTTGGAAAAATTACAATTTTGCCCCT 1 AAACTTTGGAAAAATTACAATTTTGCCCCT * * * * * 203050236 AAACTTTTGCATATTTACACTTTTGCCCCT 1 AAACTTTGGAAAAATTACAATTTTGCCCCT 203050266 A 1 A 203050267 GGCTCGGGAA Statistics Matches: 26, Mismatches: 5, Indels: 0 0.84 0.16 0.00 Matches are distributed among these distances: 30 26 1.00 ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38 Consensus pattern (30 bp): AAACTTTGGAAAAATTACAATTTTGCCCCT Found at i:203051957 original size:93 final size:93 Alignment explanation

Indices: 203051845--203052016 Score: 317 Period size: 93 Copynumber: 1.8 Consensus size: 93 203051835 GCCCATAAGT * * 203051845 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA 1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA 203051910 CGAGTTCGGATGCCTAGTTACATCTCAC 66 CGAGTTCGGATGCCTAGTTACATCTCAC * 203051938 GAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA 1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA 203052003 CGAGTTCGGATGCC 66 CGAGTTCGGATGCC 203052017 CAAATATCCA Statistics Matches: 76, Mismatches: 3, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 93 76 1.00 ACGTcount: A:0.27, C:0.30, G:0.22, T:0.20 Consensus pattern (93 bp): GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA CGAGTTCGGATGCCTAGTTACATCTCAC Found at i:203052012 original size:46 final size:46 Alignment explanation

Indices: 203051837--203052012 Score: 232 Period size: 46 Copynumber: 3.8 Consensus size: 46 203051827 TGTAACCCGC * * * 203051837 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT 1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT * * 203051883 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT 1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACG-CTCG---CAT * * 203051933 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT 1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT 203051976 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA 1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA 203052013 TGCCCAAATA Statistics Matches: 112, Mismatches: 11, Indels: 14 0.82 0.08 0.10 Matches are distributed among these distances: 43 3 0.03 44 1 0.01 45 2 0.02 46 68 0.61 47 32 0.29 48 2 0.02 49 1 0.01 50 3 0.03 ACGTcount: A:0.28, C:0.30, G:0.22, T:0.20 Consensus pattern (46 bp): CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT Found at i:203057440 original size:30 final size:30 Alignment explanation

Indices: 203057406--203057466 Score: 77 Period size: 30 Copynumber: 2.0 Consensus size: 30 203057396 TCCTTAACTC 203057406 AAACTTTGGAAAAATTACAATTTTGCCCCT 1 AAACTTTGGAAAAATTACAATTTTGCCCCT * * * * * 203057436 AAACTTTTGCATATTTACACTTTTGCCCCT 1 AAACTTTGGAAAAATTACAATTTTGCCCCT 203057466 A 1 A 203057467 GGCTCGGGAA Statistics Matches: 26, Mismatches: 5, Indels: 0 0.84 0.16 0.00 Matches are distributed among these distances: 30 26 1.00 ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38 Consensus pattern (30 bp): AAACTTTGGAAAAATTACAATTTTGCCCCT Found at i:203060680 original size:29 final size:29 Alignment explanation

Indices: 203060618--203060720 Score: 100 Period size: 29 Copynumber: 3.6 Consensus size: 29 203060608 GTGACGAGAT * * * 203060618 TGGCACTGAGTGTGCGAGCTTGTAATGTA 1 TGGCACTAAGTGTGCGAGCTTGGAATATA * * * 203060647 CGGCACTAAGTGTGCGAGTTTGGACTATA 1 TGGCACTAAGTGTGCGAGCTTGGAATATA * * ** 203060676 TGGCACTATGTGTGCGGGCTT-GAATCACG 1 TGGCACTAAGTGTGCGAGCTTGGAAT-ATA 203060705 TGGCACTAAGTGTGCG 1 TGGCACTAAGTGTGCG 203060721 TGATTGAGTA Statistics Matches: 59, Mismatches: 14, Indels: 2 0.79 0.19 0.03 Matches are distributed among these distances: 28 3 0.05 29 56 0.95 ACGTcount: A:0.20, C:0.17, G:0.34, T:0.28 Consensus pattern (29 bp): TGGCACTAAGTGTGCGAGCTTGGAATATA Found at i:203063147 original size:40 final size:39 Alignment explanation

Indices: 203063102--203063267 Score: 172 Period size: 40 Copynumber: 4.2 Consensus size: 39 203063092 CGGAATATAA 203063102 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC 1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGG-CTTAGC * * * * 203063142 CCGGATAGAATAACTCGCACGAATGCCTTCGGGCTTAGC 1 CCGGATATAATCACTAGCACAAATGCCTTCGGGCTTAGC ** * * 203063181 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC 1 CCGGATATAATCACTAGCACAAATGCCTTCGGG-CTTAGC ** * * * * 203063221 CCGGATATAATTTCCAGCATAATTGTCTTCGGGCTTAGC 1 CCGGATATAATCACTAGCACAAATGCCTTCGGGCTTAGC 203063260 CCGGATAT 1 CCGGATAT 203063268 CATTCAATTT Statistics Matches: 105, Mismatches: 19, Indels: 5 0.81 0.15 0.04 Matches are distributed among these distances: 39 46 0.44 40 59 0.56 ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26 Consensus pattern (39 bp): CCGGATATAATCACTAGCACAAATGCCTTCGGGCTTAGC Found at i:203063224 original size:79 final size:79 Alignment explanation

Indices: 203063118--203063267 Score: 205 Period size: 79 Copynumber: 1.9 Consensus size: 79 203063108 ATAATCACGT * 203063118 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATAACTC-GCACGAA-TGCCTTCGGGCTTAGC 1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAAC-CAGCA-GAATTGCCTTCGGGCTTAGC 203063181 CCGGATATAGCCACTA 64 CCGGATATAGCCACTA * * ** * * 203063197 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTCCAGCATAATTGTCTTCGGGCTTAGCCC 1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACCAGCAGAATTGCCTTCGGGCTTAGCCC 203063262 GGATAT 66 GGATAT 203063268 CATTCAATTT Statistics Matches: 62, Mismatches: 7, Indels: 4 0.85 0.10 0.05 Matches are distributed among these distances: 78 3 0.05 79 59 0.95 ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26 Consensus pattern (79 bp): GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACCAGCAGAATTGCCTTCGGGCTTAGCCC GGATATAGCCACTA Found at i:203071125 original size:40 final size:39 Alignment explanation

Indices: 203071080--203071245 Score: 172 Period size: 40 Copynumber: 4.2 Consensus size: 39 203071070 CGGAATATAA 203071080 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC 1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGG-CTTAGC * * * * 203071120 CCGGATAGAATAACTCGCACGAATGCCTTCGGGCTTAGC 1 CCGGATATAATCACTAGCACAAATGCCTTCGGGCTTAGC ** * * 203071159 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC 1 CCGGATATAATCACTAGCACAAATGCCTTCGGG-CTTAGC ** * * * * 203071199 CCGGATATAATTTCCAGCATAATTGTCTTCGGGCTTAGC 1 CCGGATATAATCACTAGCACAAATGCCTTCGGGCTTAGC 203071238 CCGGATAT 1 CCGGATAT 203071246 CATTCAATTT Statistics Matches: 105, Mismatches: 19, Indels: 5 0.81 0.15 0.04 Matches are distributed among these distances: 39 46 0.44 40 59 0.56 ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26 Consensus pattern (39 bp): CCGGATATAATCACTAGCACAAATGCCTTCGGGCTTAGC Found at i:203071202 original size:79 final size:79 Alignment explanation

Indices: 203071096--203071245 Score: 205 Period size: 79 Copynumber: 1.9 Consensus size: 79 203071086 ATAATCACGT * 203071096 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATAACTC-GCACGAA-TGCCTTCGGGCTTAGC 1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAAC-CAGCA-GAATTGCCTTCGGGCTTAGC 203071159 CCGGATATAGCCACTA 64 CCGGATATAGCCACTA * * ** * * 203071175 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTCCAGCATAATTGTCTTCGGGCTTAGCCC 1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACCAGCAGAATTGCCTTCGGGCTTAGCCC 203071240 GGATAT 66 GGATAT 203071246 CATTCAATTT Statistics Matches: 62, Mismatches: 7, Indels: 4 0.85 0.10 0.05 Matches are distributed among these distances: 78 3 0.05 79 59 0.95 ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26 Consensus pattern (79 bp): GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACCAGCAGAATTGCCTTCGGGCTTAGCCC GGATATAGCCACTA Found at i:203073872 original size:25 final size:26 Alignment explanation

Indices: 203073819--203073904 Score: 99 Period size: 25 Copynumber: 3.4 Consensus size: 26 203073809 TATGGCTCTT * 203073819 ATGAGCTTCCCATTACA-CAGCTCGA- 1 ATGAGCTTCCCATTACATGA-CTCGAC 203073844 ATGAGCTTCCCATTACATGACTC-AC 1 ATGAGCTTCCCATTACATGACTCGAC * * * 203073869 ATGAGCTTCCTATTATATGGCTCGAC 1 ATGAGCTTCCCATTACATGACTCGAC 203073895 A-GAGCTTCCC 1 ATGAGCTTCCC 203073905 GTTAGTGTGT Statistics Matches: 53, Mismatches: 5, Indels: 6 0.83 0.08 0.09 Matches are distributed among these distances: 24 1 0.02 25 48 0.91 26 4 0.08 ACGTcount: A:0.26, C:0.30, G:0.16, T:0.28 Consensus pattern (26 bp): ATGAGCTTCCCATTACATGACTCGAC Found at i:203076293 original size:17 final size:17 Alignment explanation

Indices: 203076259--203076318 Score: 50 Period size: 17 Copynumber: 3.5 Consensus size: 17 203076249 ATGTGCGAGG * 203076259 TCACCAAAGATACTAGC 1 TCACCAAAGATACAAGC ** 203076276 TCACCAAATCTACAAGC 1 TCACCAAAGATACAAGC * * * 203076293 TCATCAAACG-TGCGAGC 1 TCACCAAA-GATACAAGC 203076310 TCACCAAAG 1 TCACCAAAG 203076319 TTGTGAGTGT Statistics Matches: 34, Mismatches: 8, Indels: 3 0.76 0.18 0.07 Matches are distributed among these distances: 16 1 0.03 17 33 0.97 ACGTcount: A:0.38, C:0.32, G:0.13, T:0.17 Consensus pattern (17 bp): TCACCAAAGATACAAGC Found at i:203080380 original size:38 final size:38 Alignment explanation

Indices: 203080288--203080391 Score: 156 Period size: 38 Copynumber: 2.7 Consensus size: 38 203080278 TTAAATAGCT ** 203080288 CACAAATGCCTTCGGGA-CTTAACCCGGATTTGGAACTCG 1 CACAAATGCCTTC-GGATCTTAGTCC-GATTTGGAACTCG 203080327 CAACAAATGCCTTCGGATCTTAGTCCGATTTGGAACTCG 1 C-ACAAATGCCTTCGGATCTTAGTCCGATTTGGAACTCG 203080366 CACAAATGCCTTCGGATCTTAGTCCG 1 CACAAATGCCTTCGGATCTTAGTCCG 203080392 GATATGGTCA Statistics Matches: 61, Mismatches: 2, Indels: 5 0.90 0.03 0.07 Matches are distributed among these distances: 38 25 0.41 39 18 0.30 40 18 0.30 ACGTcount: A:0.25, C:0.28, G:0.21, T:0.26 Consensus pattern (38 bp): CACAAATGCCTTCGGATCTTAGTCCGATTTGGAACTCG Found at i:203088386 original size:40 final size:40 Alignment explanation

Indices: 203088274--203088426 Score: 148 Period size: 40 Copynumber: 3.8 Consensus size: 40 203088264 TCCGGATATG * * * * *** 203088274 ACTCGCTCAAAAGCCTTCGGGACATAGCCCGGTTATAATA 1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATGGGA * * * 203088314 GCTCGCACAAATGCCTTCGGGACTTAACCCGGATTTGGGA 1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATGGGA * ** 203088354 ACTCGCACAAATGCCTTC-GGATCTTAGTCCGGATATGGTC 1 ACTCGCACAAATGCCTTCGGGA-CTTAGCCCGGATATGGGA * 203088394 ACTTAGCACAAA-GCCTTCGGGACTTAGCCCGGA 1 AC-TCGCACAAATGCCTTCGGGACTTAGCCCGGA 203088427 CATCATTCGA Statistics Matches: 92, Mismatches: 18, Indels: 6 0.79 0.16 0.05 Matches are distributed among these distances: 39 3 0.03 40 78 0.85 41 11 0.12 ACGTcount: A:0.25, C:0.28, G:0.24, T:0.23 Consensus pattern (40 bp): ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATGGGA Found at i:203097775 original size:39 final size:40 Alignment explanation

Indices: 203097731--203097896 Score: 174 Period size: 40 Copynumber: 4.2 Consensus size: 40 203097721 CGGAATATAA * 203097731 CCGGATATAATCAGT-GCACAAATGCCTTCGGGTCTTAGC 1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC * * * * 203097770 CCGGATAGAATAACTCGCACGAATGCCTTCGGGTCTTAGC 1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC * ** * * 203097810 CCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC 1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC ** * * * * 203097850 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTTAGC 1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC 203097889 CCGGATAT 1 CCGGATAT 203097897 CATTCAATTT Statistics Matches: 104, Mismatches: 22, Indels: 2 0.81 0.17 0.02 Matches are distributed among these distances: 39 25 0.24 40 79 0.76 ACGTcount: A:0.24, C:0.27, G:0.23, T:0.27 Consensus pattern (40 bp): CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC Found at i:203098739 original size:17 final size:19 Alignment explanation

Indices: 203098716--203098761 Score: 53 Period size: 17 Copynumber: 2.5 Consensus size: 19 203098706 AAGAAGCATG 203098716 AATCATGCTCAAGAATG-C 1 AATCATGCTCAAGAATGAC * 203098734 -ATCATGGC-CAAGTATGAC 1 AATCAT-GCTCAAGAATGAC 203098752 AATCATGCTC 1 AATCATGCTC 203098762 CTTTTCAACT Statistics Matches: 23, Mismatches: 1, Indels: 7 0.74 0.03 0.23 Matches are distributed among these distances: 17 12 0.52 18 5 0.22 19 6 0.26 ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24 Consensus pattern (19 bp): AATCATGCTCAAGAATGAC Found at i:203105740 original size:40 final size:39 Alignment explanation

Indices: 203105629--203105779 Score: 151 Period size: 40 Copynumber: 3.8 Consensus size: 39 203105619 TATAATCAGT * * * 203105629 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATAACTC 1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATATAACAACTA * * 203105669 GCACGAATGCCTTCGGGTCTTAGCCCGGATATAGCCACTA 1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATATAACAACTA * *** * 203105709 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTCCA 1 GCACAA-TGCCTTCGGGTCTTAGCCCGGATATAACAACTA * * 203105749 GCATAATTGTCTTCGGG-CTTAGCCCGGATAT 1 GCACAA-TGCCTTCGGGTCTTAGCCCGGATAT 203105780 CATTCAATTT Statistics Matches: 95, Mismatches: 15, Indels: 3 0.84 0.13 0.03 Matches are distributed among these distances: 39 15 0.16 40 80 0.84 ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26 Consensus pattern (39 bp): GCACAATGCCTTCGGGTCTTAGCCCGGATATAACAACTA Found at i:203105763 original size:80 final size:79 Alignment explanation

Indices: 203105629--203105779 Score: 198 Period size: 80 Copynumber: 1.9 Consensus size: 79 203105619 TATAATCAGT * 203105629 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATAACTCGCACGAATGCCTTCGGGTCTTAGCC 1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATGCCTTCGGG-CTTAGCC 203105694 CGGATATAGCCACTA 65 CGGATATAGCCACTA * * ** * * 203105709 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCA-TAATTGTCTTCGGGCTTAGC 1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTC-GCACGAA-TGCCTTCGGGCTTAGC 203105772 CCGGATAT 64 CCGGATAT 203105780 CATTCAATTT Statistics Matches: 62, Mismatches: 7, Indels: 5 0.84 0.09 0.07 Matches are distributed among these distances: 79 17 0.27 80 45 0.73 ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26 Consensus pattern (79 bp): GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATGCCTTCGGGCTTAGCCC GGATATAGCCACTA Found at i:203106626 original size:17 final size:19 Alignment explanation

Indices: 203106603--203106648 Score: 53 Period size: 17 Copynumber: 2.5 Consensus size: 19 203106593 AAGAAGCATG 203106603 AATCATGCTCAAGAATG-C 1 AATCATGCTCAAGAATGAC * 203106621 -ATCATGGC-CAAGTATGAC 1 AATCAT-GCTCAAGAATGAC 203106639 AATCATGCTC 1 AATCATGCTC 203106649 CTTTTCAACT Statistics Matches: 23, Mismatches: 1, Indels: 7 0.74 0.03 0.23 Matches are distributed among these distances: 17 12 0.52 18 5 0.22 19 6 0.26 ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24 Consensus pattern (19 bp): AATCATGCTCAAGAATGAC Found at i:203107080 original size:22 final size:20 Alignment explanation

Indices: 203107052--203107091 Score: 80 Period size: 20 Copynumber: 2.0 Consensus size: 20 203107042 GTATGCACTC 203107052 TCTCACACACATTTTTTTTT 1 TCTCACACACATTTTTTTTT 203107072 TCTCACACACATTTTTTTTT 1 TCTCACACACATTTTTTTTT 203107092 CATTCTTTTC Statistics Matches: 20, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 20 20 1.00 ACGTcount: A:0.20, C:0.25, G:0.00, T:0.55 Consensus pattern (20 bp): TCTCACACACATTTTTTTTT Found at i:203112561 original size:2 final size:2 Alignment explanation

Indices: 203112554--203112588 Score: 70 Period size: 2 Copynumber: 17.5 Consensus size: 2 203112544 TCTGTTTATG 203112554 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T 1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T 203112589 GCTACTTTTA Statistics Matches: 33, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 33 1.00 ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51 Consensus pattern (2 bp): TA Found at i:203112876 original size:19 final size:19 Alignment explanation

Indices: 203112852--203112889 Score: 67 Period size: 19 Copynumber: 2.0 Consensus size: 19 203112842 TTGAGATTGC * 203112852 CAACCTATTTGCTTGAAAT 1 CAACCTATTTGCCTGAAAT 203112871 CAACCTATTTGCCTGAAAT 1 CAACCTATTTGCCTGAAAT 203112890 TATTCATTTC Statistics Matches: 18, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 19 18 1.00 ACGTcount: A:0.32, C:0.24, G:0.11, T:0.34 Consensus pattern (19 bp): CAACCTATTTGCCTGAAAT Found at i:203116894 original size:41 final size:40 Alignment explanation

Indices: 203116847--203117063 Score: 208 Period size: 41 Copynumber: 5.3 Consensus size: 40 203116837 GCGTTTGAAA 203116847 CAAAACGCCACTAAAAGCTGAGCAATAGTGGCGTTTTCATT 1 CAAAACGCCACTAAAAGCTGAGCAATAGTGGCGTTTT-ATT * * * 203116888 CAAAACGCCGCTAAAAACTGAGTAATAGTGGCGTTTTTATT 1 CAAAACGCCACTAAAAGCTGAGCAATAGTGGCG-TTTTATT * * * * 203116929 CAAAACGCCGCAAAAAACTGAGAAATAGTGGCGTTTTATT 1 CAAAACGCCACTAAAAGCTGAGCAATAGTGGCGTTTTATT * * * 203116969 CAAAACGCC-GTAAAAAGCTGAG-ATATAGTGGCGCTTTAGGT 1 CAAAACGCCACT-AAAAGCTGAGCA-ATAGTGGCGTTTTA-TT * * * 203117010 CCAAACGCCAC-AAAAGGTTGAGCTATAGTGGCGTTTT-TGT 1 CAAAACGCCACTAAAA-GCTGAGCAATAGTGGCGTTTTAT-T * * 203117050 AAAAACGCCGCTAA 1 CAAAACGCCACTAA 203117064 TATTTATTAT Statistics Matches: 148, Mismatches: 19, Indels: 18 0.80 0.10 0.10 Matches are distributed among these distances: 39 1 0.01 40 51 0.34 41 92 0.62 42 4 0.03 ACGTcount: A:0.35, C:0.19, G:0.22, T:0.24 Consensus pattern (40 bp): CAAAACGCCACTAAAAGCTGAGCAATAGTGGCGTTTTATT Found at i:203116997 original size:81 final size:82 Alignment explanation

Indices: 203116847--203117063 Score: 239 Period size: 81 Copynumber: 2.7 Consensus size: 82 203116837 GCGTTTGAAA * * * 203116847 CAAAACGCCACTAAAAGCTGAGCAATAGTGGCGTTTTCATTCAAAACGCCGCTAAAAACTGAGTA 1 CAAAACGCCACAAAAAACTGAGAAATAGTGGCGTTTTCATTCAAAACGCCGCTAAAAACTGAGTA 203116912 ATAGTGGCGTTTTTATT 66 ATAGTGGCGTTTTTATT * 203116929 CAAAACGCCGCAAAAAACTGAGAAATAGTGGCGTTTT-ATTCAAAACGCCG-TAAAAAGCTGAG- 1 CAAAACGCCACAAAAAACTGAGAAATAGTGGCGTTTTCATTCAAAACGCCGCTAAAAA-CTGAGT * * 203116991 ATATAGTGGCG-CTTTAGGT 65 A-ATAGTGGCGTTTTTA-TT * *** ** * 203117010 CCAAACGCCACAAAAGGTTGAGCTATAGTGGCGTTTT--TGTAAAAACGCCGCTAA 1 CAAAACGCCACAAAAAACTGAGAAATAGTGGCGTTTTCAT-TCAAAACGCCGCTAA 203117064 TATTTATTAT Statistics Matches: 116, Mismatches: 14, Indels: 10 0.83 0.10 0.07 Matches are distributed among these distances: 80 12 0.10 81 68 0.59 82 36 0.31 ACGTcount: A:0.35, C:0.19, G:0.22, T:0.24 Consensus pattern (82 bp): CAAAACGCCACAAAAAACTGAGAAATAGTGGCGTTTTCATTCAAAACGCCGCTAAAAACTGAGTA ATAGTGGCGTTTTTATT Found at i:203117626 original size:29 final size:29 Alignment explanation

Indices: 203117587--203117642 Score: 94 Period size: 29 Copynumber: 1.9 Consensus size: 29 203117577 AAAATATGAA * 203117587 GCCTAACCCCTAAATCATAACCGATGACC 1 GCCTAACCCCTAAATCATAACCCATGACC * 203117616 GCCTAATCCCTAAATCATAACCCATGA 1 GCCTAACCCCTAAATCATAACCCATGA 203117643 TCTAAACTCT Statistics Matches: 25, Mismatches: 2, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 29 25 1.00 ACGTcount: A:0.36, C:0.36, G:0.09, T:0.20 Consensus pattern (29 bp): GCCTAACCCCTAAATCATAACCCATGACC Found at i:203117838 original size:14 final size:15 Alignment explanation

Indices: 203117812--203117855 Score: 63 Period size: 15 Copynumber: 2.9 Consensus size: 15 203117802 CTTTAAACCC 203117812 TTATAATACCCTAAA- 1 TTATAA-ACCCTAAAT 203117827 TTATAAACCCTAAAT 1 TTATAAACCCTAAAT * 203117842 TTGTAAACCCTAAA 1 TTATAAACCCTAAA 203117856 AATAAATTTC Statistics Matches: 27, Mismatches: 1, Indels: 2 0.90 0.03 0.07 Matches are distributed among these distances: 14 8 0.30 15 19 0.70 ACGTcount: A:0.45, C:0.20, G:0.02, T:0.32 Consensus pattern (15 bp): TTATAAACCCTAAAT Found at i:203118837 original size:18 final size:18 Alignment explanation

Indices: 203118814--203118848 Score: 61 Period size: 18 Copynumber: 1.9 Consensus size: 18 203118804 CCCACCCAAA 203118814 TTTCCCCAAATCCCTAAC 1 TTTCCCCAAATCCCTAAC * 203118832 TTTCCCCTAATCCCTAA 1 TTTCCCCAAATCCCTAA 203118849 ATATTTCCCC Statistics Matches: 16, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 18 16 1.00 ACGTcount: A:0.26, C:0.43, G:0.00, T:0.31 Consensus pattern (18 bp): TTTCCCCAAATCCCTAAC Found at i:203118936 original size:19 final size:19 Alignment explanation

Indices: 203118881--203118937 Score: 87 Period size: 19 Copynumber: 3.0 Consensus size: 19 203118871 AAATATCCTT * 203118881 CTGCCGTTGAAGACTCCGA 1 CTGCCGTTGAAGACTCTGA * 203118900 CTGCCGTTGAAGAATCTGA 1 CTGCCGTTGAAGACTCTGA * 203118919 CTGCCATTGAAGACTCTGA 1 CTGCCGTTGAAGACTCTGA 203118938 GTGGACGACC Statistics Matches: 34, Mismatches: 4, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 19 34 1.00 ACGTcount: A:0.25, C:0.26, G:0.25, T:0.25 Consensus pattern (19 bp): CTGCCGTTGAAGACTCTGA Found at i:203122426 original size:23 final size:23 Alignment explanation

Indices: 203122396--203122444 Score: 82 Period size: 23 Copynumber: 2.1 Consensus size: 23 203122386 ACATTAATCT 203122396 AATGTATGAA-TTGCAGCCCTTTA 1 AATGTATGAATTTG-AGCCCTTTA 203122419 AATGTATGAATTTGAGCCCTTTA 1 AATGTATGAATTTGAGCCCTTTA 203122442 AAT 1 AAT 203122445 AAACTTGAAC Statistics Matches: 25, Mismatches: 0, Indels: 2 0.93 0.00 0.07 Matches are distributed among these distances: 23 22 0.88 24 3 0.12 ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37 Consensus pattern (23 bp): AATGTATGAATTTGAGCCCTTTA Found at i:203122503 original size:10 final size:10 Alignment explanation

Indices: 203122488--203122538 Score: 54 Period size: 10 Copynumber: 5.4 Consensus size: 10 203122478 TTATTATTTG 203122488 AAGTATGAAT 1 AAGTATGAAT 203122498 AAGTATGAAT 1 AAGTATGAAT * ** 203122508 AAGTTTTTAT 1 AAGTATGAAT 203122518 -A--ATGAAT 1 AAGTATGAAT 203122525 AAGTATGAAT 1 AAGTATGAAT 203122535 AAGT 1 AAGT 203122539 TTTTATATTT Statistics Matches: 32, Mismatches: 6, Indels: 6 0.73 0.14 0.14 Matches are distributed among these distances: 7 3 0.09 8 1 0.03 9 1 0.03 10 27 0.84 ACGTcount: A:0.47, C:0.00, G:0.18, T:0.35 Consensus pattern (10 bp): AAGTATGAAT Found at i:203122530 original size:27 final size:27 Alignment explanation

Indices: 203122492--203122545 Score: 108 Period size: 27 Copynumber: 2.0 Consensus size: 27 203122482 TATTTGAAGT 203122492 ATGAATAAGTATGAATAAGTTTTTATA 1 ATGAATAAGTATGAATAAGTTTTTATA 203122519 ATGAATAAGTATGAATAAGTTTTTATA 1 ATGAATAAGTATGAATAAGTTTTTATA 203122546 TTTGATTCAA Statistics Matches: 27, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 27 27 1.00 ACGTcount: A:0.44, C:0.00, G:0.15, T:0.41 Consensus pattern (27 bp): ATGAATAAGTATGAATAAGTTTTTATA Found at i:203123373 original size:240 final size:241 Alignment explanation

Indices: 203122583--203123494 Score: 1727 Period size: 241 Copynumber: 3.8 Consensus size: 241 203122573 ATGAATTAAT * * 203122583 TTTATTACCATGTAGCTTGCTTGTCCATTAAAATTACAACAATAGCTGACCTTCTCTCCAAGCTT 1 TTTATTACCATATAGCTTGCTTGTCCATTAAAATTACAACAATAGCTGACCTTCTCTCCAAGTTT 203122648 ATTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTATATCGAG 66 ATTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTATATCGAG * 203122713 CCGTAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATCTTAAAAAATTC 131 CCATAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATCTTAAAAAATTC 203122778 AAAAATACTTGAAAAAAATTCTATCCAACTCATTTACTATTGAATA 196 AAAAATACTTGAAAAAAATTCTATCCAACTCATTTACTATTGAATA 203122824 TTTATTACCATATAGCTTGCTTGTCCATTAAAATTACAACAATAGCTGACCTTCTCTCCAAGTTT 1 TTTATTACCATATAGCTTGCTTGTCCATTAAAATTACAACAATAGCTGACCTTCTCTCCAAGTTT * 203122889 ATTGTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTATATCGAG 66 ATTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTATATCGAG * 203122954 CCGTAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATCTTAAAAAATTC 131 CCATAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATCTTAAAAAATTC 203123019 AAAAATACTTGAAAAAAATTCTATCCAACTCATTTACTATTGAATA 196 AAAAATACTTGAAAAAAATTCTATCCAACTCATTTACTATTGAATA 203123065 TTTATTACCATATAGCTTGCTTGTCCATTAAAATTACAACAATAGCTGACCTTCTCTCCAAGTTT 1 TTTATTACCATATAGCTTGCTTGTCCATTAAAATTACAACAATAGCTGACCTTCTCTCCAAGTTT 203123130 ATTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTATATCGAG 66 ATTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTATATCGAG * * * * 203123195 CTATAAGATATAATGGATCCTCCCTAGGTGTAACAAC-ACGCGTATGATGAATCTTAAAAAAATC 131 CCATAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATCTTAAAAAATTC 203123259 AAAAATACTTGAAAAAAATTCTATCCAACTCATTTACTATTGAATA 196 AAAAATACTTGAAAAAAATTCTATCCAACTCATTTACTATTGAATA 203123305 TTTATTACCATATAGCTTGCTTGTCCATTAAAATTACAACAATAGCTGACCTTCTCTCCAAGTTT 1 TTTATTACCATATAGCTTGCTTGTCCATTAAAATTACAACAATAGCTGACCTTCTCTCCAAGTTT 203123370 ATTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTATATCGAG 66 ATTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTATATCGAG * 203123435 CTATAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATCTTAAAA 131 CCATAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATCTTAAAA 203123495 TTTATAACTA Statistics Matches: 659, Mismatches: 11, Indels: 2 0.98 0.02 0.00 Matches are distributed among these distances: 240 237 0.36 241 422 0.64 ACGTcount: A:0.35, C:0.18, G:0.14, T:0.33 Consensus pattern (241 bp): TTTATTACCATATAGCTTGCTTGTCCATTAAAATTACAACAATAGCTGACCTTCTCTCCAAGTTT ATTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTATATCGAG CCATAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATCTTAAAAAATTC AAAAATACTTGAAAAAAATTCTATCCAACTCATTTACTATTGAATA Found at i:203123486 original size:481 final size:482 Alignment explanation

Indices: 203122583--203123494 Score: 1727 Period size: 481 Copynumber: 1.9 Consensus size: 482 203122573 ATGAATTAAT * 203122583 TTTATTACCATGTAGCTTGCTTGTCCATTAAAATTACAACAATAGCTGACCTTCTCTCCAAGCTT 1 TTTATTACCATATAGCTTGCTTGTCCATTAAAATTACAACAATAGCTGACCTTCTCTCCAAGCTT 203122648 ATTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTATATCGAG 66 ATTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTATATCGAG * * * 203122713 CCGTAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATCTTAAAAAATTC 131 CCATAAGATATAATGGATCCTCCCTAGGTGTAACAACGACACGTATGATGAATCTTAAAAAAATC 203122778 AAAAATACTTGAAAAAAATTCTATCCAACTCATTTACTATTGAATATTTATTACCATATAGCTTG 196 AAAAATACTTGAAAAAAATTCTATCCAACTCATTTACTATTGAATATTTATTACCATATAGCTTG 203122843 CTTGTCCATTAAAATTACAACAATAGCTGACCTTCTCTCCAAGTTTATTGTAAATATTTTAAAGA 261 CTTGTCCATTAAAATTACAACAATAGCTGACCTTCTCTCCAAGTTTATTGTAAATATTTTAAAGA * 203122908 TTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTATATCGAGCCGTAAGATATAATGGATC 326 TTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTATATCGAGCCATAAGATATAATGGATC 203122973 CTCCCTAGGTGTAACAACGCCACGTATGATGAATCTTAAAAAATTCAAAAATACTTGAAAAAAAT 391 CTCCCTAGGTGTAACAACGCCACGTATGATGAATCTTAAAAAATTCAAAAATACTTGAAAAAAAT 203123038 TCTATCCAACTCATTTACTATTGAATA 456 TCTATCCAACTCATTTACTATTGAATA * 203123065 TTTATTACCATATAGCTTGCTTGTCCATTAAAATTACAACAATAGCTGACCTTCTCTCCAAGTTT 1 TTTATTACCATATAGCTTGCTTGTCCATTAAAATTACAACAATAGCTGACCTTCTCTCCAAGCTT 203123130 ATTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTATATCGAG 66 ATTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTATATCGAG * * 203123195 CTATAAGATATAATGGATCCTCCCTAGGTGTAACAAC-ACGCGTATGATGAATCTTAAAAAAATC 131 CCATAAGATATAATGGATCCTCCCTAGGTGTAACAACGACACGTATGATGAATCTTAAAAAAATC 203123259 AAAAATACTTGAAAAAAATTCTATCCAACTCATTTACTATTGAATATTTATTACCATATAGCTTG 196 AAAAATACTTGAAAAAAATTCTATCCAACTCATTTACTATTGAATATTTATTACCATATAGCTTG * 203123324 CTTGTCCATTAAAATTACAACAATAGCTGACCTTCTCTCCAAGTTTATTTTAAATATTTTAAAGA 261 CTTGTCCATTAAAATTACAACAATAGCTGACCTTCTCTCCAAGTTTATTGTAAATATTTTAAAGA * 203123389 TTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTATATCGAGCTATAAGATATAATGGATC 326 TTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTATATCGAGCCATAAGATATAATGGATC 203123454 CTCCCTAGGTGTAACAACGCCACGTATGATGAATCTTAAAA 391 CTCCCTAGGTGTAACAACGCCACGTATGATGAATCTTAAAA 203123495 TTTATAACTA Statistics Matches: 420, Mismatches: 10, Indels: 1 0.97 0.02 0.00 Matches are distributed among these distances: 481 257 0.61 482 163 0.39 ACGTcount: A:0.35, C:0.18, G:0.14, T:0.33 Consensus pattern (482 bp): TTTATTACCATATAGCTTGCTTGTCCATTAAAATTACAACAATAGCTGACCTTCTCTCCAAGCTT ATTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTATATCGAG CCATAAGATATAATGGATCCTCCCTAGGTGTAACAACGACACGTATGATGAATCTTAAAAAAATC AAAAATACTTGAAAAAAATTCTATCCAACTCATTTACTATTGAATATTTATTACCATATAGCTTG CTTGTCCATTAAAATTACAACAATAGCTGACCTTCTCTCCAAGTTTATTGTAAATATTTTAAAGA TTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTATATCGAGCCATAAGATATAATGGATC CTCCCTAGGTGTAACAACGCCACGTATGATGAATCTTAAAAAATTCAAAAATACTTGAAAAAAAT TCTATCCAACTCATTTACTATTGAATA Found at i:203123561 original size:9 final size:9 Alignment explanation

Indices: 203123538--203123650 Score: 118 Period size: 9 Copynumber: 12.2 Consensus size: 9 203123528 ATTGATCATT * 203123538 ACTTAAATA 1 ACTTACATA * 203123547 AATTACATA 1 ACTTACATA 203123556 ACTTACATA 1 ACTTACATA * * 203123565 ACTCATATA 1 ACTTACATA 203123574 ACTTACATA 1 ACTTACATA * 203123583 ATTTACATAACA 1 ACTTACAT---A 203123595 ACTTACATA 1 ACTTACATA * 203123604 ACTCACATA 1 ACTTACATA 203123613 ACTTACATA 1 ACTTACATA * 203123622 ATTTACATA 1 ACTTACATA * 203123631 ACTCACATA 1 ACTTACATA * 203123640 ACGTACATA 1 ACTTACATA 203123649 AC 1 AC 203123651 AACTTACATA Statistics Matches: 85, Mismatches: 16, Indels: 6 0.79 0.15 0.06 Matches are distributed among these distances: 9 77 0.91 12 8 0.09 ACGTcount: A:0.47, C:0.21, G:0.01, T:0.31 Consensus pattern (9 bp): ACTTACATA Found at i:203123607 original size:39 final size:39 Alignment explanation

Indices: 203123555--203123632 Score: 147 Period size: 39 Copynumber: 2.0 Consensus size: 39 203123545 TAAATTACAT * 203123555 AACTTACATAACTCATATAACTTACATAATTTACATAAC 1 AACTTACATAACTCACATAACTTACATAATTTACATAAC 203123594 AACTTACATAACTCACATAACTTACATAATTTACATAAC 1 AACTTACATAACTCACATAACTTACATAATTTACATAAC 203123633 TCACATAACG Statistics Matches: 38, Mismatches: 1, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 39 38 1.00 ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32 Consensus pattern (39 bp): AACTTACATAACTCACATAACTTACATAATTTACATAAC Found at i:203123632 original size:57 final size:57 Alignment explanation

Indices: 203123551--203123662 Score: 170 Period size: 57 Copynumber: 2.0 Consensus size: 57 203123541 TAAATAAATT * * ** 203123551 ACATAACTTACATAACTCATATAACTTACATAATTTACATAACAACTTACATAACTC 1 ACATAACTTACATAACTCACATAACTCACATAACGTACATAACAACTTACATAACTC * * 203123608 ACATAACTTACATAATTTACATAACTCACATAACGTACATAACAACTTACATAAC 1 ACATAACTTACATAACTCACATAACTCACATAACGTACATAACAACTTACATAAC 203123663 CTAACTAATA Statistics Matches: 49, Mismatches: 6, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 57 49 1.00 ACGTcount: A:0.46, C:0.23, G:0.01, T:0.29 Consensus pattern (57 bp): ACATAACTTACATAACTCACATAACTCACATAACGTACATAACAACTTACATAACTC Found at i:203129712 original size:25 final size:25 Alignment explanation

Indices: 203129678--203129736 Score: 100 Period size: 25 Copynumber: 2.4 Consensus size: 25 203129668 TTGTAGAAAA * 203129678 AGCGCCGCTAAAAGCCTTGACCTTT 1 AGCGGCGCTAAAAGCCTTGACCTTT * 203129703 AGCGGCGCTAAAAGTCTTGACCTTT 1 AGCGGCGCTAAAAGCCTTGACCTTT 203129728 AGCGGCGCT 1 AGCGGCGCT 203129737 TTTCCAAAAA Statistics Matches: 32, Mismatches: 2, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 25 32 1.00 ACGTcount: A:0.22, C:0.29, G:0.25, T:0.24 Consensus pattern (25 bp): AGCGGCGCTAAAAGCCTTGACCTTT Found at i:203129794 original size:44 final size:43 Alignment explanation

Indices: 203129708--203129908 Score: 312 Period size: 43 Copynumber: 4.6 Consensus size: 43 203129698 CCTTTAGCGG * * * * 203129708 CGCTAAAAGTCTTGACCTTTAGCGGCGCTTTTCCAAAAAAACGC 1 CGCTAAAAGCCTTGACCTTTAGCGGCGCTTCTCC-CACAAACGC * * 203129752 CCCTAAAAGCCTTGACCTTTTAGCGGTGCTTCTCCCACAAACGC 1 CGCTAAAAGCCTTGACC-TTTAGCGGCGCTTCTCCCACAAACGC * 203129796 CGCTAAAAGCCTTGACCTTTAGCGGCGTTTCTCCCACAAACGC 1 CGCTAAAAGCCTTGACCTTTAGCGGCGCTTCTCCCACAAACGC * 203129839 CGCTAAAAGCCTTGACCTTTAGCGGCGCTTTTCCCACAAACGC 1 CGCTAAAAGCCTTGACCTTTAGCGGCGCTTCTCCCACAAACGC 203129882 CGCTAAAAGCCTTGACCTTTAGCGGCG 1 CGCTAAAAGCCTTGACCTTTAGCGGCG 203129909 TTTTTTTCCA Statistics Matches: 145, Mismatches: 11, Indels: 3 0.91 0.07 0.02 Matches are distributed among these distances: 43 92 0.63 44 38 0.26 45 15 0.10 ACGTcount: A:0.24, C:0.33, G:0.19, T:0.24 Consensus pattern (43 bp): CGCTAAAAGCCTTGACCTTTAGCGGCGCTTCTCCCACAAACGC Found at i:203138375 original size:41 final size:41 Alignment explanation

Indices: 203138326--203138463 Score: 118 Period size: 41 Copynumber: 3.2 Consensus size: 41 203138316 AAGACATAGC 203138326 TGATTTGGCTTTCACGTGTTTACGTTGAAGCAGATCCAAGA 1 TGATTTGGCTTTCACGTGTTTACGTTGAAGCAGATCCAAGA * * * * ** * 203138367 TGATTTGGC-ATCTC-TGTATCAGGCGGAGAGCAGATCGAAGACA 1 TGATTTGGCTTTCACGTGT-TTACGTTGA-AGCAGATCCAAG--A * 203138410 TAGCTAATTTGGCTTTCACGTGTTTATGTTGAAGCAGATCCAAGA 1 T-G---ATTTGGCTTTCACGTGTTTACGTTGAAGCAGATCCAAGA 203138455 TGATTTGGC 1 TGATTTGGC 203138464 GTCTTGTAGC Statistics Matches: 73, Mismatches: 14, Indels: 20 0.68 0.13 0.19 Matches are distributed among these distances: 39 3 0.04 40 8 0.11 41 27 0.37 43 2 0.03 44 2 0.03 45 2 0.03 47 18 0.25 48 8 0.11 49 3 0.04 ACGTcount: A:0.25, C:0.17, G:0.26, T:0.32 Consensus pattern (41 bp): TGATTTGGCTTTCACGTGTTTACGTTGAAGCAGATCCAAGA Found at i:203138420 original size:88 final size:87 Alignment explanation

Indices: 203138273--203138492 Score: 347 Period size: 88 Copynumber: 2.6 Consensus size: 87 203138263 AGCTGAAGAT * * * 203138273 ATCCAAGATGATTTGGCATTTTGTATCAGG-GGGGAGCAGATCGAAGACATAGCTGATTTGGCTT 1 ATCCAAGATGATTTGGCATCTTGTATCAGGCGGAGAGCAGATCGAAGACATAGCTAATTTGGCTT 203138337 TCACGTGTTTACGTTGAAGCAG 66 TCACGTGTTTACGTTGAAGCAG 203138359 ATCCAAGATGATTTGGCATCTCTGTATCAGGCGGAGAGCAGATCGAAGACATAGCTAATTTGGCT 1 ATCCAAGATGATTTGGCATCT-TGTATCAGGCGGAGAGCAGATCGAAGACATAGCTAATTTGGCT * 203138424 TTCACGTGTTTATGTTGAAGCAG 65 TTCACGTGTTTACGTTGAAGCAG * * * 203138447 ATCCAAGATGATTTGGCGTCTTGTAGC-GGCAGA-AGCAGATCGAAGA 1 ATCCAAGATGATTTGGCATCTTGTATCAGGCGGAGAGCAGATCGAAGA 203138493 TAACAGATTT Statistics Matches: 125, Mismatches: 7, Indels: 5 0.91 0.05 0.04 Matches are distributed among these distances: 85 13 0.10 86 25 0.20 87 14 0.11 88 73 0.58 ACGTcount: A:0.27, C:0.16, G:0.28, T:0.28 Consensus pattern (87 bp): ATCCAAGATGATTTGGCATCTTGTATCAGGCGGAGAGCAGATCGAAGACATAGCTAATTTGGCTT TCACGTGTTTACGTTGAAGCAG Found at i:203138447 original size:47 final size:46 Alignment explanation

Indices: 203138307--203138454 Score: 130 Period size: 47 Copynumber: 3.3 Consensus size: 46 203138297 ATCAGGGGGG * 203138307 AGCAGATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGA 1 AGCAGATCCAAGACATAGCT-ATTTGGCTTTCACGTGTTTACGTTGA * * * * ** 203138354 AGCAGATCCAAG--AT-G--ATTTGGC-ATCTC-TGTATCAGGCGGA 1 AGCAGATCCAAGACATAGCTATTTGGCTTTCACGTGT-TTACGTTGA * * 203138394 GAGCAGATCGAAGACATAGCTAATTTGGCTTTCACGTGTTTATGTTGA 1 -AGCAGATCCAAGACATAGCT-ATTTGGCTTTCACGTGTTTACGTTGA 203138442 AGCAGATCCAAGA 1 AGCAGATCCAAGA 203138455 TGATTTGGCG Statistics Matches: 76, Mismatches: 15, Indels: 20 0.68 0.14 0.18 Matches are distributed among these distances: 39 3 0.04 40 8 0.11 41 18 0.24 43 2 0.03 44 2 0.03 45 2 0.03 47 30 0.39 48 8 0.11 49 3 0.04 ACGTcount: A:0.28, C:0.18, G:0.26, T:0.28 Consensus pattern (46 bp): AGCAGATCCAAGACATAGCTATTTGGCTTTCACGTGTTTACGTTGA Found at i:203138508 original size:20 final size:20 Alignment explanation

Indices: 203138485--203138523 Score: 69 Period size: 20 Copynumber: 1.9 Consensus size: 20 203138475 GCAGAAGCAG 203138485 ATCGAAGATAACAGATTTGA 1 ATCGAAGATAACAGATTTGA * 203138505 ATCGAAGATAGCAGATTTG 1 ATCGAAGATAACAGATTTG 203138524 GCATCTCTGT Statistics Matches: 18, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 20 18 1.00 ACGTcount: A:0.41, C:0.10, G:0.23, T:0.26 Consensus pattern (20 bp): ATCGAAGATAACAGATTTGA Found at i:203138592 original size:43 final size:44 Alignment explanation

Indices: 203138505--203139565 Score: 1684 Period size: 43 Copynumber: 24.7 Consensus size: 44 203138495 ACAGATTTGA * * * 203138505 ATCGAAGATAGCAGATTTGGCATCTCTGTAGCGGTGGAGAGCAG 1 ATCGAAGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAG 203138549 ATCGAAGATAACAGATTTGGCGTCT-TGTAGCGGCGGAGAGCAG 1 ATCGAAGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAG * 203138592 ATCGAAGATAACAGATTTGGCGT-TCTGTAGTGGC-GAGAGCAG 1 ATCGAAGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAG ** 203138634 ATCGAAGATAACAGATTTGGCGTCT-TGTAGCGGCGGAGAATAG 1 ATCGAAGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAG * * 203138677 ATCGAAGAT----GATTTGGCATCTCTGTAGCGGCAGAGAGCAG 1 ATCGAAGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAG * 203138717 ATCGAAGATAACAGATTTGGCGTATCTGTAGCGGCGGAGAGCAG 1 ATCGAAGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAG 203138761 ATCGAAGATAACAGATTTGGCGTCTCTGTAG-GGC--AGAGCAG 1 ATCGAAGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAG 203138802 ATCGAAGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAG 1 ATCGAAGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAG 203138846 ATCGAAGATAACAGATTTGGCGTCTCTGTAGCGG-GGAGAGCAG 1 ATCGAAGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAG 203138889 ATCGAAGATAACAGATTTGGCGTCTCTGTAGCGGC-GAGAGCA- 1 ATCGAAGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAG * 203138931 ATCGAAGAT----GATTT-G-GTCTCTGTAGCGGAGGAGAGCAG 1 ATCGAAGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAG 203138969 ATCGAAGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAG 1 ATCGAAGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAG * 203139013 ATCGAAGATAACAGATTTGGCGTCT-TGTAGTGGCGGAGAGCAG 1 ATCGAAGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAG * 203139056 ATCGAAGATAACAGATTTGGCATCTCTGTAGCGGCGGAGAGCAG 1 ATCGAAGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAG 203139100 ATCGAAGATAACAGATTTGGCGTCTCTGTAGCGGCGTAGCGGCGGAGAGCAG 1 ATCGAAGATAACAGATTTGGCGTCTC--T------GTAGCGGCGGAGAGCAG 203139152 ATC-AAGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCA- 1 ATCGAAGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAG 203139194 ATCGAAGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAG 1 ATCGAAGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAG * 203139238 ATCGAAGAT----GATTTGGCATCTCTGTAGCGGC-GAGAGCAG 1 ATCGAAGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAG 203139277 ATCGAAGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAG 1 ATCGAAGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAG 203139321 ATCGAAGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAG 1 ATCGAAGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAG 203139365 ATCGAAGATAACAGATTTGGCGTCTCTGTAGCGGC-GAGAGCAG 1 ATCGAAGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAG 203139408 ATCGAAGATAA-AGATTTGGCGTCTCTGTAGC-GCGGAGAGCAG 1 ATCGAAGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAG 203139450 ATCGAAGATAACAGATTTGGCGTCTC-GTAGCGGCGGAGAGCAG 1 ATCGAAGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAG * 203139493 ATCAAAGATAACAGATTTGGCGTCTCTGTAGCGGCGG-GAGCAG 1 ATCGAAGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAG * 203139536 ATCGAAGATAACGGATTTGGCGTCTCTGTA 1 ATCGAAGATAACAGATTTGGCGTCTCTGTA 203139566 TTAGACGGGA Statistics Matches: 951, Mismatches: 26, Indels: 81 0.90 0.02 0.08 Matches are distributed among these distances: 36 13 0.01 37 8 0.01 38 14 0.01 39 28 0.03 40 45 0.05 41 40 0.04 42 104 0.11 43 338 0.36 44 317 0.33 46 1 0.00 49 1 0.00 51 22 0.02 52 20 0.02 ACGTcount: A:0.28, C:0.17, G:0.33, T:0.22 Consensus pattern (44 bp): ATCGAAGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAG Found at i:203139097 original size:87 final size:88 Alignment explanation

Indices: 203138505--203139565 Score: 1684 Period size: 85 Copynumber: 12.3 Consensus size: 88 203138495 ACAGATTTGA * * * 203138505 ATCGAAGATAGCAGATTTGGCATCTCTGTAGCGGTGGAGAGCAGATCGAAGATAACAGATTTGGC 1 ATCGAAGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATAACAGATTTGGC 203138570 GTCT-TGTAGCGGCGGAGAGCAG 66 GTCTCTGTAGCGGCGGAGAGCAG * 203138592 ATCGAAGATAACAGATTTGGCGT-TCTGTAGTGGC-GAGAGCAGATCGAAGATAACAGATTTGGC 1 ATCGAAGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATAACAGATTTGGC ** 203138655 GTCT-TGTAGCGGCGGAGAATAG 66 GTCTCTGTAGCGGCGGAGAGCAG * * 203138677 ATCGAAGAT----GATTTGGCATCTCTGTAGCGGCAGAGAGCAGATCGAAGATAACAGATTTGGC 1 ATCGAAGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATAACAGATTTGGC * 203138738 GTATCTGTAGCGGCGGAGAGCAG 66 GTCTCTGTAGCGGCGGAGAGCAG 203138761 ATCGAAGATAACAGATTTGGCGTCTCTGTAG-GGC--AGAGCAGATCGAAGATAACAGATTTGGC 1 ATCGAAGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATAACAGATTTGGC 203138823 GTCTCTGTAGCGGCGGAGAGCAG 66 GTCTCTGTAGCGGCGGAGAGCAG 203138846 ATCGAAGATAACAGATTTGGCGTCTCTGTAGCGG-GGAGAGCAGATCGAAGATAACAGATTTGGC 1 ATCGAAGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATAACAGATTTGGC 203138910 GTCTCTGTAGCGGC-GAGAGCA- 66 GTCTCTGTAGCGGCGGAGAGCAG * 203138931 ATCGAAGAT----GATTT-G-GTCTCTGTAGCGGAGGAGAGCAGATCGAAGATAACAGATTTGGC 1 ATCGAAGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATAACAGATTTGGC 203138990 GTCTCTGTAGCGGCGGAGAGCAG 66 GTCTCTGTAGCGGCGGAGAGCAG * 203139013 ATCGAAGATAACAGATTTGGCGTCT-TGTAGTGGCGGAGAGCAGATCGAAGATAACAGATTTGGC 1 ATCGAAGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATAACAGATTTGGC * 203139077 ATCTCTGTAGCGGCGGAGAGCAG 66 GTCTCTGTAGCGGCGGAGAGCAG 203139100 ATCGAAGATAACAGATTTGGCGTCTCTGTAGCGGCGTAGCGGCGGAGAGCAGATC-AAGATAACA 1 ATCGAAGATAACAGATTTGGCGTCTC--T------GTAGCGGCGGAGAGCAGATCGAAGATAACA 203139164 GATTTGGCGTCTCTGTAGCGGCGGAGAGCA- 58 GATTTGGCGTCTCTGTAGCGGCGGAGAGCAG 203139194 ATCGAAGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGAT----GATTTGGC 1 ATCGAAGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATAACAGATTTGGC * 203139255 ATCTCTGTAGCGGC-GAGAGCAG 66 GTCTCTGTAGCGGCGGAGAGCAG 203139277 ATCGAAGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATAACAGATTTGGC 1 ATCGAAGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATAACAGATTTGGC 203139342 GTCTCTGTAGCGGCGGAGAGCAG 66 GTCTCTGTAGCGGCGGAGAGCAG 203139365 ATCGAAGATAACAGATTTGGCGTCTCTGTAGCGGC-GAGAGCAGATCGAAGATAA-AGATTTGGC 1 ATCGAAGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATAACAGATTTGGC 203139428 GTCTCTGTAGC-GCGGAGAGCAG 66 GTCTCTGTAGCGGCGGAGAGCAG * 203139450 ATCGAAGATAACAGATTTGGCGTCTC-GTAGCGGCGGAGAGCAGATCAAAGATAACAGATTTGGC 1 ATCGAAGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATAACAGATTTGGC 203139514 GTCTCTGTAGCGGCGG-GAGCAG 66 GTCTCTGTAGCGGCGGAGAGCAG * 203139536 ATCGAAGATAACGGATTTGGCGTCTCTGTA 1 ATCGAAGATAACAGATTTGGCGTCTCTGTA 203139566 TTAGACGGGA Statistics Matches: 913, Mismatches: 22, Indels: 78 0.90 0.02 0.08 Matches are distributed among these distances: 79 13 0.01 80 45 0.05 81 21 0.02 82 26 0.03 83 106 0.12 84 33 0.04 85 203 0.22 86 114 0.12 87 203 0.22 88 64 0.07 90 1 0.00 92 1 0.00 94 26 0.03 95 38 0.04 96 19 0.02 ACGTcount: A:0.28, C:0.17, G:0.33, T:0.22 Consensus pattern (88 bp): ATCGAAGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATAACAGATTTGGC GTCTCTGTAGCGGCGGAGAGCAG Found at i:203141076 original size:19 final size:19 Alignment explanation

Indices: 203141052--203141089 Score: 67 Period size: 19 Copynumber: 2.0 Consensus size: 19 203141042 TTGAGATTGC * 203141052 CAACCTATTTGCTTGAAAT 1 CAACCTATTTGCCTGAAAT 203141071 CAACCTATTTGCCTGAAAT 1 CAACCTATTTGCCTGAAAT 203141090 TATTCATTTC Statistics Matches: 18, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 19 18 1.00 ACGTcount: A:0.32, C:0.24, G:0.11, T:0.34 Consensus pattern (19 bp): CAACCTATTTGCCTGAAAT Found at i:203143882 original size:46 final size:46 Alignment explanation

Indices: 203143815--203143988 Score: 214 Period size: 46 Copynumber: 3.8 Consensus size: 46 203143805 TGTAACCCGC * 203143815 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT 1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCAT * 203143861 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT 1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG--G-C--GTTCGCAT * * * * 203143911 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGAC-ATCGCAT 1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCAT 203143953 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG 1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG 203143989 ATGCCCAAAT Statistics Matches: 110, Mismatches: 9, Indels: 19 0.80 0.07 0.14 Matches are distributed among these distances: 41 1 0.01 42 3 0.03 43 1 0.01 44 3 0.03 45 28 0.25 46 35 0.32 47 28 0.25 48 3 0.03 49 2 0.02 50 3 0.03 51 3 0.03 ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21 Consensus pattern (46 bp): CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCAT Found at i:203143981 original size:92 final size:93 Alignment explanation

Indices: 203143823--203143993 Score: 308 Period size: 92 Copynumber: 1.8 Consensus size: 93 203143813 GCCCATAAGT * * 203143823 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA 1 GAACTCGGACTCAACTCAACGAGCTCGGACGATCGCATCCATAAGTGAACTCGGACTCAACTCAA 203143888 CGAGTTCGGATGCCTAGTTACATCTCAC 66 CGAGTTCGGATGCCTAGTTACATCTCAC * 203143916 GAACTCGGACTCAACTCAACGAGTTCGGAC-ATCGCATCCATAAGTGAACTCGGACTCAACTCAA 1 GAACTCGGACTCAACTCAACGAGCTCGGACGATCGCATCCATAAGTGAACTCGGACTCAACTCAA 203143980 CGAGTTCGGATGCC 66 CGAGTTCGGATGCC 203143994 CAAATATCCC Statistics Matches: 75, Mismatches: 3, Indels: 1 0.95 0.04 0.01 Matches are distributed among these distances: 92 47 0.63 93 28 0.37 ACGTcount: A:0.28, C:0.30, G:0.22, T:0.20 Consensus pattern (93 bp): GAACTCGGACTCAACTCAACGAGCTCGGACGATCGCATCCATAAGTGAACTCGGACTCAACTCAA CGAGTTCGGATGCCTAGTTACATCTCAC Found at i:203146418 original size:30 final size:30 Alignment explanation

Indices: 203146374--203146462 Score: 101 Period size: 30 Copynumber: 3.0 Consensus size: 30 203146364 CAAAGATAAC 203146374 AAGAAAACC-GAATAAAGAAATCCAAGATA 1 AAGAAAACCAGAATAAAGAAATCCAAGATA * * 203146403 GAGAAACCCAGAATAAAGAAATCC-AGAATA 1 AAGAAAACCAGAATAAAGAAATCCAAG-ATA * * * * 203146433 AAGAGATCCAGGATAAAGAAACCCAAGATA 1 AAGAAAACCAGAATAAAGAAATCCAAGATA 203146463 CGATACTATG Statistics Matches: 50, Mismatches: 7, Indels: 5 0.81 0.11 0.08 Matches are distributed among these distances: 29 9 0.18 30 39 0.78 31 2 0.04 ACGTcount: A:0.57, C:0.16, G:0.17, T:0.10 Consensus pattern (30 bp): AAGAAAACCAGAATAAAGAAATCCAAGATA Found at i:203146422 original size:15 final size:15 Alignment explanation

Indices: 203146374--203146453 Score: 92 Period size: 15 Copynumber: 5.4 Consensus size: 15 203146364 CAAAGATAAC * 203146374 AAGAAAACC-GAATA 1 AAGAAATCCAGAATA 203146388 AAGAAATCCA-AGATA 1 AAGAAATCCAGA-ATA * * 203146403 GAGAAACCCAGAATA 1 AAGAAATCCAGAATA 203146418 AAGAAATCCAGAATA 1 AAGAAATCCAGAATA * * 203146433 AAGAGATCCAGGATA 1 AAGAAATCCAGAATA 203146448 AAGAAA 1 AAGAAA 203146454 CCCAAGATAC Statistics Matches: 55, Mismatches: 8, Indels: 5 0.81 0.12 0.07 Matches are distributed among these distances: 14 9 0.16 15 45 0.82 16 1 0.02 ACGTcount: A:0.59, C:0.14, G:0.17, T:0.10 Consensus pattern (15 bp): AAGAAATCCAGAATA Found at i:203146462 original size:15 final size:15 Alignment explanation

Indices: 203146385--203146462 Score: 79 Period size: 15 Copynumber: 5.2 Consensus size: 15 203146375 AGAAAACCGA 203146385 ATAAAGAAATCCAAG 1 ATAAAGAAATCCAAG * * 203146400 ATAGAGAAA-CCCAG 1 ATAAAGAAATCCAAG 203146414 AATAAAGAAATCC-AG 1 -ATAAAGAAATCCAAG * * 203146429 AATAAAGAGATCCAGG 1 -ATAAAGAAATCCAAG * 203146445 ATAAAGAAACCCAAG 1 ATAAAGAAATCCAAG 203146460 ATA 1 ATA 203146463 CGATACTATG Statistics Matches: 52, Mismatches: 8, Indels: 6 0.79 0.12 0.09 Matches are distributed among these distances: 14 4 0.08 15 45 0.87 16 3 0.06 ACGTcount: A:0.56, C:0.15, G:0.17, T:0.12 Consensus pattern (15 bp): ATAAAGAAATCCAAG Found at i:203149467 original size:46 final size:46 Alignment explanation

Indices: 203149400--203149573 Score: 214 Period size: 46 Copynumber: 3.8 Consensus size: 46 203149390 TGTAACCCGC * 203149400 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT 1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCAT * 203149446 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT 1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG--G-C--GTTCGCAT * * * * 203149496 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGAC-ATCGCAT 1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCAT 203149538 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG 1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG 203149574 ATGCCCAAAT Statistics Matches: 110, Mismatches: 9, Indels: 19 0.80 0.07 0.14 Matches are distributed among these distances: 41 1 0.01 42 3 0.03 43 1 0.01 44 3 0.03 45 28 0.25 46 35 0.32 47 28 0.25 48 3 0.03 49 2 0.02 50 3 0.03 51 3 0.03 ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21 Consensus pattern (46 bp): CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCAT Found at i:203149566 original size:92 final size:93 Alignment explanation

Indices: 203149408--203149578 Score: 308 Period size: 92 Copynumber: 1.8 Consensus size: 93 203149398 GCCCATAAGT * * 203149408 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA 1 GAACTCGGACTCAACTCAACGAGCTCGGACGATCGCATCCATAAGTGAACTCGGACTCAACTCAA 203149473 CGAGTTCGGATGCCTAGTTACATCTCAC 66 CGAGTTCGGATGCCTAGTTACATCTCAC * 203149501 GAACTCGGACTCAACTCAACGAGTTCGGAC-ATCGCATCCATAAGTGAACTCGGACTCAACTCAA 1 GAACTCGGACTCAACTCAACGAGCTCGGACGATCGCATCCATAAGTGAACTCGGACTCAACTCAA 203149565 CGAGTTCGGATGCC 66 CGAGTTCGGATGCC 203149579 CAAATATCCA Statistics Matches: 75, Mismatches: 3, Indels: 1 0.95 0.04 0.01 Matches are distributed among these distances: 92 47 0.63 93 28 0.37 ACGTcount: A:0.28, C:0.30, G:0.22, T:0.20 Consensus pattern (93 bp): GAACTCGGACTCAACTCAACGAGCTCGGACGATCGCATCCATAAGTGAACTCGGACTCAACTCAA CGAGTTCGGATGCCTAGTTACATCTCAC Found at i:203149592 original size:45 final size:45 Alignment explanation

Indices: 203149405--203149592 Score: 168 Period size: 46 Copynumber: 4.1 Consensus size: 45 203149395 CCCGCCCATA * * * * * * 203149405 AGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCAT-A 1 AGTGAACTCGGACTCAACTCAACGAGTTC-GG-ATGCCCATACATCC * 203149451 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTC 1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCA--TACATC-C * * * * 203149499 A-CGAACTCGGACTCAACTCAACGAGTTCGGACAT-CGCATCCAT-A 1 AGTGAACTCGGACTCAACTCAACGAGTTCGG--ATGCCCATACATCC * * 203149543 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCAAATATCC 1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCATACATCC 203149588 AGTGA 1 AGTGA 203149593 CATGTCACTT Statistics Matches: 115, Mismatches: 18, Indels: 19 0.76 0.12 0.12 Matches are distributed among these distances: 43 2 0.02 44 9 0.08 45 35 0.30 46 36 0.31 47 28 0.24 48 3 0.03 49 2 0.02 ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21 Consensus pattern (45 bp): AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCATACATCC Found at i:203152000 original size:30 final size:30 Alignment explanation

Indices: 203151956--203152044 Score: 101 Period size: 30 Copynumber: 3.0 Consensus size: 30 203151946 CAAAGATAAC 203151956 AAGAAAACC-GAATAAAGAAATCCAAGATA 1 AAGAAAACCAGAATAAAGAAATCCAAGATA * * 203151985 GAGAAACCCAGAATAAAGAAATCC-AGAATA 1 AAGAAAACCAGAATAAAGAAATCCAAG-ATA * * * * 203152015 AAGAGATCCAGGATAAAGAAACCCAAGATA 1 AAGAAAACCAGAATAAAGAAATCCAAGATA 203152045 CGATACTATG Statistics Matches: 50, Mismatches: 7, Indels: 5 0.81 0.11 0.08 Matches are distributed among these distances: 29 9 0.18 30 39 0.78 31 2 0.04 ACGTcount: A:0.57, C:0.16, G:0.17, T:0.10 Consensus pattern (30 bp): AAGAAAACCAGAATAAAGAAATCCAAGATA Found at i:203152004 original size:15 final size:15 Alignment explanation

Indices: 203151956--203152035 Score: 92 Period size: 15 Copynumber: 5.4 Consensus size: 15 203151946 CAAAGATAAC * 203151956 AAGAAAACC-GAATA 1 AAGAAATCCAGAATA 203151970 AAGAAATCCA-AGATA 1 AAGAAATCCAGA-ATA * * 203151985 GAGAAACCCAGAATA 1 AAGAAATCCAGAATA 203152000 AAGAAATCCAGAATA 1 AAGAAATCCAGAATA * * 203152015 AAGAGATCCAGGATA 1 AAGAAATCCAGAATA 203152030 AAGAAA 1 AAGAAA 203152036 CCCAAGATAC Statistics Matches: 55, Mismatches: 8, Indels: 5 0.81 0.12 0.07 Matches are distributed among these distances: 14 9 0.16 15 45 0.82 16 1 0.02 ACGTcount: A:0.59, C:0.14, G:0.17, T:0.10 Consensus pattern (15 bp): AAGAAATCCAGAATA Found at i:203152044 original size:15 final size:15 Alignment explanation

Indices: 203151967--203152044 Score: 79 Period size: 15 Copynumber: 5.2 Consensus size: 15 203151957 AGAAAACCGA 203151967 ATAAAGAAATCCAAG 1 ATAAAGAAATCCAAG * * 203151982 ATAGAGAAA-CCCAG 1 ATAAAGAAATCCAAG 203151996 AATAAAGAAATCC-AG 1 -ATAAAGAAATCCAAG * * 203152011 AATAAAGAGATCCAGG 1 -ATAAAGAAATCCAAG * 203152027 ATAAAGAAACCCAAG 1 ATAAAGAAATCCAAG 203152042 ATA 1 ATA 203152045 CGATACTATG Statistics Matches: 52, Mismatches: 8, Indels: 6 0.79 0.12 0.09 Matches are distributed among these distances: 14 4 0.08 15 45 0.87 16 3 0.06 ACGTcount: A:0.56, C:0.15, G:0.17, T:0.12 Consensus pattern (15 bp): ATAAAGAAATCCAAG Found at i:203155147 original size:93 final size:93 Alignment explanation

Indices: 203154988--203155159 Score: 317 Period size: 93 Copynumber: 1.8 Consensus size: 93 203154978 GCCCATAAGT * * 203154988 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA 1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA 203155053 CGAGTTCGGATGCCTAGTTACATCTCAC 66 CGAGTTCGGATGCCTAGTTACATCTCAC * 203155081 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA 1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA 203155146 CGAGTTCGGATGCC 66 CGAGTTCGGATGCC 203155160 CAAATATCCC Statistics Matches: 76, Mismatches: 3, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 93 76 1.00 ACGTcount: A:0.28, C:0.30, G:0.22, T:0.21 Consensus pattern (93 bp): GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA CGAGTTCGGATGCCTAGTTACATCTCAC Found at i:203155155 original size:46 final size:46 Alignment explanation

Indices: 203154980--203155155 Score: 225 Period size: 46 Copynumber: 3.8 Consensus size: 46 203154970 TGTAACCCGC * * * 203154980 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT 1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT * 203155026 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT 1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT * * 203155076 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT 1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT 203155119 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA 1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA 203155156 TGCCCAAATA Statistics Matches: 112, Mismatches: 9, Indels: 18 0.81 0.06 0.13 Matches are distributed among these distances: 42 2 0.02 43 4 0.04 44 2 0.02 45 2 0.02 46 64 0.57 47 29 0.26 48 2 0.02 49 2 0.02 50 3 0.03 51 2 0.02 ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21 Consensus pattern (46 bp): CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT Found at i:203157796 original size:2 final size:2 Alignment explanation

Indices: 203157789--203157835 Score: 94 Period size: 2 Copynumber: 23.5 Consensus size: 2 203157779 TCGATCGGAG 203157789 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT 1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT 203157831 AT AT A 1 AT AT A 203157836 GAGTACGCAC Statistics Matches: 45, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 45 1.00 ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49 Consensus pattern (2 bp): AT Found at i:203157958 original size:29 final size:29 Alignment explanation

Indices: 203157900--203157998 Score: 101 Period size: 29 Copynumber: 3.4 Consensus size: 29 203157890 TTTAAGCCCG *** * 203157900 CACACAGTGCCATACCCTTCGAGC-TCGCA 1 CACACAGTGCCATATATTTCCAGCAT-GCA * * 203157929 CACCCAGTGCCGTATATTTCCAGCATGCA 1 CACACAGTGCCATATATTTCCAGCATGCA * 203157958 CACATAGTGCCATATATTTCCAGCATGCA 1 CACACAGTGCCATATATTTCCAGCATGCA ** 203157987 CACTTAGTGCCA 1 CACACAGTGCCA 203157999 ATCTCGTCAC Statistics Matches: 59, Mismatches: 10, Indels: 2 0.83 0.14 0.03 Matches are distributed among these distances: 29 58 0.98 30 1 0.02 ACGTcount: A:0.26, C:0.34, G:0.16, T:0.23 Consensus pattern (29 bp): CACACAGTGCCATATATTTCCAGCATGCA Found at i:203165891 original size:28 final size:28 Alignment explanation

Indices: 203165830--203165927 Score: 108 Period size: 28 Copynumber: 3.5 Consensus size: 28 203165820 TCACAAATTG ** * * 203165830 GCACTAAGTGTGCGGGTTCAAATTATACA 1 GCACTAAGTGTGCAAGTTC-GATTATATA * 203165859 GCACTAAGTGTGCAAGTTTGATTATATA 1 GCACTAAGTGTGCAAGTTCGATTATATA * * 203165887 GCACTAAGTGTGCGAGTTCGACTAT-TAA 1 GCACTAAGTGTGCAAGTTCGATTATAT-A 203165915 GCACTAAGTGTGC 1 GCACTAAGTGTGC 203165928 GGGCTTATTG Statistics Matches: 60, Mismatches: 8, Indels: 3 0.85 0.11 0.04 Matches are distributed among these distances: 27 1 0.02 28 43 0.72 29 16 0.27 ACGTcount: A:0.30, C:0.16, G:0.24, T:0.30 Consensus pattern (28 bp): GCACTAAGTGTGCAAGTTCGATTATATA Found at i:203173579 original size:28 final size:28 Alignment explanation

Indices: 203173518--203173615 Score: 108 Period size: 28 Copynumber: 3.5 Consensus size: 28 203173508 TCACAAATTG ** * * 203173518 GCACTAAGTGTGCGGGTTCAAATTATACA 1 GCACTAAGTGTGCAAGTTC-GATTATATA * 203173547 GCACTAAGTGTGCAAGTTTGATTATATA 1 GCACTAAGTGTGCAAGTTCGATTATATA * * 203173575 GCACTAAGTGTGCGAGTTCGACTAT-TAA 1 GCACTAAGTGTGCAAGTTCGATTATAT-A 203173603 GCACTAAGTGTGC 1 GCACTAAGTGTGC 203173616 GGGCTTATTG Statistics Matches: 60, Mismatches: 8, Indels: 3 0.85 0.11 0.04 Matches are distributed among these distances: 27 1 0.02 28 43 0.72 29 16 0.27 ACGTcount: A:0.30, C:0.16, G:0.24, T:0.30 Consensus pattern (28 bp): GCACTAAGTGTGCAAGTTCGATTATATA Found at i:203188569 original size:132 final size:132 Alignment explanation

Indices: 203188366--203188865 Score: 797 Period size: 132 Copynumber: 3.8 Consensus size: 132 203188356 GATTACAGAT * 203188366 ATCATCAGCCTTATC-TCACTGAGCAGGAGTGGAGCAGGCTATAGACTAGATCTTATCTTCACTG 1 ATCATCAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAAGACTAGATCTTATCTTCACTG * * 203188430 ACAGGAGTGGAGTAGATCGAATTTTGATGAATCTTATCTCCACGTACCGGCGATGGAGCAGATTC 66 ACAGGAGTGAAGCAGATCGAATTTTGATGAATCTTATCTCCACGTACCGGCGATGGAGCAGATTC 203188495 CA 131 CA * * 203188497 ATCATCAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTATAGACTAGATCTTACCTTCACTG 1 ATCATCAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAAGACTAGATCTTATCTTCACTG * * * * * 203188562 ACAGGAGTGAAGCAGATCAAATTTTGA-CAAGTCTTATCTCCATGTATCGGCAATGGAGCAGATT 66 ACAGGAGTGAAGCAGATCGAATTTTGATGAA-TCTTATCTCCACGTACCGGCGATGGAGCAGATT * 203188626 TCA 130 CCA ** * * * 203188629 GCCACCAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAACACCAGATCTTATCTTCACTG 1 ATCATCAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAAGACTAGATCTTATCTTCACTG * * 203188694 ACAGGAGTGGAGCAGATCGAATTTTGATGAATTTTATCTCCACGTACCGGCGATGGAGCAGATTC 66 ACAGGAGTGAAGCAGATCGAATTTTGATGAATCTTATCTCCACGTACCGGCGATGGAGCAGATTC 203188759 CA 131 CA * 203188761 ATCATCAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAATACTAGATCTTATCTTCACTG 1 ATCATCAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAAGACTAGATCTTATCTTCACTG 203188826 AGCAGGAGTGAAGCAGATCGAATTTTGATGAATCTTATCT 66 A-CAGGAGTGAAGCAGATCGAATTTTGATGAATCTTATCT 203188866 TCGCTGAGCA Statistics Matches: 334, Mismatches: 31, Indels: 6 0.90 0.08 0.02 Matches are distributed among these distances: 131 17 0.05 132 279 0.84 133 38 0.11 ACGTcount: A:0.28, C:0.22, G:0.23, T:0.27 Consensus pattern (132 bp): ATCATCAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAAGACTAGATCTTATCTTCACTG ACAGGAGTGAAGCAGATCGAATTTTGATGAATCTTATCTCCACGTACCGGCGATGGAGCAGATTC CA Found at i:203188878 original size:46 final size:47 Alignment explanation

Indices: 203188811--203188899 Score: 144 Period size: 46 Copynumber: 1.9 Consensus size: 47 203188801 TAAATACTAG * 203188811 ATCTTATCTTCACTGAGCAGGAGTGAAGCAGA-TCGAATTTTGATGA 1 ATCTTATCTTCACTGAGCAGGAGCGAAGCAGATTCGAATTTTGATGA * * 203188857 ATCTTATCTTCGCTGAGCAGGAGCGGAGCAGATTCGAATTTTG 1 ATCTTATCTTCACTGAGCAGGAGCGAAGCAGATTCGAATTTTG 203188900 GTCTCCTATA Statistics Matches: 39, Mismatches: 3, Indels: 1 0.91 0.07 0.02 Matches are distributed among these distances: 46 29 0.74 47 10 0.26 ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30 Consensus pattern (47 bp): ATCTTATCTTCACTGAGCAGGAGCGAAGCAGATTCGAATTTTGATGA Found at i:203202632 original size:132 final size:132 Alignment explanation

Indices: 203202429--203202928 Score: 797 Period size: 132 Copynumber: 3.8 Consensus size: 132 203202419 GATTACAGAT * 203202429 ATCATCAGCCTTATC-TCACTGAGCAGGAGTGGAGCAGGCTATAGACTAGATCTTATCTTCACTG 1 ATCATCAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAAGACTAGATCTTATCTTCACTG * * 203202493 ACAGGAGTGGAGTAGATCGAATTTTGATGAATCTTATCTCCACGTACCGGCGATGGAGCAGATTC 66 ACAGGAGTGAAGCAGATCGAATTTTGATGAATCTTATCTCCACGTACCGGCGATGGAGCAGATTC 203202558 CA 131 CA * * 203202560 ATCATCAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTATAGACTAGATCTTACCTTCACTG 1 ATCATCAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAAGACTAGATCTTATCTTCACTG * * * * * 203202625 ACAGGAGTGAAGCAGATCAAATTTTGA-CAAGTCTTATCTCCATGTATCGGCAATGGAGCAGATT 66 ACAGGAGTGAAGCAGATCGAATTTTGATGAA-TCTTATCTCCACGTACCGGCGATGGAGCAGATT * 203202689 TCA 130 CCA ** * * * 203202692 GCCACCAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAACACCAGATCTTATCTTCACTG 1 ATCATCAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAAGACTAGATCTTATCTTCACTG * * 203202757 ACAGGAGTGGAGCAGATCGAATTTTGATGAATTTTATCTCCACGTACCGGCGATGGAGCAGATTC 66 ACAGGAGTGAAGCAGATCGAATTTTGATGAATCTTATCTCCACGTACCGGCGATGGAGCAGATTC 203202822 CA 131 CA * 203202824 ATCATCAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAATACTAGATCTTATCTTCACTG 1 ATCATCAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAAGACTAGATCTTATCTTCACTG 203202889 AGCAGGAGTGAAGCAGATCGAATTTTGATGAATCTTATCT 66 A-CAGGAGTGAAGCAGATCGAATTTTGATGAATCTTATCT 203202929 TCGCTGAGCA Statistics Matches: 334, Mismatches: 31, Indels: 6 0.90 0.08 0.02 Matches are distributed among these distances: 131 17 0.05 132 279 0.84 133 38 0.11 ACGTcount: A:0.28, C:0.22, G:0.23, T:0.27 Consensus pattern (132 bp): ATCATCAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAAGACTAGATCTTATCTTCACTG ACAGGAGTGAAGCAGATCGAATTTTGATGAATCTTATCTCCACGTACCGGCGATGGAGCAGATTC CA Found at i:203202941 original size:46 final size:47 Alignment explanation

Indices: 203202874--203202962 Score: 144 Period size: 46 Copynumber: 1.9 Consensus size: 47 203202864 TAAATACTAG * 203202874 ATCTTATCTTCACTGAGCAGGAGTGAAGCAGA-TCGAATTTTGATGA 1 ATCTTATCTTCACTGAGCAGGAGCGAAGCAGATTCGAATTTTGATGA * * 203202920 ATCTTATCTTCGCTGAGCAGGAGCGGAGCAGATTCGAATTTTG 1 ATCTTATCTTCACTGAGCAGGAGCGAAGCAGATTCGAATTTTG 203202963 GTCTCCCTAT Statistics Matches: 39, Mismatches: 3, Indels: 1 0.91 0.07 0.02 Matches are distributed among these distances: 46 29 0.74 47 10 0.26 ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30 Consensus pattern (47 bp): ATCTTATCTTCACTGAGCAGGAGCGAAGCAGATTCGAATTTTGATGA Found at i:203208762 original size:40 final size:39 Alignment explanation

Indices: 203208595--203208764 Score: 159 Period size: 40 Copynumber: 4.3 Consensus size: 39 203208585 AGAAATTGAA * 203208595 TGATATCCGGGCTAAG-CCCGAAGACAATTATGCTG-AAAT- 1 TGATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCAAATG * * * * * 203208634 TTATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTAG 1 TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAAT-G * * 203208674 CT-ATATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTG 1 -TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAA-ATG * * 203208714 TTAAATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG 1 TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAAT-G 203208754 TGATATCCGGG 1 TGATATCCGGG 203208765 TAAAGTCCCG Statistics Matches: 107, Mismatches: 16, Indels: 15 0.78 0.12 0.11 Matches are distributed among these distances: 37 2 0.02 38 4 0.04 39 18 0.17 40 81 0.76 41 2 0.02 ACGTcount: A:0.28, C:0.21, G:0.26, T:0.24 Consensus pattern (39 bp): TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATG Found at i:203216786 original size:40 final size:39 Alignment explanation

Indices: 203216618--203216788 Score: 159 Period size: 40 Copynumber: 4.3 Consensus size: 39 203216608 AGAAATTGAA * * 203216618 TGATATCCGGGCTAAGCCCCGAAGACAATTATGCTG-AAAT- 1 TGATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCAAATG * * * * * 203216658 TTATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTAG 1 TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAAT-G * * 203216698 CT-ATATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTG 1 -TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAA-ATG * * 203216738 TTAAATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG 1 TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAAT-G 203216778 TGATATCCGGG 1 TGATATCCGGG 203216789 TAAAGTCCCG Statistics Matches: 107, Mismatches: 17, Indels: 14 0.78 0.12 0.10 Matches are distributed among these distances: 37 2 0.02 38 4 0.04 39 4 0.04 40 95 0.89 41 2 0.02 ACGTcount: A:0.28, C:0.22, G:0.26, T:0.24 Consensus pattern (39 bp): TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATG Found at i:203226805 original size:40 final size:40 Alignment explanation

Indices: 203226742--203226842 Score: 103 Period size: 40 Copynumber: 2.5 Consensus size: 40 203226732 TGAATGATAC * ** * * * 203226742 CCGGGCTAAGCCCCGAAAACAATTATGCTGGAAATTATAT 1 CCGGGCTAAGACCCGAAGGCAATTATGCTAGAAACTACAT * * *** 203226782 CCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCTACAT 1 CCGGGCTAAGACCCGAAGGCAATTATGCTAGAAACTACAT 203226822 CCGGGCTAAGACCCGAAGGCA 1 CCGGGCTAAGACCCGAAGGCA 203226843 TTCGTGCGAG Statistics Matches: 49, Mismatches: 12, Indels: 0 0.80 0.20 0.00 Matches are distributed among these distances: 40 49 1.00 ACGTcount: A:0.30, C:0.25, G:0.27, T:0.19 Consensus pattern (40 bp): CCGGGCTAAGACCCGAAGGCAATTATGCTAGAAACTACAT Found at i:203227009 original size:14 final size:14 Alignment explanation

Indices: 203226990--203227018 Score: 58 Period size: 14 Copynumber: 2.1 Consensus size: 14 203226980 CCAAAGAATA 203226990 ACGTTTATATGTGC 1 ACGTTTATATGTGC 203227004 ACGTTTATATGTGC 1 ACGTTTATATGTGC 203227018 A 1 A 203227019 TTGGAAAGTC Statistics Matches: 15, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 14 15 1.00 ACGTcount: A:0.24, C:0.14, G:0.21, T:0.41 Consensus pattern (14 bp): ACGTTTATATGTGC Found at i:203228441 original size:40 final size:40 Alignment explanation

Indices: 203228396--203228562 Score: 185 Period size: 40 Copynumber: 4.2 Consensus size: 40 203228386 CGGAATATAA 203228396 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC 1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC * * * * * 203228436 CCGGATAGAATAACTCGCACGAATGCCTTCGGGCCTTAGC 1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC * * * 203228476 CCGGATATAACCACTAGCACAATTGCCTTCGGGTCTTAAC 1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC ** * * * * 203228516 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTTAGC 1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC 203228555 CCGGATAT 1 CCGGATAT 203228563 CATTCAATTT Statistics Matches: 107, Mismatches: 19, Indels: 3 0.83 0.15 0.02 Matches are distributed among these distances: 39 14 0.13 40 93 0.87 ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26 Consensus pattern (40 bp): CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC Found at i:203228546 original size:80 final size:79 Alignment explanation

Indices: 203228396--203228562 Score: 205 Period size: 80 Copynumber: 2.1 Consensus size: 79 203228386 CGGAATATAA * * 203228396 CCGGATATAATCACGTGCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATAACTCGCACGAATG 1 CCGGATATAACCACGTGCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATG 203228461 CCTTCGGGCCTTAGC 66 CCTTCGGG-CTTAGC * * ** * 203228476 CCGGATATAACCAC-TAGCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCA-TAA 1 CCGGATATAACCACGT-GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTC-GCACGAA * 203228538 TTGTCTTCGGGCTTAGC 64 -TGCCTTCGGGCTTAGC 203228555 CCGGATAT 1 CCGGATAT 203228563 CATTCAATTT Statistics Matches: 76, Mismatches: 8, Indels: 7 0.84 0.09 0.08 Matches are distributed among these distances: 79 18 0.24 80 58 0.76 ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26 Consensus pattern (79 bp): CCGGATATAACCACGTGCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATG CCTTCGGGCTTAGC Found at i:203229380 original size:17 final size:19 Alignment explanation

Indices: 203229357--203229402 Score: 53 Period size: 17 Copynumber: 2.5 Consensus size: 19 203229347 AAGAAGCATG 203229357 AATCATGCTCAAGAATG-C 1 AATCATGCTCAAGAATGAC * 203229375 -ATCATGGC-CAAGTATGAC 1 AATCAT-GCTCAAGAATGAC 203229393 AATCATGCTC 1 AATCATGCTC 203229403 CTTTTCAACT Statistics Matches: 23, Mismatches: 1, Indels: 7 0.74 0.03 0.23 Matches are distributed among these distances: 17 12 0.52 18 5 0.22 19 6 0.26 ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24 Consensus pattern (19 bp): AATCATGCTCAAGAATGAC Found at i:203236401 original size:40 final size:40 Alignment explanation

Indices: 203236356--203236522 Score: 185 Period size: 40 Copynumber: 4.2 Consensus size: 40 203236346 CGGAATATAA 203236356 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC 1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC * * * * * 203236396 CCGGATAGAATAACTCGCACGAATGCCTTCGGGCCTTAGC 1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC * * * 203236436 CCGGATATAACCACTAGCACAATTGCCTTCGGGTCTTAAC 1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC ** * * * * 203236476 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTTAGC 1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC 203236515 CCGGATAT 1 CCGGATAT 203236523 CATTCAATTT Statistics Matches: 107, Mismatches: 19, Indels: 3 0.83 0.15 0.02 Matches are distributed among these distances: 39 14 0.13 40 93 0.87 ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26 Consensus pattern (40 bp): CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC Found at i:203236506 original size:80 final size:79 Alignment explanation

Indices: 203236356--203236522 Score: 205 Period size: 80 Copynumber: 2.1 Consensus size: 79 203236346 CGGAATATAA * * 203236356 CCGGATATAATCACGTGCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATAACTCGCACGAATG 1 CCGGATATAACCACGTGCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATG 203236421 CCTTCGGGCCTTAGC 66 CCTTCGGG-CTTAGC * * ** * 203236436 CCGGATATAACCAC-TAGCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCA-TAA 1 CCGGATATAACCACGT-GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTC-GCACGAA * 203236498 TTGTCTTCGGGCTTAGC 64 -TGCCTTCGGGCTTAGC 203236515 CCGGATAT 1 CCGGATAT 203236523 CATTCAATTT Statistics Matches: 76, Mismatches: 8, Indels: 7 0.84 0.09 0.08 Matches are distributed among these distances: 79 18 0.24 80 58 0.76 ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26 Consensus pattern (79 bp): CCGGATATAACCACGTGCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATG CCTTCGGGCTTAGC Found at i:203237352 original size:17 final size:19 Alignment explanation

Indices: 203237329--203237374 Score: 53 Period size: 17 Copynumber: 2.5 Consensus size: 19 203237319 AAGAAGCATG 203237329 AATCATGCTCAAGAATG-C 1 AATCATGCTCAAGAATGAC * 203237347 -ATCATGGC-CAAGTATGAC 1 AATCAT-GCTCAAGAATGAC 203237365 AATCATGCTC 1 AATCATGCTC 203237375 CTTTTCAACT Statistics Matches: 23, Mismatches: 1, Indels: 7 0.74 0.03 0.23 Matches are distributed among these distances: 17 12 0.52 18 5 0.22 19 6 0.26 ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24 Consensus pattern (19 bp): AATCATGCTCAAGAATGAC Found at i:203240635 original size:40 final size:40 Alignment explanation

Indices: 203240590--203240692 Score: 134 Period size: 40 Copynumber: 2.6 Consensus size: 40 203240580 CGGAATACAA * * * 203240590 CCGGATATAACCACATGCACGAAGGCCTTCGGGTCTTAGC 1 CCGGATATAACAACTTGCACGAAGGCCTTCGGGTATTAGC * * * * 203240630 CCGGATAGAACGACTTGCACAAATGCCTTCGGGTATTAGC 1 CCGGATATAACAACTTGCACGAAGGCCTTCGGGTATTAGC * 203240670 CCGGATTTAACAACTTGCACGAA 1 CCGGATATAACAACTTGCACGAA 203240693 TCAACAATAA Statistics Matches: 53, Mismatches: 10, Indels: 0 0.84 0.16 0.00 Matches are distributed among these distances: 40 53 1.00 ACGTcount: A:0.28, C:0.27, G:0.23, T:0.21 Consensus pattern (40 bp): CCGGATATAACAACTTGCACGAAGGCCTTCGGGTATTAGC Found at i:203248019 original size:40 final size:39 Alignment explanation

Indices: 203247974--203248180 Score: 193 Period size: 40 Copynumber: 5.2 Consensus size: 39 203247964 CGGAATACAA * 203247974 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGC 1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC * * * 203248014 CCGGATAGAACGACTTGCACAAATGCCTTCGGGTATTAGC 1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC * * * 203248054 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGC 1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC * *** * 203248094 CCGGATGTGGTCACTAGCAC-AATGGCCTTCGGGTCTTAAC 1 CCGGATATAACCACT-GCACAAAT-GCCTTCGGGTCTTAGC ** * * * 203248134 CCGG-TATAATTACTAGCATAAATGTCTTCGGGACTTAGC 1 CCGGATATAACCACT-GCACAAATGCCTTCGGGTCTTAGC 203248173 CCGGATAT 1 CCGGATAT 203248181 CATTCAATTG Statistics Matches: 139, Mismatches: 24, Indels: 8 0.81 0.14 0.05 Matches are distributed among these distances: 39 31 0.22 40 108 0.78 ACGTcount: A:0.25, C:0.26, G:0.24, T:0.26 Consensus pattern (39 bp): CCGGATATAACCACTGCACAAATGCCTTCGGGTCTTAGC Found at i:203248114 original size:80 final size:80 Alignment explanation

Indices: 203247974--203248179 Score: 229 Period size: 80 Copynumber: 2.6 Consensus size: 80 203247964 CGGAATACAA * * * 203247974 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGCCCGGATAGAACGACTTGCACAAAT- 1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATAGAACGACTAGCAC-AATG * 203248038 GCCTTCGGGTATTAGC 65 GCCTTCGGGTATTAAC * * ** 203248054 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATGTGGTC-ACTAGCACAATG 1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGAT-AGAACGACTAGCACAATG * 203248118 GCCTTCGGGTCTTAAC 65 GCCTTCGGGTATTAAC ** * ** * * 203248134 CCGG-TATAATTACTAGCATAAATGTCTTCGGGACTTAGCCCGGATA 1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATA 203248180 TCATTCAATT Statistics Matches: 106, Mismatches: 18, Indels: 6 0.82 0.14 0.05 Matches are distributed among these distances: 79 36 0.34 80 68 0.64 81 2 0.02 ACGTcount: A:0.25, C:0.26, G:0.24, T:0.25 Consensus pattern (80 bp): CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATAGAACGACTAGCACAATGG CCTTCGGGTATTAAC Found at i:203256044 original size:40 final size:39 Alignment explanation

Indices: 203255999--203256205 Score: 202 Period size: 40 Copynumber: 5.2 Consensus size: 39 203255989 CGGAATACAA * 203255999 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGC 1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC * * * 203256039 CCGGATAGAACGACTTGCACAAATGCCTTCGGGTATTAGC 1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC * * * 203256079 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGC 1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC * ** * 203256119 CCGGATGT-GTCACTAGCAC-AATGGCCTTCGGGTCTTAAC 1 CCGGATATAACCACT-GCACAAAT-GCCTTCGGGTCTTAGC ** * * * 203256158 CCGGATATAATTACTAGCATAAATGTCTTCGGGACTTAGC 1 CCGGATATAACCACT-GCACAAATGCCTTCGGGTCTTAGC 203256198 CCGGATAT 1 CCGGATAT 203256206 CATACAATTG Statistics Matches: 141, Mismatches: 22, Indels: 8 0.82 0.13 0.05 Matches are distributed among these distances: 38 4 0.03 39 28 0.20 40 106 0.75 41 3 0.02 ACGTcount: A:0.25, C:0.26, G:0.23, T:0.26 Consensus pattern (39 bp): CCGGATATAACCACTGCACAAATGCCTTCGGGTCTTAGC Found at i:203256188 original size:79 final size:80 Alignment explanation

Indices: 203255999--203256204 Score: 222 Period size: 79 Copynumber: 2.6 Consensus size: 80 203255989 CGGAATACAA * * * 203255999 CCGGATATAACCAC-ATGCACGAATGCCTTCGGGTCTTAGCCCGGATAGAACGACTTGCACAAAT 1 CCGGATATAACAACTA-GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAACGACTAGCACAAAT * 203256063 GCCTTCGGGTATTAGC 65 GCCTTCGGGTATTAAC * * * ** 203256079 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGAT-GTGTC-ACTAGCAC-AAT 1 CCGGATATAACAACTAGCACAAATGCCTTCGGGTCTTAGCCCGGATAG-AACGACTAGCACAAAT * 203256141 GGCCTTCGGGTCTTAAC 65 -GCCTTCGGGTATTAAC ** * * * 203256158 CCGGATATAATTACTAGCATAAATGTCTTCGGGACTTAGCCCGGATA 1 CCGGATATAACAACTAGCACAAATGCCTTCGGGTCTTAGCCCGGATA 203256205 TCATACAATT Statistics Matches: 106, Mismatches: 16, Indels: 8 0.82 0.12 0.06 Matches are distributed among these distances: 78 3 0.03 79 60 0.57 80 43 0.41 ACGTcount: A:0.25, C:0.26, G:0.23, T:0.25 Consensus pattern (80 bp): CCGGATATAACAACTAGCACAAATGCCTTCGGGTCTTAGCCCGGATAGAACGACTAGCACAAATG CCTTCGGGTATTAAC Found at i:203257171 original size:20 final size:20 Alignment explanation

Indices: 203257146--203257183 Score: 58 Period size: 20 Copynumber: 1.9 Consensus size: 20 203257136 GTTTATTCGC * 203257146 GATTTTCAATATTTTGTAAA 1 GATTTTCAAAATTTTGTAAA * 203257166 GATTTTTAAAATTTTGTA 1 GATTTTCAAAATTTTGTA 203257184 TTTGGATGTG Statistics Matches: 16, Mismatches: 2, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 20 16 1.00 ACGTcount: A:0.34, C:0.03, G:0.11, T:0.53 Consensus pattern (20 bp): GATTTTCAAAATTTTGTAAA Found at i:203259891 original size:40 final size:40 Alignment explanation

Indices: 203259846--203260012 Score: 167 Period size: 40 Copynumber: 4.2 Consensus size: 40 203259836 CGGAATATAA 203259846 CCGGATATAACCACGT-GCACAAATGCCTTCGGGTCTTAGC 1 CCGGATATAACCAC-TAGCACAAATGCCTTCGGGTCTTAGC * ** * * 203259886 CCGGATAGAATGACTCGCACGAATGCCTTCGGGTCTTAGC 1 CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC * * * * 203259926 CCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC 1 CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC *** * * * * 203259966 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTTAGC 1 CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC 203260005 CCGGATAT 1 CCGGATAT 203260013 CATTCAATTT Statistics Matches: 104, Mismatches: 22, Indels: 3 0.81 0.17 0.02 Matches are distributed among these distances: 39 14 0.13 40 90 0.87 ACGTcount: A:0.23, C:0.28, G:0.23, T:0.26 Consensus pattern (40 bp): CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC Found at i:203267845 original size:40 final size:40 Alignment explanation

Indices: 203267800--203267967 Score: 158 Period size: 40 Copynumber: 4.2 Consensus size: 40 203267790 CGGAATATAA * 203267800 CCGGATATAACCA-TGTGCACAAATGCCTTCGGGTCTTAGC 1 CCGGATATAACCACT-AGCACAAATGCCTTCGGGTCTTAGC * ** * * 203267840 CCGGATAGAATGACTCGCACGAATGCCTTCGGGTCTTAGC 1 CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC * * * * 203267880 CCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC 1 CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC *** * * * * * 203267920 CCGGATATAATTTCCAGCATAATTGTCTTCGGGGCTTAGC 1 CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC 203267960 CCGGATAT 1 CCGGATAT 203267968 CATTCAATTT Statistics Matches: 103, Mismatches: 24, Indels: 2 0.80 0.19 0.02 Matches are distributed among these distances: 40 102 0.99 41 1 0.01 ACGTcount: A:0.23, C:0.27, G:0.24, T:0.26 Consensus pattern (40 bp): CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC Found at i:203267950 original size:80 final size:80 Alignment explanation

Indices: 203267816--203267965 Score: 196 Period size: 80 Copynumber: 1.9 Consensus size: 80 203267806 ATAACCATGT * * 203267816 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATGACTCGCACGAATGCCTTCGGGTCTTAGCC 1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGACTCGCACGAATGCCTTCGGGGCTTAGCC 203267881 CGGATGTAGCCACTA 66 CGGATGTAGCCACTA * * ** * * 203267896 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCA-TAATTGTCTTCGGGGCTTAG 1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGACTC-GCACGAA-TGCCTTCGGGGCTTAG 203267959 CCCGGAT 64 CCCGGAT 203267966 ATCATTCAAT Statistics Matches: 60, Mismatches: 8, Indels: 4 0.83 0.11 0.06 Matches are distributed among these distances: 79 3 0.05 80 57 0.95 ACGTcount: A:0.22, C:0.27, G:0.25, T:0.26 Consensus pattern (80 bp): GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGACTCGCACGAATGCCTTCGGGGCTTAGCC CGGATGTAGCCACTA Found at i:203276638 original size:13 final size:13 Alignment explanation

Indices: 203276620--203276647 Score: 56 Period size: 13 Copynumber: 2.2 Consensus size: 13 203276610 TGAAAATTCG 203276620 TTAATGGTACATT 1 TTAATGGTACATT 203276633 TTAATGGTACATT 1 TTAATGGTACATT 203276646 TT 1 TT 203276648 CCCCTATATT Statistics Matches: 15, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 15 1.00 ACGTcount: A:0.29, C:0.07, G:0.14, T:0.50 Consensus pattern (13 bp): TTAATGGTACATT Found at i:203288943 original size:21 final size:21 Alignment explanation

Indices: 203288919--203288962 Score: 54 Period size: 21 Copynumber: 2.1 Consensus size: 21 203288909 GAATCTTTAG * 203288919 TATTTATTGTATCATTT-TATT 1 TATTTAAT-TATCATTTCTATT * 203288940 TATTTAATTATCCTTTCTATT 1 TATTTAATTATCATTTCTATT 203288961 TA 1 TA 203288963 ATTAGGTCGT Statistics Matches: 20, Mismatches: 2, Indels: 2 0.83 0.08 0.08 Matches are distributed among these distances: 20 7 0.35 21 13 0.65 ACGTcount: A:0.25, C:0.09, G:0.02, T:0.64 Consensus pattern (21 bp): TATTTAATTATCATTTCTATT Found at i:203291218 original size:22 final size:22 Alignment explanation

Indices: 203291191--203291234 Score: 88 Period size: 22 Copynumber: 2.0 Consensus size: 22 203291181 CTCTCGATTT 203291191 TTTTATTGCTCCTTTTCAATCA 1 TTTTATTGCTCCTTTTCAATCA 203291213 TTTTATTGCTCCTTTTCAATCA 1 TTTTATTGCTCCTTTTCAATCA 203291235 AAAGAGATAA Statistics Matches: 22, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 22 22 1.00 ACGTcount: A:0.18, C:0.23, G:0.05, T:0.55 Consensus pattern (22 bp): TTTTATTGCTCCTTTTCAATCA Found at i:203295389 original size:32 final size:32 Alignment explanation

Indices: 203295353--203295414 Score: 115 Period size: 32 Copynumber: 1.9 Consensus size: 32 203295343 AGCTTTTGGT 203295353 TTTTTCATGTTGTCAAAGAGTTGAACAATGGA 1 TTTTTCATGTTGTCAAAGAGTTGAACAATGGA * 203295385 TTTTTCGTGTTGTCAAAGAGTTGAACAATG 1 TTTTTCATGTTGTCAAAGAGTTGAACAATG 203295415 AAAATAGATG Statistics Matches: 29, Mismatches: 1, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 32 29 1.00 ACGTcount: A:0.29, C:0.10, G:0.23, T:0.39 Consensus pattern (32 bp): TTTTTCATGTTGTCAAAGAGTTGAACAATGGA Found at i:203309069 original size:40 final size:40 Alignment explanation

Indices: 203308844--203309041 Score: 276 Period size: 40 Copynumber: 5.0 Consensus size: 40 203308834 TCGAATGATG * * * * 203308844 TCCGGGCTAAG-TCCCGAAGGC-TTTGTGCTAAGTGACTATA 1 TCCGGACTAAGAT-CCGAAGGCATTTGTGC-GAGTTACTAAA * 203308884 TCCGGACTAAGATCCGAAGGCATTCGTGCGAGTTACTAAA 1 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA * 203308924 TCTGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA 1 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA 203308964 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA 1 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA ** 203309004 TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTACTA 1 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTA 203309042 TAACCGGGCT Statistics Matches: 145, Mismatches: 10, Indels: 6 0.90 0.06 0.04 Matches are distributed among these distances: 39 1 0.01 40 137 0.94 41 7 0.05 ACGTcount: A:0.27, C:0.21, G:0.26, T:0.26 Consensus pattern (40 bp): TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA Found at i:203309076 original size:40 final size:40 Alignment explanation

Indices: 203308844--203309069 Score: 273 Period size: 40 Copynumber: 5.7 Consensus size: 40 203308834 TCGAATGATG * * * 203308844 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATA 1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA * * 203308884 TCCGGACTAAGAT-CCGAAGGCATTCGTGCGAGTTACTAAA 1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA * * 203308924 TCTGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAA 1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA * 203308964 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAA 1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA * 203309004 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA 1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA * * 203309045 -CCGGGCTATGTCCCAAAGGCATTTG 1 TCCGGGCTAAGTCCCGAAGGCATTTG 203309070 AACGAGTAGC Statistics Matches: 169, Mismatches: 13, Indels: 8 0.89 0.07 0.04 Matches are distributed among these distances: 39 1 0.01 40 159 0.94 41 9 0.05 ACGTcount: A:0.27, C:0.21, G:0.26, T:0.26 Consensus pattern (40 bp): TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA Found at i:203312026 original size:17 final size:16 Alignment explanation

Indices: 203311999--203312031 Score: 57 Period size: 17 Copynumber: 2.0 Consensus size: 16 203311989 GCTTGTAGGA 203311999 GATATGAGTAAAAGAT 1 GATATGAGTAAAAGAT 203312015 GATATAGAGTAAAAGAT 1 GATAT-GAGTAAAAGAT 203312032 TTGACGAAAA Statistics Matches: 16, Mismatches: 0, Indels: 1 0.94 0.00 0.06 Matches are distributed among these distances: 16 5 0.31 17 11 0.69 ACGTcount: A:0.52, C:0.00, G:0.24, T:0.24 Consensus pattern (16 bp): GATATGAGTAAAAGAT Found at i:203315023 original size:26 final size:27 Alignment explanation

Indices: 203314986--203315053 Score: 93 Period size: 26 Copynumber: 2.6 Consensus size: 27 203314976 AAACACGTTA * * 203314986 GAAAAGAAAGCCTTTGTGGAGAACTAT 1 GAAAAGAAAGCCTTTGTGGAAAACCAT 203315013 GAAAA-AAAGCCTTTGTGGAAAACCAT 1 GAAAAGAAAGCCTTTGTGGAAAACCAT ** 203315039 GAAGTGAAAGCCTTT 1 GAAAAGAAAGCCTTT 203315054 ATGGCTAAAA Statistics Matches: 36, Mismatches: 4, Indels: 2 0.86 0.10 0.05 Matches are distributed among these distances: 26 22 0.61 27 14 0.39 ACGTcount: A:0.41, C:0.13, G:0.24, T:0.22 Consensus pattern (27 bp): GAAAAGAAAGCCTTTGTGGAAAACCAT Found at i:203315171 original size:27 final size:27 Alignment explanation

Indices: 203315141--203315207 Score: 89 Period size: 27 Copynumber: 2.5 Consensus size: 27 203315131 CTTTGTTGCA * * * 203315141 AACTCTAGAGGAATGGTATTCATGGTG 1 AACTCTAAAGGAATGGTATGCATGGAG 203315168 AACTCTAAAGGAATGGTATGCATGGAG 1 AACTCTAAAGGAATGGTATGCATGGAG * * 203315195 AACTATGAAGGAA 1 AACTCTAAAGGAA 203315208 ATGCCCTTGT Statistics Matches: 35, Mismatches: 5, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 27 35 1.00 ACGTcount: A:0.37, C:0.10, G:0.28, T:0.24 Consensus pattern (27 bp): AACTCTAAAGGAATGGTATGCATGGAG Found at i:203315578 original size:13 final size:15 Alignment explanation

Indices: 203315544--203315580 Score: 51 Period size: 15 Copynumber: 2.6 Consensus size: 15 203315534 CGCCCCAAAT * 203315544 TTGGGCCTAGAAGTA 1 TTGGGCCTTGAAGTA 203315559 TTGGGCCTTG-AGTA 1 TTGGGCCTTGAAGTA 203315573 -TGGGCCTT 1 TTGGGCCTT 203315581 AATGTCTACT Statistics Matches: 21, Mismatches: 1, Indels: 2 0.88 0.04 0.08 Matches are distributed among these distances: 13 8 0.38 14 4 0.19 15 9 0.43 ACGTcount: A:0.16, C:0.16, G:0.35, T:0.32 Consensus pattern (15 bp): TTGGGCCTTGAAGTA Found at i:203316983 original size:22 final size:22 Alignment explanation

Indices: 203316958--203317019 Score: 88 Period size: 22 Copynumber: 2.8 Consensus size: 22 203316948 GTTGCTGTGA * 203316958 TATCTACGGCGTTGAGCCGTCC 1 TATCTATGGCGTTGAGCCGTCC * 203316980 TATCTATGGTGTTGAGCCGTCC 1 TATCTATGGCGTTGAGCCGTCC * * 203317002 TGTCTATGGCGTTCAGCC 1 TATCTATGGCGTTGAGCC 203317020 ATCTTGTTGA Statistics Matches: 35, Mismatches: 5, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 22 35 1.00 ACGTcount: A:0.13, C:0.27, G:0.27, T:0.32 Consensus pattern (22 bp): TATCTATGGCGTTGAGCCGTCC Found at i:203325493 original size:29 final size:29 Alignment explanation

Indices: 203325460--203325674 Score: 208 Period size: 29 Copynumber: 7.4 Consensus size: 29 203325450 GATCATTGAA * 203325460 TATGAAAAGGGATAGCTTCGGCTATCGAT 1 TATGAAAAGGGATAGCTTCGACTATCGAT 203325489 TATGAAAAGGGATAGCTTCGACTATCGAT 1 TATGAAAAGGGATAGCTTCGACTATCGAT 203325518 TATGAAAAGGGATAGCTTC-AGCTATC-AGT 1 TATGAAAAGGGATAGCTTCGA-CTATCGA-T * * * * * 203325547 GATGAAAAGGGAT-GGTGAT-GACCATCAAC 1 TATGAAAAGGGATAGCT--TCGACTATCGAT * * * * 203325576 TATGAAAAGGGAT-GGTGAC-ACCATCGAA 1 TATGAAAAGGGATAGCT-TCGACTATCGAT * * * 203325604 TATGAAAAGGGATAGCTTCGGCTATAGAA 1 TATGAAAAGGGATAGCTTCGACTATCGAT * 203325633 TATGAAAAAGGATAGCTTCGACTATCGAT 1 TATGAAAAGGGATAGCTTCGACTATCGAT * 203325662 TATGAAAACGGAT 1 TATGAAAAGGGAT 203325675 GGTGACGACC Statistics Matches: 157, Mismatches: 20, Indels: 18 0.81 0.10 0.09 Matches are distributed among these distances: 28 25 0.16 29 129 0.82 30 3 0.02 ACGTcount: A:0.37, C:0.13, G:0.26, T:0.24 Consensus pattern (29 bp): TATGAAAAGGGATAGCTTCGACTATCGAT Found at i:203325667 original size:115 final size:116 Alignment explanation

Indices: 203325483--203325762 Score: 350 Period size: 115 Copynumber: 2.4 Consensus size: 116 203325473 AGCTTCGGCT * * * 203325483 ATCGATTATGAAAAGGGATAGCTTCGACTATCGATTATGAAAAGGGATAGCTTCAGCTATCAGTG 1 ATCGATTATGAAAAGGGATAGCTTCGACTATAGAATATGAAAAAGGATAGCTTCAGCTATCAGTG * * * * * 203325548 ATGAAAAGGGATGGTGATGACCATCAACTATGAAAAGGGATGGTGAC-ACC 66 ATGAAAACGGATGGTGACGACCATCAACTATAAAAAAGGATGGCGACGACC * * 203325598 ATCGAATATGAAAAGGGATAGCTTCGGCTATAGAATATGAAAAAGGATAGCTTC-GACTATC-GA 1 ATCGATTATGAAAAGGGATAGCTTCGACTATAGAATATGAAAAAGGATAGCTTCAG-CTATCAG- * * 203325661 TTATGAAAACGGATGGTGACGACCATTAACTATAAAAAAGGATGGCGACGACC 64 TGATGAAAACGGATGGTGACGACCATCAACTATAAAAAAGGATGGCGACGACC * * * * * * 203325714 ATCGATTAATGAAATGGGATGGTTTCGACCATTGAATATGAAAATGGAT 1 ATCGATT-ATGAAAAGGGATAGCTTCGACTATAGAATATGAAAAAGGAT 203325763 GGTTACAACC Statistics Matches: 141, Mismatches: 20, Indels: 6 0.84 0.12 0.04 Matches are distributed among these distances: 114 2 0.01 115 96 0.68 116 9 0.06 117 34 0.24 ACGTcount: A:0.38, C:0.13, G:0.25, T:0.24 Consensus pattern (116 bp): ATCGATTATGAAAAGGGATAGCTTCGACTATAGAATATGAAAAAGGATAGCTTCAGCTATCAGTG ATGAAAACGGATGGTGACGACCATCAACTATAAAAAAGGATGGCGACGACC Found at i:203325683 original size:29 final size:28 Alignment explanation

Indices: 203325460--203325776 Score: 165 Period size: 29 Copynumber: 10.9 Consensus size: 28 203325450 GATCATTGAA * * * 203325460 TATGAAAAGGGATAGCTTCGGCTATCGAT 1 TATGAAAAGGGAT-GGTTCGACCATCGAT * * 203325489 TATGAAAAGGGATAGCTTCGACTATCGAT 1 TATGAAAAGGGAT-GGTTCGACCATCGAT * * 203325518 TATGAAAAGGGATAGCTTC-AGCTATC-AGT 1 TATGAAAAGGGAT-GGTTCGA-CCATCGA-T * * * 203325547 GATGAAAAGGGATGGTGAT-GACCATCAAC 1 TATGAAAAGGGATGGT--TCGACCATCGAT * * 203325576 TATGAAAAGGGATGGTGAC-ACCATCGAA 1 TATGAAAAGGGATGGT-TCGACCATCGAT * * * * * 203325604 TATGAAAAGGGATAGCTTCGGCTATAGAA 1 TATGAAAAGGGAT-GGTTCGACCATCGAT * * * 203325633 TATGAAAAAGGATAGCTTCGACTATCGAT 1 TATGAAAAGGGAT-GGTTCGACCATCGAT * * ** * 203325662 TATGAAAACGGATGGTGACGACCATTAAC 1 TATGAAAAGGGATGGT-TCGACCATCGAT * * ** 203325691 TATAAAAAAGGATGGCGACGACCATCGAT 1 TATGAAAAGGGATGG-TTCGACCATCGAT * * * 203325720 TAATGAAATGGGATGGTTTCGACCATTGAA 1 T-ATGAAAAGGGATGG-TTCGACCATCGAT * * 203325750 TATGAAAATGGATGGTTACAACCATCG 1 TATGAAAAGGGATGGTT-CGACCATCG 203325777 TTTAGTACTC Statistics Matches: 231, Mismatches: 44, Indels: 26 0.77 0.15 0.09 Matches are distributed among these distances: 28 29 0.13 29 178 0.77 30 24 0.10 ACGTcount: A:0.37, C:0.14, G:0.26, T:0.24 Consensus pattern (28 bp): TATGAAAAGGGATGGTTCGACCATCGAT Found at i:203325774 original size:59 final size:58 Alignment explanation

Indices: 203325548--203325776 Score: 189 Period size: 58 Copynumber: 3.9 Consensus size: 58 203325538 GCTATCAGTG * * * * 203325548 ATGAAAAGGGATGGTGAT-GACCA-TCAACTATGAAAAGGGATGGTGAC-ACCATCGAAT 1 ATGAAAAGGGATGGT-TTCGACCATTGAA-TATGAAAAAGGATGGTGACGACCATCGATT * * * * * * * * 203325605 ATGAAAAGGGATAGCTTCGGCTATAGAATATGAAAAAGGATAGCT-TCGACTATCGATT 1 ATGAAAAGGGATGGTTTCGACCATTGAATATGAAAAAGGAT-GGTGACGACCATCGATT * ** * * 203325663 ATGAAAACGGATGGTGACGACCATT-AACTATAAAAAAGGATGGCGACGACCATCGATT 1 ATGAAAAGGGATGGTTTCGACCATTGAA-TATGAAAAAGGATGGTGACGACCATCGATT * * * * 203325721 AATGAAATGGGATGGTTTCGACCATTGAATATGAAAATGGATGGTTACAACCATCG 1 -ATGAAAAGGGATGGTTTCGACCATTGAATATGAAAAAGGATGGTGACGACCATCG 203325777 TTTAGTACTC Statistics Matches: 130, Mismatches: 34, Indels: 14 0.73 0.19 0.08 Matches are distributed among these distances: 56 1 0.01 57 32 0.25 58 52 0.40 59 43 0.33 60 2 0.02 ACGTcount: A:0.38, C:0.14, G:0.25, T:0.23 Consensus pattern (58 bp): ATGAAAAGGGATGGTTTCGACCATTGAATATGAAAAAGGATGGTGACGACCATCGATT Found at i:203328575 original size:93 final size:93 Alignment explanation

Indices: 203328463--203328633 Score: 315 Period size: 93 Copynumber: 1.8 Consensus size: 93 203328453 GCCCATAAGT * * 203328463 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA 1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA 203328528 CGAGTTCGGATGCCTAGTTACATCTCAC 66 CGAGTTCGGATGCCTAGTTACATCTCAC * 203328556 GAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA 1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA 203328621 CGAGTTCGGATGC 66 CGAGTTCGGATGC 203328634 TCAACCATCC Statistics Matches: 75, Mismatches: 3, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 93 75 1.00 ACGTcount: A:0.27, C:0.30, G:0.22, T:0.20 Consensus pattern (93 bp): GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA CGAGTTCGGATGCCTAGTTACATCTCAC Found at i:203328649 original size:46 final size:46 Alignment explanation

Indices: 203328455--203328635 Score: 233 Period size: 46 Copynumber: 3.9 Consensus size: 46 203328445 TGTAACCCGC * * * 203328455 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT 1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT * * 203328501 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT 1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACG-CTCG---CAT * * 203328551 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT 1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT * 203328594 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTC 1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTC 203328636 AACCATCCTA Statistics Matches: 116, Mismatches: 12, Indels: 14 0.82 0.08 0.10 Matches are distributed among these distances: 43 3 0.03 44 1 0.01 45 2 0.02 46 72 0.62 47 32 0.28 48 2 0.02 49 1 0.01 50 3 0.03 ACGTcount: A:0.28, C:0.30, G:0.22, T:0.21 Consensus pattern (46 bp): CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT Found at i:203331061 original size:30 final size:30 Alignment explanation

Indices: 203331017--203331105 Score: 101 Period size: 30 Copynumber: 3.0 Consensus size: 30 203331007 CAAAGATAAC 203331017 AAGAAAACC-GAATAAAGAAATCCAAGATA 1 AAGAAAACCAGAATAAAGAAATCCAAGATA * * 203331046 GAGAAACCCAGAATAAAGAAATCC-AGAATA 1 AAGAAAACCAGAATAAAGAAATCCAAG-ATA * * * * 203331076 AAGAGATCCAGGATAAAGAAACCCAAGATA 1 AAGAAAACCAGAATAAAGAAATCCAAGATA 203331106 CGATACTATG Statistics Matches: 50, Mismatches: 7, Indels: 5 0.81 0.11 0.08 Matches are distributed among these distances: 29 9 0.18 30 39 0.78 31 2 0.04 ACGTcount: A:0.57, C:0.16, G:0.17, T:0.10 Consensus pattern (30 bp): AAGAAAACCAGAATAAAGAAATCCAAGATA Found at i:203331065 original size:15 final size:15 Alignment explanation

Indices: 203331017--203331096 Score: 92 Period size: 15 Copynumber: 5.4 Consensus size: 15 203331007 CAAAGATAAC * 203331017 AAGAAAACC-GAATA 1 AAGAAATCCAGAATA 203331031 AAGAAATCCA-AGATA 1 AAGAAATCCAGA-ATA * * 203331046 GAGAAACCCAGAATA 1 AAGAAATCCAGAATA 203331061 AAGAAATCCAGAATA 1 AAGAAATCCAGAATA * * 203331076 AAGAGATCCAGGATA 1 AAGAAATCCAGAATA 203331091 AAGAAA 1 AAGAAA 203331097 CCCAAGATAC Statistics Matches: 55, Mismatches: 8, Indels: 5 0.81 0.12 0.07 Matches are distributed among these distances: 14 9 0.16 15 45 0.82 16 1 0.02 ACGTcount: A:0.59, C:0.14, G:0.17, T:0.10 Consensus pattern (15 bp): AAGAAATCCAGAATA Found at i:203331105 original size:15 final size:15 Alignment explanation

Indices: 203331028--203331105 Score: 79 Period size: 15 Copynumber: 5.2 Consensus size: 15 203331018 AGAAAACCGA 203331028 ATAAAGAAATCCAAG 1 ATAAAGAAATCCAAG * * 203331043 ATAGAGAAA-CCCAG 1 ATAAAGAAATCCAAG 203331057 AATAAAGAAATCC-AG 1 -ATAAAGAAATCCAAG * * 203331072 AATAAAGAGATCCAGG 1 -ATAAAGAAATCCAAG * 203331088 ATAAAGAAACCCAAG 1 ATAAAGAAATCCAAG 203331103 ATA 1 ATA 203331106 CGATACTATG Statistics Matches: 52, Mismatches: 8, Indels: 6 0.79 0.12 0.09 Matches are distributed among these distances: 14 4 0.08 15 45 0.87 16 3 0.06 ACGTcount: A:0.56, C:0.15, G:0.17, T:0.12 Consensus pattern (15 bp): ATAAAGAAATCCAAG Found at i:203331691 original size:28 final size:28 Alignment explanation

Indices: 203331651--203331712 Score: 124 Period size: 28 Copynumber: 2.2 Consensus size: 28 203331641 TTTACCAAAG 203331651 AATTCCTTCTCTAACTGGGACAGTGCAT 1 AATTCCTTCTCTAACTGGGACAGTGCAT 203331679 AATTCCTTCTCTAACTGGGACAGTGCAT 1 AATTCCTTCTCTAACTGGGACAGTGCAT 203331707 AATTCC 1 AATTCC 203331713 AATAATCTTT Statistics Matches: 34, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 28 34 1.00 ACGTcount: A:0.26, C:0.26, G:0.16, T:0.32 Consensus pattern (28 bp): AATTCCTTCTCTAACTGGGACAGTGCAT Found at i:203337299 original size:33 final size:33 Alignment explanation

Indices: 203337252--203337317 Score: 114 Period size: 33 Copynumber: 2.0 Consensus size: 33 203337242 GGCTAGACAG * 203337252 AGATGGTGTTTAGTAGATGAGGGTAGGATATGT 1 AGATGGTGTGTAGTAGATGAGGGTAGGATATGT * 203337285 AGATGGTGTGTAGTAGATGGGGGTAGGATATGT 1 AGATGGTGTGTAGTAGATGAGGGTAGGATATGT 203337318 TATGATTATG Statistics Matches: 31, Mismatches: 2, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 33 31 1.00 ACGTcount: A:0.26, C:0.00, G:0.42, T:0.32 Consensus pattern (33 bp): AGATGGTGTGTAGTAGATGAGGGTAGGATATGT Found at i:203338517 original size:31 final size:31 Alignment explanation

Indices: 203338435--203338506 Score: 94 Period size: 31 Copynumber: 2.4 Consensus size: 31 203338425 TTAACAGCCT * * 203338435 AGTGACTTAAA-AAAAACTTTTGAATAATTC 1 AGTGACTTAAATGAAAATTTTTGAATAATTC * * 203338465 AGTGACTTAAATGAAAATTTTTGAATAGTTT 1 AGTGACTTAAATGAAAATTTTTGAATAATTC 203338496 AGTGAC-TAAAT 1 AGTGACTTAAAT 203338507 TGTAACTTTT Statistics Matches: 37, Mismatches: 4, Indels: 2 0.86 0.09 0.05 Matches are distributed among these distances: 30 16 0.43 31 21 0.57 ACGTcount: A:0.43, C:0.07, G:0.14, T:0.36 Consensus pattern (31 bp): AGTGACTTAAATGAAAATTTTTGAATAATTC Found at i:203339982 original size:40 final size:40 Alignment explanation

Indices: 203339937--203340103 Score: 185 Period size: 40 Copynumber: 4.2 Consensus size: 40 203339927 CGGAATATAA 203339937 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC 1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC * * * * 203339977 CCGGATAGAATAACTCGCACGAATGCCTTCGGGTCTTAGC 1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC ** * * 203340017 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC 1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC ** * * * * 203340057 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTTAGC 1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC 203340096 CCGGATAT 1 CCGGATAT 203340104 CATTCAATTT Statistics Matches: 107, Mismatches: 19, Indels: 3 0.83 0.15 0.02 Matches are distributed among these distances: 39 14 0.13 40 93 0.87 ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26 Consensus pattern (40 bp): CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC Found at i:203341371 original size:58 final size:58 Alignment explanation

Indices: 203341299--203341410 Score: 147 Period size: 58 Copynumber: 1.9 Consensus size: 58 203341289 CCCCCTTTTC 203341299 CCTTAGTAATTTCGGCCAAGAAGAT-GAGAAAGGATGAACAAATTTTTTTCTTTTCTTT 1 CCTTAGTAATTTCGGCCAAGAAGATGGAG-AAGGATGAACAAATTTTTTTCTTTTCTTT *** ** 203341357 CCTTAGTACA-TTCGGCCAAGCCTATGGAGAAGGATGAACATTTTTTTTTCTTTT 1 CCTTAGTA-ATTTCGGCCAAGAAGATGGAGAAGGATGAACAAATTTTTTTCTTTT 203341411 TTTTTTCCTA Statistics Matches: 47, Mismatches: 5, Indels: 4 0.84 0.09 0.07 Matches are distributed among these distances: 58 43 0.91 59 4 0.09 ACGTcount: A:0.28, C:0.16, G:0.18, T:0.38 Consensus pattern (58 bp): CCTTAGTAATTTCGGCCAAGAAGATGGAGAAGGATGAACAAATTTTTTTCTTTTCTTT Found at i:203345030 original size:33 final size:33 Alignment explanation

Indices: 203344983--203345048 Score: 114 Period size: 33 Copynumber: 2.0 Consensus size: 33 203344973 GGCTAGACAG * 203344983 AGATGGTGTTTAGTAGATGAGGGTAGGATATGT 1 AGATGGTGTGTAGTAGATGAGGGTAGGATATGT * 203345016 AGATGGTGTGTAGTAGATGGGGGTAGGATATGT 1 AGATGGTGTGTAGTAGATGAGGGTAGGATATGT 203345049 TATGATTATG Statistics Matches: 31, Mismatches: 2, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 33 31 1.00 ACGTcount: A:0.26, C:0.00, G:0.42, T:0.32 Consensus pattern (33 bp): AGATGGTGTGTAGTAGATGAGGGTAGGATATGT Found at i:203346248 original size:31 final size:31 Alignment explanation

Indices: 203346166--203346237 Score: 94 Period size: 31 Copynumber: 2.4 Consensus size: 31 203346156 TTAACAGCCT * * 203346166 AGTGACTTAAA-AAAAACTTTTGAATAATTC 1 AGTGACTTAAATGAAAATTTTTGAATAATTC * * 203346196 AGTGACTTAAATGAAAATTTTTGAATAGTTT 1 AGTGACTTAAATGAAAATTTTTGAATAATTC 203346227 AGTGAC-TAAAT 1 AGTGACTTAAAT 203346238 TGTAACTTTT Statistics Matches: 37, Mismatches: 4, Indels: 2 0.86 0.09 0.05 Matches are distributed among these distances: 30 16 0.43 31 21 0.57 ACGTcount: A:0.43, C:0.07, G:0.14, T:0.36 Consensus pattern (31 bp): AGTGACTTAAATGAAAATTTTTGAATAATTC Found at i:203347712 original size:40 final size:40 Alignment explanation

Indices: 203347667--203347833 Score: 185 Period size: 40 Copynumber: 4.2 Consensus size: 40 203347657 CGGAATATAA 203347667 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC 1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC * * * * 203347707 CCGGATAGAATAACTCGCACGAATGCCTTCGGGTCTTAGC 1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC ** * * 203347747 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC 1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC ** * * * * 203347787 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTTAGC 1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC 203347826 CCGGATAT 1 CCGGATAT 203347834 CATTCAATTT Statistics Matches: 107, Mismatches: 19, Indels: 3 0.83 0.15 0.02 Matches are distributed among these distances: 39 14 0.13 40 93 0.87 ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26 Consensus pattern (40 bp): CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC Found at i:203349101 original size:58 final size:59 Alignment explanation

Indices: 203349029--203349141 Score: 142 Period size: 58 Copynumber: 1.9 Consensus size: 59 203349019 CCCCCTTTTC 203349029 CCTTAGTAATTTCGGCCAAGAAGAT-GAGAAAGGATGAACA-AATTTTTTTCTTTTCTTT 1 CCTTAGTAATTTCGGCCAAGAAGATGGAG-AAGGATGAACATAATTTTTTTCTTTTCTTT *** ** 203349087 CCTTAGTACA-TTCGGCCAAGCCTATGGAGAAGGATGAACATTTTTTTTTTCTTTT 1 CCTTAGTA-ATTTCGGCCAAGAAGATGGAGAAGGATGAACATAATTTTTTTCTTTT 203349142 TTTTTTCCTA Statistics Matches: 47, Mismatches: 5, Indels: 5 0.82 0.09 0.09 Matches are distributed among these distances: 58 31 0.66 59 16 0.34 ACGTcount: A:0.27, C:0.16, G:0.18, T:0.39 Consensus pattern (59 bp): CCTTAGTAATTTCGGCCAAGAAGATGGAGAAGGATGAACATAATTTTTTTCTTTTCTTT Found at i:203352749 original size:18 final size:18 Alignment explanation

Indices: 203352726--203352778 Score: 60 Period size: 18 Copynumber: 3.1 Consensus size: 18 203352716 ATGGTGTTTA 203352726 GTAGATGGGGTAGGATAT 1 GTAGATGGGGTAGGATAT * 203352744 GTAGATGGTGT--G-TA- 1 GTAGATGGGGTAGGATAT 203352758 GTAGATGGGGGTAGGATAT 1 GTAGAT-GGGGTAGGATAT 203352777 GT 1 GT 203352779 TATGATTATG Statistics Matches: 28, Mismatches: 2, Indels: 9 0.72 0.05 0.23 Matches are distributed among these distances: 14 6 0.21 15 6 0.21 16 1 0.04 17 1 0.04 18 12 0.43 19 2 0.07 ACGTcount: A:0.25, C:0.00, G:0.45, T:0.30 Consensus pattern (18 bp): GTAGATGGGGTAGGATAT Found at i:203352760 original size:32 final size:33 Alignment explanation

Indices: 203352714--203352778 Score: 114 Period size: 32 Copynumber: 2.0 Consensus size: 33 203352704 GGCTAGACAG * 203352714 AGATGGTGTTTAGTAGAT-GGGGTAGGATATGT 1 AGATGGTGTGTAGTAGATGGGGGTAGGATATGT 203352746 AGATGGTGTGTAGTAGATGGGGGTAGGATATGT 1 AGATGGTGTGTAGTAGATGGGGGTAGGATATGT 203352779 TATGATTATG Statistics Matches: 31, Mismatches: 1, Indels: 1 0.94 0.03 0.03 Matches are distributed among these distances: 32 17 0.55 33 14 0.45 ACGTcount: A:0.25, C:0.00, G:0.43, T:0.32 Consensus pattern (33 bp): AGATGGTGTGTAGTAGATGGGGGTAGGATATGT Found at i:203353978 original size:31 final size:31 Alignment explanation

Indices: 203353896--203353967 Score: 94 Period size: 31 Copynumber: 2.4 Consensus size: 31 203353886 TTAACAGCCT * * 203353896 AGTGACTTAAA-AAAAACTTTTGAATAATTC 1 AGTGACTTAAATGAAAATTTTTGAATAATTC * * 203353926 AGTGACTTAAATGAAAATTTTTGAATAGTTT 1 AGTGACTTAAATGAAAATTTTTGAATAATTC 203353957 AGTGAC-TAAAT 1 AGTGACTTAAAT 203353968 TGTAACTTTT Statistics Matches: 37, Mismatches: 4, Indels: 2 0.86 0.09 0.05 Matches are distributed among these distances: 30 16 0.43 31 21 0.57 ACGTcount: A:0.43, C:0.07, G:0.14, T:0.36 Consensus pattern (31 bp): AGTGACTTAAATGAAAATTTTTGAATAATTC Found at i:203355443 original size:40 final size:40 Alignment explanation

Indices: 203355398--203355564 Score: 185 Period size: 40 Copynumber: 4.2 Consensus size: 40 203355388 CGGAATATAA 203355398 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC 1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC * * * * 203355438 CCGGATAGAATAACTCGCACGAATGCCTTCGGGTCTTAGC 1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC ** * * 203355478 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC 1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC ** * * * * 203355518 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTTAGC 1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC 203355557 CCGGATAT 1 CCGGATAT 203355565 CATTCAATTT Statistics Matches: 107, Mismatches: 19, Indels: 3 0.83 0.15 0.02 Matches are distributed among these distances: 39 14 0.13 40 93 0.87 ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26 Consensus pattern (40 bp): CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC Done.