Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Chr07 97507971 

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: 97507971
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33

Warning! 232 characters in sequence are not A, C, G, or T


File 144 of 328

Found at i:42082729 original size:80 final size:79

Alignment explanation

Indices: 42082590--42082745 Score: 183 Period size: 80 Copynumber: 2.0 Consensus size: 79 42082580 GGACTAAGAT * ** 42082590 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTA-CT 1 CCGAAGGCATTTGTGCGAGCTACTAAATCCGGACTAAGATCCGAAGGCATTTGAACGAG-TAGCT 42082654 AAATCCGGGTTAAGTC 65 AAATCC-GGTTAAGTC * * * * 42082670 CCGAAGGCCTTTGTGCGAGCTACTATAA-CCGGGCTATG-TCCCGAAGGTATTTGAACGAGTAGC 1 CCGAAGGCATTTGTGCGAGCTACTA-AATCCGGACTAAGAT-CCGAAGGCATTTGAACGAGTAGC * 42082733 TATATCCGGTTAA 64 TAAATCCGGTTAA 42082746 ACTCCGAAGG Statistics Matches: 65, Mismatches: 8, Indels: 7 0.81 0.10 0.09 Matches are distributed among these distances: 79 9 0.14 80 54 0.83 81 2 0.03 ACGTcount: A:0.26, C:0.21, G:0.26, T:0.26 Consensus pattern (79 bp): CCGAAGGCATTTGTGCGAGCTACTAAATCCGGACTAAGATCCGAAGGCATTTGAACGAGTAGCTA AATCCGGTTAAGTC Found at i:42085155 original size:22 final size:24 Alignment explanation

Indices: 42085101--42085155 Score: 64 Period size: 22 Copynumber: 2.5 Consensus size: 24 42085091 TATATAACTG 42085101 ATAATAT-TA-AAATATATACATA 1 ATAATATATATAAATATATACATA * * 42085123 ATATTATATATAAAT-TATTCAT- 1 ATAATATATATAAATATATACATA 42085145 ATAATATATAT 1 ATAATATATAT 42085156 TAAAAAAATT Statistics Matches: 28, Mismatches: 3, Indels: 4 0.80 0.09 0.11 Matches are distributed among these distances: 22 16 0.57 23 8 0.29 24 4 0.14 ACGTcount: A:0.53, C:0.04, G:0.00, T:0.44 Consensus pattern (24 bp): ATAATATATATAAATATATACATA Found at i:42085357 original size:3 final size:3 Alignment explanation

Indices: 42085344--42085399 Score: 103 Period size: 3 Copynumber: 18.7 Consensus size: 3 42085334 ATAGTAACAT * 42085344 TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA 1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA 42085392 TAA TAA TA 1 TAA TAA TA 42085400 TTGAAACACA Statistics Matches: 51, Mismatches: 2, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 3 51 1.00 ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34 Consensus pattern (3 bp): TAA Found at i:42085513 original size:3 final size:3 Alignment explanation

Indices: 42085498--42085541 Score: 61 Period size: 3 Copynumber: 14.3 Consensus size: 3 42085488 ACTAATGTAC * * 42085498 AAT AAT AAC AAT AAT AAT AAT AAT AAAT AAT AAT ATT AAT AAT A 1 AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT A 42085542 TGAAAATAAC Statistics Matches: 36, Mismatches: 4, Indels: 2 0.86 0.10 0.05 Matches are distributed among these distances: 3 33 0.92 4 3 0.08 ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32 Consensus pattern (3 bp): AAT Found at i:42087957 original size:65 final size:65 Alignment explanation

Indices: 42087844--42087974 Score: 165 Period size: 65 Copynumber: 2.0 Consensus size: 65 42087834 ATTTTACCCA * 42087844 TATTGAATTTACTATCTTTGATTACTTTATTCATTTCAAAATGCGCTCCCAATAAATTTCCTTCT 1 TATTGAATTTACTATCTTTGATTACTTTATTCATTTCAAAATACGCTCCCAATAAATTTCCTTCT * ** * ** * * 42087909 TATTGCATTTACTATCTTTGATTAAC-TTATTTGTTTCGAGCTATGCTCCCAATTAATTTCCTTC 1 TATTGAATTTACTATCTTTGATT-ACTTTATTCATTTCAAAATACGCTCCCAATAAATTTCCTTC 42087973 T 65 T 42087974 T 1 T 42087975 TTCCATTGTT Statistics Matches: 56, Mismatches: 9, Indels: 2 0.84 0.13 0.03 Matches are distributed among these distances: 65 54 0.96 66 2 0.04 ACGTcount: A:0.24, C:0.20, G:0.08, T:0.48 Consensus pattern (65 bp): TATTGAATTTACTATCTTTGATTACTTTATTCATTTCAAAATACGCTCCCAATAAATTTCCTTCT Found at i:42088442 original size:46 final size:46 Alignment explanation

Indices: 42088387--42088495 Score: 164 Period size: 46 Copynumber: 2.4 Consensus size: 46 42088377 TGAGGAAGCC * * * 42088387 ACAAGTCCTATACCCTTGAGTTGTAGTGGGATGGATTGAAGAAGAT 1 ACAAATCCTATACCCCTGAGCTGTAGTGGGATGGATTGAAGAAGAT * * * 42088433 AGAAATCCTATACCCCTGAGCTGTAGTGGGATGGATTGAAGATGGT 1 ACAAATCCTATACCCCTGAGCTGTAGTGGGATGGATTGAAGAAGAT 42088479 ACAAATCCTATACCCCT 1 ACAAATCCTATACCCCT 42088496 AAATTACATT Statistics Matches: 56, Mismatches: 7, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 46 56 1.00 ACGTcount: A:0.30, C:0.18, G:0.25, T:0.27 Consensus pattern (46 bp): ACAAATCCTATACCCCTGAGCTGTAGTGGGATGGATTGAAGAAGAT Found at i:42088509 original size:46 final size:46 Alignment explanation

Indices: 42088411--42088521 Score: 132 Period size: 46 Copynumber: 2.4 Consensus size: 46 42088401 CTTGAGTTGT * * * ** 42088411 AGTGGGATGGATTGAAGAAGATAGAAATCCTATACCCCTGAGCTGT 1 AGTGGGATGGATTGAAGAAGATACAAATCCTATACCCCTAAACTAC * * * 42088457 AGTGGGATGGATTGAAGATGGTACAAATCCTATACCCCTAAATTAC 1 AGTGGGATGGATTGAAGAAGATACAAATCCTATACCCCTAAACTAC * * 42088503 ATTGGGATGGATGGAAGAA 1 AGTGGGATGGATTGAAGAA 42088522 ACCACAAATT Statistics Matches: 54, Mismatches: 11, Indels: 0 0.83 0.17 0.00 Matches are distributed among these distances: 46 54 1.00 ACGTcount: A:0.34, C:0.14, G:0.28, T:0.24 Consensus pattern (46 bp): AGTGGGATGGATTGAAGAAGATACAAATCCTATACCCCTAAACTAC Found at i:42089163 original size:143 final size:143 Alignment explanation

Indices: 42088880--42089433 Score: 625 Period size: 143 Copynumber: 3.9 Consensus size: 143 42088870 ATAAATTTCT * * 42088880 TCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAACCTTATCT-CCTAAAGTTGCAGCGGA 1 TCTTCCTGAAGTTGCAGTGAAGCAGATTGAAGCCACCAACCTTATCTCCCTGAAGTTGCAGCGGA * ** * * * * ** 42088944 GTAGACTGAAGATAGCGGATTTTATTTCCCT-AACGTTGCACTCGAATTGATTAAAGCTACAAAT 66 GCAGACTGAAGATAGCAAATCTTATTTCCCTGAA-GTTACAGTGGAACAGATTAAAGCTACAAAT 42089008 TATGGCGAATCTTA 130 TATGGCGAATCTTA * * 42089022 TCTTCCTGAAGTTGCAGTGAAGCAGATTGAAGCCACCAGCCTTATCTCCCTGAAGTTGCAGTGGA 1 TCTTCCTGAAGTTGCAGTGAAGCAGATTGAAGCCACCAACCTTATCTCCCTGAAGTTGCAGCGGA * * * 42089087 GCAGACTGAAGATAGCAAATCTCATTTCCCTGAAGTTACAGTGGAACAGATTGATGCTACAAATT 66 GCAGACTGAAGATAGCAAATCTTATTTCCCTGAAGTTACAGTGGAACAGATTAAAGCTACAAATT * 42089152 ATGG-TAGATCTTA 131 ATGGCGA-ATCTTA * ** * * 42089165 TCTTCCT-TAGTTGGGGTGGAA-TAGATTGAAGCCACCAGCCTTATCTCCCTGAAGTTGCAGCGG 1 TCTTCCTGAAGTTGCAGT-GAAGCAGATTGAAGCCACCAACCTTATCTCCCTGAAGTTGCAGCGG * * *** * * * 42089228 AACAGACTGAAGACAGTGGATCTTATTTCCCTGATGTTGCGGTGGAACAGATTAAAGCTACAAAT 65 AGCAGACTGAAGATAGCAAATCTTATTTCCCTGAAGTTACAGTGGAACAGATTAAAGCTACAAAT * 42089293 TACGGCGAATCTTA 130 TATGGCGAATCTTA * * * * 42089307 TCTTCCTTAAGTTGCAGTGGAGCAGATTGAAGCCACCAACCTTGTCTCCCTGAAGTTGCAGTGGA 1 TCTTCCTGAAGTTGCAGTGAAGCAGATTGAAGCCACCAACCTTATCTCCCTGAAGTTGCAGCGGA * * * * ** * * * * 42089372 GTAGATTAAAGATAG-AGAATCTTGTTTCCCTGAAGACACAGAGAAATAGATTGAAGCTACAA 66 GCAGACTGAAGATAGCA-AATCTTATTTCCCTGAAGTTACAGTGGAACAGATTAAAGCTACAA 42089434 GTCACAATCC Statistics Matches: 344, Mismatches: 60, Indels: 15 0.82 0.14 0.04 Matches are distributed among these distances: 142 166 0.48 143 176 0.51 144 2 0.01 ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27 Consensus pattern (143 bp): TCTTCCTGAAGTTGCAGTGAAGCAGATTGAAGCCACCAACCTTATCTCCCTGAAGTTGCAGCGGA GCAGACTGAAGATAGCAAATCTTATTTCCCTGAAGTTACAGTGGAACAGATTAAAGCTACAAATT ATGGCGAATCTTA Found at i:42089235 original size:142 final size:142 Alignment explanation

Indices: 42088880--42089406 Score: 630 Period size: 142 Copynumber: 3.7 Consensus size: 142 42088870 ATAAATTTCT * * * 42088880 TCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAACCTTATCT-CCTAAAGTTGCAGCGGA 1 TCTTCCT-TAGTTGCAGTGGAACAGATTGAAGCCACCAACCTTATCTCCCTGAAGTTGCAGCGGA * * * * ** 42088944 GTAGACTGAAGATAGCGGATTTTATTTCCCT-AACGTTGCACTCGAATTGATTAAAGCTACAAAT 65 GCAGACTGAAGATAGCGGATCTTATTTCCCTGAA-GTTGCAGTGGAACAGATTAAAGCTACAAAT 42089008 TATGGCGAATCTTA 129 TATGGCGAATCTTA * * * 42089022 TCTTCCTGAAGTTGCAGT-GAAGCAGATTGAAGCCACCAGCCTTATCTCCCTGAAGTTGCAGTGG 1 TCTTCCT-TAGTTGCAGTGGAA-CAGATTGAAGCCACCAACCTTATCTCCCTGAAGTTGCAGCGG ** * * * * 42089086 AGCAGACTGAAGATAGCAAATCTCATTTCCCTGAAGTTACAGTGGAACAGATTGATGCTACAAAT 64 AGCAGACTGAAGATAGCGGATCTTATTTCCCTGAAGTTGCAGTGGAACAGATTAAAGCTACAAAT * 42089151 TATGG-TAGATCTTA 129 TATGGCGA-ATCTTA ** * * * 42089165 TCTTCCTTAGTTGGGGTGGAATAGATTGAAGCCACCAGCCTTATCTCCCTGAAGTTGCAGCGGAA 1 TCTTCCTTAGTTGCAGTGGAACAGATTGAAGCCACCAACCTTATCTCCCTGAAGTTGCAGCGGAG * * * * 42089230 CAGACTGAAGACAGTGGATCTTATTTCCCTGATGTTGCGGTGGAACAGATTAAAGCTACAAATTA 66 CAGACTGAAGATAGCGGATCTTATTTCCCTGAAGTTGCAGTGGAACAGATTAAAGCTACAAATTA * 42089295 CGGCGAATCTTA 131 TGGCGAATCTTA * * * 42089307 TCTTCCTTAAGTTGCAGTGGAGCAGATTGAAGCCACCAACCTTGTCTCCCTGAAGTTGCAGTGGA 1 TCTTCCTT-AGTTGCAGTGGAACAGATTGAAGCCACCAACCTTATCTCCCTGAAGTTGCAGCGGA * * * * * * 42089372 GTAGATTAAAGATAGAGAATCTTGTTTCCCTGAAG 65 GCAGACTGAAGATAGCGGATCTTATTTCCCTGAAG 42089407 ACACAGAGAA Statistics Matches: 327, Mismatches: 51, Indels: 13 0.84 0.13 0.03 Matches are distributed among these distances: 141 2 0.01 142 162 0.50 143 161 0.49 144 2 0.01 ACGTcount: A:0.29, C:0.20, G:0.23, T:0.28 Consensus pattern (142 bp): TCTTCCTTAGTTGCAGTGGAACAGATTGAAGCCACCAACCTTATCTCCCTGAAGTTGCAGCGGAG CAGACTGAAGATAGCGGATCTTATTTCCCTGAAGTTGCAGTGGAACAGATTAAAGCTACAAATTA TGGCGAATCTTA Found at i:42089402 original size:285 final size:284 Alignment explanation

Indices: 42088903--42089433 Score: 767 Period size: 285 Copynumber: 1.9 Consensus size: 284 42088893 GCAGTGGAGC ** * * 42088903 AGATTGAAGCCACCAACCTTATCTCCTAAAGTTGCAGCGGAGTAGACTGAAGATAGCGGATTTTA 1 AGATTGAAGCCACCAACCTTATCTCCTAAAGTTGCAGCGGAACAGACTGAAGACAGCGGATCTTA ** * 42088968 TTTCCCTAACGTTGCACTCGAATTGATTAAAGCTACAAATTATGGCGAATCTTATCTTCCTGAAG 66 TTTCCCTAACGTTGCACTCGAACAGATTAAAGCTACAAATTACGGCGAATCTTATCTTCCTGAAG * * 42089033 TTGCAGTGAAGCAGATTGAAGCCACCAGCCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAG 131 TTGCAGTGAAGCAGATTGAAGCCACCAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAG ** * * * 42089098 ATAGCAAATCTCATTTCCCTGAAGTTACAGTGGAACAGATTGATGCTACAAATTATGGTAGATCT 196 ATAGCAAATCTCATTTCCCTGAAGACACAGAGAAACAGATTGAAGCTACAAATTATGGTAGATCT 42089163 TATCTTCCTTAGTTGGGGTGGAAT 261 TATCTTCCTTAGTTGGGGTGGAAT * * * 42089187 AGATTGAAGCCACCAGCCTTATCTCCCTGAAGTTGCAGCGGAACAGACTGAAGACAGTGGATCTT 1 AGATTGAAGCCACCAACCTTATCT-CCTAAAGTTGCAGCGGAACAGACTGAAGACAGCGGATCTT * * ** * * 42089252 ATTTCCCTGATGTTGCGGTGGAACAGATTAAAGCTACAAATTACGGCGAATCTTATCTTCCTTAA 65 ATTTCCCTAACGTTGCACTCGAACAGATTAAAGCTACAAATTACGGCGAATCTTATCTTCCTGAA * * * * 42089317 GTTGCAGTGGAGCAGATTGAAGCCACCAACCTTGTCTCCCTGAAGTTGCAGTGGAGTAGATTAAA 130 GTTGCAGTGAAGCAGATTGAAGCCACCAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAA ** * 42089382 GATAG-AGAATCTTGTTTCCCTGAAGACACAGAGAAATAGATTGAAGCTACAA 195 GATAGCA-AATCTCATTTCCCTGAAGACACAGAGAAACAGATTGAAGCTACAA 42089434 GTCACAATCC Statistics Matches: 215, Mismatches: 30, Indels: 3 0.87 0.12 0.01 Matches are distributed among these distances: 284 24 0.11 285 191 0.89 ACGTcount: A:0.30, C:0.20, G:0.22, T:0.27 Consensus pattern (284 bp): AGATTGAAGCCACCAACCTTATCTCCTAAAGTTGCAGCGGAACAGACTGAAGACAGCGGATCTTA TTTCCCTAACGTTGCACTCGAACAGATTAAAGCTACAAATTACGGCGAATCTTATCTTCCTGAAG TTGCAGTGAAGCAGATTGAAGCCACCAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAG ATAGCAAATCTCATTTCCCTGAAGACACAGAGAAACAGATTGAAGCTACAAATTATGGTAGATCT TATCTTCCTTAGTTGGGGTGGAAT Found at i:42089639 original size:176 final size:176 Alignment explanation

Indices: 42089436--42089992 Score: 755 Period size: 176 Copynumber: 3.2 Consensus size: 176 42089426 AGCTACAAGT ** * * * * 42089436 CACAATCCTTATCTCTTTGAAGTTGCAGTAGAGTAGGAAAATACACAAACTTTATCTCCTTAAAG 1 CACAATCCTTATCTCCCTGAAGTTGCAGTAGAGCAGGAAAATACACAAACCTTATCTCCCTGAAG * ** 42089501 TTACAGTGGAGCAGGTTGAAATTACCAATTCTTATCTCCTTTAAGTTTCAGCAAAGTAGATCGAA 66 TTATAGTGGAGCAGGTTGAAATTACCAATTCTTATCTCCTTTAAGTTTCAGCGGAGTAGATCGAA * * * 42089566 GCTACAAATCTCTTCTCCCTGAAACTACATTGGAG-AGGATCGAAGC 131 GCTACAAATCTCTTCTCCCTGAAATTACATTGGAGCA-AATCGAAGA * * * * 42089612 CACAATCCTTATTTCCCT-AATGTTGCAGTGGAGCAGGAATATACAAAAACCTTATCTCCCTGAA 1 CACAATCCTTATCTCCCTGAA-GTTGCAGTAGAGCAGGAAAATACACAAACCTTATCTCCCTGAA * * * 42089676 GTTTTAGTGGAGCAGGTTGAAATTACCAATTCTTATCTCCTTAAAG-TTCTAGTGGAGTAGATCG 65 GTTATAGTGGAGCAGGTTGAAATTACCAATTCTTATCTCCTTTAAGTTTC-AGCGGAGTAGATCG * * * 42089740 ACGCTACAAATTTCTTCTCTCTGAAATTACATTGGAGCAAATCGAAGA 129 AAGCTACAAATCTCTTCTCCCTGAAATTACATTGGAGCAAATCGAAGA ** * 42089788 CGTAATCCTTATCTCCTTGAAGTTGCAGTAGAGCAGGAAAATACACAAACCTTATCTCCCTGAAG 1 CACAATCCTTATCTCCCTGAAGTTGCAGTAGAGCAGGAAAATACACAAACCTTATCTCCCTGAAG * * * * 42089853 TTGTAGTGCAGCAGGTTGAAATTACCAATTCTTATCTTCTTTAAGTTCCAGCGGAGTAGATCGAA 66 TTATAGTGGAGCAGGTTGAAATTACCAATTCTTATCTCCTTTAAGTTTCAGCGGAGTAGATCGAA * 42089918 GCTACAAATCTCTTCTCCCTGAAATTACATTGGAGTAAATCGAAG- 131 GCTACAAATCTCTTCTCCCTGAAATTACATTGGAGCAAATCGAAGA * 42089963 CTACAAGT-CTCATCTCCCTGAAGTTGCAGT 1 C-ACAA-TCCTTATCTCCCTGAAGTTGCAGT 42089993 GGATTAGAAC Statistics Matches: 331, Mismatches: 43, Indels: 14 0.85 0.11 0.04 Matches are distributed among these distances: 175 6 0.02 176 319 0.96 177 6 0.02 ACGTcount: A:0.31, C:0.21, G:0.18, T:0.30 Consensus pattern (176 bp): CACAATCCTTATCTCCCTGAAGTTGCAGTAGAGCAGGAAAATACACAAACCTTATCTCCCTGAAG TTATAGTGGAGCAGGTTGAAATTACCAATTCTTATCTCCTTTAAGTTTCAGCGGAGTAGATCGAA GCTACAAATCTCTTCTCCCTGAAATTACATTGGAGCAAATCGAAGA Found at i:42089887 original size:88 final size:88 Alignment explanation

Indices: 42089438--42089899 Score: 289 Period size: 88 Copynumber: 5.2 Consensus size: 88 42089428 CTACAAGTCA * * * * 42089438 CAATCCTTATCTCTTTGAAGTTGCAGTAGAGTAGGAAAATACACAAACTTTATCTCCTTAAAGTT 1 CAATCCTTATCTCCTTGAAGTTGCAGTAGAGTAGGAAAATACACAAACCTTATCTCCCTGAAGTT 42089503 ACAGTGGAGCAGGTTGAAATTAC 66 ACAGTGGAGCAGGTTGAAATTAC * * * * * * * * 42089526 CAATTCTTATCTCCTTTAAGTTTCAGCAAAGTA-GATCGAA-GCTACAAATCTCT-TCTCCCTGA 1 CAATCCTTATCTCCTTGAAGTTGCAGTAGAGTAGGA--AAATAC-ACAAACCT-TATCTCCCTGA ** * * *** 42089588 AACTACATTGGAG-AGGATCGAAGCCA- 62 AGTTACAGTGGAGCAGG-TTGAAATTAC * * * * * * 42089614 CAATCCTTATTTCCCT-AATGTTGCAGTGGAGCAGGAATATACAAAAACCTTATCTCCCTGAAGT 1 CAATCCTTATCTCCTTGAA-GTTGCAGTAGAGTAGGAAAATACACAAACCTTATCTCCCTGAAGT ** 42089678 TTTAGTGGAGCAGGTTGAAATTAC 65 TACAGTGGAGCAGGTTGAAATTAC * * * ** ** * * * 42089702 CAATTCTTATCTCCTTAAAGTT-CTAGTGGAGTA-GATCGACGCTACAAA-TTTCTTCTCTCTGA 1 CAATCCTTATCTCCTTGAAGTTGC-AGTAGAGTAGGA-AAATAC-ACAAACCTT-ATCTCCCTGA * * ** * * 42089764 AATTACATTGGAGCAAATCG-AA-GAC 62 AGTTACAGTGGAGCAGGTTGAAATTAC * * 42089789 GTAATCCTTATCTCCTTGAAGTTGCAGTAGAGCAGGAAAATACACAAACCTTATCTCCCTGAAGT 1 -CAATCCTTATCTCCTTGAAGTTGCAGTAGAGTAGGAAAATACACAAACCTTATCTCCCTGAAGT ** * 42089854 TGTAGTGCAGCAGGTTGAAATTAC 65 TACAGTGGAGCAGGTTGAAATTAC * * * 42089878 CAATTCTTATCTTCTTTAAGTT 1 CAATCCTTATCTCCTTGAAGTT 42089900 CCAGCGGAGT Statistics Matches: 266, Mismatches: 86, Indels: 44 0.67 0.22 0.11 Matches are distributed among these distances: 86 1 0.00 87 63 0.24 88 137 0.52 89 64 0.24 90 1 0.00 ACGTcount: A:0.31, C:0.20, G:0.17, T:0.31 Consensus pattern (88 bp): CAATCCTTATCTCCTTGAAGTTGCAGTAGAGTAGGAAAATACACAAACCTTATCTCCCTGAAGTT ACAGTGGAGCAGGTTGAAATTAC Found at i:42090010 original size:44 final size:44 Alignment explanation

Indices: 42089895--42090010 Score: 126 Period size: 44 Copynumber: 2.6 Consensus size: 44 42089885 TATCTTCTTT * * * * 42089895 AAGTTCCAGCGGAGTAGATCGAAGCTACAAATCTCTTCTCCCTG 1 AAGTTACAGTGGAGTAGAACGAAGCTACAAATCTCATCTCCCTG * * * 42089939 AAATTACATTGGAGTA-AATCGAAGCTACAAGTCTCATCTCCCTG 1 AAGTTACAGTGGAGTAGAA-CGAAGCTACAAATCTCATCTCCCTG * * * 42089983 AAGTTGCAGTGGATTAGAACGAGGCTAC 1 AAGTTACAGTGGAGTAGAACGAAGCTAC 42090011 TTGAAGAAGA Statistics Matches: 58, Mismatches: 12, Indels: 4 0.78 0.16 0.05 Matches are distributed among these distances: 43 1 0.02 44 55 0.95 45 2 0.03 ACGTcount: A:0.31, C:0.22, G:0.22, T:0.25 Consensus pattern (44 bp): AAGTTACAGTGGAGTAGAACGAAGCTACAAATCTCATCTCCCTG Found at i:42091314 original size:15 final size:14 Alignment explanation

Indices: 42091294--42091379 Score: 68 Period size: 15 Copynumber: 5.9 Consensus size: 14 42091284 TCTAATACTA 42091294 TTATTTATCTAATTT 1 TTATTTATCT-ATTT 42091309 TTATTTATCTATTT 1 TTATTTATCTATTT * * * 42091323 ATATTTCTACTATTA 1 TTATTTAT-CTATTT 42091338 TTATATT-TCTATTT 1 TTAT-TTATCTATTT 42091352 ATTATATT-TCTATTT 1 -TTAT-TTATCTATTT * * 42091367 ATATTTATATATT 1 TTATTTATCTATT 42091380 AATATTATTT Statistics Matches: 60, Mismatches: 7, Indels: 9 0.79 0.09 0.12 Matches are distributed among these distances: 13 2 0.03 14 23 0.38 15 33 0.55 16 2 0.03 ACGTcount: A:0.28, C:0.07, G:0.00, T:0.65 Consensus pattern (14 bp): TTATTTATCTATTT Found at i:42091343 original size:17 final size:15 Alignment explanation

Indices: 42091321--42091368 Score: 78 Period size: 15 Copynumber: 3.1 Consensus size: 15 42091311 ATTTATCTAT 42091321 TTATATTTCTACTATTA 1 TTATATTTCTA-T-TTA 42091338 TTATATTTCTATTTA 1 TTATATTTCTATTTA 42091353 TTATATTTCTATTTA 1 TTATATTTCTATTTA 42091368 T 1 T 42091369 ATTTATATAT Statistics Matches: 31, Mismatches: 0, Indels: 2 0.94 0.00 0.06 Matches are distributed among these distances: 15 19 0.61 16 1 0.03 17 11 0.35 ACGTcount: A:0.27, C:0.08, G:0.00, T:0.65 Consensus pattern (15 bp): TTATATTTCTATTTA Found at i:42091364 original size:44 final size:44 Alignment explanation

Indices: 42091249--42091389 Score: 122 Period size: 44 Copynumber: 3.3 Consensus size: 44 42091239 TTATTGCTAT * * 42091249 TATTATTATGTTTCT-ATTTATATTTAT-T-TTGT-TATTCTAATAC 1 TATTATTATATTTCTAATTTTTATTTATCTATT-TATATT-T-ATAC * 42091292 TATTATT-TA--TCTAATTTTTATTTATCTATTTATATTTCTAC 1 TATTATTATATTTCTAATTTTTATTTATCTATTTATATTTATAC 42091333 TATTATTATATTTCT-ATTTATTATATT-TCTATTTATATTTATA- 1 TATTATTATATTTCTAATTT-TTAT-TTATCTATTTATATTTATAC * 42091376 TATTAATATTATTT 1 TATTATTA-TATTT 42091390 TCATTATTTT Statistics Matches: 83, Mismatches: 5, Indels: 19 0.78 0.05 0.18 Matches are distributed among these distances: 40 3 0.04 41 21 0.25 42 6 0.07 43 24 0.29 44 27 0.33 45 2 0.02 ACGTcount: A:0.28, C:0.06, G:0.01, T:0.64 Consensus pattern (44 bp): TATTATTATATTTCTAATTTTTATTTATCTATTTATATTTATAC Found at i:42091371 original size:21 final size:20 Alignment explanation

Indices: 42091316--42091379 Score: 65 Period size: 21 Copynumber: 3.0 Consensus size: 20 42091306 TTTTTATTTA * 42091316 TCTATTTATATTTCTACTATTAT 1 TCTATTTATATTTATA-TA-T-T * * 42091339 TATATTTCTATTTATTATATT 1 TCTATTTATATTTA-TATATT 42091360 TCTATTTATATTTATATATT 1 TCTATTTATATTTATATATT 42091380 AATATTATTT Statistics Matches: 35, Mismatches: 5, Indels: 5 0.78 0.11 0.11 Matches are distributed among these distances: 20 6 0.17 21 13 0.37 22 1 0.03 23 13 0.37 24 2 0.06 ACGTcount: A:0.28, C:0.08, G:0.00, T:0.64 Consensus pattern (20 bp): TCTATTTATATTTATATATT Found at i:42091607 original size:3 final size:3 Alignment explanation

Indices: 42091588--42091642 Score: 65 Period size: 3 Copynumber: 18.0 Consensus size: 3 42091578 GAAAGACTTA * * * * 42091588 TAT TAT TCAT TAC TAT TAT TAT TAT TGT TGT TAT TAT TAT TAT TGT 1 TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT 42091634 TAT TAT TAT 1 TAT TAT TAT 42091643 CGTTTTTTTA Statistics Matches: 45, Mismatches: 6, Indels: 2 0.85 0.11 0.04 Matches are distributed among these distances: 3 42 0.93 4 3 0.07 ACGTcount: A:0.27, C:0.04, G:0.05, T:0.64 Consensus pattern (3 bp): TAT Found at i:42091622 original size:18 final size:18 Alignment explanation

Indices: 42091601--42091642 Score: 75 Period size: 18 Copynumber: 2.3 Consensus size: 18 42091591 TATTCATTAC * 42091601 TATTATTATTATTGTTGT 1 TATTATTATTATTGTTAT 42091619 TATTATTATTATTGTTAT 1 TATTATTATTATTGTTAT 42091637 TATTAT 1 TATTAT 42091643 CGTTTTTTTA Statistics Matches: 23, Mismatches: 1, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 18 23 1.00 ACGTcount: A:0.26, C:0.00, G:0.07, T:0.67 Consensus pattern (18 bp): TATTATTATTATTGTTAT Found at i:42091623 original size:15 final size:14 Alignment explanation

Indices: 42091603--42091687 Score: 73 Period size: 15 Copynumber: 5.8 Consensus size: 14 42091593 TTCATTACTA 42091603 TTATTATTATTGTT 1 TTATTATTATTGTT * 42091617 GTTATTATTATTATT 1 -TTATTATTATTGTT * 42091632 GTTATTATTATCGTT 1 -TTATTATTATTGTT * * 42091647 TTTTTATCATTGTT 1 TTATTATTATTGTT * 42091661 ATT-TATATTGTTGTT 1 -TTAT-TATTATTGTT 42091676 TTCATTATTATT 1 TT-ATTATTATT 42091688 ATTCTGTCAT Statistics Matches: 57, Mismatches: 9, Indels: 8 0.77 0.12 0.11 Matches are distributed among these distances: 14 14 0.25 15 42 0.74 16 1 0.02 ACGTcount: A:0.21, C:0.04, G:0.08, T:0.67 Consensus pattern (14 bp): TTATTATTATTGTT Found at i:42095101 original size:955 final size:955 Alignment explanation

Indices: 42092636--42095268 Score: 3737 Period size: 957 Copynumber: 2.8 Consensus size: 955 42092626 CATCAGAATG * * * * 42092636 GATGACACCTAGAAGATATG-GACATAGATGTGACTGACCAGATTAATAGTACGTCAGACTGGAC 1 GATGACTCCTAGAAGATA-GAGACATAGATGTGACTGACCAGATTAACAGTACATTAGACTGGAC * * * * ** 42092700 CTAAGTAGAGTAGATCCTGAAATCATTTATGGATCTATTCACTTGAGACATTTATAGAGTGACAT 65 CCAAGTAGAATAGATCCTG-AATCTTTTATGGATCTATTCACTTGTGACATTTATATTGTGACAT * ** * * * * 42092765 ATGTAAACCCTGAGTGGATGGCGGACTATGTATGTGTGACTTGAACACTTTGGTGTAAGTAAAAG 129 ACGTAATTCTTAAGTGGATGGCGGACTATGTATGCGTGACTTGAACACTTTGATGTAAGTAAAAG * * * * * * * 42092830 CTTGAGTTCAAATAGGTACAAAATTGAAAACTGGTGTGTTGGGTGTACGACTTCTATAGTGTGTA 194 CTTGAGTTCGAATAGATACAAAATCGAAAGCTGGTGCGTTGGCTGTACGACTTCTATAGTATGTA * * ** 42092895 GCATCATTCACAATGGTGGAATTCATAGCCCAAGATATGAGAAAATGATATCCTCTCATAAGCAT 259 ACGTCATTCACAATAATGGAATTCATAGCCCAAGATATGAGAAAATGATATCCTCTCATAAGCAT * * * 42092960 TACATTG-TGATGAGAAGTAAATGTGGCCAGAGGTCATTCGTCTTTGTGATGGATAACTTGATTA 324 TACATTGTTGATGAGAAGTAAATGTGGCCAG-GGTCATTCATCTTTGTGATGGATGACTTGATCA * * * * 42093024 CTATTTAATAGTGATTGACTTTTCATAAATGAAGGTGTAATGATTACCATAAGATAAAATA-TGA 388 CTATTTGATAGTGATTGACTTTTCATGAATGAAGATGTAATGATTACCATAAGATAAAAAAGT-A ** * 42093088 TCATATTGGGAGAACGAATATTATCCCAAAGAGATCAATGATATACTATAAGGGTAACACACTTA 452 TCATATTGGGAGAAC-AATATCGTCCCAAAGAGATCAATGATATACTATGAGGGTAACACACTTA * 42093153 TGACAAGGTCAATGGATGAGCACTGAATAGTTGCTCTTGTAATGGTATGGCTTTAGGGAAAGCTC 516 TGACAAGGTCAATGGATGAGCACTGAATAGTTGCTCTTGTAATGGTATGTCTTTAGGGAAAGCTC * * * 42093218 AGTCACGATACTTTAGTGGAATGCCTTCATGACTAAATGAGTTTATAATTAATAGGCGAAAAGTT 581 AGTCACGATACTTTAGTGGAAAGCCTTCGTGACTAAATGAGTTTATAATTAATAGGTGAAAAGTT * * * * 42093283 AAAACTTAATTATAAATCATTTGAGCTCTAATTACATATGTCC-AATAGGTTCCTCCGCTAGGTC 646 AAAACTTAATTATAAATCATTTAAGCCCTAATTACATATG-CCTAATAGGTCCCTCCGCTAGCTC * * * 42093347 GTTGAAACCAAAAATGAATTGCGTGTTGAATTGAAAATGAATAGAATGAATATAAATAGAGAAAC 710 GTTGAAACCAAAAATGAATTGCATGTTGAATCGAAAATGAATAGAATAAATATAAATAGAGAAAC * * * 42093412 GGAAAACATTCAAAAGTTATTACAGTTTTCTTTGAAATAAAGAAATGAAATCATTTGGAAATGAA 775 GGAAAACATTCAAAAATGATTACAGTTTTCTTTGAAATAAAGAAATGAAATCATTTAGAAATGAA * * 42093477 TATGGTTTTCTCAAAATTGAAATGGAGATGAAAAAGAAAATGAGGAATGATTCATTTGCAAATGT 840 TATGGTTCTCTCAAAATTGAAATGGAGATGAAAAAGAAAATGAGAAATGATTCATTTGCAAATGT * * * * * ** 42093542 ACATGGTTTACTCAAAAATTGTGGAGATGCTTTGTCTTGGGCAACAGAGTG 905 ACATGGATAACTAAAAAATTGTGGAGATGCTATGTCTTAGGCAACAGAGCA * * 42093593 GATGACTCCTAGAAGATAGAGACATAGATGTGACTGACCAGATTAACAGTACATTAGATTGGAGC 1 GATGACTCCTAGAAGATAGAGACATAGATGTGACTGACCAGATTAACAGTACATTAGACTGGACC * * * 42093658 CAAGTAGAATAGATCCTGAATTCTTTTATGGATCTATTCACTTATGACGTTCATATTGTGACATA 66 CAAGTAGAATAGATCCTGAA-TCTTTTATGGATCTATTCACTTGTGACATTTATATTGTGACATA * * 42093723 CGTAATTCTTAAGTGGATGGCGGAGTATGTATGCGTGACTCGAACACTTTGATGTAAGTAAAAGC 130 CGTAATTCTTAAGTGGATGGCGGACTATGTATGCGTGACTTGAACACTTTGATGTAAGTAAAAGC * * * * * * * 42093788 TTGAGTTTGAATAGATACAAAA-CTAAAAGTTGGTGCATTAGCTATACGACTTCTATAGTATGCA 195 TTGAGTTCGAATAGATACAAAATC-GAAAGCTGGTGCGTTGGCTGTACGACTTCTATAGTATGTA * * 42093852 ACGTCATTCACAATAATGGAATTCATAGCCCAAGATATGATAAAATGATATCCTCTCATAATCAT 259 ACGTCATTCACAATAATGGAATTCATAGCCCAAGATATGAGAAAATGATATCCTCTCATAAGCAT * * * * 42093917 TACACTATTGATGAGAAGTAAATGTGGCTAGGGGTCATTCATCTTTGTGATGGA-GACTTGATCG 324 TACATTGTTGATGAGAAGTAAATGTGGCCA-GGGTCATTCATCTTTGTGATGGATGACTTGATCA * 42093981 CTATTTGATAGTGATTGACTTTTCATGAATGAAGATGTAATGATTACCTTAAGATAAAAAAAG-A 388 CTATTTGATAGTGATTGACTTTTCATGAATGAAGATGTAATGATTACCATAAGAT-AAAAAAGTA * * * 42094045 TCATATTGGGAGAAAAAATATCAG-CCCAAAGAGATCAATGATATATTATGAGGGTAACACATTT 452 TCATATTGGGAG-AACAATATC-GTCCCAAAGAGATCAATGATATACTATGAGGGTAACACACTT ** * * * 42094109 ATGGTAAGGTCAATGGATGAGCACTGAATAGTTGCTCTCGTAATGGAATGTCTTTAGAGAAAGCT 515 ATGACAAGGTCAATGGATGAGCACTGAATAGTTGCTCTTGTAATGGTATGTCTTTAGGGAAAGCT * * * 42094174 CAGTTACAATACTTTAGTGGAAGGCCTTCGTGACTAAATGAGTTTATAATTAATAGGTGAAAAGT 580 CAGTCACGATACTTTAGTGGAAAGCCTTCGTGACTAAATGAGTTTATAATTAATAGGTGAAAAGT * 42094239 TAAAACTTAATTATAAATCATTTAATCCCTAATTACATATGCCTAATAGGTCCCTCCGCTAGCTC 645 TAAAACTTAATTATAAATCATTTAAGCCCTAATTACATATGCCTAATAGGTCCCTCCGCTAGCTC * 42094304 GTTGAAATCC-TAAATGAATTGCATGTTGAATCGAAAATGAATAGAATAAATATAAATAGAGAAA 710 GTTGAAA-CCAAAAATGAATTGCATGTTGAATCGAAAATGAATAGAATAAATATAAATAGAGAAA * ** * * 42094368 CGGAAAATATT-AAAAATGATTATGGTTTTCTTTGAAATAGAGAAATGAAATCGTTTAGAAATGA 774 CGGAAAACATTCAAAAATGATTACAGTTTTCTTTGAAATAAAGAAATGAAATCATTTAGAAATGA * * 42094432 ATGTGGTTCTCTCAAAATTTAAATGGAGATGAAAAAGAAAATGAGAAATGATTCATTTGCAAATG 839 ATATGGTTCTCTCAAAATTGAAATGGAGATGAAAAAGAAAATGAGAAATGATTCATTTGCAAATG ** 42094497 TACATGGATAACTAAAAAATTG-GAGAGATGCTATGTCTTAGGCATTAGAGCA 904 TACATGGATAACTAAAAAATTGTG-GAGATGCTATGTCTTAGGCAACAGAGCA * * 42094549 GATGACTCCTAGAAGATAGAGACATAGATGTGACTAACCAGATTGACAGTACATTAGACTGGACC 1 GATGACTCCTAGAAGATAGAGACATAGATGTGACTGACCAGATTAACAGTACATTAGACTGGACC * * * * 42094614 CAAGTAGAATAGATCCT-AATCTGTTTGTGGATCTACTCGCTTGTGATATTTATATTGTGACATA 66 CAAGTAGAATAGATCCTGAATCT-TTTATGGATCTATTCACTTGTGACATTTATATTGTGACATA ** 42094678 CGTAATTCTTAAGTGGATGGCGGACTATGTATGCGTGACTTGTGCACTTTGATGTAAGTAAAAGC 130 CGTAATTCTTAAGTGGATGGCGGACTATGTATGCGTGACTTGAACACTTTGATGTAAGTAAAAGC * * * 42094743 TTGAGTTCGAATAGCTACAAAATCGAAAGCTGGTGCGTTGGTTGCT-CG-TTTCTATAGTATGTA 195 TTGAGTTCGAATAGATACAAAATCGAAAGCTGGTGCGTTGGCTG-TACGACTTCTATAGTATGTA * 42094806 ACGTCATTCACAATAATGGAATTCATAGCCCAAGATATGAGAAAATGATATCCTCTCATAAGAAT 259 ACGTCATTCACAATAATGGAATTCATAGCCCAAGATATGAGAAAATGATATCCTCTCATAAGCAT * ** * * 42094871 TACATTGTTGATGAGAAGCAAACATAGCCACGGGTCATTCATCTTTGTGATGGATGACTTTATCA 324 TACATTGTTGATGAGAAGTAAATGTGGCCA-GGGTCATTCATCTTTGTGATGGATGACTTGATCA * * * 42094936 CTATTTGATAGTGATTGACTTTTTATGAATGAAGATGTAATGACTACCATAAGATAAAACAGTAT 388 CTATTTGATAGTGATTGACTTTTCATGAATGAAGATGTAATGATTACCATAAGATAAAAAAGTAT * * 42095001 CATATTAGGAGAACATAGATCGTCCCAAAGAGATCAATGATATACTATGAGGGTAACACACTTAT 453 CATATTGGGAGAACA-ATATCGTCCCAAAGAGATCAATGATATACTATGAGGGTAACACACTTAT * * * * 42095066 GACAAGGTCATTGGATGAGCACTGAATAATTGCTCTTGTAAGGGTATGTCTTTAGGGAAAGCTTA 517 GACAAGGTCAATGGATGAGCACTGAATAGTTGCTCTTGTAATGGTATGTCTTTAGGGAAAGCTCA * * * * 42095131 GTCATGATACTTTAATGAAAAGCCTTCGTGACTAAATGAGTTTATAATTAATAGGTAAAAAGTTA 582 GTCACGATACTTTAGTGGAAAGCCTTCGTGACTAAATGAGTTTATAATTAATAGGTGAAAAGTTA * ** ** * * 42095196 AAACTTAATTATAACTCATTTAAGCCCTAATTACATATTTCTAATAGGTCCCTTTGCTAGCCCAT 647 AAACTTAATTATAAATCATTTAAGCCCTAATTACATATGCCTAATAGGTCCCTCCGCTAGCTCGT 42095261 TGAAACCA 712 TGAAACCA 42095269 TATGTGACAG Statistics Matches: 1482, Mismatches: 174, Indels: 42 0.87 0.10 0.02 Matches are distributed among these distances: 954 136 0.09 955 426 0.29 956 233 0.16 957 635 0.43 958 51 0.03 959 1 0.00 ACGTcount: A:0.36, C:0.13, G:0.20, T:0.31 Consensus pattern (955 bp): GATGACTCCTAGAAGATAGAGACATAGATGTGACTGACCAGATTAACAGTACATTAGACTGGACC CAAGTAGAATAGATCCTGAATCTTTTATGGATCTATTCACTTGTGACATTTATATTGTGACATAC GTAATTCTTAAGTGGATGGCGGACTATGTATGCGTGACTTGAACACTTTGATGTAAGTAAAAGCT TGAGTTCGAATAGATACAAAATCGAAAGCTGGTGCGTTGGCTGTACGACTTCTATAGTATGTAAC GTCATTCACAATAATGGAATTCATAGCCCAAGATATGAGAAAATGATATCCTCTCATAAGCATTA CATTGTTGATGAGAAGTAAATGTGGCCAGGGTCATTCATCTTTGTGATGGATGACTTGATCACTA TTTGATAGTGATTGACTTTTCATGAATGAAGATGTAATGATTACCATAAGATAAAAAAGTATCAT ATTGGGAGAACAATATCGTCCCAAAGAGATCAATGATATACTATGAGGGTAACACACTTATGACA AGGTCAATGGATGAGCACTGAATAGTTGCTCTTGTAATGGTATGTCTTTAGGGAAAGCTCAGTCA CGATACTTTAGTGGAAAGCCTTCGTGACTAAATGAGTTTATAATTAATAGGTGAAAAGTTAAAAC TTAATTATAAATCATTTAAGCCCTAATTACATATGCCTAATAGGTCCCTCCGCTAGCTCGTTGAA ACCAAAAATGAATTGCATGTTGAATCGAAAATGAATAGAATAAATATAAATAGAGAAACGGAAAA CATTCAAAAATGATTACAGTTTTCTTTGAAATAAAGAAATGAAATCATTTAGAAATGAATATGGT TCTCTCAAAATTGAAATGGAGATGAAAAAGAAAATGAGAAATGATTCATTTGCAAATGTACATGG ATAACTAAAAAATTGTGGAGATGCTATGTCTTAGGCAACAGAGCA Found at i:42096859 original size:30 final size:30 Alignment explanation

Indices: 42096823--42096982 Score: 222 Period size: 29 Copynumber: 5.5 Consensus size: 30 42096813 GACAAGATTG * * * * * 42096823 GCACTAAGTGTGCGGGTTTAAAATTGTACA 1 GCACTAAGTGTGCGAGCTGAAAATTATATA * 42096853 GCACTAAGTGTGCGAGTTTG---ATTATATA 1 GCACTAAGTGTGCGAG-CTGAAAATTATATA 42096881 GCACTAAGTGTGCGAGCTGAAAA-TATATA 1 GCACTAAGTGTGCGAGCTGAAAATTATATA 42096910 GCACTAAGTGTGCGAGCTGAAAATTATATA 1 GCACTAAGTGTGCGAGCTGAAAATTATATA 42096940 GCACTAAGTGTGCGAGCTGAAAA-TATATA 1 GCACTAAGTGTGCGAGCTGAAAATTATATA 42096969 GCACTAAGTGTGCG 1 GCACTAAGTGTGCG 42096983 GATTCACCAT Statistics Matches: 120, Mismatches: 5, Indels: 11 0.88 0.04 0.08 Matches are distributed among these distances: 27 2 0.02 28 22 0.18 29 49 0.41 30 45 0.38 31 2 0.02 ACGTcount: A:0.33, C:0.14, G:0.26, T:0.28 Consensus pattern (30 bp): GCACTAAGTGTGCGAGCTGAAAATTATATA Found at i:42096950 original size:59 final size:57 Alignment explanation

Indices: 42096823--42096982 Score: 223 Period size: 59 Copynumber: 2.8 Consensus size: 57 42096813 GACAAGATTG * * * * * * 42096823 GCACTAAGTGTGCGGGTTTAAAATTGTACAGCACTAAGTGTGCGAGTTTGATTATATA 1 GCACTAAGTGTGCGAGCTGAAAA-TATATAGCACTAAGTGTGCGAGTCTGATTATATA 42096881 GCACTAAGTGTGCGAGCTGAAAATATATAGCACTAAGTGTGCGAG-CTGAAAATTATATA 1 GCACTAAGTGTGCGAGCTGAAAATATATAGCACTAAGTGTGCGAGTCTG---ATTATATA 42096940 GCACTAAGTGTGCGAGCTGAAAATATATAGCACTAAGTGTGCG 1 GCACTAAGTGTGCGAGCTGAAAATATATAGCACTAAGTGTGCG 42096983 GATTCACCAT Statistics Matches: 93, Mismatches: 6, Indels: 5 0.89 0.06 0.05 Matches are distributed among these distances: 56 2 0.02 57 20 0.22 58 20 0.22 59 51 0.55 ACGTcount: A:0.33, C:0.14, G:0.26, T:0.28 Consensus pattern (57 bp): GCACTAAGTGTGCGAGCTGAAAATATATAGCACTAAGTGTGCGAGTCTGATTATATA Found at i:42098487 original size:46 final size:44 Alignment explanation

Indices: 42098434--42098531 Score: 124 Period size: 45 Copynumber: 2.2 Consensus size: 44 42098424 AGAATGAATA * 42098434 TAAATAGAGAAATGGAAAACATTAAAAAATGATTATGGTTTTCTT 1 TAAATAGAGAAAT-GAAAACATTAAAAAATGAATATGGTTTTCTT * ** * * 42098479 TGAAATAGAGAAATGAAATCATTTGAAATTGAATGTGGTTTTCTT 1 T-AAATAGAGAAATGAAAACATTAAAAAATGAATATGGTTTTCTT 42098524 TAAATAGA 1 TAAATAGA 42098532 AATGAAGGTG Statistics Matches: 46, Mismatches: 6, Indels: 3 0.84 0.11 0.05 Matches are distributed among these distances: 44 7 0.15 45 27 0.59 46 12 0.26 ACGTcount: A:0.44, C:0.04, G:0.17, T:0.35 Consensus pattern (44 bp): TAAATAGAGAAATGAAAACATTAAAAAATGAATATGGTTTTCTT Found at i:42108767 original size:39 final size:39 Alignment explanation

Indices: 42108697--42108807 Score: 161 Period size: 39 Copynumber: 2.9 Consensus size: 39 42108687 CTCAATCATA * * * 42108697 TAAACAGTAATTCATTCA-ATAATAGTAATTCATCCGTT 1 TAAACAGTACTTCATCCATATAAAAGTAATTCATCCGTT * * 42108735 TAAACAGTACTTTATCCATATAAAAGTAATTCATCCTTT 1 TAAACAGTACTTCATCCATATAAAAGTAATTCATCCGTT * 42108774 TAAACAGTACTTCATCCATATAACAGTAATTCAT 1 TAAACAGTACTTCATCCATATAAAAGTAATTCAT 42108808 TCGTGTAACA Statistics Matches: 65, Mismatches: 7, Indels: 1 0.89 0.10 0.01 Matches are distributed among these distances: 38 15 0.23 39 50 0.77 ACGTcount: A:0.40, C:0.18, G:0.06, T:0.36 Consensus pattern (39 bp): TAAACAGTACTTCATCCATATAAAAGTAATTCATCCGTT Found at i:42108770 original size:19 final size:20 Alignment explanation

Indices: 42108693--42108807 Score: 121 Period size: 20 Copynumber: 6.0 Consensus size: 20 42108683 CACTCTCAAT * 42108693 CATATAAACAGTAATTCATT 1 CATATAAACAGTAATTCATC * 42108713 CA-AT-AATAGTAATTCATC 1 CATATAAACAGTAATTCATC * * * * 42108731 CGTTTAAACAGTACTTTATC 1 CATATAAACAGTAATTCATC 42108751 CATATAAA-AGTAATTCATC 1 CATATAAACAGTAATTCATC * * * 42108770 CTTTTAAACAGTACTTCATC 1 CATATAAACAGTAATTCATC 42108790 CATAT-AACAGTAATTCAT 1 CATATAAACAGTAATTCAT 42108808 TCGTGTAACA Statistics Matches: 75, Mismatches: 17, Indels: 7 0.76 0.17 0.07 Matches are distributed among these distances: 18 13 0.17 19 30 0.40 20 32 0.43 ACGTcount: A:0.40, C:0.18, G:0.06, T:0.36 Consensus pattern (20 bp): CATATAAACAGTAATTCATC Found at i:42109066 original size:26 final size:24 Alignment explanation

Indices: 42108987--42109077 Score: 87 Period size: 24 Copynumber: 3.8 Consensus size: 24 42108977 CTGATGAACA * 42108987 GTAAGCT-TTATTAAGCTG-AAATG 1 GTAAGCTCTTA-TGAGCTGAAAATG * * * 42109010 GTAAGCTCTGACGAGCTGAAAATA 1 GTAAGCTCTTATGAGCTGAAAATG * 42109034 GTAAGCTCTTATGAGCTGATATATCG 1 GTAAGCTCTTATGAGCTGA-AAAT-G * 42109060 GTAAGCTCATATGAGCTG 1 GTAAGCTCTTATGAGCTG 42109078 TGGTGAGTCC Statistics Matches: 55, Mismatches: 9, Indels: 5 0.80 0.13 0.07 Matches are distributed among these distances: 23 12 0.22 24 23 0.42 25 3 0.05 26 17 0.31 ACGTcount: A:0.32, C:0.14, G:0.24, T:0.30 Consensus pattern (24 bp): GTAAGCTCTTATGAGCTGAAAATG Found at i:42113266 original size:47 final size:47 Alignment explanation

Indices: 42113212--42113333 Score: 187 Period size: 47 Copynumber: 2.6 Consensus size: 47 42113202 GGTAAGGTGC * 42113212 CGATGCCATGTCCTAGACATAGTCTTACATTGGCTTAT-ATCTCA-AAT 1 CGATGCCATGTCCCAGACAT-GTCTTACATTGGC-TATCATCTCATAAT 42113259 CGATGCCATGTCCCAGACATGGTCTTACATTGGCTATCATCTCATAAT 1 CGATGCCATGTCCCAGACAT-GTCTTACATTGGCTATCATCTCATAAT 42113307 CGATG-CATGTCCCAGACATGTCTTACA 1 CGATGCCATGTCCCAGACATGTCTTACA 42113334 CTGGTTTACG Statistics Matches: 71, Mismatches: 2, Indels: 5 0.91 0.03 0.06 Matches are distributed among these distances: 46 11 0.15 47 52 0.73 48 8 0.11 ACGTcount: A:0.26, C:0.26, G:0.16, T:0.31 Consensus pattern (47 bp): CGATGCCATGTCCCAGACATGTCTTACATTGGCTATCATCTCATAAT Found at i:42113362 original size:46 final size:45 Alignment explanation

Indices: 42113307--42113475 Score: 160 Period size: 46 Copynumber: 3.6 Consensus size: 45 42113297 ATCTCATAAT * * 42113307 CGATGCATGTCCCAGACATGTCTTACACTGGTTTACGTCTCGAGGC 1 CGATACATGTCCCAGACATGTCTTACACTGGTCT-CGTCTCGAGGC * * ** * * 42113353 CGGTACATGTCCTAGACATGTCTTACACTAGCCCTCGTCTCAATGC 1 CGATACATGTCCCAGACATGTCTTACACT-GGTCTCGTCTCGAGGC * * * * 42113399 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAAT-GTGGC 1 CGAT-ACATGTCCCAGACAT-GTCTTACACTGG-TCTCGT-CTCGAGGC * 42113447 CGATGCATGTCCCAGACATGTCTTACACT 1 CGATACATGTCCCAGACATGTCTTACACT 42113476 AGCTTACACA Statistics Matches: 99, Mismatches: 19, Indels: 10 0.77 0.15 0.08 Matches are distributed among these distances: 46 48 0.48 47 30 0.30 48 20 0.20 49 1 0.01 ACGTcount: A:0.21, C:0.30, G:0.21, T:0.28 Consensus pattern (45 bp): CGATACATGTCCCAGACATGTCTTACACTGGTCTCGTCTCGAGGC Found at i:42113457 original size:94 final size:92 Alignment explanation

Indices: 42113307--42113478 Score: 231 Period size: 94 Copynumber: 1.8 Consensus size: 92 42113297 ATCTCATAAT * * * * * 42113307 CGATGCATGTCCCAGACATGTCTTACACTGGTTTACGTCTCGAGGCCGGTACATGTCCTAGACAT 1 CGATGCATGTCCCAGACATGTCTTACACTGGTCTACATATCGAGGCCGATACATGTCCCAGACAT 42113372 GTCTTACACTAGCCCTCGTCTCAATGC 66 GTCTTACACTAGCCCTCGTCTCAATGC * * 42113399 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCT-CATAAT-GTGGCCGATGCATGTCCCAG 1 CGATG-CATGTCCCAGACAT-GTCTTACACTGG-TCTACAT-ATCGAGGCCGATACATGTCCCAG 42113462 ACATGTCTTACACTAGC 62 ACATGTCTTACACTAGC 42113479 TTACACACGA Statistics Matches: 69, Mismatches: 7, Indels: 6 0.84 0.09 0.07 Matches are distributed among these distances: 92 5 0.07 93 14 0.20 94 47 0.68 95 3 0.04 ACGTcount: A:0.22, C:0.30, G:0.21, T:0.27 Consensus pattern (92 bp): CGATGCATGTCCCAGACATGTCTTACACTGGTCTACATATCGAGGCCGATACATGTCCCAGACAT GTCTTACACTAGCCCTCGTCTCAATGC Found at i:42117152 original size:172 final size:172 Alignment explanation

Indices: 42116859--42117204 Score: 541 Period size: 172 Copynumber: 2.0 Consensus size: 172 42116849 GACAGAAAGT * * * * 42116859 ATAAAATTTAAGGATTAAAACTATTATTATTCTAACTAAAAAATATTACTATTAGTCATTTATTG 1 ATAAAAATTAAGGATTAAAACTATTATTATACCAACTAAAAAATATTACTATTAGTCATTTATAG * * * 42116924 ATTGGGTGATAAAAGAAAAATAATTTCGAAAATGTTAGCGATCAAACTGTAATTCTTTTTTCTAA 66 ATTGGGTGACAAAAGAAAAACAATTTCAAAAATGTTAGCGATCAAACTGTAATTCTTTTTTCTAA * * 42116989 TTAAGTGATCCAAATGAAAATTTAGTCATAAATGAGTGACTA 131 TTAAGTAATCAAAATGAAAATTTAGTCATAAATGAGTGACTA * * * * 42117031 ATAAAAATTAAGGATTAAAATTGTTATTATACCAACTAAAAAGTGTTACTATTAGTCATTTAATA 1 ATAAAAATTAAGGATTAAAACTATTATTATACCAACTAAAAAATATTACTATTAGTCATTT-ATA 42117096 G-TTGGGTGACAAAAGAAAAACAATTTCAAAAATGTTAGCGATCAAACTGTAATTCTTTTTTCTA 65 GATTGGGTGACAAAAGAAAAACAATTTCAAAAATGTTAGCGATCAAACTGTAATTCTTTTTTCTA * * 42117160 GTTAAGTAATCAAAATGAAAATTTATTCATAAATGAGTGACTA 130 ATTAAGTAATCAAAATGAAAATTTAGTCATAAATGAGTGACTA 42117203 AT 1 AT 42117205 GATATAGTTT Statistics Matches: 158, Mismatches: 15, Indels: 2 0.90 0.09 0.01 Matches are distributed among these distances: 172 155 0.98 173 3 0.02 ACGTcount: A:0.43, C:0.09, G:0.12, T:0.36 Consensus pattern (172 bp): ATAAAAATTAAGGATTAAAACTATTATTATACCAACTAAAAAATATTACTATTAGTCATTTATAG ATTGGGTGACAAAAGAAAAACAATTTCAAAAATGTTAGCGATCAAACTGTAATTCTTTTTTCTAA TTAAGTAATCAAAATGAAAATTTAGTCATAAATGAGTGACTA Found at i:42129757 original size:46 final size:46 Alignment explanation

Indices: 42129690--42129865 Score: 214 Period size: 46 Copynumber: 3.8 Consensus size: 46 42129680 TATTTGGGCA * 42129690 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGCTTATGGATGCGAGCG 1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG * * * * 42129736 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA 1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG---CGA-GCG * * 42129783 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAACG 1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG * * 42129829 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG 1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG 42129866 GCGGGTTACA Statistics Matches: 111, Mismatches: 12, Indels: 14 0.81 0.09 0.10 Matches are distributed among these distances: 43 4 0.04 45 2 0.02 46 67 0.60 47 33 0.30 48 2 0.02 50 3 0.03 ACGTcount: A:0.20, C:0.22, G:0.30, T:0.28 Consensus pattern (46 bp): TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG Found at i:42129845 original size:93 final size:93 Alignment explanation

Indices: 42129686--42129857 Score: 299 Period size: 93 Copynumber: 1.8 Consensus size: 93 42129676 GGGATATTTG * * * * 42129686 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCGCTTATGGATGCGAGCGTCCGAACTCGTTGAG 1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAACGCCCGAACTCGTTGAG 42129751 TTGAGTCCGAGTTCGTGAGATGTAACTA 66 TTGAGTCCGAGTTCGTGAGATGTAACTA * 42129779 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAACGCCCGAGCTCGTTGAG 1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAACGCCCGAACTCGTTGAG 42129844 TTGAGTCCGAGTTC 66 TTGAGTCCGAGTTC 42129858 ACTTATGGGC Statistics Matches: 74, Mismatches: 5, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 93 74 1.00 ACGTcount: A:0.20, C:0.22, G:0.30, T:0.27 Consensus pattern (93 bp): GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAACGCCCGAACTCGTTGAG TTGAGTCCGAGTTCGTGAGATGTAACTA Found at i:42132718 original size:24 final size:23 Alignment explanation

Indices: 42132685--42132792 Score: 83 Period size: 24 Copynumber: 4.5 Consensus size: 23 42132675 TTCAGGCAGT 42132685 ATAATAGGAAGCTCATAAGAGCC 1 ATAATAGGAAGCTCATAAGAGCC * 42132708 ATAATTAGGAAGCTCATGAGAGCC 1 ATAA-TAGGAAGCTCATAAGAGCC ** * ** 42132732 AATAACGGGTAGCTCCGAAGAGCC 1 -ATAATAGGAAGCTCATAAGAGCC * * 42132756 ATTAACAGGAAGCTCCA-AATAGCC 1 A-TAATAGGAAGCT-CATAAGAGCC 42132780 ATACATTAGGAAG 1 ATA-A-TAGGAAG 42132793 TTCAAGCGAG Statistics Matches: 67, Mismatches: 12, Indels: 10 0.75 0.13 0.11 Matches are distributed among these distances: 23 7 0.10 24 49 0.73 25 11 0.16 ACGTcount: A:0.40, C:0.19, G:0.23, T:0.18 Consensus pattern (23 bp): ATAATAGGAAGCTCATAAGAGCC Found at i:42132857 original size:25 final size:26 Alignment explanation

Indices: 42132822--42132880 Score: 75 Period size: 26 Copynumber: 2.3 Consensus size: 26 42132812 GAAGCTTTGG 42132822 AGAGCCATTAA-TCAGAAGCTCACAA 1 AGAGCCATTAACTCAGAAGCTCACAA * ** * 42132847 AGAGCCTTTAACTGGGAAGCTCACTA 1 AGAGCCATTAACTCAGAAGCTCACAA 42132873 AGAGCCAT 1 AGAGCCAT 42132881 ATATCAAGAT Statistics Matches: 28, Mismatches: 5, Indels: 1 0.82 0.15 0.03 Matches are distributed among these distances: 25 10 0.36 26 18 0.64 ACGTcount: A:0.37, C:0.24, G:0.20, T:0.19 Consensus pattern (26 bp): AGAGCCATTAACTCAGAAGCTCACAA Found at i:42133390 original size:5 final size:5 Alignment explanation

Indices: 42133361--42133399 Score: 51 Period size: 5 Copynumber: 7.6 Consensus size: 5 42133351 TAAATTTAAC * * 42133361 TCAAT TTAAT ACAAT TCATAT TCAAT TCAAT TCAAT TCA 1 TCAAT TCAAT TCAAT TCA-AT TCAAT TCAAT TCAAT TCA 42133400 CACCTTAGGC Statistics Matches: 29, Mismatches: 4, Indels: 2 0.83 0.11 0.06 Matches are distributed among these distances: 5 24 0.83 6 5 0.17 ACGTcount: A:0.41, C:0.18, G:0.00, T:0.41 Consensus pattern (5 bp): TCAAT Found at i:42137108 original size:6 final size:6 Alignment explanation

Indices: 42137097--42137283 Score: 154 Period size: 6 Copynumber: 30.8 Consensus size: 6 42137087 AACCAAAATG * 42137097 AGAATC AGAATC AGAATC AGTAA-C AGAATC AGAATC AGAATC A-ATATT 1 AGAATC AGAATC AGAATC AG-AATC AGAATC AGAATC AGAATC AGA-ATC * * * * 42137145 AGTAA-C AGAATT AGAATT AGAATC AGAATT AG-GTGAC AGAATC AGAATC 1 AG-AATC AGAATC AGAATC AGAATC AGAATC AGAAT--C AGAATC AGAATC * * 42137194 AGAATC AGTAA-C AGAATC AGAATC AGAATC AGTATT AGTAA-C AGAATC 1 AGAATC AG-AATC AGAATC AGAATC AGAATC AGAATC AG-AATC AGAATC * * * 42137242 AAAATC AGAATC AGAATT ATGTGA-C AGAATC AGAATC AGAAT 1 AGAATC AGAATC AGAATC A-G-AATC AGAATC AGAATC AGAAT 42137284 GTGAATGCAA Statistics Matches: 147, Mismatches: 18, Indels: 32 0.75 0.09 0.16 Matches are distributed among these distances: 5 11 0.07 6 123 0.84 7 10 0.07 8 3 0.02 ACGTcount: A:0.49, C:0.13, G:0.17, T:0.21 Consensus pattern (6 bp): AGAATC Found at i:42137112 original size:30 final size:30 Alignment explanation

Indices: 42137076--42137283 Score: 209 Period size: 30 Copynumber: 7.1 Consensus size: 30 42137066 AAGAAACATT * * 42137076 ATCAGAATT-GGAACCAAAATGAGAATCAGA 1 ATCAGAATTAGGAA-CAGAATCAGAATCAGA * * 42137106 ATCAGAATCAGTAACAGAATCAGAATCAGA 1 ATCAGAATTAGGAACAGAATCAGAATCAGA * * * 42137136 ATCA-ATATTAGTAACAGAATTAGAATTAGA 1 ATCAGA-ATTAGGAACAGAATCAGAATCAGA * 42137166 ATCAGAATTAGGTGACAGAATCAGAATCAGA 1 ATCAGAATTAGG-AACAGAATCAGAATCAGA 42137197 ATCAG---T---AACAGAATCAGAATCAGA 1 ATCAGAATTAGGAACAGAATCAGAATCAGA * * * 42137221 ATCAGTATTAGTAACAGAATCAAAATCAGA 1 ATCAGAATTAGGAACAGAATCAGAATCAGA 42137251 ATCAGAATTATGTG-ACAGAATCAGAATCAGA 1 ATCAGAATTA-G-GAACAGAATCAGAATCAGA 42137282 AT 1 AT 42137284 GTGAATGCAA Statistics Matches: 150, Mismatches: 16, Indels: 23 0.79 0.08 0.12 Matches are distributed among these distances: 24 22 0.15 27 1 0.01 28 1 0.01 29 1 0.01 30 82 0.55 31 43 0.29 ACGTcount: A:0.49, C:0.13, G:0.17, T:0.21 Consensus pattern (30 bp): ATCAGAATTAGGAACAGAATCAGAATCAGA Found at i:42137197 original size:85 final size:85 Alignment explanation

Indices: 42137097--42137283 Score: 329 Period size: 85 Copynumber: 2.2 Consensus size: 85 42137087 AACCAAAATG * * 42137097 AGAATCAGAATCAGAATCAGTAACAGAATCAGAATCAGAATCAATATTAGTAACAGAATTAGAAT 1 AGAATCAGAATCAGAATCAGTAACAGAATCAGAATCAGAATCAATATTAGTAACAGAATCAAAAT * 42137162 TAGAATCAGAATTAGGTGAC 66 CAGAATCAGAATTAGGTGAC * 42137182 AGAATCAGAATCAGAATCAGTAACAGAATCAGAATCAGAATCAGTATTAGTAACAGAATCAAAAT 1 AGAATCAGAATCAGAATCAGTAACAGAATCAGAATCAGAATCAATATTAGTAACAGAATCAAAAT * 42137247 CAGAATCAGAATTATGTGAC 66 CAGAATCAGAATTAGGTGAC 42137267 AGAATCAGAATCAGAAT 1 AGAATCAGAATCAGAAT 42137284 GTGAATGCAA Statistics Matches: 97, Mismatches: 5, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 85 97 1.00 ACGTcount: A:0.49, C:0.13, G:0.17, T:0.21 Consensus pattern (85 bp): AGAATCAGAATCAGAATCAGTAACAGAATCAGAATCAGAATCAATATTAGTAACAGAATCAAAAT CAGAATCAGAATTAGGTGAC Found at i:42137438 original size:27 final size:26 Alignment explanation

Indices: 42137401--42137466 Score: 87 Period size: 27 Copynumber: 2.5 Consensus size: 26 42137391 AGCATGGCTG * 42137401 CCAGAACAGATATCGTGACAGAGTCA 1 CCAGAACAGATATCGTGACAGAGCCA * * 42137427 CCAGATACAGATATTGTGGCAGAGCCA 1 CCAGA-ACAGATATCGTGACAGAGCCA 42137454 CCAGAATCAGATA 1 CCAGAA-CAGATA 42137467 ATGTGGCAAA Statistics Matches: 35, Mismatches: 3, Indels: 3 0.85 0.07 0.07 Matches are distributed among these distances: 26 6 0.17 27 29 0.83 ACGTcount: A:0.38, C:0.23, G:0.23, T:0.17 Consensus pattern (26 bp): CCAGAACAGATATCGTGACAGAGCCA Found at i:42137471 original size:27 final size:27 Alignment explanation

Indices: 42137401--42137474 Score: 82 Period size: 27 Copynumber: 2.8 Consensus size: 27 42137391 AGCATGGCTG * * 42137401 CCAGAA-CAGAT-ATCGTGACAGAGTCA 1 CCAGAATCAGATAAT-GTGGCAGAGCCA * 42137427 CCAG-ATACAGATATTGTGGCAGAGCCA 1 CCAGAAT-CAGATAATGTGGCAGAGCCA 42137454 CCAGAATCAGATAATGTGGCA 1 CCAGAATCAGATAATGTGGCA 42137475 AACCCACCTA Statistics Matches: 40, Mismatches: 4, Indels: 7 0.78 0.08 0.14 Matches are distributed among these distances: 25 1 0.03 26 4 0.10 27 32 0.80 28 3 0.08 ACGTcount: A:0.36, C:0.22, G:0.24, T:0.18 Consensus pattern (27 bp): CCAGAATCAGATAATGTGGCAGAGCCA Found at i:42137481 original size:27 final size:27 Alignment explanation

Indices: 42137425--42137482 Score: 73 Period size: 27 Copynumber: 2.1 Consensus size: 27 42137415 GTGACAGAGT * * * 42137425 CACCAGATACAGATATTGTGGCAGAGC 1 CACCAGATACAGATAATGTGGCAAACC 42137452 CACCAGA-ATCAGATAATGTGGCAAACC 1 CACCAGATA-CAGATAATGTGGCAAACC 42137479 CACC 1 CACC 42137483 TAACAGAATA Statistics Matches: 27, Mismatches: 3, Indels: 2 0.84 0.09 0.06 Matches are distributed among these distances: 26 1 0.04 27 26 0.96 ACGTcount: A:0.36, C:0.28, G:0.21, T:0.16 Consensus pattern (27 bp): CACCAGATACAGATAATGTGGCAAACC Found at i:42137687 original size:22 final size:22 Alignment explanation

Indices: 42137639--42137697 Score: 64 Period size: 22 Copynumber: 2.7 Consensus size: 22 42137629 GTAAATACGT * 42137639 TTGGCACGAAGCCATAGTCAAG 1 TTGGCACAAAGCCATAGTCAAG * * * * 42137661 ATGGCACAAAGCCATATTTAGG 1 TTGGCACAAAGCCATAGTCAAG * 42137683 TTGGCACAGAGCCAT 1 TTGGCACAAAGCCAT 42137698 TAATAACGGG Statistics Matches: 30, Mismatches: 7, Indels: 0 0.81 0.19 0.00 Matches are distributed among these distances: 22 30 1.00 ACGTcount: A:0.32, C:0.22, G:0.25, T:0.20 Consensus pattern (22 bp): TTGGCACAAAGCCATAGTCAAG Found at i:42137850 original size:27 final size:26 Alignment explanation

Indices: 42137787--42137865 Score: 86 Period size: 27 Copynumber: 3.0 Consensus size: 26 42137777 GATCGGTCAA * * * * 42137787 CAGATATTGTGACAGAGTCACCACATA 1 CAGATATTGTGGCAGAGCCACCAGA-C * 42137814 CAGATATTGTGGTAGAGCCACCAGAC 1 CAGATATTGTGGCAGAGCCACCAGAC * 42137840 CAGATATTTGTGGCATAGCCACCAGA 1 CAGATA-TTGTGGCAGAGCCACCAGA 42137866 ACGCTTCCTC Statistics Matches: 44, Mismatches: 7, Indels: 2 0.83 0.13 0.04 Matches are distributed among these distances: 26 6 0.14 27 38 0.86 ACGTcount: A:0.33, C:0.23, G:0.23, T:0.22 Consensus pattern (26 bp): CAGATATTGTGGCAGAGCCACCAGAC Found at i:42138084 original size:27 final size:28 Alignment explanation

Indices: 42138022--42138085 Score: 69 Period size: 27 Copynumber: 2.4 Consensus size: 28 42138012 CAATCACTTG * 42138022 CCCACAAGGGCAAAACAGTCATTTAACA 1 CCCACAAGGGCAAAACAGTAATTTAACA * ** * 42138050 CCC-TAAGGGCAAAATGGTAATTTTAC- 1 CCCACAAGGGCAAAACAGTAATTTAACA 42138076 CCCACAAGGG 1 CCCACAAGGG 42138086 TATCTCGGTA Statistics Matches: 29, Mismatches: 6, Indels: 3 0.76 0.16 0.08 Matches are distributed among these distances: 26 3 0.10 27 23 0.79 28 3 0.10 ACGTcount: A:0.38, C:0.27, G:0.19, T:0.17 Consensus pattern (28 bp): CCCACAAGGGCAAAACAGTAATTTAACA Found at i:42138095 original size:27 final size:27 Alignment explanation

Indices: 42138065--42138260 Score: 248 Period size: 27 Copynumber: 7.3 Consensus size: 27 42138055 AGGGCAAAAT * * * * 42138065 GGTAATTTTACCCCACAAGGGTATCTC 1 GGTAATTCTACCCTACAGGGGTATTTC 42138092 GGTAATTCTACCCTACAGGGGTATTTC 1 GGTAATTCTACCCTACAGGGGTATTTC * * 42138119 GGTATTTCTACCCTACAAGGGTATTTC 1 GGTAATTCTACCCTACAGGGGTATTTC * * 42138146 GATAATTCTACCCTACAGGGGTATTTT 1 GGTAATTCTACCCTACAGGGGTATTTC * * * * 42138173 GGTAATTCTATCCTATAAGGGTATTTT 1 GGTAATTCTACCCTACAGGGGTATTTC * * 42138200 AGTAATTCTACCCTATAGGGGTATTTC 1 GGTAATTCTACCCTACAGGGGTATTTC * 42138227 GGAAATTCTACCCTACAGGGGTATTTC 1 GGTAATTCTACCCTACAGGGGTATTTC * 42138254 AGTAATT 1 GGTAATT 42138261 TCACAATCAA Statistics Matches: 146, Mismatches: 23, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 27 146 1.00 ACGTcount: A:0.26, C:0.19, G:0.19, T:0.36 Consensus pattern (27 bp): GGTAATTCTACCCTACAGGGGTATTTC Found at i:42138295 original size:27 final size:27 Alignment explanation

Indices: 42138265--42138539 Score: 358 Period size: 27 Copynumber: 10.2 Consensus size: 27 42138255 GTAATTTCAC * * 42138265 AATCAAGGGTGAAACGGTAATTCTGTA 1 AATCGAGGGTAAAACGGTAATTCTGTA * * 42138292 AATCGAGGGTAAAACGATAATTTTGTA 1 AATCGAGGGTAAAACGGTAATTCTGTA * * 42138319 AA-CTGAGGGTAAACCAGTAATTCTGTA 1 AATC-GAGGGTAAAACGGTAATTCTGTA * * * ** 42138346 AATCAAGGGTAAAACGATAATTTTACA 1 AATCGAGGGTAAAACGGTAATTCTGTA * 42138373 AATCGAGGGTAAAACGGTAATTCTATA 1 AATCGAGGGTAAAACGGTAATTCTGTA * 42138400 AATCGAGGGTAAAACAGTAATTCTGTA 1 AATCGAGGGTAAAACGGTAATTCTGTA 42138427 AA-CTGAGGGTAAAACGGTAATTCTGTA 1 AATC-GAGGGTAAAACGGTAATTCTGTA * 42138454 AATCGAGGGTAAAACGGTAATTTTAG-A 1 AATCGAGGGTAAAACGGTAATTCT-GTA * 42138481 AATCGAGGGTAAAACGATAATTCTGTA 1 AATCGAGGGTAAAACGGTAATTCTGTA * 42138508 AATCAAGGGTAAAACGGTAATTCTGTA 1 AATCGAGGGTAAAACGGTAATTCTGTA 42138535 AATCG 1 AATCG 42138540 GGAGTACTTT Statistics Matches: 214, Mismatches: 28, Indels: 12 0.84 0.11 0.05 Matches are distributed among these distances: 26 3 0.01 27 208 0.97 28 3 0.01 ACGTcount: A:0.40, C:0.11, G:0.23, T:0.26 Consensus pattern (27 bp): AATCGAGGGTAAAACGGTAATTCTGTA Found at i:42138559 original size:81 final size:81 Alignment explanation

Indices: 42138265--42138539 Score: 396 Period size: 81 Copynumber: 3.4 Consensus size: 81 42138255 GTAATTTCAC * * 42138265 AATCAAGGGTGAAACGGTAATTCTGTAAATCGAGGGTAAAACGATAATTTT-GTAAA-CTGAGGG 1 AATCAAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAACGGTAATTTTAG-AAATC-GAGGG * 42138328 TAAACCAGTAATTCTGTA 64 TAAAACAGTAATTCTGTA * * ** * * 42138346 AATCAAGGGTAAAACGATAATTTTACAAATCGAGGGTAAAACGGTAATTCTATAAATCGAGGGTA 1 AATCAAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAACGGTAATTTTAGAAATCGAGGGTA 42138411 AAACAGTAATTCTGTA 66 AAACAGTAATTCTGTA * 42138427 AA-CTGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAACGGTAATTTTAGAAATCGAGGGT 1 AATC-AAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAACGGTAATTTTAGAAATCGAGGGT 42138491 AAAAC-GATAATTCTGTA 65 AAAACAG-TAATTCTGTA 42138508 AATCAAGGGTAAAACGGTAATTCTGTAAATCG 1 AATCAAGGGTAAAACGGTAATTCTGTAAATCG 42138540 GGAGTACTTT Statistics Matches: 172, Mismatches: 17, Indels: 10 0.86 0.09 0.05 Matches are distributed among these distances: 80 2 0.01 81 168 0.98 82 2 0.01 ACGTcount: A:0.40, C:0.11, G:0.23, T:0.26 Consensus pattern (81 bp): AATCAAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAACGGTAATTTTAGAAATCGAGGGTA AAACAGTAATTCTGTA Found at i:42146603 original size:26 final size:26 Alignment explanation

Indices: 42146510--42146595 Score: 111 Period size: 26 Copynumber: 3.3 Consensus size: 26 42146500 GCCACATCAA * * ** 42146510 GAAGCTC-CAGAGAGCCATTAATTAG 1 GAAGCTCACAAAGAGCCTTTAATCGG * * 42146535 AAAGCTTACAAAGAGCCTTTAATCGG 1 GAAGCTCACAAAGAGCCTTTAATCGG 42146561 GAAGCTCACAAAGAGCCTTTAATCGG 1 GAAGCTCACAAAGAGCCTTTAATCGG 42146587 GAAGCTCAC 1 GAAGCTCAC 42146596 TCAGAGCCAT Statistics Matches: 52, Mismatches: 8, Indels: 1 0.85 0.13 0.02 Matches are distributed among these distances: 25 5 0.10 26 47 0.90 ACGTcount: A:0.36, C:0.22, G:0.22, T:0.20 Consensus pattern (26 bp): GAAGCTCACAAAGAGCCTTTAATCGG Found at i:42153975 original size:272 final size:272 Alignment explanation

Indices: 42153489--42154033 Score: 1054 Period size: 272 Copynumber: 2.0 Consensus size: 272 42153479 GTGTTCCACC 42153489 TCTCTTAGCTTGATATTTAGTTTGATTTCTTTGAGAAAGCTTTAAAAGTTTACACATTAATATTT 1 TCTCTTAGCTTGATATTTAGTTTGATTTCTTTGAGAAAGCTTTAAAAGTTTACACATTAATATTT 42153554 AGTTATATTTTTGTGTATGAGAAAATGATGGATAATGGAATTTCAAACTAGTGTACAATGGATTC 66 AGTTATATTTTTGTGTATGAGAAAATGATGGATAATGGAATTTCAAACTAGTGTACAATGGATTC * 42153619 AAGTGAATGAAGGTTTGGTTTTGAGTATAAATGCATCCAAGAGATAAGTACCCTTGGATACTCTT 131 AAGTGAATGAAGGTTTGGTTTTGAGTATAAATACATCCAAGAGATAAGTACCCTTGGATACTCTT * 42153684 ACTTTTCCTATACTAATATGTTTAGAAAATTGGTGGAATTGTATAATAAATATGAGACTAATCAT 196 ACTTTTCCTATACTAATATGTTTAGAAAAGTGGTGGAATTGTATAATAAATATGAGACTAATCAT 42153749 GCAATGAATATA 261 GCAATGAATATA 42153761 TCTCTTAGCTTGATATTTAGTTTGATTTCTTTGAGAAAGCTTTAAAAGTTTACACATTAATATTT 1 TCTCTTAGCTTGATATTTAGTTTGATTTCTTTGAGAAAGCTTTAAAAGTTTACACATTAATATTT 42153826 AGTTATATTTTTGTGTATGAGAAAATGATGGATAATGGAATTTCAAACTAGTGTACAATGGATTC 66 AGTTATATTTTTGTGTATGAGAAAATGATGGATAATGGAATTTCAAACTAGTGTACAATGGATTC ** 42153891 AAGTGAATGAAGGTTTGGTTTTGAGTATAAATACATCCAAGAGATAAGTATTCTTGGATACTCTT 131 AAGTGAATGAAGGTTTGGTTTTGAGTATAAATACATCCAAGAGATAAGTACCCTTGGATACTCTT 42153956 ACTTTTCCTATACTAATATGTTTAGAAAAGTGGTGGAATTGTATAATAAATATGAGACTAATCAT 196 ACTTTTCCTATACTAATATGTTTAGAAAAGTGGTGGAATTGTATAATAAATATGAGACTAATCAT 42154021 GCAATGAATATA 261 GCAATGAATATA 42154033 T 1 T 42154034 GTAAGTCTCA Statistics Matches: 269, Mismatches: 4, Indels: 0 0.99 0.01 0.00 Matches are distributed among these distances: 272 269 1.00 ACGTcount: A:0.35, C:0.09, G:0.18, T:0.39 Consensus pattern (272 bp): TCTCTTAGCTTGATATTTAGTTTGATTTCTTTGAGAAAGCTTTAAAAGTTTACACATTAATATTT AGTTATATTTTTGTGTATGAGAAAATGATGGATAATGGAATTTCAAACTAGTGTACAATGGATTC AAGTGAATGAAGGTTTGGTTTTGAGTATAAATACATCCAAGAGATAAGTACCCTTGGATACTCTT ACTTTTCCTATACTAATATGTTTAGAAAAGTGGTGGAATTGTATAATAAATATGAGACTAATCAT GCAATGAATATA Found at i:42154398 original size:24 final size:24 Alignment explanation

Indices: 42154366--42154414 Score: 98 Period size: 24 Copynumber: 2.0 Consensus size: 24 42154356 ACTGTAATCA 42154366 GTAATTTAATTGTTTGGTTGAATG 1 GTAATTTAATTGTTTGGTTGAATG 42154390 GTAATTTAATTGTTTGGTTGAATG 1 GTAATTTAATTGTTTGGTTGAATG 42154414 G 1 G 42154415 AATAGAATAG Statistics Matches: 25, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 24 25 1.00 ACGTcount: A:0.24, C:0.00, G:0.27, T:0.49 Consensus pattern (24 bp): GTAATTTAATTGTTTGGTTGAATG Found at i:42154612 original size:26 final size:25 Alignment explanation

Indices: 42154583--42154666 Score: 82 Period size: 24 Copynumber: 3.3 Consensus size: 25 42154573 TGTAATTTAA * * 42154583 TAATAATAAATAATTTAATCATATTT 1 TAATAATAAATAATTAAAT-ATAATT * 42154609 TAAT-ATAATTATTATTAAATATAATT 1 TAATAATAA--ATAATTAAATATAATT * * 42154635 TAATAA-AAATAATGATATATAATT 1 TAATAATAAATAATTAAATATAATT 42154659 TAATAATA 1 TAATAATA 42154667 TTCTTAATAT Statistics Matches: 48, Mismatches: 6, Indels: 9 0.76 0.10 0.14 Matches are distributed among these distances: 24 19 0.40 25 5 0.10 26 15 0.31 27 9 0.19 ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44 Consensus pattern (25 bp): TAATAATAAATAATTAAATATAATT Found at i:42154634 original size:55 final size:60 Alignment explanation

Indices: 42154564--42154698 Score: 181 Period size: 55 Copynumber: 2.3 Consensus size: 60 42154554 TTTTAATAAG * * 42154564 ATTATTAAATGTAATTTAAT-AATAAT-A-A-ATAATTTAATCATATT-TTAATATAATT 1 ATTATTAAATATAATTTAATAAATAATGATATATAATTTAATAATATTCTTAATATAATT 42154619 ATTATTAAATATAATTTAATAAAAATAATGATATATAATTTAATAATATTCTTAATATAATT 1 ATTATTAAATATAATTTAAT--AAATAATGATATATAATTTAATAATATTCTTAATATAATT 42154681 ATTATTAAAATATGAATT 1 ATTATT-AAATAT-AATT 42154699 AAGAAAAATT Statistics Matches: 69, Mismatches: 2, Indels: 9 0.86 0.03 0.11 Matches are distributed among these distances: 55 19 0.28 58 6 0.09 59 1 0.01 60 1 0.01 61 15 0.22 62 17 0.25 63 6 0.09 64 4 0.06 ACGTcount: A:0.50, C:0.01, G:0.02, T:0.46 Consensus pattern (60 bp): ATTATTAAATATAATTTAATAAATAATGATATATAATTTAATAATATTCTTAATATAATT Found at i:42154640 original size:24 final size:23 Alignment explanation

Indices: 42154613--42154680 Score: 66 Period size: 24 Copynumber: 2.9 Consensus size: 23 42154603 ATATTTTAAT 42154613 ATAATTATTATTAAATATAATTTA 1 ATAA-TATTATTAAATATAATTTA * * * * 42154637 ATAAAAATAATGATATATAATTTA 1 AT-AATATTATTAAATATAATTTA * 42154661 ATAATATTCTT-AATATAATT 1 ATAATATTATTAAATATAATT 42154681 ATTATTAAAA Statistics Matches: 34, Mismatches: 9, Indels: 4 0.72 0.19 0.09 Matches are distributed among these distances: 22 8 0.24 23 5 0.15 24 19 0.56 25 2 0.06 ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46 Consensus pattern (23 bp): ATAATATTATTAAATATAATTTA Found at i:42156209 original size:43 final size:43 Alignment explanation

Indices: 42156101--42156230 Score: 138 Period size: 43 Copynumber: 3.0 Consensus size: 43 42156091 CATTGTATTG * * * * 42156101 TGATTATGTGTAAGACCATGTCTGGGACATTGGAATCATTATA 1 TGATTACGTGAAAGACCATGTTTGGGACATTGGAATCGTTATA * * 42156144 TGATTACGTGTAAGACCATGTTTGGGACATTGGCATCGTTA-A 1 TGATTACGTGAAAGACCATGTTTGGGACATTGGAATCGTTATA * * * * 42156186 TCGATTTCGTGAAAGATCC-TGTTTGGGACAGTGGTATCGATATA 1 T-GATTACGTGAAAGA-CCATGTTTGGGACATTGGAATCGTTATA 42156230 T 1 T 42156231 AATAAGATGT Statistics Matches: 75, Mismatches: 9, Indels: 5 0.84 0.10 0.06 Matches are distributed among these distances: 42 2 0.03 43 69 0.92 44 4 0.05 ACGTcount: A:0.27, C:0.13, G:0.25, T:0.35 Consensus pattern (43 bp): TGATTACGTGAAAGACCATGTTTGGGACATTGGAATCGTTATA Found at i:42158084 original size:902 final size:902 Alignment explanation

Indices: 42156341--42159948 Score: 6770 Period size: 902 Copynumber: 4.0 Consensus size: 902 42156331 GATAAGAATG * 42156341 AAAGTACAATAGAATTAAGTGATACAGGTACGTACAAAACCTATATGAGAATCAAATGAAGGTAA 1 AAAGTACAATAGAATTAAGTGATACAGGTATGTACAAAACCTATATGAGAATCAAATGAAGGTAA 42156406 TTTGGCAAGTT-TTAAGTGTATCATGTATATGAAATGAGAAAGATTTATGTATAAGTATGTTTCA 66 TTTGGCAAGTTCTT-AGTGTATCATGTATATGAAATGAGAAAGATTTATGTATAAGTATGTTTCA 42156470 TGCCAAAATGTGTTTATTTGGCTATAATGAGGTATGAATTGAATGATATGTGAGATATGAGTTAT 130 TGCCAAAATGTGTTTATTTGGCTATAATGAGGTATGAATTGAATGATATGTGAGATATGAGTTAT 42156535 AGTTATTTTAACTAAATATACATATGGCATATACTGTGCGAAATACCGTTATTTGATGATATTTT 195 AGTTATTTTAACTAAATATACATATGGCATATACTGTGCGAAATACCGTTATTTGATGATATTTT 42156600 AGATAATTCACTTGACTAAAGAAAAGGTGATGGAAATTGAATTGTATAAAGTTATATATATGATT 260 AGATAATTCACTTGACTAAAGAAAAGGTGATGGAAATTGAATTGTATAAAGTTATATATATGATT * * 42156665 GCTTATGCATATGAAGATATAAATGAATCGATAAGAAGTATTCAAATCATACGTGTTTTGAATGA 325 GCTTATGCATATGAAGATGTAAATGAATTGATAAGAAGTATTCAAATCATACGTGTTTTGAATGA 42156730 ATAAACTCATGAAAATCTTGATCATTTGTGTGCATGAATTTGAGATTGAATGGTGAAATCATATG 390 ATAAACTCATGAAAATCTTGATCATTTGTGTGCATGAATTTGAGATTGAATGGTGAAATCATATG * 42156795 AATTATATCATGTTTTGAGTAATTGTTTAAAATGTGGTTATTTAATAATATAAGTTTATTACCCT 455 AATTATATCATGTTTTGAGTAATTGTTTAAAATGTGGTTATTTAATAATATGAGTTTATTACCCT 42156860 AGGAGCTTACTAAGCTTTATAGCTTACTTTGTGTTATTTTTCTATGTTTTATAGTGGTTTGAACG 520 AGGAGCTTACTAAGCTTTATAGCTTACTTTGTGTTATTTTTCTATGTTTTATAGTGGTTTGAACG * * * 42156925 TTCGCTTGGGTTTGAAGTTAGCAGAGATAACATCACACTATTCGGTTTTCGATTTTGGTATTTTT 585 TTCGCTCGGGTTTGAAGTTAGCGGAGATAACATCACACTATTCGGTTTTTGATTTTGGTATTTTT * 42156990 ACACTTGTCATTTGGTTATATGACATGTATAGGCTTGAATCTTTTTGACAAAGGTTTTGGTGACG 650 ACACTTGTCATTTGGTTATATGACATGTATAGGCTTGAATCTTTTTGACAAAGGTTTTGGTGATG * 42157055 TATTTGGTTCCTTGGTACGGCTTATTAATGACTTATGTTTGATGTGTAATTTGCCTGGTGTAATG 715 TATTTGGTTCCTTTGTACGGCTTATTAATGACTTATGTTTGATGTGTAATTTGCCTGGTGTAATG 42157120 GCATAATATAGTAAGCTTTGGTATAATTTAAGATGATGTTTGGATTCCATTTTGGTTTAGTAAAT 780 GCATAATATAGTAAGCTTTGGTATAATTTAAGATGATGTTTGGATTCCATTTTGGTTTAGTAAAT * * * 42157185 GCTTGATGATTTGGGTTGTGTCTGAATGTGGATATTAGTTAAGGTATCAATTTGATTT 845 GCTTGATGATTTGGATTGTGTCTAAATGTGGATATTAGTTAAAGTATCAATTTGATTT * 42157243 AAAGTACAATAGAATTAAGTGATACAGGTATGTACAAAACCTATATGAGAATCAAATGAAGCTAA 1 AAAGTACAATAGAATTAAGTGATACAGGTATGTACAAAACCTATATGAGAATCAAATGAAGGTAA 42157308 TTTGGCAAGTTCTTAGTGTATCATGTATATGAAATGAGAAAGATTTATGTATAAGTATGTTTCAT 66 TTTGGCAAGTTCTTAGTGTATCATGTATATGAAATGAGAAAGATTTATGTATAAGTATGTTTCAT * 42157373 GCCAAAATGTGTTTATTTGGCTACAATGAGGTATGAATTGAATGATATGTGAGATATGAGTTATA 131 GCCAAAATGTGTTTATTTGGCTATAATGAGGTATGAATTGAATGATATGTGAGATATGAGTTATA 42157438 GTTATTTTAACTAAATATACATATGGCATATACTGTGCGAAATACCGTTATTTGATGATATTTTA 196 GTTATTTTAACTAAATATACATATGGCATATACTGTGCGAAATACCGTTATTTGATGATATTTTA * * 42157503 GATAATTCACTTGACTAGAGAAAAGGTGATGGAAATTGAATTGTATAAAGTTATATATATGATTT 261 GATAATTCACTTGACTAAAGAAAAGGTGATGGAAATTGAATTGTATAAAGTTATATATATGATTG 42157568 CTTATGCATATGAAGATGTAAATGAATTGATAAGAAGTATTCAAATCATACGTGTTTTGAATGAA 326 CTTATGCATATGAAGATGTAAATGAATTGATAAGAAGTATTCAAATCATACGTGTTTTGAATGAA * * 42157633 TGAACTCATGAAAATCTTGATCATTTGTGTGCATGAATTTGAGATTGAACGGTGAAATCATATGA 391 TAAACTCATGAAAATCTTGATCATTTGTGTGCATGAATTTGAGATTGAATGGTGAAATCATATGA 42157698 ATTATATCATGTTTTGAGTAATTGTTTAAAATGTGGTTATTTAATAATATGAGTTTATTACCCTA 456 ATTATATCATGTTTTGAGTAATTGTTTAAAATGTGGTTATTTAATAATATGAGTTTATTACCCTA 42157763 GGAGCTTACTAAGCTTTATAGCTTACTTTGTGTTATTTTTCTATGTTTTATAGTGGTTTGAACGT 521 GGAGCTTACTAAGCTTTATAGCTTACTTTGTGTTATTTTTCTATGTTTTATAGTGGTTTGAACGT * * 42157828 TCGCTCGGGTTTGAAGTTAGCTGAGATAACATCACACTATTCAGTTTTTGATTTTGGTATTTTTA 586 TCGCTCGGGTTTGAAGTTAGCGGAGATAACATCACACTATTCGGTTTTTGATTTTGGTATTTTTA 42157893 CACTTGTCATTTGGTTATATGACATGTATAGGCTTGAATCTTTTTGACAAAGGTTTTGGTGATGT 651 CACTTGTCATTTGGTTATATGACATGTATAGGCTTGAATCTTTTTGACAAAGGTTTTGGTGATGT * 42157958 ATTTGGTTCCTTTGTATGGCTTATTAATGACTTATGTTTGATGTGTAATTTGCCTGGTGTAATGG 716 ATTTGGTTCCTTTGTACGGCTTATTAATGACTTATGTTTGATGTGTAATTTGCCTGGTGTAATGG * * 42158023 CATAATATAGTATGCTTTGGTATAATTTAAGATGATGTTTGGATTCCATTTTGGTTTAGTAATTG 781 CATAATATAGTAAGCTTTGGTATAATTTAAGATGATGTTTGGATTCCATTTTGGTTTAGTAAATG 42158088 CTTGATGATTTGGATTGTGTCTAAATGTGGATATTAGTTAAAGTATCAATTTGATTT 846 CTTGATGATTTGGATTGTGTCTAAATGTGGATATTAGTTAAAGTATCAATTTGATTT 42158145 AAAGTACAATAGAATTAAGTGATACAGGTATGTACAAAACCTATATGAGAATCAAATGAAGGTAA 1 AAAGTACAATAGAATTAAGTGATACAGGTATGTACAAAACCTATATGAGAATCAAATGAAGGTAA 42158210 TTTGGCAAGTTCTTAGTGTATCATGTATATGAAATGAGAAAGATTTATGTATAAGTATGTTTCAT 66 TTTGGCAAGTTCTTAGTGTATCATGTATATGAAATGAGAAAGATTTATGTATAAGTATGTTTCAT 42158275 GCCAAAATGTGTTTATTTGGCTATAATGAGGTATGAATTGAATGATATGTGAGATATGAGTTATA 131 GCCAAAATGTGTTTATTTGGCTATAATGAGGTATGAATTGAATGATATGTGAGATATGAGTTATA * * * * 42158340 GTTATTTTAACTAAATATACATATGGCATATAGTGTGCAAAATAACGTTATTTGATAATATTTTA 196 GTTATTTTAACTAAATATACATATGGCATATACTGTGCGAAATACCGTTATTTGATGATATTTTA 42158405 GATAATTCACTTGACTAAAGAAAAGGTGATGGAAATTGAATTGTATAAAGTTATATATATGATTG 261 GATAATTCACTTGACTAAAGAAAAGGTGATGGAAATTGAATTGTATAAAGTTATATATATGATTG 42158470 CTTATGCATATGAAGATGTAAATGAATTGATAAGAAGTATTCAAATCATACGTGTTTTGAATGAA 326 CTTATGCATATGAAGATGTAAATGAATTGATAAGAAGTATTCAAATCATACGTGTTTTGAATGAA 42158535 TAAACTCATGAAAATCTTGATCATTTGTGTGCATGAATTTGAGATTGAATGGTGAAATCATATGA 391 TAAACTCATGAAAATCTTGATCATTTGTGTGCATGAATTTGAGATTGAATGGTGAAATCATATGA 42158600 ATTATATCATGTTTTGAGTAATTGTTTAAAATGTGGTTATTTAATAATATGAGTTTATTACCCTA 456 ATTATATCATGTTTTGAGTAATTGTTTAAAATGTGGTTATTTAATAATATGAGTTTATTACCCTA * 42158665 GGCGCTTACTAAGCTTTATAGCTTACTTTGTGTTATTTTTCTATGTTTTATAGTGGTTTGAACGT 521 GGAGCTTACTAAGCTTTATAGCTTACTTTGTGTTATTTTTCTATGTTTTATAGTGGTTTGAACGT * * 42158730 TCGCTCGGTTTTGAAGTTAGCGGAGATAACATCACACTATTCGGTGTTTGATTTTGGTATTTTTA 586 TCGCTCGGGTTTGAAGTTAGCGGAGATAACATCACACTATTCGGTTTTTGATTTTGGTATTTTTA * * 42158795 CACTTGTCATTTGGTTATATGACATGTATAGGCTTGAATCATTTTGACAAAGGTTTTGATGATGT 651 CACTTGTCATTTGGTTATATGACATGTATAGGCTTGAATCTTTTTGACAAAGGTTTTGGTGATGT 42158860 ATTTGGTTCCTTTGTACGGCTTATTAATGACTTATGTTTGATGTGTAATTTGCCTGGTGTAATGG 716 ATTTGGTTCCTTTGTACGGCTTATTAATGACTTATGTTTGATGTGTAATTTGCCTGGTGTAATGG * * 42158925 CATAATATAGTAAGCTTTGGTATATTTTAAGATGATGTTTGGATTCCATTTTGGTTTAGTAAATA 781 CATAATATAGTAAGCTTTGGTATAATTTAAGATGATGTTTGGATTCCATTTTGGTTTAGTAAATG * 42158990 CTTGATGATTTGGGTTGTGTCTAAATGTGGATATTAGTTAAAGTATCAATTTGATTT 846 CTTGATGATTTGGATTGTGTCTAAATGTGGATATTAGTTAAAGTATCAATTTGATTT 42159047 AAAGTACAATAGAATTAAGTGATACAGGTATGTACAAAACCTATATGAGAATCAAATGAAGGTAA 1 AAAGTACAATAGAATTAAGTGATACAGGTATGTACAAAACCTATATGAGAATCAAATGAAGGTAA * * * 42159112 TTTGGCAAGTTCTTAGTGTAGCATGCATATGAAATGAGAAAGACTTATGTATAAGTATGTTTCAT 66 TTTGGCAAGTTCTTAGTGTATCATGTATATGAAATGAGAAAGATTTATGTATAAGTATGTTTCAT * 42159177 GCCAAAATGTGTTTATTTGGCTATAATGAGGTGTGAATTGAATGATATGTGAGATATGAGTTATA 131 GCCAAAATGTGTTTATTTGGCTATAATGAGGTATGAATTGAATGATATGTGAGATATGAGTTATA * * 42159242 GTTATTTTAACTAAATATACATATGGCATATACTGTGCGAAATATCGTTATTTGATGATATTTCA 196 GTTATTTTAACTAAATATACATATGGCATATACTGTGCGAAATACCGTTATTTGATGATATTTTA * 42159307 CATAATTCACTTGACTAAAGAAAAGGTGATGGAAATTGAATTGTATAAAGTTATATATATGATTG 261 GATAATTCACTTGACTAAAGAAAAGGTGATGGAAATTGAATTGTATAAAGTTATATATATGATTG 42159372 CTTATGCATATGAAGATGTAAATGAATTGATAAGAAGTATTCAAATCATACGTGTTTTGAATGAA 326 CTTATGCATATGAAGATGTAAATGAATTGATAAGAAGTATTCAAATCATACGTGTTTTGAATGAA 42159437 TAAACTCATGAAAATCTTGATCATTTGTGTGCATGAATTTGAGATTGAATGGTGAAATCATATGA 391 TAAACTCATGAAAATCTTGATCATTTGTGTGCATGAATTTGAGATTGAATGGTGAAATCATATGA 42159502 ATTATATCATGTTTTGAGTAATTGTTTAAAATGTGGTTATTTAATAATATGAGTTTATTACCCTA 456 ATTATATCATGTTTTGAGTAATTGTTTAAAATGTGGTTATTTAATAATATGAGTTTATTACCCTA 42159567 GGAGCTTACTAAGCTTTATAGCTTACTTTGTGTTATTTTTCTATGTTTTATAGTGGTTTGAACGT 521 GGAGCTTACTAAGCTTTATAGCTTACTTTGTGTTATTTTTCTATGTTTTATAGTGGTTTGAACGT 42159632 TCGCTCGGGTTTGAAGTTAGCGGAGATAACATCACACTATTCGGTTTTTGATTTTGGTATTTTTA 586 TCGCTCGGGTTTGAAGTTAGCGGAGATAACATCACACTATTCGGTTTTTGATTTTGGTATTTTTA * * 42159697 CACTTGTCATTTGGTTATATGACATGTATAGGCTTGAATCTTTTTTACAAAGGTTTTGGTAATGT 651 CACTTGTCATTTGGTTATATGACATGTATAGGCTTGAATCTTTTTGACAAAGGTTTTGGTGATGT * * 42159762 ATTTGGTTCCTTTGTATGGCTTATTAATGACTTATGTTTGATGTGTAATTTGTCTGGTGTAATGG 716 ATTTGGTTCCTTTGTACGGCTTATTAATGACTTATGTTTGATGTGTAATTTGCCTGGTGTAATGG 42159827 CATAATATAGTAAGCTTTGGTATAATTTAA-ATTGATGTTTGGATTCCATTTTGGTTTAGTAAAT 781 CATAATATAGTAAGCTTTGGTATAATTTAAGA-TGATGTTTGGATTCCATTTTGGTTTAGTAAAT 42159891 GCTTGATGATTTGGATTGTGTCTAAATGTGGATATTAGTTAAAGTATCAATTTGATTT 845 GCTTGATGATTTGGATTGTGTCTAAATGTGGATATTAGTTAAAGTATCAATTTGATTT 42159949 GGCATGCTTT Statistics Matches: 2637, Mismatches: 67, Indels: 4 0.97 0.02 0.00 Matches are distributed among these distances: 901 1 0.00 902 2634 1.00 903 2 0.00 ACGTcount: A:0.32, C:0.08, G:0.20, T:0.40 Consensus pattern (902 bp): AAAGTACAATAGAATTAAGTGATACAGGTATGTACAAAACCTATATGAGAATCAAATGAAGGTAA TTTGGCAAGTTCTTAGTGTATCATGTATATGAAATGAGAAAGATTTATGTATAAGTATGTTTCAT GCCAAAATGTGTTTATTTGGCTATAATGAGGTATGAATTGAATGATATGTGAGATATGAGTTATA GTTATTTTAACTAAATATACATATGGCATATACTGTGCGAAATACCGTTATTTGATGATATTTTA GATAATTCACTTGACTAAAGAAAAGGTGATGGAAATTGAATTGTATAAAGTTATATATATGATTG CTTATGCATATGAAGATGTAAATGAATTGATAAGAAGTATTCAAATCATACGTGTTTTGAATGAA TAAACTCATGAAAATCTTGATCATTTGTGTGCATGAATTTGAGATTGAATGGTGAAATCATATGA ATTATATCATGTTTTGAGTAATTGTTTAAAATGTGGTTATTTAATAATATGAGTTTATTACCCTA GGAGCTTACTAAGCTTTATAGCTTACTTTGTGTTATTTTTCTATGTTTTATAGTGGTTTGAACGT TCGCTCGGGTTTGAAGTTAGCGGAGATAACATCACACTATTCGGTTTTTGATTTTGGTATTTTTA CACTTGTCATTTGGTTATATGACATGTATAGGCTTGAATCTTTTTGACAAAGGTTTTGGTGATGT ATTTGGTTCCTTTGTACGGCTTATTAATGACTTATGTTTGATGTGTAATTTGCCTGGTGTAATGG CATAATATAGTAAGCTTTGGTATAATTTAAGATGATGTTTGGATTCCATTTTGGTTTAGTAAATG CTTGATGATTTGGATTGTGTCTAAATGTGGATATTAGTTAAAGTATCAATTTGATTT Found at i:42161042 original size:24 final size:24 Alignment explanation

Indices: 42160990--42161086 Score: 151 Period size: 24 Copynumber: 4.0 Consensus size: 24 42160980 ACTTTATCAT * * 42160990 ATAACTGGAGGCCT-AGCCTCTTTTA 1 ATAACTGG-GGCATAAGCC-CTTTTG 42161015 ATAACTGGGGCATAAGCCCTTTTG 1 ATAACTGGGGCATAAGCCCTTTTG 42161039 ATAACTGGGGCATAAGCCCTTTTG 1 ATAACTGGGGCATAAGCCCTTTTG 42161063 ATAACTGGGGCATAAGCCCTTTTG 1 ATAACTGGGGCATAAGCCCTTTTG 42161087 CACTTCCTCC Statistics Matches: 69, Mismatches: 2, Indels: 3 0.93 0.03 0.04 Matches are distributed among these distances: 24 57 0.83 25 12 0.17 ACGTcount: A:0.25, C:0.22, G:0.24, T:0.30 Consensus pattern (24 bp): ATAACTGGGGCATAAGCCCTTTTG Found at i:42161157 original size:9 final size:9 Alignment explanation

Indices: 42161143--42161195 Score: 52 Period size: 9 Copynumber: 5.4 Consensus size: 9 42161133 ACATCATGTG 42161143 CATATCATA 1 CATATCATA 42161152 CATATCATA 1 CATATCATA 42161161 TGCATATCATA 1 --CATATCATA * * 42161172 CATTTCATGTG 1 CATATCA--TA 42161183 CATATCATA 1 CATATCATA 42161192 CATA 1 CATA 42161196 CCATGTTTAT Statistics Matches: 36, Mismatches: 4, Indels: 8 0.75 0.08 0.17 Matches are distributed among these distances: 9 20 0.56 11 16 0.44 ACGTcount: A:0.38, C:0.21, G:0.06, T:0.36 Consensus pattern (9 bp): CATATCATA Found at i:42161164 original size:20 final size:20 Alignment explanation

Indices: 42161135--42161201 Score: 107 Period size: 20 Copynumber: 3.4 Consensus size: 20 42161125 TTATGAATAC 42161135 ATCATGTGCATATCATACAT 1 ATCATGTGCATATCATACAT * 42161155 ATCATATGCATATCATACAT 1 ATCATGTGCATATCATACAT * 42161175 TTCATGTGCATATCATACAT 1 ATCATGTGCATATCATACAT * 42161195 ACCATGT 1 ATCATGT 42161202 TTATCAAAAT Statistics Matches: 42, Mismatches: 5, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 20 42 1.00 ACGTcount: A:0.34, C:0.21, G:0.09, T:0.36 Consensus pattern (20 bp): ATCATGTGCATATCATACAT Found at i:42161166 original size:11 final size:11 Alignment explanation

Indices: 42161135--42161191 Score: 59 Period size: 11 Copynumber: 5.5 Consensus size: 11 42161125 TTATGAATAC * 42161135 ATCATGTGCAT 1 ATCATATGCAT 42161146 ATCATA--CAT 1 ATCATATGCAT 42161155 ATCATATGCAT 1 ATCATATGCAT 42161166 ATCATA--CAT 1 ATCATATGCAT * * 42161175 TTCATGTGCAT 1 ATCATATGCAT 42161186 ATCATA 1 ATCATA 42161192 CATACCATGT Statistics Matches: 37, Mismatches: 5, Indels: 8 0.74 0.10 0.16 Matches are distributed among these distances: 9 16 0.43 11 21 0.57 ACGTcount: A:0.35, C:0.19, G:0.09, T:0.37 Consensus pattern (11 bp): ATCATATGCAT Found at i:42161270 original size:25 final size:25 Alignment explanation

Indices: 42161238--42161285 Score: 69 Period size: 25 Copynumber: 1.9 Consensus size: 25 42161228 ATATATAAAC * * * 42161238 CCTAGGGGTATAATGGTCATTTTTA 1 CCTAGGGGCAAAACGGTCATTTTTA 42161263 CCTAGGGGCAAAACGGTCATTTT 1 CCTAGGGGCAAAACGGTCATTTT 42161286 CATGTTATAA Statistics Matches: 20, Mismatches: 3, Indels: 0 0.87 0.13 0.00 Matches are distributed among these distances: 25 20 1.00 ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33 Consensus pattern (25 bp): CCTAGGGGCAAAACGGTCATTTTTA Found at i:42165619 original size:20 final size:21 Alignment explanation

Indices: 42165584--42165638 Score: 78 Period size: 20 Copynumber: 2.7 Consensus size: 21 42165574 GCAGCATAAA * 42165584 GATTTAAAGAATCAAACAA-C 1 GATTTAAAGCATCAAACAATC 42165604 TGATTTAAA-CATCAAACAATC 1 -GATTTAAAGCATCAAACAATC 42165625 GATTTAAAGCATCA 1 GATTTAAAGCATCA 42165639 TTCAATCAGG Statistics Matches: 31, Mismatches: 1, Indels: 4 0.86 0.03 0.11 Matches are distributed among these distances: 20 17 0.55 21 14 0.45 ACGTcount: A:0.49, C:0.16, G:0.09, T:0.25 Consensus pattern (21 bp): GATTTAAAGCATCAAACAATC Found at i:42170670 original size:30 final size:31 Alignment explanation

Indices: 42170634--42170696 Score: 119 Period size: 31 Copynumber: 2.1 Consensus size: 31 42170624 AATGTGAAAG 42170634 TATGATAG-AAAATCAAGGTAGTTAACATGA 1 TATGATAGAAAAATCAAGGTAGTTAACATGA 42170664 TATGATAGAAAAATCAAGGTAGTTAACATGA 1 TATGATAGAAAAATCAAGGTAGTTAACATGA 42170695 TA 1 TA 42170697 GGAAATATAG Statistics Matches: 32, Mismatches: 0, Indels: 1 0.97 0.00 0.03 Matches are distributed among these distances: 30 8 0.25 31 24 0.75 ACGTcount: A:0.48, C:0.06, G:0.19, T:0.27 Consensus pattern (31 bp): TATGATAGAAAAATCAAGGTAGTTAACATGA Found at i:42173185 original size:52 final size:52 Alignment explanation

Indices: 42173108--42173209 Score: 204 Period size: 52 Copynumber: 2.0 Consensus size: 52 42173098 GTATCTCTTG 42173108 TTGTCATTGTCCAGACCGGATTGGGGTAAGGTTTTCACAGATAGGCAATACC 1 TTGTCATTGTCCAGACCGGATTGGGGTAAGGTTTTCACAGATAGGCAATACC 42173160 TTGTCATTGTCCAGACCGGATTGGGGTAAGGTTTTCACAGATAGGCAATA 1 TTGTCATTGTCCAGACCGGATTGGGGTAAGGTTTTCACAGATAGGCAATA 42173210 TCGATTTTGA Statistics Matches: 50, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 52 50 1.00 ACGTcount: A:0.25, C:0.18, G:0.27, T:0.29 Consensus pattern (52 bp): TTGTCATTGTCCAGACCGGATTGGGGTAAGGTTTTCACAGATAGGCAATACC Found at i:42178022 original size:28 final size:28 Alignment explanation

Indices: 42177957--42178057 Score: 114 Period size: 28 Copynumber: 3.5 Consensus size: 28 42177947 ATAGTGAATC * 42177957 CGCACACTTAGTGCTATATGTATTC-AACT 1 CGCACACTTAGTGCTATA--TAATCAAACT 42177986 CGCACACTTAGTGCTATATAATCAAACT 1 CGCACACTTAGTGCTATATAATCAAACT * * * * 42178014 CGCACACTTAGTGCTGTACAATTTTAAACC 1 CGCACACTTAGTGCTATATAA--TCAAACT 42178044 CGCACACTTAGTGC 1 CGCACACTTAGTGC 42178058 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:42185983 original size:28 final size:28 Alignment explanation

Indices: 42185918--42186018 Score: 114 Period size: 28 Copynumber: 3.5 Consensus size: 28 42185908 ATAGTGAATC * 42185918 CGCACACTTAGTGCTATATGTATTC-AACT 1 CGCACACTTAGTGCTATA--TAATCAAACT 42185947 CGCACACTTAGTGCTATATAATCAAACT 1 CGCACACTTAGTGCTATATAATCAAACT * * * * 42185975 CGCACACTTAGTGCTGTACAATTTTAAACC 1 CGCACACTTAGTGCTATATAA--TCAAACT 42186005 CGCACACTTAGTGC 1 CGCACACTTAGTGC 42186019 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:42188992 original size:10 final size:10 Alignment explanation

Indices: 42188964--42188997 Score: 50 Period size: 10 Copynumber: 3.3 Consensus size: 10 42188954 GAATTGTGTT * 42188964 TATAAATATA 1 TATAATTATA 42188974 TATTAATTATA 1 TA-TAATTATA 42188985 TATAATTATA 1 TATAATTATA 42188995 TAT 1 TAT 42188998 TTAATGACTT Statistics Matches: 22, Mismatches: 1, Indels: 2 0.88 0.04 0.08 Matches are distributed among these distances: 10 13 0.59 11 9 0.41 ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50 Consensus pattern (10 bp): TATAATTATA Found at i:42196182 original size:53 final size:53 Alignment explanation

Indices: 42196113--42196270 Score: 172 Period size: 53 Copynumber: 2.9 Consensus size: 53 42196103 TTCCTTTTTA * 42196113 AACTTACCATTACCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATG 1 AACTTACCATTACCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATC * * * * * * 42196166 AACTCACCATTTCCATGCCTTGGCATGGTCTTACATGGGATCTTTGCCTTATC 1 AACTTACCATTACCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATC * * * * * * * 42196219 ATAGTTTATCAATGCCATGTCTTGACATGATCTTACATGATTTCCTTGCCTT 1 A-A-CTTACCATTACCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTT 42196271 GTAAAACTTA Statistics Matches: 84, Mismatches: 19, Indels: 2 0.80 0.18 0.02 Matches are distributed among these distances: 53 47 0.56 54 1 0.01 55 36 0.43 ACGTcount: A:0.22, C:0.25, G:0.15, T:0.39 Consensus pattern (53 bp): AACTTACCATTACCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATC Found at i:42207007 original size:20 final size:21 Alignment explanation

Indices: 42206984--42207022 Score: 62 Period size: 21 Copynumber: 1.9 Consensus size: 21 42206974 CATATCATAT 42206984 AAATAAC-ATTAAATTACTTA 1 AAATAACAATTAAATTACTTA * 42207004 AAATAACAATTATATTACT 1 AAATAACAATTAAATTACT 42207023 ACATTTACAC Statistics Matches: 17, Mismatches: 1, Indels: 1 0.89 0.05 0.05 Matches are distributed among these distances: 20 7 0.41 21 10 0.59 ACGTcount: A:0.54, C:0.10, G:0.00, T:0.36 Consensus pattern (21 bp): AAATAACAATTAAATTACTTA Found at i:42208571 original size:17 final size:18 Alignment explanation

Indices: 42208529--42208577 Score: 50 Period size: 17 Copynumber: 2.8 Consensus size: 18 42208519 AGTTGAAAAG 42208529 GAGCATGATTGTCATACTT 1 GAGCATGA-TGTCATACTT * 42208548 G-GCCATGATG-CATTCTT 1 GAG-CATGATGTCATACTT 42208565 GAGCATGAT-TCAT 1 GAGCATGATGTCAT 42208578 GCTTCTTGCA Statistics Matches: 26, Mismatches: 1, Indels: 8 0.74 0.03 0.23 Matches are distributed among these distances: 17 16 0.62 18 4 0.15 19 6 0.23 ACGTcount: A:0.24, C:0.18, G:0.22, T:0.35 Consensus pattern (18 bp): GAGCATGATGTCATACTT Found at i:42209466 original size:40 final size:40 Alignment explanation

Indices: 42209400--42209566 Score: 169 Period size: 40 Copynumber: 4.2 Consensus size: 40 42209390 AAATTGAATG * * * 42209400 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT 1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT * * ** 42209439 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGTT 1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT * * 42209479 ATATCCGGGCTAAGGCCCGAAGGC-ATTCGTGC-GAGTTATT 1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-GTAATT * * ** * 42209519 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCACGTGATT 1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT 42209559 ATATCCGG 1 ATATCCGG 42209567 TTATATTCCG Statistics Matches: 105, Mismatches: 18, Indels: 9 0.80 0.14 0.07 Matches are distributed among these distances: 39 16 0.15 40 87 0.83 41 2 0.02 ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25 Consensus pattern (40 bp): ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT Found at i:42216571 original size:17 final size:18 Alignment explanation

Indices: 42216529--42216577 Score: 50 Period size: 17 Copynumber: 2.8 Consensus size: 18 42216519 AGTTGAAAAG 42216529 GAGCATGATTGTCATACTT 1 GAGCATGA-TGTCATACTT * 42216548 G-GCCATGATG-CATTCTT 1 GAG-CATGATGTCATACTT 42216565 GAGCATGAT-TCAT 1 GAGCATGATGTCAT 42216578 GCTTCTTGCA Statistics Matches: 26, Mismatches: 1, Indels: 8 0.74 0.03 0.23 Matches are distributed among these distances: 17 16 0.62 18 4 0.15 19 6 0.23 ACGTcount: A:0.24, C:0.18, G:0.22, T:0.35 Consensus pattern (18 bp): GAGCATGATGTCATACTT Found at i:42217465 original size:40 final size:39 Alignment explanation

Indices: 42217399--42217564 Score: 158 Period size: 40 Copynumber: 4.2 Consensus size: 39 42217389 AAATTGAATG * * * 42217399 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT 1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGG-TATT * * ** 42217438 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGT 1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTATT * 42217477 ATATCCGGGCTAAGGCCCGAAGGC-ATTCGTGC-GAGTTATT 1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-G-TATT * * ** 42217517 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCACGTGATT 1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGT-ATT 42217557 ATATCCGG 1 ATATCCGG 42217565 TTATATTCCG Statistics Matches: 103, Mismatches: 17, Indels: 13 0.77 0.13 0.10 Matches are distributed among these distances: 38 3 0.03 39 42 0.41 40 56 0.54 41 2 0.02 ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25 Consensus pattern (39 bp): ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTATT Found at i:42223834 original size:40 final size:40 Alignment explanation

Indices: 42223785--42223936 Score: 164 Period size: 40 Copynumber: 3.8 Consensus size: 40 42223775 ACAACCACAA * * *** * 42223785 GCACAATTGCCTTCGGGTCTTAACCCGGATTTGGTAACTT 1 GCACAATTGCCTTCGGGTCTTAGCCCGGATATAACAACTC * 42223825 GCACCATTGCCTTCGGGTCTTAGCCCGGATATAACAACTC 1 GCACAATTGCCTTCGGGTCTTAGCCCGGATATAACAACTC * * 42223865 GCACGAA-TGCCTTCGGGTCTTAGCCCGGACATAATC-ACTA 1 GCAC-AATTGCCTTCGGGTCTTAGCCCGGATATAA-CAACTC * * * 42223905 GCATAAATGCCTTCGGGACTTAGCCCGGATAT 1 GCACAATTGCCTTCGGGTCTTAGCCCGGATAT 42223937 CATTCAAATG Statistics Matches: 96, Mismatches: 13, Indels: 6 0.83 0.11 0.05 Matches are distributed among these distances: 39 2 0.02 40 92 0.96 41 2 0.02 ACGTcount: A:0.23, C:0.28, G:0.22, T:0.26 Consensus pattern (40 bp): GCACAATTGCCTTCGGGTCTTAGCCCGGATATAACAACTC Found at i:42231820 original size:40 final size:40 Alignment explanation

Indices: 42231771--42231922 Score: 164 Period size: 40 Copynumber: 3.8 Consensus size: 40 42231761 ACAACCACAA * * *** * 42231771 GCACAATTGCCTTCGGGTCTTAACCCGGATTTGGTAACTT 1 GCACAATTGCCTTCGGGTCTTAGCCCGGATATAACAACTC * 42231811 GCACCATTGCCTTCGGGTCTTAGCCCGGATATAACAACTC 1 GCACAATTGCCTTCGGGTCTTAGCCCGGATATAACAACTC * * 42231851 GCACGAA-TGCCTTCGGGTCTTAGCCCGGACATAATC-ACTA 1 GCAC-AATTGCCTTCGGGTCTTAGCCCGGATATAA-CAACTC * * * 42231891 GCATAAATGCCTTCGGGACTTAGCCCGGATAT 1 GCACAATTGCCTTCGGGTCTTAGCCCGGATAT 42231923 CATTCAAATG Statistics Matches: 96, Mismatches: 13, Indels: 6 0.83 0.11 0.05 Matches are distributed among these distances: 39 2 0.02 40 92 0.96 41 2 0.02 ACGTcount: A:0.23, C:0.28, G:0.22, T:0.26 Consensus pattern (40 bp): GCACAATTGCCTTCGGGTCTTAGCCCGGATATAACAACTC Found at i:42239395 original size:13 final size:13 Alignment explanation

Indices: 42239371--42239395 Score: 50 Period size: 13 Copynumber: 1.9 Consensus size: 13 42239361 TACAAAAAGG 42239371 TTTTACTAAAATA 1 TTTTACTAAAATA 42239384 TTTTACTAAAAT 1 TTTTACTAAAAT 42239396 TGTGGTTTAG Statistics Matches: 12, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 12 1.00 ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48 Consensus pattern (13 bp): TTTTACTAAAATA Found at i:42242562 original size:19 final size:19 Alignment explanation

Indices: 42242538--42242576 Score: 78 Period size: 19 Copynumber: 2.1 Consensus size: 19 42242528 TTGGAACAAG 42242538 TCCAATTAACAACAATATT 1 TCCAATTAACAACAATATT 42242557 TCCAATTAACAACAATATT 1 TCCAATTAACAACAATATT 42242576 T 1 T 42242577 AAATAATAGA Statistics Matches: 20, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 19 20 1.00 ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33 Consensus pattern (19 bp): TCCAATTAACAACAATATT Found at i:42244037 original size:89 final size:89 Alignment explanation

Indices: 42243931--42244109 Score: 299 Period size: 89 Copynumber: 2.0 Consensus size: 89 42243921 TGAGTACTAA 42243931 ACAAATAGTGATGTTAACATATATAATAACGC-AAATATG-TAGGAATCATATCTCTTACAACAA 1 ACAAATAGTGATGTTAACATATATAATAAC-CTAAATATGTTA-GAATCATATCTCTTACAACAA * 42243994 AAAGCAACAAAGAAAAAGACAGAAAG 64 AAAACAACAAAGAAAAAGACAGAAAG * 42244020 ACAAATAGTGATGTTAACATATATAATAACCTAAATATGTTAGAATTATATCTCTTACAACAAAA 1 ACAAATAGTGATGTTAACATATATAATAACCTAAATATGTTAGAATCATATCTCTTACAACAAAA * 42244085 AACAATAAAGAAAAAGACAGAAAG 66 AACAACAAAGAAAAAGACAGAAAG 42244109 A 1 A 42244110 AAGAAACAAT Statistics Matches: 85, Mismatches: 3, Indels: 4 0.92 0.03 0.04 Matches are distributed among these distances: 88 1 0.01 89 82 0.96 90 2 0.02 ACGTcount: A:0.54, C:0.12, G:0.12, T:0.22 Consensus pattern (89 bp): ACAAATAGTGATGTTAACATATATAATAACCTAAATATGTTAGAATCATATCTCTTACAACAAAA AACAACAAAGAAAAAGACAGAAAG Found at i:42244699 original size:3 final size:3 Alignment explanation

Indices: 42244691--42244734 Score: 88 Period size: 3 Copynumber: 14.7 Consensus size: 3 42244681 GTGATTCAAT 42244691 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT 1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT 42244735 GTGTTCATAT Statistics Matches: 41, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 3 41 1.00 ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34 Consensus pattern (3 bp): ATA Found at i:42245842 original size:16 final size:17 Alignment explanation

Indices: 42245803--42245842 Score: 50 Period size: 16 Copynumber: 2.5 Consensus size: 17 42245793 AATTAAAATG 42245803 TAATTTTATCATTATAA 1 TAATTTTATCATTATAA 42245820 TAA-TTTAT-ATT-TATA 1 TAATTTTATCATTATA-A 42245835 TAATTTTA 1 TAATTTTA 42245843 AGAAGGATTA Statistics Matches: 21, Mismatches: 0, Indels: 5 0.81 0.00 0.19 Matches are distributed among these distances: 14 2 0.10 15 7 0.33 16 9 0.43 17 3 0.14 ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57 Consensus pattern (17 bp): TAATTTTATCATTATAA Found at i:42250805 original size:1 final size:1 Alignment explanation

Indices: 42250799--42250823 Score: 50 Period size: 1 Copynumber: 25.0 Consensus size: 1 42250789 ATAGTTAAGG 42250799 TTTTTTTTTTTTTTTTTTTTTTTTT 1 TTTTTTTTTTTTTTTTTTTTTTTTT 42250824 GCTTAGAGTT Statistics Matches: 24, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 1 24 1.00 ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00 Consensus pattern (1 bp): T Found at i:42252278 original size:28 final size:29 Alignment explanation

Indices: 42252208--42252278 Score: 74 Period size: 28 Copynumber: 2.4 Consensus size: 29 42252198 TGGGTGACAC 42252208 ATTAATAATTAATTTTTAAAATTTAAAAATT 1 ATTAA-AATT-ATTTTTAAAATTTAAAAATT * * * 42252239 ATAAAAACTATTCTTTAAAA-TT-AAATTT 1 ATTAAAATTATT-TTTAAAATTTAAAAATT 42252267 ATTAAAATTATT 1 ATTAAAATTATT 42252279 AAAAAATTAA Statistics Matches: 34, Mismatches: 5, Indels: 5 0.77 0.11 0.11 Matches are distributed among these distances: 28 15 0.44 29 5 0.15 30 10 0.29 31 4 0.12 ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46 Consensus pattern (29 bp): ATTAAAATTATTTTTAAAATTTAAAAATT Found at i:42259769 original size:2 final size:2 Alignment explanation

Indices: 42259762--42259788 Score: 54 Period size: 2 Copynumber: 13.5 Consensus size: 2 42259752 CATACCTATC 42259762 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 T 42259789 GTTTTAATTT Statistics Matches: 25, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 25 1.00 ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52 Consensus pattern (2 bp): TA Found at i:42263009 original size:9 final size:9 Alignment explanation

Indices: 42262979--42263151 Score: 61 Period size: 9 Copynumber: 18.3 Consensus size: 9 42262969 TAAACTTATT 42262979 AAATTATAAA 1 AAATTAT-AA * 42262989 AAATATAAAA 1 AAAT-TATAA 42262999 AAATTATAA 1 AAATTATAA * * 42263008 AAGTAATAA 1 AAATTATAA 42263017 AAACTTATTTAA 1 AAA-TTA--TAA 42263029 AATATT-T-A 1 AA-ATTATAA * 42263037 AAATTAAATA 1 AAATTATA-A * * 42263047 AAAGTATTA 1 AAATTATAA * 42263056 GAATTATTAA 1 AAATTA-TAA * 42263066 AAA-AATAAA 1 AAATTAT-AA * 42263075 AAATTGTAA 1 AAATTATAA * 42263084 AAACTAT-A 1 AAATTATAA 42263092 AAATATATTAA 1 AAAT-TA-TAA * 42263103 AAA-TATTA 1 AAATTATAA 42263111 AAATTGATATA 1 AAATT-ATA-A * 42263122 AATTTATAA 1 AAATTATAA 42263131 AAATT-TAAA 1 AAATTAT-AA * 42263140 AAATCATAA 1 AAATTATAA 42263149 AAA 1 AAA 42263152 CTTGAACCGG Statistics Matches: 119, Mismatches: 25, Indels: 39 0.65 0.14 0.21 Matches are distributed among these distances: 7 3 0.03 8 14 0.12 9 53 0.45 10 30 0.25 11 11 0.09 12 7 0.06 13 1 0.01 ACGTcount: A:0.64, C:0.02, G:0.03, T:0.32 Consensus pattern (9 bp): AAATTATAA Found at i:42263079 original size:19 final size:18 Alignment explanation

Indices: 42262979--42263086 Score: 56 Period size: 19 Copynumber: 5.7 Consensus size: 18 42262969 TAAACTTATT 42262979 AAATTATAAAAAATATAAAA 1 AAATTATAAAAAA-AT-AAA * 42262999 AAATTATAAAAGTAATAAA 1 AAATTATAAAA-AAATAAA * * * ** 42263018 AACTTATTTAAAATATTTA 1 AAATTA-TAAAAAAATAAA * * 42263037 AAATTA-AATAAAAGTATTA 1 AAATTATAA-AAAAATA-AA * 42263056 GAATTATTAAAAAAATAAA 1 AAATTA-TAAAAAAATAAA * 42263075 AAATTGTAAAAA 1 AAATTATAAAAA 42263087 CTATAAAATA Statistics Matches: 65, Mismatches: 17, Indels: 14 0.68 0.18 0.15 Matches are distributed among these distances: 17 1 0.02 18 10 0.15 19 28 0.43 20 23 0.35 21 3 0.05 ACGTcount: A:0.65, C:0.01, G:0.04, T:0.31 Consensus pattern (18 bp): AAATTATAAAAAAATAAA Found at i:42263103 original size:19 final size:18 Alignment explanation

Indices: 42263060--42263114 Score: 58 Period size: 19 Copynumber: 2.9 Consensus size: 18 42263050 GTATTAGAAT * * 42263060 TATTAAAAAAATAAAAAA 1 TATTAAAAATATAAAATA 42263078 T-TGTAAAAACTATAAAATA 1 TAT-TAAAAA-TATAAAATA 42263097 TATTAAAAATATTAAAAT 1 TATTAAAAATA-TAAAAT 42263115 TGATATAAAT Statistics Matches: 31, Mismatches: 2, Indels: 7 0.77 0.05 0.17 Matches are distributed among these distances: 17 1 0.03 18 9 0.29 19 20 0.65 20 1 0.03 ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31 Consensus pattern (18 bp): TATTAAAAATATAAAATA Found at i:42263113 original size:8 final size:9 Alignment explanation

Indices: 42262928--42263113 Score: 69 Period size: 9 Copynumber: 20.1 Consensus size: 9 42262918 AATCTGAAAC * 42262928 AATATTAGA 1 AATATTAAA 42262937 AATATTAAA 1 AATATTAAA * 42262946 AA-CTTAAA 1 AATATTAAA * 42262954 AA-AATAAA 1 AATATTAAA * 42262962 ATTGATATAAA 1 AAT-AT-TAAA ** 42262973 CTTATT-AA 1 AATATTAAA * * 42262981 ATTATAAAA 1 AATATTAAA 42262990 AATA-TAAA 1 AATATTAAA * 42262998 AAAATTATAA 1 AATATTA-AA * 42263008 AAGTAATAAA 1 AA-TATTAAA * 42263018 AACTTATTTAA 1 AA--TATTAAA 42263029 AATATTTAAA 1 AATA-TTAAA * * 42263039 ATTAAATAAA 1 AAT-ATTAAA * * 42263049 AGTATTAGA 1 AATATTAAA * 42263058 ATTATTAAA 1 AATATTAAA * * 42263067 AAAATAAAA 1 AATATTAAA 42263076 AAT-TGTAAA 1 AATAT-TAAA 42263085 AACTA-TAAA 1 AA-TATTAAA 42263094 ATATATTAAA 1 A-ATATTAAA 42263104 AATATTAAA 1 AATATTAAA 42263113 A 1 A 42263114 TTGATATAAA Statistics Matches: 132, Mismatches: 30, Indels: 30 0.69 0.16 0.16 Matches are distributed among these distances: 8 25 0.19 9 60 0.45 10 30 0.23 11 17 0.13 ACGTcount: A:0.63, C:0.02, G:0.03, T:0.32 Consensus pattern (9 bp): AATATTAAA Found at i:42263141 original size:28 final size:27 Alignment explanation

Indices: 42263073--42263150 Score: 70 Period size: 28 Copynumber: 2.8 Consensus size: 27 42263063 TAAAAAAATA 42263073 AAAAATTGTAAAAACTATAAAATATATT 1 AAAAATT-TAAAAACTATAAAATATATT * * 42263101 AAAAATATT-AAAATTGATATAAATTTA-T 1 AAAAAT-TTAAAAACT-ATA-AAATATATT * 42263129 AAAAATTTAAAAAATCATAAAA 1 AAAAATTTAAAAACT-ATAAAA 42263151 ACTTGAACCG Statistics Matches: 42, Mismatches: 4, Indels: 9 0.76 0.07 0.16 Matches are distributed among these distances: 27 10 0.24 28 25 0.60 29 7 0.17 ACGTcount: A:0.63, C:0.03, G:0.03, T:0.32 Consensus pattern (27 bp): AAAAATTTAAAAACTATAAAATATATT Found at i:42263556 original size:19 final size:18 Alignment explanation

Indices: 42263509--42263556 Score: 51 Period size: 19 Copynumber: 2.6 Consensus size: 18 42263499 GTTTTATTAA * 42263509 AAATAATTTTTCTAATTT 1 AAATAATTTTTATAATTT * * * 42263527 AAATTAGTTTTAATACTTT 1 AAA-TAATTTTTATAATTT 42263546 AAATAATTTTT 1 AAATAATTTTT 42263557 TTATAATTTT Statistics Matches: 23, Mismatches: 6, Indels: 2 0.74 0.19 0.06 Matches are distributed among these distances: 18 9 0.39 19 14 0.61 ACGTcount: A:0.40, C:0.04, G:0.02, T:0.54 Consensus pattern (18 bp): AAATAATTTTTATAATTT Found at i:42263677 original size:29 final size:28 Alignment explanation

Indices: 42263617--42263695 Score: 81 Period size: 28 Copynumber: 2.8 Consensus size: 28 42263607 TATAAATTTC * * * 42263617 TTTTTATAA-TTTATTAGAATTTTTATAT 1 TTTTTATAATTTTAATA-AGTTTTTACAT * 42263645 TTTTTATAGTATTTAA-AAGTTTTTACAT 1 TTTTTATAAT-TTTAATAAGTTTTTACAT 42263673 GTTTTTATAATTTTAATAAGTTT 1 -TTTTTATAATTTTAATAAGTTT 42263696 ATATCAATTT Statistics Matches: 42, Mismatches: 5, Indels: 7 0.78 0.09 0.13 Matches are distributed among these distances: 28 22 0.52 29 16 0.38 30 4 0.10 ACGTcount: A:0.32, C:0.01, G:0.06, T:0.61 Consensus pattern (28 bp): TTTTTATAATTTTAATAAGTTTTTACAT Found at i:42263686 original size:9 final size:9 Alignment explanation

Indices: 42263617--42263728 Score: 66 Period size: 9 Copynumber: 12.1 Consensus size: 9 42263607 TATAAATTTC 42263617 TTTTTATAA 1 TTTTTATAA * 42263626 TTTATTAGAA 1 TTT-TTATAA * 42263636 TTTTTATAT 1 TTTTTATAA * 42263645 TTTTTATAG 1 TTTTTATAA * * 42263654 TATTTAAAA 1 TTTTTATAA * * 42263663 GTTTTTACATG 1 -TTTTTATA-A 42263674 TTTTTATAA 1 TTTTTATAA * 42263683 TTTTAATAA 1 TTTTTATAA * 42263692 GTTTATATCAA 1 -TTTTTAT-AA * 42263703 TTTTAAT-A 1 TTTTTATAA * 42263711 TTTTTCTAA 1 TTTTTATAA 42263720 TTTTT-TAA 1 TTTTTATAA 42263728 T 1 T 42263729 CATTTTTAGG Statistics Matches: 78, Mismatches: 19, Indels: 13 0.71 0.17 0.12 Matches are distributed among these distances: 8 10 0.13 9 35 0.45 10 31 0.40 11 2 0.03 ACGTcount: A:0.32, C:0.03, G:0.04, T:0.61 Consensus pattern (9 bp): TTTTTATAA Found at i:42263686 original size:19 final size:18 Alignment explanation

Indices: 42263617--42263686 Score: 59 Period size: 19 Copynumber: 3.7 Consensus size: 18 42263607 TATAAATTTC * * 42263617 TTTTTATAATTTATTAGAA 1 TTTTTATAATTT-TTACAG * * 42263636 TTTTTATATTTTTTATAG 1 TTTTTATAATTTTTACAG * * 42263654 TATTTAAAAGTTTTTACATG 1 TTTTTATAA-TTTTTACA-G 42263674 TTTTTATAATTTT 1 TTTTTATAATTTT 42263687 AATAAGTTTA Statistics Matches: 40, Mismatches: 9, Indels: 4 0.75 0.17 0.08 Matches are distributed among these distances: 18 10 0.25 19 22 0.55 20 8 0.20 ACGTcount: A:0.30, C:0.01, G:0.06, T:0.63 Consensus pattern (18 bp): TTTTTATAATTTTTACAG Found at i:42264473 original size:2 final size:2 Alignment explanation

Indices: 42264466--42264497 Score: 64 Period size: 2 Copynumber: 16.0 Consensus size: 2 42264456 CATAGAGGAA 42264466 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 42264498 GTAAAAGGCC Statistics Matches: 30, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 30 1.00 ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50 Consensus pattern (2 bp): AT Found at i:42273352 original size:51 final size:51 Alignment explanation

Indices: 42273283--42273381 Score: 198 Period size: 51 Copynumber: 1.9 Consensus size: 51 42273273 GGATTAAAGT 42273283 CTTGGTTACGTACTACTGGAAAAATATATATGTACTTTCTCCTAATTAAGC 1 CTTGGTTACGTACTACTGGAAAAATATATATGTACTTTCTCCTAATTAAGC 42273334 CTTGGTTACGTACTACTGGAAAAATATATATGTACTTTCTCCTAATTA 1 CTTGGTTACGTACTACTGGAAAAATATATATGTACTTTCTCCTAATTA 42273382 CATTTGCATT Statistics Matches: 48, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 51 48 1.00 ACGTcount: A:0.31, C:0.17, G:0.13, T:0.38 Consensus pattern (51 bp): CTTGGTTACGTACTACTGGAAAAATATATATGTACTTTCTCCTAATTAAGC Found at i:42276867 original size:40 final size:40 Alignment explanation

Indices: 42276675--42276860 Score: 227 Period size: 40 Copynumber: 4.7 Consensus size: 40 42276665 TCGAATGATG * * * 42276675 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATA 1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA * * 42276715 TCCGGACTAAGAT-CCGAAGGCATTCGTGCGAGTTACTAAA 1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA * 42276755 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAA 1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA * * 42276795 TCCGGGTTAAGTCCCGAAGGCATCTGTGCGAGTTACTATAA 1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA * 42276836 -CCGGGCTATGTCCCGAAGGCATTTG 1 TCCGGGCTAAGTCCCGAAGGCATTTG 42276861 AACGAGTAGC Statistics Matches: 130, Mismatches: 12, Indels: 8 0.87 0.08 0.05 Matches are distributed among these distances: 39 1 0.01 40 120 0.92 41 9 0.07 ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25 Consensus pattern (40 bp): TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA Found at i:42276867 original size:80 final size:80 Alignment explanation

Indices: 42276675--42276893 Score: 238 Period size: 80 Copynumber: 2.8 Consensus size: 80 42276665 TCGAATGATG * * ** 42276675 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGCATT 1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATATCCGGGTTAAGATCCGAAGGCATT 42276739 CGTGCGAGTTACTAAA 65 CGTGCGAGTTACTAAA * * 42276755 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA- 1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGTTAAGAT-CCGAAGGCAT 42276817 TCTGTGCGAGTTACTATAA 64 TC-GTGCGAGTTACTA-AA * ** 42276836 -CCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGCTATATCC-GGTTAA-ACTCCGAAGG 1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATATCCGGGTTAAGA-TCCGAAGG 42276894 TACGTGATTC Statistics Matches: 119, Mismatches: 11, Indels: 19 0.80 0.07 0.13 Matches are distributed among these distances: 79 19 0.16 80 90 0.76 81 10 0.08 ACGTcount: A:0.26, C:0.22, G:0.26, T:0.25 Consensus pattern (80 bp): TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGTTAAGATCCGAAGGCATTC GTGCGAGTTACTAAA Found at i:42284398 original size:40 final size:39 Alignment explanation

Indices: 42284207--42284391 Score: 221 Period size: 40 Copynumber: 4.6 Consensus size: 39 42284197 TCGAATGATG * * * 42284207 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATA 1 TCCGGGCTAAGT-CCGAAGGCATTTGTGC-GAGTTACTAAA * * 42284247 TCCGGACTAAGATCCGAAGGCATTCGTGCGAGTTACTAAA 1 TCCGGGCTAAG-TCCGAAGGCATTTGTGCGAGTTACTAAA * 42284287 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA 1 TCCGGGCTAAG-TCCGAAGGCATTTGTGCGAGTTACTAAA * * 42284327 TCCGGGTTAAGTCCGAAGGCATCTGTGCGAGTTACTATAA 1 TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTA-AA * 42284367 -CCGGGCTATGTCCCGAAGGCATTTG 1 TCCGGGCTAAGT-CCGAAGGCATTTG 42284392 AACGAGTAGC Statistics Matches: 129, Mismatches: 12, Indels: 8 0.87 0.08 0.05 Matches are distributed among these distances: 39 34 0.26 40 88 0.68 41 7 0.05 ACGTcount: A:0.25, C:0.22, G:0.27, T:0.25 Consensus pattern (39 bp): TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA Found at i:42284398 original size:79 final size:79 Alignment explanation

Indices: 42284207--42284424 Score: 241 Period size: 79 Copynumber: 2.7 Consensus size: 79 42284197 TCGAATGATG * * ** 42284207 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGCATT 1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATATCCGGGTTAAG-TCCGAAGGCATT 42284271 CGTGCGAGTTACTAAA 64 CGTGCGAGTTACTAAA * * 42284287 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCGAAGGCA-TC 1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGTTAAGTCCGAAGGCATTC 42284350 TGTGCGAGTTACTATAA 65 -GTGCGAGTTACTA-AA * ** * 42284367 -CCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGCTATATCC-GGTTAAACTCCGAAGG 1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATATCCGGGTT-AAGTCCGAAGG 42284425 TACGTGATTC Statistics Matches: 119, Mismatches: 12, Indels: 15 0.82 0.08 0.10 Matches are distributed among these distances: 78 9 0.08 79 65 0.55 80 37 0.31 81 8 0.07 ACGTcount: A:0.27, C:0.22, G:0.27, T:0.25 Consensus pattern (79 bp): TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGTTAAGTCCGAAGGCATTCG TGCGAGTTACTAAA Found at i:42288555 original size:2 final size:2 Alignment explanation

Indices: 42288548--42288576 Score: 58 Period size: 2 Copynumber: 14.5 Consensus size: 2 42288538 AAAATAAATA 42288548 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A 1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A 42288577 AACCTAAAAT Statistics Matches: 27, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 27 1.00 ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48 Consensus pattern (2 bp): AT Found at i:42288585 original size:44 final size:43 Alignment explanation

Indices: 42288504--42288598 Score: 122 Period size: 44 Copynumber: 2.2 Consensus size: 43 42288494 ATAATTTTAA ** 42288504 AATAGATAATATATATACATATATATAAAAGTGTAAAATAAAT 1 AATAGATAATATATATACATATATATAAAAGCCTAAAATAAAT * * 42288547 AATATATATATATATATATATATATATATAAA-CCTAAAATAAAT 1 AATAGATA-ATATATATACATATATATA-AAAGCCTAAAATAAAT 42288591 AATA-ATAA 1 AATAGATAA 42288599 AACCATTTTA Statistics Matches: 46, Mismatches: 4, Indels: 5 0.84 0.07 0.09 Matches are distributed among these distances: 42 1 0.02 43 10 0.22 44 32 0.70 45 3 0.07 ACGTcount: A:0.59, C:0.03, G:0.03, T:0.35 Consensus pattern (43 bp): AATAGATAATATATATACATATATATAAAAGCCTAAAATAAAT Found at i:42288698 original size:24 final size:23 Alignment explanation

Indices: 42288662--42288707 Score: 56 Period size: 23 Copynumber: 2.0 Consensus size: 23 42288652 GTAATAAAAC * 42288662 AATAATACGTAAAAACAAGTTTAA 1 AATAATACAT-AAAACAAGTTTAA * * 42288686 AATAATATATAAAGCAAGTTTA 1 AATAATACATAAAACAAGTTTA 42288708 CAGTAAATAG Statistics Matches: 19, Mismatches: 3, Indels: 1 0.83 0.13 0.04 Matches are distributed among these distances: 23 11 0.58 24 8 0.42 ACGTcount: A:0.57, C:0.07, G:0.09, T:0.28 Consensus pattern (23 bp): AATAATACATAAAACAAGTTTAA Found at i:42288931 original size:26 final size:26 Alignment explanation

Indices: 42288871--42288941 Score: 74 Period size: 26 Copynumber: 2.7 Consensus size: 26 42288861 CTTTAAAGTA ** * 42288871 AATAAT-ATATAAAAAGTTTTAACATG 1 AATAATAATATAAAAA-ACTTAAAATG 42288897 AATAA-AATATAAAAAACTTAAAATG 1 AATAATAATATAAAAAACTTAAAATG 42288922 AATAATAATAATAATAAAAC 1 AATAATAAT-ATAA-AAAAC 42288942 AAATATTTTT Statistics Matches: 38, Mismatches: 3, Indels: 6 0.81 0.06 0.13 Matches are distributed among these distances: 25 12 0.32 26 17 0.45 27 4 0.11 28 5 0.13 ACGTcount: A:0.63, C:0.04, G:0.04, T:0.28 Consensus pattern (26 bp): AATAATAATATAAAAAACTTAAAATG Found at i:42289762 original size:24 final size:25 Alignment explanation

Indices: 42289735--42289801 Score: 59 Period size: 25 Copynumber: 2.6 Consensus size: 25 42289725 AATCGATTTA 42289735 AAATAAAAATAAGAAAAAA-GA-AAG 1 AAATAAAAA-AAGAAAAAATGAGAAG * 42289759 AAATTGAAAAAAGGAAAAAATGAGAAG 1 AAA-T-AAAAAAAGAAAAAATGAGAAG * 42289786 AAA-ACAAAGAAGAAAA 1 AAATA-AAAAAAGAAAA 42289802 TCGAAAATCA Statistics Matches: 35, Mismatches: 3, Indels: 9 0.74 0.06 0.19 Matches are distributed among these distances: 24 4 0.11 25 18 0.51 26 7 0.20 27 6 0.17 ACGTcount: A:0.75, C:0.01, G:0.16, T:0.07 Consensus pattern (25 bp): AAATAAAAAAAGAAAAAATGAGAAG Found at i:42295003 original size:13 final size:13 Alignment explanation

Indices: 42294985--42295013 Score: 58 Period size: 13 Copynumber: 2.2 Consensus size: 13 42294975 GAACTTATCC 42294985 AAATATGGTCAGA 1 AAATATGGTCAGA 42294998 AAATATGGTCAGA 1 AAATATGGTCAGA 42295011 AAA 1 AAA 42295014 CAACCGCAGG Statistics Matches: 16, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 16 1.00 ACGTcount: A:0.52, C:0.07, G:0.21, T:0.21 Consensus pattern (13 bp): AAATATGGTCAGA Found at i:42299585 original size:49 final size:48 Alignment explanation

Indices: 42299478--42299604 Score: 130 Period size: 49 Copynumber: 2.6 Consensus size: 48 42299468 ATTACAAATA * * * 42299478 TAATATTATTTTAATATATTTAATATTAAAATAAATTAAATACTTTTTT 1 TAATAGTATTTTATTA-ATTTAATATTAAAATAAATTAAATACTTTTCT * * * 42299527 TAATAGTATTTTATTAATTTAATATTAAATTTAATTTAATA-TTTATCT 1 TAATAGTATTTTATTAATTTAATATTAAAATAAATTAAATACTTT-TCT * * * * 42299575 TGATAAGTATTATCTTGATTTAATATTAAA 1 TAAT-AGTATTTTATTAATTTAATATTAAA 42299605 GTGATTAAGA Statistics Matches: 66, Mismatches: 10, Indels: 4 0.82 0.12 0.05 Matches are distributed among these distances: 47 3 0.05 48 27 0.41 49 36 0.55 ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53 Consensus pattern (48 bp): TAATAGTATTTTATTAATTTAATATTAAAATAAATTAAATACTTTTCT Found at i:42318880 original size:21 final size:20 Alignment explanation

Indices: 42318854--42318893 Score: 53 Period size: 21 Copynumber: 1.9 Consensus size: 20 42318844 ACGTTCAAGT * 42318854 TCCACAAGGGCGTGTTGCCCG 1 TCCACAAGAGCGTG-TGCCCG * 42318875 TCCACACGAGCGTGTGCCC 1 TCCACAAGAGCGTGTGCCC 42318894 TGTTTCAAAG Statistics Matches: 17, Mismatches: 2, Indels: 1 0.85 0.10 0.05 Matches are distributed among these distances: 20 5 0.29 21 12 0.71 ACGTcount: A:0.15, C:0.38, G:0.30, T:0.17 Consensus pattern (20 bp): TCCACAAGAGCGTGTGCCCG Found at i:42320217 original size:31 final size:31 Alignment explanation

Indices: 42320182--42320258 Score: 145 Period size: 31 Copynumber: 2.5 Consensus size: 31 42320172 CCAAAGCTCA 42320182 AACAGACCAGAATGTTGGTAGTGCTCGCCCG 1 AACAGACCAGAATGTTGGTAGTGCTCGCCCG 42320213 AACAGACCAGAATGTTGGTAGTGCTCGCCCG 1 AACAGACCAGAATGTTGGTAGTGCTCGCCCG * 42320244 AATAGACCAGAATGT 1 AACAGACCAGAATGT 42320259 CCACAGTGCG Statistics Matches: 45, Mismatches: 1, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 31 45 1.00 ACGTcount: A:0.30, C:0.23, G:0.27, T:0.19 Consensus pattern (31 bp): AACAGACCAGAATGTTGGTAGTGCTCGCCCG Found at i:42320267 original size:31 final size:31 Alignment explanation

Indices: 42320182--42320267 Score: 91 Period size: 31 Copynumber: 2.8 Consensus size: 31 42320172 CCAAAGCTCA **** 42320182 AACAGACCAGAATGTTGGTAGTGCTCGCCCG 1 AACAGACCAGAATGTCCACAGTGCTCGCCCG **** 42320213 AACAGACCAGAATGTTGGTAGTGCTCGCCCG 1 AACAGACCAGAATGTCCACAGTGCTCGCCCG * 42320244 AATAGACCAGAATGTCCACAGTGC 1 AACAGACCAGAATGTCCACAGTGC 42320268 GGAAGACGTC Statistics Matches: 50, Mismatches: 5, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 31 50 1.00 ACGTcount: A:0.29, C:0.26, G:0.27, T:0.19 Consensus pattern (31 bp): AACAGACCAGAATGTCCACAGTGCTCGCCCG Found at i:42324197 original size:101 final size:100 Alignment explanation

Indices: 42324067--42324255 Score: 288 Period size: 101 Copynumber: 1.9 Consensus size: 100 42324057 TGATTTTAGG * * * * 42324067 TCACGTGTGCAGTACTAAGTGCAGGCTACTACGTGTACCAGATAGTTAGGTTGCATGTGTAATAC 1 TCACGTGTGCAGTACTAAGTGCAAGCTACTACGTGTACCAAAT-GTTAGGTCGCATGTCTAATAC 42324132 TAAGTGCAGGCTACTATGCGTACCCGACAACTTCAA 65 TAAGTGCAGGCTACTATGCGTACCCGACAACTTCAA * * * * * 42324168 TCACGTGTGTAGTACTAAGTGCAAGCTACTACGTGTACCAAATTTTTGGTCGTATGTCTAGTACT 1 TCACGTGTGCAGTACTAAGTGCAAGCTACTACGTGTACCAAATGTTAGGTCGCATGTCTAATACT 42324233 AAGTGCAGGCTACTATGCGTACC 66 AAGTGCAGGCTACTATGCGTACC 42324256 AGATAGCTTT Statistics Matches: 79, Mismatches: 9, Indels: 1 0.89 0.10 0.01 Matches are distributed among these distances: 100 39 0.49 101 40 0.51 ACGTcount: A:0.26, C:0.21, G:0.23, T:0.29 Consensus pattern (100 bp): TCACGTGTGCAGTACTAAGTGCAAGCTACTACGTGTACCAAATGTTAGGTCGCATGTCTAATACT AAGTGCAGGCTACTATGCGTACCCGACAACTTCAA Found at i:42324245 original size:49 final size:49 Alignment explanation

Indices: 42324062--42324256 Score: 160 Period size: 50 Copynumber: 3.9 Consensus size: 49 42324052 TATGATGATT * * * * * * 42324062 TTAGGTCACGTGTGCAGTACTAAGTGCAGGCTACTACGTGTACCAGATAG 1 TTAGGTCGCATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAAAT-C * * * 42324112 TTAGGTTGCATGTGTAATACTAAGTGCAGGCTACTATGCGTACCCGACAA-C 1 TTAGGTCGCATGTGTAGTACTAAGTGCAGGCTACTACGCGTA-CC-A-AATC * * * * * * 42324163 TTCA-ATCACGTGTGTAGTACTAAGTGCAAGCTACTACGTGTACCAAATT 1 TT-AGGTCGCATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAAATC * * * * 42324212 TTTGGTCGTATGTCTAGTACTAAGTGCAGGCTACTATGCGTACCA 1 TTAGGTCGCATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCA 42324257 GATAGCTTTT Statistics Matches: 112, Mismatches: 27, Indels: 13 0.74 0.18 0.09 Matches are distributed among these distances: 48 2 0.02 49 36 0.32 50 37 0.33 51 34 0.30 52 2 0.02 53 1 0.01 ACGTcount: A:0.27, C:0.21, G:0.24, T:0.29 Consensus pattern (49 bp): TTAGGTCGCATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAAATC Found at i:42324290 original size:100 final size:101 Alignment explanation

Indices: 42324077--42324258 Score: 231 Period size: 100 Copynumber: 1.8 Consensus size: 101 42324067 TCACGTGTGC * * * * * 42324077 AGTACTAAGTGCAGGCTACTACGTGTACCAGATAGTTAGGTTGCATGTGTAATACTAAGTGCAGG 1 AGTAATAAGTGCAAGCTACTACGTGTACCAAATAGTTAGGTCGCATGTCTAATACTAAGTGCAGG * ** * 42324142 CTACTATGCGTACCCGACAACTTCAATCACGTGTGT 66 CTACTATGCGTACCAGACAACTTCAATCACAAGGGT * * * * * 42324178 AGTACTAAGTGCAAGCTACTACGTGTACCAAAT-TTTTGGTCGTATGTCTAGTACTAAGTGCAGG 1 AGTAATAAGTGCAAGCTACTACGTGTACCAAATAGTTAGGTCGCATGTCTAATACTAAGTGCAGG 42324242 CTACTATGCGTACCAGA 66 CTACTATGCGTACCAGA 42324259 TAGCTTTTGT Statistics Matches: 72, Mismatches: 9, Indels: 1 0.88 0.11 0.01 Matches are distributed among these distances: 100 41 0.57 101 31 0.43 ACGTcount: A:0.28, C:0.20, G:0.23, T:0.29 Consensus pattern (101 bp): AGTAATAAGTGCAAGCTACTACGTGTACCAAATAGTTAGGTCGCATGTCTAATACTAAGTGCAGG CTACTATGCGTACCAGACAACTTCAATCACAAGGGT Found at i:42324479 original size:16 final size:15 Alignment explanation

Indices: 42324458--42324487 Score: 51 Period size: 16 Copynumber: 1.9 Consensus size: 15 42324448 GAATGGAGTA 42324458 AGTGAAATTATGTAAG 1 AGTGAAATT-TGTAAG 42324474 AGTGAAATTTGTAA 1 AGTGAAATTTGTAA 42324488 TAAAACAATT Statistics Matches: 14, Mismatches: 0, Indels: 1 0.93 0.00 0.07 Matches are distributed among these distances: 15 5 0.36 16 9 0.64 ACGTcount: A:0.43, C:0.00, G:0.23, T:0.33 Consensus pattern (15 bp): AGTGAAATTTGTAAG Found at i:42328180 original size:46 final size:48 Alignment explanation

Indices: 42328037--42328353 Score: 250 Period size: 46 Copynumber: 6.7 Consensus size: 48 42328027 TTACTTGTGT * ** * 42328037 GCTAGTGTAAGA-CATGTTTGGGACATGTGTCGGCCAT--ATTATG-AGA 1 GCTAGTGTAAGACCATGTCTGGGACATGCATCGGCC-TCGA-GATGTAGA * * * * * 42328083 GCCAGTGTAAGACCGTGTCTGGGACATGGCATCGGCATTGAGACG-AGA 1 GCTAGTGTAAGACCATGTCTGGGACAT-GCATCGGCCTCGAGATGTAGA 42328131 GCTAGTGTAAGA-CATGTCTGGGACATGCATCGGCCTCGAGATGTA-A 1 GCTAGTGTAAGACCATGTCTGGGACATGCATCGGCCTCGAGATGTAGA * 42328177 GCTAGTGTAAG-GCATGTCTGGGACATGCATCGG-CTGCGAGATGT-G- 1 GCTAGTGTAAGACCATGTCTGGGACATGCATCGGCCT-CGAGATGTAGA * * * * 42328222 TC-AGTGTAAGACCATGTCTAGGACATGGCATCGGCAC-AGATATGTGAGA 1 GCTAGTGTAAGACCATGTCTGGGACAT-GCATCGGC-CTCGAGATGT-AGA * * ** * 42328271 GCTAGTGTAAGACCATATATGGGACATGACATCGGCCTCGATTTCG-ATA 1 GCTAGTGTAAGACCATGTCTGGGACATG-CATCGGCCTCGAGAT-GTAGA * 42328320 G-TCAGTGTAAGACCATGTCTAGGACATGGCATCG 1 GCT-AGTGTAAGACCATGTCTGGGACAT-GCATCG 42328354 ACTTAATGGA Statistics Matches: 222, Mismatches: 28, Indels: 39 0.77 0.10 0.13 Matches are distributed among these distances: 44 8 0.04 45 16 0.07 46 79 0.36 47 27 0.12 48 25 0.11 49 33 0.15 50 33 0.15 51 1 0.00 ACGTcount: A:0.26, C:0.19, G:0.31, T:0.24 Consensus pattern (48 bp): GCTAGTGTAAGACCATGTCTGGGACATGCATCGGCCTCGAGATGTAGA Found at i:42328331 original size:99 final size:92 Alignment explanation

Indices: 42328134--42328353 Score: 259 Period size: 99 Copynumber: 2.3 Consensus size: 92 42328124 GACGAGAGCT * * * * * 42328134 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCTCGAGATGTAAGCTAGTGTAAGGCATGTCTG 1 AGTGTAAGACCATGTCTAGGACATGGCATCGGCCTAGAGATGTAAGCTAGTGTAAGCCATATATG 42328197 GGACATGCATCGGCTGCGAGATGTGTC 66 GGACATGCATCGGCTGCGAGATGTGTC * 42328224 AGTGTAAGACCATGTCTAGGACATGGCATCGGCAC-AGATATGTGAGAGCTAGTGTAAGACCATA 1 AGTGTAAGACCATGTCTAGGACATGGCATCGGC-CTAGAGATGT-A-AGCTAGTGTAAG-CCATA ** 42328288 TATGGGACATGACATCGGCCT-CGATTTCGATAGTC 62 TATGGGACATG-CATCGG-CTGCGAGAT-G-T-GTC 42328323 AGTGTAAGACCATGTCTAGGACATGGCATCG 1 AGTGTAAGACCATGTCTAGGACATGGCATCG 42328354 ACTTAATGGA Statistics Matches: 111, Mismatches: 8, Indels: 13 0.84 0.06 0.10 Matches are distributed among these distances: 90 9 0.08 91 13 0.12 92 14 0.13 93 2 0.02 94 12 0.11 95 13 0.12 96 10 0.09 97 3 0.03 98 1 0.01 99 34 0.31 ACGTcount: A:0.27, C:0.19, G:0.30, T:0.24 Consensus pattern (92 bp): AGTGTAAGACCATGTCTAGGACATGGCATCGGCCTAGAGATGTAAGCTAGTGTAAGCCATATATG GGACATGCATCGGCTGCGAGATGTGTC Found at i:42330402 original size:11 final size:11 Alignment explanation

Indices: 42330379--42330413 Score: 54 Period size: 11 Copynumber: 3.3 Consensus size: 11 42330369 ATTTGGTCTG 42330379 TTTT-GCTCCT 1 TTTTGGCTCCT * 42330389 TTTTGGCTCGT 1 TTTTGGCTCCT 42330400 TTTTGGCTCCT 1 TTTTGGCTCCT 42330411 TTT 1 TTT 42330414 GACTCTTGTG Statistics Matches: 22, Mismatches: 2, Indels: 1 0.88 0.08 0.04 Matches are distributed among these distances: 10 4 0.18 11 18 0.82 ACGTcount: A:0.00, C:0.23, G:0.17, T:0.60 Consensus pattern (11 bp): TTTTGGCTCCT Found at i:42332276 original size:14 final size:14 Alignment explanation

Indices: 42332259--42332288 Score: 60 Period size: 14 Copynumber: 2.1 Consensus size: 14 42332249 AATTGAAAAG 42332259 AAAATAAAAATAAA 1 AAAATAAAAATAAA 42332273 AAAATAAAAATAAA 1 AAAATAAAAATAAA 42332287 AA 1 AA 42332289 GATAGGAGGA Statistics Matches: 16, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 14 16 1.00 ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13 Consensus pattern (14 bp): AAAATAAAAATAAA Found at i:42332276 original size:19 final size:19 Alignment explanation

Indices: 42332234--42332275 Score: 59 Period size: 18 Copynumber: 2.3 Consensus size: 19 42332224 ATATGTCTTT * 42332234 AAAAAGAAAATAAAAAATT 1 AAAAAGAAAATAAAAAATA * 42332253 GAAAAGAAAAT-AAAAATA 1 AAAAAGAAAATAAAAAATA 42332271 AAAAA 1 AAAAA 42332276 ATAAAAATAA Statistics Matches: 20, Mismatches: 3, Indels: 1 0.83 0.12 0.04 Matches are distributed among these distances: 18 10 0.50 19 10 0.50 ACGTcount: A:0.81, C:0.00, G:0.07, T:0.12 Consensus pattern (19 bp): AAAAAGAAAATAAAAAATA Found at i:42333740 original size:28 final size:27 Alignment explanation

Indices: 42333697--42333749 Score: 79 Period size: 28 Copynumber: 1.9 Consensus size: 27 42333687 TAAAACTAGT * 42333697 ATATAGAAAATCCTAAAACAATATTCAA 1 ATATAGAAAATACTAAAACAA-ATTCAA * 42333725 ATATAGAAAATACTAAAGCAAATTC 1 ATATAGAAAATACTAAAACAAATTC 42333750 CTAACTTATT Statistics Matches: 23, Mismatches: 2, Indels: 1 0.88 0.08 0.04 Matches are distributed among these distances: 27 4 0.17 28 19 0.83 ACGTcount: A:0.57, C:0.13, G:0.06, T:0.25 Consensus pattern (27 bp): ATATAGAAAATACTAAAACAAATTCAA Found at i:42340560 original size:6 final size:6 Alignment explanation

Indices: 42340550--42340589 Score: 62 Period size: 6 Copynumber: 6.7 Consensus size: 6 42340540 AGAAAATAAT * * 42340550 AAAATT AAAATG AAAATA AAAATA AAAATA AAAATA AAAA 1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAA 42340590 GATAGGAGGA Statistics Matches: 32, Mismatches: 2, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 6 32 1.00 ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17 Consensus pattern (6 bp): AAAATA Found at i:42340577 original size:18 final size:18 Alignment explanation

Indices: 42340537--42340589 Score: 63 Period size: 18 Copynumber: 2.9 Consensus size: 18 42340527 TATGTATTTC * 42340537 AAAA-GAAAATAATAAAATT 1 AAAATGAAAAT-A-AAAATA 42340556 AAAATGAAAATAAAAATA 1 AAAATGAAAATAAAAATA * 42340574 AAAATAAAAATAAAAA 1 AAAATGAAAATAAAAA 42340590 GATAGGAGGA Statistics Matches: 31, Mismatches: 2, Indels: 3 0.86 0.06 0.08 Matches are distributed among these distances: 18 20 0.65 19 5 0.16 20 6 0.19 ACGTcount: A:0.79, C:0.00, G:0.04, T:0.17 Consensus pattern (18 bp): AAAATGAAAATAAAAATA Done.