Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Chr08 129432109 

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: 129432109
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32

Warning! 350 characters in sequence are not A, C, G, or T


File 224 of 425

Found at i:67912617 original size:49 final size:49

Alignment explanation

Indices: 67912467--67912645 Score: 166 Period size: 49 Copynumber: 3.7 Consensus size: 49 67912457 GATAAGATGC * ** * * * 67912467 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTAGC--ACATCAAAGT 1 CGATGCCATGTCCCAGACA-GGTCTTACACTGACTCTCATATATCGAGGT * * * 67912515 CGATGCCATGTCCCAAACAGGTCTTACACTGACTTTCATATATCGAGGC 1 CGATGCCATGTCCCAGACAGGTCTTACACTGACTCTCATATATCGAGGT * * * * * * 67912564 CGATGTCGTGTCCCAGACAGGTCTTACACTGGCTCTCATCTCTTG-GTGT 1 CGATGCCATGTCCCAGACAGGTCTTACACTGACTCTCATATATCGAG-GT * * 67912613 CGATGCCATGTCCTAGATAGGTCTTACACTGAC 1 CGATGCCATGTCCCAGACAGGTCTTACACTGAC 67912646 ACACAACAAG Statistics Matches: 106, Mismatches: 22, Indels: 5 0.80 0.17 0.04 Matches are distributed among these distances: 47 15 0.14 48 19 0.18 49 72 0.68 ACGTcount: A:0.23, C:0.28, G:0.21, T:0.27 Consensus pattern (49 bp): CGATGCCATGTCCCAGACAGGTCTTACACTGACTCTCATATATCGAGGT Found at i:67912723 original size:48 final size:48 Alignment explanation

Indices: 67912663--67912877 Score: 201 Period size: 46 Copynumber: 4.6 Consensus size: 48 67912653 AAGCTGACAC * * 67912663 CATGTCCCAGACAGGTCTGACACTAGCTTGTATATCTCAGGGCCGATG 1 CATGTCCCAGACATGTCTTACACTAGCTTGTATATCTCAGGGCCGATG * * * ** * 67912711 CATGTCCTAGACATGTCTTACACTAGC-TCT-TGTCTCAATGCTGATG 1 CATGTCCCAGACATGTCTTACACTAGCTTGTATATCTCAGGGCCGATG * * * * 67912757 CATGTCCCAGACATGTCTTACTCTAGCTTGCATCTATC-GAGGCCGATG 1 CATGTCCCAGACATGTCTTACACTAGCTTGTATATCTCAG-GGCCGATG * * * * * 67912805 CATGTCCCAGACATGTCCTACACTGGCTCCCGTA-ATGT---GGCTGATG 1 CATGTCCCAGACATGTCTTACACTAGCT--TGTATATCTCAGGGCCGATG 67912851 CATGTCCCAGACATGTCTTACACTAGC 1 CATGTCCCAGACATGTCTTACACTAGC 67912878 ACACATATCA Statistics Matches: 135, Mismatches: 27, Indels: 12 0.78 0.16 0.07 Matches are distributed among these distances: 46 69 0.51 47 3 0.02 48 59 0.44 49 2 0.01 50 2 0.01 ACGTcount: A:0.22, C:0.29, G:0.21, T:0.28 Consensus pattern (48 bp): CATGTCCCAGACATGTCTTACACTAGCTTGTATATCTCAGGGCCGATG Found at i:67912786 original size:94 final size:93 Alignment explanation

Indices: 67912663--67912877 Score: 265 Period size: 94 Copynumber: 2.3 Consensus size: 93 67912653 AAGCTGACAC * * * * * 67912663 CATGTCCCAGACAGGTCTGACACTAGCTTGTATATCTC-AGGGCCGATGCATGTCCTAGACATGT 1 CATGTCCCAGACATGTCTTACACTAGCTTGCATATATCGA-GGCCGATGCATGTCCCAGACATGT * ** 67912727 CTTACACTAGCTCTTGTCTCAA-T-GCTGATG 65 CCTACACTAGCTCCCG--T-AAGTGGCTGATG * * 67912757 CATGTCCCAGACATGTCTTACTCTAGCTTGCATCTATCGAGGCCGATGCATGTCCCAGACATGTC 1 CATGTCCCAGACATGTCTTACACTAGCTTGCATATATCGAGGCCGATGCATGTCCCAGACATGTC * 67912822 CTACACTGGCTCCCGTAATGTGGCTGATG 66 CTACACTAGCTCCCGTAA-GTGGCTGATG 67912851 CATGTCCCAGACATGTCTTACACTAGC 1 CATGTCCCAGACATGTCTTACACTAGC 67912878 ACACATATCA Statistics Matches: 105, Mismatches: 12, Indels: 8 0.84 0.10 0.06 Matches are distributed among these distances: 91 2 0.02 92 1 0.01 93 1 0.01 94 100 0.95 95 1 0.01 ACGTcount: A:0.22, C:0.29, G:0.21, T:0.28 Consensus pattern (93 bp): CATGTCCCAGACATGTCTTACACTAGCTTGCATATATCGAGGCCGATGCATGTCCCAGACATGTC CTACACTAGCTCCCGTAAGTGGCTGATG Found at i:67918115 original size:20 final size:20 Alignment explanation

Indices: 67918092--67918132 Score: 50 Period size: 19 Copynumber: 2.1 Consensus size: 20 67918082 TAATACTAAC 67918092 CTTTTAACAC-AAATATCATA 1 CTTTTAACACTAAATATC-TA * 67918112 C-TTTAATACTAAATATCTA 1 CTTTTAACACTAAATATCTA 67918131 CT 1 CT 67918133 AATATAACTA Statistics Matches: 18, Mismatches: 1, Indels: 4 0.78 0.04 0.17 Matches are distributed among these distances: 19 10 0.56 20 8 0.44 ACGTcount: A:0.41, C:0.20, G:0.00, T:0.39 Consensus pattern (20 bp): CTTTTAACACTAAATATCTA Found at i:67918882 original size:21 final size:22 Alignment explanation

Indices: 67918844--67918891 Score: 55 Period size: 21 Copynumber: 2.2 Consensus size: 22 67918834 TGGTATCTAT * 67918844 TTTATTATAAATTAATGT-TAA 1 TTTATGATAAATTAATGTATAA 67918865 TTTATGATAAAATT-ATGTAGTAA 1 TTTATGAT-AAATTAATGTA-TAA 67918888 TTTA 1 TTTA 67918892 GCATGCTAAA Statistics Matches: 23, Mismatches: 1, Indels: 4 0.82 0.04 0.14 Matches are distributed among these distances: 21 11 0.48 22 5 0.22 23 7 0.30 ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50 Consensus pattern (22 bp): TTTATGATAAATTAATGTATAA Found at i:67925426 original size:51 final size:51 Alignment explanation

Indices: 67925327--67925426 Score: 112 Period size: 51 Copynumber: 2.0 Consensus size: 51 67925317 CTGTAAGGAT * * * * * * 67925327 GGTATATGGTGTAAGATTATAAATGAAAGAGGCTATGACGATCTGGTATAA 1 GGTATACGGTATAAGACTATAAATGAAAGAGGCTATAACGACCAGGTATAA * * 67925378 GGTATACGGTATAAGACTATATATGAAAGATGCTATAAC-AGCCAGGTAT 1 GGTATACGGTATAAGACTATAAATGAAAGAGGCTATAACGA-CCAGGTAT 67925427 GATGGGTAAG Statistics Matches: 40, Mismatches: 8, Indels: 2 0.80 0.16 0.04 Matches are distributed among these distances: 50 1 0.03 51 39 0.98 ACGTcount: A:0.38, C:0.09, G:0.25, T:0.28 Consensus pattern (51 bp): GGTATACGGTATAAGACTATAAATGAAAGAGGCTATAACGACCAGGTATAA Found at i:67927321 original size:33 final size:33 Alignment explanation

Indices: 67927279--67927381 Score: 190 Period size: 33 Copynumber: 3.2 Consensus size: 33 67927269 GTCTCATCCA 67927279 TCATA-ATAAGGTTTGGTTATTGGGAAATGTAC 1 TCATAGATAAGGTTTGGTTATTGGGAAATGTAC 67927311 TCATAGATAAGGTTTGGTTATTGGGAAATGTAC 1 TCATAGATAAGGTTTGGTTATTGGGAAATGTAC * 67927344 TCATAGATAAGGTTTGGTTATTGGAAAATGTAC 1 TCATAGATAAGGTTTGGTTATTGGGAAATGTAC 67927377 TCATA 1 TCATA 67927382 TTGTAGTAAA Statistics Matches: 69, Mismatches: 1, Indels: 1 0.97 0.01 0.01 Matches are distributed among these distances: 32 5 0.07 33 64 0.93 ACGTcount: A:0.32, C:0.07, G:0.24, T:0.37 Consensus pattern (33 bp): TCATAGATAAGGTTTGGTTATTGGGAAATGTAC Found at i:67928408 original size:40 final size:41 Alignment explanation

Indices: 67928364--67928441 Score: 122 Period size: 40 Copynumber: 1.9 Consensus size: 41 67928354 CTTGATCAGA ** 67928364 AACGCCGCAAAAGATTGATC-TTTAGCGGCGTTTTTGAAAC 1 AACGCCGCAAAAGATCAATCTTTTAGCGGCGTTTTTGAAAC * 67928404 AACGCCGCTAAAGATCAATCTTTTAGCGGCGTTTTTGA 1 AACGCCGCAAAAGATCAATCTTTTAGCGGCGTTTTTGA 67928442 TTAAGCGCAG Statistics Matches: 34, Mismatches: 3, Indels: 1 0.89 0.08 0.03 Matches are distributed among these distances: 40 17 0.50 41 17 0.50 ACGTcount: A:0.28, C:0.21, G:0.22, T:0.29 Consensus pattern (41 bp): AACGCCGCAAAAGATCAATCTTTTAGCGGCGTTTTTGAAAC Found at i:67929142 original size:22 final size:22 Alignment explanation

Indices: 67929097--67929158 Score: 67 Period size: 22 Copynumber: 2.9 Consensus size: 22 67929087 CTATAGGCCT 67929097 TAAAT-CTCAAAC-CTTAAACTA 1 TAAATCCT-AAACTCTTAAACTA 67929118 TAAATCCTAAACTCTTAAA-TCA 1 TAAATCCTAAACTCTTAAACT-A * * 67929140 TAAACCCTAAAATCTTAAA 1 TAAATCCTAAACTCTTAAA 67929159 AATAAATTTT Statistics Matches: 36, Mismatches: 2, Indels: 5 0.84 0.05 0.12 Matches are distributed among these distances: 21 10 0.28 22 26 0.72 ACGTcount: A:0.48, C:0.23, G:0.00, T:0.29 Consensus pattern (22 bp): TAAATCCTAAACTCTTAAACTA Found at i:67929588 original size:41 final size:42 Alignment explanation

Indices: 67929533--67929635 Score: 127 Period size: 41 Copynumber: 2.5 Consensus size: 42 67929523 TAAAATTTAA ** * 67929533 GTTTAAGGTTTAGGGTATTGGGTTTAGAATTTAGTTTATAAG 1 GTTTAAGGGATAGGGTATTGGGTTTAGAATTTAGTCTATAAG ** * 67929575 GTTT-AGGGATAGGGTATTGGGTTTAGGGTTTAGTCTATAGG 1 GTTTAAGGGATAGGGTATTGGGTTTAGAATTTAGTCTATAAG ** 67929616 GTTTAAGGTTTAGGGTATTG 1 GTTTAAGGGATAGGGTATTG 67929636 TGTATTTGGT Statistics Matches: 52, Mismatches: 8, Indels: 2 0.84 0.13 0.03 Matches are distributed among these distances: 41 35 0.67 42 17 0.33 ACGTcount: A:0.22, C:0.01, G:0.34, T:0.43 Consensus pattern (42 bp): GTTTAAGGGATAGGGTATTGGGTTTAGAATTTAGTCTATAAG Found at i:67929603 original size:7 final size:7 Alignment explanation

Indices: 67929533--67929685 Score: 66 Period size: 7 Copynumber: 21.9 Consensus size: 7 67929523 TAAAATTTAA * 67929533 GTTTAAG 1 GTTTAGG 67929540 GTTTAGG 1 GTTTAGG 67929547 GTATT-GG 1 GT-TTAGG * 67929554 GTTTAGA 1 GTTTAGG * 67929561 ATTTA-G 1 GTTTAGG * * 67929567 TTTATAAG 1 GTT-TAGG 67929575 GTTTAGG 1 GTTTAGG * 67929582 G-ATAGG 1 GTTTAGG 67929588 GTATT-GG 1 GT-TTAGG 67929595 GTTTAGG 1 GTTTAGG * 67929602 GTTTAGT 1 GTTTAGG * * 67929609 CTATAGG 1 GTTTAGG * 67929616 GTTTAAG 1 GTTTAGG 67929623 GTTTAGG 1 GTTTAGG * 67929630 GTATT-GT 1 GT-TTAGG * 67929637 GTATT-TG 1 GT-TTAGG 67929644 GTTTAGG 1 GTTTAGG * 67929651 GTTTAGT 1 GTTTAGG * * 67929658 CTATAGG 1 GTTTAGG 67929665 GTTTAGG 1 GTTTAGG * 67929672 GTATTGGG 1 GT-TTAGG 67929680 GTTTAG 1 GTTTAG 67929686 TGTATTGGTT Statistics Matches: 107, Mismatches: 29, Indels: 20 0.69 0.19 0.13 Matches are distributed among these distances: 6 13 0.12 7 80 0.75 8 14 0.13 ACGTcount: A:0.20, C:0.01, G:0.35, T:0.44 Consensus pattern (7 bp): GTTTAGG Found at i:67929655 original size:49 final size:49 Alignment explanation

Indices: 67929571--67929696 Score: 168 Period size: 49 Copynumber: 2.6 Consensus size: 49 67929561 ATTTAGTTTA * * * 67929571 TAAGGTTTAGGG-ATAGGGTATTGGGTTTAGGGTTTAGTCTATAGGGTT 1 TAAGGTTTAGGGTATTGTGTATTTGGTTTAGGGTTTAGTCTATAGGGTT 67929619 TAAGGTTTAGGGTATTGTGTATTTGGTTTAGGGTTTAGTCTATAGGGTT 1 TAAGGTTTAGGGTATTGTGTATTTGGTTTAGGGTTTAGTCTATAGGGTT * * 67929668 TAGGGTATTGGGGT-TTAGTGTA-TTGGTTT 1 TAAGGT-TTAGGGTATT-GTGTATTTGGTTT 67929697 TGGGATTAAT Statistics Matches: 70, Mismatches: 5, Indels: 5 0.88 0.06 0.06 Matches are distributed among these distances: 48 12 0.17 49 47 0.67 50 11 0.16 ACGTcount: A:0.18, C:0.02, G:0.36, T:0.44 Consensus pattern (49 bp): TAAGGTTTAGGGTATTGTGTATTTGGTTTAGGGTTTAGTCTATAGGGTT Found at i:67929683 original size:15 final size:15 Alignment explanation

Indices: 67929663--67929693 Score: 53 Period size: 15 Copynumber: 2.1 Consensus size: 15 67929653 TTAGTCTATA 67929663 GGGTTTAGGGTATTG 1 GGGTTTAGGGTATTG * 67929678 GGGTTTAGTGTATTG 1 GGGTTTAGGGTATTG 67929693 G 1 G 67929694 TTTTGGGATT Statistics Matches: 15, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 15 15 1.00 ACGTcount: A:0.13, C:0.00, G:0.45, T:0.42 Consensus pattern (15 bp): GGGTTTAGGGTATTG Found at i:67930126 original size:84 final size:84 Alignment explanation

Indices: 67930025--67930204 Score: 272 Period size: 84 Copynumber: 2.1 Consensus size: 84 67930015 GGTAGTGGAT * * * 67930025 TTAGTGGCGCTATCTTATAAACGCCACTAATAATATGAAAAA-TCGAGTGAAAACTACGTCATTT 1 TTAGTGGCGCTACCTTATAAACGCCACTAAGAATATGAAAAACT-GAATGAAAACTACGTCATTT * 67930089 TATGTGGCACGGTTTAGGAA 65 TATGTGGCACGGTGTAGGAA * * * 67930109 TTAGTGGCGCTGCCTTATAAACGCCACTAAGAATATGAGAAACTGAATGAAAACTACGTCGTTTT 1 TTAGTGGCGCTACCTTATAAACGCCACTAAGAATATGAAAAACTGAATGAAAACTACGTCATTTT 67930174 ATGTGGCACGGTGTAGGAA 66 ATGTGGCACGGTGTAGGAA * 67930193 TTAGTAGCGCTA 1 TTAGTGGCGCTA 67930205 TCCTAAAAAC Statistics Matches: 86, Mismatches: 9, Indels: 2 0.89 0.09 0.02 Matches are distributed among these distances: 84 85 0.99 85 1 0.01 ACGTcount: A:0.33, C:0.16, G:0.23, T:0.28 Consensus pattern (84 bp): TTAGTGGCGCTACCTTATAAACGCCACTAAGAATATGAAAAACTGAATGAAAACTACGTCATTTT ATGTGGCACGGTGTAGGAA Found at i:67933620 original size:9 final size:9 Alignment explanation

Indices: 67933597--67933672 Score: 71 Period size: 9 Copynumber: 8.1 Consensus size: 9 67933587 ATTGATCATT * 67933597 ACTTAAATA 1 ACTTACATA * 67933606 AATTACATA 1 ACTTACATA 67933615 ACTTACATA 1 ACTTACATA * * 67933624 ACTCATATA 1 ACTTACATA 67933633 ACTTACATA 1 ACTTACATA * 67933642 ATTTACATAACA 1 ACTTACAT---A 67933654 ACTTACATA 1 ACTTACATA * 67933663 ACTCACATA 1 ACTTACATA 67933672 A 1 A 67933673 TTTCCTTAAA Statistics Matches: 54, Mismatches: 10, Indels: 6 0.77 0.14 0.09 Matches are distributed among these distances: 9 46 0.85 12 8 0.15 ACGTcount: A:0.49, C:0.20, G:0.00, T:0.32 Consensus pattern (9 bp): ACTTACATA Found at i:67933658 original size:21 final size:21 Alignment explanation

Indices: 67933614--67933672 Score: 70 Period size: 21 Copynumber: 3.0 Consensus size: 21 67933604 TAAATTACAT * 67933614 AACTTACATAACT--CAT-AT 1 AACTTACATAACTCACATAAC * * 67933632 AACTTACATAATTTACATAAC 1 AACTTACATAACTCACATAAC 67933653 AACTTACATAACTCACATAA 1 AACTTACATAACTCACATAA 67933673 TTTCCTTAAA Statistics Matches: 34, Mismatches: 4, Indels: 3 0.83 0.10 0.07 Matches are distributed among these distances: 18 12 0.35 20 3 0.09 21 19 0.56 ACGTcount: A:0.47, C:0.22, G:0.00, T:0.31 Consensus pattern (21 bp): AACTTACATAACTCACATAAC Found at i:67937611 original size:40 final size:40 Alignment explanation

Indices: 67937556--67937779 Score: 306 Period size: 40 Copynumber: 5.5 Consensus size: 40 67937546 TATTCGGATG 67937556 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT 1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT * 67937596 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTAGTTGCT 1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGC-A--AGTTACT * * * 67937639 ATACCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT 1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT ** * * 67937679 ATATCCGGGCTAAGTCCCGAAGGCATTCATGCTAGTGACT 1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT * * * 67937719 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCT 1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT * 67937759 ATATCC-GGCTAAATCCCGAAG 1 ATATCCGGGCTAAGTCCCGAAG 67937780 ATACTTGGGT Statistics Matches: 165, Mismatches: 16, Indels: 7 0.88 0.09 0.04 Matches are distributed among these distances: 39 13 0.08 40 114 0.69 41 1 0.01 43 37 0.22 ACGTcount: A:0.24, C:0.24, G:0.27, T:0.25 Consensus pattern (40 bp): ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT Found at i:67937699 original size:83 final size:80 Alignment explanation

Indices: 67937560--67937779 Score: 302 Period size: 83 Copynumber: 2.7 Consensus size: 80 67937550 CGGATGATAT * ** 67937560 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTG 1 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTGACTATATCCGGGCTAAGTCCCGAAGGCATTCA 67937625 TGCGAGTAGTTG-CTATAC 66 TGC---TAG-TGACTATAC * 67937643 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTCCCGAAGGCATTCA 1 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTGACTATATCCGGGCTAAGTCCCGAAGGCATTCA * 67937708 TGCTAGTGACTATAT 66 TGCTAGTGACTATAC * * * 67937723 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CTATATCC-GGCTAAATCCCGAAG 1 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAG-TGACTATATCCGGGCTAAGTCCCGAAG 67937780 ATACTTGGGT Statistics Matches: 127, Mismatches: 8, Indels: 8 0.89 0.06 0.06 Matches are distributed among these distances: 79 16 0.13 80 45 0.35 81 2 0.02 83 64 0.50 ACGTcount: A:0.24, C:0.24, G:0.27, T:0.25 Consensus pattern (80 bp): CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTGACTATATCCGGGCTAAGTCCCGAAGGCATTCA TGCTAGTGACTATAC Found at i:67945831 original size:40 final size:40 Alignment explanation

Indices: 67945776--67946038 Score: 377 Period size: 40 Copynumber: 6.5 Consensus size: 40 67945766 TATTCGGATG 67945776 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT 1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT 67945816 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT 1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT * 67945856 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTAGTTGCT 1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGC-A--AGTTACT * * * 67945899 ATACCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT 1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT ** * * 67945939 ATAT-CGGGCTAAGTCCCGAAGGCATTCATGCTAGTGACT 1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT * * * 67945978 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCT 1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT * 67946018 ATATCC-GGCTAAATCCCGAAG 1 ATATCCGGGCTAAGTCCCGAAG 67946039 ATACTTGGGT Statistics Matches: 203, Mismatches: 16, Indels: 9 0.89 0.07 0.04 Matches are distributed among these distances: 39 50 0.25 40 115 0.57 41 1 0.00 43 37 0.18 ACGTcount: A:0.24, C:0.23, G:0.27, T:0.26 Consensus pattern (40 bp): ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT Found at i:67945998 original size:122 final size:120 Alignment explanation

Indices: 67945780--67946038 Score: 396 Period size: 122 Copynumber: 2.1 Consensus size: 120 67945770 CGGATGATAT * ** 67945780 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTG 1 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTGACTATATCCGGGCTAAGTCCCGAAGGCATTCA * * 67945845 TGCAAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTAGTTGCTATAC 66 TGCAAGTGACTATATCCGGGCTAAGACCCGAAGGCATTTGTGC--G-AGTTGCTATAC * 67945903 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATAT-CGGGCTAAGTCCCGAAGGCATTCA 1 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTGACTATATCCGGGCTAAGTCCCGAAGGCATTCA * * 67945967 TGCTAGTGACTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT 66 TGCAAGTGACTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAC * 67946022 CC-GGCTAAATCCCGAAG 1 CCGGGCTAAGTCCCGAAG 67946039 ATACTTGGGT Statistics Matches: 127, Mismatches: 9, Indels: 5 0.90 0.06 0.04 Matches are distributed among these distances: 118 14 0.11 119 12 0.09 120 1 0.01 122 62 0.49 123 38 0.30 ACGTcount: A:0.24, C:0.24, G:0.27, T:0.25 Consensus pattern (120 bp): CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTGACTATATCCGGGCTAAGTCCCGAAGGCATTCA TGCAAGTGACTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAC Found at i:67951277 original size:43 final size:44 Alignment explanation

Indices: 67951194--67951279 Score: 156 Period size: 44 Copynumber: 2.0 Consensus size: 44 67951184 ACCGGGCAAA * 67951194 TTAGCGGCGCTTTTTTAAAAAACGCCGCTAAAAGTCCCTGGTCT 1 TTAGCGGCGCTTTTTTAAAAAACGCCACTAAAAGTCCCTGGTCT 67951238 TTAGCGGCGCTTTTTTAAAAAACGCCACTAAAAGT-CCTGGTC 1 TTAGCGGCGCTTTTTTAAAAAACGCCACTAAAAGTCCCTGGTC 67951280 AAAAAAACGC Statistics Matches: 41, Mismatches: 1, Indels: 1 0.95 0.02 0.02 Matches are distributed among these distances: 43 7 0.17 44 34 0.83 ACGTcount: A:0.27, C:0.24, G:0.20, T:0.29 Consensus pattern (44 bp): TTAGCGGCGCTTTTTTAAAAAACGCCACTAAAAGTCCCTGGTCT Found at i:67953204 original size:77 final size:77 Alignment explanation

Indices: 67953077--67953229 Score: 270 Period size: 77 Copynumber: 2.0 Consensus size: 77 67953067 CTATAAATAT * 67953077 GTTTAATTTTTTGTTAAGTAAGGTTTTTCCTCATTGTCTCCGGTGATATTTTTTATTGCAATGAC 1 GTTTAATTTTTTGTTAAGTAAGGTTTTTCCTCATTGTCACCGGTGATATTTTTTATTGCAATGAC 67953142 TAATAGGACAGG 66 TAATAGGACAGG * * 67953154 GTTTAATTTTTTGTTCAGTAAGGTTTTTCCTTATTGTCACCGGTGATATTTTTTATTGCAATGAC 1 GTTTAATTTTTTGTTAAGTAAGGTTTTTCCTCATTGTCACCGGTGATATTTTTTATTGCAATGAC * 67953219 TAATGGGACAG 66 TAATAGGACAG 67953230 TGAATTTAAA Statistics Matches: 72, Mismatches: 4, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 77 72 1.00 ACGTcount: A:0.23, C:0.12, G:0.20, T:0.46 Consensus pattern (77 bp): GTTTAATTTTTTGTTAAGTAAGGTTTTTCCTCATTGTCACCGGTGATATTTTTTATTGCAATGAC TAATAGGACAGG Found at i:67955771 original size:61 final size:57 Alignment explanation

Indices: 67955676--67955817 Score: 176 Period size: 61 Copynumber: 2.4 Consensus size: 57 67955666 TTGTTATTAA * * * * * 67955676 ATTTTAATAAAATTATTATTAAATATAATTTAATAAAAATAATAATAAATAATTTAATCAT 1 ATTTTAATATAATTATTATTAAATACAATTTAAT-AAAATAAT-AT--ATAATTCAATAAC * * 67955737 ATTTTAACATAATTATTGTTAAATACAATTTAATAAAATAATATATAATTCAATAAC 1 ATTTTAATATAATTATTATTAAATACAATTTAATAAAATAATATATAATTCAATAAC 67955794 ATTCTTAATATAATTATTATTAAA 1 ATT-TTAATATAATTATTATTAAA 67955818 ATATGAAATA Statistics Matches: 71, Mismatches: 9, Indels: 5 0.84 0.11 0.06 Matches are distributed among these distances: 57 13 0.18 58 18 0.25 59 2 0.03 60 8 0.11 61 30 0.42 ACGTcount: A:0.52, C:0.04, G:0.01, T:0.43 Consensus pattern (57 bp): ATTTTAATATAATTATTATTAAATACAATTTAATAAAATAATATATAATTCAATAAC Found at i:67958420 original size:66 final size:66 Alignment explanation

Indices: 67958296--67958420 Score: 153 Period size: 67 Copynumber: 1.9 Consensus size: 66 67958286 ATGTGTACAC * * * * 67958296 CATGTAGACAAGAGAACTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGAC 1 CATGTAGACAAGAGAACTACGAGATAAATG-AGCTAGGTCACATGCGTGGTACCAAGTGAAGGAC 67958361 AT 65 AT * * * * 67958363 CATGTAGACAAGAGAGCTATGAGATAAACTG-GCTAGGTCACATGGGTGGTACTAAGTG 1 CATGTAGACAAGAGAACTACGAGATAAA-TGAGCTAGGTCACATGCGTGGTACCAAGTG 67958421 TTCACCATGT Statistics Matches: 49, Mismatches: 8, Indels: 3 0.82 0.13 0.05 Matches are distributed among these distances: 66 23 0.47 67 24 0.49 68 2 0.04 ACGTcount: A:0.32, C:0.15, G:0.30, T:0.22 Consensus pattern (66 bp): CATGTAGACAAGAGAACTACGAGATAAATGAGCTAGGTCACATGCGTGGTACCAAGTGAAGGACA T Found at i:67964192 original size:38 final size:38 Alignment explanation

Indices: 67964132--67964365 Score: 297 Period size: 38 Copynumber: 6.2 Consensus size: 38 67964122 GTGGTATACT * * 67964132 TTCTGTTTGGCGTTTTGGTTGGATCAACTCTTATGAGC 1 TTCTGTTTGGCGATTCGGTTGGATCAACTCTTATGAGC * * * * 67964170 TTCTGTTTGGTGATTCGATTGGATTATCTCTTATGAGC 1 TTCTGTTTGGCGATTCGGTTGGATCAACTCTTATGAGC * ** * ** 67964208 TTCTGTTTGGCGTTTCGGTTAAATCAACTCATATGAAA 1 TTCTGTTTGGCGATTCGGTTGGATCAACTCTTATGAGC 67964246 TTCTGTTTGGCGATTCGGTTGGATCAACTCTTATGAGC 1 TTCTGTTTGGCGATTCGGTTGGATCAACTCTTATGAGC * * ** 67964284 TTCTATTTGGTGATTCATTTGGATCAACTCTTATGAGC 1 TTCTGTTTGGCGATTCGGTTGGATCAACTCTTATGAGC * * * 67964322 TTCTGTTTGGTGTTTCGGTTGGATCAGCTCTTATGAGC 1 TTCTGTTTGGCGATTCGGTTGGATCAACTCTTATGAGC 67964360 TTCTGT 1 TTCTGT 67964366 CTAGTGTGTT Statistics Matches: 165, Mismatches: 31, Indels: 0 0.84 0.16 0.00 Matches are distributed among these distances: 38 165 1.00 ACGTcount: A:0.17, C:0.16, G:0.24, T:0.44 Consensus pattern (38 bp): TTCTGTTTGGCGATTCGGTTGGATCAACTCTTATGAGC Found at i:67964365 original size:114 final size:114 Alignment explanation

Indices: 67964132--67964341 Score: 350 Period size: 114 Copynumber: 1.8 Consensus size: 114 67964122 GTGGTATACT * * * * * 67964132 TTCTGTTTGGCGTTTTGGTTGGATCAACTCTTATGAGCTTCTGTTTGGTGATTCGATTGGATTAT 1 TTCTGTTTGGCGATTCGGTTGGATCAACTCTTATGAGCTTCTATTTGGTGATTCGATTGGATCAA 67964197 CTCTTATGAGCTTCTGTTTGGCGTTTCGGTTAAATCAACTCATATGAAA 66 CTCTTATGAGCTTCTGTTTGGCGTTTCGGTTAAATCAACTCATATGAAA 67964246 TTCTGTTTGGCGATTCGGTTGGATCAACTCTTATGAGCTTCTATTTGGTGATTC-ATTTGGATCA 1 TTCTGTTTGGCGATTCGGTTGGATCAACTCTTATGAGCTTCTATTTGGTGATTCGA-TTGGATCA * 67964310 ACTCTTATGAGCTTCTGTTTGGTGTTTCGGTT 65 ACTCTTATGAGCTTCTGTTTGGCGTTTCGGTT 67964342 GGATCAGCTC Statistics Matches: 89, Mismatches: 6, Indels: 2 0.92 0.06 0.02 Matches are distributed among these distances: 113 1 0.01 114 88 0.99 ACGTcount: A:0.17, C:0.15, G:0.23, T:0.45 Consensus pattern (114 bp): TTCTGTTTGGCGATTCGGTTGGATCAACTCTTATGAGCTTCTATTTGGTGATTCGATTGGATCAA CTCTTATGAGCTTCTGTTTGGCGTTTCGGTTAAATCAACTCATATGAAA Found at i:67968641 original size:103 final size:103 Alignment explanation

Indices: 67968457--67968651 Score: 309 Period size: 103 Copynumber: 1.9 Consensus size: 103 67968447 TTAGCTGCGT * * * * * 67968457 GGCGAATTAAATTCCAAAAATTAAGTGTAGACTTCACATGGCCTGGGCACACACCCATTTCCTGA 1 GGCGAATTAAATTCCAAAAATTAAGTGCAGACTTCACACGGCCTAGCCACACACCCATATCCTGA ** * 67968522 GGTTGTGTCCTTCACACGGCTGAGACATAAGGCCGTGC 66 GGCCGTGTCCTCCACACGGCTGAGACATAAGGCCGTGC * 67968560 GGCGAATTACATTCCAAAAATTAAGTGCAGACTTCACACGGCCTAGCCACACACCCATATCCTGA 1 GGCGAATTAAATTCCAAAAATTAAGTGCAGACTTCACACGGCCTAGCCACACACCCATATCCTGA 67968625 GGCCGTGTCCTCCACACGGCTGAGACA 66 GGCCGTGTCCTCCACACGGCTGAGACA 67968652 CATGACTGTG Statistics Matches: 83, Mismatches: 9, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 103 83 1.00 ACGTcount: A:0.28, C:0.29, G:0.22, T:0.22 Consensus pattern (103 bp): GGCGAATTAAATTCCAAAAATTAAGTGCAGACTTCACACGGCCTAGCCACACACCCATATCCTGA GGCCGTGTCCTCCACACGGCTGAGACATAAGGCCGTGC Found at i:67969986 original size:20 final size:20 Alignment explanation

Indices: 67969961--67969998 Score: 67 Period size: 20 Copynumber: 1.9 Consensus size: 20 67969951 GTCACATATA 67969961 TCATGAGCTCAGACCACAAC 1 TCATGAGCTCAGACCACAAC * 67969981 TCATGAGCTCAGATCACA 1 TCATGAGCTCAGACCACA 67969999 TAGTTCCTAA Statistics Matches: 17, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 20 17 1.00 ACGTcount: A:0.34, C:0.32, G:0.16, T:0.18 Consensus pattern (20 bp): TCATGAGCTCAGACCACAAC Found at i:67973176 original size:48 final size:48 Alignment explanation

Indices: 67973111--67973258 Score: 224 Period size: 48 Copynumber: 3.1 Consensus size: 48 67973101 GGGCTATCGA * * 67973111 CATCGATATGTGATCCCATGTAAGACCATGTCTGGGACATGGCATTAG 1 CATCGATCTGTGATCCCATGTAAGACCATGTCTGGGACATGGCATTGG * * * 67973159 CATCGATCTATGATCCCACGTAAGACCATGTTTGGGACATGGCATTGG 1 CATCGATCTGTGATCCCATGTAAGACCATGTCTGGGACATGGCATTGG * * * 67973207 CATCGATCTGTGATCCCATGTAAGACCATATCTGGGATATGGCTTTGG 1 CATCGATCTGTGATCCCATGTAAGACCATGTCTGGGACATGGCATTGG 67973255 CATC 1 CATC 67973259 TTACCATGTG Statistics Matches: 89, Mismatches: 11, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 48 89 1.00 ACGTcount: A:0.25, C:0.22, G:0.24, T:0.28 Consensus pattern (48 bp): CATCGATCTGTGATCCCATGTAAGACCATGTCTGGGACATGGCATTGG Found at i:67975545 original size:40 final size:41 Alignment explanation

Indices: 67975501--67975609 Score: 116 Period size: 40 Copynumber: 2.7 Consensus size: 41 67975491 ACTATGTTTG 67975501 GCACTTAGTGTGCG-TTCCGAGATAGCTTCGGCTATATATA 1 GCACTTAGTGTGCGATTCCGAGATAGCTTCGGCTATATATA * * * * * 67975541 GCACTTAGTGTACGAATT-GGA-ATAGCTTCGGCTTTATGTG 1 GCACTTAGTGTGCG-ATTCCGAGATAGCTTCGGCTATATATA * * * 67975581 GCTCTAAGTGTGCGATACCGAGATAGCTT 1 GCACTTAGTGTGCGATTCCGAGATAGCTT 67975610 TGCTTTAATG Statistics Matches: 55, Mismatches: 10, Indels: 7 0.76 0.14 0.10 Matches are distributed among these distances: 39 2 0.04 40 42 0.76 41 9 0.16 42 2 0.04 ACGTcount: A:0.23, C:0.18, G:0.27, T:0.32 Consensus pattern (41 bp): GCACTTAGTGTGCGATTCCGAGATAGCTTCGGCTATATATA Found at i:67981906 original size:25 final size:24 Alignment explanation

Indices: 67981865--67981921 Score: 62 Period size: 25 Copynumber: 2.3 Consensus size: 24 67981855 GATTATGTAG * 67981865 AAAGAATAAAGAAATGAA-AAAAAA 1 AAAGAA-AGAGAAATGAAGAAAAAA * 67981889 AGAAGAAAGAGAATATGAAGAAAAAC 1 A-AAGAAAGAGAA-ATGAAGAAAAAA 67981915 AAAGAAA 1 AAAGAAA 67981922 AGGAAAAAAA Statistics Matches: 28, Mismatches: 2, Indels: 5 0.80 0.06 0.14 Matches are distributed among these distances: 24 6 0.21 25 16 0.57 26 6 0.21 ACGTcount: A:0.74, C:0.02, G:0.18, T:0.07 Consensus pattern (24 bp): AAAGAAAGAGAAATGAAGAAAAAA Found at i:67983127 original size:29 final size:29 Alignment explanation

Indices: 67983094--67983158 Score: 112 Period size: 29 Copynumber: 2.2 Consensus size: 29 67983084 GTGACGAGAT * 67983094 TGGCACTAAGTGTGCATGCTGGAAATATA 1 TGGCACTAAGTGTGCATGCTGGAAAAATA 67983123 TGGCACTAAGTGTGCATGCTGGAAAAATA 1 TGGCACTAAGTGTGCATGCTGGAAAAATA * 67983152 CGGCACT 1 TGGCACT 67983159 GGGTGTGCGA Statistics Matches: 34, Mismatches: 2, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 29 34 1.00 ACGTcount: A:0.31, C:0.17, G:0.28, T:0.25 Consensus pattern (29 bp): TGGCACTAAGTGTGCATGCTGGAAAAATA Found at i:67989762 original size:22 final size:22 Alignment explanation

Indices: 67989730--67989776 Score: 69 Period size: 23 Copynumber: 2.1 Consensus size: 22 67989720 TAGAAAGAAT 67989730 AAAGAAATGAA-AAAAAAAAAG 1 AAAGAAATGAAGAAAAAAAAAG * 67989751 AAAGAGAATGAAGAAAAACAAAG 1 AAAGA-AATGAAGAAAAAAAAAG 67989774 AAA 1 AAA 67989777 AGGAAAAAAA Statistics Matches: 23, Mismatches: 1, Indels: 2 0.88 0.04 0.08 Matches are distributed among these distances: 21 5 0.22 22 6 0.26 23 12 0.52 ACGTcount: A:0.77, C:0.02, G:0.17, T:0.04 Consensus pattern (22 bp): AAAGAAATGAAGAAAAAAAAAG Found at i:67989786 original size:19 final size:19 Alignment explanation

Indices: 67989742--67989787 Score: 56 Period size: 19 Copynumber: 2.4 Consensus size: 19 67989732 AGAAATGAAA * * * 67989742 AAAAAAAAGAAAGAGAATG 1 AAAAAAAACAAAGAAAAGG * 67989761 AAGAAAAACAAAGAAAAGG 1 AAAAAAAACAAAGAAAAGG 67989780 AAAAAAAA 1 AAAAAAAA 67989788 AAGTGTTCAT Statistics Matches: 22, Mismatches: 5, Indels: 0 0.81 0.19 0.00 Matches are distributed among these distances: 19 22 1.00 ACGTcount: A:0.78, C:0.02, G:0.17, T:0.02 Consensus pattern (19 bp): AAAAAAAACAAAGAAAAGG Found at i:67990948 original size:28 final size:28 Alignment explanation

Indices: 67990917--67990971 Score: 110 Period size: 28 Copynumber: 2.0 Consensus size: 28 67990907 CGGTGACGAG 67990917 ATTGGCACTAAGTGTGCATGCTGGAAAT 1 ATTGGCACTAAGTGTGCATGCTGGAAAT 67990945 ATTGGCACTAAGTGTGCATGCTGGAAA 1 ATTGGCACTAAGTGTGCATGCTGGAAA 67990972 AATACGGCAC Statistics Matches: 27, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 28 27 1.00 ACGTcount: A:0.29, C:0.15, G:0.29, T:0.27 Consensus pattern (28 bp): ATTGGCACTAAGTGTGCATGCTGGAAAT Found at i:67990990 original size:29 final size:28 Alignment explanation

Indices: 67990920--67990982 Score: 99 Period size: 28 Copynumber: 2.2 Consensus size: 28 67990910 TGACGAGATT * * 67990920 GGCACTAAGTGTGCATGCTGGAAATATT 1 GGCACTAAGTGTGCATGCTGGAAAAATC 67990948 GGCACTAAGTGTGCATGCTGGAAAAATAC 1 GGCACTAAGTGTGCATGCTGGAAAAAT-C 67990977 GGCACT 1 GGCACT 67990983 GGGTGTGCGA Statistics Matches: 32, Mismatches: 2, Indels: 1 0.91 0.06 0.03 Matches are distributed among these distances: 28 26 0.81 29 6 0.19 ACGTcount: A:0.30, C:0.17, G:0.29, T:0.24 Consensus pattern (28 bp): GGCACTAAGTGTGCATGCTGGAAAAATC Found at i:67997602 original size:24 final size:24 Alignment explanation

Indices: 67997562--67997623 Score: 72 Period size: 25 Copynumber: 2.5 Consensus size: 24 67997552 GATTATGTAG 67997562 AAAGAATAAAGAAATGAA-AAAAAA 1 AAAGAA-AAAGAAATGAAGAAAAAA * * 67997586 AAAGAAAGAGAATATGAAGAAAAAC 1 AAAGAAAAAGAA-ATGAAGAAAAAA * 67997611 AAAGAAAAGGAAA 1 AAAGAAAAAGAAA 67997624 AAAAAAGTGT Statistics Matches: 32, Mismatches: 4, Indels: 4 0.80 0.10 0.10 Matches are distributed among these distances: 23 5 0.16 24 12 0.38 25 15 0.47 ACGTcount: A:0.74, C:0.02, G:0.18, T:0.06 Consensus pattern (24 bp): AAAGAAAAAGAAATGAAGAAAAAA Found at i:67998821 original size:29 final size:29 Alignment explanation

Indices: 67998788--67998852 Score: 112 Period size: 29 Copynumber: 2.2 Consensus size: 29 67998778 GTGACGAGAT * 67998788 TGGCACTAAGTGTGCATGCTGGAAATATA 1 TGGCACTAAGTGTGCATGCTGGAAAAATA 67998817 TGGCACTAAGTGTGCATGCTGGAAAAATA 1 TGGCACTAAGTGTGCATGCTGGAAAAATA * 67998846 CGGCACT 1 TGGCACT 67998853 GGGTGTGCGA Statistics Matches: 34, Mismatches: 2, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 29 34 1.00 ACGTcount: A:0.31, C:0.17, G:0.28, T:0.25 Consensus pattern (29 bp): TGGCACTAAGTGTGCATGCTGGAAAAATA Found at i:68006715 original size:29 final size:29 Alignment explanation

Indices: 68006682--68006746 Score: 112 Period size: 29 Copynumber: 2.2 Consensus size: 29 68006672 GTGACGAGAT * 68006682 TGGCACTAAGTGTGCATGCTGGAAATATA 1 TGGCACTAAGTGTGCATGCTGGAAAAATA 68006711 TGGCACTAAGTGTGCATGCTGGAAAAATA 1 TGGCACTAAGTGTGCATGCTGGAAAAATA * 68006740 CGGCACT 1 TGGCACT 68006747 GGGTGTGCGA Statistics Matches: 34, Mismatches: 2, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 29 34 1.00 ACGTcount: A:0.31, C:0.17, G:0.28, T:0.25 Consensus pattern (29 bp): TGGCACTAAGTGTGCATGCTGGAAAAATA Found at i:68008313 original size:28 final size:28 Alignment explanation

Indices: 68008244--68008344 Score: 114 Period size: 28 Copynumber: 3.5 Consensus size: 28 68008234 GACAAGATTG * * * * 68008244 GCACTAAGTGTGCGGGTTTAAAATTGTACA 1 GCACTAAGTGTGCGAGTTT--GATTATATA 68008274 GCACTAAGTGTGCGAGTTTGATTATATA 1 GCACTAAGTGTGCGAGTTTGATTATATA * 68008302 GCACTAAGTGTGCGAG-CTGAATGTATATA 1 GCACTAAGTGTGCGAGTTTG-AT-TATATA 68008331 GCACTAAGTGTGCG 1 GCACTAAGTGTGCG 68008345 GATTCACTAT Statistics Matches: 64, Mismatches: 5, Indels: 5 0.86 0.07 0.07 Matches are distributed among these distances: 27 2 0.03 28 24 0.38 29 20 0.31 30 18 0.28 ACGTcount: A:0.29, C:0.14, G:0.28, T:0.30 Consensus pattern (28 bp): GCACTAAGTGTGCGAGTTTGATTATATA Found at i:68008338 original size:29 final size:28 Alignment explanation

Indices: 68008273--68008344 Score: 110 Period size: 29 Copynumber: 2.5 Consensus size: 28 68008263 AAAATTGTAC * 68008273 AGCACTAAGTGTGCGAGTTTGATTATAT 1 AGCACTAAGTGTGCGAGTCTGATTATAT 68008301 AGCACTAAGTGTGCGAG-CTGAATGTATAT 1 AGCACTAAGTGTGCGAGTCTG-AT-TATAT 68008330 AGCACTAAGTGTGCG 1 AGCACTAAGTGTGCG 68008345 GATTCACTAT Statistics Matches: 41, Mismatches: 1, Indels: 3 0.91 0.02 0.07 Matches are distributed among these distances: 27 2 0.05 28 19 0.46 29 20 0.49 ACGTcount: A:0.29, C:0.14, G:0.28, T:0.29 Consensus pattern (28 bp): AGCACTAAGTGTGCGAGTCTGATTATAT Found at i:68010286 original size:40 final size:40 Alignment explanation

Indices: 68010227--68010433 Score: 218 Period size: 40 Copynumber: 5.2 Consensus size: 40 68010217 CAATTGAATG * * * * 68010227 ATATCCGGGCTAAGTCCCGAAGACATTTATGCTAGTAATT 1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT * * * * 68010267 ATATCCGGGTTAAGACCCGAAGGCA-TTGTGCTAGTGACT 1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT * * ** 68010306 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTT 1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT * * ** 68010346 AAATCCGGGCTAATACCCGAAGGCATTTGTGCAAGTCGTT 1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT * * * ** 68010386 CTATCCGGGCTAAGACCCGAAGGCATTCGTGCATGTGGTT 1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT 68010426 ATATCCGG 1 ATATCCGG 68010434 TTGTATTCCG Statistics Matches: 142, Mismatches: 24, Indels: 2 0.85 0.14 0.01 Matches are distributed among these distances: 39 34 0.24 40 108 0.76 ACGTcount: A:0.26, C:0.23, G:0.26, T:0.26 Consensus pattern (40 bp): ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT Found at i:68010406 original size:80 final size:77 Alignment explanation

Indices: 68010228--68010433 Score: 241 Period size: 79 Copynumber: 2.6 Consensus size: 77 68010218 AATTGAATGA * * ** * * * 68010228 TATCCGGGCTAAGTCCCGAAGACATTTATGCTAGTAATTATATCCGGGTTAAGACCCGAAGGCAT 1 TATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGGGCTAAGACCCGAAGGCAT * 68010293 TGTGCTAGTGAC 66 TGTGCAAGTGAC * * * 68010305 TACATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTTAAATCCGGGCTAATACCCGAAGGC 1 T--ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGGGCTAAGACCCGAAGGC * 68010370 ATTTGTGCAAGTCGTTC 64 A-TTGTGCAAGT-G-AC * * 68010387 TATCCGGGCTAAGACCCGAAGGCATTCGTGCATGTGGTTATATCCGG 1 TATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGG 68010434 TTGTATTCCG Statistics Matches: 109, Mismatches: 15, Indels: 7 0.83 0.11 0.05 Matches are distributed among these distances: 77 1 0.01 79 53 0.49 80 52 0.48 81 1 0.01 82 2 0.02 ACGTcount: A:0.25, C:0.23, G:0.26, T:0.26 Consensus pattern (77 bp): TATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGGGCTAAGACCCGAAGGCAT TGTGCAAGTGAC Found at i:68018282 original size:40 final size:40 Alignment explanation

Indices: 68018223--68018429 Score: 218 Period size: 40 Copynumber: 5.2 Consensus size: 40 68018213 CAATTGAATG * * * * 68018223 ATATCCGGGCTAAGTCCCGAAGACATTTATGCTAGTAATT 1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT * * * * 68018263 ATATCCGGGTTAAGACCCGAAGGCA-TTGTGCTAGTGACT 1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT * * ** 68018302 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTT 1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT * * ** 68018342 AAATCCGGGCTAATACCCGAAGGCATTTGTGCAAGTCGTT 1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT * * * ** 68018382 CTATCCGGGCTAAGACCCGAAGGCATTCGTGCATGTGGTT 1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT 68018422 ATATCCGG 1 ATATCCGG 68018430 TTGTATTCCG Statistics Matches: 142, Mismatches: 24, Indels: 2 0.85 0.14 0.01 Matches are distributed among these distances: 39 34 0.24 40 108 0.76 ACGTcount: A:0.26, C:0.23, G:0.26, T:0.26 Consensus pattern (40 bp): ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT Found at i:68018402 original size:80 final size:77 Alignment explanation

Indices: 68018224--68018429 Score: 241 Period size: 79 Copynumber: 2.6 Consensus size: 77 68018214 AATTGAATGA * * ** * * * 68018224 TATCCGGGCTAAGTCCCGAAGACATTTATGCTAGTAATTATATCCGGGTTAAGACCCGAAGGCAT 1 TATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGGGCTAAGACCCGAAGGCAT * 68018289 TGTGCTAGTGAC 66 TGTGCAAGTGAC * * * 68018301 TACATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTTAAATCCGGGCTAATACCCGAAGGC 1 T--ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGGGCTAAGACCCGAAGGC * 68018366 ATTTGTGCAAGTCGTTC 64 A-TTGTGCAAGT-G-AC * * 68018383 TATCCGGGCTAAGACCCGAAGGCATTCGTGCATGTGGTTATATCCGG 1 TATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGG 68018430 TTGTATTCCG Statistics Matches: 109, Mismatches: 15, Indels: 7 0.83 0.11 0.05 Matches are distributed among these distances: 77 1 0.01 79 53 0.49 80 52 0.48 81 1 0.01 82 2 0.02 ACGTcount: A:0.25, C:0.23, G:0.26, T:0.26 Consensus pattern (77 bp): TATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGGGCTAAGACCCGAAGGCAT TGTGCAAGTGAC Found at i:68026772 original size:18 final size:18 Alignment explanation

Indices: 68026751--68026819 Score: 111 Period size: 18 Copynumber: 3.8 Consensus size: 18 68026741 GTGTCCCAAG * * 68026751 CCACACAGGTGTGTGTGA 1 CCACACGGGCGTGTGTGA 68026769 CCACACGGGCGTGTGTGA 1 CCACACGGGCGTGTGTGA * 68026787 CCATACGGGCGTGTGTGA 1 CCACACGGGCGTGTGTGA 68026805 CCACACGGGCGTGTG 1 CCACACGGGCGTGTG 68026820 ACCCTGTTTC Statistics Matches: 47, Mismatches: 4, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 18 47 1.00 ACGTcount: A:0.17, C:0.26, G:0.38, T:0.19 Consensus pattern (18 bp): CCACACGGGCGTGTGTGA Found at i:68029347 original size:65 final size:65 Alignment explanation

Indices: 68029218--68029352 Score: 216 Period size: 65 Copynumber: 2.1 Consensus size: 65 68029208 ATGCTAGACA * * * 68029218 GTGTGAAATCTAAGGGGGTTACTGACTTGGGTCACATGGCTGACCACAAGTCCATATGCTAGCCC 1 GTGTGAAATCTAAGGGGGTTACTAACTTGGGTCACACGGCTGACCACAAGTCCATATGCCAGCCC * * * 68029283 GTGTGAAATCTAATGGGGTTACTAACTTGGGTCACACGGCTGACCACATGTCCATGTGCCAGCCC 1 GTGTGAAATCTAAGGGGGTTACTAACTTGGGTCACACGGCTGACCACAAGTCCATATGCCAGCCC 68029348 GTGTG 1 GTGTG 68029353 CCACACACGA Statistics Matches: 64, Mismatches: 6, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 65 64 1.00 ACGTcount: A:0.23, C:0.24, G:0.28, T:0.25 Consensus pattern (65 bp): GTGTGAAATCTAAGGGGGTTACTAACTTGGGTCACACGGCTGACCACAAGTCCATATGCCAGCCC Found at i:68029381 original size:30 final size:30 Alignment explanation

Indices: 68029344--68029412 Score: 111 Period size: 30 Copynumber: 2.3 Consensus size: 30 68029334 CCATGTGCCA 68029344 GCCCGTGTGCCACACACGACCAATAGACAC 1 GCCCGTGTGCCACACACGACCAATAGACAC * * * 68029374 GCTCGTGTGCCACACACGGCCAGTAGACAC 1 GCCCGTGTGCCACACACGACCAATAGACAC 68029404 GCCCGTGTG 1 GCCCGTGTG 68029413 TCTAGGCTGT Statistics Matches: 35, Mismatches: 4, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 30 35 1.00 ACGTcount: A:0.23, C:0.38, G:0.26, T:0.13 Consensus pattern (30 bp): GCCCGTGTGCCACACACGACCAATAGACAC Found at i:68032547 original size:28 final size:28 Alignment explanation

Indices: 68032501--68032569 Score: 122 Period size: 28 Copynumber: 2.5 Consensus size: 28 68032491 TTTAAAACCC * 68032501 TAGGGGT-ATATCGGTAATTTTGCTCTT 1 TAGGGGTAATTTCGGTAATTTTGCTCTT 68032528 TAGGGGTAATTTCGGTAATTTTGCTCTT 1 TAGGGGTAATTTCGGTAATTTTGCTCTT 68032556 TAGGGGTAATTTCG 1 TAGGGGTAATTTCG 68032570 TGATCTACGC Statistics Matches: 40, Mismatches: 1, Indels: 1 0.95 0.02 0.02 Matches are distributed among these distances: 27 7 0.17 28 33 0.82 ACGTcount: A:0.19, C:0.10, G:0.28, T:0.43 Consensus pattern (28 bp): TAGGGGTAATTTCGGTAATTTTGCTCTT Found at i:68036814 original size:28 final size:28 Alignment explanation

Indices: 68036768--68036836 Score: 122 Period size: 28 Copynumber: 2.5 Consensus size: 28 68036758 TTTAAAACCC * 68036768 TAGGGGT-ATATCGGTAATTTTGCTCTT 1 TAGGGGTAATTTCGGTAATTTTGCTCTT 68036795 TAGGGGTAATTTCGGTAATTTTGCTCTT 1 TAGGGGTAATTTCGGTAATTTTGCTCTT 68036823 TAGGGGTAATTTCG 1 TAGGGGTAATTTCG 68036837 TGATCTACGC Statistics Matches: 40, Mismatches: 1, Indels: 1 0.95 0.02 0.02 Matches are distributed among these distances: 27 7 0.17 28 33 0.82 ACGTcount: A:0.19, C:0.10, G:0.28, T:0.43 Consensus pattern (28 bp): TAGGGGTAATTTCGGTAATTTTGCTCTT Found at i:68038926 original size:29 final size:29 Alignment explanation

Indices: 68038894--68038953 Score: 77 Period size: 29 Copynumber: 2.1 Consensus size: 29 68038884 GATTTTGAGT * * 68038894 AAAAGTGCATATT-AGGGATTAAATTGTG 1 AAAAATGCAAATTGAGGGATTAAATTGTG * * 68038922 AAAAATGTAAATTGAGGGGTTAAATTGTG 1 AAAAATGCAAATTGAGGGATTAAATTGTG 68038951 AAA 1 AAA 68038954 TAAATGAAAA Statistics Matches: 27, Mismatches: 4, Indels: 1 0.84 0.12 0.03 Matches are distributed among these distances: 28 10 0.37 29 17 0.63 ACGTcount: A:0.43, C:0.02, G:0.25, T:0.30 Consensus pattern (29 bp): AAAAATGCAAATTGAGGGATTAAATTGTG Found at i:68041753 original size:31 final size:31 Alignment explanation

Indices: 68041715--68041776 Score: 106 Period size: 31 Copynumber: 2.0 Consensus size: 31 68041705 TCAACAGCCC 68041715 GGTGACTTAAATAAAAACTTTTAAATAGTTT 1 GGTGACTTAAATAAAAACTTTTAAATAGTTT * * 68041746 GGTGACTTAAATGAAAACTTTTGAATAGTTT 1 GGTGACTTAAATAAAAACTTTTAAATAGTTT 68041777 AATGATCAAA Statistics Matches: 29, Mismatches: 2, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 31 29 1.00 ACGTcount: A:0.39, C:0.06, G:0.16, T:0.39 Consensus pattern (31 bp): GGTGACTTAAATAAAAACTTTTAAATAGTTT Found at i:68042663 original size:31 final size:31 Alignment explanation

Indices: 68042625--68042686 Score: 108 Period size: 31 Copynumber: 2.0 Consensus size: 31 68042615 AAAAAAGAGA 68042625 AAAAAATACCTTTTGT-CATAATTCTATGATT 1 AAAAAATACCTTTT-TCCATAATTCTATGATT 68042656 AAAAAATACCTTTTTCCATAATTCTATGATT 1 AAAAAATACCTTTTTCCATAATTCTATGATT 68042687 TTCTTTCAAA Statistics Matches: 30, Mismatches: 0, Indels: 2 0.94 0.00 0.06 Matches are distributed among these distances: 30 1 0.03 31 29 0.97 ACGTcount: A:0.39, C:0.15, G:0.05, T:0.42 Consensus pattern (31 bp): AAAAAATACCTTTTTCCATAATTCTATGATT Found at i:68044694 original size:43 final size:44 Alignment explanation

Indices: 68044625--68044729 Score: 115 Period size: 43 Copynumber: 2.4 Consensus size: 44 68044615 TCTCAGATAT * * * * * * 68044625 GGTCTTACATGTTATCAC-ATATCAATGCCACTGTCCTAGACAG 1 GGTCTTACATGTAATCTCAATATCAATGACAATGTCCCAAACAG * * 68044668 GGTCTTACACGTAATCTCAATA-CAATGACAATGTCCCAAACAT 1 GGTCTTACATGTAATCTCAATATCAATGACAATGTCCCAAACAG * 68044711 GGTCTTAAATGTAATCTCA 1 GGTCTTACATGTAATCTCA 68044730 TATTGGTAAC Statistics Matches: 51, Mismatches: 10, Indels: 2 0.81 0.16 0.03 Matches are distributed among these distances: 43 48 0.94 44 3 0.06 ACGTcount: A:0.32, C:0.24, G:0.14, T:0.30 Consensus pattern (44 bp): GGTCTTACATGTAATCTCAATATCAATGACAATGTCCCAAACAG Found at i:68046056 original size:26 final size:26 Alignment explanation

Indices: 68046020--68046071 Score: 86 Period size: 26 Copynumber: 2.0 Consensus size: 26 68046010 AAGGTATGTG 68046020 ATATATATGTGTGCATGAATGATATA 1 ATATATATGTGTGCATGAATGATATA ** 68046046 ATATATATGTGTGTGTGAATGATATA 1 ATATATATGTGTGCATGAATGATATA 68046072 CTAATAATTA Statistics Matches: 24, Mismatches: 2, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 26 24 1.00 ACGTcount: A:0.37, C:0.02, G:0.21, T:0.40 Consensus pattern (26 bp): ATATATATGTGTGCATGAATGATATA Found at i:68055250 original size:42 final size:42 Alignment explanation

Indices: 68055203--68055357 Score: 170 Period size: 42 Copynumber: 3.7 Consensus size: 42 68055193 TCAAAACTAT * 68055203 GTGTAAGACCATATCTGGGATATGGCATC-ATTATGAGATTTC 1 GTGTAAGACCATATCTGGGATATGGCATCGA-TATGAGATGTC * 68055245 GTGTAAGACCATATCTGGGAGATGGCATCGATATGAGATGTC 1 GTGTAAGACCATATCTGGGATATGGCATCGATATGAGATGTC * * * * ** 68055287 GTGTAATACCATAGT-TGGGATATTGGCGTCGAAACGAGATCCC 1 GTGTAAGACCATA-TCTGGGATA-TGGCATCGATATGAGATGTC * * * 68055330 ATATAAGACCATATCTAGGATATGGCAT 1 GTGTAAGACCATATCTGGGATATGGCAT 68055358 TAGTGTGGCA Statistics Matches: 95, Mismatches: 14, Indels: 8 0.81 0.12 0.07 Matches are distributed among these distances: 42 62 0.65 43 33 0.35 ACGTcount: A:0.30, C:0.15, G:0.26, T:0.28 Consensus pattern (42 bp): GTGTAAGACCATATCTGGGATATGGCATCGATATGAGATGTC Found at i:68059644 original size:20 final size:20 Alignment explanation

Indices: 68059607--68059644 Score: 58 Period size: 20 Copynumber: 1.9 Consensus size: 20 68059597 TTTAATAAAT ** 68059607 AAAAATAAAAATCTAAAACA 1 AAAAATAAAAATAAAAAACA 68059627 AAAAATAAAAATAAAAAA 1 AAAAATAAAAATAAAAAA 68059645 TATATAATTT Statistics Matches: 16, Mismatches: 2, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 20 16 1.00 ACGTcount: A:0.82, C:0.05, G:0.00, T:0.13 Consensus pattern (20 bp): AAAAATAAAAATAAAAAACA Found at i:68060581 original size:130 final size:131 Alignment explanation

Indices: 68060288--68060677 Score: 434 Period size: 130 Copynumber: 3.0 Consensus size: 131 68060278 ATTTGGAGAA * ** ** * * * * 68060288 CATGAGTGAAATTATAAAGGAATATTCGGTTATTTTGAACAAAC-AGGAGATCGTAACCCAGCAT 1 CATGAGTGAAAATCCAAAGGAATATTCAATTGTTTTGAACAAACGA-GAAATCGCAACCCAGAAT * * * ** 68060352 GATAGGGCATGATTCCCCGAATCGCCAAACATCGAACATTACCTTCGTTTT-GGAGAAAATTTTT 65 GATAGGGCACGATT-CCCGAATTGCCAAACACCGAGTATTACCTTCGTTTTAGGAG-AAATTTTT 68060416 AAAG 128 AAAG * 68060420 CATGTGTG-AAATCCCAAAGGAATATTCAATTGTTTTGAACAAACGAGAAATCGCAACCCAGAAT 1 CATGAGTGAAAAT-CCAAAGGAATATTCAATTGTTTTGAACAAACGAGAAATCGCAACCCAGAAT * ** * * 68060484 GATAGGGTACGATTCTTGAATTGCCAAACACCGAGTATCACCTTCGTTTTAGG-G-GATTTTTAA 65 GATAGGGCACGATTCCCGAATTGCCAAACACCGAGTATTACCTTCGTTTTAGGAGAAATTTTT-A 68060547 AAG 129 AAG * * * ** * 68060550 CATGAGTGAAAATCCAAAGGAATATTCAATTGTTTTGAACAAATGAGAAATCACAATCCATTACG 1 CATGAGTGAAAATCCAAAGGAATATTCAATTGTTTTGAACAAACGAGAAATCGCAACCCAGAATG * * 68060615 ATAGGGCACGATTCCCGAATTGCCAAACACCGAGTATTGCCTTCGTTTTA-AAG-AATTTTTAAA 66 ATAGGGCACGATTCCCGAATTGCCAAACACCGAGTATTACCTTCGTTTTAGGAGAAATTTTTAAA 68060678 TGAATAATTA Statistics Matches: 218, Mismatches: 34, Indels: 15 0.82 0.13 0.06 Matches are distributed among these distances: 129 9 0.04 130 109 0.50 131 37 0.17 132 62 0.28 133 1 0.00 ACGTcount: A:0.36, C:0.18, G:0.19, T:0.28 Consensus pattern (131 bp): CATGAGTGAAAATCCAAAGGAATATTCAATTGTTTTGAACAAACGAGAAATCGCAACCCAGAATG ATAGGGCACGATTCCCGAATTGCCAAACACCGAGTATTACCTTCGTTTTAGGAGAAATTTTTAAA G Found at i:68071760 original size:130 final size:130 Alignment explanation

Indices: 68071409--68071764 Score: 461 Period size: 130 Copynumber: 2.7 Consensus size: 130 68071399 ATTCGGCTAC * * 68071409 TTTGAACAAAC-AGGAGATCGCAACCCAGCACGATAGGGCACGATTCCCCGAATCGCCAAACA-T 1 TTTGAACAAACGA-GAAATCGCAACCCAGCACGATAGGGCACGATT-CCCGAATTGCCAAACACT ** * * * 68071472 CGAACATTACCTTCGTTTTGGAGAAAATTTT-AAAGCATGTGTGAAATCCCAAAGGAATATTCGA 64 -GAGTATTACCTTCGTTTTAGAG-AATTTTTAAAAGCATGTGTGAAATCCCAAAGGAATATTCAA 68071536 TTGT 127 TTGT * ** * 68071540 TTTGAACAAACGAGAAATCGCAACCTAGCACGATAGGGCACGATTCTTGAATTGCCAAACACCGA 1 TTTGAACAAACGAGAAATCGCAACCCAGCACGATAGGGCACGATTCCCGAATTGCCAAACACTGA * * * 68071605 GTATCACCTTCGTTTTAGGGGATTTTTAAAAGCATGAT-TGAAAAT-CCAAAGGAATATTCAATT 66 GTATTACCTTCGTTTTAGAGAATTTTTAAAAGCATG-TGTG-AAATCCCAAAGGAATATTCAATT 68071668 GT 129 GT * * 68071670 TTTGAACAAATGAGAAATCGCAACCCAGCACGATAGGGCACAATTCCCGAATTGCCAAACACTGA 1 TTTGAACAAACGAGAAATCGCAACCCAGCACGATAGGGCACGATTCCCGAATTGCCAAACACTGA * * 68071735 GTATTGCCTTCGTTTTAAAGAATTTTTAAA 66 GTATTACCTTCGTTTTAGAGAATTTTTAAA 68071765 TGAATAATTA Statistics Matches: 195, Mismatches: 25, Indels: 11 0.84 0.11 0.05 Matches are distributed among these distances: 129 5 0.03 130 143 0.73 131 46 0.24 132 1 0.01 ACGTcount: A:0.35, C:0.21, G:0.19, T:0.26 Consensus pattern (130 bp): TTTGAACAAACGAGAAATCGCAACCCAGCACGATAGGGCACGATTCCCGAATTGCCAAACACTGA GTATTACCTTCGTTTTAGAGAATTTTTAAAAGCATGTGTGAAATCCCAAAGGAATATTCAATTGT Found at i:68075082 original size:132 final size:132 Alignment explanation

Indices: 68074845--68075104 Score: 459 Period size: 132 Copynumber: 2.0 Consensus size: 132 68074835 ATCTGTAATC 68074845 TTCAGCCTACTCCACTACAACTTTAGGGAGATAGGATGGTGGCTTAAATCTGCTTCACTGCAACT 1 TTCAGCCTACTCCACTACAACTTTAGGGAGATAGGATGGTGGCTTAAATCTGCTTCACTGCAACT * 68074910 TCAGGAAGACAAGATCTGCCGTCCTCGATCTGCTCCACTGCAACTTCAGGGAAACAAGATCTACA 66 TCAGGAAGACAAGATCTGCCGTCCTCGATCTGCTCCACTGCAACTTCAAGGAAACAAGATCTACA 68074975 AT 131 AT * 68074977 TTCAGCCTACTCCACTACAACTTTAGGGAGATAGGATGGTGGGTTAAATCTGCTTCACTGCAACT 1 TTCAGCCTACTCCACTACAACTTTAGGGAGATAGGATGGTGGCTTAAATCTGCTTCACTGCAACT * * * 68075042 TCAGGAAGACAAGAT-TCGCCGTCTTCGATTTTCTCCACTGCAACTTCAAGGAAACAAGATCTA 66 TCAGGAAGACAAGATCT-GCCGTCCTCGATCTGCTCCACTGCAACTTCAAGGAAACAAGATCTA 68075105 TAGAATCGGT Statistics Matches: 122, Mismatches: 5, Indels: 2 0.95 0.04 0.02 Matches are distributed among these distances: 131 1 0.01 132 121 0.99 ACGTcount: A:0.29, C:0.25, G:0.20, T:0.26 Consensus pattern (132 bp): TTCAGCCTACTCCACTACAACTTTAGGGAGATAGGATGGTGGCTTAAATCTGCTTCACTGCAACT TCAGGAAGACAAGATCTGCCGTCCTCGATCTGCTCCACTGCAACTTCAAGGAAACAAGATCTACA AT Found at i:68086552 original size:130 final size:131 Alignment explanation

Indices: 68086251--68086627 Score: 467 Period size: 130 Copynumber: 2.9 Consensus size: 131 68086241 ATTTGGAGAA * * ** * 68086251 CATGAGTGAAATTCTAAAGGAATATTCGGCTATTTTGAACAAAC-AGGAGATCGCAACCCAGCAC 1 CATGAGTGAAAATCCAAAGGAATATTCGATTATTTTGAACAAACGA-GAAATCGCAACCCAGCAC * * * * ** 68086315 GATAGGGCACGATTCCCCGAATCGCCAAACATCAAACATTACCTTCGTTTT-GGAGAAAACTTTT 65 GATAGGGCACGATT-CCTGAATTGCCAAACACCGAGTATTACCTTCGTTTTAGGAG-AAACTTTT 68086379 AAAG 128 AAAG * * * * 68086383 CATGTGTG-AAATCCCAAAGGAATATTCGATTGTTTTGAACAAACGAGAAATCGCAACCTAGCGC 1 CATGAGTGAAAAT-CCAAAGGAATATTCGATTATTTTGAACAAACGAGAAATCGCAACCCAGCAC * * * * 68086447 GATAGGGCACGATTCTTGAATTGCCAAACACCGAGTATCACCTTCGTTTTAGG-G-GATTTTTAA 65 GATAGGGCACGATTCCTGAATTGCCAAACACCGAGTATTACCTTCGTTTTAGGAGAAACTTTTAA 68086510 ACG 130 A-G * * 68086513 CATGAGTGAAAATCCAAAGGAATATTCGATTTTTTTGAACAAATGAGAAATCGCAACCCAGCACG 1 CATGAGTGAAAATCCAAAGGAATATTCGATTATTTTGAACAAACGAGAAATCGCAACCCAGCACG * * 68086578 ATAGGGCACGATTCCTGAATTGCAAAACACCGAGTATTGCCTTCGTTTTA 66 ATAGGGCACGATTCCTGAATTGCCAAACACCGAGTATTACCTTCGTTTTA 68086628 AAGAATTTTT Statistics Matches: 212, Mismatches: 28, Indels: 12 0.84 0.11 0.05 Matches are distributed among these distances: 129 8 0.04 130 102 0.48 131 36 0.17 132 65 0.31 133 1 0.00 ACGTcount: A:0.34, C:0.21, G:0.20, T:0.25 Consensus pattern (131 bp): CATGAGTGAAAATCCAAAGGAATATTCGATTATTTTGAACAAACGAGAAATCGCAACCCAGCACG ATAGGGCACGATTCCTGAATTGCCAAACACCGAGTATTACCTTCGTTTTAGGAGAAACTTTTAAA G Found at i:68089312 original size:16 final size:16 Alignment explanation

Indices: 68089291--68089321 Score: 53 Period size: 16 Copynumber: 1.9 Consensus size: 16 68089281 TTATTATTTA * 68089291 TTTATTGTTTTGTTTT 1 TTTATTATTTTGTTTT 68089307 TTTATTATTTTGTTT 1 TTTATTATTTTGTTT 68089322 GTAACAGGCC Statistics Matches: 14, Mismatches: 1, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 16 14 1.00 ACGTcount: A:0.10, C:0.00, G:0.10, T:0.81 Consensus pattern (16 bp): TTTATTATTTTGTTTT Found at i:68091620 original size:15 final size:15 Alignment explanation

Indices: 68091600--68091631 Score: 55 Period size: 15 Copynumber: 2.1 Consensus size: 15 68091590 TCAGTGTTTC 68091600 GGACCTCCACCAAAT 1 GGACCTCCACCAAAT * 68091615 GGACCTCCAGCAAAT 1 GGACCTCCACCAAAT 68091630 GG 1 GG 68091632 GGCCACGGAC Statistics Matches: 16, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 15 16 1.00 ACGTcount: A:0.31, C:0.34, G:0.22, T:0.12 Consensus pattern (15 bp): GGACCTCCACCAAAT Found at i:68092728 original size:30 final size:30 Alignment explanation

Indices: 68092682--68092741 Score: 84 Period size: 30 Copynumber: 2.0 Consensus size: 30 68092672 TTCCCAAGCC * * 68092682 TAGGGGCAAAAGTGTAATTATGCAAAAGTT 1 TAGGGGAAAAAATGTAATTATGCAAAAGTT * * 68092712 TAGGGGAAAAAATGTAATTTTGCCAAAGTT 1 TAGGGGAAAAAATGTAATTATGCAAAAGTT 68092742 CTTATTAAAT Statistics Matches: 26, Mismatches: 4, Indels: 0 0.87 0.13 0.00 Matches are distributed among these distances: 30 26 1.00 ACGTcount: A:0.40, C:0.07, G:0.25, T:0.28 Consensus pattern (30 bp): TAGGGGAAAAAATGTAATTATGCAAAAGTT Found at i:68100251 original size:55 final size:55 Alignment explanation

Indices: 68100190--68100301 Score: 224 Period size: 55 Copynumber: 2.0 Consensus size: 55 68100180 TGCTAAATGC 68100190 TTGTTTAATTAACTATGTCAGTGGTGCTTCTAGTTTTGAGATGCTTTCTTTTGTT 1 TTGTTTAATTAACTATGTCAGTGGTGCTTCTAGTTTTGAGATGCTTTCTTTTGTT 68100245 TTGTTTAATTAACTATGTCAGTGGTGCTTCTAGTTTTGAGATGCTTTCTTTTGTT 1 TTGTTTAATTAACTATGTCAGTGGTGCTTCTAGTTTTGAGATGCTTTCTTTTGTT 68100300 TT 1 TT 68100302 TGCCCCCTTG Statistics Matches: 57, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 55 57 1.00 ACGTcount: A:0.16, C:0.11, G:0.20, T:0.54 Consensus pattern (55 bp): TTGTTTAATTAACTATGTCAGTGGTGCTTCTAGTTTTGAGATGCTTTCTTTTGTT Found at i:68100700 original size:24 final size:24 Alignment explanation

Indices: 68100668--68100716 Score: 98 Period size: 24 Copynumber: 2.0 Consensus size: 24 68100658 GCATTTAAAG 68100668 AGATACTATTCTTCTTCCCTCAAC 1 AGATACTATTCTTCTTCCCTCAAC 68100692 AGATACTATTCTTCTTCCCTCAAC 1 AGATACTATTCTTCTTCCCTCAAC 68100716 A 1 A 68100717 ATTTGCTGTT 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:0.27, C:0.33, G:0.04, T:0.37 Consensus pattern (24 bp): AGATACTATTCTTCTTCCCTCAAC Found at i:68103782 original size:21 final size:21 Alignment explanation

Indices: 68103707--68103782 Score: 80 Period size: 21 Copynumber: 3.6 Consensus size: 21 68103697 TTGTAACAGA * 68103707 TACAAATCATGCTTATCATAT 1 TACAAATCATACTTATCATAT * * 68103728 TACAGATCATACATATCATAT 1 TACAAATCATACTTATCATAT ** * * 68103749 TACAGTTTATACTTATCACAT 1 TACAAATCATACTTATCATAT * 68103770 TTCAAATCATACT 1 TACAAATCATACT 68103783 AAGCGGACAA Statistics Matches: 44, Mismatches: 11, Indels: 0 0.80 0.20 0.00 Matches are distributed among these distances: 21 44 1.00 ACGTcount: A:0.38, C:0.20, G:0.04, T:0.38 Consensus pattern (21 bp): TACAAATCATACTTATCATAT Found at i:68112854 original size:24 final size:24 Alignment explanation

Indices: 68112827--68112902 Score: 68 Period size: 24 Copynumber: 3.2 Consensus size: 24 68112817 ATGAATGTCT * 68112827 ATTGTGACGGATTTGGTTGTATGA 1 ATTGTGACGGATTTGGTTATATGA * * * 68112851 ATTGTG-CTTGTTTTGG-TAT-TGG 1 ATTGTGAC-GGATTTGGTTATATGA * * 68112873 TTTGTGACGGATTTGGTTTTATGA 1 ATTGTGACGGATTTGGTTATATGA 68112897 ATTGTG 1 ATTGTG 68112903 CTTGTTTTGG Statistics Matches: 38, Mismatches: 10, Indels: 8 0.68 0.18 0.14 Matches are distributed among these distances: 22 13 0.34 23 6 0.16 24 19 0.50 ACGTcount: A:0.16, C:0.04, G:0.32, T:0.49 Consensus pattern (24 bp): ATTGTGACGGATTTGGTTATATGA Found at i:68112896 original size:46 final size:46 Alignment explanation

Indices: 68112828--68112920 Score: 177 Period size: 46 Copynumber: 2.0 Consensus size: 46 68112818 TGAATGTCTA 68112828 TTGTGACGGATTTGGTTGTATGAATTGTGCTTGTTTTGGTATTGGT 1 TTGTGACGGATTTGGTTGTATGAATTGTGCTTGTTTTGGTATTGGT * 68112874 TTGTGACGGATTTGGTTTTATGAATTGTGCTTGTTTTGGTATTGGT 1 TTGTGACGGATTTGGTTGTATGAATTGTGCTTGTTTTGGTATTGGT 68112920 T 1 T 68112921 GGTATTTGCA Statistics Matches: 46, Mismatches: 1, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 46 46 1.00 ACGTcount: A:0.13, C:0.04, G:0.31, T:0.52 Consensus pattern (46 bp): TTGTGACGGATTTGGTTGTATGAATTGTGCTTGTTTTGGTATTGGT Found at i:68112911 original size:24 final size:24 Alignment explanation

Indices: 68112838--68112913 Score: 68 Period size: 24 Copynumber: 3.2 Consensus size: 24 68112828 TTGTGACGGA * 68112838 TTTGGTTGTATGAATTGTGCTTGT 1 TTTGGTTATATGAATTGTGCTTGT ** * * 68112862 TTTGG-TAT-TGGTTTGTGAC-GGA 1 TTTGGTTATATGAATTGTG-CTTGT * 68112884 TTTGGTTTTATGAATTGTGCTTGT 1 TTTGGTTATATGAATTGTGCTTGT 68112908 TTTGGT 1 TTTGGT 68112914 ATTGGTTGGT Statistics Matches: 38, Mismatches: 10, Indels: 8 0.68 0.18 0.14 Matches are distributed among these distances: 22 13 0.34 23 6 0.16 24 19 0.50 ACGTcount: A:0.12, C:0.04, G:0.30, T:0.54 Consensus pattern (24 bp): TTTGGTTATATGAATTGTGCTTGT Found at i:68117713 original size:10 final size:10 Alignment explanation

Indices: 68117698--68117724 Score: 54 Period size: 10 Copynumber: 2.7 Consensus size: 10 68117688 GATTATGCCT 68117698 AATGATACCA 1 AATGATACCA 68117708 AATGATACCA 1 AATGATACCA 68117718 AATGATA 1 AATGATA 68117725 AAGAATGAGA Statistics Matches: 17, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 10 17 1.00 ACGTcount: A:0.52, C:0.15, G:0.11, T:0.22 Consensus pattern (10 bp): AATGATACCA Found at i:68118128 original size:36 final size:36 Alignment explanation

Indices: 68118081--68118153 Score: 146 Period size: 36 Copynumber: 2.0 Consensus size: 36 68118071 TCTAAAAAGA 68118081 TTATTAAAACTCTTCTAAAAGAAACTCAAGAGAAAT 1 TTATTAAAACTCTTCTAAAAGAAACTCAAGAGAAAT 68118117 TTATTAAAACTCTTCTAAAAGAAACTCAAGAGAAAT 1 TTATTAAAACTCTTCTAAAAGAAACTCAAGAGAAAT 68118153 T 1 T 68118154 CTTAAAAAAA Statistics Matches: 37, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 36 37 1.00 ACGTcount: A:0.49, C:0.14, G:0.08, T:0.29 Consensus pattern (36 bp): TTATTAAAACTCTTCTAAAAGAAACTCAAGAGAAAT Found at i:68118533 original size:26 final size:26 Alignment explanation

Indices: 68118492--68118547 Score: 78 Period size: 26 Copynumber: 2.2 Consensus size: 26 68118482 AACCTGAATT * 68118492 TTTTGCTTCTAGTTTTCATTTGTTTG 1 TTTTGCTTCTAGTTTTCATTTGTTTA * 68118518 TTTTGCTT-TAGTTTTTCATTTTTTTA 1 TTTTGCTTCTAG-TTTTCATTTGTTTA 68118544 TTTT 1 TTTT 68118548 TATTGTTCCT Statistics Matches: 27, Mismatches: 2, Indels: 2 0.87 0.06 0.06 Matches are distributed among these distances: 25 3 0.11 26 24 0.89 ACGTcount: A:0.09, C:0.09, G:0.11, T:0.71 Consensus pattern (26 bp): TTTTGCTTCTAGTTTTCATTTGTTTA Found at i:68123682 original size:35 final size:35 Alignment explanation

Indices: 68123643--68123715 Score: 137 Period size: 35 Copynumber: 2.1 Consensus size: 35 68123633 ACACATTCTT 68123643 TATTCTCGTCAGATCAATCTCAAATAAATAATATA 1 TATTCTCGTCAGATCAATCTCAAATAAATAATATA * 68123678 TATTCTCGTCAGATCAATCTCACATAAATAATATA 1 TATTCTCGTCAGATCAATCTCAAATAAATAATATA 68123713 TAT 1 TAT 68123716 ATCACATACC Statistics Matches: 37, Mismatches: 1, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 35 37 1.00 ACGTcount: A:0.41, C:0.18, G:0.05, T:0.36 Consensus pattern (35 bp): TATTCTCGTCAGATCAATCTCAAATAAATAATATA Found at i:68127323 original size:29 final size:30 Alignment explanation

Indices: 68127268--68127330 Score: 85 Period size: 29 Copynumber: 2.1 Consensus size: 30 68127258 AATTCAAAGG * * 68127268 AATTTATAAAATTTATAAAATAAATATATA 1 AATTTATAAAAATTATAAAATAAATATAAA 68127298 AATTT-TAAAAATT-TAAAATAATATATAAA 1 AATTTATAAAAATTATAAAATAA-ATATAAA 68127327 AATT 1 AATT 68127331 GAAAATTTTA Statistics Matches: 30, Mismatches: 2, Indels: 3 0.86 0.06 0.09 Matches are distributed among these distances: 28 8 0.27 29 17 0.57 30 5 0.17 ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40 Consensus pattern (30 bp): AATTTATAAAAATTATAAAATAAATATAAA Found at i:68127335 original size:27 final size:28 Alignment explanation

Indices: 68127274--68127338 Score: 78 Period size: 27 Copynumber: 2.3 Consensus size: 28 68127264 AAGGAATTTA * ** 68127274 TAAAATTTATAAAATAAATATATAAATTT 1 TAAAAATT-TAAAATAAATATATAAAAAT 68127303 TAAAAATTTAAAAT-AATATATAAAAAT 1 TAAAAATTTAAAATAAATATATAAAAAT * 68127330 TGAAAATTT 1 TAAAAATTT 68127339 TATAAAAATT Statistics Matches: 32, Mismatches: 4, Indels: 2 0.84 0.11 0.05 Matches are distributed among these distances: 27 19 0.59 28 6 0.19 29 7 0.22 ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38 Consensus pattern (28 bp): TAAAAATTTAAAATAAATATATAAAAAT Found at i:68127335 original size:28 final size:27 Alignment explanation

Indices: 68127283--68127355 Score: 78 Period size: 28 Copynumber: 2.7 Consensus size: 27 68127273 ATAAAATTTA * * 68127283 TAAAATAAATATATAAATTTTAAAAATT 1 TAAAATAAATATA-AAAATTGAAAAATT * 68127311 TAAAATAATATATAAAAATTGAAAATTT 1 TAAAATAA-ATATAAAAATTGAAAAATT * 68127339 TATAA-AAAT-TAAAAATT 1 TAAAATAAATATAAAAATT 68127356 TTATTTAGAT Statistics Matches: 40, Mismatches: 4, Indels: 5 0.82 0.08 0.10 Matches are distributed among these distances: 25 8 0.20 26 2 0.05 27 2 0.05 28 23 0.57 29 5 0.12 ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37 Consensus pattern (27 bp): TAAAATAAATATAAAAATTGAAAAATT Found at i:68127344 original size:18 final size:18 Alignment explanation

Indices: 68127297--68127359 Score: 74 Period size: 18 Copynumber: 3.5 Consensus size: 18 68127287 ATAAATATAT * 68127297 AAATTTTA-AAAATTTAA 1 AAATTTTATAAAAATTAA * * * 68127314 AATAATATATAAAAATTGA 1 AA-ATTTTATAAAAATTAA 68127333 AAATTTTATAAAAATTAA 1 AAATTTTATAAAAATTAA 68127351 AAATTTTAT 1 AAATTTTAT 68127360 TTAGATTTTA Statistics Matches: 37, Mismatches: 7, Indels: 3 0.79 0.15 0.06 Matches are distributed among these distances: 17 2 0.05 18 26 0.70 19 9 0.24 ACGTcount: A:0.59, C:0.00, G:0.02, T:0.40 Consensus pattern (18 bp): AAATTTTATAAAAATTAA Found at i:68127462 original size:20 final size:18 Alignment explanation

Indices: 68127432--68127485 Score: 63 Period size: 20 Copynumber: 2.8 Consensus size: 18 68127422 AATTAGATTT 68127432 TATTTTGAATTTTTATATA 1 TATTTTGAATTTTTA-ATA * 68127451 TATTTCTGAATTTATCAATA 1 TATTT-TGAATTT-TTAATA * 68127471 TATTTTAAATTTTTA 1 TATTTTGAATTTTTA 68127486 GAATTTAAAA Statistics Matches: 30, Mismatches: 3, Indels: 5 0.79 0.08 0.13 Matches are distributed among these distances: 18 2 0.07 19 11 0.37 20 15 0.50 21 2 0.07 ACGTcount: A:0.33, C:0.04, G:0.04, T:0.59 Consensus pattern (18 bp): TATTTTGAATTTTTAATA Found at i:68129792 original size:38 final size:37 Alignment explanation

Indices: 68129705--68129794 Score: 110 Period size: 37 Copynumber: 2.4 Consensus size: 37 68129695 TAATTAAGAT * ** * 68129705 TTTAATGTGTCTTTGTTTAGTACAAATTAAATAGGTG 1 TTTAATGTGTCTTAGTGAAGTACAAATTAAAGAGGTG * 68129742 TTTAATGTGTCTTAGTGAAGTACATATTAAAGA-GTCG 1 TTTAATGTGTCTTAGTGAAGTACAAATTAAAGAGGT-G 68129779 TCTTAATGTGTCTTAG 1 T-TTAATGTGTCTTAG 68129795 CTTAAGAAAA Statistics Matches: 46, Mismatches: 5, Indels: 3 0.85 0.09 0.06 Matches are distributed among these distances: 36 2 0.04 37 30 0.65 38 14 0.30 ACGTcount: A:0.29, C:0.08, G:0.20, T:0.43 Consensus pattern (37 bp): TTTAATGTGTCTTAGTGAAGTACAAATTAAAGAGGTG Found at i:68137363 original size:40 final size:40 Alignment explanation

Indices: 68137318--68137447 Score: 165 Period size: 40 Copynumber: 3.2 Consensus size: 40 68137308 CGGAATACAA 68137318 CCGGATATAACCACGT-GCACGAATGCCTTCGGGTCTTAGC 1 CCGGATATAACCAC-TAGCACGAATGCCTTCGGGTCTTAGC * * * 68137358 CCGGATAGAACAACTCGCACGAATGCCTTCGGGTCTTAGC 1 CCGGATATAACCACTAGCACGAATGCCTTCGGGTCTTAGC * * * * 68137398 CCGGATGTAGCCGCTAGCAC-AATTGCCTTCGGGTCTTAAC 1 CCGGATATAACCACTAGCACGAA-TGCCTTCGGGTCTTAGC 68137438 CCGGATATAA 1 CCGGATATAA 68137448 TTTCCAGCAA Statistics Matches: 77, Mismatches: 11, Indels: 4 0.84 0.12 0.04 Matches are distributed among these distances: 39 3 0.04 40 74 0.96 ACGTcount: A:0.24, C:0.29, G:0.25, T:0.22 Consensus pattern (40 bp): CCGGATATAACCACTAGCACGAATGCCTTCGGGTCTTAGC Found at i:68138997 original size:52 final size:52 Alignment explanation

Indices: 68138937--68139041 Score: 210 Period size: 52 Copynumber: 2.0 Consensus size: 52 68138927 AACATGTTTC 68138937 ATGACATGTTTAGCCCATATTTCTTGGTCATGGCCGGCCACCACCTATAAAA 1 ATGACATGTTTAGCCCATATTTCTTGGTCATGGCCGGCCACCACCTATAAAA 68138989 ATGACATGTTTAGCCCATATTTCTTGGTCATGGCCGGCCACCACCTATAAAA 1 ATGACATGTTTAGCCCATATTTCTTGGTCATGGCCGGCCACCACCTATAAAA 68139041 A 1 A 68139042 GGGGAATTTG Statistics Matches: 53, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 52 53 1.00 ACGTcount: A:0.28, C:0.27, G:0.17, T:0.29 Consensus pattern (52 bp): ATGACATGTTTAGCCCATATTTCTTGGTCATGGCCGGCCACCACCTATAAAA Found at i:68148146 original size:43 final size:42 Alignment explanation

Indices: 68148099--68148246 Score: 126 Period size: 44 Copynumber: 3.5 Consensus size: 42 68148089 AATGCCAACG 68148099 TCCCAGACGTGGTCTTACATGTAATCAAACATCGATGCCACTA 1 TCCCAGACGTGGTCTTACATGTAATCAAA-ATCGATGCCACTA * * * * 68148142 TCCCAGACAG-GGTCTTACATGAAATC-AAATACGATTCTGA-TG 1 TCCCAGAC-GTGGTCTTACATGTAATCAAAAT-CGATGC-CACTA * * * 68148184 TCCCAGACATGGTCTTACACGTAAAAT-AGAAGTCGATGCCAAC-A 1 TCCCAGACGTGGTCTTACATGT--AATCA-AAATCGATGCC-ACTA 68148228 TCCCAGACGTGGTCTTACA 1 TCCCAGACGTGGTCTTACA 68148247 CGAAATCCTA Statistics Matches: 83, Mismatches: 12, Indels: 19 0.73 0.11 0.17 Matches are distributed among these distances: 41 2 0.02 42 26 0.31 43 24 0.29 44 28 0.34 45 3 0.04 ACGTcount: A:0.32, C:0.26, G:0.18, T:0.24 Consensus pattern (42 bp): TCCCAGACGTGGTCTTACATGTAATCAAAATCGATGCCACTA Found at i:68148201 original size:42 final size:43 Alignment explanation

Indices: 68148090--68148253 Score: 124 Period size: 43 Copynumber: 3.8 Consensus size: 43 68148080 AACATATACA * * 68148090 ATGCCAAC-GTCCCAGACGTGGTCTTACATGTAATCAAACATCG 1 ATGCC-ACTGTCCCAGACATGGTCTTACATGAAATCAAACATCG * * * 68148133 ATGCCACTATCCCAGACAGGGTCTTACATGAAATCAAATA-CG 1 ATGCCACTGTCCCAGACATGGTCTTACATGAAATCAAACATCG * * * * 68148175 ATTCTGA-TGTCCCAGACATGGTCTTACACGTAAAAT-AGAA-GTCG 1 ATGC-CACTGTCCCAGACATGGTCTTACA--TGAAATCA-AACATCG * * * 68148219 ATGCCAAC-ATCCCAGACGTGGTCTTACACGAAATC 1 ATGCC-ACTGTCCCAGACATGGTCTTACATGAAATC 68148254 CTATGTCATG Statistics Matches: 95, Mismatches: 17, Indels: 18 0.73 0.13 0.14 Matches are distributed among these distances: 42 30 0.32 43 34 0.36 44 31 0.33 ACGTcount: A:0.32, C:0.26, G:0.18, T:0.23 Consensus pattern (43 bp): ATGCCACTGTCCCAGACATGGTCTTACATGAAATCAAACATCG Found at i:68152381 original size:30 final size:30 Alignment explanation

Indices: 68152335--68152394 Score: 86 Period size: 30 Copynumber: 2.0 Consensus size: 30 68152325 TTCCCGAGCC 68152335 TAGGGGAAAAAGTGTAATTATGCAAAAGTT 1 TAGGGGAAAAAGTGTAATTATGCAAAAGTT * * 68152365 TAGGGGCAAAAA-TGTAATTTTGCCAAAGTT 1 TAGGGG-AAAAAGTGTAATTATGCAAAAGTT 68152395 CGTATTAAAT Statistics Matches: 27, Mismatches: 2, Indels: 2 0.87 0.06 0.06 Matches are distributed among these distances: 30 22 0.81 31 5 0.19 ACGTcount: A:0.40, C:0.07, G:0.25, T:0.28 Consensus pattern (30 bp): TAGGGGAAAAAGTGTAATTATGCAAAAGTT Found at i:68154687 original size:18 final size:18 Alignment explanation

Indices: 68154664--68154707 Score: 60 Period size: 14 Copynumber: 2.7 Consensus size: 18 68154654 TTGAGATTTG 68154664 GATAATTACTAGAAATGT 1 GATAATTACTAGAAATGT 68154682 GAT-A--A-TAGAAATGT 1 GATAATTACTAGAAATGT 68154696 GATAATTACTAG 1 GATAATTACTAG 68154708 GAATTGTAGT Statistics Matches: 22, Mismatches: 0, Indels: 8 0.73 0.00 0.27 Matches are distributed among these distances: 14 12 0.55 15 2 0.09 17 2 0.09 18 6 0.27 ACGTcount: A:0.45, C:0.05, G:0.18, T:0.32 Consensus pattern (18 bp): GATAATTACTAGAAATGT Found at i:68156909 original size:31 final size:31 Alignment explanation

Indices: 68156861--68156944 Score: 143 Period size: 31 Copynumber: 2.7 Consensus size: 31 68156851 TTAGTCTTGA * 68156861 CATAT-ACTGGGCTGAAGCCTTTTCATAAAT 1 CATATCACTGGGCCGAAGCCTTTTCATAAAT 68156891 CATATCACTGGGCCGAAGCCTTTTCATAAAT 1 CATATCACTGGGCCGAAGCCTTTTCATAAAT * 68156922 CATATCATTGGGCCGAAGCCTTT 1 CATATCACTGGGCCGAAGCCTTT 68156945 ACTATAAACG Statistics Matches: 51, Mismatches: 2, Indels: 1 0.94 0.04 0.02 Matches are distributed among these distances: 30 5 0.10 31 46 0.90 ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31 Consensus pattern (31 bp): CATATCACTGGGCCGAAGCCTTTTCATAAAT Found at i:68157196 original size:25 final size:26 Alignment explanation

Indices: 68157163--68157260 Score: 128 Period size: 25 Copynumber: 3.8 Consensus size: 26 68157153 CTCTTTTAAT * 68157163 AACTAGGGCA-AAGCCCTTTTCGGTA 1 AACTGGGGCATAAGCCCTTTTCGGTA ** 68157188 AACTGGGGCA-AAGCCCTTTTCAATA 1 AACTGGGGCATAAGCCCTTTTCGGTA * 68157213 AACTGGGGCATAAGCCCTTTTTTTGGTA 1 AACTGGGGCATAAGCCC--TTTTCGGTA 68157241 AACTGGGGCATAAGCCCTTT 1 AACTGGGGCATAAGCCCTTT 68157261 CGCACTTCCT Statistics Matches: 64, Mismatches: 6, Indels: 5 0.85 0.08 0.07 Matches are distributed among these distances: 25 32 0.50 26 9 0.14 28 23 0.36 ACGTcount: A:0.27, C:0.22, G:0.23, T:0.28 Consensus pattern (26 bp): AACTGGGGCATAAGCCCTTTTCGGTA Found at i:68158092 original size:27 final size:27 Alignment explanation

Indices: 68158062--68158153 Score: 107 Period size: 27 Copynumber: 3.4 Consensus size: 27 68158052 GGGCACATTC * * 68158062 GTCATTTTACCATATAGGGG-TATTACG 1 GTCATTTTACCCTACAGGGGCT-TTACG * 68158089 GTCACTTTACCCTACAGGGGCTTTACG 1 GTCATTTTACCCTACAGGGGCTTTACG * 68158116 GTC-TCTTTACCCTACAGGGGCTTTACA 1 GTCAT-TTTACCCTACAGGGGCTTTACG * 68158143 GTCTTTTTACC 1 GTCATTTTACC 68158154 TAATAGGGGT Statistics Matches: 57, Mismatches: 5, Indels: 6 0.84 0.07 0.09 Matches are distributed among these distances: 27 55 0.96 28 2 0.04 ACGTcount: A:0.20, C:0.25, G:0.20, T:0.36 Consensus pattern (27 bp): GTCATTTTACCCTACAGGGGCTTTACG Found at i:68158356 original size:54 final size:54 Alignment explanation

Indices: 68158184--68158422 Score: 158 Period size: 54 Copynumber: 4.4 Consensus size: 54 68158174 TTTCATCCTA * * * * * ** 68158184 CAAGGGTGTTTTGGTAAATCTACAAACCAAGGGTATTTCAGTAATTTTGTTAAAC 1 CAAGGGTATTTTGGTAATTTTACAAACCAAGGGTATTTCGGTAACTTT-ACAAAC * *** * * * ** * 68158239 CAATGGTATTTCCATAATTTTTAGAAAGTCAAGGGTATTTCTGTAACTTTGTAAAT 1 CAAGGGTATTTTGGTAA-TTTTACAAA-CCAAGGGTATTTCGGTAACTTTACAAAC * ** 68158295 CAGGGGTATTTTGGTAATTTTACAAATTAAGGGTATTTCGGTAA-TTTCACAAAC 1 CAAGGGTATTTTGGTAATTTTACAAACCAAGGGTATTTCGGTAACTTT-ACAAAC * * * * * * ** * 68158349 CAAGGGTATTTTAGCAATTTTACAGA-CTAGGGTATTTTGGTAATTTTACTGAT 1 CAAGGGTATTTTGGTAATTTTACAAACCAAGGGTATTTCGGTAACTTTACAAAC * 68158402 CGAGGGTATTTTGGTAATTTT 1 CAAGGGTATTTTGGTAATTTT 68158423 GTAAACTGAG Statistics Matches: 143, Mismatches: 37, Indels: 10 0.75 0.19 0.05 Matches are distributed among these distances: 53 38 0.27 54 44 0.31 55 20 0.14 56 22 0.15 57 19 0.13 ACGTcount: A:0.30, C:0.10, G:0.20, T:0.39 Consensus pattern (54 bp): CAAGGGTATTTTGGTAATTTTACAAACCAAGGGTATTTCGGTAACTTTACAAAC Found at i:68158391 original size:80 final size:80 Alignment explanation

Indices: 68158298--68158449 Score: 205 Period size: 80 Copynumber: 1.9 Consensus size: 80 68158288 TGTAAATCAG * 68158298 GGGTATTTTGGTAATTTTACAAATTAAGGGTATTTCGGTAATTTCACAAACCAAGGGTATTTTAG 1 GGGTATTTTGGTAATTTTACAAATCAAGGGTATTTCGGTAATTTCACAAACCAAGGGTATTTTAG 68158363 CAATTTTACAGACTA 66 CAATTTTACAGACTA ** * * *** ** 68158378 GGGTATTTTGGTAATTTTACTGATCGAGGGTATTTTGGTAATTTTGTAAACTGAGGGTATTTTAG 1 GGGTATTTTGGTAATTTTACAAATCAAGGGTATTTCGGTAATTTCACAAACCAAGGGTATTTTAG * 68158443 TAATTTT 66 CAATTTT 68158450 GTAAATCGAG Statistics Matches: 61, Mismatches: 11, Indels: 0 0.85 0.15 0.00 Matches are distributed among these distances: 80 61 1.00 ACGTcount: A:0.28, C:0.08, G:0.22, T:0.42 Consensus pattern (80 bp): GGGTATTTTGGTAATTTTACAAATCAAGGGTATTTCGGTAATTTCACAAACCAAGGGTATTTTAG CAATTTTACAGACTA Found at i:68158447 original size:54 final size:53 Alignment explanation

Indices: 68158298--68158449 Score: 169 Period size: 53 Copynumber: 2.8 Consensus size: 53 68158288 TGTAAATCAG * * * 68158298 GGGTATTTTGGTAATTTTACAAATTAAGGGTATTTCGGTAATTTCACAAACCAA 1 GGGTATTTTGGTAATTTTACAAACT-AGGGTATTTTGGTAATTTTACAAACCAA * * * ** * * 68158352 GGGTATTTTAGCAATTTTACAGACTAGGGTATTTTGGTAATTTTACTGATCGA 1 GGGTATTTTGGTAATTTTACAAACTAGGGTATTTTGGTAATTTTACAAACCAA ** * 68158405 GGGTATTTTGGTAATTTTGTAAACTGAGGGTATTTTAGTAATTTT 1 GGGTATTTTGGTAATTTTACAAACT-AGGGTATTTTGGTAATTTT 68158450 GTAAATCGAG Statistics Matches: 81, Mismatches: 16, Indels: 2 0.82 0.16 0.02 Matches are distributed among these distances: 53 42 0.52 54 39 0.48 ACGTcount: A:0.28, C:0.08, G:0.22, T:0.42 Consensus pattern (53 bp): GGGTATTTTGGTAATTTTACAAACTAGGGTATTTTGGTAATTTTACAAACCAA Found at i:68158462 original size:27 final size:27 Alignment explanation

Indices: 68158213--68158616 Score: 165 Period size: 27 Copynumber: 14.9 Consensus size: 27 68158203 CTACAAACCA * * 68158213 AGGGTATTTCAGTAATTTTGTTAAACCA 1 AGGGTATTTCAGTAATTTTG-TAAATCG * * 68158241 ATGGTATTTCCA-TAATTTT-TAGAAAGTCA 1 AGGGTATTT-CAGTAATTTTGT--AAA-TCG * * 68158270 AGGGTATTTCTGTAACTTTGTAAATC- 1 AGGGTATTTCAGTAATTTTGTAAATCG ** ** ** 68158296 AGGGGTATTTTGGTAATTTTACAAATTA 1 A-GGGTATTTCAGTAATTTTGTAAATCG * *** * * 68158324 AGGGTATTTCGGTAATTTCACAAACCA 1 AGGGTATTTCAGTAATTTTGTAAATCG * * ** * * 68158351 AGGGTATTTTAGCAATTTTACAGA-CT 1 AGGGTATTTCAGTAATTTTGTAAATCG ** * * 68158377 AGGGTATTTTGGTAATTTTACT-GATCG 1 AGGGTATTTCAGTAATTTT-GTAAATCG ** 68158404 AGGGTATTTTGGTAATTTTGTAAA-CTG 1 AGGGTATTTCAGTAATTTTGTAAATC-G * 68158431 AGGGTATTTTAGTAATTTTGTAAATCG 1 AGGGTATTTCAGTAATTTTGTAAATCG *** * * 68158458 AGGGTAAAACAGTAATTCTGTAAATCA 1 AGGGTATTTCAGTAATTTTGTAAATCG ** * * 68158485 AGGGTATAACAGTAATTCTATAAATCG 1 AGGGTATTTCAGTAATTTTGTAAATCG *** * * 68158512 AGGGTAAAACGGTAATTCTGTAAATCG 1 AGGGTATTTCAGTAATTTTGTAAATCG *** * * * 68158539 AGGGTAAAACGGTAATTCTATAAATCG 1 AGGGTATTTCAGTAATTTTGTAAATCG * ** * * 68158566 AGGGTACTTT-GGTAATTTTACAATTTG 1 AGGGTA-TTTCAGTAATTTTGTAAATCG * 68158593 AGGGTATTTCAGTAATTTGGTAAA 1 AGGGTATTTCAGTAATTTTGTAAA 68158617 CTAAAGTATT Statistics Matches: 307, Mismatches: 54, Indels: 31 0.78 0.14 0.08 Matches are distributed among these distances: 26 27 0.09 27 237 0.77 28 24 0.08 29 18 0.06 30 1 0.00 ACGTcount: A:0.33, C:0.09, G:0.21, T:0.37 Consensus pattern (27 bp): AGGGTATTTCAGTAATTTTGTAAATCG Found at i:68158473 original size:54 final size:54 Alignment explanation

Indices: 68158415--68158571 Score: 208 Period size: 54 Copynumber: 2.9 Consensus size: 54 68158405 GGGTATTTTG * *** * * 68158415 GTAATTTTGTAAA-CTGAGGGTATTTTAGTAATTTTGTAAATCGAGGGTAAAACA 1 GTAATTCTGTAAATC-GAGGGTATAACAGTAATTCTATAAATCGAGGGTAAAACA * * 68158469 GTAATTCTGTAAATCAAGGGTATAACAGTAATTCTATAAATCGAGGGTAAAACG 1 GTAATTCTGTAAATCGAGGGTATAACAGTAATTCTATAAATCGAGGGTAAAACA * * 68158523 GTAATTCTGTAAATCGAGGGTAAAACGGTAATTCTATAAATCGAGGGTA 1 GTAATTCTGTAAATCGAGGGTATAACAGTAATTCTATAAATCGAGGGTA 68158572 CTTTGGTAAT Statistics Matches: 91, Mismatches: 11, Indels: 2 0.88 0.11 0.02 Matches are distributed among these distances: 54 90 0.99 55 1 0.01 ACGTcount: A:0.38, C:0.09, G:0.22, T:0.31 Consensus pattern (54 bp): GTAATTCTGTAAATCGAGGGTATAACAGTAATTCTATAAATCGAGGGTAAAACA Found at i:68158608 original size:81 final size:80 Alignment explanation

Indices: 68158400--68158609 Score: 231 Period size: 81 Copynumber: 2.6 Consensus size: 80 68158390 AATTTTACTG * * * * 68158400 ATCGAGGGTATTTTGGTAATTTTGTAAACTGAGGGTATTTTAGTAATTTTGTAAATCGAGGGTAA 1 ATCGAGGGTA-TTTGGTAATTTTATAAATTGAGGGTATTTCAGTAATTCTGTAAATCGAGGGTAA * 68158465 AACAGTAATTCTGTAA 65 AACAGTAATTCTATAA * *** * * *** * 68158481 ATCAAGGGTATAACAGTAATTCTATAAATCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAA 1 ATCGAGGGTAT-TTGGTAATTTTATAAATTGAGGGTATTTCAGTAATTCTGTAAATCGAGGGTAA * 68158546 AACGGTAATTCTATAA 65 AACAGTAATTCTATAA * * 68158562 ATCGAGGGTACTTTGGTAATTTTACAATTTGAGGGTATTTCAGTAATT 1 ATCGAGGGTA-TTTGGTAATTTTATAAATTGAGGGTATTTCAGTAATT 68158610 TGGTAAACTA Statistics Matches: 99, Mismatches: 28, Indels: 4 0.76 0.21 0.03 Matches are distributed among these distances: 80 1 0.01 81 97 0.98 82 1 0.01 ACGTcount: A:0.34, C:0.09, G:0.22, T:0.35 Consensus pattern (80 bp): ATCGAGGGTATTTGGTAATTTTATAAATTGAGGGTATTTCAGTAATTCTGTAAATCGAGGGTAAA ACAGTAATTCTATAA Found at i:68166918 original size:40 final size:39 Alignment explanation

Indices: 68166873--68167002 Score: 181 Period size: 40 Copynumber: 3.3 Consensus size: 39 68166863 ATGCTGGAAA * 68166873 TTATATCCGGGTTAAGACCCGAAGGCAATT-GTGCTAGTGG 1 TTATATCCGGGCTAAGACCCGAAGGC-ATTCGTGC-AGTGG * * 68166913 CTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCG 1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGC-AGTGG * 68166953 TTCTATCCGGGCTAAGACCCGAAGGCATTCGTGCACGTGG 1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCA-GTGG 68166993 TTATATCCGG 1 TTATATCCGG 68167003 TTGTATTCCG Statistics Matches: 80, Mismatches: 8, Indels: 4 0.87 0.09 0.04 Matches are distributed among these distances: 39 4 0.05 40 76 0.95 ACGTcount: A:0.22, C:0.24, G:0.29, T:0.25 Consensus pattern (39 bp): TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCAGTGG Found at i:68172645 original size:40 final size:40 Alignment explanation

Indices: 68172518--68172647 Score: 174 Period size: 40 Copynumber: 3.2 Consensus size: 40 68172508 ATGCTGGAAA * * 68172518 TTATATCCGGGTTAAGACCCGAAGGCAATT-GTGCTAGTGG 1 TTATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTGG * * * 68172558 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCG 1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGG * 68172598 TTCTATCCGGGCTAAGACCCGAAGGCATTCGTGC-ACGTGG 1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGA-GTGG 68172638 TTATATCCGG 1 TTATATCCGG 68172648 TTGTATTCCG Statistics Matches: 78, Mismatches: 10, Indels: 4 0.85 0.11 0.04 Matches are distributed among these distances: 39 4 0.05 40 74 0.95 ACGTcount: A:0.22, C:0.25, G:0.29, T:0.24 Consensus pattern (40 bp): TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGG Found at i:68180547 original size:40 final size:39 Alignment explanation

Indices: 68180502--68180631 Score: 181 Period size: 40 Copynumber: 3.3 Consensus size: 39 68180492 ATGCTGGAAA * 68180502 TTATATCCGGGTTAAGACCCGAAGGCAATT-GTGCTAGTGG 1 TTATATCCGGGCTAAGACCCGAAGGC-ATTCGTGC-AGTGG * * 68180542 CTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCG 1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGC-AGTGG * 68180582 TTCTATCCGGGCTAAGACCCGAAGGCATTCGTGCACGTGG 1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCA-GTGG 68180622 TTATATCCGG 1 TTATATCCGG 68180632 TTGTATTCCG Statistics Matches: 80, Mismatches: 8, Indels: 4 0.87 0.09 0.04 Matches are distributed among these distances: 39 4 0.05 40 76 0.95 ACGTcount: A:0.22, C:0.24, G:0.29, T:0.25 Consensus pattern (39 bp): TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCAGTGG Found at i:68183318 original size:29 final size:29 Alignment explanation

Indices: 68183279--68183353 Score: 107 Period size: 29 Copynumber: 2.6 Consensus size: 29 68183269 GGTTGAGAGA * * 68183279 ATGGCACTAAGTGTGCGGGCTTGAAA-TGC 1 ATGGCACTAAGTGTGCGAG-TTGAAAGTAC * 68183308 ATGGCACTAAGTGTGCGAGTTTAAAGTAC 1 ATGGCACTAAGTGTGCGAGTTGAAAGTAC 68183337 ATGGCACTAAGTGTGCG 1 ATGGCACTAAGTGTGCG 68183354 TGGTTGATTA Statistics Matches: 42, Mismatches: 3, Indels: 2 0.89 0.06 0.04 Matches are distributed among these distances: 28 5 0.12 29 37 0.88 ACGTcount: A:0.27, C:0.16, G:0.32, T:0.25 Consensus pattern (29 bp): ATGGCACTAAGTGTGCGAGTTGAAAGTAC Found at i:68190498 original size:21 final size:21 Alignment explanation

Indices: 68190474--68190543 Score: 54 Period size: 21 Copynumber: 3.2 Consensus size: 21 68190464 TGATCTGAAC 68190474 TCATTGAGTTATGGTCTGAGT 1 TCATTGAGTTATGGTCTGAGT * ** 68190495 TCA-TGA-TATATGTGGCATTTGAAA 1 TCATTGAGT-TA--TGG--TCTGAGT 68190519 TCATTGAGTTATGGTCTGAGT 1 TCATTGAGTTATGGTCTGAGT 68190540 TCAT 1 TCAT 68190544 GATATATGTG Statistics Matches: 36, Mismatches: 6, Indels: 14 0.64 0.11 0.25 Matches are distributed among these distances: 19 1 0.03 20 5 0.14 21 11 0.31 22 3 0.08 23 3 0.08 24 7 0.19 25 5 0.14 26 1 0.03 ACGTcount: A:0.24, C:0.10, G:0.24, T:0.41 Consensus pattern (21 bp): TCATTGAGTTATGGTCTGAGT Found at i:68192202 original size:18 final size:19 Alignment explanation

Indices: 68192179--68192216 Score: 51 Period size: 20 Copynumber: 2.0 Consensus size: 19 68192169 AGGACACGGC * 68192179 CCCAAG-ACACTGGCGTGT 1 CCCAAGCACACGGGCGTGT 68192197 CCCAAGCCACACGGGCGTGT 1 CCCAAG-CACACGGGCGTGT 68192217 GTATGACCAC Statistics Matches: 17, Mismatches: 1, Indels: 2 0.85 0.05 0.10 Matches are distributed among these distances: 18 6 0.35 20 11 0.65 ACGTcount: A:0.21, C:0.37, G:0.29, T:0.13 Consensus pattern (19 bp): CCCAAGCACACGGGCGTGT Found at i:68193540 original size:13 final size:13 Alignment explanation

Indices: 68193522--68193550 Score: 58 Period size: 13 Copynumber: 2.2 Consensus size: 13 68193512 GGTTGTTTAT 68193522 TAAACTAATTAAC 1 TAAACTAATTAAC 68193535 TAAACTAATTAAC 1 TAAACTAATTAAC 68193548 TAA 1 TAA 68193551 TTAAACTAAA 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:0.55, C:0.14, G:0.00, T:0.31 Consensus pattern (13 bp): TAAACTAATTAAC Found at i:68201635 original size:13 final size:13 Alignment explanation

Indices: 68201617--68201645 Score: 58 Period size: 13 Copynumber: 2.2 Consensus size: 13 68201607 GGTTGTTTAT 68201617 TAAACTAATTAAC 1 TAAACTAATTAAC 68201630 TAAACTAATTAAC 1 TAAACTAATTAAC 68201643 TAA 1 TAA 68201646 TTAAACTAAA 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:0.55, C:0.14, G:0.00, T:0.31 Consensus pattern (13 bp): TAAACTAATTAAC Found at i:68206793 original size:40 final size:39 Alignment explanation

Indices: 68206732--68206977 Score: 212 Period size: 40 Copynumber: 6.2 Consensus size: 39 68206722 GGATGATAAC * * 68206732 CGGGCTAAGTCCCG-AGAGCATTTGAGCTAGTGGCTAAATT 1 CGGGCTAAGTCCCGAAG-GCATTTGTGCTAGTGACTAAA-T * * * 68206772 CGGGCTAAGTCCCGAAGGCATTCGTGCGAGCT-ACTATAT 1 CGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TGACTAAAT * * * 68206811 CTGGGCTAAGTCCCGAAGGCGTTTGTG-TGAGCT-ATTATAT 1 C-GGGCTAAGTCCCGAAGGCATTTGTGCT-AG-TGACTAAAT * * * * 68206851 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTATTATAT 1 -CGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAAAT * * * 68206891 CGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTATAAC 1 CGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-AAT * * * * 68206931 CGGGTTAAGTCCCGAAGGCATTTGAGCTAGTGGCTATAT 1 CGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAAAT * 68206970 CCGGCTAA 1 CGGGCTAA 68206978 ACTCCGAAGG Statistics Matches: 174, Mismatches: 24, Indels: 17 0.81 0.11 0.08 Matches are distributed among these distances: 39 44 0.25 40 126 0.72 41 4 0.02 ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27 Consensus pattern (39 bp): CGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAAAT Found at i:68206943 original size:119 final size:120 Alignment explanation

Indices: 68206731--68206954 Score: 308 Period size: 119 Copynumber: 1.9 Consensus size: 120 68206721 CGGATGATAA * * 68206731 CCGGGCTAAGTCCCGAGAGCATTTGAGCTAGTGGCTAAATTCGGGCTAAGTCCCGAAGGCATTCG 1 CCGGGCTAAGTCCCGAGAGCATTTGAGCGAGTGACTAAATTCGGGCTAAGTCCCGAAGGCATTCG * * * * 68206796 TGCGAGCTACTATATCTGGGCTAAGTCCCGAAGGCGTTTGTGTGAGCTATTATAT 66 TGCAAGCTACTATAACCGGGCTAAGTCCCGAAGGCATTTGTGTGAGCTATTATAT * * * * * 68206851 CCGGGCTAAGTCCCGA-AGGCATTTGTGCGAGTTATTATA-TCGGGCTAAGTCCCGAAGGCATTT 1 CCGGGCTAAGTCCCGAGA-GCATTTGAGCGAGTGACTAAATTCGGGCTAAGTCCCGAAGGCATTC * * 68206914 GTGCAAGTTACTATAACCGGGTTAAGTCCCGAAGGCATTTG 65 GTGCAAGCTACTATAACCGGGCTAAGTCCCGAAGGCATTTG 68206955 AGCTAGTGGC Statistics Matches: 90, Mismatches: 13, Indels: 3 0.85 0.12 0.03 Matches are distributed among these distances: 119 59 0.66 120 31 0.34 ACGTcount: A:0.23, C:0.21, G:0.29, T:0.27 Consensus pattern (120 bp): CCGGGCTAAGTCCCGAGAGCATTTGAGCGAGTGACTAAATTCGGGCTAAGTCCCGAAGGCATTCG TGCAAGCTACTATAACCGGGCTAAGTCCCGAAGGCATTTGTGTGAGCTATTATAT Found at i:68206969 original size:79 final size:78 Alignment explanation

Indices: 68206732--68206977 Score: 262 Period size: 79 Copynumber: 3.1 Consensus size: 78 68206722 GGATGATAAC * * ** * * 68206732 CGGGCTAAGTCCCG-AGAGCATTTGAGCTAGTGGCTA-AATTCGGGCTAAGTCCCGAAGGCATTC 1 CGGGCTAAGTCCCGAAG-GCATTTGTGCAAGTTACTATAA-CCGGGCTAAGTCCCGAAGGCATTT 68206795 GTGCGAGCTACTATAT 64 GTGCGAG-TACTATAT * ** * * * 68206811 CTGGGCTAAGTCCCGAAGGCGTTTGTGTGAGCTATTATATCCGGGCTAAGTCCCGAAGGCATTTG 1 C-GGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTATAACCGGGCTAAGTCCCGAAGGCATTTG * 68206876 TGCGAGTTATTATAT 65 TGCGAG-TACTATAT * * 68206891 CGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTATAACCGGGTTAAGTCCCGAAGGCATTTGA 1 CGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTATAACCGGGCTAAGTCCCGAAGGCATTTGT * * 68206956 GCTAGTGGCTATAT 66 GCGAGT-ACTATAT * 68206970 CCGGCTAA 1 CGGGCTAA 68206978 ACTCCGAAGG Statistics Matches: 138, Mismatches: 25, Indels: 8 0.81 0.15 0.05 Matches are distributed among these distances: 78 1 0.01 79 73 0.53 80 61 0.44 81 3 0.02 ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27 Consensus pattern (78 bp): CGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTATAACCGGGCTAAGTCCCGAAGGCATTTGT GCGAGTACTATAT Found at i:68214906 original size:40 final size:40 Alignment explanation

Indices: 68214851--68215097 Score: 244 Period size: 40 Copynumber: 6.2 Consensus size: 40 68214841 CGGATGATAA * * 68214851 CCGGGCTAAGTCCCG-AGAGCATTTGAGCTAGTGGCTAAT-T 1 CCGGGCTAAGTCCCGAAG-GCATTTGTGCGAGT-GCTAATAT * * 68214891 CCGGGCTAAGTCCCGAAGGCATTCGTGCGAGCTACT-ATAT 1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TGCTAATAT * 68214931 CCGGGCTAAGTCCCGAAGGCGTTTGTGCGA--GCTATTATAT 1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGCTA--ATAT * 68214971 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGT--TATTAT 1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGCTAATAT * * * 68215009 ACCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT-ATAA 1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TGCTAATAT * * * 68215050 CCGGGTTAAGTCCCGAAGGCATTTGAGCTAGTGGCT-ATAT 1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGT-GCTAATAT 68215090 CC-GGCTAA 1 CCGGGCTAA 68215098 ACTCCGAAGG Statistics Matches: 176, Mismatches: 18, Indels: 27 0.80 0.08 0.12 Matches are distributed among these distances: 37 2 0.01 38 3 0.02 39 38 0.22 40 127 0.72 41 5 0.03 42 1 0.01 ACGTcount: A:0.23, C:0.23, G:0.28, T:0.26 Consensus pattern (40 bp): CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGCTAATAT Found at i:68215063 original size:119 final size:120 Alignment explanation

Indices: 68214851--68215074 Score: 317 Period size: 119 Copynumber: 1.9 Consensus size: 120 68214841 CGGATGATAA * * * 68214851 CCGGGCTAAGTCCCGAGAGCATTTGAGCTAGTGGCTAATTCCGGGCTAAGTCCCGAAGGCATTCG 1 CCGGGCTAAGTCCCGAGAGCATTTGAGCGAGTGGATAATACCGGGCTAAGTCCCGAAGGCATTCG * * * 68214916 TGCGAGCTACTATATCCGGGCTAAGTCCCGAAGGCGTTTGTGCGAGCTATTATAT 66 TGCAAGCTACTATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGCTATTATAT * * * * 68214971 CCGGGCTAAGTCCCGA-AGGCATTTGTGCGAGT-TATTATACCGGGCTAAGTCCCGAAGGCATTT 1 CCGGGCTAAGTCCCGAGA-GCATTTGAGCGAGTGGATAATACCGGGCTAAGTCCCGAAGGCATTC * * 68215034 GTGCAAGTTACTATAACCGGGTTAAGTCCCGAAGGCATTTG 65 GTGCAAGCTACTATAACCGGGCTAAGTCCCGAAGGCATTTG 68215075 AGCTAGTGGC Statistics Matches: 91, Mismatches: 12, Indels: 3 0.86 0.11 0.03 Matches are distributed among these distances: 119 63 0.69 120 28 0.31 ACGTcount: A:0.23, C:0.23, G:0.29, T:0.25 Consensus pattern (120 bp): CCGGGCTAAGTCCCGAGAGCATTTGAGCGAGTGGATAATACCGGGCTAAGTCCCGAAGGCATTCG TGCAAGCTACTATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGCTATTATAT Found at i:68215107 original size:79 final size:79 Alignment explanation

Indices: 68214891--68215097 Score: 274 Period size: 79 Copynumber: 2.6 Consensus size: 79 68214881 GTGGCTAATT * * 68214891 CCGGGCTAAGTCCCGAAGGCATTCGTGCGAGCTACTATATCCGGGCTAAGTCCCGAAGGCGTTTG 1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TACTATATCCGGGCTAAGTCCCGAAGGCATTTG * * * 68214956 TGCGAGCTATTATAT 65 TGCAAGCTACTATAA * 68214971 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTATTATA-CCGGGCTAAGTCCCGAAGGCATTTG 1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TACTATATCCGGGCTAAGTCCCGAAGGCATTTG * 68215035 TGCAAGTTACTATAA 65 TGCAAGCTACTATAA * * * * 68215050 CCGGGTTAAGTCCCGAAGGCATTTGAGCTAGTGGCTATATCC-GGCTAA 1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGT-ACTATATCCGGGCTAA 68215098 ACTCCGAAGG Statistics Matches: 112, Mismatches: 13, Indels: 5 0.86 0.10 0.04 Matches are distributed among these distances: 78 1 0.01 79 73 0.65 80 38 0.34 ACGTcount: A:0.23, C:0.23, G:0.28, T:0.26 Consensus pattern (79 bp): CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTACTATATCCGGGCTAAGTCCCGAAGGCATTTGT GCAAGCTACTATAA Found at i:68216676 original size:44 final size:46 Alignment explanation

Indices: 68216622--68216737 Score: 139 Period size: 44 Copynumber: 2.5 Consensus size: 46 68216612 TATGCGTGGT 68216622 GATGCATGTCCCAGACATGTCTTACACTAGCACAACTCT-T-A-GCC 1 GATGCATGTCCCAGACATGTCTTACACTAGC-CAACTCTGTCAGGCC * * * * * * 68216666 GATGCGTGTCCCAGACACGTCTTACACTGGCTATCTTTGTCGAGGCC 1 GATGCATGTCCCAGACATGTCTTACACTAGCCAACTCTGTC-AGGCC 68216713 GATGCATGTCCCAGACATGTCTTAC 1 GATGCATGTCCCAGACATGTCTTAC 68216738 TCTGGCACTC Statistics Matches: 60, Mismatches: 8, Indels: 5 0.82 0.11 0.07 Matches are distributed among these distances: 43 4 0.07 44 29 0.48 46 1 0.02 47 26 0.43 ACGTcount: A:0.22, C:0.30, G:0.21, T:0.27 Consensus pattern (46 bp): GATGCATGTCCCAGACATGTCTTACACTAGCCAACTCTGTCAGGCC Found at i:68216726 original size:47 final size:46 Alignment explanation

Indices: 68216571--68216743 Score: 165 Period size: 47 Copynumber: 3.7 Consensus size: 46 68216561 GATATATTGT * * 68216571 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCTTATATGCGTGG- 1 CGATG-CATGTCCCAGACAT-GTCTTACACTGGCTATCTT-T-T-CGAGGC * * * * * 68216621 TGATGCATGTCCCAGACATGTCTTACACTAGCACAACTCTT--A-GC 1 CGATGCATGTCCCAGACATGTCTTACACTGGC-TATCTTTTCGAGGC * * 68216665 CGATGCGTGTCCCAGACACGTCTTACACTGGCTATCTTTGTCGAGGC 1 CGATGCATGTCCCAGACATGTCTTACACTGGCTATCTTT-TCGAGGC * 68216712 CGATGCATGTCCCAGACATGTCTTACTCTGGC 1 CGATGCATGTCCCAGACATGTCTTACACTGGC 68216744 ACTCATAATA Statistics Matches: 100, Mismatches: 17, Indels: 15 0.76 0.13 0.11 Matches are distributed among these distances: 43 5 0.05 44 29 0.29 46 1 0.01 47 32 0.32 48 13 0.13 49 16 0.16 50 4 0.04 ACGTcount: A:0.20, C:0.29, G:0.22, T:0.28 Consensus pattern (46 bp): CGATGCATGTCCCAGACATGTCTTACACTGGCTATCTTTTCGAGGC Found at i:68224227 original size:44 final size:46 Alignment explanation

Indices: 68224173--68224340 Score: 123 Period size: 46 Copynumber: 3.7 Consensus size: 46 68224163 TATGCGTGCT 68224173 GATGCATGTCCCAGACATGTCTTACACTAGCACAACTCT-T-A-GCC 1 GATGCATGTCCCAGACATGTCTTACACTAGC-CAACTCTGTCAGGCC * * * * * * 68224217 GATGCGTGTCCCAAACACGTCTTACACTGGCTATCTCTGTCGAGGCC 1 GATGCATGTCCCAGACATGTCTTACACTAGCCAACTCTGTC-AGGCC * * * * * * 68224264 GGTGCCTGTCCCAGACATGTCTTACTCT-GGC-ACTCATAAT-ATGGCT 1 GATGCATGTCCCAGACATGTCTTACACTAGCCAACTC-T-GTCA-GGCC * * 68224310 GAAGCATGTTCCAGACATGTCTTACACTAGC 1 GATGCATGTCCCAGACATGTCTTACACTAGC 68224341 TCTCGTCTGG Statistics Matches: 94, Mismatches: 22, Indels: 13 0.73 0.17 0.10 Matches are distributed among these distances: 43 5 0.05 44 28 0.30 45 4 0.04 46 29 0.31 47 28 0.30 ACGTcount: A:0.23, C:0.30, G:0.20, T:0.27 Consensus pattern (46 bp): GATGCATGTCCCAGACATGTCTTACACTAGCCAACTCTGTCAGGCC Found at i:68224286 original size:47 final size:44 Alignment explanation

Indices: 68224173--68224296 Score: 124 Period size: 47 Copynumber: 2.8 Consensus size: 44 68224163 TATGCGTGCT * * 68224173 GATGCATGTCCCAGACATGTCTTACACTAGCACAACTCTTAGCC 1 GATGCCTGTCCCAGACATGTCTTACACTGGCACAACTCTTAGCC * * * * * 68224217 GATGCGTGTCCCAAACACGTCTTACACTGGC-TATCTCTGTCGAGGCC 1 GATGCCTGTCCCAGACATGTCTTACACTGGCACAACTCT-T--A-GCC * * 68224264 GGTGCCTGTCCCAGACATGTCTTACTCTGGCAC 1 GATGCCTGTCCCAGACATGTCTTACACTGGCAC 68224297 TCATAATATG Statistics Matches: 63, Mismatches: 12, Indels: 6 0.78 0.15 0.07 Matches are distributed among these distances: 43 5 0.08 44 28 0.44 46 1 0.02 47 29 0.46 ACGTcount: A:0.21, C:0.32, G:0.21, T:0.26 Consensus pattern (44 bp): GATGCCTGTCCCAGACATGTCTTACACTGGCACAACTCTTAGCC Found at i:68228527 original size:21 final size:21 Alignment explanation

Indices: 68228503--68228578 Score: 55 Period size: 21 Copynumber: 3.5 Consensus size: 21 68228493 CTAGGAACTA 68228503 TGTGATCTGAACTCATTGAGT 1 TGTGATCTGAACTCATTGAGT * ** * 68228524 TGTGGTCTGAGTTCA-TGATAT 1 TGTGATCTGAACTCATTGA-GT 68228545 ATGTGGCATCTGAACTCATTGAGT 1 -TGT-G-ATCTGAACTCATTGAGT * * 68228569 TATGGTCTGA 1 TGTGATCTGA 68228579 GTTCATGATG Statistics Matches: 40, Mismatches: 10, Indels: 10 0.67 0.17 0.17 Matches are distributed among these distances: 20 3 0.08 21 18 0.45 22 4 0.10 23 3 0.08 24 9 0.22 25 3 0.08 ACGTcount: A:0.22, C:0.13, G:0.26, T:0.38 Consensus pattern (21 bp): TGTGATCTGAACTCATTGAGT Found at i:68228563 original size:45 final size:45 Alignment explanation

Indices: 68228507--68228594 Score: 158 Period size: 45 Copynumber: 2.0 Consensus size: 45 68228497 GAACTATGTG * 68228507 ATCTGAACTCATTGAGTTGTGGTCTGAGTTCATGATATATGTGGC 1 ATCTGAACTCATTGAGTTATGGTCTGAGTTCATGATATATGTGGC * 68228552 ATCTGAACTCATTGAGTTATGGTCTGAGTTCATGATGTATGTG 1 ATCTGAACTCATTGAGTTATGGTCTGAGTTCATGATATATGTG 68228595 ACACATGTTT Statistics Matches: 41, Mismatches: 2, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 45 41 1.00 ACGTcount: A:0.23, C:0.12, G:0.26, T:0.39 Consensus pattern (45 bp): ATCTGAACTCATTGAGTTATGGTCTGAGTTCATGATATATGTGGC Found at i:68232687 original size:2 final size:2 Alignment explanation

Indices: 68232680--68232712 Score: 66 Period size: 2 Copynumber: 16.5 Consensus size: 2 68232670 TGTCCTTGCT 68232680 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T 1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T 68232713 GTTTTGGATC Statistics Matches: 31, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 31 1.00 ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52 Consensus pattern (2 bp): TA Found at i:68238405 original size:9 final size:9 Alignment explanation

Indices: 68238393--68238433 Score: 50 Period size: 9 Copynumber: 4.6 Consensus size: 9 68238383 AATTTAATTA 68238393 TTTTTAAAT 1 TTTTTAAAT 68238402 TTTTTAAA- 1 TTTTTAAAT 68238410 -TTTTAAAT 1 TTTTTAAAT 68238418 TTTTTATATAT 1 TTTTTA-A-AT 68238429 TTTTT 1 TTTTT 68238434 TGGTTTTTTT Statistics Matches: 28, Mismatches: 0, Indels: 6 0.82 0.00 0.18 Matches are distributed among these distances: 7 7 0.25 9 13 0.46 10 1 0.04 11 7 0.25 ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71 Consensus pattern (9 bp): TTTTTAAAT Found at i:68238733 original size:80 final size:75 Alignment explanation

Indices: 68238558--68238734 Score: 230 Period size: 80 Copynumber: 2.3 Consensus size: 75 68238548 AGTTTTTTTG * * 68238558 AAAATT-ATTTTTTTCTTTTTTGAATTCTTAGAAACTATATCGACATATTTTACAATTTTATAAA 1 AAAATTAATTTTTTT-TTTTTTGAATTCTTAGAAACTATATCAAAATATTTTACAATTTTATAAA * 68238622 ATTTTATTTAA 65 ATTTTATTAAA * 68238633 AAAATTCAATTTTTCCTTTTTTTATAGAATTTTTAGAAACTATATCAAAATATTTTACAATTTTA 1 AAAATT-AATTTTT--TTTTTTT-T-GAATTCTTAGAAACTATATCAAAATATTTTACAATTTTA 68238698 TAAAATTTTATTCAAAAA 61 TAAAATTTTATT---AAA 68238716 AAAATTAATTTTTTTTTTT 1 AAAATTAATTTTTTTTTTT 68238735 AGAATGTACA Statistics Matches: 89, Mismatches: 4, Indels: 13 0.84 0.04 0.12 Matches are distributed among these distances: 75 6 0.07 77 6 0.07 78 5 0.06 79 3 0.03 80 54 0.61 82 7 0.08 83 8 0.09 ACGTcount: A:0.38, C:0.07, G:0.03, T:0.51 Consensus pattern (75 bp): AAAATTAATTTTTTTTTTTTTGAATTCTTAGAAACTATATCAAAATATTTTACAATTTTATAAAA TTTTATTAAA Found at i:68242457 original size:51 final size:52 Alignment explanation

Indices: 68242381--68242487 Score: 207 Period size: 51 Copynumber: 2.1 Consensus size: 52 68242371 ATAGATTCTT 68242381 TTATAGTAAAGTCGTCATGACCTTAACAAAA-TTAGAATTGGGTTGAGAAAA 1 TTATAGTAAAGTCGTCATGACCTTAACAAAATTTAGAATTGGGTTGAGAAAA 68242432 TTATAGTAAAGTCGTCATGACCTTAACAAAATTTAGAATTGGGTTGAGAAAA 1 TTATAGTAAAGTCGTCATGACCTTAACAAAATTTAGAATTGGGTTGAGAAAA 68242484 TTAT 1 TTAT 68242488 TTAATTAAAA Statistics Matches: 55, Mismatches: 0, Indels: 1 0.98 0.00 0.02 Matches are distributed among these distances: 51 31 0.56 52 24 0.44 ACGTcount: A:0.40, C:0.09, G:0.19, T:0.32 Consensus pattern (52 bp): TTATAGTAAAGTCGTCATGACCTTAACAAAATTTAGAATTGGGTTGAGAAAA Found at i:68242505 original size:4 final size:4 Alignment explanation

Indices: 68242482--68242537 Score: 57 Period size: 4 Copynumber: 15.0 Consensus size: 4 68242472 GGGTTGAGAA * ** 68242482 AATT ATTT AATT AAAA AATT AATT AATT AATT AATT AA-- AATT AATT 1 AATT AATT AATT AATT AATT AATT AATT AATT AATT AATT AATT AATT 68242528 AA-- AATT AATT 1 AATT AATT AATT 68242538 TAATAAGATT Statistics Matches: 42, Mismatches: 6, Indels: 8 0.75 0.11 0.14 Matches are distributed among these distances: 2 4 0.10 4 38 0.90 ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45 Consensus pattern (4 bp): AATT Done.