Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: At_chr3

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: 100348136
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31

Warning! 3062571 characters in sequence are not A, C, G, or T


File 253 of 290

Found at i:87130861 original size:82 final size:81

Alignment explanation

Indices: 87130743--87130898 Score: 233 Period size: 82 Copynumber: 1.9 Consensus size: 81 87130733 TGCTATATAA * * 87130743 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA 1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA 87130808 CACTTAGTGCCGCATGG 65 CACTTAGTGCCGCATGG * * ** 87130825 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA 1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA 87130889 CACTTAGTGC 65 CACTTAGTGC 87130899 TGTACAATTT Statistics Matches: 67, Mismatches: 6, Indels: 3 0.88 0.08 0.04 Matches are distributed among these distances: 81 16 0.24 82 51 0.76 ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27 Consensus pattern (81 bp): TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC ACTTAGTGCCGCATGG Found at i:87131397 original size:12 final size:12 Alignment explanation

Indices: 87131380--87131406 Score: 54 Period size: 12 Copynumber: 2.2 Consensus size: 12 87131370 ATGGCATACT 87131380 TATGTATATATA 1 TATGTATATATA 87131392 TATGTATATATA 1 TATGTATATATA 87131404 TAT 1 TAT 87131407 ACTTCGGAAT Statistics Matches: 15, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 12 15 1.00 ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52 Consensus pattern (12 bp): TATGTATATATA Found at i:87143254 original size:45 final size:45 Alignment explanation

Indices: 87143199--87143288 Score: 162 Period size: 45 Copynumber: 2.0 Consensus size: 45 87143189 AAGCTTAAAA 87143199 ATTTTAACACATGCACATGTACATATAATGAGCATAAGTTATGAC 1 ATTTTAACACATGCACATGTACATATAATGAGCATAAGTTATGAC * * 87143244 ATTTTCACACATGCACATGTACATATAATGAGCATCAGTTATGAC 1 ATTTTAACACATGCACATGTACATATAATGAGCATAAGTTATGAC 87143289 GGTTAATTAT Statistics Matches: 43, Mismatches: 2, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 45 43 1.00 ACGTcount: A:0.38, C:0.18, G:0.13, T:0.31 Consensus pattern (45 bp): ATTTTAACACATGCACATGTACATATAATGAGCATAAGTTATGAC Found at i:87146144 original size:43 final size:43 Alignment explanation

Indices: 87146092--87146201 Score: 139 Period size: 43 Copynumber: 2.6 Consensus size: 43 87146082 AGGATTACCC * * * 87146092 ATATGTGATTACATGTAAGACCATGTCTTGGACATTGGCATCG 1 ATATATGATTACATGTAAGACCATGTCTGGGACAGTGGCATCG * * * * 87146135 TTATATGATTTCATGTAAGACCCTGTCTGGGACAGTGGCTTCG 1 ATATATGATTACATGTAAGACCATGTCTGGGACAGTGGCATCG * * 87146178 ATATGTGATAACATGTAAGACCAT 1 ATATATGATTACATGTAAGACCAT 87146202 ATCCGGGATA Statistics Matches: 55, Mismatches: 12, Indels: 0 0.82 0.18 0.00 Matches are distributed among these distances: 43 55 1.00 ACGTcount: A:0.28, C:0.16, G:0.23, T:0.33 Consensus pattern (43 bp): ATATATGATTACATGTAAGACCATGTCTGGGACAGTGGCATCG Found at i:87152976 original size:43 final size:43 Alignment explanation

Indices: 87152928--87153074 Score: 161 Period size: 43 Copynumber: 3.4 Consensus size: 43 87152918 GATTACCGAG * 87152928 ATGTGATTACATGTAAGACCATGTCTAGGACATTGGCATTGTA 1 ATGTGATTACATGTAAGACCATGTCTGGGACATTGGCATTGTA * * * 87152971 ATGTGATTACGTGTAAGACCATGTCTGGGACATTGGCATCGTT 1 ATGTGATTACATGTAAGACCATGTCTGGGACATTGGCATTGTA * * * * * * * * 87153014 ATATGATTTCGTGTAAGACCCTATCTGGGACAGTGTCA-TCTA 1 ATGTGATTACATGTAAGACCATGTCTGGGACATTGGCATTGTA * 87153056 TATGTGATAACATGTAAGA 1 -ATGTGATTACATGTAAGA 87153075 ACATATCCGG Statistics Matches: 86, Mismatches: 17, Indels: 2 0.82 0.16 0.02 Matches are distributed among these distances: 42 1 0.01 43 85 0.99 ACGTcount: A:0.29, C:0.15, G:0.24, T:0.33 Consensus pattern (43 bp): ATGTGATTACATGTAAGACCATGTCTGGGACATTGGCATTGTA Found at i:87158564 original size:34 final size:33 Alignment explanation

Indices: 87158504--87158574 Score: 81 Period size: 34 Copynumber: 2.1 Consensus size: 33 87158494 GCATTTCTGT 87158504 TACTATTACAATAATAGGCTAAGGCCCACACTGA 1 TACTATTACAATAATAGGCTAAGGCCC-CACTGA ** * * 87158538 TACTATTACTGTAAT-GGTCTATGGCCCTACTGA 1 TACTATTACAATAATAGG-CTAAGGCCCCACTGA 87158571 TACT 1 TACT 87158575 GGACTATCAC Statistics Matches: 32, Mismatches: 4, Indels: 3 0.82 0.10 0.08 Matches are distributed among these distances: 33 11 0.34 34 21 0.66 ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31 Consensus pattern (33 bp): TACTATTACAATAATAGGCTAAGGCCCCACTGA Found at i:87161048 original size:78 final size:78 Alignment explanation

Indices: 87160914--87161069 Score: 276 Period size: 78 Copynumber: 2.0 Consensus size: 78 87160904 TAATTCTATT * 87160914 CCCAAAATTTATTTTAAGTTATGGAAGCTAATTTTAAAAGTAATTGATTTACGAAAACGTGATGT 1 CCCAAAATTTATTTTAAGTTACGGAAGCTAATTTTAAAAGTAATTGATTTACGAAAACGTGATGT * 87160979 CAAAAACAACTAA 66 CAAAAAAAACTAA * * 87160992 CCCAAAATTTCTTTTAAGTTACGGAAGCTAATTTTAAAAGTAATTGATTTATGAAAACGTGATGT 1 CCCAAAATTTATTTTAAGTTACGGAAGCTAATTTTAAAAGTAATTGATTTACGAAAACGTGATGT 87161057 CAAAAAAAACTAA 66 CAAAAAAAACTAA 87161070 GTTGCGAAAC Statistics Matches: 74, Mismatches: 4, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 78 74 1.00 ACGTcount: A:0.44, C:0.12, G:0.13, T:0.32 Consensus pattern (78 bp): CCCAAAATTTATTTTAAGTTACGGAAGCTAATTTTAAAAGTAATTGATTTACGAAAACGTGATGT CAAAAAAAACTAA Found at i:87161529 original size:31 final size:33 Alignment explanation

Indices: 87161473--87161537 Score: 89 Period size: 32 Copynumber: 2.0 Consensus size: 33 87161463 TTTGGGTCAC * * 87161473 AACCTATAACAGAATCAATTGGGCCT-AGCCCA 1 AACCAATAACAGAATCAAGTGGGCCTAAGCCCA * 87161505 AACCAATAACAGGA-CAAGTGGGCCTAAGCCCA 1 AACCAATAACAGAATCAAGTGGGCCTAAGCCCA 87161537 A 1 A 87161538 TACAGTGACA Statistics Matches: 29, Mismatches: 3, Indels: 2 0.85 0.09 0.06 Matches are distributed among these distances: 31 10 0.34 32 19 0.66 ACGTcount: A:0.40, C:0.28, G:0.18, T:0.14 Consensus pattern (33 bp): AACCAATAACAGAATCAAGTGGGCCTAAGCCCA Found at i:87161785 original size:32 final size:32 Alignment explanation

Indices: 87161740--87161822 Score: 103 Period size: 32 Copynumber: 2.6 Consensus size: 32 87161730 CTCTAAGTCT * 87161740 TCAGTAGCGGTATTATAATTGGCACAAAGCCA 1 TCAGTAACGGTATTATAATTGGCACAAAGCCA * ** * 87161772 TCAGTAACTGTATTATGTTTGGCACATAGCCA 1 TCAGTAACGGTATTATAATTGGCACAAAGCCA * * 87161804 TCAGCAACGGTAATATAAT 1 TCAGTAACGGTATTATAAT 87161823 CGACACAGAG Statistics Matches: 41, Mismatches: 10, Indels: 0 0.80 0.20 0.00 Matches are distributed among these distances: 32 41 1.00 ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29 Consensus pattern (32 bp): TCAGTAACGGTATTATAATTGGCACAAAGCCA Found at i:87162326 original size:27 final size:27 Alignment explanation

Indices: 87162294--87162408 Score: 112 Period size: 27 Copynumber: 4.3 Consensus size: 27 87162284 CAAAACAATC 87162294 ATTTTACCTTAC-AGGAGTATTTCGATA 1 ATTTTACCTTACAAGG-GTATTTCGATA 87162321 ATTTTACAC-TACAAGGGTATTTCGGA-A 1 ATTTTAC-CTTACAAGGGTATTTC-GATA * * 87162348 ATTTTTCATTACAAGGGTATTTCGATA 1 ATTTTACCTTACAAGGGTATTTCGATA * * * * 87162375 ATTTTACAATT-CAAGGATATTTTGGTA 1 ATTTTAC-CTTACAAGGGTATTTCGATA 87162402 ATTTTAC 1 ATTTTAC 87162409 AAATAGAGGT Statistics Matches: 76, Mismatches: 6, Indels: 12 0.81 0.06 0.13 Matches are distributed among these distances: 26 2 0.03 27 65 0.86 28 9 0.12 ACGTcount: A:0.31, C:0.12, G:0.15, T:0.42 Consensus pattern (27 bp): ATTTTACCTTACAAGGGTATTTCGATA Found at i:87162352 original size:54 final size:54 Alignment explanation

Indices: 87162294--87162409 Score: 153 Period size: 54 Copynumber: 2.1 Consensus size: 54 87162284 CAAAACAATC * * * 87162294 ATTTTACCTTAC-AGGAGTATTTCGATAATTTTACACTACAAGGGTATTTCGGAA 1 ATTTTACATTACAAGG-GTATTTCGATAATTTTACAATACAAGGATATTTCGGAA * * * * 87162348 ATTTTTCATTACAAGGGTATTTCGATAATTTTACAATTCAAGGATATTTTGGTA 1 ATTTTACATTACAAGGGTATTTCGATAATTTTACAATACAAGGATATTTCGGAA 87162402 ATTTTACA 1 ATTTTACA 87162410 AATAGAGGTC Statistics Matches: 53, Mismatches: 8, Indels: 2 0.84 0.13 0.03 Matches are distributed among these distances: 54 50 0.94 55 3 0.06 ACGTcount: A:0.32, C:0.12, G:0.15, T:0.41 Consensus pattern (54 bp): ATTTTACATTACAAGGGTATTTCGATAATTTTACAATACAAGGATATTTCGGAA Found at i:87162409 original size:27 final size:27 Alignment explanation

Indices: 87162310--87162410 Score: 114 Period size: 27 Copynumber: 3.7 Consensus size: 27 87162300 CCTTACAGGA * * * 87162310 GTATTTCGATAATTTTACACTACAAGG 1 GTATTTCGGTAATTTTACAATTCAAGG * * 87162337 GTATTTCGGAAATTTTTC-ATTACAAGG 1 GTATTTCGGTAATTTTACAATT-CAAGG * 87162364 GTATTTCGATAATTTTACAATTCAAGG 1 GTATTTCGGTAATTTTACAATTCAAGG * * 87162391 ATATTTTGGTAATTTTACAA 1 GTATTTCGGTAATTTTACAA 87162411 ATAGAGGTCT Statistics Matches: 61, Mismatches: 11, Indels: 4 0.80 0.14 0.05 Matches are distributed among these distances: 26 1 0.02 27 57 0.93 28 3 0.05 ACGTcount: A:0.33, C:0.11, G:0.15, T:0.42 Consensus pattern (27 bp): GTATTTCGGTAATTTTACAATTCAAGG Found at i:87182666 original size:13 final size:13 Alignment explanation

Indices: 87182645--87182677 Score: 57 Period size: 13 Copynumber: 2.5 Consensus size: 13 87182635 TGGGCTTCCT 87182645 CACACGGGTAAGC 1 CACACGGGTAAGC * 87182658 CACATGGGTAAGC 1 CACACGGGTAAGC 87182671 CACACGG 1 CACACGG 87182678 CCGTGTCCAT Statistics Matches: 18, Mismatches: 2, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 13 18 1.00 ACGTcount: A:0.30, C:0.30, G:0.30, T:0.09 Consensus pattern (13 bp): CACACGGGTAAGC Found at i:87191515 original size:54 final size:54 Alignment explanation

Indices: 87191363--87191519 Score: 154 Period size: 54 Copynumber: 2.9 Consensus size: 54 87191353 GTGTTGGTAG * * * * * 87191363 ACTATCCCACGTTTATTGTCCCAGTGGATTATCCCATGTCTA-CTATCCTAGCAG 1 ACTAACCCACGTTTATTGTCACAATGGATTATCCCATGTCTATC-GTCCTAGCAA * ** * * * * * * 87191417 ACTAACCCACGTTTATTTTCATGACGGACTATCCCGTGTTTATCGTCTTGGCAA 1 ACTAACCCACGTTTATTGTCACAATGGATTATCCCATGTCTATCGTCCTAGCAA * * 87191471 ACTAACCCACATTTATTGTCACAATGGATTATCCCATGCCTATCGTCCT 1 ACTAACCCACGTTTATTGTCACAATGGATTATCCCATGTCTATCGTCCT 87191520 GGTGGACCGT Statistics Matches: 78, Mismatches: 24, Indels: 2 0.75 0.23 0.02 Matches are distributed among these distances: 54 77 0.99 55 1 0.01 ACGTcount: A:0.24, C:0.29, G:0.14, T:0.34 Consensus pattern (54 bp): ACTAACCCACGTTTATTGTCACAATGGATTATCCCATGTCTATCGTCCTAGCAA Found at i:87197842 original size:57 final size:58 Alignment explanation

Indices: 87197761--87197871 Score: 143 Period size: 58 Copynumber: 1.9 Consensus size: 58 87197751 AAATCCACAT * * 87197761 ACCTCTATCTGGCCCATTAAGCCC-AATCATACTCATATGGCCTATTAGGCCCAAACC 1 ACCTCTATATGGCCCATTAAGCCCAAATCACACTCATATGGCCTATTAGGCCCAAACC * * * * * * 87197818 ACCTGTATATGGCCCATTAGGCCCAAATCACATTTATATGGCTTGTTAGGCCCA 1 ACCTCTATATGGCCCATTAAGCCCAAATCACACTCATATGGCCTATTAGGCCCA 87197872 GTCACATCCA Statistics Matches: 45, Mismatches: 8, Indels: 1 0.83 0.15 0.02 Matches are distributed among these distances: 57 21 0.47 58 24 0.53 ACGTcount: A:0.27, C:0.31, G:0.15, T:0.27 Consensus pattern (58 bp): ACCTCTATATGGCCCATTAAGCCCAAATCACACTCATATGGCCTATTAGGCCCAAACC Found at i:87197866 original size:29 final size:29 Alignment explanation

Indices: 87197795--87197871 Score: 100 Period size: 29 Copynumber: 2.7 Consensus size: 29 87197785 AATCATACTC * 87197795 ATATGGCCTATTAGGCCCAAACCACCTGT 1 ATATGGCCTATTAGGCCCAAACCACATGT * * * 87197824 ATATGGCCCATTAGGCCCAAATCACATTT 1 ATATGGCCTATTAGGCCCAAACCACATGT * * 87197853 ATATGGCTTGTTAGGCCCA 1 ATATGGCCTATTAGGCCCA 87197872 GTCACATCCA Statistics Matches: 41, Mismatches: 7, Indels: 0 0.85 0.15 0.00 Matches are distributed among these distances: 29 41 1.00 ACGTcount: A:0.27, C:0.27, G:0.18, T:0.27 Consensus pattern (29 bp): ATATGGCCTATTAGGCCCAAACCACATGT Found at i:87197965 original size:17 final size:18 Alignment explanation

Indices: 87197943--87197976 Score: 52 Period size: 17 Copynumber: 1.9 Consensus size: 18 87197933 TGCCTATTAT 87197943 GGGCCCAAC-AGCCCATC 1 GGGCCCAACTAGCCCATC * 87197960 GGGCCCATCTAGCCCAT 1 GGGCCCAACTAGCCCAT 87197977 TCTGGCTCGT Statistics Matches: 15, Mismatches: 1, Indels: 1 0.88 0.06 0.06 Matches are distributed among these distances: 17 8 0.53 18 7 0.47 ACGTcount: A:0.21, C:0.44, G:0.24, T:0.12 Consensus pattern (18 bp): GGGCCCAACTAGCCCATC Found at i:87198108 original size:8 final size:8 Alignment explanation

Indices: 87198095--87198140 Score: 56 Period size: 8 Copynumber: 5.8 Consensus size: 8 87198085 GTAGCTAAAC * 87198095 TTTCGACT 1 TTTCGACA 87198103 TTTCGACA 1 TTTCGACA * 87198111 TTTAGACA 1 TTTCGACA * 87198119 TTTCGGCA 1 TTTCGACA * 87198127 TTTCGGCA 1 TTTCGACA 87198135 TTTCGA 1 TTTCGA 87198141 GTTTTACCGA Statistics Matches: 33, Mismatches: 5, Indels: 0 0.87 0.13 0.00 Matches are distributed among these distances: 8 33 1.00 ACGTcount: A:0.20, C:0.22, G:0.17, T:0.41 Consensus pattern (8 bp): TTTCGACA Found at i:87202392 original size:29 final size:29 Alignment explanation

Indices: 87202326--87202433 Score: 110 Period size: 29 Copynumber: 3.8 Consensus size: 29 87202316 TCCAAATACC * * * * 87202326 TGTATCTGGCCCATTAAGCCC-AATCATA 1 TGTATATGGCCCATTAGGCCCAAACCACA * * * * 87202354 TTTATATGGCCTATTGGGCCCAAACCACC 1 TGTATATGGCCCATTAGGCCCAAACCACA * 87202383 TGTATATGGCCCATTAGGCCCAAATCACA 1 TGTATATGGCCCATTAGGCCCAAACCACA * * 87202412 TTTATATGGCCCGTTAGGCCCA 1 TGTATATGGCCCATTAGGCCCA 87202434 GCCACATTCA Statistics Matches: 64, Mismatches: 15, Indels: 1 0.80 0.19 0.01 Matches are distributed among these distances: 28 16 0.25 29 48 0.75 ACGTcount: A:0.26, C:0.29, G:0.18, T:0.28 Consensus pattern (29 bp): TGTATATGGCCCATTAGGCCCAAACCACA Found at i:87203406 original size:412 final size:412 Alignment explanation

Indices: 87202636--87203410 Score: 1496 Period size: 412 Copynumber: 1.9 Consensus size: 412 87202626 GCTTTTTGAC * * * 87202636 ATTTCAGCATTTCGACTTTTATCGATCTACTTGTGTGTACTGTGTATGTACACACCTGGTAAGCA 1 ATTTCAGCATTTCGACTTTTACCGAACTACTTGTGTGTACAGTGTATGTACACACCTGGTAAGCA 87202701 AGCGTGCTACAATTCCCTTAGTTACCAACCTACAACGATATCATCCTTCAATTAATCGCATGCCT 66 AGCGTGCTACAATTCCCTTAGTTACCAACCTACAACGATATCATCCTTCAATTAATCGCATGCCT 87202766 AATGCATATCTTTAATAAAACCGAAACCTCACCTTAACCTTACCTTGAACACCAATCCCTAATAG 131 AATGCATATCTTTAATAAAACCGAAACCTCACCTTAACCTTACCTTGAACACCAATCCCTAATAG 87202831 TTTTTCCTCAATCACGTACTCCTTGGATCTATATTAATCTTACTTATTAAAACTAGAATAATAGG 196 TTTTTCCTCAATCACGTACTCCTTGGATCTATATTAATCTTACTTATTAAAACTAGAATAATAGG 87202896 TGACTCGTATCCAAAACAAGTCCCATTACCTTAACTATGACCATTTGGCCAACCAATATCAAGAG 261 TGACTCGTATCCAAAACAAGTCCCATTACCTTAACTATGACCATTTGGCCAACCAATATCAAGAG 87202961 CACTTACCAAAGTCTTTCACCTGAGGAGCAAATCGGAAAGGCTACCGTAGCTAAACTTTCGACTT 326 CACTTACCAAAGTCTTTCACCTGAGGAGCAAATCGGAAAGGCTACCGTAGCTAAACTTTCGACTT 87203026 TTCGACATTTAGACATTTCGGT 391 TTCGACATTTAGACATTTCGGT * * * 87203048 ATTTCGGCATTTCGAGTTTTACCGAACTACTTGTGTGTGCAGTGTATGTACACACCTGGTAAGCA 1 ATTTCAGCATTTCGACTTTTACCGAACTACTTGTGTGTACAGTGTATGTACACACCTGGTAAGCA 87203113 AGCGTGCTACAATTCCCTTAGTTACCAACCTACAACGATATCATCCTTCAATTAATCGCATGCCT 66 AGCGTGCTACAATTCCCTTAGTTACCAACCTACAACGATATCATCCTTCAATTAATCGCATGCCT 87203178 AATGCATATCTTTAATAAAACCGAAACCTCACCTTAACCTTACCTTGAACACCAATCCCTAATAG 131 AATGCATATCTTTAATAAAACCGAAACCTCACCTTAACCTTACCTTGAACACCAATCCCTAATAG 87203243 TTTTTCCTCAATCACGTACTCCTTGGATCTATATTAATCTTACTTATTAAAACTAGAATAATAGG 196 TTTTTCCTCAATCACGTACTCCTTGGATCTATATTAATCTTACTTATTAAAACTAGAATAATAGG 87203308 TGACTCGTATCCAAAACAAGTCCCATTACCTTAACTATGACCATTTGGCCAACCAATATCAAGAG 261 TGACTCGTATCCAAAACAAGTCCCATTACCTTAACTATGACCATTTGGCCAACCAATATCAAGAG 87203373 CACTTACCAAAGTCTTTCACCTGAGGAGCAAATCGGAA 326 CACTTACCAAAGTCTTTCACCTGAGGAGCAAATCGGAA 87203411 GATATCCAAG Statistics Matches: 357, Mismatches: 6, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 412 357 1.00 ACGTcount: A:0.31, C:0.25, G:0.13, T:0.30 Consensus pattern (412 bp): ATTTCAGCATTTCGACTTTTACCGAACTACTTGTGTGTACAGTGTATGTACACACCTGGTAAGCA AGCGTGCTACAATTCCCTTAGTTACCAACCTACAACGATATCATCCTTCAATTAATCGCATGCCT AATGCATATCTTTAATAAAACCGAAACCTCACCTTAACCTTACCTTGAACACCAATCCCTAATAG TTTTTCCTCAATCACGTACTCCTTGGATCTATATTAATCTTACTTATTAAAACTAGAATAATAGG TGACTCGTATCCAAAACAAGTCCCATTACCTTAACTATGACCATTTGGCCAACCAATATCAAGAG CACTTACCAAAGTCTTTCACCTGAGGAGCAAATCGGAAAGGCTACCGTAGCTAAACTTTCGACTT TTCGACATTTAGACATTTCGGT Found at i:87204534 original size:29 final size:29 Alignment explanation

Indices: 87204471--87204541 Score: 88 Period size: 29 Copynumber: 2.4 Consensus size: 29 87204461 GTCGACCATC * 87204471 AGGCCCAATTCACATTCATATAGCCTATA 1 AGGCCCAATTCACATTCATATAGCCGATA * * * * 87204500 AAGCCCAATTCATATTCATATGGCCGATT 1 AGGCCCAATTCACATTCATATAGCCGATA * 87204529 AGGCCCAAATCAC 1 AGGCCCAATTCAC 87204542 CTTTATATGT Statistics Matches: 34, Mismatches: 8, Indels: 0 0.81 0.19 0.00 Matches are distributed among these distances: 29 34 1.00 ACGTcount: A:0.34, C:0.28, G:0.13, T:0.25 Consensus pattern (29 bp): AGGCCCAATTCACATTCATATAGCCGATA Found at i:87204549 original size:29 final size:28 Alignment explanation

Indices: 87204517--87204577 Score: 88 Period size: 29 Copynumber: 2.1 Consensus size: 28 87204507 ATTCATATTC 87204517 ATATGGC-CGATTAGGCCCAAATCACCTTT 1 ATATGGCTCG-TTAGGCCCAAATCACC-TT * 87204546 ATATGTCTCGTTAGGCCCAAATCACCTT 1 ATATGGCTCGTTAGGCCCAAATCACCTT 87204574 ATAT 1 ATAT 87204578 TCATGCTCAC Statistics Matches: 30, Mismatches: 1, Indels: 3 0.88 0.03 0.09 Matches are distributed among these distances: 28 6 0.20 29 22 0.73 30 2 0.07 ACGTcount: A:0.28, C:0.26, G:0.15, T:0.31 Consensus pattern (28 bp): ATATGGCTCGTTAGGCCCAAATCACCTT Found at i:87204831 original size:16 final size:16 Alignment explanation

Indices: 87204789--87204823 Score: 52 Period size: 16 Copynumber: 2.2 Consensus size: 16 87204779 GCAACCAAAC * * 87204789 TTTCGACTTTTGGGCA 1 TTTCGCCTTTTCGGCA 87204805 TTTCGCCTTTTCGGCA 1 TTTCGCCTTTTCGGCA 87204821 TTT 1 TTT 87204824 TGGCTTTTGT Statistics Matches: 17, Mismatches: 2, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 16 17 1.00 ACGTcount: A:0.09, C:0.23, G:0.20, T:0.49 Consensus pattern (16 bp): TTTCGCCTTTTCGGCA Found at i:87209933 original size:42 final size:42 Alignment explanation

Indices: 87209874--87210040 Score: 201 Period size: 42 Copynumber: 4.0 Consensus size: 42 87209864 GGAAATATTT * 87209874 GAGATAGCTTCAGCTATGCATTAGCACTTAGTGTGCGAGATC 1 GAGATAGCTTCAGCTATGCATTGGCACTTAGTGTGCGAGATC * * 87209916 GAGATAGCTTCGGCTATGCATTGGCACTTAGTGTTCGAGATC 1 GAGATAGCTTCAGCTATGCATTGGCACTTAGTGTGCGAGATC * * * * 87209958 AAGATAGCTTC-GACTATGCATTGGCACTTAGTGTGTGTGATT 1 GAGATAGCTTCAG-CTATGCATTGGCACTTAGTGTGCGAGATC * *** * * 87210000 GAGTTAGCTTCAGCTACATATTGGCACTTAGTTTACGAGAT 1 GAGATAGCTTCAGCTATGCATTGGCACTTAGTGTGCGAGAT 87210041 TCCCGAGTAA Statistics Matches: 106, Mismatches: 17, Indels: 4 0.83 0.13 0.03 Matches are distributed among these distances: 41 1 0.01 42 104 0.98 43 1 0.01 ACGTcount: A:0.25, C:0.17, G:0.26, T:0.32 Consensus pattern (42 bp): GAGATAGCTTCAGCTATGCATTGGCACTTAGTGTGCGAGATC Found at i:87210156 original size:32 final size:32 Alignment explanation

Indices: 87210111--87210174 Score: 110 Period size: 32 Copynumber: 2.0 Consensus size: 32 87210101 ATGAGATTGG * * 87210111 TACGAGATTGTACAGGTATGTACGAAAATTCA 1 TACGAGATGGTACAAGTATGTACGAAAATTCA 87210143 TACGAGATGGTACAAGTATGTACGAAAATTCA 1 TACGAGATGGTACAAGTATGTACGAAAATTCA 87210175 ATTGAGTGTT 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:0.39, C:0.12, G:0.22, T:0.27 Consensus pattern (32 bp): TACGAGATGGTACAAGTATGTACGAAAATTCA Found at i:87211731 original size:24 final size:24 Alignment explanation

Indices: 87211703--87211800 Score: 115 Period size: 24 Copynumber: 4.0 Consensus size: 24 87211693 AAGGCTGACA * 87211703 GGAGAAGATTTAGGAGCTGATAAG 1 GGAGAAGATTTAGAAGCTGATAAG * * 87211727 GGAGAGGATTTAGGAGCTGATAAG 1 GGAGAAGATTTAGAAGCTGATAAG * * * * * 87211751 GGAGAGGTTTTAGAATCTAATAAA 1 GGAGAAGATTTAGAAGCTGATAAG 87211775 GGAGAAGATTTAGAAGCTGATCAAG 1 GGAGAAGATTTAGAAGCTGAT-AAG 87211800 G 1 G 87211801 AGCAGGAGTT Statistics Matches: 62, Mismatches: 11, Indels: 1 0.84 0.15 0.01 Matches are distributed among these distances: 24 59 0.95 25 3 0.05 ACGTcount: A:0.38, C:0.05, G:0.35, T:0.22 Consensus pattern (24 bp): GGAGAAGATTTAGAAGCTGATAAG Found at i:87219674 original size:24 final size:24 Alignment explanation

Indices: 87219641--87219738 Score: 133 Period size: 24 Copynumber: 4.0 Consensus size: 24 87219631 AAGGCTATCA * 87219641 GGAGAAGATTTAGGAGCTGTTAAG 1 GGAGAAGATTTAGGAGCTGATAAG * 87219665 GGAGAGGATTTAGGAGCTGATAAG 1 GGAGAAGATTTAGGAGCTGATAAG * * * 87219689 GGAGAGGATTTAGGAGATGATAAA 1 GGAGAAGATTTAGGAGCTGATAAG * 87219713 GGAGAAGATTTAGAAGCTGATCAAG 1 GGAGAAGATTTAGGAGCTGAT-AAG 87219738 G 1 G 87219739 AGCAGGAGTT Statistics Matches: 65, Mismatches: 8, Indels: 1 0.88 0.11 0.01 Matches are distributed among these distances: 24 62 0.95 25 3 0.05 ACGTcount: A:0.37, C:0.04, G:0.38, T:0.21 Consensus pattern (24 bp): GGAGAAGATTTAGGAGCTGATAAG Found at i:87227981 original size:47 final size:47 Alignment explanation

Indices: 87227912--87228834 Score: 1648 Period size: 47 Copynumber: 19.7 Consensus size: 47 87227902 GGCCATAAGT 87227912 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCAC 1 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCAC * * * * 87227959 GAACTCGGACTCAACTCAACGAGTTC-G--GCGT--TTGCATCCATGAGT 1 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT-C-TCA-C * * * * * 87228004 GAACTCAGACTCAACTCAACGAGTTCGGA---C-ATTTGCATCCATAAGT 1 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT-C-TCA-C 87228050 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCAC 1 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCAC 87228097 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCAC 1 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCAC 87228144 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCAC 1 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCAC 87228191 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCAC 1 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCAC 87228238 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCAC 1 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCAC 87228285 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCAC 1 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCAC 87228332 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCAC 1 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCAC 87228379 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCAC 1 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCAC 87228426 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCAC 1 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCAC 87228473 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCAC 1 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCAC 87228520 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCAC 1 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCAC 87228567 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCAC 1 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCAC 87228614 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCAC 1 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCAC 87228661 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCAC 1 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCAC 87228708 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCAC 1 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCAC 87228755 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCAC 1 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCAC 87228802 GAACTCGGACTCAACTCAACGAGTTCGGATGCC 1 GAACTCGGACTCAACTCAACGAGTTCGGATGCC 87228835 CAAATATCCC Statistics Matches: 853, Mismatches: 12, Indels: 22 0.96 0.01 0.02 Matches are distributed among these distances: 42 5 0.01 43 1 0.00 44 5 0.01 45 25 0.03 46 43 0.05 47 764 0.90 48 2 0.00 49 2 0.00 50 6 0.01 ACGTcount: A:0.28, C:0.29, G:0.20, T:0.23 Consensus pattern (47 bp): GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCAC Found at i:87229328 original size:47 final size:47 Alignment explanation

Indices: 87229274--87229366 Score: 177 Period size: 47 Copynumber: 2.0 Consensus size: 47 87229264 TACAATTTTA * 87229274 CCCCTAAACTTTTGCATATTTACACTTTTGCCCCAAAGCTCGTAAAG 1 CCCCTAAACTTTTCCATATTTACACTTTTGCCCCAAAGCTCGTAAAG 87229321 CCCCTAAACTTTTCCATATTTACACTTTTGCCCCAAAGCTCGTAAA 1 CCCCTAAACTTTTCCATATTTACACTTTTGCCCCAAAGCTCGTAAA 87229367 TTAAACTTCA Statistics Matches: 45, Mismatches: 1, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 47 45 1.00 ACGTcount: A:0.28, C:0.31, G:0.09, T:0.32 Consensus pattern (47 bp): CCCCTAAACTTTTCCATATTTACACTTTTGCCCCAAAGCTCGTAAAG Found at i:87233099 original size:26 final size:26 Alignment explanation

Indices: 87233070--87233131 Score: 97 Period size: 26 Copynumber: 2.4 Consensus size: 26 87233060 CAACCTTAAC * * 87233070 CCTAGTGGTATATCAGTAATTTTGCT 1 CCTAGGGGCATATCAGTAATTTTGCT * 87233096 CCTAGGGGCATATCAGTAATTTTTCT 1 CCTAGGGGCATATCAGTAATTTTGCT 87233122 CCTAGGGGCA 1 CCTAGGGGCA 87233132 AATCTATAAA Statistics Matches: 33, Mismatches: 3, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 26 33 1.00 ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35 Consensus pattern (26 bp): CCTAGGGGCATATCAGTAATTTTGCT Found at i:87233152 original size:27 final size:26 Alignment explanation

Indices: 87233081--87233152 Score: 83 Period size: 26 Copynumber: 2.7 Consensus size: 26 87233071 CTAGTGGTAT * * 87233081 ATCAGTAATTTTGCTCCTAGGGGCAT 1 ATCAGTAATTTTCCTCCTAGGGGCAA * 87233107 ATCAGTAATTTTTCTCCTAGGGGCAA 1 ATCAGTAATTTTCCTCCTAGGGGCAA * 87233133 ATCTA-TAAATTTTCCACCTA 1 ATC-AGT-AATTTTCCTCCTA 87233153 TAAAGGTATT Statistics Matches: 40, Mismatches: 4, Indels: 3 0.85 0.09 0.06 Matches are distributed among these distances: 26 28 0.70 27 12 0.30 ACGTcount: A:0.28, C:0.21, G:0.15, T:0.36 Consensus pattern (26 bp): ATCAGTAATTTTCCTCCTAGGGGCAA Found at i:87236532 original size:28 final size:27 Alignment explanation

Indices: 87236469--87236593 Score: 187 Period size: 28 Copynumber: 4.6 Consensus size: 27 87236459 ATATTAAGTC * * 87236469 CGCACACTCAGTGCTATATAATCAACT 1 CGCACACTTAGTGCTACATAATCAACT 87236496 CGCACACTTAGTGCTACATAATCAAACT 1 CGCACACTTAGTGCTACATAATC-AACT * 87236524 CGCACACTTAGTGCTACATAGTCAAACT 1 CGCACACTTAGTGCTACATAATC-AACT * * 87236552 CGCACACTTAGTGCTACATAGTCAATT 1 CGCACACTTAGTGCTACATAATCAACT 87236579 CGCACACTTAGTGCT 1 CGCACACTTAGTGCT 87236594 GCACAATTTA Statistics Matches: 93, Mismatches: 4, Indels: 2 0.94 0.04 0.02 Matches are distributed among these distances: 27 39 0.42 28 54 0.58 ACGTcount: A:0.31, C:0.29, G:0.14, T:0.26 Consensus pattern (27 bp): CGCACACTTAGTGCTACATAATCAACT Found at i:87236614 original size:56 final size:56 Alignment explanation

Indices: 87236469--87236593 Score: 173 Period size: 55 Copynumber: 2.3 Consensus size: 56 87236459 ATATTAAGTC * * * * 87236469 CGCACACTCAGTGCTATATAATC-AACTCGCACACTTAGTGCTACATAATCAAACT 1 CGCACACTTAGTGCTACATAGTCAAACCCGCACACTTAGTGCTACATAATCAAACT * * * 87236524 CGCACACTTAGTGCTACATAGTCAAACTCGCACACTTAGTGCTACATAGTC-AATT 1 CGCACACTTAGTGCTACATAGTCAAACCCGCACACTTAGTGCTACATAATCAAACT 87236579 CGCACACTTAGTGCT 1 CGCACACTTAGTGCT 87236594 GCACAATTTA Statistics Matches: 64, Mismatches: 5, Indels: 2 0.90 0.07 0.03 Matches are distributed among these distances: 55 38 0.59 56 26 0.41 ACGTcount: A:0.31, C:0.29, G:0.14, T:0.26 Consensus pattern (56 bp): CGCACACTTAGTGCTACATAGTCAAACCCGCACACTTAGTGCTACATAATCAAACT Found at i:87240118 original size:93 final size:93 Alignment explanation

Indices: 87240006--87240178 Score: 274 Period size: 93 Copynumber: 1.9 Consensus size: 93 87239996 CGCCGATAAG * * * 87240006 CGAACTCGGACTAAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCAGACTCAACTCA 1 CGAACTCAGACTAAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCAGACTCAACTCA 87240071 ACAAGCTCGGATGCCTAGTTACATCTCA 66 ACAAGCTCGGATGCCTAGTTACATCTCA * * * 87240099 CGAACTCAGACTCAACTCAACGAGTTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCA 1 CGAACTCAGACTAAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCAGACTCAACTCA * * 87240164 ACGAGTTCGGATGCC 66 ACAAGCTCGGATGCC 87240179 CAAATATCCC Statistics Matches: 72, Mismatches: 8, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 93 72 1.00 ACGTcount: A:0.29, C:0.31, G:0.20, T:0.20 Consensus pattern (93 bp): CGAACTCAGACTAAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCAGACTCAACTCA ACAAGCTCGGATGCCTAGTTACATCTCA Found at i:87240174 original size:46 final size:46 Alignment explanation

Indices: 87240001--87240174 Score: 174 Period size: 46 Copynumber: 3.8 Consensus size: 46 87239991 TAACCCGCCG * * * * 87240001 ATAAGCGAACTCGGACTAAACTCAACGAGCTCGGGCGTTCGCATCC 1 ATAAGCGAACTCAGACTCAACTCAACGAGCTCGGACGCTCGCATCC * * * * 87240047 ATAAGTGAACTCAGACTCAACTCAACAAGCTCGGATGCCTAGTTACAT-C 1 ATAAGCGAACTCAGACTCAACTCAACGAGCTCGGACG-CTCG---CATCC * * 87240096 -TCA-CGAACTCAGACTCAACTCAACGAGTTCGGACGCTCGCATCC 1 ATAAGCGAACTCAGACTCAACTCAACGAGCTCGGACGCTCGCATCC * * * 87240140 ATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA 1 ATAAGCGAACTCAGACTCAACTCAACGAGCTCGGA 87240175 TGCCCAAATA Statistics Matches: 104, Mismatches: 17, Indels: 14 0.77 0.13 0.10 Matches are distributed among these distances: 43 3 0.03 44 1 0.01 45 2 0.02 46 62 0.60 47 30 0.29 48 2 0.02 49 1 0.01 50 3 0.03 ACGTcount: A:0.31, C:0.29, G:0.20, T:0.20 Consensus pattern (46 bp): ATAAGCGAACTCAGACTCAACTCAACGAGCTCGGACGCTCGCATCC Found at i:87240193 original size:46 final size:45 Alignment explanation

Indices: 87240050--87240193 Score: 121 Period size: 46 Copynumber: 3.1 Consensus size: 45 87240040 CGCATCCATA * * * * 87240050 AGTGAACTCAGACTCAACTCAACAAGCTCGGATGCCTAGTTACATCTC 1 AGTGAACTCAGACTCAACTCAACGAGTTCGGATGCCCA---ACATCCC * * * * * 87240098 A-CGAACTCAGACTCAACTCAACGAGTTCGGACGCTC-GCATCCATA 1 AGTGAACTCAGACTCAACTCAACGAGTTCGGATGCCCAACATCC--C * * 87240143 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCAAATATCCC 1 AGTGAACTCAGACTCAACTCAACGAGTTCGGATGCCC-AACATCCC 87240189 AGTGA 1 AGTGA 87240194 CATGTCACTT Statistics Matches: 75, Mismatches: 16, Indels: 12 0.73 0.16 0.12 Matches are distributed among these distances: 43 4 0.05 45 1 0.01 46 36 0.48 47 29 0.39 48 5 0.07 ACGTcount: A:0.31, C:0.30, G:0.19, T:0.20 Consensus pattern (45 bp): AGTGAACTCAGACTCAACTCAACGAGTTCGGATGCCCAACATCCC Found at i:87240767 original size:74 final size:74 Alignment explanation

Indices: 87240646--87240793 Score: 278 Period size: 74 Copynumber: 2.0 Consensus size: 74 87240636 ATACACTTTT * 87240646 GCCCCAAAGCTCGTAAATTAAACTTCAGCCTATTTTCTTATGTTTTATGACATGCTGATCATTTT 1 GCCCCAAAGCTCGTAAATTAAACTTCAGCATATTTTCTTATGTTTTATGACATGCTGATCATTTT 87240711 TCCCTTCTA 66 TCCCTTCTA * 87240720 GCCCCAAATCTCGTAAATTAAACTTCAGCATATTTTCTTATGTTTTATGACATGCTGATCATTTT 1 GCCCCAAAGCTCGTAAATTAAACTTCAGCATATTTTCTTATGTTTTATGACATGCTGATCATTTT 87240785 TCCCTTCTA 66 TCCCTTCTA 87240794 TGGAAACATC Statistics Matches: 72, Mismatches: 2, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 74 72 1.00 ACGTcount: A:0.25, C:0.24, G:0.10, T:0.41 Consensus pattern (74 bp): GCCCCAAAGCTCGTAAATTAAACTTCAGCATATTTTCTTATGTTTTATGACATGCTGATCATTTT TCCCTTCTA Found at i:87240886 original size:76 final size:76 Alignment explanation

Indices: 87240760--87240912 Score: 306 Period size: 76 Copynumber: 2.0 Consensus size: 76 87240750 TATTTTCTTA 87240760 TGTTTTATGACATGCTGATCATTTTTCCCTTCTATGGAAACATCAAATTCTCACTCTAACATGTA 1 TGTTTTATGACATGCTGATCATTTTTCCCTTCTATGGAAACATCAAATTCTCACTCTAACATGTA 87240825 CTTATGACTAT 66 CTTATGACTAT 87240836 TGTTTTATGACATGCTGATCATTTTTCCCTTCTATGGAAACATCAAATTCTCACTCTAACATGTA 1 TGTTTTATGACATGCTGATCATTTTTCCCTTCTATGGAAACATCAAATTCTCACTCTAACATGTA 87240901 CTTATGACTAT 66 CTTATGACTAT 87240912 T 1 T 87240913 AGGTATTTTT Statistics Matches: 77, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 76 77 1.00 ACGTcount: A:0.27, C:0.21, G:0.10, T:0.41 Consensus pattern (76 bp): TGTTTTATGACATGCTGATCATTTTTCCCTTCTATGGAAACATCAAATTCTCACTCTAACATGTA CTTATGACTAT Found at i:87242994 original size:46 final size:47 Alignment explanation

Indices: 87242927--87243140 Score: 187 Period size: 46 Copynumber: 4.6 Consensus size: 47 87242917 TCATTTGTGT * 87242927 GCTAGTGTAAGA-CATGTCTGGGACATGCATCAGCCTCGGA-ATGTAA 1 GCTAGTGTAAGACCATGTCTGGGACATGCATC-GGCTCGGAGATGTAA ** 87242973 GCTAGTGTAAGA-CATGTCTGGGACATGCA-CTGGCTATGAGATGT-- 1 GCTAGTGTAAGACCATGTCTGGGACATGCATC-GGCTCGGAGATGTAA * * * * * 87243017 GCCAGTGTAA-ACCATGTCTGGGATATGGAATCGGCACGGATATGTGAGA 1 GCTAGTGTAAGACCATGTCTGGGACAT-GCATCGGCTCGGAGATGT-A-A * * 87243066 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGACT-TGATGGATG-AA 1 GCTAGTGTAAGACCATGTCTGGGACAT-GCATCGGCTCGGA--GATGTAA * 87243114 -CTAGTGTAAGACCATGTCTGGGTCATG 1 GCTAGTGTAAGACCATGTCTGGGACATG 87243141 GCATTAACAT Statistics Matches: 138, Mismatches: 19, Indels: 22 0.77 0.11 0.12 Matches are distributed among these distances: 43 1 0.01 44 22 0.16 45 17 0.12 46 35 0.25 47 25 0.18 48 1 0.01 49 12 0.09 50 22 0.16 51 3 0.02 ACGTcount: A:0.27, C:0.17, G:0.31, T:0.25 Consensus pattern (47 bp): GCTAGTGTAAGACCATGTCTGGGACATGCATCGGCTCGGAGATGTAA Found at i:87243126 original size:47 final size:48 Alignment explanation

Indices: 87242928--87243144 Score: 165 Period size: 47 Copynumber: 4.6 Consensus size: 48 87242918 CATTTGTGTG * 87242928 CTAGTGTAAGA-CATGTCTGGGACAT-GCATCAGCCTCG--GA-ATGTAA 1 CTAGTGTAAGACCATGTCTGGGACATGGCATCAGACT-GATGAGATG-AA * * ** 87242973 GCTAGTGTAAGA-CATGTCTGGGACAT-GCA-CTGGCT-ATGAGATGTG 1 -CTAGTGTAAGACCATGTCTGGGACATGGCATCAGACTGATGAGATGAA * * * * * 87243018 CCAGTGTAA-ACCATGTCTGGGATATGGAATCGGCACGGAT-ATG-TGAGA 1 CTAGTGTAAGACCATGTCTGGGACATGGCATCAG-ACTGATGA-GATGA-A 87243066 GCTAGTGTAAGACCATGTCTGGGACATGGCATC-GACTTGATG-GATGAA 1 -CTAGTGTAAGACCATGTCTGGGACATGGCATCAGAC-TGATGAGATGAA * 87243114 CTAGTGTAAGACCATGTCTGGGTCATGGCAT 1 CTAGTGTAAGACCATGTCTGGGACATGGCAT 87243145 TAACATTATA Statistics Matches: 139, Mismatches: 17, Indels: 29 0.75 0.09 0.16 Matches are distributed among these distances: 43 1 0.01 44 21 0.15 45 8 0.06 46 33 0.24 47 34 0.24 48 7 0.05 49 15 0.11 50 20 0.14 ACGTcount: A:0.27, C:0.18, G:0.30, T:0.25 Consensus pattern (48 bp): CTAGTGTAAGACCATGTCTGGGACATGGCATCAGACTGATGAGATGAA Found at i:87249283 original size:42 final size:42 Alignment explanation

Indices: 87249177--87249335 Score: 180 Period size: 43 Copynumber: 3.7 Consensus size: 42 87249167 ATATGTGTTA * * 87249177 TCATGTAAGACCACGTCTAGGACGTTGGCATCGACT-TATGTTT 1 TCATGTAAGACCACGTCTGGGACGTTGGCATCGA-TAT-TGATT * * 87249220 TACTTGTAAGACCACGCCTGGGACGTTGGCATCGATATTGATT 1 T-CATGTAAGACCACGTCTGGGACGTTGGCATCGATATTGATT * 87249263 TCATGTAAGACC-CTGTCTGGGATAG-TGGCATCGATATTTGATT 1 TCATGTAAGACCAC-GTCTGGGA-CGTTGGCATCGATA-TTGATT * * 87249306 ACATGTAAGACCACGTCTGGGACATTGGCA 1 TCATGTAAGACCACGTCTGGGACGTTGGCA 87249336 CTTATGAGCT Statistics Matches: 99, Mismatches: 10, Indels: 14 0.80 0.08 0.11 Matches are distributed among these distances: 41 1 0.01 42 28 0.28 43 38 0.38 44 32 0.32 ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30 Consensus pattern (42 bp): TCATGTAAGACCACGTCTGGGACGTTGGCATCGATATTGATT Found at i:87249324 original size:43 final size:43 Alignment explanation

Indices: 87249178--87249335 Score: 182 Period size: 42 Copynumber: 3.7 Consensus size: 43 87249168 TATGTGTTAT * 87249178 CATGTAAGACCACGTCTAGGACGTTGGCATCGACTTATGTT--TTA 1 CATGTAAGACCACGTCTGGGACGTTGGCATCGA--TAT-TTGATTA * * * 87249222 CTTGTAAGACCACGCCTGGGACGTTGGCATCGATA-TTGATTT 1 CATGTAAGACCACGTCTGGGACGTTGGCATCGATATTTGATTA * 87249264 CATGTAAGACC-CTGTCTGGGATAG-TGGCATCGATATTTGATTA 1 CATGTAAGACCAC-GTCTGGGA-CGTTGGCATCGATATTTGATTA * 87249307 CATGTAAGACCACGTCTGGGACATTGGCA 1 CATGTAAGACCACGTCTGGGACGTTGGCA 87249336 CTTATGAGCT Statistics Matches: 97, Mismatches: 10, Indels: 15 0.80 0.08 0.12 Matches are distributed among these distances: 40 2 0.02 41 1 0.01 42 32 0.33 43 31 0.32 44 31 0.32 ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30 Consensus pattern (43 bp): CATGTAAGACCACGTCTGGGACGTTGGCATCGATATTTGATTA Found at i:87254817 original size:25 final size:25 Alignment explanation

Indices: 87254762--87254823 Score: 70 Period size: 25 Copynumber: 2.5 Consensus size: 25 87254752 AATCAAAATG ** 87254762 AGAATCAGAATCAAAATCAGGTGAC 1 AGAATCAGAATCAAAATCAGGAAAC * * ** 87254787 AAAATCAAAATCAGTATCAGGAAAC 1 AGAATCAGAATCAAAATCAGGAAAC 87254812 AGAATCAGAATC 1 AGAATCAGAATC 87254824 TGAATGTGAA Statistics Matches: 29, Mismatches: 8, Indels: 0 0.78 0.22 0.00 Matches are distributed among these distances: 25 29 1.00 ACGTcount: A:0.52, C:0.16, G:0.16, T:0.16 Consensus pattern (25 bp): AGAATCAGAATCAAAATCAGGAAAC Found at i:87254980 original size:27 final size:28 Alignment explanation

Indices: 87254950--87255010 Score: 81 Period size: 27 Copynumber: 2.2 Consensus size: 28 87254940 GGTTGCCAGA * * 87254950 ACAGATATTGTGATAGAGTCACCA-AAT 1 ACAGATATTGTGACAGAGCCACCAGAAT * 87254977 ACAGATATTGTGGCAGAGCCACCAGAAT 1 ACAGATATTGTGACAGAGCCACCAGAAT 87255005 -CAGATA 1 ACAGATA 87255011 ATGTAGCAAA Statistics Matches: 30, Mismatches: 3, Indels: 2 0.86 0.09 0.06 Matches are distributed among these distances: 27 27 0.90 28 3 0.10 ACGTcount: A:0.39, C:0.18, G:0.21, T:0.21 Consensus pattern (28 bp): ACAGATATTGTGACAGAGCCACCAGAAT Found at i:87255023 original size:27 final size:27 Alignment explanation

Indices: 87254969--87255024 Score: 69 Period size: 27 Copynumber: 2.1 Consensus size: 27 87254959 GTGATAGAGT * * * 87254969 CACCAAATACAGATATTGTGGCAGAGC 1 CACCAAATACAGATAATGTAGCAAAGC 87254996 CACCAGAAT-CAGATAATGTAGCAAAGC 1 CACCA-AATACAGATAATGTAGCAAAGC 87255023 CA 1 CA 87255025 ATTAACAGAA Statistics Matches: 25, Mismatches: 3, Indels: 2 0.83 0.10 0.07 Matches are distributed among these distances: 27 22 0.88 28 3 0.12 ACGTcount: A:0.41, C:0.23, G:0.20, T:0.16 Consensus pattern (27 bp): CACCAAATACAGATAATGTAGCAAAGC Found at i:87255100 original size:20 final size:20 Alignment explanation

Indices: 87255075--87255129 Score: 92 Period size: 20 Copynumber: 2.8 Consensus size: 20 87255065 TATAATTCGC * 87255075 ACGAAGCCCACAATACCGAT 1 ACGAAGCCCACAATACCAAT * 87255095 ACGAAGCCCACAATATCAAT 1 ACGAAGCCCACAATACCAAT 87255115 ACGAAGCCCACAATA 1 ACGAAGCCCACAATA 87255130 ACGGCACACA Statistics Matches: 33, Mismatches: 2, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 20 33 1.00 ACGTcount: A:0.44, C:0.33, G:0.13, T:0.11 Consensus pattern (20 bp): ACGAAGCCCACAATACCAAT Found at i:87255840 original size:81 final size:80 Alignment explanation

Indices: 87255714--87255880 Score: 244 Period size: 81 Copynumber: 2.1 Consensus size: 80 87255704 CAAAATGGTA * * * 87255714 ATTTTACCCCACAAGGGTATCTCGGTAATTCTACCCTATAGGGGTATTTCGGTATTTCTACCCTA 1 ATTTTACCCCACAAGGGTATCTCGGTAATTCTACCCTACAGGGGTATTTCAGTAATTCTACCCTA 87255779 CAGGGGTATTTCGAT 66 CAGGGGTATTTCGAT * * * 87255794 ATTTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACATGGGTATTTCAGTAATTCTACCCT 1 ATTT-TACCCCACAAGGGTATCTCGGTAATTCTACCCTACAGGGGTATTTCAGTAATTCTACCCT * * 87255859 ATAGGGGTATTTCAAT 65 ACAGGGGTATTTCGAT 87255875 AATTTT 1 -ATTTT 87255881 GTAAATCGAG Statistics Matches: 77, Mismatches: 8, Indels: 3 0.88 0.09 0.03 Matches are distributed among these distances: 80 4 0.05 81 69 0.90 82 4 0.05 ACGTcount: A:0.25, C:0.21, G:0.17, T:0.37 Consensus pattern (80 bp): ATTTTACCCCACAAGGGTATCTCGGTAATTCTACCCTACAGGGGTATTTCAGTAATTCTACCCTA CAGGGGTATTTCGAT Found at i:87255878 original size:27 final size:27 Alignment explanation

Indices: 87255710--87255871 Score: 216 Period size: 27 Copynumber: 6.0 Consensus size: 27 87255700 GGGGCAAAAT * * * * 87255710 GGTAATTTTACCCCACAAGGGTATCTC 1 GGTAATTCTACCCTACAGGGGTATTTC * 87255737 GGTAATTCTACCCTATAGGGGTATTTC 1 GGTAATTCTACCCTACAGGGGTATTTC * 87255764 GGTATTTCTACCCTACAGGGGTATTTC 1 GGTAATTCTACCCTACAGGGGTATTTC * * * 87255791 GATATTTCTACCCTACAAGGGTATTTC 1 GGTAATTCTACCCTACAGGGGTATTTC * 87255818 GGTAATTCTACCCTACATGGGTATTTC 1 GGTAATTCTACCCTACAGGGGTATTTC * * 87255845 AGTAATTCTACCCTATAGGGGTATTTC 1 GGTAATTCTACCCTACAGGGGTATTTC 87255872 AATAATTTTG Statistics Matches: 120, Mismatches: 15, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 27 120 1.00 ACGTcount: A:0.23, C:0.22, G:0.19, T:0.36 Consensus pattern (27 bp): GGTAATTCTACCCTACAGGGGTATTTC Found at i:87255947 original size:27 final size:26 Alignment explanation

Indices: 87255910--87256149 Score: 241 Period size: 27 Copynumber: 8.9 Consensus size: 26 87255900 GTAATTCTGT * 87255910 AAATAGGGGGTACTTTGGTAATTTTAC 1 AAATA-GGGGTATTTTGGTAATTTTAC ** 87255937 AAGAT-GAGGGTATTTCAGTAATTTTAC 1 AA-ATAG-GGGTATTTTGGTAATTTTAC * * * 87255964 AGGA-CGAGGGTATTTTAGTAATTTTAC 1 A-AATAG-GGGTATTTTGGTAATTTTAC 87255991 AAATTAGGGGTATTTTGGTAATTTTAC 1 AAA-TAGGGGTATTTTGGTAATTTTAC * 87256018 AAACTAGGGGTATTTTGGTAATTTTAT 1 AAA-TAGGGGTATTTTGGTAATTTTAC 87256045 AAACTAGGGGTATTTTGGTAATTTTAC 1 AAA-TAGGGGTATTTTGGTAATTTTAC * * 87256072 AAACTAGGGGTATTTTGGAAATTTTATG 1 AAA-TAGGGGTATTTTGGTAATTTTA-C * * * 87256100 AACTAGGGGTATTTTGGTCATTTTTC 1 AAATAGGGGTATTTTGGTAATTTTAC * * 87256126 TAATCGAGGGTATTTTGGTAATTT 1 AAATAG-GGGTATTTTGGTAATTT 87256150 GGTAAACTAA Statistics Matches: 183, Mismatches: 22, Indels: 16 0.83 0.10 0.07 Matches are distributed among these distances: 26 5 0.03 27 173 0.95 28 5 0.03 ACGTcount: A:0.29, C:0.06, G:0.24, T:0.41 Consensus pattern (26 bp): AAATAGGGGTATTTTGGTAATTTTAC Found at i:87256158 original size:54 final size:54 Alignment explanation

Indices: 87255916--87256158 Score: 269 Period size: 54 Copynumber: 4.5 Consensus size: 54 87255906 CTGTAAATAG * * ** * 87255916 GGGGTACTTTGGTAATTTTACAAGA-T-GAGGGTATTTCAGTAATTTTACAGGACGA 1 GGGGTATTTTGGTAATTTTATAA-ACTAG-GGGTATTTTGGTAATTTTACA-AACGA * * * * 87255971 -GGGTATTTTAGTAATTTTACAAATTAGGGGTATTTTGGTAATTTTACAAACTA 1 GGGGTATTTTGGTAATTTTATAAACTAGGGGTATTTTGGTAATTTTACAAACGA * 87256024 GGGGTATTTTGGTAATTTTATAAACTAGGGGTATTTTGGTAATTTTACAAACTA 1 GGGGTATTTTGGTAATTTTATAAACTAGGGGTATTTTGGTAATTTTACAAACGA * * * * * 87256078 GGGGTATTTTGGAAATTTTATGAACTAGGGGTATTTTGGTCATTTTTCTAATCGA 1 GGGGTATTTTGGTAATTTTATAAACTAGGGGTATTTTGGTAATTTTAC-AAACGA ** 87256133 -GGGTATTTTGGTAATTTGGTAAACTA 1 GGGGTATTTTGGTAATTTTATAAACTA 87256159 AAGTATTCTA Statistics Matches: 165, Mismatches: 19, Indels: 9 0.85 0.10 0.05 Matches are distributed among these distances: 53 4 0.02 54 156 0.95 55 5 0.03 ACGTcount: A:0.28, C:0.07, G:0.24, T:0.41 Consensus pattern (54 bp): GGGGTATTTTGGTAATTTTATAAACTAGGGGTATTTTGGTAATTTTACAAACGA Found at i:87256158 original size:81 final size:80 Alignment explanation

Indices: 87255916--87256149 Score: 274 Period size: 81 Copynumber: 2.9 Consensus size: 80 87255906 CTGTAAATAG * * ** * * 87255916 GGGGTACTTTGGTAATTTTACAAGA-T-GAGGGTATTTCAGTAATTTTACAGGACGAGGGTATTT 1 GGGGTATTTTGGAAATTTTACAA-ACTAG-GGGTATTTTGGTAATTTTATA-AACGAGGGTATTT * * 87255979 TAGTAATTTTACAAATTA 63 TGGTAATTTTACAAACTA * * 87255997 GGGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTATAAACTAGGGGTATTTTG 1 GGGGTATTTTGGAAATTTTACAAACTAGGGGTATTTTGGTAATTTTATAAACGA-GGGTATTTTG 87256062 GTAATTTTACAAACTA 65 GTAATTTTACAAACTA ** * * * 87256078 GGGGTATTTTGGAAATTTTATGAACTAGGGGTATTTTGGTCATTTTTCTAATCGAGGGTATTTTG 1 GGGGTATTTTGGAAATTTTACAAACTAGGGGTATTTTGGT-AATTTTATAAACGAGGGTATTTTG 87256143 GTAATTT 65 GTAATTT 87256150 GGTAAACTAA Statistics Matches: 134, Mismatches: 15, Indels: 8 0.85 0.10 0.05 Matches are distributed among these distances: 80 4 0.03 81 119 0.89 82 11 0.08 ACGTcount: A:0.28, C:0.06, G:0.24, T:0.42 Consensus pattern (80 bp): GGGGTATTTTGGAAATTTTACAAACTAGGGGTATTTTGGTAATTTTATAAACGAGGGTATTTTGG TAATTTTACAAACTA Found at i:87261311 original size:68 final size:64 Alignment explanation

Indices: 87261246--87261453 Score: 206 Period size: 67 Copynumber: 3.2 Consensus size: 64 87261236 CATCATGTGT * 87261246 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATG 1 ACAAGAGAGCTAC--GAGA-TAT-ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATG 87261311 TAG 62 TAG * * * * * * 87261314 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGATGGACACCATGT 1 ACAAGAGAGCTACGAGATATATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACCATGT 87261379 AG 63 AG * * * * * 87261381 ACAAGAGAGCTACGAGATAAACTG--GCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-G 1 ACAAGAGAGCTACGAGATATA-TGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAG 87261443 TACAAGAGAGC 1 -ACAAGAGAGC 87261454 CGAACTATAT Statistics Matches: 118, Mismatches: 17, Indels: 15 0.79 0.11 0.10 Matches are distributed among these distances: 62 1 0.01 63 20 0.17 64 21 0.18 65 11 0.09 66 18 0.15 67 32 0.27 68 15 0.13 ACGTcount: A:0.31, C:0.17, G:0.29, T:0.23 Consensus pattern (64 bp): ACAAGAGAGCTACGAGATATATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAG Found at i:87267243 original size:43 final size:43 Alignment explanation

Indices: 87267077--87267243 Score: 164 Period size: 43 Copynumber: 3.9 Consensus size: 43 87267067 TATAAGCTCG * * * * 87267077 TACAATGCC-ATGTCCCAGATATGGTCATACATGCT-ATCAC-A 1 TACAATGCCAATGTCCCAGACATGGTCTTACACG-TAATCTCAA * * * * 87267118 TATCAATGCCACTGTCCTAGACAGGGTCTTACACG-AA-ATCAA 1 TA-CAATGCCAATGTCCCAGACATGGTCTTACACGTAATCTCAA * * 87267160 TTAACGATGCCGATGTCCCAGACATGGTCTTACACGTAATCTCAA 1 -T-ACAATGCCAATGTCCCAGACATGGTCTTACACGTAATCTCAA * 87267205 TACAATGCCAATGTCCCAGACATGGTCTTACATGTAATC 1 TACAATGCCAATGTCCCAGACATGGTCTTACACGTAATC 87267244 ACATCTCGAT Statistics Matches: 101, Mismatches: 17, Indels: 14 0.77 0.13 0.11 Matches are distributed among these distances: 41 3 0.03 42 9 0.09 43 81 0.80 44 4 0.04 45 4 0.04 ACGTcount: A:0.31, C:0.26, G:0.16, T:0.26 Consensus pattern (43 bp): TACAATGCCAATGTCCCAGACATGGTCTTACACGTAATCTCAA Found at i:87269302 original size:20 final size:19 Alignment explanation

Indices: 87269266--87269316 Score: 54 Period size: 20 Copynumber: 2.7 Consensus size: 19 87269256 AAGGGCTATT * 87269266 TTGTAAA-GTTGTAAAATAAA 1 TTGTAAATG-TGTGAAAT-AA 87269286 TTGTAAATGTGTGAAATAA 1 TTGTAAATGTGTGAAATAA 87269305 TTG-AAAT-TGTGA 1 TTGTAAATGTGTGA 87269317 GTTGCTATAG Statistics Matches: 29, Mismatches: 1, Indels: 5 0.83 0.03 0.14 Matches are distributed among these distances: 17 5 0.17 18 4 0.14 19 5 0.17 20 14 0.48 21 1 0.03 ACGTcount: A:0.43, C:0.00, G:0.20, T:0.37 Consensus pattern (19 bp): TTGTAAATGTGTGAAATAA Found at i:87271309 original size:15 final size:15 Alignment explanation

Indices: 87271289--87271319 Score: 62 Period size: 15 Copynumber: 2.1 Consensus size: 15 87271279 CTTATTATTT 87271289 TTTATACGGTCTTAC 1 TTTATACGGTCTTAC 87271304 TTTATACGGTCTTAC 1 TTTATACGGTCTTAC 87271319 T 1 T 87271320 AAGCTATAAA Statistics Matches: 16, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 15 16 1.00 ACGTcount: A:0.19, C:0.19, G:0.13, T:0.48 Consensus pattern (15 bp): TTTATACGGTCTTAC Found at i:87275647 original size:20 final size:18 Alignment explanation

Indices: 87275622--87275672 Score: 59 Period size: 20 Copynumber: 2.7 Consensus size: 18 87275612 AATGGCTATT 87275622 TTGTAAAGTTGTAAAATAAA 1 TTGTAAA-TTGTAAAAT-AA * 87275642 TTGTAAATGTGTGAAATAA 1 TTGTAAAT-TGTAAAATAA 87275661 TTG-AAATTGTAA 1 TTGTAAATTGTAA 87275673 GTGGCTATAG Statistics Matches: 28, Mismatches: 2, Indels: 5 0.80 0.06 0.14 Matches are distributed among these distances: 17 4 0.14 18 4 0.14 19 6 0.21 20 14 0.50 ACGTcount: A:0.45, C:0.00, G:0.18, T:0.37 Consensus pattern (18 bp): TTGTAAATTGTAAAATAA Found at i:87278265 original size:45 final size:45 Alignment explanation

Indices: 87278215--87278347 Score: 185 Period size: 45 Copynumber: 3.0 Consensus size: 45 87278205 GCTCGATATC * * 87278215 ATTTCATCGGCATTATAGCCTACTAGGGTCAAAGGCCCGAATAGT 1 ATTTCACCGGCATTATAGCCTGCTAGGGTCAAAGGCCCGAATAGT ** * 87278260 ATTTCACCATCATTGTAGCCTGCTAGGGTCAAAGGCCCGAATAGT 1 ATTTCACCGGCATTATAGCCTGCTAGGGTCAAAGGCCCGAATAGT * * * * 87278305 ATCTCACCGGCATCATAGCCTGCTAGGCTCAAAGGCTCGAATA 1 ATTTCACCGGCATTATAGCCTGCTAGGGTCAAAGGCCCGAATA 87278348 TTACTGTACG Statistics Matches: 76, Mismatches: 12, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 45 76 1.00 ACGTcount: A:0.28, C:0.26, G:0.22, T:0.25 Consensus pattern (45 bp): ATTTCACCGGCATTATAGCCTGCTAGGGTCAAAGGCCCGAATAGT Found at i:87285407 original size:93 final size:93 Alignment explanation

Indices: 87285282--87285452 Score: 297 Period size: 93 Copynumber: 1.8 Consensus size: 93 87285272 CCCATAAGTG * 87285282 AACTCGGACTCAACTCAACAAGCTCGGGCATTCGCATCCATAAGTGAACTCGGACTCAACTCAAC 1 AACTCGGACTCAACTCAACAAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAAC 87285347 GAGCTCGGATGCCTAGTTACATCTCTCA 66 GAGCTCGGATGCCTAGTTACATCTCTCA * * * 87285375 AACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAAT 1 AACTCGGACTCAACTCAACAAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAAC * 87285440 GAGTTCGGATGCC 66 GAGCTCGGATGCC 87285453 CAAATATCCT Statistics Matches: 73, Mismatches: 5, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 93 73 1.00 ACGTcount: A:0.29, C:0.30, G:0.19, T:0.22 Consensus pattern (93 bp): AACTCGGACTCAACTCAACAAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAAC GAGCTCGGATGCCTAGTTACATCTCTCA Found at i:87285448 original size:46 final size:46 Alignment explanation

Indices: 87285273--87285448 Score: 200 Period size: 46 Copynumber: 3.8 Consensus size: 46 87285263 TGTAACCCGC * * 87285273 CCATAAGTGAACTCGGACTCAACTCAACAAGCTCGGGCATTCGCAT 1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT * 87285319 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTT-ACAT 1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA---C-A-TTCGCAT * * 87285369 CTC-TCA---AACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT 1 C-CATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT * * 87285412 CCATAAGTGAACTCGGACTCAACTCAATGAGTTCGGA 1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA 87285449 TGCCCAAATA Statistics Matches: 111, Mismatches: 8, Indels: 22 0.79 0.06 0.16 Matches are distributed among these distances: 42 3 0.03 43 7 0.06 44 1 0.01 46 62 0.56 47 27 0.24 49 1 0.01 50 7 0.06 51 3 0.03 ACGTcount: A:0.30, C:0.29, G:0.19, T:0.22 Consensus pattern (46 bp): CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT Found at i:87316660 original size:57 final size:57 Alignment explanation

Indices: 87316542--87316660 Score: 132 Period size: 57 Copynumber: 2.1 Consensus size: 57 87316532 ATGTTATTCC * * * * 87316542 ATTAACAACAAAGTTAACGTGTAATGATTAAAATGTCAGCTTTTCAAACGTACTGAN 1 ATTAACAACAAAGTTAACGTGTAAGGATTAAAATATCAGCTTTTCAAACGTACTAAG * * * ** * 87316599 ATTAACAACAAAGTTAACGTTTAGGGATTGAAATATCTTCTTTTCAAATGTA-TAAAG 1 ATTAACAACAAAGTTAACGTGTAAGGATTAAAATATCAGCTTTTCAAACGTACT-AAG 87316656 ATTAA 1 ATTAA 87316661 AATATTTCTT Statistics Matches: 51, Mismatches: 10, Indels: 2 0.81 0.16 0.03 Matches are distributed among these distances: 56 1 0.02 57 50 0.98 ACGTcount: A:0.41, C:0.12, G:0.13, T:0.33 Consensus pattern (57 bp): ATTAACAACAAAGTTAACGTGTAAGGATTAAAATATCAGCTTTTCAAACGTACTAAG Found at i:87330610 original size:29 final size:29 Alignment explanation

Indices: 87330575--87330649 Score: 116 Period size: 29 Copynumber: 2.6 Consensus size: 29 87330565 GTTGTGAGAT * 87330575 TGGCACTAAGTGTGCGAGCTTGAAA-TGCA 1 TGGCACTAAGTGTGCGAG-TTGAAAGTACA * 87330604 TGGCACTAAGTGTGCGAGTTTAAAGTACA 1 TGGCACTAAGTGTGCGAGTTGAAAGTACA 87330633 TGGCACTAAGTGTGCGA 1 TGGCACTAAGTGTGCGA 87330650 ACCCACTATA Statistics Matches: 43, Mismatches: 2, Indels: 2 0.91 0.04 0.04 Matches are distributed among these distances: 28 5 0.12 29 38 0.88 ACGTcount: A:0.28, C:0.16, G:0.31, T:0.25 Consensus pattern (29 bp): TGGCACTAAGTGTGCGAGTTGAAAGTACA Found at i:87331551 original size:18 final size:18 Alignment explanation

Indices: 87331528--87331570 Score: 86 Period size: 18 Copynumber: 2.4 Consensus size: 18 87331518 GTGACATGTA 87331528 AGATGAATTATTAGTAAC 1 AGATGAATTATTAGTAAC 87331546 AGATGAATTATTAGTAAC 1 AGATGAATTATTAGTAAC 87331564 AGATGAA 1 AGATGAA 87331571 AAATCACGAA Statistics Matches: 25, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 18 25 1.00 ACGTcount: A:0.47, C:0.05, G:0.19, T:0.30 Consensus pattern (18 bp): AGATGAATTATTAGTAAC Found at i:87345349 original size:20 final size:20 Alignment explanation

Indices: 87345326--87345364 Score: 78 Period size: 20 Copynumber: 1.9 Consensus size: 20 87345316 TAAACATGGT 87345326 ATGTATGATATGCACATGAC 1 ATGTATGATATGCACATGAC 87345346 ATGTATGATATGCACATGA 1 ATGTATGATATGCACATGA 87345365 TGTAATCATA Statistics Matches: 19, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 20 19 1.00 ACGTcount: A:0.36, C:0.13, G:0.21, T:0.31 Consensus pattern (20 bp): ATGTATGATATGCACATGAC Found at i:87345468 original size:22 final size:23 Alignment explanation

Indices: 87345416--87345533 Score: 166 Period size: 23 Copynumber: 5.1 Consensus size: 23 87345406 AGGAAGTGTA 87345416 AAAGGGCTTATGCCCCAGTTATT 1 AAAGGGCTTATGCCCCAGTTATT * 87345439 AAAAGGCTTATGCCCCAGTTATT 1 AAAGGGCTTATGCCCCAGTTATT 87345462 AAA-GGCTTATGCCCCAGTTATT 1 AAAGGGCTTATGCCCCAGTTATT * * ** 87345484 AAAGGGCTTGTACCTTAGTTATT 1 AAAGGGCTTATGCCCCAGTTATT * 87345507 AAAAGGGCTTTTGCCCCAGTTATT 1 -AAAGGGCTTATGCCCCAGTTATT 87345531 AAA 1 AAA 87345534 AGAGGCTAGG Statistics Matches: 84, Mismatches: 9, Indels: 4 0.87 0.09 0.04 Matches are distributed among these distances: 22 22 0.26 23 43 0.51 24 19 0.23 ACGTcount: A:0.29, C:0.19, G:0.19, T:0.32 Consensus pattern (23 bp): AAAGGGCTTATGCCCCAGTTATT Found at i:87345481 original size:45 final size:47 Alignment explanation

Indices: 87345414--87345535 Score: 176 Period size: 45 Copynumber: 2.6 Consensus size: 47 87345404 GGAGGAAGTG * 87345414 TAAAAGGGCTTATGCCCCAGTTATTAAAAGGCTTATGCCCCAGTTAT 1 TAAAAGGGCTTATGCCCCAGTTATTAAAAGGCTTATACCCCAGTTAT * * ** 87345461 T-AAA-GGCTTATGCCCCAGTTATTAAAGGGCTTGTACCTTAGTTAT 1 TAAAAGGGCTTATGCCCCAGTTATTAAAAGGCTTATACCCCAGTTAT * 87345506 TAAAAGGGCTTTTGCCCCAGTTATTAAAAG 1 TAAAAGGGCTTATGCCCCAGTTATTAAAAG 87345536 AGGCTAGGCC Statistics Matches: 66, Mismatches: 7, Indels: 4 0.86 0.09 0.05 Matches are distributed among these distances: 45 37 0.56 46 6 0.09 47 23 0.35 ACGTcount: A:0.30, C:0.19, G:0.20, T:0.32 Consensus pattern (47 bp): TAAAAGGGCTTATGCCCCAGTTATTAAAAGGCTTATACCCCAGTTAT Found at i:87345550 original size:25 final size:24 Alignment explanation

Indices: 87345414--87345554 Score: 141 Period size: 23 Copynumber: 6.0 Consensus size: 24 87345404 GGAGGAAGTG * 87345414 TAAAAGGGCTTATGCCCCAGTTAT 1 TAAAAGGGCTTAGGCCCCAGTTAT * 87345438 TAAAA-GGCTTATGCCCCAGTTAT 1 TAAAAGGGCTTAGGCCCCAGTTAT * 87345461 T-AAA-GGCTTATGCCCCAGTTAT 1 TAAAAGGGCTTAGGCCCCAGTTAT * ** 87345483 T-AAAGGGCTT-GTACCTTAGTTAT 1 TAAAAGGGCTTAG-GCCCCAGTTAT ** 87345506 TAAAAGGGCTTTTGCCCCAGTTAT 1 TAAAAGGGCTTAGGCCCCAGTTAT 87345530 TAAAAGAGGC-TAGGCCTCCAGTTAT 1 TAAAAG-GGCTTAGGCC-CCAGTTAT 87345555 ATGATAAAGC Statistics Matches: 101, Mismatches: 10, Indels: 11 0.83 0.08 0.09 Matches are distributed among these distances: 22 25 0.25 23 33 0.33 24 32 0.32 25 11 0.11 ACGTcount: A:0.28, C:0.20, G:0.21, T:0.31 Consensus pattern (24 bp): TAAAAGGGCTTAGGCCCCAGTTAT Found at i:87351778 original size:40 final size:40 Alignment explanation

Indices: 87351734--87352212 Score: 737 Period size: 40 Copynumber: 12.0 Consensus size: 40 87351724 CTAGTTACTA * * * * 87351734 TTGTGCAAATTGATATATCCGGGTTAAGACCCGAAGGCAT 1 TTGTGCGAATTGATATATCCAGGCTAAGACCTGAAGGCAT * * 87351774 TTGTGCGAATTGATATATCCGGGTTAAGACCTGAAGGCAT 1 TTGTGCGAATTGATATATCCAGGCTAAGACCTGAAGGCAT 87351814 TTGTGCGAATTGATATATCCAGGCTAAGACCTGAAGGCAT 1 TTGTGCGAATTGATATATCCAGGCTAAGACCTGAAGGCAT 87351854 TTGTGCGAATTGATATATCCAGGCTAAGACCTGAAGGCAT 1 TTGTGCGAATTGATATATCCAGGCTAAGACCTGAAGGCAT 87351894 TTGTGCGAATTGATATATCCAGGCTAAGACCTGAAGGCAT 1 TTGTGCGAATTGATATATCCAGGCTAAGACCTGAAGGCAT 87351934 TTGTGCGAATTGATATATCCAGGCTAAGACCTGAAGGCAT 1 TTGTGCGAATTGATATATCCAGGCTAAGACCTGAAGGCAT 87351974 TTGTGCGAATTGATATATCCAGGCTAAGACCTGAAGGCAT 1 TTGTGCGAATTGATATATCCAGGCTAAGACCTGAAGGCAT 87352014 TTGTGCGAATTGATATATCCAGGCTAAGACCTGAAGGCAT 1 TTGTGCGAATTGATATATCCAGGCTAAGACCTGAAGGCAT * * * 87352054 TTGTGCGAATTGATATATCCGGGCTAAGACCCGAAGGCAA 1 TTGTGCGAATTGATATATCCAGGCTAAGACCTGAAGGCAT * * * 87352094 TTGTGC-AAGTTGATATATCCGGGCTAAGACCCGAAGGCAA 1 TTGTGCGAA-TTGATATATCCAGGCTAAGACCTGAAGGCAT * * 87352134 TTGTGC-AAGTTGATATATCCGGGCTAAGACCCGAAGGCAT 1 TTGTGCGAA-TTGATATATCCAGGCTAAGACCTGAAGGCAT * * * * * * * 87352174 TCGTGCGAGTTGCTATACCCGGGTTAAGACCCGAAGGCA 1 TTGTGCGAATTGATATATCCAGGCTAAGACCTGAAGGCA 87352213 ATTGAGCTTG Statistics Matches: 424, Mismatches: 13, Indels: 4 0.96 0.03 0.01 Matches are distributed among these distances: 39 2 0.00 40 421 0.99 41 1 0.00 ACGTcount: A:0.29, C:0.19, G:0.26, T:0.26 Consensus pattern (40 bp): TTGTGCGAATTGATATATCCAGGCTAAGACCTGAAGGCAT Found at i:87358258 original size:40 final size:40 Alignment explanation

Indices: 87358203--87358297 Score: 154 Period size: 40 Copynumber: 2.4 Consensus size: 40 87358193 NNNNNNNNNN * * 87358203 TAAGACCCGAAGGCATTTGTGCGAGTTGATATATCCGGGC 1 TAAGACCCGAAGGCATTCGTGCGAGTTGATATACCCGGGC * * 87358243 TAAGACCCGAAGGCATTCGTGCGAGTTGCTATACCCGGGT 1 TAAGACCCGAAGGCATTCGTGCGAGTTGATATACCCGGGC 87358283 TAAGACCCGAAGGCA 1 TAAGACCCGAAGGCA 87358298 ATTGAGCTTG Statistics Matches: 51, Mismatches: 4, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 40 51 1.00 ACGTcount: A:0.26, C:0.23, G:0.29, T:0.21 Consensus pattern (40 bp): TAAGACCCGAAGGCATTCGTGCGAGTTGATATACCCGGGC Found at i:87361021 original size:20 final size:20 Alignment explanation

Indices: 87360996--87361040 Score: 63 Period size: 20 Copynumber: 2.2 Consensus size: 20 87360986 AGGGACTAAA * * 87360996 ATGAAAAGTTGTAAAATTTG 1 ATGAAAAATTCTAAAATTTG * 87361016 ATGAAAAATTCTAAAATTTT 1 ATGAAAAATTCTAAAATTTG 87361036 ATGAA 1 ATGAA 87361041 TACATGTGCT Statistics Matches: 22, Mismatches: 3, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 20 22 1.00 ACGTcount: A:0.49, C:0.02, G:0.13, T:0.36 Consensus pattern (20 bp): ATGAAAAATTCTAAAATTTG Found at i:87363731 original size:24 final size:24 Alignment explanation

Indices: 87363690--87363761 Score: 67 Period size: 25 Copynumber: 3.0 Consensus size: 24 87363680 GCTTTATCAT ** 87363690 ATAACTGGAGGCCTAGCCTCTTTTA 1 ATAACTGGAGGCAAAGCC-CTTTTA * 87363715 ATAACT-GAGGCAAAGCCCTTTTTG 1 ATAACTGGAGGCAAAGCCC-TTTTA * 87363739 GTAAACTGG-GGCAAAGCCCTTTT 1 AT-AACTGGAGGCAAAGCCCTTTT 87363762 CGCACTTCCT Statistics Matches: 40, Mismatches: 4, Indels: 7 0.78 0.08 0.14 Matches are distributed among these distances: 23 1 0.03 24 18 0.45 25 20 0.50 26 1 0.03 ACGTcount: A:0.26, C:0.22, G:0.22, T:0.29 Consensus pattern (24 bp): ATAACTGGAGGCAAAGCCCTTTTA Found at i:87364015 original size:27 final size:27 Alignment explanation

Indices: 87363985--87364269 Score: 374 Period size: 27 Copynumber: 10.6 Consensus size: 27 87363975 ACCCCACAAA * * 87363985 GGTATCTCAGTAATTCTACCCTACAGG 1 GGTATTTCGGTAATTCTACCCTACAGG * * 87364012 GGTATTTCGGTATTTCTACCCTACAAG 1 GGTATTTCGGTAATTCTACCCTACAGG * 87364039 GGTATTTTGGTAATTCTACCCTACAGG 1 GGTATTTCGGTAATTCTACCCTACAGG * * 87364066 GGTATTTCGGTATTTCTACCCTACAAG 1 GGTATTTCGGTAATTCTACCCTACAGG * 87364093 GGTATTTTGGTAATTCTACCCTACAGG 1 GGTATTTCGGTAATTCTACCCTACAGG * * 87364120 GGTATTTCGGTATTTCTACCCTACAAG 1 GGTATTTCGGTAATTCTACCCTACAGG * 87364147 GGTATTTTGGTAATTCTACCCTACAGG 1 GGTATTTCGGTAATTCTACCCTACAGG * * 87364174 GGTATTTCGGTATTTCTACCCTACAAG 1 GGTATTTCGGTAATTCTACCCTACAGG * * 87364201 GGTATTTCGGTAACTCTACCCTATAGG 1 GGTATTTCGGTAATTCTACCCTACAGG * * ** 87364228 GGTATTTTGGTAATTTTA-CAAACCAGG 1 GGTATTTCGGTAATTCTACCCTA-CAGG * 87364255 GGTATTTTGGTAATT 1 GGTATTTCGGTAATT 87364270 TTGTAAACCA Statistics Matches: 225, Mismatches: 32, Indels: 2 0.87 0.12 0.01 Matches are distributed among these distances: 26 2 0.01 27 223 0.99 ACGTcount: A:0.23, C:0.19, G:0.21, T:0.37 Consensus pattern (27 bp): GGTATTTCGGTAATTCTACCCTACAGG Found at i:87364032 original size:54 final size:54 Alignment explanation

Indices: 87363994--87364269 Score: 457 Period size: 54 Copynumber: 5.1 Consensus size: 54 87363984 AGGTATCTCA 87363994 GTAATTCTACCCTACAGGGGTATTTCGGTATTTCTACCCTACAAGGGTATTTTG 1 GTAATTCTACCCTACAGGGGTATTTCGGTATTTCTACCCTACAAGGGTATTTTG 87364048 GTAATTCTACCCTACAGGGGTATTTCGGTATTTCTACCCTACAAGGGTATTTTG 1 GTAATTCTACCCTACAGGGGTATTTCGGTATTTCTACCCTACAAGGGTATTTTG 87364102 GTAATTCTACCCTACAGGGGTATTTCGGTATTTCTACCCTACAAGGGTATTTTG 1 GTAATTCTACCCTACAGGGGTATTTCGGTATTTCTACCCTACAAGGGTATTTTG * 87364156 GTAATTCTACCCTACAGGGGTATTTCGGTATTTCTACCCTACAAGGGTATTTCG 1 GTAATTCTACCCTACAGGGGTATTTCGGTATTTCTACCCTACAAGGGTATTTTG * * * ** * 87364210 GTAACTCTACCCTATAGGGGTATTTTGGTAATTT-TA-CAAACCAGGGGTATTTTG 1 GTAATTCTACCCTACAGGGGTATTTCGGT-ATTTCTACCCTA-CAAGGGTATTTTG 87364264 GTAATT 1 GTAATT 87364270 TTGTAAACCA Statistics Matches: 211, Mismatches: 9, Indels: 4 0.94 0.04 0.02 Matches are distributed among these distances: 53 2 0.01 54 205 0.97 55 4 0.02 ACGTcount: A:0.23, C:0.19, G:0.21, T:0.37 Consensus pattern (54 bp): GTAATTCTACCCTACAGGGGTATTTCGGTATTTCTACCCTACAAGGGTATTTTG Found at i:87364282 original size:81 final size:79 Alignment explanation

Indices: 87364007--87364432 Score: 292 Period size: 81 Copynumber: 5.3 Consensus size: 79 87363997 ATTCTACCCT * ** * 87364007 ACAGGGGTATTTCGGT-ATTTCTACCCTACAAGGGTATTTTGGTAATTCTACCCTACAGGGGTAT 1 ACAGGGGTATTTTGGTAATTTCTAAAC--CAAGGGTATTTTGGTAATTCTACCCTATAGGGGTAT * ** 87364071 TTCGGT-ATTTCTACCCT 64 TTTGGTAATTT-TA-CAA * * * * * * 87364088 ACAAGGGTATTTTGGTAA-TTCT-ACCCTACAGGGGTATTTCGGTATTTCTACCCTACAAGGGTA 1 ACAGGGGTATTTTGGTAATTTCTAAACC-A-A-GGGTATTTTGGTAATTCTACCCTATAGGGGTA * ** 87364151 TTTTGGTAATTCTACCCT 63 TTTTGGTAATTTTA-CAA * ** * * 87364169 ACAGGGGTATTTCGGT-ATTTCTACCCTACAAGGGTATTTCGGTAACTCTACCCTATAGGGGTAT 1 ACAGGGGTATTTTGGTAATTTCTAAAC--CAAGGGTATTTTGGTAATTCTACCCTATAGGGGTAT 87364233 TTTGGTAATTTTACAA 64 TTTGGTAATTTTACAA * * * * 87364249 ACCAGGGGTATTTTGGTAATTTTGTAAACCAAGGGTATTTTGGTAATTTTA--CAAGTCGAGGGT 1 A-CAGGGGTATTTTGGTAA-TTTCTAAACCAAGGGTATTTTGGTAATTCTACCCTA-TAG-GGGT ** * 87364312 ATTTCAGTAATTTCACAA 62 ATTTTGGTAATTTTACAA * ** * * * * *** 87364330 ATTAGGGGTATTTTGGTAGGTTCACAAACTAGGGGTATTTTGGTAATTTTA-TAAACTAGGGGTA 1 A-CAGGGGTATTTTGGTAATTTC-TAAACCAAGGGTATTTTGGTAATTCTACCCTA-TAGGGGTA 87364394 TTTTGGTAATTTTACAA 63 TTTTGGTAATTTTACAA 87364411 ACTAGGGGTATTTTGGTAATTT 1 AC-AGGGGTATTTTGGTAATTT 87364433 TGCTAATCGA Statistics Matches: 281, Mismatches: 47, Indels: 34 0.78 0.13 0.09 Matches are distributed among these distances: 78 1 0.00 79 3 0.01 80 10 0.04 81 247 0.88 82 12 0.04 83 7 0.02 84 1 0.00 ACGTcount: A:0.25, C:0.15, G:0.22, T:0.38 Consensus pattern (79 bp): ACAGGGGTATTTTGGTAATTTCTAAACCAAGGGTATTTTGGTAATTCTACCCTATAGGGGTATTT TGGTAATTTTACAA Found at i:87364447 original size:27 final size:27 Alignment explanation

Indices: 87364224--87364433 Score: 269 Period size: 27 Copynumber: 7.8 Consensus size: 27 87364214 CTCTACCCTA 87364224 TAGGGGTATTTTGGTAATTTTACAAAC 1 TAGGGGTATTTTGGTAATTTTACAAAC * ** 87364251 CAGGGGTATTTTGGTAATTTTGTAAAC 1 TAGGGGTATTTTGGTAATTTTACAAAC * * * 87364278 CAAGGGTATTTTGGTAATTTTAC-AAG 1 TAGGGGTATTTTGGTAATTTTACAAAC * ** * * 87364304 TCGAGGGTATTTCAGTAATTTCACAAAT 1 TAG-GGGTATTTTGGTAATTTTACAAAC ** * 87364332 TAGGGGTATTTTGGTAGGTTCACAAAC 1 TAGGGGTATTTTGGTAATTTTACAAAC * 87364359 TAGGGGTATTTTGGTAATTTTATAAAC 1 TAGGGGTATTTTGGTAATTTTACAAAC 87364386 TAGGGGTATTTTGGTAATTTTACAAAC 1 TAGGGGTATTTTGGTAATTTTACAAAC 87364413 TAGGGGTATTTTGGTAATTTT 1 TAGGGGTATTTTGGTAATTTT 87364434 GCTAATCGAG Statistics Matches: 156, Mismatches: 25, Indels: 4 0.84 0.14 0.02 Matches are distributed among these distances: 26 2 0.01 27 150 0.96 28 4 0.03 ACGTcount: A:0.28, C:0.08, G:0.24, T:0.40 Consensus pattern (27 bp): TAGGGGTATTTTGGTAATTTTACAAAC Found at i:87364447 original size:81 final size:80 Alignment explanation

Indices: 87364223--87364486 Score: 280 Period size: 81 Copynumber: 3.3 Consensus size: 80 87364213 ACTCTACCCT * 87364223 ATAGGGGTATTTTGGTAATTTTACAAACCAGGGGTATTTTGGTAATTTTG-TAAACCAAGGGTAT 1 ATAGGGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTGCTAAA-CAAGGGTAT * 87364287 TTTGGTAATTTTACAA 65 TTTGGTAATTTTATAA * * ** * * ** ** * 87364303 GTCGAGGGTATTTCAGTAATTTCACAAATTAGGGGTATTTTGGTAGGTTCAC-AAACTAGGGGTA 1 ATAG-GGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTGCTAAAC-AAGGGTA 87364367 TTTTGGTAATTTTATAA 64 TTTTGGTAATTTTATAA * * * 87364384 ACTAGGGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTGCTAATCGAGGGTAA 1 A-TAGGGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTGCTAAACAAGGGTAT *** * 87364449 AACGGTAATTCTATAA 65 TTTGGTAATTTTATAA * 87364465 ATCAGGGGTACTTTGGTAATTT 1 AT-AGGGGTATTTTGGTAATTT 87364487 GGTAAACTAA Statistics Matches: 146, Mismatches: 32, Indels: 11 0.77 0.17 0.06 Matches are distributed among these distances: 80 4 0.03 81 137 0.94 82 5 0.03 ACGTcount: A:0.29, C:0.08, G:0.24, T:0.39 Consensus pattern (80 bp): ATAGGGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTGCTAAACAAGGGTATT TTGGTAATTTTATAA Found at i:87364482 original size:27 final size:27 Alignment explanation

Indices: 87364225--87364486 Score: 237 Period size: 27 Copynumber: 9.7 Consensus size: 27 87364215 TCTACCCTAT * 87364225 AGGGGTATTTTGGTAATTTTACAAACC 1 AGGGGTATTTTGGTAATTTTACAAATC ** * 87364252 AGGGGTATTTTGGTAATTTTGTAAACC 1 AGGGGTATTTTGGTAATTTTACAAATC * * 87364279 AAGGGTATTTTGGTAATTTTACAAGTC 1 AGGGGTATTTTGGTAATTTTACAAATC ** * * 87364306 -GAGGGTATTTCAGTAATTTCACAAATT 1 AG-GGGTATTTTGGTAATTTTACAAATC ** * 87364333 AGGGGTATTTTGGTAGGTTCACAAA-C 1 AGGGGTATTTTGGTAATTTTACAAATC * 87364359 TAGGGGTATTTTGGTAATTTTATAAA-C 1 -AGGGGTATTTTGGTAATTTTACAAATC 87364386 TAGGGGTATTTTGGTAATTTTACAAA-C 1 -AGGGGTATTTTGGTAATTTTACAAATC * * 87364413 TAGGGGTATTTTGGTAATTTTGCTAATC 1 -AGGGGTATTTTGGTAATTTTACAAATC **** * * 87364441 -GAGGGTAAAACGGTAATTCTATAAATC 1 AG-GGGTATTTTGGTAATTTTACAAATC * 87364468 AGGGGTACTTTGGTAATTT 1 AGGGGTATTTTGGTAATTT 87364487 GGTAAACTAA Statistics Matches: 191, Mismatches: 38, Indels: 12 0.79 0.16 0.05 Matches are distributed among these distances: 26 1 0.01 27 187 0.98 28 3 0.02 ACGTcount: A:0.29, C:0.08, G:0.24, T:0.39 Consensus pattern (27 bp): AGGGGTATTTTGGTAATTTTACAAATC Found at i:87366950 original size:19 final size:19 Alignment explanation

Indices: 87366926--87366963 Score: 67 Period size: 19 Copynumber: 2.0 Consensus size: 19 87366916 GCGTGGCCAG * 87366926 GCAGTGTGACAGAGCCCAA 1 GCAGTGTGACAAAGCCCAA 87366945 GCAGTGTGACAAAGCCCAA 1 GCAGTGTGACAAAGCCCAA 87366964 TTCGTATGGC Statistics Matches: 18, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 19 18 1.00 ACGTcount: A:0.34, C:0.26, G:0.29, T:0.11 Consensus pattern (19 bp): GCAGTGTGACAAAGCCCAA Found at i:87371641 original size:27 final size:27 Alignment explanation

Indices: 87371600--87371653 Score: 81 Period size: 27 Copynumber: 2.0 Consensus size: 27 87371590 TGTCATGTGA * 87371600 AATTGAATGACAAATTATTATTACATG 1 AATTGAATGACAAATTACTATTACATG ** 87371627 AATTGAATGTTAAATTACTATTACATG 1 AATTGAATGACAAATTACTATTACATG 87371654 GGTTGTACCT Statistics Matches: 24, Mismatches: 3, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 27 24 1.00 ACGTcount: A:0.43, C:0.07, G:0.11, T:0.39 Consensus pattern (27 bp): AATTGAATGACAAATTACTATTACATG Found at i:87372025 original size:49 final size:51 Alignment explanation

Indices: 87371882--87372025 Score: 157 Period size: 51 Copynumber: 2.9 Consensus size: 51 87371872 TATTGTGATG * * * * 87371882 TCACGTGTGTAGTACTAAGTGCAGGCTATTATGCATACCCGATATCTTCGA 1 TCACATGTGTAGTACTAAGTGCAGGCTATTATGCGTACCAGATATATTCGA ** * * * * 87371933 TCATGTGTGTAGTACTAAGTGCAGGCTATTACGTGTACTAGATA-ATT-GG 1 TCACATGTGTAGTACTAAGTGCAGGCTATTATGCGTACCAGATATATTCGA * * * 87371982 TCGCATGTGTAGTACTAAGTGCAGGCCACTATGCGTACCAGATA 1 TCACATGTGTAGTACTAAGTGCAGGCTATTATGCGTACCAGATA 87372026 GCCTTGTCTA Statistics Matches: 77, Mismatches: 16, Indels: 2 0.81 0.17 0.02 Matches are distributed among these distances: 49 37 0.48 50 2 0.03 51 38 0.49 ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31 Consensus pattern (51 bp): TCACATGTGTAGTACTAAGTGCAGGCTATTATGCGTACCAGATATATTCGA Found at i:87380917 original size:27 final size:27 Alignment explanation

Indices: 87380887--87381064 Score: 180 Period size: 27 Copynumber: 6.6 Consensus size: 27 87380877 ATATTGAGCC * * 87380887 CGCACACTCAGTGCTATATAATCAACT 1 CGCACACTTAGTGCTACATAATCAACT * * 87380914 CGCACACTTAGTGCTACGTAATCAAAT 1 CGCACACTTAGTGCTACATAATCAACT * 87380941 CGCACACTTAGTGCTACATAGTCAGACT 1 CGCACACTTAGTGCTACATAATCA-ACT ** ** * 87380969 CGCACACTTAGTGCCGCATGGTCAATT 1 CGCACACTTAGTGCTACATAATCAACT * ** 87380996 CGCACACTTAGTGC-ATCATATTCATTT 1 CGCACACTTAGTGCTA-CATAATCAACT * * 87381023 CGCACACTTAGTGCAACATAGTCGAA-T 1 CGCACACTTAGTGCTACATAATC-AACT 87381050 CGCACACTTAGTGCT 1 CGCACACTTAGTGCT 87381065 GTACAATTTA Statistics Matches: 129, Mismatches: 18, Indels: 8 0.83 0.12 0.05 Matches are distributed among these distances: 27 104 0.81 28 25 0.19 ACGTcount: A:0.29, C:0.28, G:0.16, T:0.27 Consensus pattern (27 bp): CGCACACTTAGTGCTACATAATCAACT Found at i:87381026 original size:82 final size:81 Alignment explanation

Indices: 87380908--87381063 Score: 224 Period size: 82 Copynumber: 1.9 Consensus size: 81 87380898 TGCTATATAA * * * 87380908 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAGACTCGCA 1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTC-GAATCGCA 87380973 CACTTAGTGCCGCATGG 65 CACTTAGTGCCGCATGG * * ** 87380990 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCGAATCGCA 1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCGAATCGCA 87381054 CACTTAGTGC 65 CACTTAGTGC 87381064 TGTACAATTT Statistics Matches: 66, Mismatches: 7, Indels: 3 0.87 0.09 0.04 Matches are distributed among these distances: 81 18 0.27 82 48 0.73 ACGTcount: A:0.28, C:0.28, G:0.17, T:0.27 Consensus pattern (81 bp): TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCGAATCGCAC ACTTAGTGCCGCATGG Found at i:87382922 original size:50 final size:50 Alignment explanation

Indices: 87382847--87382946 Score: 200 Period size: 50 Copynumber: 2.0 Consensus size: 50 87382837 CATCGAGCTC 87382847 TCGGTTTCCCAGGTTGCTTCCTCGATCCCGTGTTTAAGCCACAACACCTT 1 TCGGTTTCCCAGGTTGCTTCCTCGATCCCGTGTTTAAGCCACAACACCTT 87382897 TCGGTTTCCCAGGTTGCTTCCTCGATCCCGTGTTTAAGCCACAACACCTT 1 TCGGTTTCCCAGGTTGCTTCCTCGATCCCGTGTTTAAGCCACAACACCTT 87382947 AACCAACGGA Statistics Matches: 50, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 50 50 1.00 ACGTcount: A:0.16, C:0.34, G:0.18, T:0.32 Consensus pattern (50 bp): TCGGTTTCCCAGGTTGCTTCCTCGATCCCGTGTTTAAGCCACAACACCTT Found at i:87387316 original size:4 final size:4 Alignment explanation

Indices: 87387307--87387334 Score: 56 Period size: 4 Copynumber: 7.0 Consensus size: 4 87387297 TTAAACTAAG 87387307 TAAA TAAA TAAA TAAA TAAA TAAA TAAA 1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA 87387335 AATAAAACTT Statistics Matches: 24, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 4 24 1.00 ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25 Consensus pattern (4 bp): TAAA Found at i:87389693 original size:43 final size:43 Alignment explanation

Indices: 87389646--87389731 Score: 163 Period size: 43 Copynumber: 2.0 Consensus size: 43 87389636 TTAGTGACAG * 87389646 TTGCTCAGGAAGATAGCTTGCAGTGAAATTATGATTATGTGGT 1 TTGCTCAGGAAGACAGCTTGCAGTGAAATTATGATTATGTGGT 87389689 TTGCTCAGGAAGACAGCTTGCAGTGAAATTATGATTATGTGGT 1 TTGCTCAGGAAGACAGCTTGCAGTGAAATTATGATTATGTGGT 87389732 AAACATTGAC Statistics Matches: 42, Mismatches: 1, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 43 42 1.00 ACGTcount: A:0.28, C:0.10, G:0.28, T:0.34 Consensus pattern (43 bp): TTGCTCAGGAAGACAGCTTGCAGTGAAATTATGATTATGTGGT Found at i:87390913 original size:38 final size:39 Alignment explanation

Indices: 87390806--87390972 Score: 203 Period size: 38 Copynumber: 4.3 Consensus size: 39 87390796 ATTTGATGTG * 87390806 TATCCGGGCTTAAATACCCGCAGGCTTTGTGCTGGTAAAA 1 TATCCGGGCTTAAAT-CCCGCAGGCTTCGTGCTGGTAAAA * 87390846 TATCCGGGCTTAAAGACCCGCAGGCTTCGTGCTGGTAAAA 1 TATCCGGGCTTAAA-TCCCGCAGGCTTCGTGCTGGTAAAA * ** 87390886 TATCCAGG-TTAAATCCCGCAGGCTTCGTGCTGGTATTA 1 TATCCGGGCTTAAATCCCGCAGGCTTCGTGCTGGTAAAA * * * ** 87390924 TATCCGGG-ATAAATCCCGCAGGCCTAGTGCTGGTATTA 1 TATCCGGGCTTAAATCCCGCAGGCTTCGTGCTGGTAAAA * 87390962 TATTCGGGCTT 1 TATCCGGGCTT 87390973 TCGTGCCTAG Statistics Matches: 113, Mismatches: 12, Indels: 5 0.87 0.09 0.04 Matches are distributed among these distances: 38 63 0.56 39 6 0.05 40 44 0.39 ACGTcount: A:0.23, C:0.23, G:0.26, T:0.28 Consensus pattern (39 bp): TATCCGGGCTTAAATCCCGCAGGCTTCGTGCTGGTAAAA Found at i:87390916 original size:78 final size:78 Alignment explanation

Indices: 87390806--87390958 Score: 202 Period size: 78 Copynumber: 2.0 Consensus size: 78 87390796 ATTTGATGTG * * * 87390806 TATCCGGGCTTAAATACCCGCAGGCTTTGTGCTGGTAAAATATCCGGGCTTAAAGACCCGCAGGC 1 TATCCAGGCTTAAATACCCGCAGGCTTCGTGCTGGTAAAATATCCGGG-ATAAA-ACCCGCAGGC * * 87390871 TTCGTGCTGGTAAAA 64 CTAGTGCTGGTAAAA ** * 87390886 TATCCAGG-TTAAAT-CCCGCAGGCTTCGTGCTGGTATTATATCCGGGATAAATCCCGCAGGCCT 1 TATCCAGGCTTAAATACCCGCAGGCTTCGTGCTGGTAAAATATCCGGGATAAAACCCGCAGGCCT 87390949 AGTGCTGGTA 66 AGTGCTGGTA 87390959 TTATATTCGG Statistics Matches: 65, Mismatches: 8, Indels: 4 0.84 0.10 0.05 Matches are distributed among these distances: 76 19 0.29 77 4 0.06 78 29 0.45 79 6 0.09 80 7 0.11 ACGTcount: A:0.24, C:0.24, G:0.26, T:0.26 Consensus pattern (78 bp): TATCCAGGCTTAAATACCCGCAGGCTTCGTGCTGGTAAAATATCCGGGATAAAACCCGCAGGCCT AGTGCTGGTAAAA Found at i:87391301 original size:43 final size:43 Alignment explanation

Indices: 87390962--87391288 Score: 528 Period size: 43 Copynumber: 7.6 Consensus size: 43 87390952 GCTGGTATTA * * * 87390962 TATTCGGGCTTTCGTGCCTAGCAGGCTTTGTTCCGGTGATGTG 1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG * 87391005 TATTCGGGCCTTCGTCCCTAGCAGGCTTCGTGCCGGTGATGTG 1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG * * 87391048 TATTCGGGCCTCCGTGCCTAGTAGGCTTCGTGCCGGTGATGTG 1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG * * 87391091 TATTCGGGCCTCCGTGCCTAGCAGGCTTCGTGCCAGTGATGTG 1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG * * * * 87391134 TATTCAGGCCTTCATGCCTAGCAGGCTTCGTGTCGGTGATTTG 1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG 87391177 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG 1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG 87391220 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG 1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG * * 87391263 TATTTGGGCCTTCGTACCTAGCAGGC 1 TATTCGGGCCTTCGTGCCTAGCAGGC 87391289 GTAATGCCGG Statistics Matches: 263, Mismatches: 21, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 43 263 1.00 ACGTcount: A:0.11, C:0.25, G:0.32, T:0.31 Consensus pattern (43 bp): TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG Found at i:87401103 original size:29 final size:28 Alignment explanation

Indices: 87401068--87401126 Score: 84 Period size: 29 Copynumber: 2.1 Consensus size: 28 87401058 TTATATTCAC * 87401068 ATGGCCC-ATTAGGTCCAAATCACATTTAT 1 ATGGCCCTA-TAGGCCCAAATCAC-TTTAT 87401097 ATGGCCCTATAGGCCCAAATCACTTTAT 1 ATGGCCCTATAGGCCCAAATCACTTTAT 87401125 AT 1 AT 87401127 TCATGCTCAC Statistics Matches: 28, Mismatches: 1, Indels: 3 0.88 0.03 0.09 Matches are distributed among these distances: 28 7 0.25 29 20 0.71 30 1 0.04 ACGTcount: A:0.31, C:0.25, G:0.14, T:0.31 Consensus pattern (28 bp): ATGGCCCTATAGGCCCAAATCACTTTAT Found at i:87406461 original size:47 final size:47 Alignment explanation

Indices: 87406278--87406500 Score: 165 Period size: 47 Copynumber: 4.7 Consensus size: 47 87406268 TATACTATGA * * * 87406278 GAGCCAGTGCAAGACCATGTCTGGGACATGGTATC-AGC-ATCAAGATGA- 1 GAGCCAGTGTAAGACCATGTCTGGGACAT-GCATCGA-CTAT-GAGAT-AT * * * * * * * * 87406326 GTGCTAGCGTAAGA-CTTGTTTGGGACATGCATCGCCCT-CGAGATGT 1 GAGCCAGTGTAAGACCATGTCTGGGACATGCATCG-ACTATGAGATAT * * 87406372 AAGCCAGTGTAAGA-CATGTCTAGGACATGCATCGACTATGAGATGAT 1 GAGCCAGTGTAAGACCATGTCTGGGACATGCATCGACTATGAGAT-AT * * * * 87406419 -AGTCAGTGTAAGACCATGTTTGGGACATGGCATTGAGT-TGAGATAT 1 GAGCCAGTGTAAGACCATGTCTGGGACAT-GCATCGACTATGAGATAT 87406465 GAGCCAGTGTAAGACCATGTCTGGGACATAGCATCG 1 GAGCCAGTGTAAGACCATGTCTGGGACAT-GCATCG 87406501 GCACCTTACT Statistics Matches: 136, Mismatches: 30, Indels: 19 0.74 0.16 0.10 Matches are distributed among these distances: 45 2 0.01 46 54 0.40 47 63 0.46 48 17 0.12 ACGTcount: A:0.28, C:0.18, G:0.29, T:0.24 Consensus pattern (47 bp): GAGCCAGTGTAAGACCATGTCTGGGACATGCATCGACTATGAGATAT Found at i:87417733 original size:40 final size:40 Alignment explanation

Indices: 87417689--87417767 Score: 149 Period size: 40 Copynumber: 2.0 Consensus size: 40 87417679 ATGGATTTAA 87417689 AGCTCTAATTTTGTTATGTGATGATTTTATCAAGTGATTG 1 AGCTCTAATTTTGTTATGTGATGATTTTATCAAGTGATTG * 87417729 AGCTCTAATTTTGTTATGTGATGATTTTATGAAGTGATT 1 AGCTCTAATTTTGTTATGTGATGATTTTATCAAGTGATT 87417768 TCAATAGAAG Statistics Matches: 38, Mismatches: 1, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 40 38 1.00 ACGTcount: A:0.25, C:0.06, G:0.20, T:0.48 Consensus pattern (40 bp): AGCTCTAATTTTGTTATGTGATGATTTTATCAAGTGATTG Found at i:87436169 original size:26 final size:26 Alignment explanation

Indices: 87436101--87436159 Score: 111 Period size: 26 Copynumber: 2.3 Consensus size: 26 87436091 TTTCTACTAC 87436101 TCACTTTTACATCTTTTGCAACTTGG 1 TCACTTTTACATCTTTTGCAACTTGG 87436127 TCACTTTTACATCTTTTGCAACTTGG 1 TCACTTTTACATCTTTTGCAACTTGG 87436153 TC-CTTTT 1 TCACTTTT 87436160 TAGGTGTTTT Statistics Matches: 33, Mismatches: 0, Indels: 1 0.97 0.00 0.03 Matches are distributed among these distances: 25 5 0.15 26 28 0.85 ACGTcount: A:0.17, C:0.24, G:0.10, T:0.49 Consensus pattern (26 bp): TCACTTTTACATCTTTTGCAACTTGG Found at i:87441128 original size:24 final size:24 Alignment explanation

Indices: 87441083--87441128 Score: 58 Period size: 24 Copynumber: 1.9 Consensus size: 24 87441073 CCTTATTAAC * * 87441083 ATTTCTTATTTCTCTTTTCTTTTA 1 ATTTCTTATTTCTCCTTCCTTTTA 87441107 ATTTCTT-TTTCTCGCTTCCTTT 1 ATTTCTTATTTCTC-CTTCCTTT 87441129 CATTACAAGA Statistics Matches: 19, Mismatches: 2, Indels: 2 0.83 0.09 0.09 Matches are distributed among these distances: 23 6 0.32 24 13 0.68 ACGTcount: A:0.09, C:0.22, G:0.02, T:0.67 Consensus pattern (24 bp): ATTTCTTATTTCTCCTTCCTTTTA Found at i:87451196 original size:46 final size:48 Alignment explanation

Indices: 87450996--87451268 Score: 296 Period size: 46 Copynumber: 5.8 Consensus size: 48 87450986 AGGGTATAAT * * ** 87450996 GCCGATGCCATGTCCCAGACATGGTCTTACACTAACTAT-CAAAATCGAG 1 GCCGATGCCATGTCCCAGACAT-GTCTTACACTAGCTCTAC-ATCTCGAG * * * * 87451045 GCCGACGCCATGTCCCAGACATGATCTTACACTAGCTCTCACATATCCAT 1 GCCGATGCCATGTCCCAGACATG-TCTTACACTAGCTCT-ACATCTCGAG * 87451095 GCCGATGCCATGTCCTAGACATGGTCTTACACTA---C-ACATCTCGTA- 1 GCCGATGCCATGTCCCAGACAT-GTCTTACACTAGCTCTACATCTCG-AG * 87451140 GCCGATG-CATGTCCCAGACATGTCTTACACTAGCT-TACATCTTGAG 1 GCCGATGCCATGTCCCAGACATGTCTTACACTAGCTCTACATCTCGAG * * * 87451186 GCTGATG-CATGTCCCAGACATGTCTTACACTAGCTCT-CATCTCAAT 1 GCCGATGCCATGTCCCAGACATGTCTTACACTAGCTCTACATCTCGAG * 87451232 GCCGATGCCATGTCCCGGACATGTCTTACACTAGCTC 1 GCCGATGCCATGTCCCAGACATGTCTTACACTAGCTC 87451269 CCAAATAACC Statistics Matches: 194, Mismatches: 18, Indels: 26 0.82 0.08 0.11 Matches are distributed among these distances: 43 11 0.06 44 13 0.07 45 14 0.07 46 54 0.28 47 30 0.15 48 1 0.01 49 34 0.18 50 35 0.18 51 2 0.01 ACGTcount: A:0.25, C:0.32, G:0.18, T:0.26 Consensus pattern (48 bp): GCCGATGCCATGTCCCAGACATGTCTTACACTAGCTCTACATCTCGAG Found at i:87451244 original size:93 final size:95 Alignment explanation

Indices: 87450996--87451268 Score: 308 Period size: 93 Copynumber: 2.9 Consensus size: 95 87450986 AGGGTATAAT * ** * * 87450996 GCCGATGCCATGTCCCAGACATGGTCTTACACTAACTATCAAAATCGAGGCCGACGCCATGTCCC 1 GCCGATGCCATGTCCCAGACATGGTCTTACACT-ACTCTC-ATCTC-ATGCCGATGCCATGTCCC * 87451061 AGACATGATCTTACACTAGCTCTCACATATCCAT 63 AGACATG-TCTTACACTAGCTCTCACATATCCAG * * * 87451095 GCCGATGCCATGTCCTAGACATGGTCTTACACTA--CACATCTCGTAGCCGATG-CATGTCCCAG 1 GCCGATGCCATGTCCCAGACATGGTCTTACACTACTCTCATCTCAT-GCCGATGCCATGTCCCAG * ** 87451157 ACATGTCTTACACTAGCT-T-ACATCTTGAG 65 ACATGTCTTACACTAGCTCTCACATATCCAG * * 87451186 GCTGATG-CATGTCCCAGACAT-GTCTTACACTAGCTCTCATCTCAATGCCGATGCCATGTCCCG 1 GCCGATGCCATGTCCCAGACATGGTCTTACACTA-CTCTCATCTC-ATGCCGATGCCATGTCCCA 87451249 GACATGTCTTACACTAGCTC 64 GACATGTCTTACACTAGCTC 87451269 CCAAATAACC Statistics Matches: 150, Mismatches: 17, Indels: 19 0.81 0.09 0.10 Matches are distributed among these distances: 89 11 0.07 90 13 0.09 91 12 0.08 92 15 0.10 93 41 0.27 94 15 0.10 95 9 0.06 96 1 0.01 98 1 0.01 99 32 0.21 ACGTcount: A:0.25, C:0.32, G:0.18, T:0.26 Consensus pattern (95 bp): GCCGATGCCATGTCCCAGACATGGTCTTACACTACTCTCATCTCATGCCGATGCCATGTCCCAGA CATGTCTTACACTAGCTCTCACATATCCAG Found at i:87455632 original size:24 final size:22 Alignment explanation

Indices: 87455600--87455645 Score: 56 Period size: 22 Copynumber: 2.0 Consensus size: 22 87455590 ATTTTCCCAT * 87455600 GAAACAGGGTCACACGCCTGTGTG 1 GAAACAGGG--ACACACCTGTGTG * 87455624 GAAATAGGGACACACCTGTGTG 1 GAAACAGGGACACACCTGTGTG 87455646 CCTTTGGCAC Statistics Matches: 20, Mismatches: 2, Indels: 2 0.83 0.08 0.08 Matches are distributed among these distances: 22 12 0.60 24 8 0.40 ACGTcount: A:0.28, C:0.22, G:0.33, T:0.17 Consensus pattern (22 bp): GAAACAGGGACACACCTGTGTG Found at i:87457233 original size:28 final size:28 Alignment explanation

Indices: 87457193--87457248 Score: 112 Period size: 28 Copynumber: 2.0 Consensus size: 28 87457183 ATCGATTCAA 87457193 GATAAGCTCTTATTCAGAGGAGGAATAG 1 GATAAGCTCTTATTCAGAGGAGGAATAG 87457221 GATAAGCTCTTATTCAGAGGAGGAATAG 1 GATAAGCTCTTATTCAGAGGAGGAATAG 87457249 ACCCTGTTTA Statistics Matches: 28, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 28 28 1.00 ACGTcount: A:0.36, C:0.11, G:0.29, T:0.25 Consensus pattern (28 bp): GATAAGCTCTTATTCAGAGGAGGAATAG Found at i:87459154 original size:46 final size:48 Alignment explanation

Indices: 87458899--87459211 Score: 206 Period size: 46 Copynumber: 6.6 Consensus size: 48 87458889 GGGTATAATA ** * * 87458899 CCGATGCCATGTCCCAGACATGGTCTTACACAGGC-T-CATCCATC-AAG 1 CCGATGCCATGTCCCAGACATGGTCTTACACTTGCTTACAT--TTCGAGG * * * ** 87458946 TCAATGCCCATGTCCCAGATATGGTCTTACAC-TGAC-TATCGAAATCGAGG 1 CCGATG-CCATGTCCCAGACATGGTCTTACACTTG-CTTA-C-ATTTCGAGG * * * * * * 87458996 CGGATGCCATGTCCCAGACCTGGTTTTACACTAGCTCTCACATATCCG-TG 1 CCGATGCCATGTCCCAGACATGGTCTTACACTTGCT-T-ACAT-TTCGAGG * 87459046 CCGATGCCATGTCCCAGACATGGTCTTACAC-TGAC--ACATCTCGTA-G 1 CCGATGCCATGTCCCAGACATGGTCTTACACTTG-CTTACATTTCG-AGG 87459092 CCGATG-CATGTCCCAGACAT-GTCTTACACTTGCTTACATTTCGAGG 1 CCGATGCCATGTCCCAGACATGGTCTTACACTTGCTTACATTTCGAGG * * * * * 87459138 CTGATG-CATGTCCCAGACAT-GTCTTACACTAGCTCT-CATCTCAATG 1 CCGATGCCATGTCCCAGACATGGTCTTACACTTGCT-TACATTTCGAGG * * 87459184 CCGATGCCATGTCCCATATATGGTCTTA 1 CCGATGCCATGTCCCAGACATGGTCTTA 87459212 TACTGGCTCC Statistics Matches: 213, Mismatches: 32, Indels: 41 0.74 0.11 0.14 Matches are distributed among these distances: 44 10 0.05 45 19 0.09 46 63 0.30 47 18 0.08 48 32 0.15 49 27 0.13 50 38 0.18 51 5 0.02 52 1 0.00 ACGTcount: A:0.24, C:0.30, G:0.19, T:0.27 Consensus pattern (48 bp): CCGATGCCATGTCCCAGACATGGTCTTACACTTGCTTACATTTCGAGG Found at i:87472798 original size:15 final size:15 Alignment explanation

Indices: 87472778--87472807 Score: 60 Period size: 15 Copynumber: 2.0 Consensus size: 15 87472768 CATTATTATT 87472778 CATACATTCAGATCA 1 CATACATTCAGATCA 87472793 CATACATTCAGATCA 1 CATACATTCAGATCA 87472808 TACATTTAGC Statistics Matches: 15, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 15 15 1.00 ACGTcount: A:0.40, C:0.27, G:0.07, T:0.27 Consensus pattern (15 bp): CATACATTCAGATCA Found at i:87472811 original size:13 final size:13 Alignment explanation

Indices: 87472777--87472813 Score: 56 Period size: 15 Copynumber: 2.7 Consensus size: 13 87472767 GCATTATTAT 87472777 TCATACATTCAGA 1 TCATACATTCAGA 87472790 TCACATACATTCAGA 1 T--CATACATTCAGA 87472805 TCATACATT 1 TCATACATT 87472814 TAGCGGTCTA Statistics Matches: 22, Mismatches: 0, Indels: 4 0.85 0.00 0.15 Matches are distributed among these distances: 13 9 0.41 15 13 0.59 ACGTcount: A:0.38, C:0.24, G:0.05, T:0.32 Consensus pattern (13 bp): TCATACATTCAGA Found at i:87485223 original size:15 final size:16 Alignment explanation

Indices: 87485190--87485223 Score: 52 Period size: 16 Copynumber: 2.2 Consensus size: 16 87485180 ATCAGGATAT * 87485190 TACATGTATGTCATCA 1 TACATGTATCTCATCA 87485206 TACATGTATCTC-TCA 1 TACATGTATCTCATCA 87485221 TAC 1 TAC 87485224 TCATTTTACC Statistics Matches: 17, Mismatches: 1, Indels: 1 0.89 0.05 0.05 Matches are distributed among these distances: 15 6 0.35 16 11 0.65 ACGTcount: A:0.29, C:0.24, G:0.09, T:0.38 Consensus pattern (16 bp): TACATGTATCTCATCA Found at i:87489588 original size:28 final size:28 Alignment explanation

Indices: 87489544--87489600 Score: 105 Period size: 28 Copynumber: 2.0 Consensus size: 28 87489534 ACCTCGAGAG * 87489544 TAAGCTCTTTTTTCCCTTTGGTACATTA 1 TAAGCTCTTTTTGCCCTTTGGTACATTA 87489572 TAAGCTCTTTTTGCCCTTTGGTACATTA 1 TAAGCTCTTTTTGCCCTTTGGTACATTA 87489600 T 1 T 87489601 TGTCATACAT Statistics Matches: 28, Mismatches: 1, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 28 28 1.00 ACGTcount: A:0.18, C:0.21, G:0.12, T:0.49 Consensus pattern (28 bp): TAAGCTCTTTTTGCCCTTTGGTACATTA Found at i:87493835 original size:40 final size:40 Alignment explanation

Indices: 87493739--87493962 Score: 319 Period size: 40 Copynumber: 5.5 Consensus size: 40 87493729 TATTCGGATG * 87493739 ATATCCGGGCTAAGTCCCGAAGGCATTTGTACGAGTAGTTG-CT 1 ATATCCGGGCTAAGTCCCGAAGGCATTTGT--G-CTAG-TGACT * 87493782 ATACCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT 1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT 87493822 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT 1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT ** 87493862 ATATCCGGGCTAAGTCCCGAAGGCATTCATGCTAGTGACT 1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT * * 87493902 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT 1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TGACT * 87493942 ATATCC-GGCTAAATCCCGAAG 1 ATATCCGGGCTAAGTCCCGAAG 87493963 ATACTTGGGT Statistics Matches: 168, Mismatches: 11, Indels: 8 0.90 0.06 0.04 Matches are distributed among these distances: 39 15 0.09 40 121 0.72 41 3 0.02 43 29 0.17 ACGTcount: A:0.24, C:0.24, G:0.27, T:0.25 Consensus pattern (40 bp): ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT Found at i:87502500 original size:16 final size:16 Alignment explanation

Indices: 87502479--87502531 Score: 70 Period size: 16 Copynumber: 3.1 Consensus size: 16 87502469 CACACACGCC 87502479 CGTGTGGCTTGGGACA 1 CGTGTGGCTTGGGACA 87502495 CGTGTGGCTTGGGACA 1 CGTGTGGCTTGGGACA 87502511 CGCCCGTGTGGCTTGGGACA 1 ----CGTGTGGCTTGGGACA 87502531 C 1 C 87502532 TCCCGTGTCC Statistics Matches: 33, Mismatches: 0, Indels: 8 0.80 0.00 0.20 Matches are distributed among these distances: 16 17 0.52 20 16 0.48 ACGTcount: A:0.11, C:0.25, G:0.42, T:0.23 Consensus pattern (16 bp): CGTGTGGCTTGGGACA Found at i:87502520 original size:20 final size:20 Alignment explanation

Indices: 87502472--87502539 Score: 99 Period size: 20 Copynumber: 3.6 Consensus size: 20 87502462 GTGTGGTCAC 87502472 ACACGCCCGTGTGGCTTGGG 1 ACACGCCCGTGTGGCTTGGG 87502492 ACA----CGTGTGGCTTGGG 1 ACACGCCCGTGTGGCTTGGG 87502508 ACACGCCCGTGTGGCTTGGG 1 ACACGCCCGTGTGGCTTGGG * 87502528 ACACTCCCGTGT 1 ACACGCCCGTGT 87502540 CCTCAGCCTA Statistics Matches: 43, Mismatches: 1, Indels: 8 0.83 0.02 0.15 Matches are distributed among these distances: 16 16 0.37 20 27 0.63 ACGTcount: A:0.12, C:0.29, G:0.37, T:0.22 Consensus pattern (20 bp): ACACGCCCGTGTGGCTTGGG Found at i:87504977 original size:80 final size:79 Alignment explanation

Indices: 87504893--87505064 Score: 220 Period size: 79 Copynumber: 2.2 Consensus size: 79 87504883 GGACTAAGAT * 87504893 CCGAAGGCATTTGTGCGAGATA-CAAATTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACT 1 CCGAAGGCATTTGTGCGAGATATCAAA-TCCGGGTTAAGCCCCGAAGG-CATTGTGCGAGATACT * * 87504957 AAATCCGGGTTAAGTC 64 AAAACCGGGCTAAGTC * * * * * * * 87504973 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAA 1 CCGAAGGCATTTGTGCGAGATATCAAATCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAA * 87505038 AACCGGGCTATGTC 66 AACCGGGCTAAGTC 87505052 CCGAAGGCATTTG 1 CCGAAGGCATTTG 87505065 AACGAGGAGC Statistics Matches: 79, Mismatches: 12, Indels: 3 0.84 0.13 0.03 Matches are distributed among these distances: 79 38 0.48 80 38 0.48 81 3 0.04 ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26 Consensus pattern (79 bp): CCGAAGGCATTTGTGCGAGATATCAAATCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAA AACCGGGCTAAGTC Found at i:87505044 original size:39 final size:39 Alignment explanation

Indices: 87504840--87505062 Score: 209 Period size: 40 Copynumber: 5.6 Consensus size: 39 87504830 TTGAATGCTG * * * * * 87504840 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTA-AGTGAATATA 1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGA-T-ACTAAA ** 87504880 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATAC-AAA 1 TCCGGGTTAAG-TCCCGAAGGCA-TTGTGCGAGATACTAAA * * 87504919 TTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAA 1 -TCCGGGTTAAGTCCCGAAGG-CATTGTGCGAGATACTAAA * * 87504960 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA 1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGATACTAAA * * * 87505000 TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAA 1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGATACTAAA * * * 87505039 ACCGGGCTATGTCCCGAAGGCATT 1 TCCGGGTTAAGTCCCGAAGGCATT 87505063 TGAACGAGGA Statistics Matches: 157, Mismatches: 18, Indels: 17 0.82 0.09 0.09 Matches are distributed among these distances: 39 40 0.25 40 103 0.66 41 13 0.08 42 1 0.01 ACGTcount: A:0.26, C:0.22, G:0.27, T:0.26 Consensus pattern (39 bp): TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGATACTAAA Found at i:87505082 original size:79 final size:80 Alignment explanation

Indices: 87504920--87505097 Score: 191 Period size: 79 Copynumber: 2.2 Consensus size: 80 87504910 AGATACAAAT * * * * 87504920 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTC 1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC ** * * 87504985 GTGCGAGTTATTAAA 66 GAACGAGTGACTAAA * * * * * 87505000 TCCGGGTTATGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTT 1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC * 87505064 GAACGAG-GAGCTATA 66 GAACGAGTGA-CTAAA * 87505079 TCC-GGTTAAATCCCGAAGG 1 TCCGGGTTAAGTCCCGAAGG 87505098 TACGTGATTT Statistics Matches: 81, Mismatches: 16, Indels: 4 0.80 0.16 0.04 Matches are distributed among these distances: 78 15 0.19 79 48 0.59 80 18 0.22 ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25 Consensus pattern (80 bp): TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC GAACGAGTGACTAAA Found at i:87508482 original size:480 final size:480 Alignment explanation

Indices: 87507565--87508526 Score: 1789 Period size: 480 Copynumber: 2.0 Consensus size: 480 87507555 ATGAACGTCG * 87507565 AGACAGGACGAAATGCCGATATTGCGGTAAATGGCATTCGGGGAGTTGTAGATTCCCTGACCGCT 1 AGACAGAACGAAATGCCGATATTGCGGTAAATGGCATTCGGGGAGTTGTAGATTCCCTGACCGCT * * * 87507630 CCTGTTACAAGTGCGGATCAGTTGACCACTTCATTAAAGATTGCCCGAGGTTGTCGGGACAGAAT 66 CCTGTTACAAATGCGGATCAGTGGACCACTTCATTAAAGATTGCCCGAGGTTGTCGGAACAGAAT * * 87507695 GCAAATCAGAGTGGGAGACCGGGTGCTACCACTGCTCGAGGTAGACCATCTGGAAATACGGGCAA 131 GAAAATCAGAGTGGGAAACCGGGTGCTACCACTGCTCGAGGTAGACCATCTGGAAATACGGGCAA 87507760 TGCTAGTGGTGGTCAGAGAGGATCTAGAGATGATATAACCAGATCCGAAGCCCGTGCGCCTGCTA 196 TGCTAGTGGTGGTCAGAGAGGATCTAGAGATGATATAACCAGATCCGAAGCCCGTGCGCCTGCTA 87507825 GAGCTTATGCTATACGTGCCCGCGAGGATGCTTCTTCGCCTGATGTTATTACCGGTACATTCACC 261 GAGCTTATGCTATACGTGCCCGCGAGGATGCTTCTTCGCCTGATGTTATTACCGGTACATTCACC 87507890 CTCTTTGATACTAATGTAATTGCTTTGATTGACCCCGGTTCTACTCATTCCTACATATGTGAAAC 326 CTCTTTGATACTAATGTAATTGCTTTGATTGACCCCGGTTCTACTCATTCCTACATATGTGAAAC 87507955 CTTAGCATCCAGTAAGACTTTACCTATTGAGTCTACTGAGTTCGTAATTCGGGTGTCAAATCCCT 391 CTTAGCATCCAGTAAGACTTTACCTATTGAGTCTACTGAGTTCGTAATTCGGGTGTCAAATCCCT 87508020 TGGGTCGTTACGTGCTTGTCGACAA 456 TGGGTCGTTACGTGCTTGTCGACAA * * * 87508045 AGACAGAACGGAATGTCGATATTGCGGTAAATGGCATTCGGGGAGTTGTAGATTTCCTGACCGCT 1 AGACAGAACGAAATGCCGATATTGCGGTAAATGGCATTCGGGGAGTTGTAGATTCCCTGACCGCT ** 87508110 CCTGTTACAAATGCGGATCAGTGGACCACTTCATTAAAGATTGCCCGAGGTTGTTTGAACAGAAT 66 CCTGTTACAAATGCGGATCAGTGGACCACTTCATTAAAGATTGCCCGAGGTTGTCGGAACAGAAT * 87508175 GAAAATCAGAGTGGGAAACCGGGTGCTACCACTGCTCGAGGTAGACCATCTGGAAATATGGGCAA 131 GAAAATCAGAGTGGGAAACCGGGTGCTACCACTGCTCGAGGTAGACCATCTGGAAATACGGGCAA * 87508240 TGCTGGTGGTGGTCAGAGAGGATCTAGAGATGATATAACCAGATCCGAAGCCCGTGCGCCTGCTA 196 TGCTAGTGGTGGTCAGAGAGGATCTAGAGATGATATAACCAGATCCGAAGCCCGTGCGCCTGCTA * 87508305 GAGCTTATGCTATACGTGCCCGCGAGGATGCTTCTTCGCCTGATGTTATTACCGGTACATTCACT 261 GAGCTTATGCTATACGTGCCCGCGAGGATGCTTCTTCGCCTGATGTTATTACCGGTACATTCACC * 87508370 CTCTTTGATACTAATGTAATTGCTTTGATTGACCCCGGTTCTACTCATTCTTACATATGTGAAAC 326 CTCTTTGATACTAATGTAATTGCTTTGATTGACCCCGGTTCTACTCATTCCTACATATGTGAAAC 87508435 CTTAGCATCCAGTAAGACTTTACCTATTGAGTCTACTGAGTTCGTAATTCGGGTGTCAAATCCCT 391 CTTAGCATCCAGTAAGACTTTACCTATTGAGTCTACTGAGTTCGTAATTCGGGTGTCAAATCCCT 87508500 TGGGTCGTTACGTGCTTGTCGACAA 456 TGGGTCGTTACGTGCTTGTCGACAA 87508525 AG 1 AG 87508527 TGTGTAAGAA Statistics Matches: 467, Mismatches: 15, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 480 467 1.00 ACGTcount: A:0.25, C:0.22, G:0.25, T:0.28 Consensus pattern (480 bp): AGACAGAACGAAATGCCGATATTGCGGTAAATGGCATTCGGGGAGTTGTAGATTCCCTGACCGCT CCTGTTACAAATGCGGATCAGTGGACCACTTCATTAAAGATTGCCCGAGGTTGTCGGAACAGAAT GAAAATCAGAGTGGGAAACCGGGTGCTACCACTGCTCGAGGTAGACCATCTGGAAATACGGGCAA TGCTAGTGGTGGTCAGAGAGGATCTAGAGATGATATAACCAGATCCGAAGCCCGTGCGCCTGCTA GAGCTTATGCTATACGTGCCCGCGAGGATGCTTCTTCGCCTGATGTTATTACCGGTACATTCACC CTCTTTGATACTAATGTAATTGCTTTGATTGACCCCGGTTCTACTCATTCCTACATATGTGAAAC CTTAGCATCCAGTAAGACTTTACCTATTGAGTCTACTGAGTTCGTAATTCGGGTGTCAAATCCCT TGGGTCGTTACGTGCTTGTCGACAA Found at i:87513314 original size:40 final size:40 Alignment explanation

Indices: 87513231--87513493 Score: 316 Period size: 40 Copynumber: 6.6 Consensus size: 40 87513221 TTGAATGCTG * * * * * * 87513231 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA 1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAA * * * * * 87513271 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA 1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTATTAAA 87513311 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA 1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA * 87513351 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA 1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA * 87513391 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA 1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA * * * 87513431 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA 1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA * * * 87513470 ACCGGGCTATGTCCCGAAGGCATT 1 TCCGGGTTAAGTCCCGAAGGCATT 87513494 TGAACGAGGA Statistics Matches: 201, Mismatches: 19, Indels: 7 0.89 0.08 0.03 Matches are distributed among these distances: 39 35 0.17 40 158 0.79 41 8 0.04 ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27 Consensus pattern (40 bp): TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA Found at i:87513513 original size:79 final size:80 Alignment explanation

Indices: 87513270--87513528 Score: 247 Period size: 80 Copynumber: 3.3 Consensus size: 80 87513260 AAGTGAATAT * * * * * * 87513270 ATCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCAT 1 ATCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAT ** * * 87513334 TCGTGCGAGTTA-TTAA 65 TCGAACGAG-GAGCTAA ** * * 87513350 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTCCCGAAGGCATT 1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT ** ** * 87513415 CGTGCGAGTTGTTAA 66 CGAACGAGGAGCTAA * * * 87513430 ATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATT 1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT * * 87513494 TGAACGAGGAGCTAT 66 CGAACGAGGAGCTAA * 87513509 ATCC-GGTTAAATCCCGAAGG 1 ATCCGGGTTAAGTCCCGAAGG 87513529 TACGTGATTT Statistics Matches: 154, Mismatches: 23, Indels: 6 0.84 0.13 0.03 Matches are distributed among these distances: 78 14 0.09 79 47 0.31 80 93 0.60 ACGTcount: A:0.25, C:0.20, G:0.28, T:0.26 Consensus pattern (80 bp): ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT CGAACGAGGAGCTAA Found at i:87516916 original size:26 final size:26 Alignment explanation

Indices: 87516887--87516950 Score: 83 Period size: 26 Copynumber: 2.5 Consensus size: 26 87516877 ACAAAGCCTA * * * 87516887 CTAAATATACATCATCCCGAAGCTTG 1 CTAAATATACACCAGCACGAAGCTTG * * 87516913 CTAAATATACACCAGGATGAAGCTTG 1 CTAAATATACACCAGCACGAAGCTTG 87516939 CTAAATATACAC 1 CTAAATATACAC 87516951 TGACACAAAG Statistics Matches: 33, Mismatches: 5, Indels: 0 0.87 0.13 0.00 Matches are distributed among these distances: 26 33 1.00 ACGTcount: A:0.39, C:0.23, G:0.12, T:0.25 Consensus pattern (26 bp): CTAAATATACACCAGCACGAAGCTTG Found at i:87516961 original size:26 final size:27 Alignment explanation

Indices: 87516876--87516967 Score: 73 Period size: 26 Copynumber: 3.5 Consensus size: 27 87516866 AAAACACTGT * * 87516876 CACAAAGCCTACTAAATATACA-TCAT 1 CACAAAGCCTGCTAAATATACACTCAG * * * 87516902 CCCGAAGCTTGCTAAATATACAC-CAG 1 CACAAAGCCTGCTAAATATACACTCAG * ** * * 87516928 GATGAAGCTTGCTAAATATACACTGA- 1 CACAAAGCCTGCTAAATATACACTCAG 87516954 CACAAAGCCTGCTA 1 CACAAAGCCTGCTA 87516968 TGCCCTAATG Statistics Matches: 51, Mismatches: 13, Indels: 4 0.75 0.19 0.06 Matches are distributed among these distances: 26 50 0.98 27 1 0.02 ACGTcount: A:0.39, C:0.26, G:0.13, T:0.22 Consensus pattern (27 bp): CACAAAGCCTGCTAAATATACACTCAG Found at i:87525926 original size:14 final size:14 Alignment explanation

Indices: 87525909--87525959 Score: 54 Period size: 13 Copynumber: 3.9 Consensus size: 14 87525899 ACCTCATATA 87525909 AATTTTTTATAAAT 1 AATTTTTTATAAAT * 87525923 AA-TTTTTAAAAAT 1 AATTTTTTATAAAT * 87525936 AAATTTTTAT-AAT 1 AATTTTTTATAAAT * 87525949 -TTTTTTTATAA 1 AATTTTTTATAA 87525960 TTATTTAAGT Statistics Matches: 31, Mismatches: 4, Indels: 5 0.77 0.10 0.12 Matches are distributed among these distances: 12 7 0.23 13 16 0.52 14 8 0.26 ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57 Consensus pattern (14 bp): AATTTTTTATAAAT Found at i:87525930 original size:13 final size:14 Alignment explanation

Indices: 87525906--87525947 Score: 59 Period size: 14 Copynumber: 3.0 Consensus size: 14 87525896 ATTACCTCAT 87525906 ATAAATTTTTTATAA 1 ATAAA-TTTTTATAA * 87525921 AT-AATTTTTAAAA 1 ATAAATTTTTATAA 87525934 ATAAATTTTTATAA 1 ATAAATTTTTATAA 87525948 TTTTTTTTAT Statistics Matches: 24, Mismatches: 2, Indels: 3 0.83 0.07 0.10 Matches are distributed among these distances: 13 10 0.42 14 12 0.50 15 2 0.08 ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50 Consensus pattern (14 bp): ATAAATTTTTATAA Found at i:87526071 original size:10 final size:10 Alignment explanation

Indices: 87526056--87526145 Score: 64 Period size: 10 Copynumber: 9.2 Consensus size: 10 87526046 TTTTAACATT 87526056 ATTTTTAATA 1 ATTTTTAATA 87526066 ATTTTTAATA 1 ATTTTTAATA * 87526076 A-TTTTAACA 1 ATTTTTAATA * 87526085 ATTTCTT-ATC 1 ATTT-TTAATA * 87526095 ATTTTAAATA 1 ATTTTTAATA * * 87526105 CTTTCCT-ATA 1 ATTT-TTAATA 87526115 ATTTTCT-A-A 1 ATTTT-TAATA * 87526124 ATTTTTTATA 1 ATTTTTAATA 87526134 ATTTTTAATA 1 ATTTTTAATA 87526144 AT 1 AT 87526146 AATTTGAAAA Statistics Matches: 62, Mismatches: 11, Indels: 14 0.71 0.13 0.16 Matches are distributed among these distances: 8 1 0.02 9 16 0.26 10 43 0.69 11 2 0.03 ACGTcount: A:0.36, C:0.08, G:0.00, T:0.57 Consensus pattern (10 bp): ATTTTTAATA Found at i:87526082 original size:19 final size:19 Alignment explanation

Indices: 87526058--87526145 Score: 72 Period size: 19 Copynumber: 4.5 Consensus size: 19 87526048 TTAACATTAT 87526058 TTTTAATAATTT-TTAATAA 1 TTTTAATAATTTCTT-ATAA * * 87526077 TTTTAACAATTTCTTATCA 1 TTTTAATAATTTCTTATAA * * 87526096 TTTTAAATACTTTCCTATAA 1 TTTT-AATAATTTCTTATAA * * 87526116 TTTT-CTAAATTTTTTATAA 1 TTTTAAT-AATTTCTTATAA 87526135 TTTTTAATAAT 1 -TTTTAATAAT 87526146 AATTTGAAAA Statistics Matches: 53, Mismatches: 11, Indels: 9 0.73 0.15 0.12 Matches are distributed among these distances: 18 1 0.02 19 27 0.51 20 24 0.45 21 1 0.02 ACGTcount: A:0.35, C:0.08, G:0.00, T:0.57 Consensus pattern (19 bp): TTTTAATAATTTCTTATAA Found at i:87526976 original size:21 final size:21 Alignment explanation

Indices: 87526923--87526976 Score: 51 Period size: 21 Copynumber: 2.6 Consensus size: 21 87526913 ATGCTTTTTG 87526923 TTTTT-TTATACTTTTATATAA 1 TTTTTATT-TACTTTTATATAA * 87526944 TCCTTTCA--TACTTTTATATAA 1 T--TTTTATTTACTTTTATATAA 87526965 TTTTTATTTACT 1 TTTTTATTTACT 87526977 CTAATCTAAT Statistics Matches: 26, Mismatches: 2, Indels: 10 0.68 0.05 0.26 Matches are distributed among these distances: 19 4 0.15 21 19 0.73 23 3 0.12 ACGTcount: A:0.26, C:0.11, G:0.00, T:0.63 Consensus pattern (21 bp): TTTTTATTTACTTTTATATAA Found at i:87529819 original size:24 final size:24 Alignment explanation

Indices: 87529762--87529820 Score: 59 Period size: 24 Copynumber: 2.5 Consensus size: 24 87529752 TACTACCGAT 87529762 CAGGATGCTCGCAGAACTATATAA 1 CAGGATGCTCGCAGAACTATATAA * * * 87529786 CGGGAAGCTCG-AGAGGACTA-ATAC 1 CAGGATGCTCGCAGA--ACTATATAA 87529810 CAGGATGCTCG 1 CAGGATGCTCG 87529821 TAAGAGCTAT Statistics Matches: 28, Mismatches: 5, Indels: 4 0.76 0.14 0.11 Matches are distributed among these distances: 23 3 0.11 24 21 0.75 25 4 0.14 ACGTcount: A:0.32, C:0.22, G:0.29, T:0.17 Consensus pattern (24 bp): CAGGATGCTCGCAGAACTATATAA Found at i:87530009 original size:21 final size:22 Alignment explanation

Indices: 87529969--87530011 Score: 70 Period size: 22 Copynumber: 2.0 Consensus size: 22 87529959 AACATTTATA 87529969 CAATTCAAACAAATTTAACATT 1 CAATTCAAACAAATTTAACATT * 87529991 CAATTCAAATAAA-TTAACATT 1 CAATTCAAACAAATTTAACATT 87530012 TATAATCTAG Statistics Matches: 20, Mismatches: 1, Indels: 1 0.91 0.05 0.05 Matches are distributed among these distances: 21 8 0.40 22 12 0.60 ACGTcount: A:0.51, C:0.16, G:0.00, T:0.33 Consensus pattern (22 bp): CAATTCAAACAAATTTAACATT Found at i:87535082 original size:8 final size:8 Alignment explanation

Indices: 87535071--87535104 Score: 68 Period size: 8 Copynumber: 4.2 Consensus size: 8 87535061 TATTTTAATC 87535071 ACTCTTAT 1 ACTCTTAT 87535079 ACTCTTAT 1 ACTCTTAT 87535087 ACTCTTAT 1 ACTCTTAT 87535095 ACTCTTAT 1 ACTCTTAT 87535103 AC 1 AC 87535105 CATGCTCAAT Statistics Matches: 26, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 8 26 1.00 ACGTcount: A:0.26, C:0.26, G:0.00, T:0.47 Consensus pattern (8 bp): ACTCTTAT Done.