Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Chr03 135709677 

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: 135709677
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 172 of 438

Found at i:52879048 original size:96 final size:95

Alignment explanation

Indices: 52878806--52879082 Score: 278 Period size: 96 Copynumber: 2.9 Consensus size: 95 52878796 TGCCGATGCT * * * * * 52878806 ATGTCCCAGACATGGTCTTACATTGGCT-TACAT-GTCGAGGCCGATGCCATGTCCCAGACATGG 1 ATGTCCCAGACATGGTCTTACACTGGATCT-CATACT-GTGGCCAATGCCATGTCCCAGACATGG * * * * 52878869 TCTTACACTAGCTCGCATTTCAATGCTGATGCC 64 TCTTACACTAG-TCACATATCAACGCTGAAGCC * * 52878902 ATGTCCCAGACATGGTCTTACACTGGCTCTCATACTGTGGCCAATGCCATGGCCCAGACATGGTC 1 ATGTCCCAGACATGGTCTTACACTGGATCTCATACTGTGGCCAATGCCATGTCCCAGACATGGTC 52878967 TTACACTAGTGCACATATCAACG-TCGAAGCC 66 TTACACTAGT-CACATATCAACGCT-GAAGCC * * * * * 52878998 ATGTCCCA-AGCATGGTCTTACACTGGATCTCATACCAT-TGTCGACT-CCATGTTCCAGGCATG 1 ATGTCCCAGA-CATGGTCTTACACTGGATCTCATA-C-TGTGGCCAATGCCATGTCCCAGACATG * 52879060 GTCTTACACTAGCACACATATCA 63 GTCTTACACTAG-TCACATATCA 52879083 CTCAAATGTC Statistics Matches: 156, Mismatches: 17, Indels: 16 0.83 0.09 0.08 Matches are distributed among these distances: 95 3 0.02 96 144 0.92 97 8 0.05 98 1 0.01 ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27 Consensus pattern (95 bp): ATGTCCCAGACATGGTCTTACACTGGATCTCATACTGTGGCCAATGCCATGTCCCAGACATGGTC TTACACTAGTCACATATCAACGCTGAAGCC Found at i:52880071 original size:40 final size:39 Alignment explanation

Indices: 52880004--52880081 Score: 93 Period size: 40 Copynumber: 2.0 Consensus size: 39 52879994 GACTTATCGA ** 52880004 CTAAAATGACACTTAGTGTGCGGTTTGAAATAGCTTCGG 1 CTAAAATGACACTTAGTGTGCAATTTGAAATAGCTTCGG * * * * 52880043 CTAAAAGTGGCACTTGGTGTGCAATTTGAGATAGTTTCG 1 CTAAAA-TGACACTTAGTGTGCAATTTGAAATAGCTTCG 52880082 TCTATATTTA Statistics Matches: 32, Mismatches: 6, Indels: 1 0.82 0.15 0.03 Matches are distributed among these distances: 39 6 0.19 40 26 0.81 ACGTcount: A:0.27, C:0.14, G:0.27, T:0.32 Consensus pattern (39 bp): CTAAAATGACACTTAGTGTGCAATTTGAAATAGCTTCGG Found at i:52880160 original size:28 final size:28 Alignment explanation

Indices: 52880102--52880160 Score: 64 Period size: 28 Copynumber: 2.1 Consensus size: 28 52880092 TATAAATGGA ** * * ** 52880102 ACTTAGTGTGCAAAGTATCGAGGATGGC 1 ACTTAGTGTGCAAAACATCCAGAATAAC 52880130 ACTTAGTGTGCAAAACATCCAGAATAAC 1 ACTTAGTGTGCAAAACATCCAGAATAAC 52880158 ACT 1 ACT 52880161 CAGCGTGCGA Statistics Matches: 25, Mismatches: 6, Indels: 0 0.81 0.19 0.00 Matches are distributed among these distances: 28 25 1.00 ACGTcount: A:0.36, C:0.19, G:0.22, T:0.24 Consensus pattern (28 bp): ACTTAGTGTGCAAAACATCCAGAATAAC Found at i:52882868 original size:50 final size:50 Alignment explanation

Indices: 52882804--52882939 Score: 184 Period size: 50 Copynumber: 2.7 Consensus size: 50 52882794 CAATACATGT * * * 52882804 GAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCAC-GGAAAGAGGA 1 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGC-CTCGAAAGAAGA * * * * * 52882854 GATCCAGTGTAAGACCATGTCTGGGATATGGCATCAGCCTCGATATAAGA 1 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGAAAGAAGA 52882904 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCG 1 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCG 52882940 ACTCGATATG Statistics Matches: 74, Mismatches: 11, Indels: 2 0.85 0.13 0.02 Matches are distributed among these distances: 49 1 0.01 50 73 0.99 ACGTcount: A:0.29, C:0.20, G:0.32, T:0.20 Consensus pattern (50 bp): GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGAAAGAAGA Found at i:52882979 original size:47 final size:49 Alignment explanation

Indices: 52882809--52882979 Score: 174 Period size: 50 Copynumber: 3.5 Consensus size: 49 52882799 CATGTGAGCT * * 52882809 AGTGTAAGACCATGTCTGGGACATGGCATCGGCAC-GGA-A-AGAGGAGATCC 1 AGTGTAAGACCATGTCTGGGACATGGCATCAG-ACTCGATATAGA-GAGA--C * * * 52882859 AGTGTAAGACCATGTCTGGGATATGGCATCAGCCTCGATATAAGAGAGCC 1 AGTGTAAGACCATGTCTGGGACATGGCATCAGACTCGATAT-AGAGAGAC * * 52882909 AGTGTAAGACCATGTCTGGGACATGGCATC-GACTCGATAT-GTGATTAC 1 AGTGTAAGACCATGTCTGGGACATGGCATCAGACTCGATATAGAGA-GAC * 52882957 A-TGTAAGACCATGTTTGGGACAT 1 AGTGTAAGACCATGTCTGGGACAT 52882980 TAGCATTGTA Statistics Matches: 105, Mismatches: 11, Indels: 13 0.81 0.09 0.10 Matches are distributed among these distances: 47 24 0.23 48 2 0.02 49 10 0.10 50 62 0.59 51 1 0.01 52 3 0.03 53 3 0.03 ACGTcount: A:0.29, C:0.19, G:0.29, T:0.23 Consensus pattern (49 bp): AGTGTAAGACCATGTCTGGGACATGGCATCAGACTCGATATAGAGAGAC Found at i:52883038 original size:43 final size:43 Alignment explanation

Indices: 52882911--52883054 Score: 139 Period size: 43 Copynumber: 3.3 Consensus size: 43 52882901 AGAGAGCCAG * * 52882911 TGTAAGACCATGTCTGGGACATGGCATCGACTCGATATGTGATTACA 1 TGTAAGACCATGTGTGGGACAT-G-AGC-A-TCGATATGTGATTACA * * * * * 52882958 TGTAAGACCATGTTTGGGACATTAGCATTG-TATTGTGATTTCG 1 TGTAAGACCATGTGTGGGACATGAGCATCGATA-TGTGATTACA * * 52883001 TGTAAGACCCTGTGTGGGACAGTGA-CATCGATATGTGATAACA 1 TGTAAGACCATGTGTGGGACA-TGAGCATCGATATGTGATTACA 52883044 TGTAAGACCAT 1 TGTAAGACCAT 52883055 ATCTAGGATA Statistics Matches: 80, Mismatches: 14, Indels: 10 0.77 0.13 0.10 Matches are distributed among these distances: 42 2 0.03 43 50 0.62 44 5 0.06 45 2 0.03 47 21 0.26 ACGTcount: A:0.28, C:0.16, G:0.26, T:0.31 Consensus pattern (43 bp): TGTAAGACCATGTGTGGGACATGAGCATCGATATGTGATTACA Found at i:52887906 original size:40 final size:39 Alignment explanation

Indices: 52887835--52887920 Score: 102 Period size: 40 Copynumber: 2.2 Consensus size: 39 52887825 TAATGACTTA ** * 52887835 TCGGCTAAAATGGCACTTAGTGTGCGGTTTGAAATAGCT 1 TCGGCTAAAATGGCACTTAGTGTGCAATTTGAAATAACT * 52887874 TCGGCTAAAAGTGGCACTT-GATGTGCAATTTGAGATAACT 1 TCGGCTAAAA-TGGCACTTAG-TGTGCAATTTGAAATAACT * 52887914 TTGGCTA 1 TCGGCTA 52887921 TATTTATATA Statistics Matches: 40, Mismatches: 5, Indels: 3 0.83 0.10 0.06 Matches are distributed among these distances: 39 11 0.28 40 29 0.73 ACGTcount: A:0.27, C:0.15, G:0.27, T:0.31 Consensus pattern (39 bp): TCGGCTAAAATGGCACTTAGTGTGCAATTTGAAATAACT Found at i:52889524 original size:43 final size:43 Alignment explanation

Indices: 52889401--52889611 Score: 216 Period size: 43 Copynumber: 5.0 Consensus size: 43 52889391 ATTATCGAGA * * 52889401 TGTGATTACATGTAAGACCATGTCTGGGACATTGGCACTGTAT 1 TGTGATTACATGTAAGACCATGTCTGGGATATTGGCATTGTAT * 52889444 TGTGATTACATGTAAGACCATGTCTAGGATATTGGCATTGTAT 1 TGTGATTACATGTAAGACCATGTCTGGGATATTGGCATTGTAT * * 52889487 TGTGATTACGTGTAAGACCATGTCTGGGATATTGGCATCGT-T 1 TGTGATTACATGTAAGACCATGTCTGGGATATTGGCATTGTAT *** * * * * * * 52889529 ATACAATTACATGTAA-ACCCTGTTTAGGACAGTGGCATCG-AT 1 -TGTGATTACATGTAAGACCATGTCTGGGATATTGGCATTGTAT * * * 52889571 ATGTGATAACATGTAAGA-CATATTTGGGATA-TGGCATTGTA 1 -TGTGATTACATGTAAGACCATGTCTGGGATATTGGCATTGTA 52889612 CGAGGTTTAT Statistics Matches: 140, Mismatches: 24, Indels: 9 0.81 0.14 0.05 Matches are distributed among these distances: 41 7 0.05 42 43 0.31 43 90 0.64 ACGTcount: A:0.28, C:0.14, G:0.24, T:0.34 Consensus pattern (43 bp): TGTGATTACATGTAAGACCATGTCTGGGATATTGGCATTGTAT Found at i:52896225 original size:42 final size:43 Alignment explanation

Indices: 52896146--52896247 Score: 118 Period size: 42 Copynumber: 2.4 Consensus size: 43 52896136 TCCCGGACGT * * ** 52896146 GGTCTTACATGTAATTCAGTATCGATGCCTCTGTCCCAAACAG 1 GGTCTTACACGTAAATCAGTATCGATGCCGATGTCCCAAACAG * * 52896189 GGTCTTACACG-AAATCAG-ATACGATGCCGATGTCCCAGACAT 1 GGTCTTACACGTAAATCAGTAT-CGATGCCGATGTCCCAAACAG * 52896231 GGTCTTACACATAAATC 1 GGTCTTACACGTAAATC 52896248 TCAAATCGAG Statistics Matches: 50, Mismatches: 7, Indels: 4 0.82 0.11 0.07 Matches are distributed among these distances: 41 2 0.04 42 33 0.66 43 15 0.30 ACGTcount: A:0.29, C:0.25, G:0.19, T:0.26 Consensus pattern (43 bp): GGTCTTACACGTAAATCAGTATCGATGCCGATGTCCCAAACAG Found at i:52897919 original size:51 final size:51 Alignment explanation

Indices: 52897843--52897942 Score: 157 Period size: 51 Copynumber: 2.0 Consensus size: 51 52897833 GGACACACGG * 52897843 CCAGATCACACGCCCATGGGGCAGACCGTGTGTCACACACGGCCAAGACGA 1 CCAGATCACACGCCCATGGGGCAGACCGTATGTCACACACGGCCAAGACGA * * 52897894 CCAGATCACAC-CCTTATGGGGCAGACTGTATGTCACACACGGCCAAGAC 1 CCAGATCACACGCC-CATGGGGCAGACCGTATGTCACACACGGCCAAGAC 52897943 ACATTCCTGT Statistics Matches: 45, Mismatches: 3, Indels: 2 0.90 0.06 0.04 Matches are distributed among these distances: 50 2 0.04 51 43 0.96 ACGTcount: A:0.28, C:0.34, G:0.25, T:0.13 Consensus pattern (51 bp): CCAGATCACACGCCCATGGGGCAGACCGTATGTCACACACGGCCAAGACGA Found at i:52899114 original size:45 final size:45 Alignment explanation

Indices: 52899059--52899145 Score: 129 Period size: 45 Copynumber: 1.9 Consensus size: 45 52899049 AAACATGTGT * * 52899059 ACATACATCATGAACTCAGACCACAACTCAATGAGTTCAGATGTC 1 ACATACATCATGAACTCAGACCACAACCCAATAAGTTCAGATGTC * * * 52899104 ACATATATCATGAACTCAGACCAGAACCCAATAAGTTTAGAT 1 ACATACATCATGAACTCAGACCACAACCCAATAAGTTCAGAT 52899146 CACATAGTTC Statistics Matches: 37, Mismatches: 5, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 45 37 1.00 ACGTcount: A:0.40, C:0.24, G:0.13, T:0.23 Consensus pattern (45 bp): ACATACATCATGAACTCAGACCACAACCCAATAAGTTCAGATGTC Found at i:52901477 original size:37 final size:37 Alignment explanation

Indices: 52901427--52901509 Score: 141 Period size: 37 Copynumber: 2.2 Consensus size: 37 52901417 AAGTCTTACT 52901427 CGGACATAATCTCCACACGTAGTCATCGGGTCGT-ACC 1 CGGACATAATCTCCACACGTAGTCATCGGGTC-TCACC 52901464 CGGACATAATCTCCACACGTAGTCATCGGGTCTCACC 1 CGGACATAATCTCCACACGTAGTCATCGGGTCTCACC 52901501 CGGAACATA 1 CGG-ACATA 52901510 TTTCCAAGAT Statistics Matches: 44, Mismatches: 0, Indels: 3 0.94 0.00 0.06 Matches are distributed among these distances: 36 1 0.02 37 38 0.86 38 5 0.11 ACGTcount: A:0.27, C:0.33, G:0.20, T:0.20 Consensus pattern (37 bp): CGGACATAATCTCCACACGTAGTCATCGGGTCTCACC Found at i:52901604 original size:48 final size:48 Alignment explanation

Indices: 52901549--52901685 Score: 204 Period size: 48 Copynumber: 2.9 Consensus size: 48 52901539 TATTACAACA 52901549 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT 1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT * ** * 52901597 TTCACATTAGCCATTTGGCTTTACCACATATACATATCTTATATATAT 1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT * * * 52901645 TTCACATTAGCCATTCGGCCTTATCACATATATATAT-ACAC 1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACAC 52901686 TTTCACATTC Statistics Matches: 78, Mismatches: 11, Indels: 1 0.87 0.12 0.01 Matches are distributed among these distances: 47 1 0.01 48 77 0.99 ACGTcount: A:0.32, C:0.25, G:0.07, T:0.36 Consensus pattern (48 bp): TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT Found at i:52901709 original size:51 final size:51 Alignment explanation

Indices: 52901654--52901978 Score: 613 Period size: 51 Copynumber: 6.5 Consensus size: 51 52901644 TTTCACATTA * 52901654 GCCATTCGGCCTTATCACATATATATATACACTTTCACATTCATCACATCG 1 GCCATTAGGCCTTATCACATATATATATACACTTTCACATTCATCACATCG 52901705 GCCATTAGGCCTTATCACATATATATATACACTTTCACATTCATCACATCG 1 GCCATTAGGCCTTATCACATATATATATACACTTTCACATTCATCACATCG 52901756 GCCATTAGGCCTTATCAC--ATATATATACACTTTCACATTCATCACATCG 1 GCCATTAGGCCTTATCACATATATATATACACTTTCACATTCATCACATCG 52901805 GCCATTAGGCCTTATCACATATATATATACACTTTCACATTCATCACATCG 1 GCCATTAGGCCTTATCACATATATATATACACTTTCACATTCATCACATCG 52901856 GCCATTAGGCCTTATCAC--ATATATATACACTTTCACATTCATCACATCG 1 GCCATTAGGCCTTATCACATATATATATACACTTTCACATTCATCACATCG 52901905 GCCATTAGGCCTTATCACATATATATATACACTTTCACATTCATCACATCG 1 GCCATTAGGCCTTATCACATATATATATACACTTTCACATTCATCACATCG 52901956 GCCATTAGGCCTTATCACATATA 1 GCCATTAGGCCTTATCACATATA 52901979 CCATTATGTA Statistics Matches: 269, Mismatches: 1, Indels: 8 0.97 0.00 0.03 Matches are distributed among these distances: 49 98 0.36 51 171 0.64 ACGTcount: A:0.31, C:0.28, G:0.08, T:0.33 Consensus pattern (51 bp): GCCATTAGGCCTTATCACATATATATATACACTTTCACATTCATCACATCG Found at i:52901805 original size:100 final size:100 Alignment explanation

Indices: 52901654--52901978 Score: 623 Period size: 100 Copynumber: 3.2 Consensus size: 100 52901644 TTTCACATTA * 52901654 GCCATTCGGCCTTATCACATATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA 1 GCCATTAGGCCTTATCAC--ATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA 52901719 TCACATATATATATACACTTTCACATTCATCACATCG 64 TCACATATATATATACACTTTCACATTCATCACATCG 52901756 GCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATC 1 GCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATC 52901821 ACATATATATATACACTTTCACATTCATCACATCG 66 ACATATATATATACACTTTCACATTCATCACATCG 52901856 GCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATC 1 GCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATC 52901921 ACATATATATATACACTTTCACATTCATCACATCG 66 ACATATATATATACACTTTCACATTCATCACATCG 52901956 GCCATTAGGCCTTATCACATATA 1 GCCATTAGGCCTTATCACATATA 52901979 CCATTATGTA Statistics Matches: 222, Mismatches: 1, Indels: 2 0.99 0.00 0.01 Matches are distributed among these distances: 100 205 0.92 102 17 0.08 ACGTcount: A:0.31, C:0.28, G:0.08, T:0.33 Consensus pattern (100 bp): GCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATC ACATATATATATACACTTTCACATTCATCACATCG Found at i:52901818 original size:151 final size:150 Alignment explanation

Indices: 52901654--52901978 Score: 607 Period size: 151 Copynumber: 2.2 Consensus size: 150 52901644 TTTCACATTA * 52901654 GCCATTCGGCCTTATCACATATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA 1 GCCATTAGGCCTTATCACATATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA 52901719 TCACATATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC-ATATATATA 66 TCAC--ATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACAATATATATA 52901783 CACTTTCACATTCATCACATCG 129 CACTTTCACATTCATCACATCG 52901805 GCCATTAGGCCTTATCACATATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA 1 GCCATTAGGCCTTATCACATATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA 52901870 TCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATATAC 66 TCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACA-ATATATATAC 52901935 ACTTTCACATTCATCACATCG 130 ACTTTCACATTCATCACATCG 52901956 GCCATTAGGCCTTATCACATATA 1 GCCATTAGGCCTTATCACATATA 52901979 CCATTATGTA Statistics Matches: 171, Mismatches: 1, Indels: 4 0.97 0.01 0.02 Matches are distributed among these distances: 149 49 0.29 151 122 0.71 ACGTcount: A:0.31, C:0.28, G:0.08, T:0.33 Consensus pattern (150 bp): GCCATTAGGCCTTATCACATATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA TCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACAATATATATACA CTTTCACATTCATCACATCG Found at i:52906476 original size:46 final size:46 Alignment explanation

Indices: 52906425--52906564 Score: 253 Period size: 46 Copynumber: 3.0 Consensus size: 46 52906415 AGTTAAATAT * 52906425 ATATATGTGTGGTAAAGCCAAATGGCTAGTGTGAAATATGTATGTG 1 ATATATGTGTGGTAAAGCCAAATGGCTAGTGTGAAATATGTATGAG 52906471 ATATATGTGTGGTAAAGCCAAATGGCTAGTGTGAAATATGTATGAG 1 ATATATGTGTGGTAAAGCCAAATGGCTAGTGTGAAATATGTATGAG * * 52906517 ATATATGTGTGGTAAAGCCAAATGGCTAGTATGAAACATGTATGAG 1 ATATATGTGTGGTAAAGCCAAATGGCTAGTGTGAAATATGTATGAG 52906563 AT 1 AT 52906565 GTATATATGT Statistics Matches: 91, Mismatches: 3, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 46 91 1.00 ACGTcount: A:0.35, C:0.07, G:0.27, T:0.31 Consensus pattern (46 bp): ATATATGTGTGGTAAAGCCAAATGGCTAGTGTGAAATATGTATGAG Found at i:52906476 original size:48 final size:48 Alignment explanation

Indices: 52906423--52906590 Score: 227 Period size: 46 Copynumber: 3.6 Consensus size: 48 52906413 CAAGTTAAAT 52906423 ATATATATGTGTGGTAAAGCCAAATGGCTAGTGTGAAATATGTATGTG 1 ATATATATGTGTGGTAAAGCCAAATGGCTAGTGTGAAATATGTATGTG 52906471 --ATATATGTGTGGTAAAGCCAAATGGCTAGTGTGAAATATGTA--TG 1 ATATATATGTGTGGTAAAGCCAAATGGCTAGTGTGAAATATGTATGTG * * * * 52906515 AGATATATGTGTGGTAAAGCCAAATGGCTAGTATGAAACATGTATGAG 1 ATATATATGTGTGGTAAAGCCAAATGGCTAGTGTGAAATATGTATGTG * * * * * 52906563 ATGTATATATGTGATAAGGCCGAATGGC 1 ATATATATGTGTGGTAAAGCCAAATGGC 52906591 CGATGTGATG Statistics Matches: 107, Mismatches: 9, Indels: 8 0.86 0.07 0.06 Matches are distributed among these distances: 44 2 0.02 46 82 0.77 48 23 0.21 ACGTcount: A:0.35, C:0.08, G:0.27, T:0.30 Consensus pattern (48 bp): ATATATATGTGTGGTAAAGCCAAATGGCTAGTGTGAAATATGTATGTG Found at i:52906618 original size:47 final size:47 Alignment explanation

Indices: 52906564--52906674 Score: 168 Period size: 47 Copynumber: 2.4 Consensus size: 47 52906554 ATGTATGAGA * * * 52906564 TGTATATATGTGATAAGGCCGAATGGCCGATGTGATGAATGTCAAAG 1 TGTATATATGTGATAAGGCCGAATGGCCAATGCGATGAATATCAAAG * * 52906611 TGTATATAAGTGATAAGGCCGAATGGCCAATGCGATGAATATGAAAG 1 TGTATATATGTGATAAGGCCGAATGGCCAATGCGATGAATATCAAAG * 52906658 TGTATAAATGTGATAAG 1 TGTATATATGTGATAAG 52906675 TCCCGAGGGG Statistics Matches: 57, Mismatches: 7, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 47 57 1.00 ACGTcount: A:0.36, C:0.09, G:0.28, T:0.27 Consensus pattern (47 bp): TGTATATATGTGATAAGGCCGAATGGCCAATGCGATGAATATCAAAG Found at i:52909290 original size:40 final size:40 Alignment explanation

Indices: 52909232--52909495 Score: 438 Period size: 40 Copynumber: 6.6 Consensus size: 40 52909222 CTCGACGATG * 52909232 ATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATAT 1 ATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATAT 52909272 ATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATAT 1 ATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATAT 52909312 ATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATAT 1 ATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATAT * ** 52909352 ATCCGGGCTAAGTTCCGAAGAGCATTCATGCTAGTGACGT 1 ATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATAT * * 52909392 ATCCGGACTAAGTTCCGAAGAGCATTCGTGCTAGTGATGT 1 ATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATAT * * 52909432 ATCCGGACTAAGTTCCGAAGAGCATTCGTGCTAGTGATGT 1 ATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATAT * * 52909472 ATCCGGGCTAGGTCCCGAAGAGCA 1 ATCCGGGCTAAGTTCCGAAGAGCA 52909496 ATCATGCTGG Statistics Matches: 214, Mismatches: 10, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 40 214 1.00 ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25 Consensus pattern (40 bp): ATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATAT Found at i:52910223 original size:40 final size:40 Alignment explanation

Indices: 52910159--52910294 Score: 116 Period size: 40 Copynumber: 3.4 Consensus size: 40 52910149 AATGGTATCT * ** * 52910159 GGGCTAAGTCCCGAAGGCTTTTGTGCGAGTTACTAAATCC 1 GGGCTAATTCCCGAAGGCAATTGTGCGAGTCACTAAATCC * * 52910199 GGGCTAATTCCCGAAGGCAATTGTGTGAATCACTATAA-CC 1 GGGCTAATTCCCGAAGGCAATTGTGCGAGTCACTA-AATCC * * * * * 52910239 GGGCT-ATGTCCCGAAGACAATCGAGCGAGTCGCTATATCC 1 GGGCTAAT-TCCCGAAGGCAATTGTGCGAGTCACTAAATCC * * 52910279 -GGTTAAATCCCGAAGG 1 GGGCTAATTCCCGAAGG 52910295 TACGTGATTC Statistics Matches: 76, Mismatches: 16, Indels: 9 0.75 0.16 0.09 Matches are distributed among these distances: 39 14 0.18 40 60 0.79 41 2 0.03 ACGTcount: A:0.26, C:0.24, G:0.26, T:0.24 Consensus pattern (40 bp): GGGCTAATTCCCGAAGGCAATTGTGCGAGTCACTAAATCC Found at i:52913011 original size:46 final size:46 Alignment explanation

Indices: 52912960--52913141 Score: 337 Period size: 46 Copynumber: 4.0 Consensus size: 46 52912950 AGTTAAATAT 52912960 ATATATGTGTGGTAAAGCCAAATGGCTAGTGTGAAATATGTATGTG 1 ATATATGTGTGGTAAAGCCAAATGGCTAGTGTGAAATATGTATGTG 52913006 ATATATGTGTGGTAAAGCCAAATGGCTAGTGTGAAATATGTATGTG 1 ATATATGTGTGGTAAAGCCAAATGGCTAGTGTGAAATATGTATGTG * 52913052 ATATATGTGTGGTAAAGCCAAATGGCTAGTGTGAAATATGTATGAG 1 ATATATGTGTGGTAAAGCCAAATGGCTAGTGTGAAATATGTATGTG * * 52913098 ATATATGTGTGGTAAAGCCAAATGGCTAGTATGAAACATGTATG 1 ATATATGTGTGGTAAAGCCAAATGGCTAGTGTGAAATATGTATG 52913142 AGATGTATAT Statistics Matches: 133, Mismatches: 3, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 46 133 1.00 ACGTcount: A:0.34, C:0.07, G:0.27, T:0.31 Consensus pattern (46 bp): ATATATGTGTGGTAAAGCCAAATGGCTAGTGTGAAATATGTATGTG Found at i:52913199 original size:47 final size:47 Alignment explanation

Indices: 52913145--52913255 Score: 168 Period size: 47 Copynumber: 2.4 Consensus size: 47 52913135 ATGTATGAGA * * * 52913145 TGTATATATGTGATAAGGCCGAATGGCCGATGTGATGAATGTCAAAG 1 TGTATATATGTGATAAGGCCGAATGGCCAATGCGATGAATATCAAAG * * 52913192 TGTATATAAGTGATAAGGCCGAATGGCCAATGCGATGAATATGAAAG 1 TGTATATATGTGATAAGGCCGAATGGCCAATGCGATGAATATCAAAG * 52913239 TGTATAAATGTGATAAG 1 TGTATATATGTGATAAG 52913256 TCCCGAGGGG Statistics Matches: 57, Mismatches: 7, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 47 57 1.00 ACGTcount: A:0.36, C:0.09, G:0.28, T:0.27 Consensus pattern (47 bp): TGTATATATGTGATAAGGCCGAATGGCCAATGCGATGAATATCAAAG Found at i:52915873 original size:40 final size:40 Alignment explanation

Indices: 52915815--52916078 Score: 438 Period size: 40 Copynumber: 6.6 Consensus size: 40 52915805 CTCGACGATG * 52915815 ATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATAT 1 ATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATAT 52915855 ATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATAT 1 ATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATAT 52915895 ATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATAT 1 ATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATAT * ** 52915935 ATCCGGGCTAAGTTCCGAAGAGCATTCATGCTAGTGACGT 1 ATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATAT * * 52915975 ATCCGGACTAAGTTCCGAAGAGCATTCGTGCTAGTGATGT 1 ATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATAT * * 52916015 ATCCGGACTAAGTTCCGAAGAGCATTCGTGCTAGTGATGT 1 ATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATAT * * 52916055 ATCCGGGCTAGGTCCCGAAGAGCA 1 ATCCGGGCTAAGTTCCGAAGAGCA 52916079 ATCATGCTGG Statistics Matches: 214, Mismatches: 10, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 40 214 1.00 ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25 Consensus pattern (40 bp): ATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATAT Found at i:52916834 original size:40 final size:41 Alignment explanation

Indices: 52916738--52916841 Score: 110 Period size: 40 Copynumber: 2.6 Consensus size: 41 52916728 TTCGAATGGT * * * * 52916738 ATCCGGGCTAAGTCCCGAAGGC--TTTTGTGCAGTTACTAA 1 ATCCGGGCTATGTCCCGAAGGCAATTGTGTGCAATCACTAA 52916777 ATCCGGGCTAAT-TCCCGAAGGCAATTGTGTG-AATCACTATA 1 ATCCGGGCT-ATGTCCCGAAGGCAATTGTGTGCAATCACTA-A * 52916818 A-CCGGGCTATGTCCCGAAGACAAT 1 ATCCGGGCTATGTCCCGAAGGCAAT 52916842 CGAGCGAGTC Statistics Matches: 55, Mismatches: 5, Indels: 9 0.80 0.07 0.13 Matches are distributed among these distances: 39 21 0.38 40 26 0.47 41 8 0.15 ACGTcount: A:0.27, C:0.24, G:0.24, T:0.25 Consensus pattern (41 bp): ATCCGGGCTATGTCCCGAAGGCAATTGTGTGCAATCACTAA Found at i:52919594 original size:46 final size:46 Alignment explanation

Indices: 52919543--52919706 Score: 319 Period size: 46 Copynumber: 3.6 Consensus size: 46 52919533 AGTTAAATAT 52919543 ATATATGTGTGGTAAAGCCAAATGGCTAGTGTGAAATATGTATGTG 1 ATATATGTGTGGTAAAGCCAAATGGCTAGTGTGAAATATGTATGTG 52919589 ATATATGTGTGGTAAAGCCAAATGGCTAGTGTGAAATATGTATGTG 1 ATATATGTGTGGTAAAGCCAAATGGCTAGTGTGAAATATGTATGTG * 52919635 ATATATGTGTGGTAAAGCCAAATGGCTAGTGTGAAATATGTATGAG 1 ATATATGTGTGGTAAAGCCAAATGGCTAGTGTGAAATATGTATGTG 52919681 ATATATGTGTGGTAAAGCCAAATGGC 1 ATATATGTGTGGTAAAGCCAAATGGC 52919707 CGTAAGATGG Statistics Matches: 117, Mismatches: 1, Indels: 0 0.99 0.01 0.00 Matches are distributed among these distances: 46 117 1.00 ACGTcount: A:0.34, C:0.07, G:0.28, T:0.31 Consensus pattern (46 bp): ATATATGTGTGGTAAAGCCAAATGGCTAGTGTGAAATATGTATGTG Found at i:52922260 original size:53 final size:53 Alignment explanation

Indices: 52922197--52922303 Score: 189 Period size: 53 Copynumber: 2.0 Consensus size: 53 52922187 TCGACGAATG 52922197 TACATAGATACGAAGGC-GACTAATCCAATAATTTTCCTTTGTCCCGATCTAAC 1 TACATAGATACGAAGGCGGACTAATCCAATAATTTTCCTTTGT-CCGATCTAAC * 52922250 TACATAGATACGAAGGCGGACTAATCCAATAATTTTTCTTTGTCCGATCTAAC 1 TACATAGATACGAAGGCGGACTAATCCAATAATTTTCCTTTGTCCGATCTAAC 52922303 T 1 T 52922304 TCGTATGAGG Statistics Matches: 52, Mismatches: 1, Indels: 2 0.95 0.02 0.04 Matches are distributed among these distances: 53 28 0.54 54 24 0.46 ACGTcount: A:0.32, C:0.22, G:0.14, T:0.32 Consensus pattern (53 bp): TACATAGATACGAAGGCGGACTAATCCAATAATTTTCCTTTGTCCGATCTAAC Found at i:52929487 original size:40 final size:39 Alignment explanation

Indices: 52929442--52929649 Score: 202 Period size: 40 Copynumber: 5.2 Consensus size: 39 52929432 CGGAATACAA * 52929442 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGC 1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC * * * 52929482 CCGGATAGAACGACTTGCACAAATGCCTTCGGGTATTAGC 1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC * * * 52929522 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGC 1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC * *** * 52929562 CCGGATGTGGTCACTAGCAC-AATGGCCTTCGGGTCTTAAC 1 CCGGATATAACCACT-GCACAAAT-GCCTTCGGGTCTTAGC ** * * * 52929602 CCGGATATAATTACTAGCATAAATGTCTTCGGGACTTAGC 1 CCGGATATAACCACT-GCACAAATGCCTTCGGGTCTTAGC 52929642 CCGGATAT 1 CCGGATAT 52929650 CATTCAATTG Statistics Matches: 141, Mismatches: 24, Indels: 6 0.82 0.14 0.04 Matches are distributed among these distances: 39 4 0.03 40 134 0.95 41 3 0.02 ACGTcount: A:0.25, C:0.26, G:0.24, T:0.25 Consensus pattern (39 bp): CCGGATATAACCACTGCACAAATGCCTTCGGGTCTTAGC Found at i:52929582 original size:80 final size:80 Alignment explanation

Indices: 52929442--52929648 Score: 238 Period size: 80 Copynumber: 2.6 Consensus size: 80 52929432 CGGAATACAA * * * 52929442 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGCCCGGATAGAACGACTTGCACAAAT- 1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATAGAACGACTAGCAC-AATG * 52929506 GCCTTCGGGTATTAGC 65 GCCTTCGGGTATTAAC * * ** 52929522 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATGTGGTC-ACTAGCACAATG 1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGAT-AGAACGACTAGCACAATG * 52929586 GCCTTCGGGTCTTAAC 65 GCCTTCGGGTATTAAC ** * ** * * 52929602 CCGGATATAATTACTAGCATAAATGTCTTCGGGACTTAGCCCGGATA 1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATA 52929649 TCATTCAATT Statistics Matches: 107, Mismatches: 18, Indels: 5 0.82 0.14 0.04 Matches are distributed among these distances: 79 3 0.03 80 102 0.95 81 2 0.02 ACGTcount: A:0.25, C:0.26, G:0.24, T:0.25 Consensus pattern (80 bp): CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATAGAACGACTAGCACAATGG CCTTCGGGTATTAAC Found at i:52932440 original size:28 final size:28 Alignment explanation

Indices: 52932386--52932523 Score: 111 Period size: 28 Copynumber: 4.9 Consensus size: 28 52932376 TTCTCAAATT * * * 52932386 TCGCACACTCAGTGCCTTCAC-GAATGTA 1 TCGCACACTAAGTGCCATC-CTGGATGTA * * 52932414 TCGCGCACTAAGTGCCATCCTGGATGTC 1 TCGCACACTAAGTGCCATCCTGGATGTA * * * 52932442 TCGCACACTAAGTGCCAT-TTGCAAT-AA 1 TCGCACACTAAGTGCCATCCTG-GATGTA * * * 52932469 TTCGCACACTAAGTGCCATTTCTAGATGTT 1 -TCGCACACTAAGTGCCA-TCCTGGATGTA * 52932499 TCGCACACTAAGTGCCATCTTGGAT 1 TCGCACACTAAGTGCCATCCTGGAT 52932524 ATCTCGCGTA Statistics Matches: 86, Mismatches: 18, Indels: 12 0.74 0.16 0.10 Matches are distributed among these distances: 27 3 0.03 28 62 0.72 29 20 0.23 30 1 0.01 ACGTcount: A:0.25, C:0.28, G:0.19, T:0.28 Consensus pattern (28 bp): TCGCACACTAAGTGCCATCCTGGATGTA Found at i:52932456 original size:56 final size:57 Alignment explanation

Indices: 52932386--52932516 Score: 151 Period size: 56 Copynumber: 2.3 Consensus size: 57 52932376 TTCTCAAATT * * * * 52932386 TCGCACACTCAGTGCC-TTCACGAAT-GTATCGCGCACTAAGTGCCA-TCCTGGATGTC 1 TCGCACACTAAGTGCCATTCAC-AATAAT-TCGCACACTAAGTGCCATTCCTAGATGTC ** * * 52932442 TCGCACACTAAGTGCCATTTGCAATAATTCGCACACTAAGTGCCATTTCTAGATGTT 1 TCGCACACTAAGTGCCATTCACAATAATTCGCACACTAAGTGCCATTCCTAGATGTC 52932499 TCGCACACTAAGTGCCAT 1 TCGCACACTAAGTGCCAT 52932517 CTTGGATATC Statistics Matches: 64, Mismatches: 8, Indels: 5 0.83 0.10 0.06 Matches are distributed among these distances: 56 34 0.53 57 30 0.47 ACGTcount: A:0.25, C:0.29, G:0.18, T:0.27 Consensus pattern (57 bp): TCGCACACTAAGTGCCATTCACAATAATTCGCACACTAAGTGCCATTCCTAGATGTC Found at i:52932523 original size:85 final size:84 Alignment explanation

Indices: 52932385--52932546 Score: 211 Period size: 85 Copynumber: 1.9 Consensus size: 84 52932375 ATTCTCAAAT * * * 52932385 TTCGCACACTCAGTGCCTTCACGAATGTATCGCGCACTAAGTGCCATCCTGGATGTCTCGCACAC 1 TTCGCACACTAAGTGCCTTCACGAATGTATCGCACACTAAGTGCCATCCTGGATATCTCGCACAC 52932450 TAAGTGCCATTTGCAATAA 66 TAAGTGCCATTTGCAATAA * * * 52932469 TTCGCACACTAAGTGCCATTTCTA-G-ATGTTTCGCACACTAAGTGCCATCTTGGATATCTCGCG 1 TTCGCACACTAAGTGCC--TTC-ACGAATGTATCGCACACTAAGTGCCATCCTGGATATCTCGCA * * 52932532 TACTAAGTGTCATTT 63 CACTAAGTGCCATTT 52932547 TCACAATCAA Statistics Matches: 67, Mismatches: 8, Indels: 5 0.84 0.10 0.06 Matches are distributed among these distances: 84 16 0.24 85 46 0.69 86 4 0.06 87 1 0.01 ACGTcount: A:0.24, C:0.27, G:0.19, T:0.30 Consensus pattern (84 bp): TTCGCACACTAAGTGCCTTCACGAATGTATCGCACACTAAGTGCCATCCTGGATATCTCGCACAC TAAGTGCCATTTGCAATAA Found at i:52932537 original size:57 final size:57 Alignment explanation

Indices: 52932414--52932546 Score: 164 Period size: 57 Copynumber: 2.4 Consensus size: 57 52932404 CACGAATGTA * * 52932414 TCGCGCACTAAGTGCCA-TCCTGGATGTCTCGCACACTAAGTGCCATTTGCAATAAT 1 TCGCGCACTAAGTGCCATTTCTAGATGTCTCGCACACTAAGTGCCATTTGCAATAAT * * * 52932470 TCGCACACTAAGTGCCATTTCTAGATGTTTCGCACACTAAGTGCCATCTTG-GAT-AT 1 TCGCGCACTAAGTGCCATTTCTAGATGTCTCGCACACTAAGTGCCAT-TTGCAATAAT * * 52932526 CTCGCGTACTAAGTGTCATTT 1 -TCGCGCACTAAGTGCCATTT 52932547 TCACAATCAA Statistics Matches: 66, Mismatches: 8, Indels: 5 0.84 0.10 0.06 Matches are distributed among these distances: 56 18 0.27 57 45 0.68 58 3 0.05 ACGTcount: A:0.24, C:0.26, G:0.19, T:0.31 Consensus pattern (57 bp): TCGCGCACTAAGTGCCATTTCTAGATGTCTCGCACACTAAGTGCCATTTGCAATAAT Found at i:52932539 original size:28 final size:28 Alignment explanation

Indices: 52932414--52932540 Score: 123 Period size: 28 Copynumber: 4.5 Consensus size: 28 52932404 CACGAATGTA * * * 52932414 TCGCGCACTAAGTGCCATCCTGGATGTC 1 TCGCACACTAAGTGCCATCTTGGATATC * 52932442 TCGCACACTAAGTGCCAT-TTGCAATAAT- 1 TCGCACACTAAGTGCCATCTTG-GAT-ATC * * * * 52932470 TCGCACACTAAGTGCCATTTCTAGATGTT 1 TCGCACACTAAGTGCCATCT-TGGATATC 52932499 TCGCACACTAAGTGCCATCTTGGATATC 1 TCGCACACTAAGTGCCATCTTGGATATC ** 52932527 TCGCGTACTAAGTG 1 TCGCACACTAAGTG 52932541 TCATTTTCAC Statistics Matches: 81, Mismatches: 13, Indels: 10 0.78 0.12 0.10 Matches are distributed among these distances: 27 2 0.02 28 55 0.68 29 23 0.28 30 1 0.01 ACGTcount: A:0.24, C:0.27, G:0.20, T:0.29 Consensus pattern (28 bp): TCGCACACTAAGTGCCATCTTGGATATC Found at i:52939976 original size:28 final size:28 Alignment explanation

Indices: 52939945--52940012 Score: 84 Period size: 29 Copynumber: 2.4 Consensus size: 28 52939935 GTCTCACACG 52939945 CTAAGTGCCATTT-GCAATAATTCGCACA 1 CTAAGTGCCATTTCG-AATAATTCGCACA * ** 52939973 CTAAGTGCCATTTCTGGATGTTTCGCACA 1 CTAAGTGCCATTTC-GAATAATTCGCACA 52940002 CTAAGTGCCAT 1 CTAAGTGCCAT 52940013 CTTGGATATC Statistics Matches: 35, Mismatches: 3, Indels: 3 0.85 0.07 0.07 Matches are distributed among these distances: 28 13 0.37 29 21 0.60 30 1 0.03 ACGTcount: A:0.26, C:0.25, G:0.18, T:0.31 Consensus pattern (28 bp): CTAAGTGCCATTTCGAATAATTCGCACA Found at i:52940031 original size:28 final size:29 Alignment explanation

Indices: 52939919--52940036 Score: 104 Period size: 28 Copynumber: 4.2 Consensus size: 29 52939909 ATCGTGCACA * * * 52939919 AAGTGCCATC-CTGGATGTCTCACACGCT 1 AAGTGCCATCTCTGGATATCTCGCACACT * 52939947 AAGTGCCAT-T-TGCAATAAT-TCGCACACT 1 AAGTGCCATCTCTG-GAT-ATCTCGCACACT * * * 52939975 AAGTGCCATTTCTGGATGTTTCGCACACT 1 AAGTGCCATCTCTGGATATCTCGCACACT 52940004 AAGTGCCATCT-TGGATATCTCG-AGCACT 1 AAGTGCCATCTCTGGATATCTCGCA-CACT 52940032 AAGTG 1 AAGTG 52940037 TCGTTTTCAC Statistics Matches: 74, Mismatches: 9, Indels: 14 0.76 0.09 0.14 Matches are distributed among these distances: 27 3 0.04 28 46 0.62 29 23 0.31 30 2 0.03 ACGTcount: A:0.25, C:0.25, G:0.20, T:0.29 Consensus pattern (29 bp): AAGTGCCATCTCTGGATATCTCGCACACT Found at i:52940032 original size:57 final size:57 Alignment explanation

Indices: 52939914--52940036 Score: 137 Period size: 57 Copynumber: 2.2 Consensus size: 57 52939904 GATGTATCGT * * 52939914 GCACAAAGTGCCATCCTGGATGTCTCACACGCTAAGTGCCATTTGCAATAATTCGCA 1 GCACTAAGTGCCATCCTGGATGTCTCACACACTAAGTGCCATTTGCAATAATTCGCA * * * * 52939971 -CACTAAGTGCCATTTCTGGATGTTTCGCACACTAAGTGCCATCTTG-GAT-ATCTCG-A 1 GCACTAAGTGCCA-TCCTGGATGTCTCACACACTAAGTGCCAT-TTGCAATAAT-TCGCA 52940027 GCACTAAGTG 1 GCACTAAGTG 52940037 TCGTTTTCAC Statistics Matches: 56, Mismatches: 6, Indels: 8 0.80 0.09 0.11 Matches are distributed among these distances: 56 14 0.25 57 39 0.70 58 3 0.05 ACGTcount: A:0.26, C:0.26, G:0.20, T:0.28 Consensus pattern (57 bp): GCACTAAGTGCCATCCTGGATGTCTCACACACTAAGTGCCATTTGCAATAATTCGCA Found at i:52942556 original size:48 final size:45 Alignment explanation

Indices: 52942500--52942623 Score: 128 Period size: 46 Copynumber: 2.7 Consensus size: 45 52942490 TTATGAGAAC * 52942500 CAGTGTAAGACCATGTCTAGGACATGGCATCAACGT-TGAGATGTAAGT 1 CAGTGTAAGACCATGTCT-GGACATGGCATCAAC-TATGAAATGT--GT ** 52942548 CAGTGTAAGA-CATGTCTGAGACAT-GCATCGGCTATGAAATGTGT 1 CAGTGTAAGACCATGTCTG-GACATGGCATCAACTATGAAATGTGT ** 52942592 CAGTGTAAGACCATAACTGGGACATGGCATCA 1 CAGTGTAAGACCATGTCT-GGACATGGCATCA 52942624 GCACTTTACC Statistics Matches: 65, Mismatches: 6, Indels: 12 0.78 0.07 0.14 Matches are distributed among these distances: 44 12 0.18 45 11 0.17 46 20 0.31 47 12 0.18 48 10 0.15 ACGTcount: A:0.31, C:0.18, G:0.27, T:0.24 Consensus pattern (45 bp): CAGTGTAAGACCATGTCTGGACATGGCATCAACTATGAAATGTGT Found at i:52946709 original size:13 final size:13 Alignment explanation

Indices: 52946691--52946724 Score: 68 Period size: 13 Copynumber: 2.6 Consensus size: 13 52946681 CACGCGGGCT 52946691 TGTGACTTGGCCA 1 TGTGACTTGGCCA 52946704 TGTGACTTGGCCA 1 TGTGACTTGGCCA 52946717 TGTGACTT 1 TGTGACTT 52946725 TAATTTATTG Statistics Matches: 21, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 21 1.00 ACGTcount: A:0.15, C:0.21, G:0.29, T:0.35 Consensus pattern (13 bp): TGTGACTTGGCCA Found at i:52950737 original size:3 final size:3 Alignment explanation

Indices: 52950729--52950774 Score: 92 Period size: 3 Copynumber: 15.3 Consensus size: 3 52950719 TATTGAAGAA 52950729 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T 1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T 52950775 TTATGCTTTA Statistics Matches: 43, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 3 43 1.00 ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67 Consensus pattern (3 bp): TCT Found at i:52950848 original size:30 final size:28 Alignment explanation

Indices: 52950792--52950857 Score: 87 Period size: 28 Copynumber: 2.3 Consensus size: 28 52950782 TTATTTAATC * 52950792 TGTTTATTTCTAGGCTTTGCAAAGTTTA 1 TGTTTGTTTCTAGGCTTTGCAAAGTTTA * 52950820 TGTTTGTTTCTAGGTTTTGCATAAAGTTTA 1 TGTTTGTTTCTAGGCTTTGC--AAAGTTTA * 52950850 TGCTTGTT 1 TGTTTGTT 52950858 GTTCGTTAGA Statistics Matches: 33, Mismatches: 3, Indels: 2 0.87 0.08 0.05 Matches are distributed among these distances: 28 18 0.55 30 15 0.45 ACGTcount: A:0.18, C:0.09, G:0.20, T:0.53 Consensus pattern (28 bp): TGTTTGTTTCTAGGCTTTGCAAAGTTTA Found at i:52952872 original size:52 final size:52 Alignment explanation

Indices: 52952794--52952897 Score: 199 Period size: 52 Copynumber: 2.0 Consensus size: 52 52952784 GGGCAAAATG 52952794 GTCATTTTACTAAAGATGTGGATTTATGATTGAATAATTGTAATTAGTGACT 1 GTCATTTTACTAAAGATGTGGATTTATGATTGAATAATTGTAATTAGTGACT * 52952846 GTCATTTTGCTAAAGATGTGGATTTATGATTGAATAATTGTAATTAGTGACT 1 GTCATTTTACTAAAGATGTGGATTTATGATTGAATAATTGTAATTAGTGACT 52952898 AAATGAGTAC Statistics Matches: 51, Mismatches: 1, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 52 51 1.00 ACGTcount: A:0.32, C:0.06, G:0.20, T:0.42 Consensus pattern (52 bp): GTCATTTTACTAAAGATGTGGATTTATGATTGAATAATTGTAATTAGTGACT Found at i:52953309 original size:47 final size:46 Alignment explanation

Indices: 52953200--52953464 Score: 209 Period size: 47 Copynumber: 5.7 Consensus size: 46 52953190 TACTTGTGCC * * ** 52953200 CCAGTGTAAGACATGTCTGGGACATGCATCGGCGTAGAGATGAGTG 1 CCAGTATAAGACATGTCTGGGACATGCATCAGCACAGAGATGAGTG * * 52953246 CTAGTATAAGACCATGTCTAGGACATGGCATCAGCACAGAGATGAGTG 1 CCAGTATAAGA-CATGTCTGGGACAT-GCATCAGCACAGAGATGAGTG * * 52953294 CCAGTATAAGACATGTCTGGGACATGCATCGGC-CTCGATGATGA-TAG 1 CCAGTATAAGACATGTCTGGGACATGCATCAGCAC-AGA-GATGAGT-G * * * * * * 52953341 CCAGTGTAAGACGTGTCTAGGATACGCATCAGCTA-AGAG-T-TGTG 1 CCAGTATAAGACATGTCTGGGACATGCATCAGC-ACAGAGATGAGTG * * * * * 52953385 CTAGTGTAAGACATGTTTGGGACATGCATCAGCAC-GTGTATACGAGAG 1 CCAGTATAAGACATGTCTGGGACATGCATCAGCACAGAG-AT--GAGTG * 52953433 CTAGTATAAGACCATGTCTGGGACATGGCATC 1 CCAGTATAAGA-CATGTCTGGGACAT-GCATC 52953465 GGCCTCGATG Statistics Matches: 174, Mismatches: 29, Indels: 28 0.75 0.13 0.12 Matches are distributed among these distances: 43 3 0.02 44 28 0.16 45 4 0.02 46 20 0.11 47 61 0.35 48 40 0.23 49 13 0.07 50 5 0.03 ACGTcount: A:0.29, C:0.19, G:0.29, T:0.23 Consensus pattern (46 bp): CCAGTATAAGACATGTCTGGGACATGCATCAGCACAGAGATGAGTG Found at i:52953361 original size:94 final size:91 Alignment explanation

Indices: 52953200--52953414 Score: 256 Period size: 94 Copynumber: 2.3 Consensus size: 91 52953190 TACTTGTGCC * * 52953200 CCAGTGTAAGACATGTCTGGGACATGCATCGGCGTAGAGATGAGTGCTAGTATAAGACCATGTCT 1 CCAGTGTAAGACATGTCTGGGACATGCATCGGCCTAGAGATGAGTGCCAGTATAAGACCATGTCT * 52953265 AGGACATGGCATCAGC-ACAGAGATGAGTG 66 AGGACA-CGCATCAGCTA-AGAG-T-AGTG * * * * 52953294 CCAGTATAAGACATGTCTGGGACATGCATCGGCCTCGATGATGA-TAGCCAGTGTAAGA-CGTGT 1 CCAGTGTAAGACATGTCTGGGACATGCATCGGCCTAGA-GATGAGT-GCCAGTATAAGACCATGT * * 52953357 CTAGGATACGCATCAGCTAAGAGTTGTG 64 CTAGGACACGCATCAGCTAAGAGTAGTG * * 52953385 CTAGTGTAAGACATGTTTGGGACATGCATC 1 CCAGTGTAAGACATGTCTGGGACATGCATC 52953415 AGCACGTGTA Statistics Matches: 106, Mismatches: 12, Indels: 9 0.83 0.09 0.07 Matches are distributed among these distances: 91 30 0.28 92 1 0.01 93 12 0.11 94 48 0.45 95 15 0.14 ACGTcount: A:0.28, C:0.19, G:0.29, T:0.24 Consensus pattern (91 bp): CCAGTGTAAGACATGTCTGGGACATGCATCGGCCTAGAGATGAGTGCCAGTATAAGACCATGTCT AGGACACGCATCAGCTAAGAGTAGTG Found at i:52953820 original size:11 final size:11 Alignment explanation

Indices: 52953804--52953838 Score: 61 Period size: 11 Copynumber: 3.2 Consensus size: 11 52953794 TTATGCTTAC 52953804 TCTCTTTCCTT 1 TCTCTTTCCTT 52953815 TCTCTTTCCTT 1 TCTCTTTCCTT * 52953826 TCTCTTTTCTT 1 TCTCTTTCCTT 52953837 TC 1 TC 52953839 AGTGCTGCTT Statistics Matches: 23, Mismatches: 1, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 11 23 1.00 ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66 Consensus pattern (11 bp): TCTCTTTCCTT Found at i:52954457 original size:19 final size:19 Alignment explanation

Indices: 52954413--52954457 Score: 54 Period size: 19 Copynumber: 2.4 Consensus size: 19 52954403 CTAAGGGCAT 52954413 GGGCGTGCCCAAGCCACAC 1 GGGCGTGCCCAAGCCACAC ** * * 52954432 GAACGTGCGCAAGCCATAC 1 GGGCGTGCCCAAGCCACAC 52954451 GGGCGTG 1 GGGCGTG 52954458 TGGAGCCTAA Statistics Matches: 20, Mismatches: 6, Indels: 0 0.77 0.23 0.00 Matches are distributed among these distances: 19 20 1.00 ACGTcount: A:0.22, C:0.33, G:0.36, T:0.09 Consensus pattern (19 bp): GGGCGTGCCCAAGCCACAC Found at i:52957095 original size:28 final size:27 Alignment explanation

Indices: 52957034--52957103 Score: 113 Period size: 27 Copynumber: 2.6 Consensus size: 27 52957024 ATAGTGAGTC * 52957034 CGCACACTCAGTGCTATATAATCAACT 1 CGCACACTTAGTGCTATATAATCAACT * 52957061 CGCACACTTAGTGCTATATGATCCAACT 1 CGCACACTTAGTGCTATATAAT-CAACT 52957089 CGCACACTTAGTGCT 1 CGCACACTTAGTGCT 52957104 GTACAAATTT Statistics Matches: 40, Mismatches: 2, Indels: 1 0.93 0.05 0.02 Matches are distributed among these distances: 27 20 0.50 28 20 0.50 ACGTcount: A:0.29, C:0.30, G:0.14, T:0.27 Consensus pattern (27 bp): CGCACACTTAGTGCTATATAATCAACT Found at i:52964999 original size:28 final size:27 Alignment explanation

Indices: 52964938--52965007 Score: 113 Period size: 27 Copynumber: 2.6 Consensus size: 27 52964928 ATAGTGAGTC * 52964938 CGCACACTCAGTGCTATATAATCAACT 1 CGCACACTTAGTGCTATATAATCAACT * 52964965 CGCACACTTAGTGCTATATGATCCAACT 1 CGCACACTTAGTGCTATATAAT-CAACT 52964993 CGCACACTTAGTGCT 1 CGCACACTTAGTGCT 52965008 GTACAAATTT Statistics Matches: 40, Mismatches: 2, Indels: 1 0.93 0.05 0.02 Matches are distributed among these distances: 27 20 0.50 28 20 0.50 ACGTcount: A:0.29, C:0.30, G:0.14, T:0.27 Consensus pattern (27 bp): CGCACACTTAGTGCTATATAATCAACT Found at i:52967597 original size:32 final size:32 Alignment explanation

Indices: 52967548--52967631 Score: 107 Period size: 32 Copynumber: 2.6 Consensus size: 32 52967538 TTGAAATTTT * 52967548 AGTTTGTTGGATTTTGAAATTATTATGTCTTGA 1 AGTTTGTTGGATATTGAAATTATTATGT-TTGA * * * 52967581 A-TTTGTTAGATATTGAATTTATTATGTTTTA 1 AGTTTGTTGGATATTGAAATTATTATGTTTGA * 52967612 AGCTTGTTGGATATTGAAAT 1 AGTTTGTTGGATATTGAAAT 52967632 GATTGACAAT Statistics Matches: 43, Mismatches: 7, Indels: 3 0.81 0.13 0.06 Matches are distributed among these distances: 31 4 0.09 32 38 0.88 33 1 0.02 ACGTcount: A:0.27, C:0.02, G:0.19, T:0.51 Consensus pattern (32 bp): AGTTTGTTGGATATTGAAATTATTATGTTTGA Found at i:52974424 original size:2 final size:2 Alignment explanation

Indices: 52974417--52974455 Score: 78 Period size: 2 Copynumber: 19.5 Consensus size: 2 52974407 TTTGGAGTAA 52974417 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A 1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A 52974456 GAAATTGTAA Statistics Matches: 37, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 37 1.00 ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49 Consensus pattern (2 bp): AT Found at i:52975800 original size:40 final size:39 Alignment explanation

Indices: 52975756--52975855 Score: 96 Period size: 40 Copynumber: 2.5 Consensus size: 39 52975746 AAAGAATACA * * 52975756 AAAATTTCTAAGGGCATATTCTTA-AATATTTTGATATTTC 1 AAAATTTCTAA-GGCATATACATACAA-ATTTTGATATTTC * * 52975796 AAAATATCTAA-GCATACGTACATACAAATTTTGGTATTTC 1 AAAATTTCTAAGGCATA--TACATACAAATTTTGATATTTC 52975836 AAAATTTCTAAAGAGCATAT 1 AAAATTTCT-AAG-GCATAT 52975856 CACTAGCTAT Statistics Matches: 49, Mismatches: 5, Indels: 11 0.75 0.08 0.17 Matches are distributed among these distances: 38 5 0.10 40 34 0.69 41 5 0.10 43 5 0.10 ACGTcount: A:0.40, C:0.12, G:0.10, T:0.38 Consensus pattern (39 bp): AAAATTTCTAAGGCATATACATACAAATTTTGATATTTC Found at i:52980196 original size:19 final size:20 Alignment explanation

Indices: 52980172--52980216 Score: 56 Period size: 19 Copynumber: 2.3 Consensus size: 20 52980162 CAACTATTTT 52980172 TATGTAAGTATGCAA-TACA 1 TATGTAAGTATGCAAGTACA * * * 52980191 TATGTATGTGTGCAAGTATA 1 TATGTAAGTATGCAAGTACA 52980211 TATGTA 1 TATGTA 52980217 TTTCGTAAAG Statistics Matches: 22, Mismatches: 3, Indels: 1 0.85 0.12 0.04 Matches are distributed among these distances: 19 13 0.59 20 9 0.41 ACGTcount: A:0.36, C:0.07, G:0.20, T:0.38 Consensus pattern (20 bp): TATGTAAGTATGCAAGTACA Found at i:52983834 original size:31 final size:31 Alignment explanation

Indices: 52983798--52983862 Score: 94 Period size: 31 Copynumber: 2.1 Consensus size: 31 52983788 TTCTAACGTG * * 52983798 GCATGCCACATTAGCACCATTTTTCATGTCA 1 GCATGCCACATCAGCACCATTTATCATGTCA * * 52983829 GCATGCTACATCAGCATCATTTATCATGTCA 1 GCATGCCACATCAGCACCATTTATCATGTCA 52983860 GCA 1 GCA 52983863 AAATTAACGA Statistics Matches: 30, Mismatches: 4, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 31 30 1.00 ACGTcount: A:0.28, C:0.28, G:0.14, T:0.31 Consensus pattern (31 bp): GCATGCCACATCAGCACCATTTATCATGTCA Found at i:52984168 original size:17 final size:18 Alignment explanation

Indices: 52984146--52984184 Score: 62 Period size: 17 Copynumber: 2.2 Consensus size: 18 52984136 CACTACAATT * 52984146 TTTTTAAATAAATT-TTA 1 TTTTTAAAAAAATTATTA 52984163 TTTTTAAAAAAATTATTA 1 TTTTTAAAAAAATTATTA 52984181 TTTT 1 TTTT 52984185 ATTAGTAGTG Statistics Matches: 20, Mismatches: 1, Indels: 1 0.91 0.05 0.05 Matches are distributed among these distances: 17 13 0.65 18 7 0.35 ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59 Consensus pattern (18 bp): TTTTTAAAAAAATTATTA Found at i:52984339 original size:23 final size:22 Alignment explanation

Indices: 52984313--52984365 Score: 58 Period size: 20 Copynumber: 2.5 Consensus size: 22 52984303 AAAAAATAGG 52984313 GAAAGAAAGGAGAGGAAGGAGAA 1 GAAAGAAAGGAGA-GAAGGAGAA * * 52984336 GAAATAAA--AGAGAAGTAGAA 1 GAAAGAAAGGAGAGAAGGAGAA 52984356 G-AAGAAAGGA 1 GAAAGAAAGGA 52984366 AAAAAAAAAG Statistics Matches: 25, Mismatches: 3, Indels: 6 0.74 0.09 0.18 Matches are distributed among these distances: 19 5 0.20 20 9 0.36 21 4 0.16 23 7 0.28 ACGTcount: A:0.60, C:0.00, G:0.36, T:0.04 Consensus pattern (22 bp): GAAAGAAAGGAGAGAAGGAGAA Found at i:52984999 original size:48 final size:48 Alignment explanation

Indices: 52984947--52985091 Score: 110 Period size: 48 Copynumber: 3.1 Consensus size: 48 52984937 ATTTTATTAA * 52984947 TAATTTATGATTAGGTTATAAAATGTTAGTGTTTAGTTTAGTATTTTG 1 TAATTTATGATTAGGTTATAAAATGTTAGTATTTAGTTTAGTATTTTG * * * * * 52984995 TAATTT-T--TTATG-AATGTAAAT-TT--TTTTATAG-TTA-TTTTATTAG 1 TAATTTATGATTAGGTTAT-AAAATGTTAGTATT-TAGTTTAGTATT-TT-G * * * 52985038 TAATTTATGATTAGATTATAAATTGTTAGTATTTAGTTTAGTGTTTTG 1 TAATTTATGATTAGGTTATAAAATGTTAGTATTTAGTTTAGTATTTTG 52985086 TAATTT 1 TAATTT 52985092 TTTATGAATG Statistics Matches: 72, Mismatches: 12, Indels: 26 0.65 0.11 0.24 Matches are distributed among these distances: 41 3 0.04 42 8 0.11 43 10 0.14 44 5 0.07 45 8 0.11 46 6 0.08 47 5 0.07 48 16 0.22 49 8 0.11 50 3 0.04 ACGTcount: A:0.30, C:0.00, G:0.14, T:0.56 Consensus pattern (48 bp): TAATTTATGATTAGGTTATAAAATGTTAGTATTTAGTTTAGTATTTTG Found at i:52985002 original size:104 final size:101 Alignment explanation

Indices: 52984816--52985108 Score: 356 Period size: 91 Copynumber: 3.0 Consensus size: 101 52984806 ACTGTCCTTC * * * 52984816 AAAATTATTTTATAGTTATTTTGTTAATAACTTATAATTAGGTTATAAATTGTT-GTGTTTAGTT 1 AAAATTATTTTATAGTTATTTTATTAATAATTTATGATTAGGTTATAAATTGTTAGTGTTTAGTT * * 52984880 TAGTGTTTTGTGATTTTTTATTAATGTAAATTTATTTTTT 66 TAGTGTTTTGT-AATTTTTATTAATGTAAATTTA---TGT * 52984920 AAAATTATTTTATAGTTATTTTATTAATAATTTATGATTAGGTTATAAAATGTTAGTGTTTAGTT 1 AAAATTATTTTATAGTTATTTTATTAATAATTTATGATTAGGTTATAAATTGTTAGTGTTTAGTT * 52984985 TAGTATTTTGTAA-TTTT-TT-ATG---A---ATGT 66 TAGTGTTTTGTAATTTTTATTAATGTAAATTTATGT * * * * 52985012 -AAATTTTTTTATAGTTATTTTATTAGTAATTTATGATTAGATTATAAATTGTTAGTATTTAGTT 1 AAAATTATTTTATAGTTATTTTATTAATAATTTATGATTAGGTTATAAATTGTTAGTGTTTAGTT * 52985076 TAGTGTTTTGTAATTTTTTATGAATGTAAATTT 66 TAGTGTTTTGTAA-TTTTTATTAATGTAAATTT 52985109 TTTATAATGT Statistics Matches: 164, Mismatches: 14, Indels: 25 0.81 0.07 0.12 Matches are distributed among these distances: 91 71 0.43 92 2 0.01 93 4 0.02 94 1 0.01 95 4 0.02 98 2 0.01 101 3 0.02 102 2 0.01 103 4 0.02 104 51 0.31 105 20 0.12 ACGTcount: A:0.31, C:0.00, G:0.13, T:0.56 Consensus pattern (101 bp): AAAATTATTTTATAGTTATTTTATTAATAATTTATGATTAGGTTATAAATTGTTAGTGTTTAGTT TAGTGTTTTGTAATTTTTATTAATGTAAATTTATGT Found at i:52985109 original size:17 final size:16 Alignment explanation

Indices: 52985087--52985124 Score: 67 Period size: 16 Copynumber: 2.3 Consensus size: 16 52985077 AGTGTTTTGT 52985087 AATTTTTTATGAATGTA 1 AATTTTTTAT-AATGTA 52985104 AATTTTTTATAATGTA 1 AATTTTTTATAATGTA 52985120 AATTT 1 AATTT 52985125 ATTTGTTTTT Statistics Matches: 21, Mismatches: 0, Indels: 1 0.95 0.00 0.05 Matches are distributed among these distances: 16 11 0.52 17 10 0.48 ACGTcount: A:0.37, C:0.00, G:0.08, T:0.55 Consensus pattern (16 bp): AATTTTTTATAATGTA Found at i:52985293 original size:19 final size:21 Alignment explanation

Indices: 52985260--52985298 Score: 55 Period size: 19 Copynumber: 2.0 Consensus size: 21 52985250 TCGTATGTTT * 52985260 TTTATATTTAGATATTTTATG 1 TTTATATTTAGATATATTATG 52985281 TTTAT-TTTA-ATATATTAT 1 TTTATATTTAGATATATTAT 52985299 TATTGTAAAC Statistics Matches: 17, Mismatches: 1, Indels: 2 0.85 0.05 0.10 Matches are distributed among these distances: 19 8 0.47 20 4 0.24 21 5 0.29 ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64 Consensus pattern (21 bp): TTTATATTTAGATATATTATG Found at i:52988096 original size:19 final size:19 Alignment explanation

Indices: 52988061--52988103 Score: 61 Period size: 19 Copynumber: 2.3 Consensus size: 19 52988051 TCTTTCTTTC * 52988061 CTTTTTCTTTATTTTATTT 1 CTTTTTCTTTATATTATTT 52988080 CTTTATTCTTT-TATTATTT 1 CTTT-TTCTTTATATTATTT 52988099 CTTTT 1 CTTTT 52988104 ATTATATTAT Statistics Matches: 22, Mismatches: 1, Indels: 3 0.85 0.04 0.12 Matches are distributed among these distances: 18 1 0.05 19 15 0.68 20 6 0.27 ACGTcount: A:0.12, C:0.12, G:0.00, T:0.77 Consensus pattern (19 bp): CTTTTTCTTTATATTATTT Found at i:52988113 original size:8 final size:8 Alignment explanation

Indices: 52988102--52988139 Score: 51 Period size: 8 Copynumber: 4.8 Consensus size: 8 52988092 ATTATTTCTT 52988102 TTATTATA 1 TTATTATA 52988110 TTATTA-A 1 TTATTATA * 52988117 CTATTATA 1 TTATTATA 52988125 TTATTATAA 1 TTATTAT-A 52988134 TTATTA 1 TTATTA 52988140 ATTTCTTAAA Statistics Matches: 26, Mismatches: 2, Indels: 3 0.84 0.06 0.10 Matches are distributed among these distances: 7 6 0.23 8 13 0.50 9 7 0.27 ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58 Consensus pattern (8 bp): TTATTATA Found at i:52994204 original size:22 final size:20 Alignment explanation

Indices: 52994157--52994205 Score: 62 Period size: 22 Copynumber: 2.3 Consensus size: 20 52994147 ATACATTATC * 52994157 CTTCTTTTTTCTTCTCCTTT 1 CTTCTTTTTTCTTCTCCTCT 52994177 CTTTCTTTCTTTCTTCTCCCTCT 1 C-TTCTTT-TTTCTTCT-CCTCT 52994200 CTTCTT 1 CTTCTT 52994206 CATTTTCTTT Statistics Matches: 25, Mismatches: 1, Indels: 4 0.83 0.03 0.13 Matches are distributed among these distances: 20 1 0.04 21 6 0.24 22 13 0.52 23 5 0.20 ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65 Consensus pattern (20 bp): CTTCTTTTTTCTTCTCCTCT Found at i:52996290 original size:15 final size:15 Alignment explanation

Indices: 52996266--52996295 Score: 51 Period size: 15 Copynumber: 2.0 Consensus size: 15 52996256 ACTAACTGAT * 52996266 AAAAAGAACAAAAAA 1 AAAAAAAACAAAAAA 52996281 AAAAAAAACAAAAAA 1 AAAAAAAACAAAAAA 52996296 GATATAAAAG Statistics Matches: 14, Mismatches: 1, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 15 14 1.00 ACGTcount: A:0.90, C:0.07, G:0.03, T:0.00 Consensus pattern (15 bp): AAAAAAAACAAAAAA Found at i:52999179 original size:32 final size:32 Alignment explanation

Indices: 52999143--52999206 Score: 110 Period size: 32 Copynumber: 2.0 Consensus size: 32 52999133 TAGGATACTA 52999143 AATGTATATTTATTATCTGTATATAAGCATGT 1 AATGTATATTTATTATCTGTATATAAGCATGT * * 52999175 AATGTATGTTTGTTATCTGTATATAAGCATGT 1 AATGTATATTTATTATCTGTATATAAGCATGT 52999207 GGAGCATGTC Statistics Matches: 30, Mismatches: 2, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 32 30 1.00 ACGTcount: A:0.31, C:0.06, G:0.16, T:0.47 Consensus pattern (32 bp): AATGTATATTTATTATCTGTATATAAGCATGT Found at i:52999471 original size:13 final size:14 Alignment explanation

Indices: 52999447--52999477 Score: 55 Period size: 13 Copynumber: 2.3 Consensus size: 14 52999437 GGGGTAGGAT 52999447 TCTGTGTATCTGTA 1 TCTGTGTATCTGTA 52999461 TCTGT-TATCTGTA 1 TCTGTGTATCTGTA 52999474 TCTG 1 TCTG 52999478 AATTGGACAA Statistics Matches: 17, Mismatches: 0, Indels: 1 0.94 0.00 0.06 Matches are distributed among these distances: 13 12 0.71 14 5 0.29 ACGTcount: A:0.13, C:0.16, G:0.19, T:0.52 Consensus pattern (14 bp): TCTGTGTATCTGTA Found at i:53002011 original size:22 final size:22 Alignment explanation

Indices: 53001964--53002013 Score: 57 Period size: 22 Copynumber: 2.3 Consensus size: 22 53001954 ACTCATTAGT * * 53001964 TTATAATATAGATTTTTAGGAT 1 TTATAATATAAATTTTTAGGAC * 53001986 TTATAATATAAATTGTTTATG-C 1 TTATAATATAAATT-TTTAGGAC 53002008 TTATAA 1 TTATAA 53002014 CACAATCTTT Statistics Matches: 24, Mismatches: 3, Indels: 2 0.83 0.10 0.07 Matches are distributed among these distances: 22 19 0.79 23 5 0.21 ACGTcount: A:0.38, C:0.02, G:0.10, T:0.50 Consensus pattern (22 bp): TTATAATATAAATTTTTAGGAC Found at i:53007179 original size:18 final size:18 Alignment explanation

Indices: 53007120--53007179 Score: 56 Period size: 18 Copynumber: 3.4 Consensus size: 18 53007110 AAAGGGTGGG 53007120 AAGTAAAAGTTT-AGGGAA 1 AAGTAAAAGTTTGAGGG-A * 53007138 AAATAAAAAGTTTTG-GGG- 1 AAGT-AAAAG-TTTGAGGGA 53007156 -AGTAAAAGTTTGAGGGA 1 AAGTAAAAGTTTGAGGGA 53007173 AAGTAAA 1 AAGTAAA 53007180 TAGGAGGGAG Statistics Matches: 34, Mismatches: 2, Indels: 12 0.71 0.04 0.25 Matches are distributed among these distances: 15 4 0.12 16 8 0.24 17 2 0.06 18 9 0.26 19 5 0.15 20 6 0.18 ACGTcount: A:0.48, C:0.00, G:0.28, T:0.23 Consensus pattern (18 bp): AAGTAAAAGTTTGAGGGA Found at i:53007255 original size:7 final size:7 Alignment explanation

Indices: 53007245--53007277 Score: 66 Period size: 7 Copynumber: 4.7 Consensus size: 7 53007235 TTGGGGTAGA 53007245 TGGGAGG 1 TGGGAGG 53007252 TGGGAGG 1 TGGGAGG 53007259 TGGGAGG 1 TGGGAGG 53007266 TGGGAGG 1 TGGGAGG 53007273 TGGGA 1 TGGGA 53007278 TGGGATGGGA Statistics Matches: 26, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 7 26 1.00 ACGTcount: A:0.15, C:0.00, G:0.70, T:0.15 Consensus pattern (7 bp): TGGGAGG Found at i:53007549 original size:18 final size:18 Alignment explanation

Indices: 53007526--53007562 Score: 56 Period size: 18 Copynumber: 2.1 Consensus size: 18 53007516 TATAGTTTGA * 53007526 TATTCGATTTACTCGAAT 1 TATTCGAGTTACTCGAAT * 53007544 TATTCGAGTTATTCGAAT 1 TATTCGAGTTACTCGAAT 53007562 T 1 T 53007563 TGAAAACTCA Statistics Matches: 17, Mismatches: 2, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 18 17 1.00 ACGTcount: A:0.27, C:0.14, G:0.14, T:0.46 Consensus pattern (18 bp): TATTCGAGTTACTCGAAT Found at i:53011956 original size:17 final size:17 Alignment explanation

Indices: 53011934--53011966 Score: 66 Period size: 17 Copynumber: 1.9 Consensus size: 17 53011924 CCTCATAAGG 53011934 TTAGTAATTATAACATA 1 TTAGTAATTATAACATA 53011951 TTAGTAATTATAACAT 1 TTAGTAATTATAACAT 53011967 TACATGTAAG Statistics Matches: 16, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 17 16 1.00 ACGTcount: A:0.45, C:0.06, G:0.06, T:0.42 Consensus pattern (17 bp): TTAGTAATTATAACATA Found at i:53034702 original size:145 final size:145 Alignment explanation

Indices: 53034444--53034722 Score: 441 Period size: 145 Copynumber: 1.9 Consensus size: 145 53034434 GAACAAAACG * 53034444 TATTTCACCAAAATTATTCTTTACAAATGATCTTGAGAAAAGAGGTGATATAAATGTTCAACAAA 1 TATTTCACCAAAATTATTCTTCACAAATGATCTTGAGAAAAGAGGTGATATAAATGTTCAACAAA * * * 53034509 TTTGTTCTAGTAAGAATTTAATAGATCTTTTTATTAAGGCATTACCAACTCCAACATTTGAAAGA 66 TTCGTTCTAGTAAGAATTTAACAGATCTTTTTACTAAGGCATTACCAACTCCAACATTTGAAAGA 53034574 CTACAGAACGAAATA 131 CTACAGAACGAAATA ** * * 53034589 TATTTCACCAAAATTATTCTTCACCTATGATCTTGAGAAAAGATGTGCTATAAATGTTCAACAAA 1 TATTTCACCAAAATTATTCTTCACAAATGATCTTGAGAAAAGAGGTGATATAAATGTTCAACAAA * * * * * 53034654 TTCGTTCTAGTGAGAATTTAGCAGATCTTTTTACTAAGGTATTGCCAACTTCAACATTTGAAAGA 66 TTCGTTCTAGTAAGAATTTAACAGATCTTTTTACTAAGGCATTACCAACTCCAACATTTGAAAGA 53034719 CTAC 131 CTAC 53034723 TACACAAGAT Statistics Matches: 121, Mismatches: 13, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 145 121 1.00 ACGTcount: A:0.38, C:0.15, G:0.13, T:0.34 Consensus pattern (145 bp): TATTTCACCAAAATTATTCTTCACAAATGATCTTGAGAAAAGAGGTGATATAAATGTTCAACAAA TTCGTTCTAGTAAGAATTTAACAGATCTTTTTACTAAGGCATTACCAACTCCAACATTTGAAAGA CTACAGAACGAAATA Found at i:53044958 original size:31 final size:31 Alignment explanation

Indices: 53044894--53044968 Score: 93 Period size: 31 Copynumber: 2.5 Consensus size: 31 53044884 AAATGACGTT * * 53044894 AAAGTTCAAATA-T-TAAAATTGATTTTTTA 1 AAAGTTCAAATACTATAAAAATGATTTTGTA * 53044923 AAAGTTCAAATACTATAAAAGATGA-TTTGTC 1 AAAGTTCAAATACTATAAAA-ATGATTTTGTA 53044954 AAAGTTCAAATACTA 1 AAAGTTCAAATACTA 53044969 AATATGACAT Statistics Matches: 40, Mismatches: 3, Indels: 4 0.85 0.06 0.09 Matches are distributed among these distances: 29 12 0.30 30 1 0.03 31 24 0.60 32 3 0.08 ACGTcount: A:0.47, C:0.08, G:0.09, T:0.36 Consensus pattern (31 bp): AAAGTTCAAATACTATAAAAATGATTTTGTA Found at i:53048278 original size:46 final size:46 Alignment explanation

Indices: 53048211--53048392 Score: 258 Period size: 46 Copynumber: 4.0 Consensus size: 46 53048201 AGTGTGCTCT * 53048211 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC 1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC * 53048257 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC 1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC * ** 53048303 GTGATATGAAATGAACAAGACCATGGTTGAAAGATACCATGGCAAC 1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC * * * * * 53048349 ATGACA-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCA 1 CTGATATG-AAATGAGTAAGACCATGGTTGAAAGATACCATGGCA 53048393 TCATGTCAAA Statistics Matches: 124, Mismatches: 11, Indels: 2 0.91 0.08 0.01 Matches are distributed among these distances: 45 1 0.01 46 123 0.99 ACGTcount: A:0.40, C:0.15, G:0.24, T:0.21 Consensus pattern (46 bp): CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC Found at i:53053249 original size:40 final size:40 Alignment explanation

Indices: 53053156--53053372 Score: 282 Period size: 40 Copynumber: 5.5 Consensus size: 40 53053146 AAGCCAAGTA * * * 53053156 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCGCTC-AATG 1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG * * 53053194 CCTTCGGGACATAGCCCGGATATAGTAACTCGCACCAATG 1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG 53053234 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG 1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG * * 53053274 CCTTCGGGACTTAGCCCGGATGTAATAACTCGCACAAATG 1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG * * 53053314 CCTTCGGGACTTAGCCCGGA-ACTAGTCACTAG-AGCAAAATG 1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCA-C-AAATG 53053355 CCTTCGGGACTTAGCCCG 1 CCTTCGGGACTTAGCCCG 53053373 ATTATCATCC Statistics Matches: 161, Mismatches: 12, Indels: 9 0.88 0.07 0.05 Matches are distributed among these distances: 38 12 0.07 39 18 0.11 40 108 0.67 41 23 0.14 ACGTcount: A:0.26, C:0.29, G:0.23, T:0.23 Consensus pattern (40 bp): CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG Found at i:53062807 original size:22 final size:21 Alignment explanation

Indices: 53062779--53062862 Score: 73 Period size: 22 Copynumber: 3.8 Consensus size: 21 53062769 GCTGATAAAT 53062779 AGTAAGCTCTATTGAGCTGAAC 1 AGTAAGCTCT-TTGAGCTGAAC 53062801 AGTAAGCTCTTTCGAGCTGAATC 1 AGTAAGCTCTTT-GAGCTGAA-C * ** 53062824 GGTAA-CTCCAATGAGCTGGAAC 1 AGTAAGCT-CTTTGAGCT-GAAC 53062846 A-TAAGCTCTTATGAGCT 1 AGTAAGCTCTT-TGAGCT 53062863 ATGGTGAGTT Statistics Matches: 50, Mismatches: 6, Indels: 12 0.74 0.09 0.18 Matches are distributed among these distances: 21 6 0.12 22 34 0.68 23 10 0.20 ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27 Consensus pattern (21 bp): AGTAAGCTCTTTGAGCTGAAC Found at i:53065065 original size:39 final size:39 Alignment explanation

Indices: 53065029--53065154 Score: 153 Period size: 39 Copynumber: 3.2 Consensus size: 39 53065019 AAGCATATAT * * 53065029 CAATACTCATATAATTACATAACGTTCGAGCACATATCG 1 CAATACTCATATAATTACATAACATTCAAGCACATATCG * * * * 53065068 CAATGCTTATATAATCACATAACATTCAAGCATATATCG 1 CAATACTCATATAATTACATAACATTCAAGCACATATCG * * * * * 53065107 CAATACTCATATAATTAAACAACATTTAAGCATATGTCG 1 CAATACTCATATAATTACATAACATTCAAGCACATATCG 53065146 CAATACTCA 1 CAATACTCA 53065155 AAAACATGTT Statistics Matches: 74, Mismatches: 13, Indels: 0 0.85 0.15 0.00 Matches are distributed among these distances: 39 74 1.00 ACGTcount: A:0.41, C:0.21, G:0.08, T:0.29 Consensus pattern (39 bp): CAATACTCATATAATTACATAACATTCAAGCACATATCG Found at i:53065141 original size:76 final size:75 Alignment explanation

Indices: 53064999--53065141 Score: 173 Period size: 76 Copynumber: 1.9 Consensus size: 75 53064989 TCACATTACA * * * * * 53064999 TATACAATCACATTAAATTTAAGCATATATCAATACTCATATAATTACATAACGTTCGAGCACAT 1 TATACAATCACATTAAATTCAAGCATATATCAATACTCATATAATTAAACAACATTCAAG-ACAT 53065064 ATCGCAATGCT 65 ATCGCAATGCT * * 53065075 TATATAATCACA-TAACATTCAAGCATATATCGCAATACTCATATAATTAAACAACATTTAAG-C 1 TATACAATCACATTAA-ATTCAAGCATATAT--CAATACTCATATAATTAAACAACATTCAAGAC 53065138 ATAT 63 ATAT 53065142 GTCGCAATAC Statistics Matches: 57, Mismatches: 7, Indels: 6 0.81 0.10 0.09 Matches are distributed among these distances: 75 3 0.05 76 29 0.51 78 25 0.44 ACGTcount: A:0.43, C:0.19, G:0.06, T:0.31 Consensus pattern (75 bp): TATACAATCACATTAAATTCAAGCATATATCAATACTCATATAATTAAACAACATTCAAGACATA TCGCAATGCT Found at i:53065147 original size:78 final size:76 Alignment explanation

Indices: 53064999--53065149 Score: 187 Period size: 78 Copynumber: 2.0 Consensus size: 76 53064989 TCACATTACA * * * * * 53064999 TATACAATCACATTAAATTTAAGCATATATCAATACTCATATAATTACATAACGTTCGAGCACAT 1 TATACAATCACATTAAATTCAAGCATATATCAATACTCATATAATTAAACAACATTCAAGCACAT 53065064 ATCGCAATGCT 66 ATCGCAATGCT * * 53065075 TATATAATCACA-TAACATTCAAGCATATATCGCAATACTCATATAATTAAACAACATTTAAGCA 1 TATACAATCACATTAA-ATTCAAGCATATAT--CAATACTCATATAATTAAACAACATTCAAGCA * * 53065139 TATGTCGCAAT 63 CATATCGCAAT 53065150 ACTCAAAAAC Statistics Matches: 63, Mismatches: 9, Indels: 4 0.83 0.12 0.05 Matches are distributed among these distances: 75 3 0.05 76 24 0.38 78 36 0.57 ACGTcount: A:0.42, C:0.19, G:0.07, T:0.31 Consensus pattern (76 bp): TATACAATCACATTAAATTCAAGCATATATCAATACTCATATAATTAAACAACATTCAAGCACAT ATCGCAATGCT Found at i:53066969 original size:17 final size:17 Alignment explanation

Indices: 53066957--53066991 Score: 70 Period size: 17 Copynumber: 2.1 Consensus size: 17 53066947 TCATATTATT 53066957 ACAATAATCATATTTCA 1 ACAATAATCATATTTCA 53066974 ACAATAATCATATTTCA 1 ACAATAATCATATTTCA 53066991 A 1 A 53066992 TAACAAAGAT Statistics Matches: 18, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 17 18 1.00 ACGTcount: A:0.49, C:0.17, G:0.00, T:0.34 Consensus pattern (17 bp): ACAATAATCATATTTCA Found at i:53067738 original size:21 final size:21 Alignment explanation

Indices: 53067714--53067753 Score: 55 Period size: 21 Copynumber: 1.9 Consensus size: 21 53067704 AAATGTCTAG 53067714 ATTT-CTTTAAATTTCATTTTT 1 ATTTACTTT-AATTTCATTTTT * 53067735 ATTTACTTTAATTTTATTT 1 ATTTACTTTAATTTCATTT 53067754 ATTTCCCATT Statistics Matches: 17, Mismatches: 1, Indels: 2 0.85 0.05 0.10 Matches are distributed among these distances: 21 13 0.76 22 4 0.24 ACGTcount: A:0.25, C:0.07, G:0.00, T:0.68 Consensus pattern (21 bp): ATTTACTTTAATTTCATTTTT Found at i:53071428 original size:24 final size:25 Alignment explanation

Indices: 53071374--53071430 Score: 71 Period size: 25 Copynumber: 2.3 Consensus size: 25 53071364 GAGGTAGTAC 53071374 AATAGAACAAAGCAAAACAAAACAG 1 AATAGAACAAAGCAAAACAAAACAG * * ** 53071399 AGTAGAACAACGCAATTC-AAACAG 1 AATAGAACAAAGCAAAACAAAACAG 53071423 AATAGAAC 1 AATAGAAC 53071431 CGAATAAAAT Statistics Matches: 27, Mismatches: 5, Indels: 1 0.82 0.15 0.03 Matches are distributed among these distances: 24 13 0.48 25 14 0.52 ACGTcount: A:0.60, C:0.18, G:0.14, T:0.09 Consensus pattern (25 bp): AATAGAACAAAGCAAAACAAAACAG Found at i:53080170 original size:39 final size:37 Alignment explanation

Indices: 53080034--53080175 Score: 140 Period size: 38 Copynumber: 3.7 Consensus size: 37 53080024 CCGCACCAAG * * * * 53080034 GCCTACGGGACTTAACCCGGATATCACGATTTGCACAAAT 1 GCCTTCGGGTCTTAACCCGGATAT-AC-ACTAGCAC-AAT * * * * 53080074 GCCTTCGGGTCTTAGCCCGGATAGAAACTCGCACGAAT 1 GCCTTCGGGTCTTAACCCGGATATACACTAGCAC-AAT * 53080112 GCCTTCGGGTCTTAGCCCGGATATAGCACTAGCACAATT 1 GCCTTCGGGTCTTAACCCGGATATA-CACTAGCACAA-T * 53080151 GCCTTCGGGTCTTAACCCGGTTATA 1 GCCTTCGGGTCTTAACCCGGATATA 53080176 ATTTCCAGCA Statistics Matches: 87, Mismatches: 13, Indels: 5 0.83 0.12 0.05 Matches are distributed among these distances: 38 35 0.40 39 32 0.37 40 20 0.23 ACGTcount: A:0.24, C:0.28, G:0.23, T:0.25 Consensus pattern (37 bp): GCCTTCGGGTCTTAACCCGGATATACACTAGCACAAT Found at i:53087896 original size:40 final size:40 Alignment explanation

Indices: 53087852--53088003 Score: 148 Period size: 40 Copynumber: 3.8 Consensus size: 40 53087842 ATATCACGAT 53087852 TTGCACAAATGCCTTCGGGTCTTAGCCCGGATTTAACAAC 1 TTGCACAAATGCCTTCGGGTCTTAGCCCGGATTTAACAAC * * * * 53087892 TTGCACGAATGCCTTCGGGTCTTAGCCCGGATATAGCTAC 1 TTGCACAAATGCCTTCGGGTCTTAGCCCGGATTTAACAAC * * * * * * 53087932 TAGCACAATTACCTTCGGGTCTTAACCCGG--TT-ATAAT 1 TTGCACAAATGCCTTCGGGTCTTAGCCCGGATTTAACAAC * * 53087969 TTCCAGCATAATTGTCTTCGGGTCTTAGCCCGGAT 1 TTGCA-CA-AA-TGCCTTCGGGTCTTAGCCCGGAT 53088004 ATCATTCAAT Statistics Matches: 87, Mismatches: 20, Indels: 8 0.76 0.17 0.07 Matches are distributed among these distances: 37 4 0.05 38 3 0.03 39 1 0.01 40 79 0.91 ACGTcount: A:0.22, C:0.26, G:0.21, T:0.30 Consensus pattern (40 bp): TTGCACAAATGCCTTCGGGTCTTAGCCCGGATTTAACAAC Found at i:53096910 original size:16 final size:16 Alignment explanation

Indices: 53096889--53096919 Score: 53 Period size: 16 Copynumber: 1.9 Consensus size: 16 53096879 ATTGGGTTGA * 53096889 GAAAATTATTTAATTG 1 GAAAATTAATTAATTG 53096905 GAAAATTAATTAATT 1 GAAAATTAATTAATT 53096920 TAAATTAATT 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:0.48, C:0.00, G:0.10, T:0.42 Consensus pattern (16 bp): GAAAATTAATTAATTG Found at i:53105553 original size:40 final size:40 Alignment explanation

Indices: 53105508--53105795 Score: 271 Period size: 40 Copynumber: 7.2 Consensus size: 40 53105498 CGGAATACAA * * * 53105508 CCGGATATGACCACATGCTCGAATGCCTTCGGGTCTTAGC 1 CCGGATATGACAACTTGCACGAATGCCTTCGGGTCTTAGC * * * 53105548 CCGGATA-GA-ATGACTTGCGCAAATGCCTTCGGGTATTAGC 1 CCGGATATGACA--ACTTGCACGAATGCCTTCGGGTCTTAGC * * 53105588 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGC 1 CCGGATATGACAACTTGCACGAATGCCTTCGGGTCTTAGC * * * 53105628 CCGGATA-GAACGACTTGCACAAATGCCTTCGGGTATTAGC 1 CCGGATATG-ACAACTTGCACGAATGCCTTCGGGTCTTAGC * * 53105668 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGC 1 CCGGATATGACAACTTGCACGAATGCCTTCGGGTCTTAGC * * * * 53105708 CCGGATGTAGTC-ACTAGCAC-AATTGCCTTCGGGTCTTAAC 1 CCGGATAT-GACAACTTGCACGAA-TGCCTTCGGGTCTTAGC * ** * ** * * 53105748 CCGGATATAATTACTAGCATAAATGTCTTCGGGACTTAGC 1 CCGGATATGACAACTTGCACGAATGCCTTCGGGTCTTAGC 53105788 CCGGATAT 1 CCGGATAT 53105796 CATTCAATTG Statistics Matches: 205, Mismatches: 33, Indels: 20 0.79 0.13 0.08 Matches are distributed among these distances: 39 4 0.02 40 196 0.96 41 4 0.02 42 1 0.00 ACGTcount: A:0.24, C:0.26, G:0.24, T:0.26 Consensus pattern (40 bp): CCGGATATGACAACTTGCACGAATGCCTTCGGGTCTTAGC Found at i:53105643 original size:80 final size:79 Alignment explanation

Indices: 53105527--53105794 Score: 367 Period size: 80 Copynumber: 3.4 Consensus size: 79 53105517 ACCACATGCT * 53105527 CGAATGCCTTCGGGTCTTAGCCCGGATAGAATGACTTGCGCAAATGCCTTCGGGTATTAGCCCGG 1 CGAATGCCTTCGGGTCTTAGCCCGGATAGAA-GACTTGCACAAATGCCTTCGGGTATTAGCCCGG 53105592 ATTTAACAACTTGCA 65 ATTTAACAACTTGCA 53105607 CGAATGCCTTCGGGTCTTAGCCCGGATAGAACGACTTGCACAAATGCCTTCGGGTATTAGCCCGG 1 CGAATGCCTTCGGGTCTTAGCCCGGATAGAA-GACTTGCACAAATGCCTTCGGGTATTAGCCCGG 53105672 ATTTAACAACTTGCA 65 ATTTAACAACTTGCA * * * * * 53105687 CGAATGCCTTCGGGTCTTAGCCCGGAT-GTAGTCACTAGCACAATTGCCTTCGGGTCTTAACCCG 1 CGAATGCCTTCGGGTCTTAGCCCGGATAGAAG--ACTTGCACAAATGCCTTCGGGTATTAGCCCG * ** * 53105751 GATATAATTACTAGCA 64 GATTTAACAACTTGCA ** * * 53105767 TAAATGTCTTCGGGACTTAGCCCGGATA 1 CGAATGCCTTCGGGTCTTAGCCCGGATA 53105795 TCATTCAATT Statistics Matches: 170, Mismatches: 15, Indels: 5 0.89 0.08 0.03 Matches are distributed among these distances: 78 1 0.01 79 2 0.01 80 167 0.98 ACGTcount: A:0.24, C:0.25, G:0.24, T:0.26 Consensus pattern (79 bp): CGAATGCCTTCGGGTCTTAGCCCGGATAGAAGACTTGCACAAATGCCTTCGGGTATTAGCCCGGA TTTAACAACTTGCA Found at i:53105735 original size:120 final size:120 Alignment explanation

Indices: 53105529--53105794 Score: 322 Period size: 120 Copynumber: 2.2 Consensus size: 120 53105519 CACATGCTCG * ** * 53105529 AATGCCTTCGGGTCTTAGCCCGGATAGAATGACTTGCGCAAATGCCTTCGGGTATTAGCCCGGAT 1 AATGCCTTCGGGTATTAGCCCGGATAGAACAACTTGCACAAATGCCTTCGGGTATTAGCCCGGAT * * * * 53105594 TTAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATAGAACGACTTGCACA 66 GTAACAACTAGCACGAATGCCTTCGGGTCTTAACCCGGATAGAACGACTAGCACA ** * * 53105649 AATGCCTTCGGGTATTAGCCCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGAT 1 AATGCCTTCGGGTATTAGCCCGGATAGAACAACTTGCACAAATGCCTTCGGGTATTAGCCCGGAT * * ** * 53105714 GTAGTC-ACTAGCAC-AATTGCCTTCGGGTCTTAACCCGGATATAATTACTAGCATA 66 GTA-ACAACTAGCACGAA-TGCCTTCGGGTCTTAACCCGGATAGAACGACTAGCACA * 53105769 AATGTCTTCGGG-ACTTAGCCCGGATA 1 AATGCCTTCGGGTA-TTAGCCCGGATA 53105795 TCATTCAATT Statistics Matches: 124, Mismatches: 19, Indels: 6 0.83 0.13 0.04 Matches are distributed among these distances: 119 3 0.02 120 120 0.97 121 1 0.01 ACGTcount: A:0.24, C:0.25, G:0.24, T:0.27 Consensus pattern (120 bp): AATGCCTTCGGGTATTAGCCCGGATAGAACAACTTGCACAAATGCCTTCGGGTATTAGCCCGGAT GTAACAACTAGCACGAATGCCTTCGGGTCTTAACCCGGATAGAACGACTAGCACA Found at i:53113611 original size:40 final size:40 Alignment explanation

Indices: 53113567--53113793 Score: 276 Period size: 40 Copynumber: 5.7 Consensus size: 40 53113557 CACATGCTCG * ** * 53113567 AATGCCTTCGGGTCTTAGCCCGGATAGAATGACTTGCGCA 1 AATGCCTTCGGGTCTTAGCCCGGATATAACAACTTGCACA * * * 53113607 AATGCCTTCGGGTATTAGCCCGGATTTAACAACTTGCACG 1 AATGCCTTCGGGTCTTAGCCCGGATATAACAACTTGCACA * * 53113647 AATGCCTTCGGGTCTTAGCCCGGATAGAACGACTTGCACA 1 AATGCCTTCGGGTCTTAGCCCGGATATAACAACTTGCACA * * * 53113687 AATGCCTTCGGGTATTAGCCC-GAGTTTAACAACTTGCACG 1 AATGCCTTCGGGTCTTAGCCCGGA-TATAACAACTTGCACA ** * * 53113727 AATGCCTTCGGGTCTTAGCCCGGATATAATTACTAGCATA 1 AATGCCTTCGGGTCTTAGCCCGGATATAACAACTTGCACA * * 53113767 AATGTCTTCGGGACTTAGCCCGGATAT 1 AATGCCTTCGGGTCTTAGCCCGGATAT 53113794 CTTTCAATTG Statistics Matches: 159, Mismatches: 26, Indels: 4 0.84 0.14 0.02 Matches are distributed among these distances: 39 2 0.01 40 155 0.97 41 2 0.01 ACGTcount: A:0.25, C:0.25, G:0.24, T:0.27 Consensus pattern (40 bp): AATGCCTTCGGGTCTTAGCCCGGATATAACAACTTGCACA Found at i:53113681 original size:80 final size:80 Alignment explanation

Indices: 53113565--53113788 Score: 344 Period size: 80 Copynumber: 2.8 Consensus size: 80 53113555 ACCACATGCT * * 53113565 CGAATGCCTTCGGGTCTTAGCCCGGATAGAATGACTTGCGCAAATGCCTTCGGGTATTAGCCCG- 1 CGAATGCCTTCGGGTCTTAGCCCGGATAGAACGACTTGCACAAATGCCTTCGGGTATTAGCCCGA 53113629 GATTTAACAACTTGCA 66 G-TTTAACAACTTGCA 53113645 CGAATGCCTTCGGGTCTTAGCCCGGATAGAACGACTTGCACAAATGCCTTCGGGTATTAGCCCGA 1 CGAATGCCTTCGGGTCTTAGCCCGGATAGAACGACTTGCACAAATGCCTTCGGGTATTAGCCCGA 53113710 GTTTAACAACTTGCA 66 GTTTAACAACTTGCA * ** * * * 53113725 CGAATGCCTTCGGGTCTTAGCCCGGATATAATTACTAGCATAAATGTCTTCGGG-ACTTAGCCCG 1 CGAATGCCTTCGGGTCTTAGCCCGGATAGAACGACTTGCACAAATGCCTTCGGGTA-TTAGCCCG 53113789 GATATCTTTC Statistics Matches: 134, Mismatches: 8, Indels: 4 0.92 0.05 0.03 Matches are distributed among these distances: 79 1 0.01 80 132 0.99 81 1 0.01 ACGTcount: A:0.24, C:0.25, G:0.24, T:0.26 Consensus pattern (80 bp): CGAATGCCTTCGGGTCTTAGCCCGGATAGAACGACTTGCACAAATGCCTTCGGGTATTAGCCCGA GTTTAACAACTTGCA Found at i:53120567 original size:50 final size:50 Alignment explanation

Indices: 53120475--53120599 Score: 207 Period size: 50 Copynumber: 2.5 Consensus size: 50 53120465 TGGAAGATCA * 53120475 AATATATCATCACATAAAT-CTTACCCATATGTCCAAATATACAAGGTTC 1 AATATATCATCACATAAATACTTACCCATATGACCAAATATACAAGGTTC ** * 53120524 AATATATCATCACATAAATACTTACTTATATGACTAAATATACAAGGTTC 1 AATATATCATCACATAAATACTTACCCATATGACCAAATATACAAGGTTC 53120574 AATATATCATCACATAAATACTTACC 1 AATATATCATCACATAAATACTTACC 53120600 TACATAGCCA Statistics Matches: 70, Mismatches: 5, Indels: 1 0.92 0.07 0.01 Matches are distributed among these distances: 49 19 0.27 50 51 0.73 ACGTcount: A:0.43, C:0.20, G:0.05, T:0.32 Consensus pattern (50 bp): AATATATCATCACATAAATACTTACCCATATGACCAAATATACAAGGTTC Found at i:53120627 original size:50 final size:51 Alignment explanation

Indices: 53120468--53120635 Score: 177 Period size: 50 Copynumber: 3.4 Consensus size: 51 53120458 CCGAATATGG * * 53120468 AAGATCAAATATATCATCACATAAAT-CTTACC--CATATGTCCAAATATAC 1 AAGATCCAATATATCATCACATAAATACTTACCTACATA-GACCAAATATAC * * * * * 53120517 AAGGTTCAATATATCATCACATAAATACTTACTTATAT-GACTAAATATAC 1 AAGATCCAATATATCATCACATAAATACTTACCTACATAGACCAAATATAC * * * * 53120567 AAGGTTCAATATATCATCACATAAATACTTACCTACATAG-CCAAAAATAT 1 AAGATCCAATATATCATCACATAAATACTTACCTACATAGACCAAATATAC 53120617 AAGATCCAATA-ATACATCA 1 AAGATCCAATATAT-CATCA 53120636 TATATGTACG Statistics Matches: 100, Mismatches: 14, Indels: 9 0.81 0.11 0.07 Matches are distributed among these distances: 49 25 0.25 50 72 0.72 51 1 0.01 52 2 0.02 ACGTcount: A:0.46, C:0.20, G:0.05, T:0.29 Consensus pattern (51 bp): AAGATCCAATATATCATCACATAAATACTTACCTACATAGACCAAATATAC Found at i:53120673 original size:99 final size:99 Alignment explanation

Indices: 53120475--53120687 Score: 218 Period size: 100 Copynumber: 2.2 Consensus size: 99 53120465 TGGAAGATCA * * * 53120475 AATATATCATCACATAAATCTTACCCATATGTCCAAATATACAAGGTTCAATATATCATCACATA 1 AATATATCATCACATAAATCTTACCCATATGTCCAAAAATACAAGATCCAATATATCATCACATA * * * * 53120540 AATACTTACTTATATGACTAAATATACAAGGTTC 66 AATACGTACCTATATGACCAAACATACAAGGTTC * 53120574 AATATATCATCACATAAATACTTACCTACATA-G-CCAAAAATATAAGATCCAATA-ATACATCA 1 AATATATCATCACATAAAT-CTTACC--CATATGTCCAAAAATACAAGATCCAATATAT-CATCA * ** * * * 53120636 TATATGTACGTACCTATGTGGCCAAACATTCAA-GTTC 62 CATAAATACGTACCTATATGACCAAACATACAAGGTTC * * 53120673 AATAAAACATCACAT 1 AATATATCATCACAT 53120688 TTGTACATAC Statistics Matches: 94, Mismatches: 16, Indels: 8 0.80 0.14 0.07 Matches are distributed among these distances: 99 38 0.40 100 51 0.54 101 1 0.01 102 4 0.04 ACGTcount: A:0.44, C:0.20, G:0.07, T:0.30 Consensus pattern (99 bp): AATATATCATCACATAAATCTTACCCATATGTCCAAAAATACAAGATCCAATATATCATCACATA AATACGTACCTATATGACCAAACATACAAGGTTC Found at i:53123329 original size:31 final size:31 Alignment explanation

Indices: 53123294--53123357 Score: 101 Period size: 31 Copynumber: 2.1 Consensus size: 31 53123284 CCTTTTCATG 53123294 TTTCATATTCCATAACACTGGGCCGAAGCCT 1 TTTCATATTCCATAACACTGGGCCGAAGCCT * ** 53123325 TTTCATATTTCATATTACTGGGCCGAAGCCT 1 TTTCATATTCCATAACACTGGGCCGAAGCCT 53123356 TT 1 TT 53123358 ACTGTAAACG Statistics Matches: 30, Mismatches: 3, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 31 30 1.00 ACGTcount: A:0.23, C:0.25, G:0.16, T:0.36 Consensus pattern (31 bp): TTTCATATTCCATAACACTGGGCCGAAGCCT Found at i:53123600 original size:24 final size:24 Alignment explanation

Indices: 53123549--53123691 Score: 209 Period size: 24 Copynumber: 6.0 Consensus size: 24 53123539 GCTTTATCAT * 53123549 ATAACTGGAGGCCT-AGCCTCTTTTA 1 ATAACTGG-GGCATAAGCC-CTTTTA * * 53123574 ATAACTGGGGCAAAAGCCCTTTCA 1 ATAACTGGGGCATAAGCCCTTTTA 53123598 ATAACTGGGGCATAAGCCCTTTT- 1 ATAACTGGGGCATAAGCCCTTTTA * 53123621 ATAACTGGGGCATAAGCCCTTTTG 1 ATAACTGGGGCATAAGCCCTTTTA * 53123645 ATAACTGGGGCATAAGCCCTTTTG 1 ATAACTGGGGCATAAGCCCTTTTA 53123669 ATAACTGGGGCATAAGCCCTTTT 1 ATAACTGGGGCATAAGCCCTTTT 53123692 TCACTTCCTC Statistics Matches: 111, Mismatches: 5, Indels: 5 0.92 0.04 0.04 Matches are distributed among these distances: 23 23 0.21 24 76 0.68 25 12 0.11 ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29 Consensus pattern (24 bp): ATAACTGGGGCATAAGCCCTTTTA Found at i:53123628 original size:47 final size:48 Alignment explanation

Indices: 53123549--53123690 Score: 207 Period size: 47 Copynumber: 3.0 Consensus size: 48 53123539 GCTTTATCAT * * 53123549 ATAACTGGAGGCCT-AGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTCA 1 ATAACTGG-GGCATAAGCC-CTTTTAATAACTGGGGCATAAGCCCTTTCA ** 53123598 ATAACTGGGGCATAAGCCCTTTT-ATAACTGGGGCATAAGCCCTTTTG 1 ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTCA * 53123645 ATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCCTTT 1 ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTT 53123691 TTCACTTCCT Statistics Matches: 87, Mismatches: 4, Indels: 5 0.91 0.04 0.05 Matches are distributed among these distances: 47 44 0.51 48 31 0.36 49 12 0.14 ACGTcount: A:0.27, C:0.23, G:0.23, T:0.28 Consensus pattern (48 bp): ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTCA Found at i:53123649 original size:71 final size:72 Alignment explanation

Indices: 53123548--53123691 Score: 220 Period size: 71 Copynumber: 2.0 Consensus size: 72 53123538 TGCTTTATCA * 53123548 TATAACTGGAGGCCTAGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTCAATAACTGGGGCATAA 1 TATAACTGGAGGCATAGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTCAATAACTGGGGCATAA 53123613 GCCCTTT 66 GCCCTTT * * ** 53123620 TATAACTGG-GGCATAAGCC-CTTTTGATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATA 1 TATAACTGGAGGCAT-AGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTCAATAACTGGGGCATA 53123683 AGCCCTTT 65 AGCCCTTT 53123691 T 1 T 53123692 TCACTTCCTC Statistics Matches: 66, Mismatches: 5, Indels: 3 0.89 0.07 0.04 Matches are distributed among these distances: 71 53 0.80 72 13 0.20 ACGTcount: A:0.26, C:0.22, G:0.22, T:0.29 Consensus pattern (72 bp): TATAACTGGAGGCATAGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTCAATAACTGGGGCATAA GCCCTTT Found at i:53123766 original size:20 final size:20 Alignment explanation

Indices: 53123741--53123801 Score: 104 Period size: 20 Copynumber: 3.0 Consensus size: 20 53123731 TTATGATTAC 53123741 ATCATGTGCATATCATACAT 1 ATCATGTGCATATCATACAT 53123761 ATCATGTGCATATCATACAT 1 ATCATGTGCATATCATACAT * * 53123781 GTCATGTGCATCTCATACAT 1 ATCATGTGCATATCATACAT 53123801 A 1 A 53123802 CCATATTTAT Statistics Matches: 38, Mismatches: 3, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 20 38 1.00 ACGTcount: A:0.33, C:0.21, G:0.11, T:0.34 Consensus pattern (20 bp): ATCATGTGCATATCATACAT Found at i:53123876 original size:25 final size:25 Alignment explanation

Indices: 53123844--53123891 Score: 69 Period size: 25 Copynumber: 1.9 Consensus size: 25 53123834 ATACATAAAC * * * 53123844 CCTAGGGGTATAATGGTCATTTTTA 1 CCTAGGGGCAAAACGGTCATTTTTA 53123869 CCTAGGGGCAAAACGGTCATTTT 1 CCTAGGGGCAAAACGGTCATTTT 53123892 CATGGTATAA Statistics Matches: 20, Mismatches: 3, Indels: 0 0.87 0.13 0.00 Matches are distributed among these distances: 25 20 1.00 ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33 Consensus pattern (25 bp): CCTAGGGGCAAAACGGTCATTTTTA Found at i:53125138 original size:27 final size:27 Alignment explanation

Indices: 53125047--53125130 Score: 125 Period size: 27 Copynumber: 3.1 Consensus size: 27 53125037 GGGCATATTC * 53125047 GTCATTTTACCATACAGGGG-TATTACG 1 GTCACTTTACCATACAGGGGCT-TTACG * 53125074 GTCACTTTACCTTACAGGGGCTTTACG 1 GTCACTTTACCATACAGGGGCTTTACG * 53125101 GTCACTTTACCCTACAGGGGCTTTACG 1 GTCACTTTACCATACAGGGGCTTTACG 53125128 GTC 1 GTC 53125131 TTTTTACCTA Statistics Matches: 53, Mismatches: 3, Indels: 2 0.91 0.05 0.03 Matches are distributed among these distances: 27 52 0.98 28 1 0.02 ACGTcount: A:0.20, C:0.25, G:0.23, T:0.32 Consensus pattern (27 bp): GTCACTTTACCATACAGGGGCTTTACG Found at i:53125147 original size:27 final size:26 Alignment explanation

Indices: 53125047--53125140 Score: 118 Period size: 27 Copynumber: 3.5 Consensus size: 26 53125037 GGGCATATTC * 53125047 GTCATTTTACCATACAGGGG-TATTACG 1 GTCACTTTACC-TACAGGGGCT-TTACG 53125074 GTCACTTTACCTTACAGGGGCTTTACG 1 GTCACTTTACC-TACAGGGGCTTTACG 53125101 GTCACTTTACCCTACAGGGGCTTTACG 1 GTCACTTTA-CCTACAGGGGCTTTACG ** 53125128 GTCTTTTTACCTA 1 GTCACTTTACCTA 53125141 ATAGGGGTAT Statistics Matches: 61, Mismatches: 4, Indels: 5 0.87 0.06 0.07 Matches are distributed among these distances: 26 4 0.07 27 54 0.89 28 3 0.05 ACGTcount: A:0.20, C:0.24, G:0.20, T:0.35 Consensus pattern (26 bp): GTCACTTTACCTACAGGGGCTTTACG Found at i:53125222 original size:27 final size:27 Alignment explanation

Indices: 53125196--53125628 Score: 123 Period size: 27 Copynumber: 16.0 Consensus size: 27 53125186 ATCTACAAAC * 53125196 CAAGGGTATTTCAGTAATTTTGTAAAC 1 CAAGGGTATTTCAGTAATTTTGTAAAT * 53125223 CAATGGTATTTCTA-TAATTTT-TAGAAAGT 1 CAAGGGTATTTC-AGTAATTTTGT--AAA-T * * 53125252 CAAGGGTATTTCTGTAACTTTGTAAAT 1 CAAGGGTATTTCAGTAATTTTGTAAAT ** * 53125279 C-AGGGTAAAAT-AGTAATTCTGTAAAT 1 CAAGGGT-ATTTCAGTAATTTTGTAAAT ** * * 53125305 CAAGGGTAAAAT-AGTAATTCTATAAAT 1 CAAGGGT-ATTTCAGTAATTTTGTAAAT * * *** 53125332 CGACGGTAAAAC-GATAATTTTGTAAAT 1 CAAGGGTATTTCAG-TAATTTTGTAAAT * *** * * 53125359 CGAGGGTAAAACAATAATTCTGTAAAT 1 CAAGGGTATTTCAGTAATTTTGTAAAT *** * * 53125386 CAAGGGTAAAACGGTAATTTTATAAAT 1 CAAGGGTATTTCAGTAATTTTGTAAAT * * *** * 53125413 CGAGGATAAAACAGTAATTCTGTAAAT 1 CAAGGGTATTTCAGTAATTTTGTAAAT * *** * 53125440 CGAGGGTAAAACGGTAATTTTGTAAAT 1 CAAGGGTATTTCAGTAATTTTGTAAAT * *** * * 53125467 CGAGGGTAAAACGGTAATTATGTAAAT 1 CAAGGGTATTTCAGTAATTTTGTAAAT ** *** * 53125494 CGGGGGTAAAAC-GATAATTCTGTAAAT 1 CAAGGGTATTTCAG-TAATTTTGTAAAT ** * ** * 53125521 CGGGGGTACTTT-GGTAATTTTACAAGT 1 CAAGGGTA-TTTCAGTAATTTTGTAAAT ** 53125548 CGAA-GGTATTTCAGTAATTTTACAAAT 1 C-AAGGGTATTTCAGTAATTTTGTAAAT * * 53125575 CGAGGGTATTTCAGT-ATTTT-TACAAA 1 CAAGGGTATTTCAGTAATTTTGTA-AAT * 53125601 CTAAGGGTATTTCGGTAATTTTAGTAAA 1 C-AAGGGTATTTCAGTAATTTT-GTAAA 53125629 CTAAAGTATT Statistics Matches: 333, Mismatches: 51, Indels: 42 0.78 0.12 0.10 Matches are distributed among these distances: 25 1 0.00 26 36 0.11 27 261 0.78 28 13 0.04 29 19 0.06 30 3 0.01 ACGTcount: A:0.37, C:0.09, G:0.20, T:0.33 Consensus pattern (27 bp): CAAGGGTATTTCAGTAATTTTGTAAAT Found at i:53125356 original size:54 final size:54 Alignment explanation

Indices: 53125272--53125528 Score: 338 Period size: 54 Copynumber: 4.8 Consensus size: 54 53125262 TCTGTAACTT * * * * 53125272 TGTAAATC-AGGGTAAAA-TAGTAATTCTGTAAATCAAGGGTAAAATAGTAATTC 1 TGTAAATCGAGGGTAAAACGA-TAATTTTGTAAATCGAGGGTAAAACAGTAATTC * * * 53125325 TATAAATCGACGGTAAAACGATAATTTTGTAAATCGAGGGTAAAACAATAATTC 1 TGTAAATCGAGGGTAAAACGATAATTTTGTAAATCGAGGGTAAAACAGTAATTC * * * * 53125379 TGTAAATCAAGGGTAAAACGGTAATTTTATAAATCGAGGATAAAACAGTAATTC 1 TGTAAATCGAGGGTAAAACGATAATTTTGTAAATCGAGGGTAAAACAGTAATTC * * * 53125433 TGTAAATCGAGGGTAAAACGGTAATTTTGTAAATCGAGGGTAAAACGGTAATTA 1 TGTAAATCGAGGGTAAAACGATAATTTTGTAAATCGAGGGTAAAACAGTAATTC * * * 53125487 TGTAAATCGGGGGTAAAACGATAATTCTGTAAATCGGGGGTA 1 TGTAAATCGAGGGTAAAACGATAATTTTGTAAATCGAGGGTA 53125529 CTTTGGTAAT Statistics Matches: 179, Mismatches: 23, Indels: 3 0.87 0.11 0.01 Matches are distributed among these distances: 53 7 0.04 54 171 0.96 55 1 0.01 ACGTcount: A:0.41, C:0.09, G:0.22, T:0.28 Consensus pattern (54 bp): TGTAAATCGAGGGTAAAACGATAATTTTGTAAATCGAGGGTAAAACAGTAATTC Found at i:53125541 original size:81 final size:81 Alignment explanation

Indices: 53125272--53125528 Score: 347 Period size: 81 Copynumber: 3.2 Consensus size: 81 53125262 TCTGTAACTT ** ** * * 53125272 TGTAAATC-AGGGTAAAATAGTAATTCTGTAAATCAAGGGTAAAATAGTAATTCTATAAATCGAC 1 TGTAAATCGAGGGTAAAACGGTAATTCTGTAAATCAAGGGTAAAACGGTAATTATATAAATCGAG * 53125336 GGTAAAACGATAATTT 66 GGTAAAACGATAATTC ** * 53125352 TGTAAATCGAGGGTAAAACAATAATTCTGTAAATCAAGGGTAAAACGGTAATTTTATAAATCGAG 1 TGTAAATCGAGGGTAAAACGGTAATTCTGTAAATCAAGGGTAAAACGGTAATTATATAAATCGAG * 53125417 GATAAAAC-AGTAATTC 66 GGTAAAACGA-TAATTC * * * * 53125433 TGTAAATCGAGGGTAAAACGGTAATTTTGTAAATCGAGGGTAAAACGGTAATTATGTAAATCGGG 1 TGTAAATCGAGGGTAAAACGGTAATTCTGTAAATCAAGGGTAAAACGGTAATTATATAAATCGAG 53125498 GGTAAAACGATAATTC 66 GGTAAAACGATAATTC * 53125514 TGTAAATCGGGGGTA 1 TGTAAATCGAGGGTA 53125529 CTTTGGTAAT Statistics Matches: 157, Mismatches: 17, Indels: 5 0.88 0.09 0.03 Matches are distributed among these distances: 80 9 0.06 81 147 0.94 82 1 0.01 ACGTcount: A:0.41, C:0.09, G:0.22, T:0.28 Consensus pattern (81 bp): TGTAAATCGAGGGTAAAACGGTAATTCTGTAAATCAAGGGTAAAACGGTAATTATATAAATCGAG GGTAAAACGATAATTC Found at i:53128314 original size:31 final size:31 Alignment explanation

Indices: 53128279--53128342 Score: 101 Period size: 31 Copynumber: 2.1 Consensus size: 31 53128269 CCTTTTCATG 53128279 TTTCATATTCCATAACACTGGGCCGAAGCCT 1 TTTCATATTCCATAACACTGGGCCGAAGCCT * ** 53128310 TTTCATATTTCATATTACTGGGCCGAAGCCT 1 TTTCATATTCCATAACACTGGGCCGAAGCCT 53128341 TT 1 TT 53128343 ACTGTAAACG Statistics Matches: 30, Mismatches: 3, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 31 30 1.00 ACGTcount: A:0.23, C:0.25, G:0.16, T:0.36 Consensus pattern (31 bp): TTTCATATTCCATAACACTGGGCCGAAGCCT Found at i:53128585 original size:24 final size:24 Alignment explanation

Indices: 53128534--53128700 Score: 248 Period size: 24 Copynumber: 7.0 Consensus size: 24 53128524 GCTTTATCAT * * 53128534 ATAACTGGAGGCCT-AGCCTCTTTTA 1 ATAACTGG-GGCATAAGCC-CTTTTG * * ** 53128559 ATAACTGGGGCAAAAACCCTTTCA 1 ATAACTGGGGCATAAGCCCTTTTG 53128583 ATAACTGGGGCATAAGCCCTTTT- 1 ATAACTGGGGCATAAGCCCTTTTG 53128606 ATAACTGGGGCATAAGCCCTTTTG 1 ATAACTGGGGCATAAGCCCTTTTG 53128630 ATAACTGGGGCATAAGCCCTTTTG 1 ATAACTGGGGCATAAGCCCTTTTG 53128654 ATAACTGGGGCATAAGCCCTTTTG 1 ATAACTGGGGCATAAGCCCTTTTG 53128678 ATAACTGGGGCATAAGCCCTTTT 1 ATAACTGGGGCATAAGCCCTTTT 53128701 TCACTTCCTC Statistics Matches: 133, Mismatches: 7, Indels: 5 0.92 0.05 0.03 Matches are distributed among these distances: 23 23 0.17 24 99 0.74 25 11 0.08 ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29 Consensus pattern (24 bp): ATAACTGGGGCATAAGCCCTTTTG Found at i:53128634 original size:71 final size:71 Alignment explanation

Indices: 53128533--53128700 Score: 248 Period size: 71 Copynumber: 2.3 Consensus size: 71 53128523 TGCTTTATCA * 53128533 TATAACTGGAGGCCT-AGCCTCTTTTAATAACTGGGGCAAAAACCCTTTCAATAACTGGGGCATA 1 TATAACTGG-GGCATAAGCC-CTTTTAATAACTGGGGCAAAAACCCTTTCAATAACTGGGGCATA 53128597 AGCCCTTT 64 AGCCCTTT * * * ** 53128605 TATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAG 1 TATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCAAAAACCCTTTCAATAACTGGGGCATAAG 53128670 CCCTTT 66 CCCTTT 53128676 TGATAACTGGGGCATAAGCCCTTTT 1 T-ATAACTGGGGCATAAGCCCTTTT 53128701 TCACTTCCTC Statistics Matches: 88, Mismatches: 6, Indels: 4 0.90 0.06 0.04 Matches are distributed among these distances: 71 52 0.59 72 36 0.41 ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29 Consensus pattern (71 bp): TATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCAAAAACCCTTTCAATAACTGGGGCATAAG CCCTTT Found at i:53128775 original size:20 final size:20 Alignment explanation

Indices: 53128750--53128810 Score: 104 Period size: 20 Copynumber: 3.0 Consensus size: 20 53128740 TTATGATTAC 53128750 ATCATGTGCATATCATACAT 1 ATCATGTGCATATCATACAT 53128770 ATCATGTGCATATCATACAT 1 ATCATGTGCATATCATACAT * * 53128790 GTCATGTGCATCTCATACAT 1 ATCATGTGCATATCATACAT 53128810 A 1 A 53128811 CCATATTTAT Statistics Matches: 38, Mismatches: 3, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 20 38 1.00 ACGTcount: A:0.33, C:0.21, G:0.11, T:0.34 Consensus pattern (20 bp): ATCATGTGCATATCATACAT Found at i:53128885 original size:25 final size:25 Alignment explanation

Indices: 53128853--53128900 Score: 69 Period size: 25 Copynumber: 1.9 Consensus size: 25 53128843 ATACATAAAC * * * 53128853 CCTAGGGGTATAATGGTCATTTTTA 1 CCTAGGGGCAAAACGGTCATTTTTA 53128878 CCTAGGGGCAAAACGGTCATTTT 1 CCTAGGGGCAAAACGGTCATTTT 53128901 CATGGTATAA Statistics Matches: 20, Mismatches: 3, Indels: 0 0.87 0.13 0.00 Matches are distributed among these distances: 25 20 1.00 ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33 Consensus pattern (25 bp): CCTAGGGGCAAAACGGTCATTTTTA Found at i:53130150 original size:27 final size:27 Alignment explanation

Indices: 53130059--53130142 Score: 125 Period size: 27 Copynumber: 3.1 Consensus size: 27 53130049 GGGCATATTC * 53130059 GTCATTTTACCATACAGGGG-TATTACG 1 GTCACTTTACCATACAGGGGCT-TTACG * 53130086 GTCACTTTACCTTACAGGGGCTTTACG 1 GTCACTTTACCATACAGGGGCTTTACG * 53130113 GTCACTTTACCCTACAGGGGCTTTACG 1 GTCACTTTACCATACAGGGGCTTTACG 53130140 GTC 1 GTC 53130143 TTTTTACCTA Statistics Matches: 53, Mismatches: 3, Indels: 2 0.91 0.05 0.03 Matches are distributed among these distances: 27 52 0.98 28 1 0.02 ACGTcount: A:0.20, C:0.25, G:0.23, T:0.32 Consensus pattern (27 bp): GTCACTTTACCATACAGGGGCTTTACG Found at i:53130159 original size:27 final size:26 Alignment explanation

Indices: 53130059--53130152 Score: 118 Period size: 27 Copynumber: 3.5 Consensus size: 26 53130049 GGGCATATTC * 53130059 GTCATTTTACCATACAGGGG-TATTACG 1 GTCACTTTACC-TACAGGGGCT-TTACG 53130086 GTCACTTTACCTTACAGGGGCTTTACG 1 GTCACTTTACC-TACAGGGGCTTTACG 53130113 GTCACTTTACCCTACAGGGGCTTTACG 1 GTCACTTTA-CCTACAGGGGCTTTACG ** 53130140 GTCTTTTTACCTA 1 GTCACTTTACCTA 53130153 ATAGGGGTAT Statistics Matches: 61, Mismatches: 4, Indels: 5 0.87 0.06 0.07 Matches are distributed among these distances: 26 4 0.07 27 54 0.89 28 3 0.05 ACGTcount: A:0.20, C:0.24, G:0.20, T:0.35 Consensus pattern (26 bp): GTCACTTTACCTACAGGGGCTTTACG Found at i:53130234 original size:27 final size:27 Alignment explanation

Indices: 53130204--53130298 Score: 95 Period size: 27 Copynumber: 3.4 Consensus size: 27 53130194 GTAAATCTAC 53130204 AAACCAAGGGTATTTCAGTAATTTTGT 1 AAACCAAGGGTATTTCAGTAATTTTGT * 53130231 AAACCAATGGTATTTCTA-TAATTTT-T 1 AAACCAAGGGTATTTC-AGTAATTTTGT * * * 53130257 AGAAAGTCAAGGGTATTTCTGTAACTTTGT 1 --AAA-CCAAGGGTATTTCAGTAATTTTGT * 53130287 AAATCAAGGGTA 1 AAACCAAGGGTA 53130299 AAATAGTAAT Statistics Matches: 57, Mismatches: 5, Indels: 12 0.77 0.07 0.16 Matches are distributed among these distances: 26 1 0.02 27 31 0.54 28 7 0.12 29 17 0.30 30 1 0.02 ACGTcount: A:0.35, C:0.11, G:0.18, T:0.37 Consensus pattern (27 bp): AAACCAAGGGTATTTCAGTAATTTTGT Found at i:53130307 original size:27 final size:27 Alignment explanation

Indices: 53130284--53130540 Score: 304 Period size: 27 Copynumber: 9.6 Consensus size: 27 53130274 TCTGTAACTT * * 53130284 TGTAAATCAAGGGTAAAATAGTAATTC 1 TGTAAATCGAGGGTAAAACAGTAATTC * * * 53130311 GGTAAATCAAGGGTAAAATAGTAATTC 1 TGTAAATCGAGGGTAAAACAGTAATTC * * * 53130338 TATAAATCGACGGTAAAAC-GATAATTT 1 TGTAAATCGAGGGTAAAACAG-TAATTC 53130365 TGTAAATCGAGGGTAAAACAGTAATTC 1 TGTAAATCGAGGGTAAAACAGTAATTC * * * 53130392 TGTAAATCAAGGGTAAAACGGTAATTT 1 TGTAAATCGAGGGTAAAACAGTAATTC * * 53130419 TATAAATCGAGGGTAAAATAGTAATTC 1 TGTAAATCGAGGGTAAAACAGTAATTC * * 53130446 TGTAAATCGAGGGTAAAACGGTAATTT 1 TGTAAATCGAGGGTAAAACAGTAATTC * * 53130473 TGTAAATCGAGGGTAAAACGGTAATTA 1 TGTAAATCGAGGGTAAAACAGTAATTC * 53130500 TGTAAATTG-GGGTAAAAC-GATAATTC 1 TGTAAATCGAGGGTAAAACAG-TAATTC * 53130526 TGTAAATCGGGGGTA 1 TGTAAATCGAGGGTA 53130541 CTTTGGTAAT Statistics Matches: 200, Mismatches: 26, Indels: 8 0.85 0.11 0.03 Matches are distributed among these distances: 25 1 0.00 26 23 0.12 27 175 0.88 28 1 0.00 ACGTcount: A:0.41, C:0.08, G:0.23, T:0.28 Consensus pattern (27 bp): TGTAAATCGAGGGTAAAACAGTAATTC Found at i:53130381 original size:81 final size:81 Alignment explanation

Indices: 53130284--53130540 Score: 347 Period size: 81 Copynumber: 3.2 Consensus size: 81 53130274 TCTGTAACTT * * * ** * * 53130284 TGTAAATCAAGGGTAAAATAGTAATTCGGTAAATCAAGGGTAAAATAGTAATTCTATAAATCGAC 1 TGTAAATCGAGGGTAAAACAGTAATTCTGTAAATCAAGGGTAAAACGGTAATTATATAAATCGAG * 53130349 GGTAAAACGATAATTT 66 GGTAAAACGATAATTC * 53130365 TGTAAATCGAGGGTAAAACAGTAATTCTGTAAATCAAGGGTAAAACGGTAATTTTATAAATCGAG 1 TGTAAATCGAGGGTAAAACAGTAATTCTGTAAATCAAGGGTAAAACGGTAATTATATAAATCGAG * 53130430 GGTAAAA-TAGTAATTC 66 GGTAAAACGA-TAATTC * * * * * 53130446 TGTAAATCGAGGGTAAAACGGTAATTTTGTAAATCGAGGGTAAAACGGTAATTATGTAAATTG-G 1 TGTAAATCGAGGGTAAAACAGTAATTCTGTAAATCAAGGGTAAAACGGTAATTATATAAATCGAG 53130510 GGTAAAACGATAATTC 66 GGTAAAACGATAATTC * 53130526 TGTAAATCGGGGGTA 1 TGTAAATCGAGGGTA 53130541 CTTTGGTAAT Statistics Matches: 157, Mismatches: 17, Indels: 5 0.88 0.09 0.03 Matches are distributed among these distances: 80 29 0.18 81 128 0.82 ACGTcount: A:0.41, C:0.08, G:0.23, T:0.28 Consensus pattern (81 bp): TGTAAATCGAGGGTAAAACAGTAATTCTGTAAATCAAGGGTAAAACGGTAATTATATAAATCGAG GGTAAAACGATAATTC Found at i:53130567 original size:27 final size:26 Alignment explanation

Indices: 53130537--53130635 Score: 92 Period size: 27 Copynumber: 3.7 Consensus size: 26 53130527 GTAAATCGGG * * 53130537 GGTACTTTGGTAATTTTACAAGTCGAA 1 GGTA-TTTAGTAATTTTACAAATCGAA * 53130564 GGTATTTCAGTAATTTTACAAATCGAG 1 GGTATTT-AGTAATTTTACAAATCGAA * * 53130591 GGTATTTTAGTATTTTTACAAA-CTAA 1 GGTA-TTTAGTAATTTTACAAATCGAA * 53130617 GGGTATTTCGGTAATTTTA 1 -GGTATTT-AGTAATTTTA 53130636 GTAAACTAAA Statistics Matches: 60, Mismatches: 8, Indels: 8 0.79 0.11 0.11 Matches are distributed among these distances: 26 8 0.13 27 49 0.82 28 3 0.05 ACGTcount: A:0.30, C:0.09, G:0.19, T:0.41 Consensus pattern (26 bp): GGTATTTAGTAATTTTACAAATCGAA Found at i:53130594 original size:54 final size:54 Alignment explanation

Indices: 53130529--53130635 Score: 135 Period size: 54 Copynumber: 2.0 Consensus size: 54 53130519 ATAATTCTGT * * * 53130529 AAATCGGGGGTACTTTGGTAATTTTACAAGTCGAA-GGTATTTCAGTAATTTTAC 1 AAATCGAGGGTACTTTAGTAATTTTACAA-ACGAAGGGTATTTCAGTAATTTTAC * * * * 53130583 AAATCGAGGGTATTTTAGTATTTTTACAAACTAAGGGTATTTCGGTAATTTTA 1 AAATCGAGGGTACTTTAGTAATTTTACAAACGAAGGGTATTTCAGTAATTTTA 53130636 GTAAACTAAA Statistics Matches: 45, Mismatches: 7, Indels: 2 0.83 0.13 0.04 Matches are distributed among these distances: 53 3 0.07 54 42 0.93 ACGTcount: A:0.31, C:0.09, G:0.21, T:0.39 Consensus pattern (54 bp): AAATCGAGGGTACTTTAGTAATTTTACAAACGAAGGGTATTTCAGTAATTTTAC Found at i:53137238 original size:24 final size:24 Alignment explanation

Indices: 53137211--53137286 Score: 59 Period size: 24 Copynumber: 3.1 Consensus size: 24 53137201 CAAGGTTTAA 53137211 TATATCATCACATAAATACTTACC 1 TATATCATCACATAAATACTTACC * * * 53137235 TATATGACTGA-ATATACA-AGGTT-CC 1 TATATCA-TCACATA-A-ATA-CTTACC 53137260 ATATATCATCACATAAATACTTACC 1 -TATATCATCACATAAATACTTACC 53137285 TA 1 TA 53137287 CATGGCTGAA Statistics Matches: 38, Mismatches: 6, Indels: 16 0.63 0.10 0.27 Matches are distributed among these distances: 24 14 0.37 25 12 0.32 26 12 0.32 ACGTcount: A:0.41, C:0.21, G:0.05, T:0.33 Consensus pattern (24 bp): TATATCATCACATAAATACTTACC Found at i:53137285 original size:50 final size:50 Alignment explanation

Indices: 53137159--53137304 Score: 211 Period size: 50 Copynumber: 2.9 Consensus size: 50 53137149 TGCAAGATCA * * ** * 53137159 AATATATCATCACATAAATACTTACCCATATGTCCAAATATACAAGGTTT 1 AATATATCATCACATAAATACTTACCTATATGACTGAATATACAAGGTTC 53137209 AATATATCATCACATAAATACTTACCTATATGACTGAATATACAAGGTTC 1 AATATATCATCACATAAATACTTACCTATATGACTGAATATACAAGGTTC * * * * 53137259 CATATATCATCACATAAATACTTACCTACATGGCTGAAAATACAAG 1 AATATATCATCACATAAATACTTACCTATATGACTGAATATACAAG 53137305 ATCCAATAAT Statistics Matches: 87, Mismatches: 9, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 50 87 1.00 ACGTcount: A:0.42, C:0.20, G:0.08, T:0.30 Consensus pattern (50 bp): AATATATCATCACATAAATACTTACCTATATGACTGAATATACAAGGTTC Found at i:53137320 original size:50 final size:50 Alignment explanation

Indices: 53137151--53137320 Score: 193 Period size: 50 Copynumber: 3.4 Consensus size: 50 53137141 GCCGAATATG * * * * 53137151 CAAGATCAAATATATCATCACATAAATACTTACCCATATGTC-CAAATATA 1 CAAGATCCAATATATCATCACATAAATACTTACCTATATGACTGAAA-ATA * ** * 53137201 CAAGGTTTAATATATCATCACATAAATACTTACCTATATGACTGAATATA 1 CAAGATCCAATATATCATCACATAAATACTTACCTATATGACTGAAAATA * * * 53137251 CAAGGTTCC-ATATATCATCACATAAATACTTACCTACATGGCTGAAAATA 1 CAA-GATCCAATATATCATCACATAAATACTTACCTATATGACTGAAAATA 53137301 CAAGATCCAATA-ATACATCA 1 CAAGATCCAATATAT-CATCA 53137321 TTTATGTACG Statistics Matches: 102, Mismatches: 14, Indels: 8 0.82 0.11 0.06 Matches are distributed among these distances: 49 6 0.06 50 92 0.90 51 4 0.04 ACGTcount: A:0.44, C:0.21, G:0.07, T:0.29 Consensus pattern (50 bp): CAAGATCCAATATATCATCACATAAATACTTACCTATATGACTGAAAATA Found at i:53140059 original size:40 final size:40 Alignment explanation

Indices: 53140002--53140266 Score: 313 Period size: 40 Copynumber: 6.7 Consensus size: 40 53139992 CTAACGGGGT * * * * * 53140002 TAAGTCCCAAAGACATTTGTGCTAGTGATTAATTCCGGGC 1 TAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCCGGGC * 53140042 TAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCTGGGC 1 TAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCCGGGC 53140082 TAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCCGGGC 1 TAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCCGGGC * * * 53140122 TAAGTCCCGAAGGCTTTTGTGCGAGTTACAAATTTCGGGC 1 TAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCCGGGC * * 53140162 TAAG-CCCTGAAGGCATTTGTGCAAGTTA-TTATATCCGGGC 1 TAAGTCCC-GAAGGCATTTGTGCGAGTTACTAAT-TCCGGGC * * * * * 53140202 TAAGTCCCGAAGGCATCTGTGCTAGTGAC-CATATCCGGAC 1 TAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT-TCCGGGC * * 53140242 TAAGACCCGAAGGC-CTTGTGCGAGT 1 TAAGTCCCGAAGGCATTTGTGCGAGT 53140267 GGTTATATCC Statistics Matches: 197, Mismatches: 24, Indels: 9 0.86 0.10 0.04 Matches are distributed among these distances: 39 13 0.07 40 181 0.92 41 3 0.02 ACGTcount: A:0.24, C:0.22, G:0.26, T:0.28 Consensus pattern (40 bp): TAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCCGGGC Found at i:53148381 original size:41 final size:40 Alignment explanation

Indices: 53148254--53148398 Score: 202 Period size: 40 Copynumber: 3.6 Consensus size: 40 53148244 CTCGCACAAG * * * * 53148254 GCCTTCGGGTCTTAGCCCGGATATGGTCACTAGCATAAAT 1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT 53148294 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT 1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT * * * 53148334 GCCTTC-GGATCTTAGTCCGGATGTAGTCGCTTAGCACAAAA 1 GCCTTCGGGA-CTTAGCCCGGATATAGTCGC-TAGCACAAAT 53148375 GCCTTCGGGACTTAGCCCGGATAT 1 GCCTTCGGGACTTAGCCCGGATAT 53148399 CATTCGAGTA Statistics Matches: 93, Mismatches: 9, Indels: 5 0.87 0.08 0.05 Matches are distributed among these distances: 39 3 0.03 40 60 0.65 41 27 0.29 42 3 0.03 ACGTcount: A:0.23, C:0.26, G:0.26, T:0.26 Consensus pattern (40 bp): GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT Done.