Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: A05

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: 100714657
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32

Warning! 3970000 characters in sequence are not A, C, G, or T


File 270 of 318

Found at i:86334542 original size:16 final size:15

Alignment explanation

Indices: 86334502--86334543 Score: 50 Period size: 16 Copynumber: 2.7 Consensus size: 15 86334492 AGATGATAAT 86334502 TATTAATATATAATTA 1 TATTAAT-TATAATTA 86334518 TATCT-ATTATAATATA 1 TAT-TAATTATAAT-TA 86334534 TATTAATTAT 1 TATTAATTAT 86334544 TATTTATTTT Statistics Matches: 23, Mismatches: 0, Indels: 6 0.79 0.00 0.21 Matches are distributed among these distances: 15 7 0.30 16 15 0.65 17 1 0.04 ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52 Consensus pattern (15 bp): TATTAATTATAATTA Found at i:86334547 original size:22 final size:23 Alignment explanation

Indices: 86334500--86334547 Score: 68 Period size: 22 Copynumber: 2.3 Consensus size: 23 86334490 GAAGATGATA 86334500 ATTATTAATATATAATTATATCT 1 ATTATTAATATATAATTATATCT 86334523 ATTA-TAATATAT-ATTA-AT-T 1 ATTATTAATATATAATTATATCT 86334542 ATTATT 1 ATTATT 86334548 TATTTTATCT Statistics Matches: 24, Mismatches: 0, Indels: 5 0.83 0.00 0.17 Matches are distributed among these distances: 19 5 0.21 20 3 0.12 21 4 0.17 22 8 0.33 23 4 0.17 ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54 Consensus pattern (23 bp): ATTATTAATATATAATTATATCT Found at i:86341126 original size:27 final size:27 Alignment explanation

Indices: 86341088--86341201 Score: 149 Period size: 27 Copynumber: 4.2 Consensus size: 27 86341078 GTTGTTAAGA 86341088 CCCTCGATTTGTGAAATTATCGAAATAC 1 CCCT-GATTTGTGAAATTATCGAAATAC ** * 86341116 CCCTGGGTTGT-AAACTTACCGAAATAC 1 CCCTGATTTGTGAAA-TTATCGAAATAC * 86341143 CCCTGATTTGTGAAATTATCGAAATAT 1 CCCTGATTTGTGAAATTATCGAAATAC * * 86341170 CCCTAATTTGTAAAATTATCGAAATAC 1 CCCTGATTTGTGAAATTATCGAAATAC 86341197 CCCTG 1 CCCTG 86341202 TAAGGTAGGA Statistics Matches: 73, Mismatches: 11, Indels: 5 0.82 0.12 0.06 Matches are distributed among these distances: 26 3 0.04 27 63 0.86 28 7 0.10 ACGTcount: A:0.32, C:0.22, G:0.14, T:0.32 Consensus pattern (27 bp): CCCTGATTTGTGAAATTATCGAAATAC Found at i:86341157 original size:54 final size:54 Alignment explanation

Indices: 86341088--86341201 Score: 165 Period size: 54 Copynumber: 2.1 Consensus size: 54 86341078 GTTGTTAAGA ** * 86341088 CCCTCGATTTGTGAAATTATCGAAATACCCCTGGGTTGTAAACTTACCGAAATAC 1 CCCT-GATTTGTGAAATTATCGAAATACCCCTAAGTTGTAAAATTACCGAAATAC * * * 86341143 CCCTGATTTGTGAAATTATCGAAATATCCCTAATTTGTAAAATTATCGAAATAC 1 CCCTGATTTGTGAAATTATCGAAATACCCCTAAGTTGTAAAATTACCGAAATAC 86341197 CCCTG 1 CCCTG 86341202 TAAGGTAGGA Statistics Matches: 53, Mismatches: 6, Indels: 1 0.88 0.10 0.02 Matches are distributed among these distances: 54 49 0.92 55 4 0.08 ACGTcount: A:0.32, C:0.22, G:0.14, T:0.32 Consensus pattern (54 bp): CCCTGATTTGTGAAATTATCGAAATACCCCTAAGTTGTAAAATTACCGAAATAC Found at i:86341221 original size:23 final size:23 Alignment explanation

Indices: 86341194--86341238 Score: 81 Period size: 23 Copynumber: 2.0 Consensus size: 23 86341184 ATTATCGAAA 86341194 TACCCCTGTAAGGTAGGATTACC 1 TACCCCTGTAAGGTAGGATTACC * 86341217 TACCCCTGTAGGGTAGGATTAC 1 TACCCCTGTAAGGTAGGATTAC 86341239 TGTAATCTAT Statistics Matches: 21, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 23 21 1.00 ACGTcount: A:0.24, C:0.24, G:0.24, T:0.27 Consensus pattern (23 bp): TACCCCTGTAAGGTAGGATTACC Found at i:86344797 original size:15 final size:15 Alignment explanation

Indices: 86344777--86344808 Score: 55 Period size: 15 Copynumber: 2.1 Consensus size: 15 86344767 TAATTATGTT * 86344777 TTAAATGCTTTATTA 1 TTAAATGCTTCATTA 86344792 TTAAATGCTTCATTA 1 TTAAATGCTTCATTA 86344807 TT 1 TT 86344809 GTATGAATTT Statistics Matches: 16, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 15 16 1.00 ACGTcount: A:0.31, C:0.09, G:0.06, T:0.53 Consensus pattern (15 bp): TTAAATGCTTCATTA Found at i:86344972 original size:42 final size:42 Alignment explanation

Indices: 86344909--86345059 Score: 171 Period size: 42 Copynumber: 3.6 Consensus size: 42 86344899 CTGATATTAC * * 86344909 GTGTAAGACCACATCTAGGATATGGCATCGATATGAGACTTT 1 GTGTAAGACCATATCTGGGATATGGCATCGATATGAGACTTT * * 86344951 GTGTAAAACCATATCTGGGATATGGCATCGATATGAGACCTT 1 GTGTAAGACCATATCTGGGATATGGCATCGATATGAGACTTT * * * * 86344993 GTATAAGACCATAGT-TGAGCTATTGGCATCGATACGAGA-TTT 1 GTGTAAGACCATA-TCTGGGATA-TGGCATCGATATGAGACTTT * * 86345035 CATGTAAGACCATATTTGGGATATG 1 -GTGTAAGACCATATCTGGGATATG 86345060 ACATTAGTAC Statistics Matches: 91, Mismatches: 14, Indels: 8 0.81 0.12 0.07 Matches are distributed among these distances: 42 59 0.65 43 32 0.35 ACGTcount: A:0.31, C:0.15, G:0.24, T:0.30 Consensus pattern (42 bp): GTGTAAGACCATATCTGGGATATGGCATCGATATGAGACTTT Found at i:86350146 original size:42 final size:41 Alignment explanation

Indices: 86350041--86350171 Score: 120 Period size: 42 Copynumber: 3.0 Consensus size: 41 86350031 CGATATGTGT * * * 86350041 TTTTGTGTAAGACCTCGTCTGGGACGTTGACATCG-ACTTATGA 1 TTTTGTGTAAGACCTTGTCTGGGAC-ATGGCATCGTA-TT-TGA * * * * 86350084 TTTACGTGTAATACCATGTCTGGGACATCGGTATCGTATTTGA 1 TTT-TGTGTAAGACCTTGTCTGGGACAT-GGCATCGTATTTGA * 86350127 TTTTGTGTAAGACCTTGTCTGGGCCAGTGGCATCGATATTTGA 1 TTTTGTGTAAGACCTTGTCTGGGACA-TGGCATCG-TATTTGA 86350170 TT 1 TT 86350172 ACATGTAAGA Statistics Matches: 71, Mismatches: 12, Indels: 10 0.76 0.13 0.11 Matches are distributed among these distances: 42 25 0.35 43 20 0.28 44 25 0.35 45 1 0.01 ACGTcount: A:0.21, C:0.17, G:0.25, T:0.37 Consensus pattern (41 bp): TTTTGTGTAAGACCTTGTCTGGGACATGGCATCGTATTTGA Found at i:86350201 original size:43 final size:43 Alignment explanation

Indices: 86350045--86350202 Score: 137 Period size: 43 Copynumber: 3.7 Consensus size: 43 86350035 ATGTGTTTTT * * 86350045 GTGTAAGACCTCGTCTGGGACGTTGACATCGACT-TATGATTTAC 1 GTGTAAGACCTCGTCTGGGACGTTGGCATCGA-TATTTGA-TTAC * * * * ** 86350089 GTGTAATACCAT-GTCTGGGACATCGGTATCG-TATTTGATTTT 1 GTGTAAGACC-TCGTCTGGGACGTTGGCATCGATATTTGATTAC * * 86350131 GTGTAAGACCTTGTCTGGGCCAG-TGGCATCGATATTTGATTAC 1 GTGTAAGACCTCGTCTGGGAC-GTTGGCATCGATATTTGATTAC * 86350174 ATGTAAGA-CTACGTCTGGGACGTTGGCAT 1 GTGTAAGACCT-CGTCTGGGACGTTGGCAT 86350203 TATATGAGCT Statistics Matches: 89, Mismatches: 18, Indels: 15 0.73 0.15 0.12 Matches are distributed among these distances: 41 1 0.01 42 29 0.33 43 34 0.38 44 24 0.27 45 1 0.01 ACGTcount: A:0.22, C:0.18, G:0.27, T:0.34 Consensus pattern (43 bp): GTGTAAGACCTCGTCTGGGACGTTGGCATCGATATTTGATTAC Found at i:86361309 original size:14 final size:14 Alignment explanation

Indices: 86361290--86361317 Score: 56 Period size: 14 Copynumber: 2.0 Consensus size: 14 86361280 GTATACATAG 86361290 TTTTTATTTTTTTA 1 TTTTTATTTTTTTA 86361304 TTTTTATTTTTTTA 1 TTTTTATTTTTTTA 86361318 AGAACAAGTT Statistics Matches: 14, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 14 14 1.00 ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86 Consensus pattern (14 bp): TTTTTATTTTTTTA Found at i:86362360 original size:13 final size:13 Alignment explanation

Indices: 86362344--86362383 Score: 53 Period size: 13 Copynumber: 3.1 Consensus size: 13 86362334 GAAATAACTG * 86362344 AAATTAATAATAA 1 AAATTAAAAATAA * 86362357 AAATAAAAAATAA 1 AAATTAAAAATAA * 86362370 AAAATAAAAATAA 1 AAATTAAAAATAA 86362383 A 1 A 86362384 CTTTCTAAAA Statistics Matches: 23, Mismatches: 4, Indels: 0 0.85 0.15 0.00 Matches are distributed among these distances: 13 23 1.00 ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20 Consensus pattern (13 bp): AAATTAAAAATAA Found at i:86362367 original size:7 final size:7 Alignment explanation

Indices: 86362355--86362383 Score: 51 Period size: 7 Copynumber: 4.3 Consensus size: 7 86362345 AATTAATAAT 86362355 AAAAATA 1 AAAAATA 86362362 AAAAATA 1 AAAAATA 86362369 AAAAAT- 1 AAAAATA 86362375 AAAAATA 1 AAAAATA 86362382 AA 1 AA 86362384 CTTTCTAAAA Statistics Matches: 21, Mismatches: 0, Indels: 2 0.91 0.00 0.09 Matches are distributed among these distances: 6 6 0.29 7 15 0.71 ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14 Consensus pattern (7 bp): AAAAATA Found at i:86371477 original size:63 final size:65 Alignment explanation

Indices: 86371359--86371492 Score: 193 Period size: 64 Copynumber: 2.1 Consensus size: 65 86371349 ATAAAAATGG * * * 86371359 TGAAAATGGATAAATGAGAAATCATTTGAAAATTATTTTGGTTTCTCCAAAATGAAAAT-GAAAA 1 TGAAAATGGATAAATGAGAAATCATTTGAAAATGAATGTGGTTTCTCCAAAATGAAAATGGAAAA * * 86371423 TGAAAATGGATAAAT-AG-AATTATTTGGAAATGAATGTGGTTTTCTCCAAAATGAAAATGGAAA 1 TGAAAATGGATAAATGAGAAATCATTTGAAAATGAATGTGG-TTTCTCCAAAATGAAAATGGAAA 86371486 A 65 A 86371487 TGAAAA 1 TGAAAA 86371493 ATGAAAATGA Statistics Matches: 63, Mismatches: 5, Indels: 4 0.88 0.07 0.06 Matches are distributed among these distances: 62 17 0.27 63 20 0.32 64 26 0.41 ACGTcount: A:0.47, C:0.05, G:0.18, T:0.30 Consensus pattern (65 bp): TGAAAATGGATAAATGAGAAATCATTTGAAAATGAATGTGGTTTCTCCAAAATGAAAATGGAAAA Found at i:86372465 original size:134 final size:134 Alignment explanation

Indices: 86372220--86372489 Score: 522 Period size: 134 Copynumber: 2.0 Consensus size: 134 86372210 CACACAGTTA * * 86372220 TACAGATTTACATTCGATTACAATTATTTAATTATAAATTTCTCTAAGAAATACATAAGTGTGAA 1 TACAAATTTACATTCGATTACAATTATTTAATTATAAATTTCCCTAAGAAATACATAAGTGTGAA 86372285 TAAGACGAGAATTCAATTGGTATACACAAAGAATTTATTTACAACTATGATTGAATAGATGTCCT 66 TAAGACGAGAATTCAATTGGTATACACAAAGAATTTATTTACAACTATGATTGAATAGATGTCCT 86372350 GGTC 131 GGTC 86372354 TACAAATTTACATTCGATTACAATTATTTAATTATAAATTTCCCTAAGAAATACATAAGTGTGAA 1 TACAAATTTACATTCGATTACAATTATTTAATTATAAATTTCCCTAAGAAATACATAAGTGTGAA 86372419 TAAGACGAGAATTCAATTGGTATACACAAAGAATTTATTTACAACTATGATTGAATAGATGTCCT 66 TAAGACGAGAATTCAATTGGTATACACAAAGAATTTATTTACAACTATGATTGAATAGATGTCCT 86372484 GGTC 131 GGTC 86372488 TA 1 TA 86372490 TTATAATTAT Statistics Matches: 134, Mismatches: 2, Indels: 0 0.99 0.01 0.00 Matches are distributed among these distances: 134 134 1.00 ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35 Consensus pattern (134 bp): TACAAATTTACATTCGATTACAATTATTTAATTATAAATTTCCCTAAGAAATACATAAGTGTGAA TAAGACGAGAATTCAATTGGTATACACAAAGAATTTATTTACAACTATGATTGAATAGATGTCCT GGTC Found at i:86374506 original size:48 final size:48 Alignment explanation

Indices: 86374432--86374699 Score: 288 Period size: 48 Copynumber: 5.6 Consensus size: 48 86374422 TAAAGTACCA * * * * * 86374432 ATGCCATGTCCCCGACATGCTCTTACATGAATC-CACATATCATCCCCG 1 ATGCCATGTCCCAGACATGGTCTTACA-CAAGCACACATATCATCGCCG * * * 86374480 ATGCCATGTCCCAGACATGGTTTTACACAGGCACACATATCATCGCTG 1 ATGCCATGTCCCAGACATGGTCTTACACAAGCACACATATCATCGCCG * * 86374528 ATACCATGTCCCAGACATGGTCTTACACAAGCACACATATCATCACCG 1 ATGCCATGTCCCAGACATGGTCTTACACAAGCACACATATCATCGCCG * * * * * 86374576 ACGCCATGTCCCAGACATGGTCTTACACAGGCACATATATCATTGCCA 1 ATGCCATGTCCCAGACATGGTCTTACACAAGCACACATATCATCGCCG * * * * * * * 86374624 ATGCTATGTCCCAGACATGGTCTTACATAGGCACACGTCTAGAT-GTCG 1 ATGCCATGTCCCAGACATGGTCTTACACAAGCACACATAT-CATCGCCG * * 86374672 ATGCCATGTCCTAGACATGGACTTACAC 1 ATGCCATGTCCCAGACATGGTCTTACAC 86374700 GGGATCTCAT Statistics Matches: 185, Mismatches: 33, Indels: 4 0.83 0.15 0.02 Matches are distributed among these distances: 47 2 0.01 48 181 0.98 49 2 0.01 ACGTcount: A:0.28, C:0.31, G:0.17, T:0.24 Consensus pattern (48 bp): ATGCCATGTCCCAGACATGGTCTTACACAAGCACACATATCATCGCCG Found at i:86376692 original size:27 final size:27 Alignment explanation

Indices: 86376662--86376751 Score: 117 Period size: 27 Copynumber: 3.3 Consensus size: 27 86376652 TTCAAAGAAT * 86376662 GCCACAAAGGCTTCCTTATCATAGATC 1 GCCACAAAGGCTTCCTTTTCATAGATC * 86376689 GCCACAAAGGCTTCCTTTTCATAGCTC 1 GCCACAAAGGCTTCCTTTTCATAGATC * * * 86376716 GCCAGAAAGGATTCATTTTCATAGATC 1 GCCACAAAGGCTTCCTTTTCATAGATC ** 86376743 AACACAAAG 1 GCCACAAAG 86376752 ATCACCACAA Statistics Matches: 54, Mismatches: 9, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 27 54 1.00 ACGTcount: A:0.32, C:0.27, G:0.16, T:0.26 Consensus pattern (27 bp): GCCACAAAGGCTTCCTTTTCATAGATC Found at i:86376791 original size:66 final size:67 Alignment explanation

Indices: 86376684--86376818 Score: 182 Period size: 66 Copynumber: 2.0 Consensus size: 67 86376674 TCCTTATCAT * * * * 86376684 AGATCGCCACAAAGGCTTCCTTTTCATAGCTCGCCAGAAAGG-ATTCATTTTCATAGATCAACAC 1 AGATCACCACAAAAGCTCCCTTTTCATAGATCGCCAGAAAGGCATTCATTTTCATAGATCAACAC 86376748 AA 66 AA * * * ** 86376750 AGATCACCACAAAAGCTCCCTTTTCATAGATCGCCATAAAGGCTTTTATTTTCATAGATCGTCAC 1 AGATCACCACAAAAGCTCCCTTTTCATAGATCGCCAGAAAGGCATTCATTTTCATAGATCAACAC 86376815 AA 66 AA 86376817 AG 1 AG 86376819 GCTTTCTTTT Statistics Matches: 59, Mismatches: 9, Indels: 1 0.86 0.13 0.01 Matches are distributed among these distances: 66 37 0.63 67 22 0.37 ACGTcount: A:0.33, C:0.25, G:0.14, T:0.27 Consensus pattern (67 bp): AGATCACCACAAAAGCTCCCTTTTCATAGATCGCCAGAAAGGCATTCATTTTCATAGATCAACAC AA Found at i:86376836 original size:27 final size:28 Alignment explanation

Indices: 86376769--86376845 Score: 111 Period size: 27 Copynumber: 2.8 Consensus size: 28 86376759 CAAAAGCTCC * 86376769 CTTTTCATAGATCGCCATAAAGGCTTTT 1 CTTTTCATAGATCGTCATAAAGGCTTTT * * 86376797 ATTTTCATAGATCGTCACAAAGGC-TTT 1 CTTTTCATAGATCGTCATAAAGGCTTTT * 86376824 CTTTTCAAAGATCGTCATAAAG 1 CTTTTCATAGATCGTCATAAAG 86376846 ACTTCCATTT Statistics Matches: 43, Mismatches: 6, Indels: 1 0.86 0.12 0.02 Matches are distributed among these distances: 27 22 0.51 28 21 0.49 ACGTcount: A:0.30, C:0.19, G:0.14, T:0.36 Consensus pattern (28 bp): CTTTTCATAGATCGTCATAAAGGCTTTT Found at i:86376846 original size:94 final size:93 Alignment explanation

Indices: 86376663--86376836 Score: 224 Period size: 93 Copynumber: 1.9 Consensus size: 93 86376653 TCAAAGAATG * * * * * 86376663 CCACAAAGGCTTCCTTATCATAGATCGCCACAAAGGCTTCCTTTTCATAGCTCGCCAGAAAGGAT 1 CCACAAAAGCTCCCTTATCATAGATCGCCACAAAGGCTTCATTTTCATAGATCGCCACAAAGGAT * 86376728 TCATTTTCATAGATCAACACAAAGATCA 66 TCATTTTCAAAGATCAACACAAAGATCA * * * * 86376756 CCACAAAAGCTCCCTTTTCATAGATCGCCATAAAGGCTTTTATTTTCATAGATCGTCACAAAGGC 1 CCACAAAAGCTCCCTTATCATAGATCGCCACAAAGGC-TTCATTTTCATAGATCGCCACAAAGG- * 86376821 TTTC-TTTTCAAAGATC 64 ATTCATTTTCAAAGATC 86376837 GTCATAAAGA Statistics Matches: 68, Mismatches: 11, Indels: 3 0.83 0.13 0.04 Matches are distributed among these distances: 93 33 0.49 94 32 0.47 95 3 0.04 ACGTcount: A:0.32, C:0.26, G:0.13, T:0.29 Consensus pattern (93 bp): CCACAAAAGCTCCCTTATCATAGATCGCCACAAAGGCTTCATTTTCATAGATCGCCACAAAGGAT TCATTTTCAAAGATCAACACAAAGATCA Found at i:86388545 original size:120 final size:120 Alignment explanation

Indices: 86388421--86388645 Score: 310 Period size: 122 Copynumber: 1.9 Consensus size: 120 86388411 CCAAAATAAC ** * * 86388421 CATGAGAATGTGAATAATAATGTAATAGGTATGAGGTTTTCCTAAT-CTCGATTTAACACAGAAT 1 CATGAGAATAAGAATAATAATGCAATAGGTATGAGGTTTCCCTAATACTCGATTTAACA-AGAA- 86388485 AT-ATGATAACTAACCTAAGAATGCAAATTAAATGATAGACAGTGGCATGGTAATAG 64 ATCATGATAACTAACCTAAGAATGCAAATTAAATGATAGACAGTGGCATGGTAATAG * * * * * 86388541 CATGAGAATAAGCATAGTAATGCCATGGGTTTGAGGTTTCCCTAATAACTCGATTTAACAAGAAA 1 CATGAGAATAAGAATAATAATGCAATAGGTATGAGGTTTCCCTAAT-ACTCGATTTAACAAGAAA * 86388606 TGCATGATAACTAACCTAAGAATTCAAATTAAATGATAGA 65 T-CATGATAACTAACCTAAGAATGCAAATTAAATGATAGA 86388646 ATAATGAGAA Statistics Matches: 91, Mismatches: 10, Indels: 6 0.85 0.09 0.06 Matches are distributed among these distances: 120 39 0.43 121 4 0.04 122 48 0.53 ACGTcount: A:0.41, C:0.12, G:0.18, T:0.28 Consensus pattern (120 bp): CATGAGAATAAGAATAATAATGCAATAGGTATGAGGTTTCCCTAATACTCGATTTAACAAGAAAT CATGATAACTAACCTAAGAATGCAAATTAAATGATAGACAGTGGCATGGTAATAG Found at i:86394519 original size:21 final size:20 Alignment explanation

Indices: 86394482--86394520 Score: 51 Period size: 21 Copynumber: 1.9 Consensus size: 20 86394472 GTTCGCATCT * 86394482 GAATATACATCTGTTTGTCA 1 GAATATACATCTATTTGTCA * 86394502 GAATATTCTATCTATTTGT 1 GAATATAC-ATCTATTTGT 86394521 GTGACCTTTT Statistics Matches: 16, Mismatches: 2, Indels: 1 0.84 0.11 0.05 Matches are distributed among these distances: 20 7 0.44 21 9 0.56 ACGTcount: A:0.28, C:0.13, G:0.13, T:0.46 Consensus pattern (20 bp): GAATATACATCTATTTGTCA Found at i:86396183 original size:6 final size:6 Alignment explanation

Indices: 86396172--86396228 Score: 69 Period size: 6 Copynumber: 9.5 Consensus size: 6 86396162 TTCTGTTATT * * * * 86396172 TGAATC TAAATC TGAATC TGAATC TAAATC TGAATC TGAATC TAAAAC 1 TGAATC TGAATC TGAATC TGAATC TGAATC TGAATC TGAATC TGAATC * 86396220 TGTATC TGA 1 TGAATC TGA 86396229 TTGTGTATAT Statistics Matches: 41, Mismatches: 10, Indels: 0 0.80 0.20 0.00 Matches are distributed among these distances: 6 41 1.00 ACGTcount: A:0.39, C:0.16, G:0.12, T:0.33 Consensus pattern (6 bp): TGAATC Found at i:86396195 original size:18 final size:18 Alignment explanation

Indices: 86396172--86396228 Score: 96 Period size: 18 Copynumber: 3.2 Consensus size: 18 86396162 TTCTGTTATT 86396172 TGAATCTAAATCTGAATC 1 TGAATCTAAATCTGAATC 86396190 TGAATCTAAATCTGAATC 1 TGAATCTAAATCTGAATC * * 86396208 TGAATCTAAAACTGTATC 1 TGAATCTAAATCTGAATC 86396226 TGA 1 TGA 86396229 TTGTGTATAT Statistics Matches: 37, Mismatches: 2, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 18 37 1.00 ACGTcount: A:0.39, C:0.16, G:0.12, T:0.33 Consensus pattern (18 bp): TGAATCTAAATCTGAATC Found at i:86408148 original size:46 final size:46 Alignment explanation

Indices: 86408081--86408378 Score: 465 Period size: 46 Copynumber: 6.5 Consensus size: 46 86408071 TGGCAACCTG * 86408081 TGTGTAAGACAATGGTTGAAAGATACCATGGCAACCTGATATGAAA 1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAA 86408127 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAA 1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAA * 86408173 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACTTGATATGAAA 1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAA * 86408219 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAGA 1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAA * * 86408265 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGACATGAAA 1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAA * ** * * 86408311 AGAATAAGACCATGGTTGAAAGATACCAT-GCAACATGACA-GAAAA 1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATG-AAA * * 86408356 TGAGTAAGACCATAGTTGAAAGA 1 TGTGTAAGACCATGGTTGAAAGA 86408379 CGCTATGGCA Statistics Matches: 237, Mismatches: 14, Indels: 3 0.93 0.06 0.01 Matches are distributed among these distances: 44 1 0.00 45 33 0.14 46 203 0.86 ACGTcount: A:0.39, C:0.14, G:0.24, T:0.22 Consensus pattern (46 bp): TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAA Found at i:86408272 original size:138 final size:136 Alignment explanation

Indices: 86408032--86408378 Score: 485 Period size: 138 Copynumber: 2.6 Consensus size: 136 86408022 AGTGTGCTCT * * * 86408032 CTGATATGAAATGTGTAAGACTATGATTGAAAGATACCATGGCAAC---CTG---TGTGTAAGAC 1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACTGAATGAAATGTGTAAGAC * 86408091 AATGGTTGAAAGATACCATGGCAACCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCAT 66 CATGGTTGAAAGATACCATGGCAACCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCAT 86408156 GGCAAC 131 GGCAAC 86408162 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACTTGATATGAAATGTGTAAG 1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC-TGA-ATGAAATGTGTAAG * 86408227 ACCATGGTTGAAAGATACCATGGCAACCTGATATGAGATGTGTAAGACCATGGTTGAAAGATACC 64 ACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACC 86408292 ATGGCAAC 129 ATGGCAAC * * * ** * 86408300 GTGACATGAAAAGAATAAGACCATGGTTGAAAGATACCAT-GCAACATGACA-GAAAATGAGTAA 1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC-TGA-ATG-AAATGTGTAA * 86408363 GACCATAGTTGAAAGA 63 GACCATGGTTGAAAGA 86408379 CGCTATGGCA Statistics Matches: 194, Mismatches: 14, Indels: 11 0.89 0.06 0.05 Matches are distributed among these distances: 130 44 0.23 135 2 0.01 136 1 0.01 137 33 0.17 138 114 0.59 ACGTcount: A:0.39, C:0.14, G:0.24, T:0.23 Consensus pattern (136 bp): CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACTGAATGAAATGTGTAAGAC CATGGTTGAAAGATACCATGGCAACCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCAT GGCAAC Found at i:86408694 original size:23 final size:25 Alignment explanation

Indices: 86408649--86408695 Score: 62 Period size: 25 Copynumber: 2.0 Consensus size: 25 86408639 GATAAATATA * 86408649 CATAAAATATATGGAAATGATGAAG 1 CATAAAATATATGGAAATAATGAAG * 86408674 CATAAAATAT-T-GATATAATGAA 1 CATAAAATATATGGAAATAATGAA 86408696 ATGAATGATA Statistics Matches: 20, Mismatches: 2, Indels: 2 0.83 0.08 0.08 Matches are distributed among these distances: 23 9 0.45 24 1 0.05 25 10 0.50 ACGTcount: A:0.53, C:0.04, G:0.15, T:0.28 Consensus pattern (25 bp): CATAAAATATATGGAAATAATGAAG Found at i:86424638 original size:12 final size:12 Alignment explanation

Indices: 86424621--86424645 Score: 50 Period size: 12 Copynumber: 2.1 Consensus size: 12 86424611 ACCGTAGACA 86424621 GCACAAATAGGG 1 GCACAAATAGGG 86424633 GCACAAATAGGG 1 GCACAAATAGGG 86424645 G 1 G 86424646 TGGCATAAGG Statistics Matches: 13, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 12 13 1.00 ACGTcount: A:0.40, C:0.16, G:0.36, T:0.08 Consensus pattern (12 bp): GCACAAATAGGG Found at i:86429763 original size:25 final size:26 Alignment explanation

Indices: 86429735--86429789 Score: 67 Period size: 25 Copynumber: 2.2 Consensus size: 26 86429725 TGAAACAACA ** * 86429735 AAAAAATCTAATTTAAAAA-GAAAAG 1 AAAAAATCTAACCTAAAAACAAAAAG * 86429760 AAAATATCTAACCTAAAAACAAAAAG 1 AAAAAATCTAACCTAAAAACAAAAAG 86429786 AAAA 1 AAAA 86429790 CAAACCTTAA Statistics Matches: 25, Mismatches: 4, Indels: 1 0.83 0.13 0.03 Matches are distributed among these distances: 25 16 0.64 26 9 0.36 ACGTcount: A:0.69, C:0.09, G:0.05, T:0.16 Consensus pattern (26 bp): AAAAAATCTAACCTAAAAACAAAAAG Found at i:86435094 original size:24 final size:25 Alignment explanation

Indices: 86435062--86435118 Score: 71 Period size: 24 Copynumber: 2.3 Consensus size: 25 86435052 GTATCATTAA * * 86435062 ATATAATTAAAATTAAACGATTA-TT 1 ATAT-ATTAAAAATAAAAGATTATTT * 86435087 ATATATTAAAAATAAAATATTATTT 1 ATATATTAAAAATAAAAGATTATTT 86435112 ATATATT 1 ATATATT 86435119 TTTTGAGGAA Statistics Matches: 28, Mismatches: 3, Indels: 2 0.85 0.09 0.06 Matches are distributed among these distances: 24 15 0.54 25 13 0.46 ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44 Consensus pattern (25 bp): ATATATTAAAAATAAAAGATTATTT Found at i:86440307 original size:68 final size:66 Alignment explanation

Indices: 86440195--86440459 Score: 219 Period size: 68 Copynumber: 3.9 Consensus size: 66 86440185 TACATCTCGG * * ** 86440195 CTATGTCAACAAATAGAGTCCACTAGGACAATAAACGTGAGGTTATATTGTGTAAGATTATAGCA 1 CTATGTCAACAAATA-AGTCCACTAGGACGATAAACATG-GGTTATATTGTGTAAGACCATAGCA * * 86440260 TGC 64 CGA * * 86440263 CTATGTCAACAAATATAGTCCACCAGGACGATAAACATAGGGTTATATTATGTAAGACCATAGCA 1 CTATGTCAACAAATA-AGTCCACTAGGACGATAAACAT-GGGTTATATTGTGTAAGACCATAGCA 86440328 CGA 64 CGA ** * ** ** * 86440331 CTATGGAAACAAATGAAGTTCGTTATAACGATAAACATGGGTTATATTGTGTAAGACCATAGCTC 1 CTATGTCAACAAAT-AAGTCCACTAGGACGATAAACATGGGTTATATTGTGTAAGACCATAGCAC 86440396 -A 65 GA * * * * * * * * * 86440397 GCTATGACAACATATGGAGTTCACCAGAAC-ATTAAACATGGGGTATGTTGTGTAAGACAATAG 1 -CTATGTCAACAAAT-AAGTCCACTAGGACGA-TAAACATGGGTTATATTGTGTAAGACCATAG 86440460 TTAGGTTAAG Statistics Matches: 163, Mismatches: 30, Indels: 9 0.81 0.15 0.04 Matches are distributed among these distances: 66 2 0.01 67 74 0.45 68 85 0.52 69 2 0.01 ACGTcount: A:0.38, C:0.15, G:0.20, T:0.26 Consensus pattern (66 bp): CTATGTCAACAAATAAGTCCACTAGGACGATAAACATGGGTTATATTGTGTAAGACCATAGCACG A Found at i:86440402 original size:67 final size:67 Alignment explanation

Indices: 86440225--86440459 Score: 217 Period size: 67 Copynumber: 3.5 Consensus size: 67 86440215 CACTAGGACA * ** * * * * 86440225 ATAAACGTGAGGTTATATTGTGTAAGATTATAGCATGCCTATGTCAACAAAT-ATAGTCCACCAG 1 ATAAACATG-GGTTATATTGTGTAAGACCATAGCACGACTATGACAACAAATGA-AGTTCACCAG * 86440289 GACG 64 AACG * *** * 86440293 ATAAACATAGGGTTATATTATGTAAGACCATAGCACGACTATGGA-AACAAATGAAGTTCGTTAT 1 ATAAACAT-GGGTTATATTGTGTAAGACCATAGCACGACTAT-GACAACAAATGAAGTTCACCAG 86440357 AACG 64 AACG * * * 86440361 ATAAACATGGGTTATATTGTGTAAGACCATAGCTC-AGCTATGACAACATATGGAGTTCACCAGA 1 ATAAACATGGGTTATATTGTGTAAGACCATAGCACGA-CTATGACAACAAATGAAGTTCACCAGA 86440425 AC- 65 ACG * * * 86440427 ATTAAACATGGGGTATGTTGTGTAAGACAATAG 1 A-TAAACATGGGTTATATTGTGTAAGACCATAG 86440460 TTAGGTTAAG Statistics Matches: 137, Mismatches: 24, Indels: 13 0.79 0.14 0.07 Matches are distributed among these distances: 66 4 0.03 67 73 0.53 68 57 0.42 69 3 0.02 ACGTcount: A:0.37, C:0.14, G:0.21, T:0.27 Consensus pattern (67 bp): ATAAACATGGGTTATATTGTGTAAGACCATAGCACGACTATGACAACAAATGAAGTTCACCAGAA CG Found at i:86441527 original size:41 final size:41 Alignment explanation

Indices: 86441447--86441567 Score: 118 Period size: 42 Copynumber: 2.9 Consensus size: 41 86441437 AGTTAACTCG * * * * * 86441447 TATGAGTTTTAGTTTAACCTATTGGGTTTCTGTTCAGCT-C 1 TATGAGCTTCAGTTTAACCTTTTGGGTTTCCGTTTAGCTCC * * 86441487 TCTGAGCTTCAGTTTAATCCTTTTGGGTTTCCATTTAGCTCC 1 TATGAGCTTCAGTTTAA-CCTTTTGGGTTTCCGTTTAGCTCC * * ** 86441529 TATGAGCTTCTGTTCAACCCTTACGGGTTTCCGTTTAGC 1 TATGAGCTTCAGTTTAA-CCTTTTGGGTTTCCGTTTAGC 86441568 ACTTATGTGC Statistics Matches: 65, Mismatches: 14, Indels: 2 0.80 0.17 0.02 Matches are distributed among these distances: 40 14 0.22 41 18 0.28 42 33 0.51 ACGTcount: A:0.16, C:0.21, G:0.19, T:0.44 Consensus pattern (41 bp): TATGAGCTTCAGTTTAACCTTTTGGGTTTCCGTTTAGCTCC Found at i:86454141 original size:16 final size:15 Alignment explanation

Indices: 86454120--86454149 Score: 51 Period size: 15 Copynumber: 1.9 Consensus size: 15 86454110 TTAAGAATTT 86454120 AAATAAAATAATTTTA 1 AAAT-AAATAATTTTA 86454136 AAATAAATAATTTT 1 AAATAAATAATTTT 86454150 GACACTCCCA Statistics Matches: 14, Mismatches: 0, Indels: 1 0.93 0.00 0.07 Matches are distributed among these distances: 15 10 0.71 16 4 0.29 ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40 Consensus pattern (15 bp): AAATAAATAATTTTA Found at i:86456137 original size:46 final size:46 Alignment explanation

Indices: 86456017--86456222 Score: 154 Period size: 46 Copynumber: 4.5 Consensus size: 46 86456007 TATATCTGTG * * 86456017 CCAGACATGGTCTTACACT-G-ACACATCTCGTA-GCCGATGCATGTC 1 CCAGACAT-GTCTTACACTAGCACTCGTCTCG-AGGCCGATGCATGTC * * * 86456062 TCAGACATGTCTTACGCTAGCTTA-T-GTCTCGAGGCCGATACATGTC 1 CCAGACATGTCTTACACTAGC--ACTCGTCTCGAGGCCGATGCATGTC * * ** * 86456108 CCAAACATGTCTTACACTAGCACTCGTCTCAATACTGATGCCATGTC 1 CCAGACATGTCTTACACTAGCACTCGTCTCGAGGCCGATG-CATGTC * * * * * * 86456155 CCAGACATGGTCTTACATTGGCTCTCATAAT-GTGGCCGATGCATGTC 1 CCAGACAT-GTCTTACACTAGCACTCGT-CTCGAGGCCGATGCATGTC * 86456202 CTAGACATGTCTTACACTAGC 1 CCAGACATGTCTTACACTAGC 86456223 TCACACGAGT Statistics Matches: 124, Mismatches: 27, Indels: 19 0.73 0.16 0.11 Matches are distributed among these distances: 44 10 0.08 45 10 0.08 46 56 0.45 47 26 0.21 48 21 0.17 49 1 0.01 ACGTcount: A:0.24, C:0.29, G:0.19, T:0.28 Consensus pattern (46 bp): CCAGACATGTCTTACACTAGCACTCGTCTCGAGGCCGATGCATGTC Found at i:86463688 original size:46 final size:45 Alignment explanation

Indices: 86463638--86463810 Score: 159 Period size: 46 Copynumber: 3.7 Consensus size: 45 86463628 ATGTCGTAGT 86463638 CGATGCATGTCCCAGACATGTCTTACACTAGCTTACGTCTCGAGGC 1 CGATGCATGTCCCAGACATGTCTTACACTAGCTT-CGTCTCGAGGC * * * * ** 86463684 CGATGCATGTACCAAACATGTCTTACACTAGCACTCGTCTCAATAC 1 CGATGCATGTCCCAGACATGTCTTACACTAGC-TTCGTCTCGAGGC * * * * * * * 86463730 CGATGCCATGTCCTAGACATGGTTTTACACTGGCTCTCATAAT-GTGGT 1 CGATG-CATGTCCCAGACAT-GTCTTACACTAGCT-TCGT-CTCGAGGC * 86463778 CGATGCATGTCCTAGACATGTCTTACACTAGCT 1 CGATGCATGTCCCAGACATGTCTTACACTAGCT 86463811 CACACGAGTG Statistics Matches: 101, Mismatches: 21, Indels: 10 0.77 0.16 0.08 Matches are distributed among these distances: 46 55 0.54 47 26 0.26 48 19 0.19 49 1 0.01 ACGTcount: A:0.24, C:0.28, G:0.19, T:0.29 Consensus pattern (45 bp): CGATGCATGTCCCAGACATGTCTTACACTAGCTTCGTCTCGAGGC Found at i:86465591 original size:22 final size:22 Alignment explanation

Indices: 86465552--86465593 Score: 57 Period size: 22 Copynumber: 1.9 Consensus size: 22 86465542 ATAACATAGA *** 86465552 TTTAATAAATGCTGAAAAATAT 1 TTTAATAAATGAAAAAAAATAT 86465574 TTTAATAAATGAAAAAAAAT 1 TTTAATAAATGAAAAAAAAT 86465594 TAAACTATTA Statistics Matches: 17, Mismatches: 3, Indels: 0 0.85 0.15 0.00 Matches are distributed among these distances: 22 17 1.00 ACGTcount: A:0.57, C:0.02, G:0.07, T:0.33 Consensus pattern (22 bp): TTTAATAAATGAAAAAAAATAT Found at i:86470017 original size:24 final size:24 Alignment explanation

Indices: 86469986--86470037 Score: 97 Period size: 24 Copynumber: 2.2 Consensus size: 24 86469976 ATTCTATATT 86469986 TTCA-TTTTTTTTAGTTTTTGATA 1 TTCATTTTTTTTTAGTTTTTGATA 86470009 TTCATTTTTTTTTAGTTTTTGATA 1 TTCATTTTTTTTTAGTTTTTGATA 86470033 TTCAT 1 TTCAT 86470038 GAAGAAATTT Statistics Matches: 28, Mismatches: 0, Indels: 1 0.97 0.00 0.03 Matches are distributed among these distances: 23 4 0.14 24 24 0.86 ACGTcount: A:0.17, C:0.06, G:0.08, T:0.69 Consensus pattern (24 bp): TTCATTTTTTTTTAGTTTTTGATA Found at i:86486054 original size:37 final size:37 Alignment explanation

Indices: 86486001--86486089 Score: 151 Period size: 37 Copynumber: 2.4 Consensus size: 37 86485991 TCATAGTTAG * * 86486001 CGGGTCTCACCAGGACAAAATCTCCACACGTAGTCAT 1 CGGGTCTTACCCGGACAAAATCTCCACACGTAGTCAT * 86486038 CGGGTCTTACCCGGACATAATCTCCACACGTAGTCAT 1 CGGGTCTTACCCGGACAAAATCTCCACACGTAGTCAT 86486075 CGGGTCTTACCCGGA 1 CGGGTCTTACCCGGA 86486090 ATATATTTCC Statistics Matches: 49, Mismatches: 3, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 37 49 1.00 ACGTcount: A:0.25, C:0.33, G:0.21, T:0.21 Consensus pattern (37 bp): CGGGTCTTACCCGGACAAAATCTCCACACGTAGTCAT Found at i:86486567 original size:48 final size:48 Alignment explanation

Indices: 86486230--86486558 Score: 561 Period size: 48 Copynumber: 6.9 Consensus size: 48 86486220 ATATACACAC * * * 86486230 ATCTCCTACATATTTCACATTAGCCATTCGGCTTTACCAAATATACAT 1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT 86486278 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT 1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT 86486326 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT 1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT * 86486374 ATCTCATATATATTTCACACTAGCCATTCGGCTTTACCACATATACAT 1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT 86486422 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT 1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT * ** * 86486470 ATCTCATATATATTTCAC-CTTAGCCATAGGGCTTTACCACATATATAT 1 ATCTCATACATATTTCACAC-TAGCCATTCGGCTTTACCACATATACAT * 86486518 ATCTCATACATATTTCACACTAGCCATTCGGCTTTAACACA 1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACA 86486559 CACATATATA Statistics Matches: 266, Mismatches: 13, Indels: 4 0.94 0.05 0.01 Matches are distributed among these distances: 47 1 0.00 48 264 0.99 49 1 0.00 ACGTcount: A:0.31, C:0.28, G:0.07, T:0.34 Consensus pattern (48 bp): ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT Found at i:86490656 original size:5 final size:5 Alignment explanation

Indices: 86490640--86490671 Score: 57 Period size: 5 Copynumber: 6.6 Consensus size: 5 86490630 CAAATAATTC 86490640 AGAAA A-AAA AGAAA AGAAA AGAAA AGAAA AGA 1 AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA AGA 86490672 GATTATTTAT Statistics Matches: 26, Mismatches: 0, Indels: 2 0.93 0.00 0.07 Matches are distributed among these distances: 4 4 0.15 5 22 0.85 ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00 Consensus pattern (5 bp): AGAAA Found at i:86501250 original size:20 final size:20 Alignment explanation

Indices: 86501227--86501315 Score: 96 Period size: 20 Copynumber: 4.5 Consensus size: 20 86501217 CAATCTAAAT 86501227 TAAAATACTGAAATTCAGGA 1 TAAAATACTGAAATTCAGGA * * 86501247 TAAAAT-C--AAATCCA-AA 1 TAAAATACTGAAATTCAGGA * 86501263 TTAAAATACTGAAATTTAGGA 1 -TAAAATACTGAAATTCAGGA * 86501284 TAAAATCCTGAAATTCAGGA 1 TAAAATACTGAAATTCAGGA 86501304 TAAGAATACTGA 1 TAA-AATACTGA 86501316 TGTGGCATAA Statistics Matches: 55, Mismatches: 8, Indels: 11 0.74 0.11 0.15 Matches are distributed among these distances: 16 1 0.02 17 12 0.22 18 1 0.02 19 1 0.02 20 32 0.58 21 8 0.15 ACGTcount: A:0.51, C:0.11, G:0.12, T:0.26 Consensus pattern (20 bp): TAAAATACTGAAATTCAGGA Found at i:86501264 original size:37 final size:37 Alignment explanation

Indices: 86501211--86501290 Score: 133 Period size: 37 Copynumber: 2.2 Consensus size: 37 86501201 TATCCTGAAA * * 86501211 AAAATCCAATCTAAATTAAAATACTGAAATTCAGGAT 1 AAAATCAAATCCAAATTAAAATACTGAAATTCAGGAT * 86501248 AAAATCAAATCCAAATTAAAATACTGAAATTTAGGAT 1 AAAATCAAATCCAAATTAAAATACTGAAATTCAGGAT 86501285 AAAATC 1 AAAATC 86501291 CTGAAATTCA Statistics Matches: 40, Mismatches: 3, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 37 40 1.00 ACGTcount: A:0.54, C:0.12, G:0.07, T:0.26 Consensus pattern (37 bp): AAAATCAAATCCAAATTAAAATACTGAAATTCAGGAT Found at i:86502445 original size:11 final size:10 Alignment explanation

Indices: 86502427--86502482 Score: 58 Period size: 10 Copynumber: 5.2 Consensus size: 10 86502417 TTGTTGTTTG 86502427 ATTTTAATTT 1 ATTTTAATTT 86502437 ATCTTTAATTTT 1 AT-TTTAA-TTT * 86502449 ATGTTAATTT 1 ATTTTAATTT * 86502459 AATTTAATTT 1 ATTTTAATTT 86502469 AATTCTTAATTT 1 -ATT-TTAATTT 86502481 AT 1 AT 86502483 GCTCTTTTAT Statistics Matches: 38, Mismatches: 4, Indels: 7 0.78 0.08 0.14 Matches are distributed among these distances: 10 13 0.34 11 13 0.34 12 12 0.32 ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62 Consensus pattern (10 bp): ATTTTAATTT Found at i:86502458 original size:22 final size:23 Alignment explanation

Indices: 86502430--86502482 Score: 65 Period size: 22 Copynumber: 2.4 Consensus size: 23 86502420 TTGTTTGATT * * * 86502430 TTAATTTATCTTTAATTTTA-TG 1 TTAATTTATATTTAATTTAATTC 86502452 TTAATTTA-ATTTAATTTAATTC 1 TTAATTTATATTTAATTTAATTC 86502474 TTAATTTAT 1 TTAATTTAT 86502483 GCTCTTTTAT Statistics Matches: 26, Mismatches: 3, Indels: 3 0.81 0.09 0.09 Matches are distributed among these distances: 21 9 0.35 22 17 0.65 ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62 Consensus pattern (23 bp): TTAATTTATATTTAATTTAATTC Found at i:86502462 original size:5 final size:5 Alignment explanation

Indices: 86502429--86502472 Score: 52 Period size: 5 Copynumber: 8.4 Consensus size: 5 86502419 GTTGTTTGAT * * 86502429 TTTAA TTTATC TTTAA TTTTA TGTTAA TTTAA TTTAA TTTAA TT 1 TTTAA TTTA-A TTTAA TTTAA T-TTAA TTTAA TTTAA TTTAA TT 86502473 CTTAATTTAT Statistics Matches: 33, Mismatches: 4, Indels: 4 0.80 0.10 0.10 Matches are distributed among these distances: 5 25 0.76 6 8 0.24 ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64 Consensus pattern (5 bp): TTTAA Found at i:86502465 original size:10 final size:10 Alignment explanation

Indices: 86502429--86502472 Score: 52 Period size: 11 Copynumber: 4.2 Consensus size: 10 86502419 GTTGTTTGAT * 86502429 TTTAATTTATC 1 TTTAATTTA-A * 86502440 TTTAATTTTA 1 TTTAATTTAA 86502450 TGTTAATTTAA 1 T-TTAATTTAA 86502461 TTTAATTTAA 1 TTTAATTTAA 86502471 TT 1 TT 86502473 CTTAATTTAT Statistics Matches: 29, Mismatches: 3, Indels: 3 0.83 0.09 0.09 Matches are distributed among these distances: 10 12 0.41 11 17 0.59 ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64 Consensus pattern (10 bp): TTTAATTTAA Found at i:86507405 original size:39 final size:38 Alignment explanation

Indices: 86507338--86507599 Score: 371 Period size: 39 Copynumber: 6.7 Consensus size: 38 86507328 ACAAAGCATG * * * 86507338 CGGGACTTTAAGCCCGGATATAATACCAGCACAAAGCCTG 1 CGGGAC-TT-AGCCCGGATATAACACCAGCACAATGCCTT 86507378 CGGGACTTTAGCCCGGATATAACACCAGCACGAATGCCTT 1 CGGGAC-TTAGCCCGGATATAACACCAGCAC-AATGCCTT * * * 86507418 CGGGGCTTAGCCCGAATATAACACGAGCACAAATGCCTT 1 CGGGACTTAGCCCGGATATAACACCAGCAC-AATGCCTT 86507457 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT 1 CGGGACTTAGCCCGGATATAACACCAGCAC-AATGCCTT * 86507496 CGGGACTTAGCCCGGATATAACACCAGCATGAATGCCTT 1 CGGGACTTAGCCCGGATATAACACCAGCA-CAATGCCTT * * 86507535 CAGGATTTAGCCCGGATATAACACCAGCACGAATGCCTT 1 CGGGACTTAGCCCGGATATAACACCAGCAC-AATGCCTT 86507574 CGGGACTTAGCCCGGATATAACACCA 1 CGGGACTTAGCCCGGATATAACACCA 86507600 TTATAAAGTC Statistics Matches: 202, Mismatches: 17, Indels: 7 0.89 0.08 0.03 Matches are distributed among these distances: 39 182 0.90 40 20 0.10 ACGTcount: A:0.30, C:0.29, G:0.23, T:0.19 Consensus pattern (38 bp): CGGGACTTAGCCCGGATATAACACCAGCACAATGCCTT Found at i:86507467 original size:78 final size:78 Alignment explanation

Indices: 86507338--86507599 Score: 409 Period size: 78 Copynumber: 3.3 Consensus size: 78 86507328 ACAAAGCATG * * 86507338 CGGGACTTTAAGCCCGGATATAATACCAGCACAAA-GCCTGCGGGACTTTAGCCCGGATATAACA 1 CGGGAC-TT-AGCCCGGATATAACACCAGCACAAATGCCTTCGGGAC-TTAGCCCGGATATAACA 86507402 CCAGCACGAATGCCTT 63 CCAGCACGAATGCCTT * * * 86507418 CGGGGCTTAGCCCGAATATAACACGAGCACAAATGCCTTCGGGACTTAGCCCGGATATAACACCA 1 CGGGACTTAGCCCGGATATAACACCAGCACAAATGCCTTCGGGACTTAGCCCGGATATAACACCA 86507483 GCACGAATGCCTT 66 GCACGAATGCCTT ** * * 86507496 CGGGACTTAGCCCGGATATAACACCAGCATGAATGCCTTCAGGATTTAGCCCGGATATAACACCA 1 CGGGACTTAGCCCGGATATAACACCAGCACAAATGCCTTCGGGACTTAGCCCGGATATAACACCA 86507561 GCACGAATGCCTT 66 GCACGAATGCCTT 86507574 CGGGACTTAGCCCGGATATAACACCA 1 CGGGACTTAGCCCGGATATAACACCA 86507600 TTATAAAGTC Statistics Matches: 169, Mismatches: 12, Indels: 4 0.91 0.06 0.02 Matches are distributed among these distances: 78 152 0.90 79 12 0.07 80 5 0.03 ACGTcount: A:0.30, C:0.29, G:0.23, T:0.19 Consensus pattern (78 bp): CGGGACTTAGCCCGGATATAACACCAGCACAAATGCCTTCGGGACTTAGCCCGGATATAACACCA GCACGAATGCCTT Found at i:86509748 original size:3 final size:3 Alignment explanation

Indices: 86509734--86509768 Score: 52 Period size: 3 Copynumber: 11.7 Consensus size: 3 86509724 CTCTTCCTTG * * 86509734 TCA TCG TCA TCA TCA TCA TCA TCA TTA TCA TCA TC 1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TC 86509769 CTCTCCTTTA Statistics Matches: 28, Mismatches: 4, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 3 28 1.00 ACGTcount: A:0.29, C:0.31, G:0.03, T:0.37 Consensus pattern (3 bp): TCA Found at i:86511841 original size:18 final size:17 Alignment explanation

Indices: 86511802--86511844 Score: 52 Period size: 18 Copynumber: 2.5 Consensus size: 17 86511792 GACAAGGTAC 86511802 ATAAAAAATTTATTGAA 1 ATAAAAAATTTATTGAA 86511819 ATAAAAACATTTACTT-AA 1 ATAAAAA-ATTTA-TTGAA * 86511837 CTAAAAAA 1 ATAAAAAA 86511845 AAATAAAAAT Statistics Matches: 23, Mismatches: 1, Indels: 4 0.82 0.04 0.14 Matches are distributed among these distances: 17 8 0.35 18 13 0.57 19 2 0.09 ACGTcount: A:0.60, C:0.07, G:0.02, T:0.30 Consensus pattern (17 bp): ATAAAAAATTTATTGAA Found at i:86517512 original size:23 final size:22 Alignment explanation

Indices: 86517462--86517517 Score: 67 Period size: 23 Copynumber: 2.5 Consensus size: 22 86517452 TTTAGTTAAA * 86517462 ATTTAAATTTATTATATCCTTT 1 ATTTAAATTTATTATATCCTAT * * 86517484 ATTTTAAGTTTATTTTATCCATAT 1 A-TTTAAATTTATTATATCC-TAT 86517508 ATTTAAATTT 1 ATTTAAATTT 86517518 TGAAATCTTG Statistics Matches: 28, Mismatches: 4, Indels: 3 0.80 0.11 0.09 Matches are distributed among these distances: 22 1 0.04 23 24 0.86 24 3 0.11 ACGTcount: A:0.32, C:0.07, G:0.02, T:0.59 Consensus pattern (22 bp): ATTTAAATTTATTATATCCTAT Found at i:86523228 original size:39 final size:38 Alignment explanation

Indices: 86523144--86523228 Score: 107 Period size: 39 Copynumber: 2.2 Consensus size: 38 86523134 AATTCAATAA * 86523144 TAAAAAACGCCACTAAAAACCAGCATTAGCAGCGCTTC 1 TAAAAAACGCCACTAAAAACCAGCATTAGCAGCGATTC * * * * 86523182 TATAAAAACGCCACTAAAAACGATCATTAGCGGCGATTT 1 TA-AAAAACGCCACTAAAAACCAGCATTAGCAGCGATTC 86523221 TGAAAAAA 1 T-AAAAAA 86523229 TGCCGCTATA Statistics Matches: 40, Mismatches: 5, Indels: 3 0.83 0.10 0.06 Matches are distributed among these distances: 38 2 0.05 39 37 0.93 40 1 0.03 ACGTcount: A:0.45, C:0.22, G:0.14, T:0.19 Consensus pattern (38 bp): TAAAAAACGCCACTAAAAACCAGCATTAGCAGCGATTC Found at i:86523307 original size:41 final size:40 Alignment explanation

Indices: 86523207--86523314 Score: 121 Period size: 40 Copynumber: 2.7 Consensus size: 40 86523197 AAAAACGATC * * * 86523207 ATTAGCGGCGATTT-TGAAAAAATGCCGCTATAGATTGACA 1 ATTAGCGGCGCTTTAAG-AAAAACGCCGCTATAGATTGACA * * * * 86523247 ATTAGTGGCGCTTTTAGAAAAACGCCGCTATAGGTTGACT 1 ATTAGCGGCGCTTTAAGAAAAACGCCGCTATAGATTGACA 86523287 ATTAGCGGCGCTTTAA-AGAAAACGCCGC 1 ATTAGCGGCGCTTTAAGA-AAAACGCCGC 86523315 AAAACAATAA Statistics Matches: 58, Mismatches: 8, Indels: 4 0.83 0.11 0.06 Matches are distributed among these distances: 39 1 0.02 40 56 0.97 41 1 0.02 ACGTcount: A:0.31, C:0.19, G:0.24, T:0.26 Consensus pattern (40 bp): ATTAGCGGCGCTTTAAGAAAAACGCCGCTATAGATTGACA Found at i:86523924 original size:21 final size:19 Alignment explanation

Indices: 86523888--86523967 Score: 70 Period size: 21 Copynumber: 3.8 Consensus size: 19 86523878 TAGTTGGAGT * 86523888 TTAAGATTTAGCGGTTATGGG 1 TTAAGATTAAG-GGTTA-GGG 86523909 TTAAGAATTAAGGGTTAGGGG 1 TTAAG-ATTAAGGGTTA-GGG * 86523930 ATAATGATTAAGGGTTAGTGG 1 TTAA-GATTAAGGGTTAG-GG * 86523951 TTAAGGGTTAAGGGTTA 1 TTAA-GATTAAGGGTTA 86523968 AAAGTTTATG Statistics Matches: 50, Mismatches: 6, Indels: 6 0.81 0.10 0.10 Matches are distributed among these distances: 20 1 0.02 21 43 0.86 22 6 0.12 ACGTcount: A:0.30, C:0.01, G:0.35, T:0.34 Consensus pattern (19 bp): TTAAGATTAAGGGTTAGGG Found at i:86523959 original size:7 final size:7 Alignment explanation

Indices: 86523900--86523968 Score: 59 Period size: 7 Copynumber: 9.9 Consensus size: 7 86523890 AAGATTTAGC * 86523900 GGTTATG 1 GGTTAAG 86523907 GGTTAAG 1 GGTTAAG ** 86523914 AATTAAG 1 GGTTAAG * 86523921 GGTTAGG 1 GGTTAAG * * 86523928 GGATAAT 1 GGTTAAG * 86523935 GATTAAG 1 GGTTAAG 86523942 GGTT-AG 1 GGTTAAG 86523948 TGGTTAAG 1 -GGTTAAG 86523956 GGTTAAG 1 GGTTAAG 86523963 GGTTAA 1 GGTTAA 86523969 AAGTTTATGG Statistics Matches: 47, Mismatches: 13, Indels: 4 0.73 0.20 0.06 Matches are distributed among these distances: 6 2 0.04 7 43 0.91 8 2 0.04 ACGTcount: A:0.30, C:0.00, G:0.38, T:0.32 Consensus pattern (7 bp): GGTTAAG Found at i:86525137 original size:82 final size:81 Alignment explanation

Indices: 86524875--86525139 Score: 217 Period size: 75 Copynumber: 3.3 Consensus size: 81 86524865 AAATTAAGAG * * * * * * 86524875 ATTAGTGGCGTTTTTCCAAAAAAACGCTGCAAAAAACAGTATAGTTTAAAGAAAACGACGTCGTT 1 ATTAGCGGCGTTTTT--TAAAAAACGCCGCAAAAAACATTATAGTTTAATGGAAACGACGTCGTT * * 86524940 TTAGTTGGATATTTAGGGG 64 TTAGTT-GATATATAGGGA * * ** * * 86524959 ATTAGCGGC-ATTTTT-AAAAATGCCACTGCAAAAAAGTTTATAGTTTAATAG-AACGGCGTCGT 1 ATTAGCGGCGTTTTTTAAAAAACG-C-C-GCAAAAAACATTATAGTTTAATGGAAACGACGTCGT * 86525021 TTTAGTTG---GATAGGGA 63 TTTAGTTGATATATAGGGA * * * 86525037 A-TAGTGGCG-TTTATAAAAAACGCCGCAAAAAGA-ATTAAAGTTT-ATGGAAACGACGTCGTTT 1 ATTAGCGGCGTTTTTTAAAAAACGCCGCAAAAA-ACATTATAGTTTAATGGAAACGACGTCGTTT 86525098 TAGTTGAATATATAGGGA 65 TAGTTG-ATATATAGGGA 86525116 ATTAGCGGCGTTTTTTCAAAAAAC 1 ATTAGCGGCGTTTTTT-AAAAAAC 86525140 ATTAGTGCTT Statistics Matches: 142, Mismatches: 25, Indels: 30 0.72 0.13 0.15 Matches are distributed among these distances: 74 3 0.02 75 33 0.23 76 2 0.01 77 11 0.08 78 12 0.08 79 8 0.06 80 13 0.09 81 6 0.04 82 24 0.17 83 22 0.15 84 8 0.06 ACGTcount: A:0.36, C:0.12, G:0.22, T:0.30 Consensus pattern (81 bp): ATTAGCGGCGTTTTTTAAAAAACGCCGCAAAAAACATTATAGTTTAATGGAAACGACGTCGTTTT AGTTGATATATAGGGA Found at i:86526670 original size:20 final size:19 Alignment explanation

Indices: 86526647--86526685 Score: 51 Period size: 20 Copynumber: 2.0 Consensus size: 19 86526637 CCAAACAAAT 86526647 AAAAAATAATATAATAACCC 1 AAAAAATAATATAA-AACCC * * 86526667 AAAACATTATATAAAACCC 1 AAAAAATAATATAAAACCC 86526686 TTTTAGGTGA Statistics Matches: 17, Mismatches: 2, Indels: 1 0.85 0.10 0.05 Matches are distributed among these distances: 19 5 0.29 20 12 0.71 ACGTcount: A:0.62, C:0.18, G:0.00, T:0.21 Consensus pattern (19 bp): AAAAAATAATATAAAACCC Found at i:86527970 original size:24 final size:24 Alignment explanation

Indices: 86527942--86527988 Score: 67 Period size: 24 Copynumber: 2.0 Consensus size: 24 86527932 TTAATAAATT * 86527942 AAATATTCTCATACGTTTTATCAC 1 AAATATTATCATACGTTTTATCAC * * 86527966 AAATATTATCGTCCGTTTTATCA 1 AAATATTATCATACGTTTTATCA 86527989 TTTAAGTTAA Statistics Matches: 20, Mismatches: 3, Indels: 0 0.87 0.13 0.00 Matches are distributed among these distances: 24 20 1.00 ACGTcount: A:0.32, C:0.19, G:0.06, T:0.43 Consensus pattern (24 bp): AAATATTATCATACGTTTTATCAC Found at i:86528196 original size:39 final size:39 Alignment explanation

Indices: 86528153--86528228 Score: 134 Period size: 39 Copynumber: 1.9 Consensus size: 39 86528143 GACATGCTAT * 86528153 TTTAATTAATATGATTTGGATTAATTTATTTAAATATTA 1 TTTAATTAATATAATTTGGATTAATTTATTTAAATATTA * 86528192 TTTAATTAATATAATTTGTATTAATTTATTTAAATAT 1 TTTAATTAATATAATTTGGATTAATTTATTTAAATAT 86528229 ATAAGAATTT Statistics Matches: 35, Mismatches: 2, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 39 35 1.00 ACGTcount: A:0.39, C:0.00, G:0.05, T:0.55 Consensus pattern (39 bp): TTTAATTAATATAATTTGGATTAATTTATTTAAATATTA Found at i:86528198 original size:20 final size:21 Alignment explanation

Indices: 86528172--86528228 Score: 66 Period size: 19 Copynumber: 2.9 Consensus size: 21 86528162 TATGATTTGG 86528172 ATTAATTTATTTAAATATTAT 1 ATTAATTTATTTAAATATTAT * * * 86528193 -TTAATTAATAT-AAT-TTGT 1 ATTAATTTATTTAAATATTAT 86528211 ATTAATTTATTTAAATAT 1 ATTAATTTATTTAAATAT 86528229 ATAAGAATTT Statistics Matches: 28, Mismatches: 5, Indels: 6 0.72 0.13 0.15 Matches are distributed among these distances: 18 3 0.11 19 12 0.43 20 12 0.43 21 1 0.04 ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56 Consensus pattern (21 bp): ATTAATTTATTTAAATATTAT Found at i:86528217 original size:19 final size:19 Alignment explanation

Indices: 86528154--86528217 Score: 58 Period size: 19 Copynumber: 3.3 Consensus size: 19 86528144 ACATGCTATT * * 86528154 TTAATTAATATGATTTGGA 1 TTAATTAATATAATTTGTA * * * 86528173 TTAATTTATTTAAATAT-TA 1 TTAATTAATAT-AATTTGTA 86528192 TTTAATTAATATAATTTGTA 1 -TTAATTAATATAATTTGTA 86528212 TTAATT 1 TTAATT 86528218 TATTTAAATA Statistics Matches: 34, Mismatches: 8, Indels: 6 0.71 0.17 0.12 Matches are distributed among these distances: 19 20 0.59 20 14 0.41 ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55 Consensus pattern (19 bp): TTAATTAATATAATTTGTA Found at i:86528392 original size:27 final size:27 Alignment explanation

Indices: 86528332--86528496 Score: 194 Period size: 27 Copynumber: 6.1 Consensus size: 27 86528322 ATACTGGAAT 86528332 TTACATAACTCACATAACTTACACATAAC 1 TTACATAACTCACATAACTT--ACATAAC * 86528361 TTATATAACTCACATAACTTACATAAC 1 TTACATAACTCACATAACTTACATAAC * 86528388 TTATATAACTCACATAACTTACATAAC 1 TTACATAACTCACATAACTTACATAAC * 86528415 TTACATAACTCACATAACTCACATAAC 1 TTACATAACTCACATAACTTACATAAC * * 86528442 TCACATAACTTACATAA--TACATAA- 1 TTACATAACTCACATAACTTACATAAC * * * 86528466 GTAGATATCAT-ATCATAACTTACATAAC 1 TTACATAAC-TCA-CATAACTTACATAAC 86528494 TTA 1 TTA 86528497 ATTATACTTA Statistics Matches: 120, Mismatches: 11, Indels: 11 0.85 0.08 0.08 Matches are distributed among these distances: 24 6 0.05 25 12 0.10 27 81 0.68 28 2 0.02 29 19 0.16 ACGTcount: A:0.45, C:0.23, G:0.01, T:0.31 Consensus pattern (27 bp): TTACATAACTCACATAACTTACATAAC Found at i:86528493 original size:9 final size:9 Alignment explanation

Indices: 86528332--86528496 Score: 174 Period size: 9 Copynumber: 18.3 Consensus size: 9 86528322 ATACTGGAAT 86528332 TTACATAAC 1 TTACATAAC * 86528341 TCACATAAC 1 TTACATAAC 86528350 TTACACATAAC 1 TT--ACATAAC * 86528361 TTATATAAC 1 TTACATAAC * 86528370 TCACATAAC 1 TTACATAAC 86528379 TTACATAAC 1 TTACATAAC * 86528388 TTATATAAC 1 TTACATAAC * 86528397 TCACATAAC 1 TTACATAAC 86528406 TTACATAAC 1 TTACATAAC 86528415 TTACATAAC 1 TTACATAAC * 86528424 TCACATAAC 1 TTACATAAC * 86528433 TCACATAAC 1 TTACATAAC * 86528442 TCACATAAC 1 TTACATAAC 86528451 TTACATAA- 1 TTACATAAC 86528459 -TACATAA- 1 TTACATAAC * * * 86528466 GTAGATATC 1 TTACATAAC * 86528475 ATATCATAAC 1 TTA-CATAAC 86528485 TTACATAAC 1 TTACATAAC 86528494 TTA 1 TTA 86528497 ATTATACTTA Statistics Matches: 133, Mismatches: 18, Indels: 10 0.83 0.11 0.06 Matches are distributed among these distances: 7 7 0.05 8 5 0.04 9 106 0.80 10 6 0.05 11 9 0.07 ACGTcount: A:0.45, C:0.23, G:0.01, T:0.31 Consensus pattern (9 bp): TTACATAAC Found at i:86533988 original size:21 final size:21 Alignment explanation

Indices: 86533956--86534028 Score: 92 Period size: 21 Copynumber: 3.5 Consensus size: 21 86533946 TAGAGCGGAT * ** 86533956 GCAGCAGTGAGGGAGGCAGTG 1 GCAGCAGCGAGGGAGGCAACG * 86533977 GCAGTAGCGAGGGAGGCAACG 1 GCAGCAGCGAGGGAGGCAACG ** 86533998 GCAGCAGCGAGGGAGGCAAAA 1 GCAGCAGCGAGGGAGGCAACG 86534019 GCAGCAGCGA 1 GCAGCAGCGA 86534029 TGGCAGTAGA Statistics Matches: 45, Mismatches: 7, Indels: 0 0.87 0.13 0.00 Matches are distributed among these distances: 21 45 1.00 ACGTcount: A:0.30, C:0.19, G:0.47, T:0.04 Consensus pattern (21 bp): GCAGCAGCGAGGGAGGCAACG Found at i:86534323 original size:31 final size:31 Alignment explanation

Indices: 86534261--86534341 Score: 99 Period size: 31 Copynumber: 2.5 Consensus size: 31 86534251 TTAGATTTAA * * 86534261 TGTTTTTTATTGTATTTTTTATGTTACATTTGC 1 TGTTTTTTATTGGA--TTTCATGTTACATTTGC * 86534294 TGTTTTTTATTGGATTTCATGTTATATTTGC 1 TGTTTTTTATTGGATTTCATGTTACATTTGC ** 86534325 TGTTTTTGGTTGGATTT 1 TGTTTTTTATTGGATTT 86534342 AATGCAGGAA Statistics Matches: 43, Mismatches: 5, Indels: 2 0.86 0.10 0.04 Matches are distributed among these distances: 31 30 0.70 33 13 0.30 ACGTcount: A:0.14, C:0.05, G:0.17, T:0.64 Consensus pattern (31 bp): TGTTTTTTATTGGATTTCATGTTACATTTGC Found at i:86541036 original size:40 final size:40 Alignment explanation

Indices: 86540986--86541088 Score: 170 Period size: 41 Copynumber: 2.5 Consensus size: 40 86540976 GTTTGCATAA * 86540986 AAACGCCGCTAAAACTGAGTAATAGCGGCGTTTTTGGTCC 1 AAACGCCGCTAAAACTGAGTAATAGCGGCGTTTTTAGTCC * * 86541026 AAACGCCGCTAAAAACTTAGAAATAGCGGCGTTTTTAGTCC 1 AAACGCCGCT-AAAACTGAGTAATAGCGGCGTTTTTAGTCC 86541067 AAACGCCGCTAAAACTGAGTAA 1 AAACGCCGCTAAAACTGAGTAA 86541089 AAAACGCCGC Statistics Matches: 57, Mismatches: 5, Indels: 2 0.89 0.08 0.03 Matches are distributed among these distances: 40 20 0.35 41 37 0.65 ACGTcount: A:0.34, C:0.22, G:0.21, T:0.22 Consensus pattern (40 bp): AAACGCCGCTAAAACTGAGTAATAGCGGCGTTTTTAGTCC Found at i:86541256 original size:18 final size:17 Alignment explanation

Indices: 86541224--86541258 Score: 52 Period size: 17 Copynumber: 2.0 Consensus size: 17 86541214 ATTTTCTTAT * 86541224 TTTTGTTTTGAATTTGA 1 TTTTATTTTGAATTTGA 86541241 TTTTATTTTGATATTTGA 1 TTTTATTTTGA-ATTTGA 86541259 AACTGATTTT Statistics Matches: 16, Mismatches: 1, Indels: 1 0.89 0.06 0.06 Matches are distributed among these distances: 17 10 0.62 18 6 0.38 ACGTcount: A:0.20, C:0.00, G:0.14, T:0.66 Consensus pattern (17 bp): TTTTATTTTGAATTTGA Found at i:86541844 original size:18 final size:18 Alignment explanation

Indices: 86541821--86541859 Score: 69 Period size: 18 Copynumber: 2.2 Consensus size: 18 86541811 TAATTAGTAC 86541821 ATGTTTAGAGTATTATAT 1 ATGTTTAGAGTATTATAT * 86541839 ATGTTTATAGTATTATAT 1 ATGTTTAGAGTATTATAT 86541857 ATG 1 ATG 86541860 GTTCTAGGGT Statistics Matches: 20, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 18 20 1.00 ACGTcount: A:0.33, C:0.00, G:0.15, T:0.51 Consensus pattern (18 bp): ATGTTTAGAGTATTATAT Found at i:86542024 original size:29 final size:29 Alignment explanation

Indices: 86541982--86542038 Score: 71 Period size: 29 Copynumber: 2.0 Consensus size: 29 86541972 TTAGGGTTTA 86541982 GAGTTTAAAATTTAAGGTT-TAAGGTATTT 1 GAGTTTAAAATTT-AGGTTATAAGGTATTT ** * 86542011 GAGTTTAATGTTTAGTTTATAAGGTATT 1 GAGTTTAAAATTTAGGTTATAAGGTATT 86542039 CGGGGGTTTA Statistics Matches: 24, Mismatches: 3, Indels: 2 0.83 0.10 0.07 Matches are distributed among these distances: 28 4 0.17 29 20 0.83 ACGTcount: A:0.32, C:0.00, G:0.21, T:0.47 Consensus pattern (29 bp): GAGTTTAAAATTTAGGTTATAAGGTATTT Found at i:86545086 original size:64 final size:64 Alignment explanation

Indices: 86545018--86545151 Score: 223 Period size: 64 Copynumber: 2.1 Consensus size: 64 86545008 TAATATTTCT * * 86545018 ATATTTCTATCACGATTTTTAATAAATTTATTTATTGATATAATATGTCTCATCTAATATAAAA 1 ATATTTCTATCACGATTTTTAATAAATTTATTTATTAATATAATATGTCCCATCTAATATAAAA * * * 86545082 ATATTTCTATCACGATTTTTGATAAATTTATTTATTAATATAATTTGTCCCATCTAATATACAA 1 ATATTTCTATCACGATTTTTAATAAATTTATTTATTAATATAATATGTCCCATCTAATATAAAA 86545146 ATATTT 1 ATATTT 86545152 AATAAAATAT Statistics Matches: 65, Mismatches: 5, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 64 65 1.00 ACGTcount: A:0.37, C:0.10, G:0.04, T:0.48 Consensus pattern (64 bp): ATATTTCTATCACGATTTTTAATAAATTTATTTATTAATATAATATGTCCCATCTAATATAAAA Found at i:86545164 original size:64 final size:64 Alignment explanation

Indices: 86545031--86545165 Score: 175 Period size: 64 Copynumber: 2.1 Consensus size: 64 86545021 TTTCTATCAC * * * * * 86545031 GATTTTTAATAAATTTATTTATTGATATAATATGTCTCATCTAATATAAAAATATTTCTATCAC 1 GATTTTTAATAAATTTATTTATTAATATAATATGTCCCATCTAATATAAAAATATTTATATAAA * * * 86545095 GATTTTTGATAAATTTATTTATTAATATAATTTGTCCCATCTAATATACAAATATTTA-ATAAA 1 GATTTTTAATAAATTTATTTATTAATATAATATGTCCCATCTAATATAAAAATATTTATATAAA 86545158 -ATATTTTA 1 GAT-TTTTA 86545166 TATAGTTCTT Statistics Matches: 61, Mismatches: 9, Indels: 3 0.84 0.12 0.04 Matches are distributed among these distances: 62 2 0.03 63 7 0.11 64 52 0.85 ACGTcount: A:0.40, C:0.08, G:0.04, T:0.47 Consensus pattern (64 bp): GATTTTTAATAAATTTATTTATTAATATAATATGTCCCATCTAATATAAAAATATTTATATAAA Found at i:86545227 original size:24 final size:24 Alignment explanation

Indices: 86545199--86545269 Score: 81 Period size: 24 Copynumber: 3.0 Consensus size: 24 86545189 ATTATTATTG * 86545199 AAATATTCTCTTCCGTTTTATCAC 1 AAATATTATCTTCCGTTTTATCAC * * 86545223 GAATATTAT-TGTCTGTTTTATCAC 1 AAATATTATCT-TCCGTTTTATCAC * * 86545247 AAATATTATCGTCCATTTTATCA 1 AAATATTATCTTCCGTTTTATCA 86545270 TTTAAGTTAA Statistics Matches: 38, Mismatches: 7, Indels: 4 0.78 0.14 0.08 Matches are distributed among these distances: 23 1 0.03 24 37 0.97 ACGTcount: A:0.28, C:0.18, G:0.07, T:0.46 Consensus pattern (24 bp): AAATATTATCTTCCGTTTTATCAC Found at i:86545734 original size:241 final size:241 Alignment explanation

Indices: 86545311--86546015 Score: 1324 Period size: 241 Copynumber: 2.9 Consensus size: 241 86545301 ATACCTTTTT * 86545311 AAGTTCTATCGAGCTCAGTTACTATTGAATATTTATTACCATGTAGCTTGCTTGTGCATTAAAAT 1 AAGTTCTATCGAGCTCATTTACTATTGAATATTTATTACCATGTAGCTTGCTTGTGCATTAAAAT 86545376 TACAACAATAGCTGACCTTCTCTCCAACCTTTTTTTAAATATTTTAAAGATTCAAAGTATATAGG 66 TACAACAATAGCTGACCTTCTCTCCAACCTTTTTTTAAATATTTTAAAGATTCAAAGTATATAGG 86545441 CTGGAAACCTGACGGGTTGCCTTATATCGAGCTGTAAGATATAATGGATCCTCCCTAGGTGTAAC 131 CTGGAAACCTGACGGGTTGCCTTATATCGAGCTGTAAGATATAATGGATCCTCCCTAGGTGTAAC 86545506 AACGTCACGTATGATGAATCTTAAAAAATTTAAAAAGACTTGAAAA 196 AACGTCACGTATGATGAATCTTAAAAAATTTAAAAAGACTTGAAAA * 86545552 AAGTTCTATCGAGTTCATTTACTATTGAATATTTATTACCATGTAGCTTGCTTGTGCATTAAAAT 1 AAGTTCTATCGAGCTCATTTACTATTGAATATTTATTACCATGTAGCTTGCTTGTGCATTAAAAT * 86545617 TACAACAATAGCTGACCTTCTGTCCAACCTTTTTTTAAATATTTTAAAGATTCAAAGTATATAGG 66 TACAACAATAGCTGACCTTCTCTCCAACCTTTTTTTAAATATTTTAAAGATTCAAAGTATATAGG 86545682 CTGGAAACCTGACGGGTTGCCTTATATCGAGCTGTAAGATATAATGGATCCTCCCTAGGTGTAAC 131 CTGGAAACCTGACGGGTTGCCTTATATCGAGCTGTAAGATATAATGGATCCTCCCTAGGTGTAAC * 86545747 AACGTCACGTATGATGAATCTTAAAAAA-TTCAAAAGACTTGAAAA 196 AACGTCACGTATGATGAATCTTAAAAAATTTAAAAAGACTTGAAAA * * * 86545792 AATTTCTATCGAGCTCATTTACTATTGAATATTCATTACCATGTAGCTTGCTTGTCCATTAAAAT 1 AAGTTCTATCGAGCTCATTTACTATTGAATATTTATTACCATGTAGCTTGCTTGTGCATTAAAAT 86545857 TACAACAATAGCTGACCTTCTCTCCAACC-TTTTTTAAATATTTTAAAGATTCAAAGTATATAGG 66 TACAACAATAGCTGACCTTCTCTCCAACCTTTTTTTAAATATTTTAAAGATTCAAAGTATATAGG 86545921 CTGGAAACCTGACGGGTTGCCTTATATCGAGCTGTAAGATATAATGGATCCTCCCTAGGTGTAAC 131 CTGGAAACCTGACGGGTTGCCTTATATCGAGCTGTAAGATATAATGGATCCTCCCTAGGTGTAAC * 86545986 AACGCCACGTATGATGAATCTTAAAAAATT 196 AACGTCACGTATGATGAATCTTAAAAAATT 86546016 ACTATATTCA Statistics Matches: 453, Mismatches: 10, Indels: 3 0.97 0.02 0.01 Matches are distributed among these distances: 239 127 0.28 240 106 0.23 241 220 0.49 ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34 Consensus pattern (241 bp): AAGTTCTATCGAGCTCATTTACTATTGAATATTTATTACCATGTAGCTTGCTTGTGCATTAAAAT TACAACAATAGCTGACCTTCTCTCCAACCTTTTTTTAAATATTTTAAAGATTCAAAGTATATAGG CTGGAAACCTGACGGGTTGCCTTATATCGAGCTGTAAGATATAATGGATCCTCCCTAGGTGTAAC AACGTCACGTATGATGAATCTTAAAAAATTTAAAAAGACTTGAAAA Found at i:86546157 original size:9 final size:9 Alignment explanation

Indices: 86546134--86546261 Score: 121 Period size: 9 Copynumber: 13.6 Consensus size: 9 86546124 ATTGATCATT * 86546134 ACTTAAATA 1 ACTTACATA * 86546143 AATTACATA 1 ACTTACATA 86546152 ACTTACATA 1 ACTTACATA * * 86546161 ACTCATATA 1 ACTTACATA 86546170 ACTTACATA 1 ACTTACATA * 86546179 ATTTACATAACA 1 ACTTACAT---A 86546191 ACTTACATA 1 ACTTACATA * 86546200 ACTCACATA 1 ACTTACATA 86546209 ACTTACATA 1 ACTTACATA * 86546218 ATTTACATA 1 ACTTACATA * 86546227 ACTCACATA 1 ACTTACATA * 86546236 ACGTACATAACA 1 ACTTACAT---A 86546248 ACTTACATA 1 ACTTACATA 86546257 ACTTA 1 ACTTA 86546262 ACTAATACAT Statistics Matches: 96, Mismatches: 17, Indels: 12 0.77 0.14 0.10 Matches are distributed among these distances: 9 80 0.83 12 16 0.17 ACGTcount: A:0.47, C:0.21, G:0.01, T:0.31 Consensus pattern (9 bp): ACTTACATA Found at i:86546203 original size:39 final size:39 Alignment explanation

Indices: 86546151--86546228 Score: 147 Period size: 39 Copynumber: 2.0 Consensus size: 39 86546141 TAAATTACAT * 86546151 AACTTACATAACTCATATAACTTACATAATTTACATAAC 1 AACTTACATAACTCACATAACTTACATAATTTACATAAC 86546190 AACTTACATAACTCACATAACTTACATAATTTACATAAC 1 AACTTACATAACTCACATAACTTACATAATTTACATAAC 86546229 TCACATAACG Statistics Matches: 38, Mismatches: 1, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 39 38 1.00 ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32 Consensus pattern (39 bp): AACTTACATAACTCACATAACTTACATAATTTACATAAC Found at i:86546228 original size:57 final size:57 Alignment explanation

Indices: 86546147--86546259 Score: 172 Period size: 57 Copynumber: 2.0 Consensus size: 57 86546137 TAAATAAATT * * ** 86546147 ACATAACTTACATAACTCATATAACTTACATAATTTACATAACAACTTACATAACTC 1 ACATAACTTACATAACTCACATAACTCACATAACGTACATAACAACTTACATAACTC * * 86546204 ACATAACTTACATAATTTACATAACTCACATAACGTACATAACAACTTACATAACT 1 ACATAACTTACATAACTCACATAACTCACATAACGTACATAACAACTTACATAACT 86546260 TAACTAATAC Statistics Matches: 50, Mismatches: 6, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 57 50 1.00 ACGTcount: A:0.46, C:0.23, G:0.01, T:0.30 Consensus pattern (57 bp): ACATAACTTACATAACTCACATAACTCACATAACGTACATAACAACTTACATAACTC Found at i:86552148 original size:33 final size:33 Alignment explanation

Indices: 86552102--86552179 Score: 88 Period size: 31 Copynumber: 2.4 Consensus size: 33 86552092 AATTAATGAC * * * 86552102 TTTGGTTGTATTTTTTATGTTAAATTTGTTGTT 1 TTTGGTTGCATTTTTTATATTAAATTTGTTGTA * * 86552135 TTTGGCTGCA--TTTTATATTATATTTGTTGTA 1 TTTGGTTGCATTTTTTATATTAAATTTGTTGTA * 86552166 TTTGGTTGGATTTT 1 TTTGGTTGCATTTT 86552180 AATGCAGGAA Statistics Matches: 36, Mismatches: 7, Indels: 4 0.77 0.15 0.09 Matches are distributed among these distances: 31 26 0.72 33 10 0.28 ACGTcount: A:0.15, C:0.03, G:0.19, T:0.63 Consensus pattern (33 bp): TTTGGTTGCATTTTTTATATTAAATTTGTTGTA Found at i:86552160 original size:31 final size:31 Alignment explanation

Indices: 86552114--86552180 Score: 89 Period size: 31 Copynumber: 2.2 Consensus size: 31 86552104 TGGTTGTATT * * 86552114 TTTTATGTTAAATTTGTTGTTTTTGGCTGCA 1 TTTTATATTAAATTTGTTGTATTTGGCTGCA * * * 86552145 TTTTATATTATATTTGTTGTATTTGGTTGGA 1 TTTTATATTAAATTTGTTGTATTTGGCTGCA 86552176 TTTTA 1 TTTTA 86552181 ATGCAGGAAG Statistics Matches: 31, Mismatches: 5, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 31 31 1.00 ACGTcount: A:0.18, C:0.03, G:0.18, T:0.61 Consensus pattern (31 bp): TTTTATATTAAATTTGTTGTATTTGGCTGCA Found at i:86552281 original size:43 final size:43 Alignment explanation

Indices: 86552255--86552412 Score: 280 Period size: 43 Copynumber: 3.7 Consensus size: 43 86552245 GTGGGAAAAG * * 86552255 CGCCGCTAAAAGCCTTGATCTTTAGCGGCGCTTTTCCTACAAA 1 CGCCGCTAAAAGCCTTGACCTTTAGCGGCGCTTTTCCAACAAA * 86552298 CGCCGCTAAAAGCCTTGACCTTTTGCGGCGCTTTTCCAACAAA 1 CGCCGCTAAAAGCCTTGACCTTTAGCGGCGCTTTTCCAACAAA * 86552341 CGCCGCTAAAAGCCTTGACCTTTTGCGGCGCTTTTCCAACAAA 1 CGCCGCTAAAAGCCTTGACCTTTAGCGGCGCTTTTCCAACAAA 86552384 CGCCGCTAAAAGCCTTGACCTTTAGCGGC 1 CGCCGCTAAAAGCCTTGACCTTTAGCGGC 86552413 ATTTTTTTCA Statistics Matches: 111, Mismatches: 4, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 43 111 1.00 ACGTcount: A:0.23, C:0.32, G:0.20, T:0.25 Consensus pattern (43 bp): CGCCGCTAAAAGCCTTGACCTTTAGCGGCGCTTTTCCAACAAA Found at i:86563169 original size:16 final size:16 Alignment explanation

Indices: 86563150--86563181 Score: 64 Period size: 16 Copynumber: 2.0 Consensus size: 16 86563140 GTGGATTATC 86563150 AGGATTCTTATTCTAT 1 AGGATTCTTATTCTAT 86563166 AGGATTCTTATTCTAT 1 AGGATTCTTATTCTAT 86563182 TTCTTAATAA Statistics Matches: 16, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 16 16 1.00 ACGTcount: A:0.25, C:0.12, G:0.12, T:0.50 Consensus pattern (16 bp): AGGATTCTTATTCTAT Found at i:86564855 original size:16 final size:15 Alignment explanation

Indices: 86564829--86564858 Score: 51 Period size: 16 Copynumber: 1.9 Consensus size: 15 86564819 ATCATGCATG 86564829 TGTATATATATAATA 1 TGTATATATATAATA 86564844 TGTATGATATATAAT 1 TGTAT-ATATATAAT 86564859 GTTGAATATC Statistics Matches: 14, Mismatches: 0, Indels: 1 0.93 0.00 0.07 Matches are distributed among these distances: 15 5 0.36 16 9 0.64 ACGTcount: A:0.43, C:0.00, G:0.10, T:0.47 Consensus pattern (15 bp): TGTATATATATAATA Found at i:86589103 original size:46 final size:48 Alignment explanation

Indices: 86589031--86589133 Score: 147 Period size: 46 Copynumber: 2.2 Consensus size: 48 86589021 GACAGGACAG * * * 86589031 GACAGAAATGAGCCATGTAAGTCCATA-T-CAGATATATGGCTTTGGA 1 GACAGGAATGAGCCATGTAAGCCCATATTACAGATATATGGCATTGGA * * 86589077 GACAGGAATGAGCCATGTAAGCCCATATTATATATATATGGCATTGGA 1 GACAGGAATGAGCCATGTAAGCCCATATTACAGATATATGGCATTGGA 86589125 GACAGGAAT 1 GACAGGAAT 86589134 AATTCAAGTA Statistics Matches: 50, Mismatches: 5, Indels: 2 0.88 0.09 0.04 Matches are distributed among these distances: 46 25 0.50 47 1 0.02 48 24 0.48 ACGTcount: A:0.36, C:0.15, G:0.24, T:0.25 Consensus pattern (48 bp): GACAGGAATGAGCCATGTAAGCCCATATTACAGATATATGGCATTGGA Found at i:86609320 original size:46 final size:48 Alignment explanation

Indices: 86609248--86609350 Score: 147 Period size: 46 Copynumber: 2.2 Consensus size: 48 86609238 GACAGGACAG * * * 86609248 GACAGAAATGAGCCATGTAAGTCCATA-T-CAGATATATGGCTTTGGA 1 GACAGGAATGAGCCATGTAAGCCCATATTACAGATATATGGCATTGGA * * 86609294 GACAGGAATGAGCCATGTAAGCCCATATTATATATATATGGCATTGGA 1 GACAGGAATGAGCCATGTAAGCCCATATTACAGATATATGGCATTGGA 86609342 GACAGGAAT 1 GACAGGAAT 86609351 AATTCAAGTA Statistics Matches: 50, Mismatches: 5, Indels: 2 0.88 0.09 0.04 Matches are distributed among these distances: 46 25 0.50 47 1 0.02 48 24 0.48 ACGTcount: A:0.36, C:0.15, G:0.24, T:0.25 Consensus pattern (48 bp): GACAGGAATGAGCCATGTAAGCCCATATTACAGATATATGGCATTGGA Found at i:86617152 original size:39 final size:41 Alignment explanation

Indices: 86617057--86617240 Score: 199 Period size: 40 Copynumber: 4.6 Consensus size: 41 86617047 TTGGATGATG * 86617057 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTAAGTGAC-AATA 1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGT-ACTAATA * * 86617096 TCCGGACTAAGAT-CCGAAGGCATTCGTGCG-AGATACTAAT- 1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAAG-TACTAATA 86617136 TCCGGGCTAAG-CCCGAAGGCATTTGTGCG-AGTTACTAA-A 1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAG-TACTAATA * * 86617175 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACT-ATA 1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGTACTAATA * * 86617215 ACCGGGCTATGTCCCGAAGGCATTTG 1 TCCGGGCTAAGTCCCGAAGGCATTTG 86617241 AACGAGGAGC Statistics Matches: 124, Mismatches: 11, Indels: 19 0.81 0.07 0.12 Matches are distributed among these distances: 39 53 0.43 40 61 0.49 41 10 0.08 ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24 Consensus pattern (41 bp): TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGTACTAATA Found at i:86617192 original size:79 final size:81 Alignment explanation

Indices: 86617057--86617240 Score: 213 Period size: 79 Copynumber: 2.3 Consensus size: 81 86617047 TTGGATGATG 86617057 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTAAGTGACAATATCCGGACTAAGATCCGAAGGCATT 1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACAATATCCGGACTAAGATCCGAAGGCATT 86617120 CGTGCGAGA-TACTA-A 66 CGTGCGA-ATTACTATA * * ** 86617135 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAA-ATCCGGGTTAAG-TCCCGAAGGC 1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGAC-AATATCCGGACTAAGAT-CCGAAGGC * 86617196 ATTTGTGCGAATTACTATA 63 ATTCGTGCGAATTACTATA * * 86617215 ACCGGGCTATGTCCCGAAGGCATTTG 1 TCCGGGCTAAGTCCCGAAGGCATTTG 86617241 AACGAGGAGC Statistics Matches: 91, Mismatches: 7, Indels: 13 0.82 0.06 0.12 Matches are distributed among these distances: 78 11 0.12 79 57 0.63 80 23 0.25 ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24 Consensus pattern (81 bp): TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACAATATCCGGACTAAGATCCGAAGGCATT CGTGCGAATTACTATA Found at i:86617262 original size:79 final size:79 Alignment explanation

Indices: 86617109--86617273 Score: 185 Period size: 79 Copynumber: 2.1 Consensus size: 79 86617099 GGACTAAGAT * ** * 86617109 CCGAAGGCATTCGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA 1 CCGAAGGCATTCGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAA * 86617174 ATCCGGGTTAAGTC 66 ATCCGGGTTAAATC * * 86617188 CCGAAGGCATTTGTGCGA-ATTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAG 1 CCGAAGGCATTCGTGCGAGA-TACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTGA- * * 86617250 CTATATCC-GGTTAAATT 62 CTAAATCCGGGTTAAATC 86617267 CCGAAGG 1 CCGAAGG 86617274 TACGTGATTT Statistics Matches: 73, Mismatches: 9, Indels: 8 0.81 0.10 0.09 Matches are distributed among these distances: 78 3 0.04 79 45 0.62 80 25 0.34 ACGTcount: A:0.27, C:0.22, G:0.27, T:0.24 Consensus pattern (79 bp): CCGAAGGCATTCGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAA ATCCGGGTTAAATC Found at i:86625306 original size:374 final size:375 Alignment explanation

Indices: 86624606--86625351 Score: 1352 Period size: 374 Copynumber: 2.0 Consensus size: 375 86624596 GCCAAATTAC 86624606 AACAGATCAAGGGACAAGCCTGCACTGATAAAGGTTGGGTGTGGACCCTCAGCAATACCAATGCT 1 AACAGATCAAGGGACAAGCCTGCACTGATAAAGGTTGGGTGTGGACCCTCAGCAATACCAATGCT * * 86624671 AACTTGTTTTAACTCATTAATAGTGGCTGGATTTCCTTCTTCAAATGATGAAGAAGCTTATTAGG 66 AACTTGTTTCAACTCATTAATAGTGGCTGGATTTCCTTCTTCAAATGACGAAGAAGCTTATTAGG 86624736 CTTTCTCTTCTCGAGACTCTTCATTGATCTCTTTAACAAATAGACAATAAGATGTAAGGGCTTCA 131 CTTTCTCTTCTCGAGACTCTTCATTGATCTCTTTAACAAATAGACAATAAGATGTAAGGGCTTCA 86624801 TATTTTAACACTCTTCCTTCATGGATGTATTAGTTATGACTACCATGTATTATTTGGATTTTAAG 196 TATTTTAACACTCTTCCTTCATGGATGTATTAGTTATGACTACCATGTATTATTTGGATTTTAAG * 86624866 ACTTCACCAGTAGTTATCTTCAATTAGGACTGCCTTTTCATCCACGAGCTAATTTCACTGTGAAA 261 ACTTCACCAGTAGTTATCTTCAATTAGGACTGCCTTTTCATCCACGAGCTAATTTCACTATGAAA * 86624931 ATGCGTTAATATTTTTCGAGCAGGAGC-TTTTTTTCCCTAATGCGACTAT 326 ATGCGTTAATATTTTTCGAGCAGGAGCTTTTTTTTCCCTAATACGACTAT * 86624980 AACAGA-CAAAGGGACAAGCCTGCACTGATAAAGGTTGGGTGTGGATCCTCAGCAATACCAATGC 1 AACAGATC-AAGGGACAAGCCTGCACTGATAAAGGTTGGGTGTGGACCCTCAGCAATACCAATGC * * 86625044 TAACTTGTTTCAACTCATTAATAGTGGCTTGATTTCCTTCTTCAAATGACGAAGAAGCTTATTGG 65 TAACTTGTTTCAACTCATTAATAGTGGCTGGATTTCCTTCTTCAAATGACGAAGAAGCTTATTAG * 86625109 GCTTTCTCTTCTCGAGACTCTTCATTGATCTCTTTAACAGATAGACAATAAGATGTAAGGGCTTC 130 GCTTTCTCTTCTCGAGACTCTTCATTGATCTCTTTAACAAATAGACAATAAGATGTAAGGGCTTC * 86625174 ATATTTTAACACTCTTCCTTCATGGATGTATTAGTTATGACTACCATGTATTATTTGGCTTTTAA 195 ATATTTTAACACTCTTCCTTCATGGATGTATTAGTTATGACTACCATGTATTATTTGGATTTTAA * * 86625239 GACTTCACCAGTAGTTATCTTCAATTAGGACTGCCTTTTCATCCACGAGGTAATTTCGCTATGAA 260 GACTTCACCAGTAGTTATCTTCAATTAGGACTGCCTTTTCATCCACGAGCTAATTTCACTATGAA * * 86625304 AATGTGTTAATATTTTTCGAGCGGGAGCTTTTTTTTCCCTAATACGAC 325 AATGCGTTAATATTTTTCGAGCAGGAGCTTTTTTTTCCCTAATACGAC 86625352 CAACCTTTCC Statistics Matches: 357, Mismatches: 13, Indels: 3 0.96 0.03 0.01 Matches are distributed among these distances: 373 1 0.00 374 338 0.95 375 18 0.05 ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35 Consensus pattern (375 bp): AACAGATCAAGGGACAAGCCTGCACTGATAAAGGTTGGGTGTGGACCCTCAGCAATACCAATGCT AACTTGTTTCAACTCATTAATAGTGGCTGGATTTCCTTCTTCAAATGACGAAGAAGCTTATTAGG CTTTCTCTTCTCGAGACTCTTCATTGATCTCTTTAACAAATAGACAATAAGATGTAAGGGCTTCA TATTTTAACACTCTTCCTTCATGGATGTATTAGTTATGACTACCATGTATTATTTGGATTTTAAG ACTTCACCAGTAGTTATCTTCAATTAGGACTGCCTTTTCATCCACGAGCTAATTTCACTATGAAA ATGCGTTAATATTTTTCGAGCAGGAGCTTTTTTTTCCCTAATACGACTAT Found at i:86628031 original size:12 final size:12 Alignment explanation

Indices: 86628014--86628038 Score: 50 Period size: 12 Copynumber: 2.1 Consensus size: 12 86628004 TGATGATCTT 86628014 TGGCTACTTGTA 1 TGGCTACTTGTA 86628026 TGGCTACTTGTA 1 TGGCTACTTGTA 86628038 T 1 T 86628039 ATTGGATTGT Statistics Matches: 13, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 12 13 1.00 ACGTcount: A:0.16, C:0.16, G:0.24, T:0.44 Consensus pattern (12 bp): TGGCTACTTGTA Found at i:86632007 original size:20 final size:20 Alignment explanation

Indices: 86631984--86632047 Score: 56 Period size: 20 Copynumber: 3.2 Consensus size: 20 86631974 TTGACTAAAT 86631984 TACTGGTAGTTTATCTGCAA 1 TACTGGTAGTTTATCTGCAA * ** * * 86632004 TACTGGCAGCCTGTCTGCAC 1 TACTGGTAGTTTATCTGCAA * * * 86632024 TAGTGGTAGTTTATTTGCAT 1 TACTGGTAGTTTATCTGCAA 86632044 TACT 1 TACT 86632048 AGTTACTTGA Statistics Matches: 31, Mismatches: 13, Indels: 0 0.70 0.30 0.00 Matches are distributed among these distances: 20 31 1.00 ACGTcount: A:0.20, C:0.19, G:0.22, T:0.39 Consensus pattern (20 bp): TACTGGTAGTTTATCTGCAA Found at i:86635295 original size:4 final size:4 Alignment explanation

Indices: 86635288--86635329 Score: 84 Period size: 4 Copynumber: 10.5 Consensus size: 4 86635278 GTTAGGAACT 86635288 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT 1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT 86635330 CTTATTGAAT Statistics Matches: 38, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 4 38 1.00 ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76 Consensus pattern (4 bp): TTTA Found at i:86638338 original size:24 final size:25 Alignment explanation

Indices: 86638291--86638338 Score: 73 Period size: 24 Copynumber: 2.0 Consensus size: 25 86638281 TAACCTTAGA 86638291 ATCAAAACTCTCCGTTTTACTTAAG 1 ATCAAAACTCTCCGTTTTACTTAAG 86638316 ATCAAAACTC-CC-TGTTTACTTAA 1 ATCAAAACTCTCCGT-TTTACTTAA 86638339 ATGAGGTTAG Statistics Matches: 22, Mismatches: 0, Indels: 3 0.88 0.00 0.12 Matches are distributed among these distances: 23 1 0.05 24 11 0.50 25 10 0.45 ACGTcount: A:0.33, C:0.25, G:0.06, T:0.35 Consensus pattern (25 bp): ATCAAAACTCTCCGTTTTACTTAAG Found at i:86639549 original size:79 final size:79 Alignment explanation

Indices: 86639418--86639575 Score: 255 Period size: 79 Copynumber: 2.0 Consensus size: 79 86639408 ACTAAAATAA * 86639418 AGTTTGTCATGTTTGAATTAGGCAACCCTTCAATGAAATCCAAGCTAACAACTGACCAAGCTCTG 1 AGTTTGTCATGTTTGAATTAGGCAACCCTTCAATGAAATCCAAGCTAACAACTAACCAAGCTCTG 86639483 CCAGGCATCGGTAG 66 CCAGGCATCGGTAG * * 86639497 AGTTTTTCTTGTTTGAATT-GAGCAACCCTTCAATGAAATCCAAGCTAACAACTAACCAAGCTCT 1 AGTTTGTCATGTTTGAATTAG-GCAACCCTTCAATGAAATCCAAGCTAACAACTAACCAAGCTCT * * 86639561 GTCAGGTATCGGTAG 65 GCCAGGCATCGGTAG 86639576 TGGCTGAAGG Statistics Matches: 73, Mismatches: 5, Indels: 2 0.91 0.06 0.03 Matches are distributed among these distances: 78 1 0.01 79 72 0.99 ACGTcount: A:0.30, C:0.23, G:0.19, T:0.28 Consensus pattern (79 bp): AGTTTGTCATGTTTGAATTAGGCAACCCTTCAATGAAATCCAAGCTAACAACTAACCAAGCTCTG CCAGGCATCGGTAG Found at i:86642782 original size:15 final size:16 Alignment explanation

Indices: 86642757--86642786 Score: 53 Period size: 15 Copynumber: 1.9 Consensus size: 16 86642747 CGTGACCCCG 86642757 TTAGCTGGAGGTCCAC 1 TTAGCTGGAGGTCCAC 86642773 TTAG-TGGAGGTCCA 1 TTAGCTGGAGGTCCA 86642787 AAATACTAGC Statistics Matches: 14, Mismatches: 0, Indels: 1 0.93 0.00 0.07 Matches are distributed among these distances: 15 10 0.71 16 4 0.29 ACGTcount: A:0.20, C:0.20, G:0.33, T:0.27 Consensus pattern (16 bp): TTAGCTGGAGGTCCAC Found at i:86643265 original size:26 final size:26 Alignment explanation

Indices: 86643236--86643287 Score: 104 Period size: 26 Copynumber: 2.0 Consensus size: 26 86643226 CCCGTTTACT 86643236 TAAATGAGGTTAACTGTTTATAACTA 1 TAAATGAGGTTAACTGTTTATAACTA 86643262 TAAATGAGGTTAACTGTTTATAACTA 1 TAAATGAGGTTAACTGTTTATAACTA 86643288 ACTTCTTTTC Statistics Matches: 26, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 26 26 1.00 ACGTcount: A:0.38, C:0.08, G:0.15, T:0.38 Consensus pattern (26 bp): TAAATGAGGTTAACTGTTTATAACTA Found at i:86649367 original size:32 final size:29 Alignment explanation

Indices: 86649328--86649409 Score: 87 Period size: 32 Copynumber: 2.7 Consensus size: 29 86649318 AATTTTTTTA * 86649328 TCCCCTTT-ACATCCAAAAATTTTTACTTTCCC 1 TCCCCTTTAAC-TCCAAAAATCTTTA-TTT--C * 86649360 TCCCCTTTAACTCCCAAAATCTTTATTTC 1 TCCCCTTTAACTCCAAAAATCTTTATTTC 86649389 TCCCCTTTAAC-CCTAAAAATC 1 TCCCCTTTAACTCC-AAAAATC 86649410 AAAATCCTCT Statistics Matches: 45, Mismatches: 3, Indels: 7 0.82 0.05 0.13 Matches are distributed among these distances: 28 2 0.04 29 18 0.40 31 3 0.07 32 20 0.44 33 2 0.04 ACGTcount: A:0.27, C:0.35, G:0.00, T:0.38 Consensus pattern (29 bp): TCCCCTTTAACTCCAAAAATCTTTATTTC Found at i:86663789 original size:95 final size:95 Alignment explanation

Indices: 86663626--86663907 Score: 537 Period size: 95 Copynumber: 3.0 Consensus size: 95 86663616 CAATAACCTA 86663626 TAGGAATTTGATCTTTCAAAAAGATATTAAGAGGAGGAAATTCTTGTTACCTGGCCCATTTTCCG 1 TAGGAATTTGATCTTTCAAAAAGATATTAAGAGGAGGAAATTCTTGTTACCTGGCCCATTTTCCG * 86663691 TTCAACTAAAAGGATAATAGCTAGCTTGTG 66 TTCAACTAAAAGGATAATAGCTAGCTTCTG 86663721 TAGGAATTTGATCTTTCAAAAAGATATTAAGAGGAGGAAATTCTTGTTACCTGGCCCATTTTCCG 1 TAGGAATTTGATCTTTCAAAAAGATATTAAGAGGAGGAAATTCTTGTTACCTGGCCCATTTTCCG * 86663786 TTCAACTAAAAGGATACTAGCTAGCTTCTG 66 TTCAACTAAAAGGATAATAGCTAGCTTCTG * 86663816 TAGGAATTTGATCTTTCAAAAAGATATTAAGAGGAGGAAATTCTTGTTACCTGACCCATTTTCCG 1 TAGGAATTTGATCTTTCAAAAAGATATTAAGAGGAGGAAATTCTTGTTACCTGGCCCATTTTCCG 86663881 TTCAACTAAAAGGATAATAGCTAGCTT 66 TTCAACTAAAAGGATAATAGCTAGCTT 86663908 TGAAACAGTC Statistics Matches: 183, Mismatches: 4, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 95 183 1.00 ACGTcount: A:0.33, C:0.16, G:0.19, T:0.33 Consensus pattern (95 bp): TAGGAATTTGATCTTTCAAAAAGATATTAAGAGGAGGAAATTCTTGTTACCTGGCCCATTTTCCG TTCAACTAAAAGGATAATAGCTAGCTTCTG Found at i:86671282 original size:69 final size:69 Alignment explanation

Indices: 86671196--86671331 Score: 209 Period size: 69 Copynumber: 2.0 Consensus size: 69 86671186 CTGTTGTAAC * * * * 86671196 TTTTTGATGCTGTAAAATTTAACATATAGATTATGATATATAAGCTAATGAGATAATGCAACTTT 1 TTTTTGATGCTATAAAATTTAACATATAGATAATGACATATAAGCTAACGAGATAATGCAACTTT 86671261 TTAT 66 TTAT * * * 86671265 TTTTTGATGCTATAAAATTTAACATATAGATAATGGCATATAAGCTAACGAGATCATGTAACTTT 1 TTTTTGATGCTATAAAATTTAACATATAGATAATGACATATAAGCTAACGAGATAATGCAACTTT 86671330 TT 66 TT 86671332 GTTTATGTAT Statistics Matches: 60, Mismatches: 7, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 69 60 1.00 ACGTcount: A:0.38, C:0.09, G:0.13, T:0.40 Consensus pattern (69 bp): TTTTTGATGCTATAAAATTTAACATATAGATAATGACATATAAGCTAACGAGATAATGCAACTTT TTAT Found at i:86671826 original size:16 final size:16 Alignment explanation

Indices: 86671789--86671834 Score: 56 Period size: 16 Copynumber: 2.9 Consensus size: 16 86671779 TAAATTATTG ** 86671789 ATTACAACTCTATTTT 1 ATTACAACTCTATTCC * 86671805 AGTACAACTCTATTCC 1 ATTACAACTCTATTCC * 86671821 ATTACATCTCTATT 1 ATTACAACTCTATT 86671835 TCAATATAGC Statistics Matches: 25, Mismatches: 5, Indels: 0 0.83 0.17 0.00 Matches are distributed among these distances: 16 25 1.00 ACGTcount: A:0.30, C:0.24, G:0.02, T:0.43 Consensus pattern (16 bp): ATTACAACTCTATTCC Found at i:86676343 original size:16 final size:16 Alignment explanation

Indices: 86676320--86676367 Score: 60 Period size: 18 Copynumber: 2.9 Consensus size: 16 86676310 TTATATTAAA 86676320 TTTCTTATATATATTC 1 TTTCTTATATATATTC * * 86676336 TTTTTTATATATTACTTG 1 TTTCTTATATA-TA-TTC 86676354 TTTCTTATATATAT 1 TTTCTTATATATAT 86676368 ATTCATATAT Statistics Matches: 27, Mismatches: 3, Indels: 4 0.79 0.09 0.12 Matches are distributed among these distances: 16 11 0.41 17 4 0.15 18 12 0.44 ACGTcount: A:0.25, C:0.08, G:0.02, T:0.65 Consensus pattern (16 bp): TTTCTTATATATATTC Found at i:86676577 original size:27 final size:26 Alignment explanation

Indices: 86676526--86676577 Score: 61 Period size: 26 Copynumber: 2.0 Consensus size: 26 86676516 TCATACTATT * * 86676526 TATTTTAAATTGCTTTTTGTAATATC 1 TATTTTAAAGTGCTTTTTATAATATC 86676552 TATTTTAAACGTG-TTTTTATATATAT 1 TATTTTAAA-GTGCTTTTTATA-ATAT 86676578 TACTCATCTA Statistics Matches: 22, Mismatches: 2, Indels: 3 0.81 0.07 0.11 Matches are distributed among these distances: 26 16 0.73 27 6 0.27 ACGTcount: A:0.29, C:0.06, G:0.08, T:0.58 Consensus pattern (26 bp): TATTTTAAAGTGCTTTTTATAATATC Found at i:86676642 original size:26 final size:26 Alignment explanation

Indices: 86676613--86676722 Score: 80 Period size: 26 Copynumber: 4.3 Consensus size: 26 86676603 TCATTTTTTT * * 86676613 TATTTTTTATTTTAATTTGCTTTGTA 1 TATTATTTATTTTAATTTGCTTTATA * * * 86676639 TATTATTTGTTTTAAATTGTTTTATA 1 TATTATTTATTTTAATTTGCTTTATA * * * 86676665 CATTATTCATTTTAATTTG-TTT-CA 1 TATTATTTATTTTAATTTGCTTTATA * * * * * * 86676689 TACTAGTTACTTCAAGTTGTTTTATA 1 TATTATTTATTTTAATTTGCTTTATA 86676715 TATTATTT 1 TATTATTT 86676723 TGTTTCATTT Statistics Matches: 62, Mismatches: 20, Indels: 4 0.72 0.23 0.05 Matches are distributed among these distances: 24 13 0.21 25 6 0.10 26 43 0.69 ACGTcount: A:0.25, C:0.06, G:0.07, T:0.62 Consensus pattern (26 bp): TATTATTTATTTTAATTTGCTTTATA Found at i:86678223 original size:27 final size:27 Alignment explanation

Indices: 86678191--86678245 Score: 74 Period size: 27 Copynumber: 2.0 Consensus size: 27 86678181 CCTCCTCGCC * * 86678191 TCTTCTGATCAGGTAGTTTTTTTTTCT 1 TCTTCTAATCAGGTAGATTTTTTTTCT ** 86678218 TCTTCTAATCTTGTAGATTTTTTTTCT 1 TCTTCTAATCAGGTAGATTTTTTTTCT 86678245 T 1 T 86678246 TTTTCCCTGA Statistics Matches: 24, Mismatches: 4, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 27 24 1.00 ACGTcount: A:0.13, C:0.15, G:0.11, T:0.62 Consensus pattern (27 bp): TCTTCTAATCAGGTAGATTTTTTTTCT Found at i:86679199 original size:27 final size:26 Alignment explanation

Indices: 86679164--86679291 Score: 69 Period size: 27 Copynumber: 4.7 Consensus size: 26 86679154 GTATTGTTGC * 86679164 AGTGCGTTCAACACCCAGTGGTGTTTT 1 AGTGAGTTCAACA-CCAGTGGTGTTTT * * 86679191 AGTGAGTTCAA-ATGCCAGTGATGCTTT 1 AGTGAGTTCAACA--CCAGTGGTGTTTT ** ** 86679218 AGCCAGTTCGAACACCAGTGGTGTCGT 1 AGTGAGTTC-AACACCAGTGGTGTTTT * * * ** 86679245 AGCGAGTTTGAACAACAGTGGAATTTT 1 AGTGAG-TTCAACACCAGTGGTGTTTT * * 86679272 AGGGAGTTCAAAAACCAGTG 1 AGTGAGTTC-AACACCAGTG 86679292 TTATCAATGC Statistics Matches: 75, Mismatches: 21, Indels: 10 0.71 0.20 0.09 Matches are distributed among these distances: 26 3 0.04 27 67 0.89 28 4 0.05 29 1 0.01 ACGTcount: A:0.27, C:0.18, G:0.27, T:0.27 Consensus pattern (26 bp): AGTGAGTTCAACACCAGTGGTGTTTT Found at i:86679450 original size:81 final size:81 Alignment explanation

Indices: 86679299--86679496 Score: 218 Period size: 81 Copynumber: 2.4 Consensus size: 81 86679289 GTGTTATCAA * * ** * * *** 86679299 TGCTGATAGTGTTACAGCTAGTTTAAATGCTGGTAGTTTTGCTTCAAGTTCTAATGCTTTGGGTG 1 TGCTGATAGTGCTGCAGCTAGTTTAAATGCTGGTAGCATTGCCTCAAGTTCTAAAGCTTCCAGTG * 86679364 TTGCAATGAGTTCTAC 66 CTGCAATGAGTTCTAC * * * 86679380 TGCTGGTAGTGCTGCAGCTTGTTTTAATGCTGGTAGCATTGCCTCAAGTTCTAAAGCTTCCAGTG 1 TGCTGATAGTGCTGCAGCTAGTTTAAATGCTGGTAGCATTGCCTCAAGTTCTAAAGCTTCCAGTG 86679445 CTGCAATGAGTTCTAC 66 CTGCAATGAGTTCTAC * * * * * 86679461 TTCTGTTAGT-CTTGCGGGTAGTTTGAATGCTGGTAG 1 TGCTGATAGTGC-TGCAGCTAGTTTAAATGCTGGTAG 86679497 TGTTGCTGAA Statistics Matches: 97, Mismatches: 19, Indels: 2 0.82 0.16 0.02 Matches are distributed among these distances: 80 1 0.01 81 96 0.99 ACGTcount: A:0.19, C:0.16, G:0.26, T:0.38 Consensus pattern (81 bp): TGCTGATAGTGCTGCAGCTAGTTTAAATGCTGGTAGCATTGCCTCAAGTTCTAAAGCTTCCAGTG CTGCAATGAGTTCTAC Found at i:86681000 original size:93 final size:93 Alignment explanation

Indices: 86680841--86681120 Score: 434 Period size: 93 Copynumber: 3.0 Consensus size: 93 86680831 ATTACATGGT * * * * * 86680841 GGTGTTGCAACTCACGCAGAACATTTTATGCAAGCTAAAGAAACTGAGGCCAGTGTTGAGGCCCA 1 GGTGTTACAACTCATGCAGAACATTTTATGCAAGCTAAAGAAACTGAGCCCAGTGGTGAGGGCCA * 86680906 GGTTGCTTCTAAAATGATTTCTTCTGCG 66 GGTTGCTTCTAAAATGATTTCTTCTGCA * * 86680934 GGTGTTACAACTAATGCTGAACATTTTATGCAAGCTAAAGAAACTGAGCCCAGTGGTGAGGGCCA 1 GGTGTTACAACTCATGCAGAACATTTTATGCAAGCTAAAGAAACTGAGCCCAGTGGTGAGGGCCA * 86680999 GGTTGCTTCTCAAATGATTTCTTCTGCA 66 GGTTGCTTCTAAAATGATTTCTTCTGCA * * * * 86681027 GATGTTACAACTCATGCCGAGCATTTTATGCAAGCTAAAGAAACTGAGCCCAGTGGTGAGGGCCT 1 GGTGTTACAACTCATGCAGAACATTTTATGCAAGCTAAAGAAACTGAGCCCAGTGGTGAGGGCCA * 86681092 GGTTGCTTCTGAAATGATTTCTTCTGCA 66 GGTTGCTTCTAAAATGATTTCTTCTGCA 86681120 G 1 G 86681121 ACCATGATGT Statistics Matches: 172, Mismatches: 15, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 93 172 1.00 ACGTcount: A:0.27, C:0.20, G:0.25, T:0.29 Consensus pattern (93 bp): GGTGTTACAACTCATGCAGAACATTTTATGCAAGCTAAAGAAACTGAGCCCAGTGGTGAGGGCCA GGTTGCTTCTAAAATGATTTCTTCTGCA Found at i:86685941 original size:20 final size:21 Alignment explanation

Indices: 86685916--86685956 Score: 75 Period size: 20 Copynumber: 2.0 Consensus size: 21 86685906 GATTTTGCTA 86685916 AACGAACTTTGGG-ATTTAAG 1 AACGAACTTTGGGAATTTAAG 86685936 AACGAACTTTGGGAATTTAAG 1 AACGAACTTTGGGAATTTAAG 86685957 TACTATCTAT Statistics Matches: 20, Mismatches: 0, Indels: 1 0.95 0.00 0.05 Matches are distributed among these distances: 20 13 0.65 21 7 0.35 ACGTcount: A:0.37, C:0.10, G:0.24, T:0.29 Consensus pattern (21 bp): AACGAACTTTGGGAATTTAAG Found at i:86686845 original size:66 final size:66 Alignment explanation

Indices: 86686766--86686895 Score: 165 Period size: 66 Copynumber: 2.0 Consensus size: 66 86686756 TTAACTCACC ** * 86686766 TTTTCTCTTTATTAAGAAACTTCCAAAAAGAGATGTGATAAACA-AGAGGAGGATAGAGTGCAAA 1 TTTTCTCTTTATTAAGAAACTTCCAAAAAGAGACATGATAAACATA-AGGAGGATAGAATGCAAA 86686830 CA 65 CA * * * * 86686832 TTTTCT-TTCTATTAAGAAACTTGCAAGAAGGGACATTATAAACATAAGGAGGATAGAATGCAAA 1 TTTTCTCTT-TATTAAGAAACTTCCAAAAAGAGACATGATAAACATAAGGAGGATAGAATGCAAA 86686896 AAGAGAATTC Statistics Matches: 55, Mismatches: 7, Indels: 4 0.83 0.11 0.06 Matches are distributed among these distances: 65 2 0.04 66 52 0.95 67 1 0.02 ACGTcount: A:0.42, C:0.12, G:0.19, T:0.27 Consensus pattern (66 bp): TTTTCTCTTTATTAAGAAACTTCCAAAAAGAGACATGATAAACATAAGGAGGATAGAATGCAAAC A Found at i:86688246 original size:11 final size:11 Alignment explanation

Indices: 86688230--86688255 Score: 52 Period size: 11 Copynumber: 2.4 Consensus size: 11 86688220 GTTAAATCAA 86688230 CTTATAATACT 1 CTTATAATACT 86688241 CTTATAATACT 1 CTTATAATACT 86688252 CTTA 1 CTTA 86688256 GCGTGTTCGA Statistics Matches: 15, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 11 15 1.00 ACGTcount: A:0.35, C:0.19, G:0.00, T:0.46 Consensus pattern (11 bp): CTTATAATACT Found at i:86688645 original size:60 final size:59 Alignment explanation

Indices: 86688576--86688695 Score: 222 Period size: 60 Copynumber: 2.0 Consensus size: 59 86688566 TTTCAAAACA 86688576 AAGGATTTTTGTGTGTTCCAAGGGTAACAGTTCAATATTATACATATTTTTCAATTATC 1 AAGGATTTTTGTGTGTTCCAAGGGTAACAGTTCAATATTATACATATTTTTCAATTATC * 86688635 AAGGAATTTTTGTGTGTTCCAAGGGTAACAGTTCAATATTATACATATTTTTCAGTTATC 1 AAGG-ATTTTTGTGTGTTCCAAGGGTAACAGTTCAATATTATACATATTTTTCAATTATC 86688695 A 1 A 86688696 TGGTGTTAGG Statistics Matches: 59, Mismatches: 1, Indels: 1 0.97 0.02 0.02 Matches are distributed among these distances: 59 4 0.07 60 55 0.93 ACGTcount: A:0.31, C:0.12, G:0.16, T:0.42 Consensus pattern (59 bp): AAGGATTTTTGTGTGTTCCAAGGGTAACAGTTCAATATTATACATATTTTTCAATTATC Found at i:86693996 original size:31 final size:32 Alignment explanation

Indices: 86693961--86694028 Score: 120 Period size: 31 Copynumber: 2.2 Consensus size: 32 86693951 CTATTAAACT * 86693961 AATTTATTTGTATTTGTAAAGCATGAGCTT-A 1 AATTTATTTGCATTTGTAAAGCATGAGCTTGA 86693992 AATTTATTTGCATTTGTAAAGCATGAGCTTGA 1 AATTTATTTGCATTTGTAAAGCATGAGCTTGA 86694024 AATTT 1 AATTT 86694029 TGAAATCTCC Statistics Matches: 35, Mismatches: 1, Indels: 1 0.95 0.03 0.03 Matches are distributed among these distances: 31 29 0.83 32 6 0.17 ACGTcount: A:0.32, C:0.07, G:0.16, T:0.44 Consensus pattern (32 bp): AATTTATTTGCATTTGTAAAGCATGAGCTTGA Found at i:86698393 original size:21 final size:21 Alignment explanation

Indices: 86698367--86698428 Score: 124 Period size: 21 Copynumber: 3.0 Consensus size: 21 86698357 CGGGTGGATC 86698367 AGCTCTTATGAGCTTCTATTA 1 AGCTCTTATGAGCTTCTATTA 86698388 AGCTCTTATGAGCTTCTATTA 1 AGCTCTTATGAGCTTCTATTA 86698409 AGCTCTTATGAGCTTCTATT 1 AGCTCTTATGAGCTTCTATT 86698429 GGCGTGTTTC Statistics Matches: 41, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 21 41 1.00 ACGTcount: A:0.23, C:0.19, G:0.15, T:0.44 Consensus pattern (21 bp): AGCTCTTATGAGCTTCTATTA Found at i:86698489 original size:40 final size:40 Alignment explanation

Indices: 86698340--86698506 Score: 126 Period size: 40 Copynumber: 4.2 Consensus size: 40 86698330 GCGTTATACT * * * 86698340 TTCTGTTTGGCGTGTTTCGGGTGGATCAGCTCTTATGAGC 1 TTCTGTTTGGCGTCTTTCGGGTGAATAAGCTCTTATGAGC * ** * * * 86698380 TTCTATTAAGC-TCTTAT-GAGCTTCTATTAAGCTCTTATGAGC 1 TTCTGTTTGGCGTCTT-TCG-G-GT-GAATAAGCTCTTATGAGC * * * 86698422 TTCT-ATTGGCGTGTTTCGGGTGGATAAGCTCTTATGAGC 1 TTCTGTTTGGCGTCTTTCGGGTGAATAAGCTCTTATGAGC * * * 86698461 TTCTGTTTGGCGTACTTT-TGTTGAATAAGCTTTTATGAGC 1 TTCTGTTTGGCGT-CTTTCGGGTGAATAAGCTCTTATGAGC 86698501 TTCTGT 1 TTCTGT 86698507 CTGGTATGTT Statistics Matches: 96, Mismatches: 23, Indels: 16 0.71 0.17 0.12 Matches are distributed among these distances: 39 23 0.24 40 42 0.44 41 9 0.09 42 22 0.23 ACGTcount: A:0.16, C:0.16, G:0.25, T:0.43 Consensus pattern (40 bp): TTCTGTTTGGCGTCTTTCGGGTGAATAAGCTCTTATGAGC Found at i:86699604 original size:20 final size:20 Alignment explanation

Indices: 86699579--86699621 Score: 59 Period size: 20 Copynumber: 2.1 Consensus size: 20 86699569 TCCCTACAAT * * * 86699579 CTAAAATTTTCAACTTTTTC 1 CTAAAATTTCCAAATGTTTC 86699599 CTAAAATTTCCAAATGTTTC 1 CTAAAATTTCCAAATGTTTC 86699619 CTA 1 CTA 86699622 TTTAGTCCCG Statistics Matches: 20, Mismatches: 3, Indels: 0 0.87 0.13 0.00 Matches are distributed among these distances: 20 20 1.00 ACGTcount: A:0.33, C:0.21, G:0.02, T:0.44 Consensus pattern (20 bp): CTAAAATTTCCAAATGTTTC Found at i:86712232 original size:9 final size:10 Alignment explanation

Indices: 86712213--86712237 Score: 50 Period size: 10 Copynumber: 2.5 Consensus size: 10 86712203 CTATAATATC 86712213 TTTTTGTTTT 1 TTTTTGTTTT 86712223 TTTTTGTTTT 1 TTTTTGTTTT 86712233 TTTTT 1 TTTTT 86712238 TCTTTCCCTT Statistics Matches: 15, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 10 15 1.00 ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92 Consensus pattern (10 bp): TTTTTGTTTT Found at i:86730995 original size:31 final size:31 Alignment explanation

Indices: 86730959--86731026 Score: 109 Period size: 31 Copynumber: 2.2 Consensus size: 31 86730949 CTGCACCGAG 86730959 GCCTTTTCATAAATCATATCACTGGGCCAAA 1 GCCTTTTCATAAATCATATCACTGGGCCAAA * * * 86730990 GCCTTTTCATAAATCATTTCACTGGGTCGAA 1 GCCTTTTCATAAATCATATCACTGGGCCAAA 86731021 GCCTTT 1 GCCTTT 86731027 ACTGTAAACG Statistics Matches: 34, Mismatches: 3, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 31 34 1.00 ACGTcount: A:0.26, C:0.25, G:0.15, T:0.34 Consensus pattern (31 bp): GCCTTTTCATAAATCATATCACTGGGCCAAA Found at i:86731101 original size:42 final size:42 Alignment explanation

Indices: 86731054--86731141 Score: 131 Period size: 42 Copynumber: 2.1 Consensus size: 42 86731044 CCATAGGTCA * ** * 86731054 ATTTCAATATCACATGTAATGTCAATGGATGTATGCAAGCCC 1 ATTTCAATATCACATGAAATACCAATGAATGTATGCAAGCCC * 86731096 ATTTCAATATCACGTGAAATACCAATGAATGTATGCAAGCCC 1 ATTTCAATATCACATGAAATACCAATGAATGTATGCAAGCCC 86731138 ATTT 1 ATTT 86731142 GGGGAGACTA Statistics Matches: 41, Mismatches: 5, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 42 41 1.00 ACGTcount: A:0.35, C:0.19, G:0.15, T:0.31 Consensus pattern (42 bp): ATTTCAATATCACATGAAATACCAATGAATGTATGCAAGCCC Found at i:86731334 original size:26 final size:26 Alignment explanation

Indices: 86731298--86731432 Score: 216 Period size: 26 Copynumber: 5.2 Consensus size: 26 86731288 CTAGGGCAAA 86731298 CTTTTCGATAAACTGGGGCATAAGCC 1 CTTTTCGATAAACTGGGGCATAAGCC * * 86731324 CTTTTCAATAAACTGGGGCATAAACC 1 CTTTTCGATAAACTGGGGCATAAGCC * 86731350 CTTTTCGGTAAACTGGGGCATAAGCC 1 CTTTTCGATAAACTGGGGCATAAGCC * 86731376 CTTTTCAATAAACTGGGGCATAAGCC 1 CTTTTCGATAAACTGGGGCATAAGCC * 86731402 CTTTTCGGTAAACTGGGGCATAAGCC 1 CTTTTCGATAAACTGGGGCATAAGCC * 86731428 ATTTT 1 CTTTT 86731433 GCACTTCCTC Statistics Matches: 99, Mismatches: 10, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 26 99 1.00 ACGTcount: A:0.27, C:0.22, G:0.21, T:0.29 Consensus pattern (26 bp): CTTTTCGATAAACTGGGGCATAAGCC Found at i:86731356 original size:52 final size:52 Alignment explanation

Indices: 86731298--86731432 Score: 243 Period size: 52 Copynumber: 2.6 Consensus size: 52 86731288 CTAGGGCAAA * 86731298 CTTTTCGATAAACTGGGGCATAAGCCCTTTTCAATAAACTGGGGCATAAACC 1 CTTTTCGGTAAACTGGGGCATAAGCCCTTTTCAATAAACTGGGGCATAAACC * 86731350 CTTTTCGGTAAACTGGGGCATAAGCCCTTTTCAATAAACTGGGGCATAAGCC 1 CTTTTCGGTAAACTGGGGCATAAGCCCTTTTCAATAAACTGGGGCATAAACC * 86731402 CTTTTCGGTAAACTGGGGCATAAGCCATTTT 1 CTTTTCGGTAAACTGGGGCATAAGCCCTTTT 86731433 GCACTTCCTC Statistics Matches: 80, Mismatches: 3, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 52 80 1.00 ACGTcount: A:0.27, C:0.22, G:0.21, T:0.29 Consensus pattern (52 bp): CTTTTCGGTAAACTGGGGCATAAGCCCTTTTCAATAAACTGGGGCATAAACC Found at i:86733232 original size:31 final size:31 Alignment explanation

Indices: 86733194--86733263 Score: 122 Period size: 31 Copynumber: 2.3 Consensus size: 31 86733184 TATTGCGCCG 86733194 AAGCCTTTTCATAAATCATATCACTGGGCCA 1 AAGCCTTTTCATAAATCATATCACTGGGCCA * * 86733225 AAGCCTTTTCATAAATCATTTCACTGGGCCG 1 AAGCCTTTTCATAAATCATATCACTGGGCCA 86733256 AAGCCTTT 1 AAGCCTTT 86733264 ACTGTAAACG Statistics Matches: 37, Mismatches: 2, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 31 37 1.00 ACGTcount: A:0.29, C:0.26, G:0.14, T:0.31 Consensus pattern (31 bp): AAGCCTTTTCATAAATCATATCACTGGGCCA Found at i:86733338 original size:42 final size:42 Alignment explanation

Indices: 86733291--86733378 Score: 122 Period size: 42 Copynumber: 2.1 Consensus size: 42 86733281 CCATAGGCCA * * ** * 86733291 ATTTCAATATCATATGTAATGTCAATGGATGTATGCAAGCCC 1 ATTTCAATATCACATGAAATACCAATGAATGTATGCAAGCCC * 86733333 ATTTCAATATCACGTGAAATACCAATGAATGTATGCAAGCCC 1 ATTTCAATATCACATGAAATACCAATGAATGTATGCAAGCCC 86733375 ATTT 1 ATTT 86733379 GGGGAGACTA Statistics Matches: 40, Mismatches: 6, Indels: 0 0.87 0.13 0.00 Matches are distributed among these distances: 42 40 1.00 ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32 Consensus pattern (42 bp): ATTTCAATATCACATGAAATACCAATGAATGTATGCAAGCCC Done.