Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: A06

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: 121513442
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31

Warning! 5870000 characters in sequence are not A, C, G, or T


File 249 of 366

Found at i:83926061 original size:29 final size:28

Alignment explanation

Indices: 83926019--83926090 Score: 99 Period size: 29 Copynumber: 2.5 Consensus size: 28 83926009 CATTGGTTTT 83926019 AAAAGATATTTATTGAGATTATGAATGAG 1 AAAA-ATATTTATTGAGATTATGAATGAG * 83926048 AAAAATATTCTATTGAGATTGTGAATGAG 1 AAAAATATT-TATTGAGATTATGAATGAG * 83926077 GAAAATATTATATT 1 AAAAATATT-TATT 83926091 TCATATGAAT Statistics Matches: 39, Mismatches: 3, Indels: 2 0.89 0.07 0.05 Matches are distributed among these distances: 28 5 0.13 29 34 0.87 ACGTcount: A:0.44, C:0.01, G:0.18, T:0.36 Consensus pattern (28 bp): AAAAATATTTATTGAGATTATGAATGAG Found at i:83929346 original size:25 final size:26 Alignment explanation

Indices: 83929318--83929398 Score: 83 Period size: 29 Copynumber: 3.0 Consensus size: 26 83929308 TTTGACAGAT * 83929318 TAAAAAAATTAAGAGTTGAAAA-AAA 1 TAAAAAAATTAAGTGTTGAAAATAAA * 83929343 TAAAAGATAAATAAGTGTTGAAAAATAAA 1 TAAAA-A-AATTAAGTGTTG-AAAATAAA * 83929372 TATTAAAAAATTAAGTGTTGAATATAA 1 TA--AAAAAATTAAGTGTTGAAAATAA 83929399 GTTATAAAAT Statistics Matches: 46, Mismatches: 4, Indels: 9 0.78 0.07 0.15 Matches are distributed among these distances: 25 5 0.11 26 1 0.02 27 10 0.22 28 10 0.22 29 16 0.35 30 1 0.02 31 3 0.07 ACGTcount: A:0.60, C:0.00, G:0.12, T:0.27 Consensus pattern (26 bp): TAAAAAAATTAAGTGTTGAAAATAAA Found at i:83929370 original size:14 final size:14 Alignment explanation

Indices: 83929351--83929393 Score: 50 Period size: 14 Copynumber: 3.0 Consensus size: 14 83929341 AATAAAAGAT 83929351 AAATAAGTGTTGAA 1 AAATAAGTGTTGAA * * * 83929365 AAATAAATATTAAA 1 AAATAAGTGTTGAA 83929379 AAATTAAGTGTTGAA 1 AAA-TAAGTGTTGAA 83929394 TATAAGTTAT Statistics Matches: 22, Mismatches: 6, Indels: 1 0.76 0.21 0.03 Matches are distributed among these distances: 14 14 0.64 15 8 0.36 ACGTcount: A:0.56, C:0.00, G:0.14, T:0.30 Consensus pattern (14 bp): AAATAAGTGTTGAA Found at i:83934672 original size:59 final size:59 Alignment explanation

Indices: 83934500--83934673 Score: 258 Period size: 59 Copynumber: 2.9 Consensus size: 59 83934490 CAGATCATAG * * 83934500 AATCACATGCCTTTCAACGGGGCTACTCAAAAGCACCCAGACCCTAGCATGTATCACAT 1 AATCACATGCCTCTCAACGGGGCTACTCAAAAGCACCCAGACCCTAGCATGTATTACAT * * * * * 83934559 ATTCACATCCCTCTCAACGGGGCTACTCAAAAGCATCTAGACCCTAGCATGTATTACTT 1 AATCACATGCCTCTCAACGGGGCTACTCAAAAGCACCCAGACCCTAGCATGTATTACAT * * * 83934618 AATCACATGCCTCTCAACGGTGCTACTTAAAAGCACCCAAACCCTAGCATGTATTA 1 AATCACATGCCTCTCAACGGGGCTACTCAAAAGCACCCAGACCCTAGCATGTATTA 83934674 GGTATCAATT Statistics Matches: 101, Mismatches: 14, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 59 101 1.00 ACGTcount: A:0.32, C:0.31, G:0.14, T:0.24 Consensus pattern (59 bp): AATCACATGCCTCTCAACGGGGCTACTCAAAAGCACCCAGACCCTAGCATGTATTACAT Found at i:83943625 original size:14 final size:14 Alignment explanation

Indices: 83943606--83943641 Score: 63 Period size: 14 Copynumber: 2.6 Consensus size: 14 83943596 TTGATATTTT 83943606 GAAATTTCGAGGAC 1 GAAATTTCGAGGAC 83943620 GAAATTTCGAGGAC 1 GAAATTTCGAGGAC * 83943634 AAAATTTC 1 GAAATTTC 83943642 TTTAAGGGGA Statistics Matches: 21, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 14 21 1.00 ACGTcount: A:0.39, C:0.14, G:0.22, T:0.25 Consensus pattern (14 bp): GAAATTTCGAGGAC Found at i:83951541 original size:105 final size:105 Alignment explanation

Indices: 83951415--83951673 Score: 457 Period size: 105 Copynumber: 2.5 Consensus size: 105 83951405 GTGTGCTTGA * * 83951415 GCCGTGTGGGTCACACGGGCAAGGACATGAGCATGTGTCCAGGCCGTGTAACTCACTGTTTACAT 1 GCCGTGTGAGTTACACGGGCAAGGACATGAGCATGTGTCCAGGCCGTGTAACTCACTGTTTACAT 83951480 TTTTAAACCATATGGGCAGAGGATATGGACTTGTACCCAG 66 TTTTAAACCATATGGGCAGAGGATATGGACTTGTACCCAG 83951520 GCCGTGTGAGTTACACGGGCAAGGACATGAGCATGTGTCCAGGCCGTGTAACTCACTGTTTACAT 1 GCCGTGTGAGTTACACGGGCAAGGACATGAGCATGTGTCCAGGCCGTGTAACTCACTGTTTACAT 83951585 TTTTAAACCATATGGGCAGAGGATATGGACTTGTACCCAG 66 TTTTAAACCATATGGGCAGAGGATATGGACTTGTACCCAG * ** 83951625 GCCGTGTGAGTTACACGGGTAAGGACAT-AGGTGTGTGTCCAGGCCGTGT 1 GCCGTGTGAGTTACACGGGCAAGGACATGA-GCATGTGTCCAGGCCGTGT 83951674 GACCCACACG Statistics Matches: 148, Mismatches: 5, Indels: 2 0.95 0.03 0.01 Matches are distributed among these distances: 104 1 0.01 105 147 0.99 ACGTcount: A:0.24, C:0.21, G:0.30, T:0.25 Consensus pattern (105 bp): GCCGTGTGAGTTACACGGGCAAGGACATGAGCATGTGTCCAGGCCGTGTAACTCACTGTTTACAT TTTTAAACCATATGGGCAGAGGATATGGACTTGTACCCAG Found at i:83951704 original size:42 final size:42 Alignment explanation

Indices: 83951621--83951716 Score: 113 Period size: 42 Copynumber: 2.3 Consensus size: 42 83951611 GGACTTGTAC *** ** 83951621 CCAGGCCGTGTGAGTTACACGGGTAAGGACATAGGTGTGTGT 1 CCAGGCCGTGTGACCCACACGGGTAAGGACATAGGCATGTGT 83951663 CCAGGCCGTGTGACCCACACGGGTAAGGACAT-GAGCATGTGT 1 CCAGGCCGTGTGACCCACACGGGTAAGGACATAG-GCATGTGT * * 83951705 CCATGCTGTGTG 1 CCAGGCCGTGTG 83951717 GCATATGAAT Statistics Matches: 46, Mismatches: 7, Indels: 2 0.84 0.13 0.04 Matches are distributed among these distances: 41 1 0.02 42 45 0.98 ACGTcount: A:0.21, C:0.22, G:0.35, T:0.22 Consensus pattern (42 bp): CCAGGCCGTGTGACCCACACGGGTAAGGACATAGGCATGTGT Found at i:83959678 original size:104 final size:102 Alignment explanation

Indices: 83959568--83959755 Score: 236 Period size: 102 Copynumber: 1.8 Consensus size: 102 83959558 CATTTCAAGA * * * 83959568 CTTTTTTT-AATCTATTTTTTTATAATTAAATTTTTAAAAAGATAATATTTTA-TTTGGTGGAGC 1 CTTTTTTTAAATCTATTTTTTAAT-ATAAAAATTTT-AAAA-ATAATATTTTATTTTGGTGGAGC 83959631 CATTCTAAATGGCGCCACCACTTTATTACTAGTGTAATTT 63 CATTCTAAATGGCGCCACCACTTTATTACTAGTGTAATTT * * * * * 83959671 CTTTTTTTAAATGTGTTTTTTAATCTAAAAATTTTAAAAATGATATTTTATTTTGGTGGAGTCAT 1 CTTTTTTTAAATCTATTTTTTAATATAAAAATTTTAAAAATAATATTTTATTTTGGTGGAGCCAT ** * 83959736 TCTTTATGGCTCCACCACTT 66 TCTAAATGGCGCCACCACTT 83959756 GGTTCTTCAA Statistics Matches: 72, Mismatches: 11, Indels: 5 0.82 0.12 0.06 Matches are distributed among these distances: 101 10 0.14 102 34 0.47 103 16 0.22 104 12 0.17 ACGTcount: A:0.29, C:0.12, G:0.11, T:0.48 Consensus pattern (102 bp): CTTTTTTTAAATCTATTTTTTAATATAAAAATTTTAAAAATAATATTTTATTTTGGTGGAGCCAT TCTAAATGGCGCCACCACTTTATTACTAGTGTAATTT Found at i:83961305 original size:38 final size:36 Alignment explanation

Indices: 83961263--83961403 Score: 124 Period size: 38 Copynumber: 3.8 Consensus size: 36 83961253 ATTGTAATGT * 83961263 TATTCGGGCTAC-GTGCCTAGCAGGCTTTACACTGGTGA 1 TATTCGGGCT-CTGTGCCTAGCAGGCTTTAC-C-AGTGA * * * * 83961301 TATTCGAGCTCTGTGCCTAACAGGCTGAGTGCCAGTGA 1 TATTCGGGCTCTGTGCCTAGCAGGCT--TTACCAGTGA * 83961339 TATTCGGGCTCTGTGCCTAGCAGGCTTTGTGCCAGT-A 1 TATTCGGGCTCTGTGCCTAGCAGGC-TT-TACCAGTGA * * 83961376 TTATTCGAGCTCTGTGCCTACCAGGCTT 1 -TATTCGGGCTCTGTGCCTAGCAGGCTT 83961404 CGTGCCGGTG Statistics Matches: 87, Mismatches: 10, Indels: 13 0.79 0.09 0.12 Matches are distributed among these distances: 37 4 0.05 38 79 0.91 39 2 0.02 40 2 0.02 ACGTcount: A:0.17, C:0.25, G:0.28, T:0.30 Consensus pattern (36 bp): TATTCGGGCTCTGTGCCTAGCAGGCTTTACCAGTGA Found at i:83961409 original size:38 final size:38 Alignment explanation

Indices: 83961297--83961409 Score: 156 Period size: 38 Copynumber: 3.0 Consensus size: 38 83961287 CTTTACACTG * 83961297 GTGATATTCGAGCTCTGTGCCTAACAGGCTGAGTGCCA 1 GTGATATTCGAGCTCTGTGCCTAACAGGCTTAGTGCCA * * * 83961335 GTGATATTCGGGCTCTGTGCCTAGCAGGCTTTGTGCCA 1 GTGATATTCGAGCTCTGTGCCTAACAGGCTTAGTGCCA * * 83961373 GT-ATTATTCGAGCTCTGTGCCTACCAGGCTTCGTGCC 1 GTGA-TATTCGAGCTCTGTGCCTAACAGGCTTAGTGCC 83961410 GGTGTAACTG Statistics Matches: 67, Mismatches: 7, Indels: 2 0.88 0.09 0.03 Matches are distributed among these distances: 37 1 0.01 38 66 0.99 ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30 Consensus pattern (38 bp): GTGATATTCGAGCTCTGTGCCTAACAGGCTTAGTGCCA Found at i:83964771 original size:46 final size:44 Alignment explanation

Indices: 83964687--83964807 Score: 136 Period size: 46 Copynumber: 2.7 Consensus size: 44 83964677 ATATCCGTGT * 83964687 CGATGCCATGTCCCAGACATCATCTTACACTGACACATCTC-ATAGC 1 CGATG-CATGTCCCAGACAT-GTCTTACACTGACACATCTCGA-AGC * * * 83964733 CGATGCACGTCCCAGACATGTCTTACACTGGCTTACATCTCGAGGC 1 CGATGCATGTCCCAGACATGTCTTACACTGAC--ACATCTCGAAGC * * 83964779 CGATGCGTGTCCTAGACATGTCTTACACT 1 CGATGCATGTCCCAGACATGTCTTACACT 83964808 AGCTCTCGTC Statistics Matches: 65, Mismatches: 7, Indels: 6 0.83 0.09 0.08 Matches are distributed among these distances: 44 11 0.17 45 13 0.20 46 40 0.62 47 1 0.02 ACGTcount: A:0.24, C:0.32, G:0.18, T:0.26 Consensus pattern (44 bp): CGATGCATGTCCCAGACATGTCTTACACTGACACATCTCGAAGC Found at i:83968480 original size:22 final size:22 Alignment explanation

Indices: 83968452--83968495 Score: 79 Period size: 22 Copynumber: 2.0 Consensus size: 22 83968442 TATGTAACCT 83968452 ATAGTTCAAATTCAACAGAACA 1 ATAGTTCAAATTCAACAGAACA * 83968474 ATAGTTCAAATTCAATAGAACA 1 ATAGTTCAAATTCAACAGAACA 83968496 TCACATATAG Statistics Matches: 21, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 22 21 1.00 ACGTcount: A:0.50, C:0.16, G:0.09, T:0.25 Consensus pattern (22 bp): ATAGTTCAAATTCAACAGAACA Found at i:83979640 original size:47 final size:47 Alignment explanation

Indices: 83979589--83979725 Score: 213 Period size: 47 Copynumber: 2.9 Consensus size: 47 83979579 TTAGGATTTT 83979589 ATGTGATGAATGTGAACATGAGTATGTGTGATAAGGCCGAATGACCA 1 ATGTGATGAATGTGAACATGAGTATGTGTGATAAGGCCGAATGACCA * * * 83979636 ATGTGATGAATGTGAGCATGCGTATGTGTGATAAGGCCGAATGGCCA 1 ATGTGATGAATGTGAACATGAGTATGTGTGATAAGGCCGAATGACCA * * 83979683 ATGTGATGAATGTGAACATGTA-TATATGTGGTAAGGCCGAATG 1 ATGTGATGAATGTGAACATG-AGTATGTGTGATAAGGCCGAATG 83979726 GCTAATGCGA Statistics Matches: 82, Mismatches: 7, Indels: 2 0.90 0.08 0.02 Matches are distributed among these distances: 47 82 1.00 ACGTcount: A:0.31, C:0.10, G:0.31, T:0.27 Consensus pattern (47 bp): ATGTGATGAATGTGAACATGAGTATGTGTGATAAGGCCGAATGACCA Found at i:83979772 original size:46 final size:46 Alignment explanation

Indices: 83979706--83979796 Score: 137 Period size: 46 Copynumber: 2.0 Consensus size: 46 83979696 GAACATGTAT * * * 83979706 ATATGTGGTAAGGCCGAATGGCTAATGCGAAATGTGTATGAGATGG 1 ATATGTGGTAAAGCCAAATGGCTAATGCGAAATATGTATGAGATGG * * 83979752 ATATGTGGTAAAGCCAAATGGCTAATGTGAGATATGTATGAGATG 1 ATATGTGGTAAAGCCAAATGGCTAATGCGAAATATGTATGAGATG 83979797 TGTATATATA Statistics Matches: 40, Mismatches: 5, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 46 40 1.00 ACGTcount: A:0.33, C:0.08, G:0.32, T:0.27 Consensus pattern (46 bp): ATATGTGGTAAAGCCAAATGGCTAATGCGAAATATGTATGAGATGG Found at i:83983210 original size:35 final size:35 Alignment explanation

Indices: 83983171--83983275 Score: 129 Period size: 35 Copynumber: 3.0 Consensus size: 35 83983161 TACATATGAC * 83983171 CGAATACACAAATTCAATATAAACTCACATGTAAT 1 CGAATATACAAATTCAATATAAACTCACATGTAAT * * * * * 83983206 CGAATATTCAAATTCAACATAACCTCACATGCAAC 1 CGAATATACAAATTCAATATAAACTCACATGTAAT * * * 83983241 CGAATATACAAGTTCAATATAAGCTTACATGTAAT 1 CGAATATACAAATTCAATATAAACTCACATGTAAT 83983276 TACCTATGTG Statistics Matches: 57, Mismatches: 13, Indels: 0 0.81 0.19 0.00 Matches are distributed among these distances: 35 57 1.00 ACGTcount: A:0.45, C:0.21, G:0.08, T:0.27 Consensus pattern (35 bp): CGAATATACAAATTCAATATAAACTCACATGTAAT Found at i:83988229 original size:21 final size:22 Alignment explanation

Indices: 83988186--83988229 Score: 56 Period size: 21 Copynumber: 2.0 Consensus size: 22 83988176 CTTTCGGACG * 83988186 TCGTAACTCGATCGATTCATGC 1 TCGTAACACGATCGATTCATGC 83988208 TCGTAACAC-ATC-ATTCCATGC 1 TCGTAACACGATCGATT-CATGC 83988229 T 1 T 83988230 AAATTCAATT Statistics Matches: 20, Mismatches: 1, Indels: 3 0.83 0.04 0.12 Matches are distributed among these distances: 20 3 0.15 21 9 0.45 22 8 0.40 ACGTcount: A:0.25, C:0.30, G:0.14, T:0.32 Consensus pattern (22 bp): TCGTAACACGATCGATTCATGC Found at i:83989260 original size:15 final size:13 Alignment explanation

Indices: 83989227--83989251 Score: 50 Period size: 13 Copynumber: 1.9 Consensus size: 13 83989217 AAAAACGCTA 83989227 AAATTTTCACACG 1 AAATTTTCACACG 83989240 AAATTTTCACAC 1 AAATTTTCACAC 83989252 ATATAATTTA Statistics Matches: 12, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 12 1.00 ACGTcount: A:0.40, C:0.24, G:0.04, T:0.32 Consensus pattern (13 bp): AAATTTTCACACG Found at i:83996618 original size:26 final size:26 Alignment explanation

Indices: 83996586--83996637 Score: 95 Period size: 26 Copynumber: 2.0 Consensus size: 26 83996576 GGAATTGATG * 83996586 ATTGTTTAATGCTCTGAAATAGGATT 1 ATTGTTTAATGCTCCGAAATAGGATT 83996612 ATTGTTTAATGCTCCGAAATAGGATT 1 ATTGTTTAATGCTCCGAAATAGGATT 83996638 TGTGTATCGA Statistics Matches: 25, Mismatches: 1, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 26 25 1.00 ACGTcount: A:0.31, C:0.10, G:0.19, T:0.40 Consensus pattern (26 bp): ATTGTTTAATGCTCCGAAATAGGATT Found at i:83999245 original size:23 final size:23 Alignment explanation

Indices: 83999219--83999302 Score: 134 Period size: 23 Copynumber: 3.7 Consensus size: 23 83999209 CGTAAAAGTG * * 83999219 TACTGTTTTAGCTCAATAGAGCT 1 TACTGTTTCAGCTCGATAGAGCT 83999242 TACTGTTTCAGCTCGATAGAGCT 1 TACTGTTTCAGCTCGATAGAGCT * 83999265 TACCGTTTCAGCTCGATAGAGCT 1 TACTGTTTCAGCTCGATAGAGCT 83999288 TACTG-TTCAGCTCGA 1 TACTGTTTCAGCTCGA 83999303 AGGAACTTGC Statistics Matches: 57, Mismatches: 4, Indels: 1 0.92 0.06 0.02 Matches are distributed among these distances: 22 10 0.18 23 47 0.82 ACGTcount: A:0.23, C:0.23, G:0.20, T:0.35 Consensus pattern (23 bp): TACTGTTTCAGCTCGATAGAGCT Found at i:84018642 original size:12 final size:12 Alignment explanation

Indices: 84018625--84018649 Score: 50 Period size: 12 Copynumber: 2.1 Consensus size: 12 84018615 TGGTCGTGTG 84018625 TGGCACACAGGC 1 TGGCACACAGGC 84018637 TGGCACACAGGC 1 TGGCACACAGGC 84018649 T 1 T 84018650 TGTGGTCGAC 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:0.24, C:0.32, G:0.32, T:0.12 Consensus pattern (12 bp): TGGCACACAGGC Found at i:84018978 original size:24 final size:23 Alignment explanation

Indices: 84018937--84018984 Score: 60 Period size: 24 Copynumber: 2.0 Consensus size: 23 84018927 TTTGTATTGA * 84018937 AAATGAATGATCTATGATTTTTG 1 AAATGAATGATCTATGATATTTG * * 84018960 AAATGAGATGATTTTTGATATTTG 1 AAATGA-ATGATCTATGATATTTG 84018984 A 1 A 84018985 TTGTTCTGTT Statistics Matches: 21, Mismatches: 3, Indels: 1 0.84 0.12 0.04 Matches are distributed among these distances: 23 6 0.29 24 15 0.71 ACGTcount: A:0.35, C:0.02, G:0.19, T:0.44 Consensus pattern (23 bp): AAATGAATGATCTATGATATTTG Found at i:84020411 original size:16 final size:15 Alignment explanation

Indices: 84020395--84020424 Score: 51 Period size: 15 Copynumber: 2.0 Consensus size: 15 84020385 AATTAATTTA 84020395 AAAATATTTTTTATT 1 AAAATATTTTTTATT * 84020410 AAATTATTTTTTATT 1 AAAATATTTTTTATT 84020425 TAAGTTAAAT Statistics Matches: 14, Mismatches: 1, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 15 14 1.00 ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63 Consensus pattern (15 bp): AAAATATTTTTTATT Found at i:84025495 original size:26 final size:26 Alignment explanation

Indices: 84025456--84025563 Score: 180 Period size: 26 Copynumber: 4.2 Consensus size: 26 84025446 TGATACAAAT * 84025456 TGATAGTGGGTTAGGTAAATGTTCCA 1 TGATAATGGGTTAGGTAAATGTTCCA * * 84025482 TGATAATGGATTAGGTAAATATTCCA 1 TGATAATGGGTTAGGTAAATGTTCCA 84025508 TGATAATGGGTTAGGTAAATGTTCCA 1 TGATAATGGGTTAGGTAAATGTTCCA * 84025534 TGATAATGGTTTAGGTAAATGTTCCA 1 TGATAATGGGTTAGGTAAATGTTCCA 84025560 TGAT 1 TGAT 84025564 GGGCATTTCA Statistics Matches: 76, Mismatches: 6, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 26 76 1.00 ACGTcount: A:0.31, C:0.07, G:0.25, T:0.36 Consensus pattern (26 bp): TGATAATGGGTTAGGTAAATGTTCCA Found at i:84029543 original size:50 final size:50 Alignment explanation

Indices: 84029423--84029714 Score: 329 Period size: 50 Copynumber: 5.9 Consensus size: 50 84029413 AGGGTAAGGA * * * ** * * * 84029423 GCCGACGCCATGTCCCGGACATGGTCTTAGAC--GGGCTCATACATCAAA 1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATATCGAG * * * * * 84029471 GTCGATGCCATGTTCCAGACATGGTCTTACA-TTGACTCTCGTATATCAAG 1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAG-CTCTCATATATCGAG * * * * * * 84029521 GCCAATGTCATGTCCCAAACATGGTCTTACACTAGCTTTCATCTATCGAT 1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATATCGAG * * 84029571 GCCGATGCCATGTCCCAAACATGGTCTTACACTAGCTCTCATATCTCGAG 1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATATCGAG * * 84029621 GCCGATGCTATGTCCCAGACATGGTCTTACACTAGCTCTCATATCTCGAG 1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATATCGAG * * 84029671 GCTGATGCCATGTCCGAGACATGGTCTTACACTAGCTCTCATAT 1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATAT 84029715 CTTCCTAGCA Statistics Matches: 208, Mismatches: 32, Indels: 6 0.85 0.13 0.02 Matches are distributed among these distances: 48 26 0.12 49 1 0.00 50 179 0.86 51 2 0.01 ACGTcount: A:0.24, C:0.29, G:0.20, T:0.28 Consensus pattern (50 bp): GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATATCGAG Found at i:84034895 original size:40 final size:40 Alignment explanation

Indices: 84034850--84035041 Score: 222 Period size: 40 Copynumber: 4.8 Consensus size: 40 84034840 TATAACCACA ** * 84034850 AGCACAAATGCCTTCGGGTCTTAGCCCGGATTTAGTAACT 1 AGCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATAACT * * * * * 84034890 CGCACAAATGCCTTCGGATCTTAGTCTGGATAAAATCACT 1 AGCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATAACT * * * * ** 84034930 AGCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACT 1 AGCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATAACT * * 84034970 CGCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATCACT 1 AGCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATAACT * * 84035010 AGCACAATTGCCTTCGGGACTTAGCCCGGATA 1 AGCACAAATGCCTTCGGGTCTTAGCCCGGATA 84035042 TCATTCAAAT Statistics Matches: 122, Mismatches: 30, Indels: 0 0.80 0.20 0.00 Matches are distributed among these distances: 40 122 1.00 ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25 Consensus pattern (40 bp): AGCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATAACT Found at i:84034970 original size:80 final size:80 Alignment explanation

Indices: 84034822--84035042 Score: 311 Period size: 80 Copynumber: 2.8 Consensus size: 80 84034812 ACCCAAGTTT * * * * * 84034822 CTTCGGAAT-TTAG-CCGGATATAACCACAAGCACAAATGCCTTCGGGTCTTAGCCCGGATTTAG 1 CTTCGG-ATCTTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAGCCCGGATATAG * 84034885 TAACTCGCACAAATGC 65 CAACTCGCACAAATGC * * * * 84034901 CTTCGGATCTTAGTCTGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAACCCGGGTATAGC 1 CTTCGGATCTTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAGCCCGGATATAGC 84034966 AACTCGCACAAATGC 66 AACTCGCACAAATGC * * 84034981 CTTCGGGTCTTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGACTTAGCCCGGATAT 1 CTTCGGATCTTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAGCCCGGATAT 84035043 CATTCAAATG Statistics Matches: 125, Mismatches: 15, Indels: 3 0.87 0.10 0.02 Matches are distributed among these distances: 78 2 0.02 79 10 0.08 80 113 0.90 ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25 Consensus pattern (80 bp): CTTCGGATCTTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAGCCCGGATATAGC AACTCGCACAAATGC Found at i:84042927 original size:40 final size:40 Alignment explanation

Indices: 84042882--84043073 Score: 222 Period size: 40 Copynumber: 4.8 Consensus size: 40 84042872 TATAACCACA ** * 84042882 AGCACAAATGCCTTCGGGTCTTAGCCCGGATTTAGTAACT 1 AGCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATAACT * * * * 84042922 CGCACAAATGCCTTCGGATCTTAGTCCGGATAAAATCACT 1 AGCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATAACT * * * * ** 84042962 AGCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACT 1 AGCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATAACT * * * 84043002 CGCACAAATGCCTTCGGGTCTTAGCCCAGATAAAATCACT 1 AGCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATAACT * * 84043042 AGCACAATTGCCTTCGGGACTTAGCCCGGATA 1 AGCACAAATGCCTTCGGGTCTTAGCCCGGATA 84043074 TCATTCAAAT Statistics Matches: 122, Mismatches: 30, Indels: 0 0.80 0.20 0.00 Matches are distributed among these distances: 40 122 1.00 ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24 Consensus pattern (40 bp): AGCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATAACT Found at i:84043002 original size:80 final size:79 Alignment explanation

Indices: 84042854--84043074 Score: 309 Period size: 80 Copynumber: 2.8 Consensus size: 79 84042844 ACCCAAGTTT * * * * * * 84042854 CTTCGGAAT-TTAGCCGGATATAACCACAAGCACAAATGCCTTCGGGTCTTAGCCCGGATTTAGT 1 CTTCGG-ATCTTAGCCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAGCCCGGATATAGC 84042918 AACTCGCACAAATGC 65 AACTCGCACAAATGC * * 84042933 CTTCGGATCTTAGTCCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAACCCGGGTATAGC 1 CTTCGGATCTTAG-CCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAGCCCGGATATAGC 84042998 AACTCGCACAAATGC 65 AACTCGCACAAATGC * * * 84043013 CTTCGGGTCTTAGCCCAGATAAAATCACTAGCACAATTGCCTTCGGGACTTAGCCCGGATAT 1 CTTCGGATCTTAG-CCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAGCCCGGATAT 84043075 CATTCAAATG Statistics Matches: 126, Mismatches: 14, Indels: 3 0.88 0.10 0.02 Matches are distributed among these distances: 78 2 0.02 79 10 0.08 80 114 0.90 ACGTcount: A:0.28, C:0.27, G:0.20, T:0.25 Consensus pattern (79 bp): CTTCGGATCTTAGCCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAGCCCGGATATAGCA ACTCGCACAAATGC Found at i:84045785 original size:19 final size:20 Alignment explanation

Indices: 84045761--84045798 Score: 53 Period size: 19 Copynumber: 1.9 Consensus size: 20 84045751 GGTACCACCA 84045761 AAACAT-ATATCA-CATCTTT 1 AAACATCAT-TCATCATCTTT 84045780 AAACATCATTCATCATCTT 1 AAACATCATTCATCATCTT 84045799 ACCACCTTAT Statistics Matches: 17, Mismatches: 0, Indels: 3 0.85 0.00 0.15 Matches are distributed among these distances: 19 9 0.53 20 8 0.47 ACGTcount: A:0.39, C:0.24, G:0.00, T:0.37 Consensus pattern (20 bp): AAACATCATTCATCATCTTT Found at i:84046133 original size:93 final size:93 Alignment explanation

Indices: 84046026--84046196 Score: 315 Period size: 93 Copynumber: 1.8 Consensus size: 93 84046016 GCCCCTAAGT * * 84046026 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA 1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA 84046091 CGAGTTCGGATGCCTAGTTACATTTCAC 66 CGAGTTCGGATGCCTAGTTACATTTCAC * 84046119 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA 1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA 84046184 CGAGTTCGGATGC 66 CGAGTTCGGATGC 84046197 TCAACCATCC Statistics Matches: 75, Mismatches: 3, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 93 75 1.00 ACGTcount: A:0.28, C:0.29, G:0.22, T:0.22 Consensus pattern (93 bp): GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA CGAGTTCGGATGCCTAGTTACATTTCAC Found at i:84046193 original size:46 final size:46 Alignment explanation

Indices: 84046021--84046193 Score: 210 Period size: 46 Copynumber: 3.7 Consensus size: 46 84046011 AACCCGCCCC * * * 84046021 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA 1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA * * 84046067 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT--T 1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCATCCA * * 84046115 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA 1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA 84046160 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA 1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA 84046194 TGCTCAACCA Statistics Matches: 107, Mismatches: 11, Indels: 18 0.79 0.08 0.13 Matches are distributed among these distances: 42 2 0.02 43 4 0.04 44 1 0.01 45 2 0.02 46 61 0.57 47 29 0.27 48 2 0.02 49 1 0.01 50 3 0.03 51 2 0.02 ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22 Consensus pattern (46 bp): TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA Found at i:84052904 original size:19 final size:20 Alignment explanation

Indices: 84052880--84052917 Score: 53 Period size: 19 Copynumber: 1.9 Consensus size: 20 84052870 GGTACCACCA 84052880 AAACAT-ATATCA-CATCTTT 1 AAACATCAT-TCATCATCTTT 84052899 AAACATCATTCATCATCTT 1 AAACATCATTCATCATCTT 84052918 ACCACCTTAT Statistics Matches: 17, Mismatches: 0, Indels: 3 0.85 0.00 0.15 Matches are distributed among these distances: 19 9 0.53 20 8 0.47 ACGTcount: A:0.39, C:0.24, G:0.00, T:0.37 Consensus pattern (20 bp): AAACATCATTCATCATCTTT Found at i:84053208 original size:46 final size:46 Alignment explanation

Indices: 84053141--84053312 Score: 181 Period size: 46 Copynumber: 3.7 Consensus size: 46 84053131 AACCCGCCCC * * 84053141 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA 1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCATCCT * 84053187 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT--T 1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG--G-C--GTTCGCATCCT * * * ** * 84053235 TCA-CGAACTCGAACTCAACTCAACGAGTTCGTACATTCGCATCCT 1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCATCCT * 84053280 TAAGTGAACTCGGACTCAACTCAATGAGTTCGG 1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG 84053313 ATGCTCAACC Statistics Matches: 102, Mismatches: 15, Indels: 18 0.76 0.11 0.13 Matches are distributed among these distances: 42 2 0.02 43 3 0.03 44 1 0.01 45 3 0.03 46 57 0.56 47 26 0.25 48 3 0.03 49 1 0.01 50 3 0.03 51 3 0.03 ACGTcount: A:0.28, C:0.27, G:0.20, T:0.24 Consensus pattern (46 bp): TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCATCCT Found at i:84053255 original size:93 final size:93 Alignment explanation

Indices: 84053146--84053316 Score: 279 Period size: 93 Copynumber: 1.8 Consensus size: 93 84053136 GCCCCTAAGT * * * 84053146 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA 1 GAACTCGAACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA 84053211 CGAGTTCGGATGCCTAGTTACATTTCAC 66 CGAGTTCGGATGCCTAGTTACATTTCAC * * * 84053239 GAACTCGAACTCAACTCAACGAGTTCGTACATTCGCATCCTTAAGTGAACTCGGACTCAACTCAA 1 GAACTCGAACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA * 84053304 TGAGTTCGGATGC 66 CGAGTTCGGATGC 84053317 TCAACCATCC Statistics Matches: 71, Mismatches: 7, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 93 71 1.00 ACGTcount: A:0.28, C:0.28, G:0.20, T:0.23 Consensus pattern (93 bp): GAACTCGAACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA CGAGTTCGGATGCCTAGTTACATTTCAC Found at i:84071261 original size:46 final size:45 Alignment explanation

Indices: 84071205--84071373 Score: 160 Period size: 46 Copynumber: 3.6 Consensus size: 45 84071195 ATCGCTTAGT * 84071205 CGATGCATGTCCCAGACATGTCTTACACTGGCTTACATTTCAAGGC 1 CGATGCATGTCCCAGACATGTCTTACACTGGCTT-CATATCAAGGC * * * * * * 84071251 CGATGCATGTCCCAAACATGTCTTACACTAGCACTCATATCTATGT 1 CGATGCATGTCCCAGACATGTCTTACACTGGC-TTCATATCAAGGC * * * ** 84071297 CGATGCCATGTCACAGACATGGTTTTACATTGGCTCTCATAAT-GTGGC 1 CGATG-CATGTCCCAGACAT-GTCTTACACTGGCT-TCAT-ATCAAGGC * 84071345 CGATGCATGTCCCAGACATGTTTTACACT 1 CGATGCATGTCCCAGACATGTCTTACACT 84071374 AGCTCACACA Statistics Matches: 99, Mismatches: 19, Indels: 10 0.77 0.15 0.08 Matches are distributed among these distances: 46 51 0.52 47 26 0.26 48 20 0.20 49 2 0.02 ACGTcount: A:0.25, C:0.27, G:0.18, T:0.30 Consensus pattern (45 bp): CGATGCATGTCCCAGACATGTCTTACACTGGCTTCATATCAAGGC Found at i:84071306 original size:138 final size:143 Alignment explanation

Indices: 84071066--84071325 Score: 354 Period size: 138 Copynumber: 1.8 Consensus size: 143 84071056 TTGCCGATCC * ** * 84071066 CATGTCCCCGACATGGTATTACACTGGCTATCATTATTGAGGCCGATGCCATGTCCCAGACATGG 1 CATGTCCCAGACATGGTATTACACTGGCTATCATTATCAAGGCCGATGCCATGTCCCAAACATGG * * * * 84071131 TCTTATACTAGCTCTCGTATATCTGTGTTGATGCCATGTC-CTAGACATGGTCTTACACTAACAC 66 TCTTACACTAGCACTCG-ATATCTATGTCGATGCCATGTCAC-AGACATGGTCTTACACTAACAC 84071195 ATCGCTTAGTCGATG 129 ATCGCTTAGTCGATG * 84071210 CATGTCCCAGACAT-GTCTTACACTGGCT-TACATT-TCAAGGCCGATG-CATGTCCCAAACAT- 1 CATGTCCCAGACATGGTATTACACTGGCTAT-CATTATCAAGGCCGATGCCATGTCCCAAACATG * 84071270 GTCTTACACTAGCACTC-ATATCTATGTCGATGCCATGTCACAGACATGGTTTTACA 65 GTCTTACACTAGCACTCGATATCTATGTCGATGCCATGTCACAGACATGGTCTTACA 84071326 TTGGCTCTCA Statistics Matches: 104, Mismatches: 10, Indels: 10 0.84 0.08 0.08 Matches are distributed among these distances: 138 34 0.33 139 1 0.01 140 15 0.14 141 13 0.12 142 11 0.11 143 17 0.16 144 13 0.12 ACGTcount: A:0.25, C:0.27, G:0.18, T:0.30 Consensus pattern (143 bp): CATGTCCCAGACATGGTATTACACTGGCTATCATTATCAAGGCCGATGCCATGTCCCAAACATGG TCTTACACTAGCACTCGATATCTATGTCGATGCCATGTCACAGACATGGTCTTACACTAACACAT CGCTTAGTCGATG Found at i:84071363 original size:140 final size:142 Alignment explanation

Indices: 84071066--84071373 Score: 335 Period size: 140 Copynumber: 2.2 Consensus size: 142 84071056 TTGCCGATCC * ** * 84071066 CATGTCCCCGACATGGTATTACACTGGCTATCATTATTGAGGCCGATGCCATGTCCCAGACATGG 1 CATGTCCCAGACAT-GTATTACACTGGCTATCATTATCAAGGCCGATGCCATGTCCCAAACATGG * * * * 84071131 TCTTATACTAGCTCTCGTATATCTGTGTTGATGCCATGTCCTAGACATGGTCTTACACTAACACA 65 TCTTACACTAGCACTCG-ATATCTATGTCGATGCCATGTCCTAGACATGGTCTTACACTAACACA * * 84071196 TCGCTTAGTCGATG 129 TCGATAAGTCGATG * 84071210 CATGTCCCAGACATGTCTTACACTGGCT-TACATT-TCAAGGCCGATG-CATGTCCCAAACAT-G 1 CATGTCCCAGACATGTATTACACTGGCTAT-CATTATCAAGGCCGATGCCATGTCCCAAACATGG * * ** * 84071271 TCTTACACTAGCACTC-ATATCTATGTCGATGCCATGTCAC-AGACATGGTTTTACATTGGCTC- 65 TCTTACACTAGCACTCGATATCTATGTCGATGCCATGTC-CTAGACATGGTCTTACACTAACACA 84071333 TC-ATAATGTGGCCGATG 129 TCGATAA-GT---CGATG * 84071350 CATGTCCCAGACATGTTTTACACT 1 CATGTCCCAGACATGTATTACACT 84071374 AGCTCACACA Statistics Matches: 141, Mismatches: 17, Indels: 16 0.81 0.10 0.09 Matches are distributed among these distances: 136 2 0.01 137 4 0.03 138 37 0.26 139 1 0.01 140 43 0.30 141 13 0.09 142 11 0.08 143 17 0.12 144 13 0.09 ACGTcount: A:0.24, C:0.26, G:0.19, T:0.31 Consensus pattern (142 bp): CATGTCCCAGACATGTATTACACTGGCTATCATTATCAAGGCCGATGCCATGTCCCAAACATGGT CTTACACTAGCACTCGATATCTATGTCGATGCCATGTCCTAGACATGGTCTTACACTAACACATC GATAAGTCGATG Found at i:84073524 original size:41 final size:39 Alignment explanation

Indices: 84073400--84073525 Score: 121 Period size: 37 Copynumber: 3.2 Consensus size: 39 84073390 CAACCAGTAC * * 84073400 CTCATCGGATAATTCGAAGTAATAATTTGACACCCAGTGT 1 CTCATCGAATAATTCGAAGT-ATAATTTGACACCCAATGT ** ** * * * * 84073440 CTCATCGGCTAAACCAAAGTA-AA-TTGGCACCCACTGC 1 CTCATCGAATAATTCGAAGTATAATTTGACACCCAATGT 84073477 CTCATCGAATATATTCGAAGTGATAATTTGACACCCAATGT 1 CTCATCGAATA-ATTCGAAGT-ATAATTTGACACCCAATGT 84073518 CTCATCGA 1 CTCATCGA 84073526 CTTGAAGTCA Statistics Matches: 67, Mismatches: 15, Indels: 7 0.75 0.17 0.08 Matches are distributed among these distances: 37 20 0.30 38 8 0.12 39 2 0.03 40 18 0.27 41 19 0.28 ACGTcount: A:0.33, C:0.25, G:0.16, T:0.27 Consensus pattern (39 bp): CTCATCGAATAATTCGAAGTATAATTTGACACCCAATGT Found at i:84074508 original size:26 final size:26 Alignment explanation

Indices: 84074479--84074546 Score: 77 Period size: 26 Copynumber: 2.6 Consensus size: 26 84074469 TTTTTCTTTC 84074479 TTTATTTATTT-CATTTACTTATT-TAT 1 TTTATTTATTTAC-TTTA-TTATTATAT 84074505 TTTATTATATTTACTTTATTATTATAT 1 TTTATT-TATTTACTTTATTATTATAT * * 84074532 TCTATATATTTACTT 1 TTTATTTATTTACTT 84074547 AAATATTAAG Statistics Matches: 37, Mismatches: 2, Indels: 6 0.82 0.04 0.13 Matches are distributed among these distances: 26 20 0.54 27 16 0.43 28 1 0.03 ACGTcount: A:0.26, C:0.07, G:0.00, T:0.66 Consensus pattern (26 bp): TTTATTTATTTACTTTATTATTATAT Found at i:84074516 original size:22 final size:23 Alignment explanation

Indices: 84074479--84074547 Score: 65 Period size: 22 Copynumber: 3.0 Consensus size: 23 84074469 TTTTTCTTTC 84074479 TTTA-TTTATT-TCATTTACTTA- 1 TTTATTTTATTAT-ATTTACTTAT 84074500 TTTATTTTATTATATTTACTTTAT 1 TTTATTTTATTATATTTAC-TTAT 84074524 TATTATATTCTA-TATATTTACTTA 1 T-TTAT-TT-TATTATATTTACTTA 84074548 AATATTAAGT Statistics Matches: 41, Mismatches: 0, Indels: 10 0.80 0.00 0.20 Matches are distributed among these distances: 21 4 0.10 22 12 0.29 23 4 0.10 24 1 0.02 25 7 0.17 26 11 0.27 27 2 0.05 ACGTcount: A:0.28, C:0.07, G:0.00, T:0.65 Consensus pattern (23 bp): TTTATTTTATTATATTTACTTAT Found at i:84074517 original size:14 final size:14 Alignment explanation

Indices: 84074498--84074543 Score: 51 Period size: 14 Copynumber: 3.4 Consensus size: 14 84074488 TTCATTTACT 84074498 TATTTATTTTATTA 1 TATTTATTTTATTA * 84074512 TATTTACTTTATTA 1 TATTTATTTTATTA * * 84074526 T-TATATTCTA-TA 1 TATTTATTTTATTA 84074538 TATTTA 1 TATTTA 84074544 CTTAAATATT Statistics Matches: 26, Mismatches: 5, Indels: 3 0.76 0.15 0.09 Matches are distributed among these distances: 12 3 0.12 13 9 0.35 14 14 0.54 ACGTcount: A:0.30, C:0.04, G:0.00, T:0.65 Consensus pattern (14 bp): TATTTATTTTATTA Found at i:84079355 original size:10 final size:12 Alignment explanation

Indices: 84079327--84079359 Score: 50 Period size: 11 Copynumber: 2.8 Consensus size: 12 84079317 TTTTTGAAAC 84079327 ATTTATTTTTACA 1 ATTT-TTTTTACA 84079340 ATTTTTTTTA-A 1 ATTTTTTTTACA 84079351 ATTTTTTTT 1 ATTTTTTTT 84079360 CTTTGGTATT Statistics Matches: 20, Mismatches: 0, Indels: 2 0.91 0.00 0.09 Matches are distributed among these distances: 11 10 0.50 12 6 0.30 13 4 0.20 ACGTcount: A:0.24, C:0.03, G:0.00, T:0.73 Consensus pattern (12 bp): ATTTTTTTTACA Found at i:84082294 original size:46 final size:46 Alignment explanation

Indices: 84082242--84082515 Score: 359 Period size: 46 Copynumber: 6.0 Consensus size: 46 84082232 AGTGTGCTCT * ** * 84082242 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCTAC 1 CTGACATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC * ** 84082288 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC 1 CTGACATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC * * 84082334 CTGATATGAAATGAATAAGACCATGGTAGAAAGATACCATGGCAAC 1 CTGACATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC * ** 84082380 ATGACGGGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC 1 CTGACATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC * ** * 84082426 ATGACGGGAAATGAATAAGACCATGGTTGAAAGATATCATGGCAAC 1 CTGACATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC * ** * * 84082472 GTGACATGAAATGTGTAAGACCATGGTTGAAAGACACTATGGCA 1 CTGACATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCA 84082516 TCATGTCAAA Statistics Matches: 210, Mismatches: 18, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 46 210 1.00 ACGTcount: A:0.39, C:0.15, G:0.25, T:0.22 Consensus pattern (46 bp): CTGACATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC Found at i:84082822 original size:16 final size:17 Alignment explanation

Indices: 84082801--84082833 Score: 59 Period size: 17 Copynumber: 2.0 Consensus size: 17 84082791 ATGATGGTGC 84082801 ATGAAAT-ATTGATATA 1 ATGAAATGATTGATATA 84082817 ATGAAATGATTGATATA 1 ATGAAATGATTGATATA 84082834 TACTTATGAA Statistics Matches: 16, Mismatches: 0, Indels: 1 0.94 0.00 0.06 Matches are distributed among these distances: 16 7 0.44 17 9 0.56 ACGTcount: A:0.48, C:0.00, G:0.15, T:0.36 Consensus pattern (17 bp): ATGAAATGATTGATATA Found at i:84096147 original size:28 final size:27 Alignment explanation

Indices: 84096106--84096184 Score: 95 Period size: 28 Copynumber: 2.8 Consensus size: 27 84096096 CTCAATCTCT * 84096106 TTCATATGGGCCATTAGGCCCATTCATA 1 TTCATAT-GGCCATTAGGCCCAATCATA * * 84096134 TTTATGTGGCCCATTAGGCCCAAATCATA 1 TTCATATGG-CCATTAGGCCC-AATCATA * 84096163 TTCATATGGCCACTAGGCCCAA 1 TTCATATGGCCATTAGGCCCAA 84096185 ATTACATTTA Statistics Matches: 43, Mismatches: 6, Indels: 5 0.80 0.11 0.09 Matches are distributed among these distances: 27 4 0.09 28 26 0.60 29 13 0.30 ACGTcount: A:0.27, C:0.27, G:0.18, T:0.29 Consensus pattern (27 bp): TTCATATGGCCATTAGGCCCAATCATA Found at i:84099582 original size:40 final size:40 Alignment explanation

Indices: 84099500--84099681 Score: 192 Period size: 40 Copynumber: 4.5 Consensus size: 40 84099490 GAATGCTGTT * * * * 84099500 CGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACT-ATATC 1 CGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTATTAAT-TC ** 84099540 CGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTATTAATTC 1 CGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTATTAATTC * * * 84099580 CGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAATTC 1 CGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAATTC * * * 84099620 CAGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAAATC 1 CGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATT-AATTC 84099660 CGGGTTAAGTCCCGAAGGCATT 1 CGGGTTAAGTCCCGAAGGCATT 84099682 GTATGAGTTA Statistics Matches: 121, Mismatches: 16, Indels: 10 0.82 0.11 0.07 Matches are distributed among these distances: 39 2 0.02 40 109 0.90 41 10 0.08 ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27 Consensus pattern (40 bp): CGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAATTC Found at i:84105817 original size:28 final size:28 Alignment explanation

Indices: 84105774--84105867 Score: 107 Period size: 28 Copynumber: 3.3 Consensus size: 28 84105764 TACCTATATA * * * * 84105774 TATATAGCCCACTAGGCCCAATCTCTTT 1 TATATGGCCCATTAGGCCCAATCACATT * 84105802 TATATGGCCCATTAGGCCCATTCACATT 1 TATATGGCCCATTAGGCCCAATCACATT * * 84105830 TATGTGGCCCATTAGGCCCAAATCACACT 1 TATATGGCCCATTAGGCCC-AATCACATT * 84105859 CATATGGCC 1 TATATGGCC 84105868 ACTAGGCTTA Statistics Matches: 55, Mismatches: 10, Indels: 1 0.83 0.15 0.02 Matches are distributed among these distances: 28 41 0.75 29 14 0.25 ACGTcount: A:0.26, C:0.31, G:0.15, T:0.29 Consensus pattern (28 bp): TATATGGCCCATTAGGCCCAATCACATT Found at i:84109697 original size:17 final size:17 Alignment explanation

Indices: 84109675--84109708 Score: 68 Period size: 17 Copynumber: 2.0 Consensus size: 17 84109665 CTGAAGCTTG 84109675 TAAAGAAACTATTTGGT 1 TAAAGAAACTATTTGGT 84109692 TAAAGAAACTATTTGGT 1 TAAAGAAACTATTTGGT 84109709 GAACTTAGTA Statistics Matches: 17, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 17 17 1.00 ACGTcount: A:0.41, C:0.06, G:0.18, T:0.35 Consensus pattern (17 bp): TAAAGAAACTATTTGGT Found at i:84110030 original size:29 final size:29 Alignment explanation

Indices: 84109997--84110055 Score: 109 Period size: 29 Copynumber: 2.0 Consensus size: 29 84109987 TTATGGAAGA * 84109997 GGTGAAGAACTTGTTTGTTGAGAGTTTGT 1 GGTGAAGAACTTGTTTGTTGAGAATTTGT 84110026 GGTGAAGAACTTGTTTGTTGAGAATTTGT 1 GGTGAAGAACTTGTTTGTTGAGAATTTGT 84110055 G 1 G 84110056 TCAAGGTAGA Statistics Matches: 29, Mismatches: 1, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 29 29 1.00 ACGTcount: A:0.22, C:0.03, G:0.34, T:0.41 Consensus pattern (29 bp): GGTGAAGAACTTGTTTGTTGAGAATTTGT Found at i:84111360 original size:27 final size:27 Alignment explanation

Indices: 84111330--84111391 Score: 97 Period size: 27 Copynumber: 2.3 Consensus size: 27 84111320 ACCTAAATTC * * 84111330 AAATGTAAAACCCTTATAGTTTCATTA 1 AAATGTAAAAACCTTATAGTGTCATTA * 84111357 AAATGTAAAAACCTTATGGTGTCATTA 1 AAATGTAAAAACCTTATAGTGTCATTA 84111384 AAATGTAA 1 AAATGTAA 84111392 CACTTACTTA Statistics Matches: 32, Mismatches: 3, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 27 32 1.00 ACGTcount: A:0.44, C:0.11, G:0.11, T:0.34 Consensus pattern (27 bp): AAATGTAAAAACCTTATAGTGTCATTA Found at i:84112470 original size:22 final size:21 Alignment explanation

Indices: 84112396--84112469 Score: 69 Period size: 22 Copynumber: 3.3 Consensus size: 21 84112386 AAAAACCAGA * 84112396 TTTTTATTTTAAAAATCTAAAC 1 TTTTT-TTTTAAAAATCAAAAC * 84112418 TTTCTCTTTTAAAAAT-AAATCAC 1 TTT-TTTTTTAAAAATCAAA--AC * 84112441 TATTTTTCTTAAAAATCAAAAC 1 T-TTTTTTTTAAAAATCAAAAC 84112463 TTTTTTT 1 TTTTTTT 84112470 CGAAATAGTT Statistics Matches: 42, Mismatches: 5, Indels: 11 0.72 0.09 0.19 Matches are distributed among these distances: 21 7 0.17 22 16 0.38 23 14 0.33 24 5 0.12 ACGTcount: A:0.38, C:0.12, G:0.00, T:0.50 Consensus pattern (21 bp): TTTTTTTTTAAAAATCAAAAC Found at i:84116552 original size:60 final size:62 Alignment explanation

Indices: 84116482--84116601 Score: 183 Period size: 60 Copynumber: 2.0 Consensus size: 62 84116472 TATCTCGACT 84116482 TGTAATAGGGCTATGGCCCAGATTGATACTGATATGAGCT-AGGCCCAG-TATACTCTGATAC 1 TGTAATAGGGCTATGGCCCAGATTGATACTGATATGAGCTAAGGCCCAGTTA-ACTCTGATAC * * * 84116543 TGTAA-AGGGCTATGGCCCAGATTGTTATTGATATGGGCTAAGGCCCAGTTAACTCTGAT 1 TGTAATAGGGCTATGGCCCAGATTGATACTGATATGAGCTAAGGCCCAGTTAACTCTGAT 84116602 TTTTGAATGG Statistics Matches: 54, Mismatches: 3, Indels: 4 0.89 0.05 0.07 Matches are distributed among these distances: 60 31 0.57 61 21 0.39 62 2 0.04 ACGTcount: A:0.27, C:0.18, G:0.26, T:0.29 Consensus pattern (62 bp): TGTAATAGGGCTATGGCCCAGATTGATACTGATATGAGCTAAGGCCCAGTTAACTCTGATAC Found at i:84119786 original size:23 final size:25 Alignment explanation

Indices: 84119750--84119819 Score: 72 Period size: 27 Copynumber: 2.8 Consensus size: 25 84119740 AATAGGGTAT * * 84119750 TTCAATACATAATTCAAT-TTCCAA 1 TTCAATATACAATTCAATCTTCCAA 84119774 -TCAATATACAATTTCAATCCATTCCAA 1 TTCAATATACAA-TTCAAT-C-TTCCAA * 84119801 TTCAATATACTATTCAATC 1 TTCAATATACAATTCAATC 84119820 ATACGCATAC Statistics Matches: 38, Mismatches: 3, Indels: 8 0.78 0.06 0.16 Matches are distributed among these distances: 23 9 0.24 24 6 0.16 26 1 0.03 27 12 0.32 28 10 0.26 ACGTcount: A:0.40, C:0.23, G:0.00, T:0.37 Consensus pattern (25 bp): TTCAATATACAATTCAATCTTCCAA Found at i:84119800 original size:27 final size:27 Alignment explanation

Indices: 84119768--84119819 Score: 79 Period size: 27 Copynumber: 1.9 Consensus size: 27 84119758 ATAATTCAAT 84119768 TTCCAA-TCAATATACAATTTCAATCCA 1 TTCCAATTCAATATACAA-TTCAATCCA * 84119795 TTCCAATTCAATATACTATTCAATC 1 TTCCAATTCAATATACAATTCAATC 84119820 ATACGCATAC Statistics Matches: 23, Mismatches: 1, Indels: 2 0.88 0.04 0.08 Matches are distributed among these distances: 27 13 0.57 28 10 0.43 ACGTcount: A:0.38, C:0.25, G:0.00, T:0.37 Consensus pattern (27 bp): TTCCAATTCAATATACAATTCAATCCA Found at i:84120417 original size:29 final size:29 Alignment explanation

Indices: 84120352--84120418 Score: 100 Period size: 29 Copynumber: 2.3 Consensus size: 29 84120342 ACCCACATCT 84120352 AAAAATCAACTAACTTTCAAATTTTCCAC 1 AAAAATCAACTAACTTTCAAATTTTCCAC * * 84120381 ATAAATCAATTAACTTTCAAATTTTCCA- 1 AAAAATCAACTAACTTTCAAATTTTCCAC 84120409 AAAACATCAA 1 AAAA-ATCAA 84120419 AATTACAAGA Statistics Matches: 34, Mismatches: 3, Indels: 2 0.87 0.08 0.05 Matches are distributed among these distances: 28 3 0.09 29 31 0.91 ACGTcount: A:0.48, C:0.21, G:0.00, T:0.31 Consensus pattern (29 bp): AAAAATCAACTAACTTTCAAATTTTCCAC Found at i:84120998 original size:26 final size:26 Alignment explanation

Indices: 84120959--84121010 Score: 95 Period size: 26 Copynumber: 2.0 Consensus size: 26 84120949 CATTCACTTC * 84120959 AGGGAATGAGGCAAAACTAGTGGGAA 1 AGGGAATGAAGCAAAACTAGTGGGAA 84120985 AGGGAATGAAGCAAAACTAGTGGGAA 1 AGGGAATGAAGCAAAACTAGTGGGAA 84121011 GAATTTCTTA Statistics Matches: 25, Mismatches: 1, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 26 25 1.00 ACGTcount: A:0.44, C:0.08, G:0.37, T:0.12 Consensus pattern (26 bp): AGGGAATGAAGCAAAACTAGTGGGAA Found at i:84123494 original size:42 final size:42 Alignment explanation

Indices: 84123447--84123917 Score: 606 Period size: 42 Copynumber: 11.3 Consensus size: 42 84123437 CTTCATATAC * * * 84123447 AATGCAATGAAAAGTAAATGGACATCCACACTTGGGCCTTTA 1 AATGCAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTA * * * 84123489 AATGCAATGAAAAGTAAACGGACCTCCACACCTAGGCCTTTA 1 AATGCAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTA * * * 84123531 GATGCAATGAAAAGTCAATGGACCTCCACACCCGGGCCTCTA 1 AATGCAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTA * * * * 84123573 AATGCAATGAAAA-TAAATGGAACTCCAAACCTAGGCCTTTA 1 AATGCAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTA * * * 84123614 AATGCAATAAAAAGTAAATGAACCTCCACACCTTGGCCTCTA 1 AATGCAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTA ** 84123656 AATGCAATGAAAAGTAAATGGACCTCCACACCTGGGTTTCTA 1 AATGCAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTA * * * * 84123698 AATGCAAT-AAAAGTAAATGAACCTCTACGCCTAGGCCTCTA 1 AATGCAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTA * * 84123739 AATGCAATGAAAAGTAAATGGACCTCCACACTTGAGCCTCTA 1 AATGCAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTA * * 84123781 AATACAATAAAAAGTAAATGGACCTCCACACCTGGGCCTCTA 1 AATGCAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTA * * * 84123823 AATACAATGAAAAGTAAATAGACCTCCACACCTAGGCCTCTA 1 AATGCAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTA * * *** 84123865 AGTGTAATGAAAAGTAAAT-GACCCTCCACACCTATTCCTCTA 1 AATGCAATGAAAAGTAAATGGA-CCTCCACACCTGGGCCTCTA 84123907 AATGCAATGAA 1 AATGCAATGAA 84123918 TGTTTTCCTT Statistics Matches: 372, Mismatches: 54, Indels: 6 0.86 0.12 0.01 Matches are distributed among these distances: 41 71 0.19 42 301 0.81 ACGTcount: A:0.39, C:0.24, G:0.16, T:0.21 Consensus pattern (42 bp): AATGCAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTA Found at i:84123629 original size:125 final size:126 Alignment explanation

Indices: 84123447--84123917 Score: 621 Period size: 125 Copynumber: 3.8 Consensus size: 126 84123437 CTTCATATAC * * * * 84123447 AATGCAATGAAAAGTAAATGG-ACATCCACACTTGGGCCTTTAAATGCAATGAAAAGTAAACGGA 1 AATGCAATGAAAAGTAAATGGAAC-TCCACACCTAGGCCTCTAAATGCAATGAAAAGTAAATGGA * * * * 84123511 CCTCCACACCTAGGCCTTTAGATGCAATGAAAAGTCAATGGACCTCCACACCCGGGCCTCTA 65 CCTCCACACCTAGGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTA * * * * 84123573 AATGCAATGAAAA-TAAATGGAACTCCAAACCTAGGCCTTTAAATGCAATAAAAAGTAAATGAAC 1 AATGCAATGAAAAGTAAATGGAACTCCACACCTAGGCCTCTAAATGCAATGAAAAGTAAATGGAC * ** 84123637 CTCCACACCTTGGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACCTGGGTTTCTA 66 CTCCACACCTAGGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTA * * 84123698 AATGCAAT-AAAAGTAAAT-GAACCTCTACGCCTAGGCCTCTAAATGCAATGAAAAGTAAATGGA 1 AATGCAATGAAAAGTAAATGGAA-CTCCACACCTAGGCCTCTAAATGCAATGAAAAGTAAATGGA * * * 84123761 CCTCCACA-CTTGAGCCTCTAAATACAATAAAAAGTAAATGGACCTCCACACCTGGGCCTCTA 65 CCTCCACACCTAG-GCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTA * * * * * 84123823 AATACAATGAAAAGTAAATAGACCTCCACACCTAGGCCTCTAAGTGTAATGAAAAGTAAAT-GAC 1 AATGCAATGAAAAGTAAATGGAACTCCACACCTAGGCCTCTAAATGCAATGAAAAGTAAATGGA- ** 84123887 CCTCCACACCTATTCCTCTAAATGCAATGAA 65 CCTCCACACCTAGGCCTCTAAATGCAATGAA 84123918 TGTTTTCCTT Statistics Matches: 303, Mismatches: 34, Indels: 16 0.86 0.10 0.05 Matches are distributed among these distances: 124 11 0.04 125 206 0.68 126 82 0.27 127 4 0.01 ACGTcount: A:0.39, C:0.24, G:0.16, T:0.21 Consensus pattern (126 bp): AATGCAATGAAAAGTAAATGGAACTCCACACCTAGGCCTCTAAATGCAATGAAAAGTAAATGGAC CTCCACACCTAGGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTA Found at i:84128765 original size:50 final size:51 Alignment explanation

Indices: 84128604--84128762 Score: 176 Period size: 51 Copynumber: 3.1 Consensus size: 51 84128594 TTACCACCCT * * * 84128604 TGTGACCGAAGCTATTTGGTACGCATAGTAGCCTGCGCTTAATACTACACA 1 TGTGACCGAAGCTATCTGGTACGCATAGTAGCCTGCACTTAGTACTACACA * * * * * * 84128655 TGTGATCGAAGTTGTCGGGTACGCATAGTAGCCTACACATAGTACTACACA 1 TGTGACCGAAGCTATCTGGTACGCATAGTAGCCTGCACTTAGTACTACACA ** * * * 84128706 TGCAACCTAA-CTATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACA 1 TGTGACCGAAGCTATCTGGTACGCATAGTAGCCTGCACTTAGTACTACACA * 84128756 CGTGACC 1 TGTGACC 84128763 TAAAACCATC Statistics Matches: 85, Mismatches: 23, Indels: 1 0.78 0.21 0.01 Matches are distributed among these distances: 50 37 0.44 51 48 0.56 ACGTcount: A:0.28, C:0.25, G:0.21, T:0.26 Consensus pattern (51 bp): TGTGACCGAAGCTATCTGGTACGCATAGTAGCCTGCACTTAGTACTACACA Found at i:84131529 original size:30 final size:30 Alignment explanation

Indices: 84131495--84131553 Score: 82 Period size: 30 Copynumber: 2.0 Consensus size: 30 84131485 ATAGATAACA * * * 84131495 AGAAAACTAAGATTAAGAAGTCCAAGATAG 1 AGAAAACCAAGATAAAGAAATCCAAGATAG * 84131525 AGAAATCCAAGATAAAGAAATCCAAGATA 1 AGAAAACCAAGATAAAGAAATCCAAGATA 84131554 CAATATCATA Statistics Matches: 25, Mismatches: 4, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 30 25 1.00 ACGTcount: A:0.56, C:0.12, G:0.17, T:0.15 Consensus pattern (30 bp): AGAAAACCAAGATAAAGAAATCCAAGATAG Found at i:84131553 original size:15 final size:15 Alignment explanation

Indices: 84131503--84131553 Score: 75 Period size: 15 Copynumber: 3.4 Consensus size: 15 84131493 CAAGAAAACT * * 84131503 AAGATTAAGAAGTCC 1 AAGATAAAGAAATCC * 84131518 AAGATAGAGAAATCC 1 AAGATAAAGAAATCC 84131533 AAGATAAAGAAATCC 1 AAGATAAAGAAATCC 84131548 AAGATA 1 AAGATA 84131554 CAATATCATA Statistics Matches: 32, Mismatches: 4, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 15 32 1.00 ACGTcount: A:0.55, C:0.12, G:0.18, T:0.16 Consensus pattern (15 bp): AAGATAAAGAAATCC Found at i:84134991 original size:16 final size:15 Alignment explanation

Indices: 84134967--84134996 Score: 51 Period size: 16 Copynumber: 1.9 Consensus size: 15 84134957 AACTGTTTTA 84134967 TTACAAATTTCACTC 1 TTACAAATTTCACTC 84134982 TTACATAATTTCACT 1 TTACA-AATTTCACT 84134997 TACTCTATTC 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:0.33, C:0.23, G:0.00, T:0.43 Consensus pattern (15 bp): TTACAAATTTCACTC Found at i:84140646 original size:26 final size:27 Alignment explanation

Indices: 84140617--84140669 Score: 81 Period size: 27 Copynumber: 2.0 Consensus size: 27 84140607 CACACAAGTC 84140617 AGTCATTT-ACGCACGAGGGGCAAAAT 1 AGTCATTTAACGCACGAGGGGCAAAAT * * 84140643 AGTCATTTAACGCCCTAGGGGCAAAAT 1 AGTCATTTAACGCACGAGGGGCAAAAT 84140670 GGTAATTTTA Statistics Matches: 24, Mismatches: 2, Indels: 1 0.89 0.07 0.04 Matches are distributed among these distances: 26 8 0.33 27 16 0.67 ACGTcount: A:0.34, C:0.21, G:0.25, T:0.21 Consensus pattern (27 bp): AGTCATTTAACGCACGAGGGGCAAAAT Found at i:84140702 original size:27 final size:27 Alignment explanation

Indices: 84140672--84140842 Score: 191 Period size: 27 Copynumber: 6.3 Consensus size: 27 84140662 GGCAAAATGG * * * 84140672 TAATTTTACCCCACAAGGGTATCTCGA 1 TAATTCTACCCTACAAGGGTATTTCGA * * 84140699 TAATTCTACCCTACAGGGGTATTTCGG 1 TAATTCTACCCTACAAGGGTATTTCGA * * 84140726 TATTTCTATCCTAC-AGGGTTATTTCGA 1 TAATTCTACCCTACAAGGG-TATTTCGA * * 84140753 TAATTCTACCCTACAGGGGTATTTCAA 1 TAATTCTACCCTACAAGGGTATTTCGA * * 84140780 TAATTCTACCCTACAAGGTTATTTCGG 1 TAATTCTACCCTACAAGGGTATTTCGA * * * * 84140807 TAATTCTACCTTACAGGGGTATTTTGG 1 TAATTCTACCCTACAAGGGTATTTCGA 84140834 TAATTCTAC 1 TAATTCTAC 84140843 AACTTATCCA Statistics Matches: 121, Mismatches: 21, Indels: 4 0.83 0.14 0.03 Matches are distributed among these distances: 26 3 0.02 27 115 0.95 28 3 0.02 ACGTcount: A:0.26, C:0.21, G:0.16, T:0.37 Consensus pattern (27 bp): TAATTCTACCCTACAAGGGTATTTCGA Found at i:84140753 original size:54 final size:54 Alignment explanation

Indices: 84140670--84140842 Score: 231 Period size: 54 Copynumber: 3.2 Consensus size: 54 84140660 GGGGCAAAAT * * * 84140670 GGTAATTTTACCCCACAAGGG-TATCTCGATAATTCTACCCTACAGGGGTATTTC 1 GGTAATTCTACCCTAC-AGGGTTATTTCGATAATTCTACCCTACAGGGGTATTTC * * 84140724 GGTATTTCTATCCTACAGGGTTATTTCGATAATTCTACCCTACAGGGGTATTTC 1 GGTAATTCTACCCTACAGGGTTATTTCGATAATTCTACCCTACAGGGGTATTTC ** * * * * 84140778 AATAATTCTACCCTACAAGGTTATTTCGGTAATTCTACCTTACAGGGGTATTTT 1 GGTAATTCTACCCTACAGGGTTATTTCGATAATTCTACCCTACAGGGGTATTTC 84140832 GGTAATTCTAC 1 GGTAATTCTAC 84140843 AACTTATCCA Statistics Matches: 103, Mismatches: 15, Indels: 2 0.86 0.12 0.02 Matches are distributed among these distances: 53 4 0.04 54 99 0.96 ACGTcount: A:0.25, C:0.21, G:0.17, T:0.36 Consensus pattern (54 bp): GGTAATTCTACCCTACAGGGTTATTTCGATAATTCTACCCTACAGGGGTATTTC Found at i:84140786 original size:81 final size:81 Alignment explanation

Indices: 84140672--84140842 Score: 227 Period size: 81 Copynumber: 2.1 Consensus size: 81 84140662 GGCAAAATGG * * * * 84140672 TAATTTTACCCCACAAGGGTATCTCGATAATTCTACCCTACAGGGGTATTTCGGTATTTCTATCC 1 TAATTCTACCCCACAAGGGTATCTCAATAATTCTACCCTACAAGGGTATTTCGGTAATTCTA-CC * 84140737 -TACAGGGTTATTTCGA 65 TTACAGGGGTATTTCGA * * * * 84140753 TAATTCTACCCTACAGGGGTATTTCAATAATTCTACCCTACAAGGTTATTTCGGTAATTCTACCT 1 TAATTCTACCCCACAAGGGTATCTCAATAATTCTACCCTACAAGGGTATTTCGGTAATTCTACCT * * 84140818 TACAGGGGTATTTTGG 66 TACAGGGGTATTTCGA 84140834 TAATTCTAC 1 TAATTCTAC 84140843 AACTTATCCA Statistics Matches: 78, Mismatches: 11, Indels: 2 0.86 0.12 0.02 Matches are distributed among these distances: 80 2 0.03 81 76 0.97 ACGTcount: A:0.26, C:0.21, G:0.16, T:0.37 Consensus pattern (81 bp): TAATTCTACCCCACAAGGGTATCTCAATAATTCTACCCTACAAGGGTATTTCGGTAATTCTACCT TACAGGGGTATTTCGA Found at i:84143878 original size:3 final size:3 Alignment explanation

Indices: 84143870--84143913 Score: 88 Period size: 3 Copynumber: 14.7 Consensus size: 3 84143860 ATTCGATCTT 84143870 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT 1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT 84143914 TAAAATATTT Statistics Matches: 41, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 3 41 1.00 ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68 Consensus pattern (3 bp): TTA Found at i:84145142 original size:26 final size:26 Alignment explanation

Indices: 84145113--84145166 Score: 108 Period size: 26 Copynumber: 2.1 Consensus size: 26 84145103 CTTTCATTTC 84145113 ATTTCATCTATATATATTATTTTTTA 1 ATTTCATCTATATATATTATTTTTTA 84145139 ATTTCATCTATATATATTATTTTTTA 1 ATTTCATCTATATATATTATTTTTTA 84145165 AT 1 AT 84145167 CTTGTTTATT Statistics Matches: 28, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 26 28 1.00 ACGTcount: A:0.31, C:0.07, G:0.00, T:0.61 Consensus pattern (26 bp): ATTTCATCTATATATATTATTTTTTA Found at i:84146883 original size:14 final size:14 Alignment explanation

Indices: 84146864--84146903 Score: 55 Period size: 14 Copynumber: 2.9 Consensus size: 14 84146854 TTAATATTTT 84146864 AATTAAACTAATTA 1 AATTAAACTAATTA 84146878 AATT-AACTAACTTA 1 AATTAAACTAA-TTA * 84146892 AATTAACCTAAT 1 AATTAAACTAAT 84146904 GGACTTTCCT Statistics Matches: 23, Mismatches: 1, Indels: 4 0.82 0.04 0.14 Matches are distributed among these distances: 13 6 0.26 14 12 0.52 15 5 0.22 ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35 Consensus pattern (14 bp): AATTAAACTAATTA Found at i:84150074 original size:38 final size:39 Alignment explanation

Indices: 84150031--84150116 Score: 102 Period size: 40 Copynumber: 2.2 Consensus size: 39 84150021 AACCAGCCTA * * 84150031 ACACACCA-TGTGAGGATAGAATCGACCCACCCAACCCT 1 ACACACCAGTATGAGGATAGAATCAACCCACCCAACCCT * * * * 84150069 ACACACCAAGTATGGGGATATAATTAACCCATCCAACCCT 1 ACACACC-AGTATGAGGATAGAATCAACCCACCCAACCCT 84150109 ACACACCA 1 ACACACCA 84150117 CAAAGTACCG Statistics Matches: 40, Mismatches: 6, Indels: 3 0.82 0.12 0.06 Matches are distributed among these distances: 38 7 0.17 39 2 0.05 40 31 0.77 ACGTcount: A:0.37, C:0.35, G:0.13, T:0.15 Consensus pattern (39 bp): ACACACCAGTATGAGGATAGAATCAACCCACCCAACCCT Found at i:84150513 original size:17 final size:19 Alignment explanation

Indices: 84150486--84150521 Score: 58 Period size: 17 Copynumber: 2.0 Consensus size: 19 84150476 TGCCCTGCCT 84150486 GTGTGGGCCCACAC-GCCC 1 GTGTGGGCCCACACAGCCC 84150504 GTGT-GGCCCACACAGCCC 1 GTGTGGGCCCACACAGCCC 84150522 AACTTGGCTT Statistics Matches: 17, Mismatches: 0, Indels: 2 0.89 0.00 0.11 Matches are distributed among these distances: 17 9 0.53 18 8 0.47 ACGTcount: A:0.14, C:0.44, G:0.31, T:0.11 Consensus pattern (19 bp): GTGTGGGCCCACACAGCCC Found at i:84152558 original size:93 final size:93 Alignment explanation

Indices: 84152446--84152616 Score: 315 Period size: 93 Copynumber: 1.8 Consensus size: 93 84152436 GCCCATAAGT * * 84152446 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA 1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA 84152511 CGAGTTCGGATGCCTAGTTACATTTCAC 66 CGAGTTCGGATGCCTAGTTACATTTCAC * 84152539 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA 1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA 84152604 CGAGTTCGGATGC 66 CGAGTTCGGATGC 84152617 TCAACCATCC Statistics Matches: 75, Mismatches: 3, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 93 75 1.00 ACGTcount: A:0.28, C:0.29, G:0.22, T:0.22 Consensus pattern (93 bp): GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA CGAGTTCGGATGCCTAGTTACATTTCAC Found at i:84152613 original size:46 final size:46 Alignment explanation

Indices: 84152438--84152613 Score: 216 Period size: 46 Copynumber: 3.8 Consensus size: 46 84152428 TGCAACCCGC * * * 84152438 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT 1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT * 84152484 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT 1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT * * * 84152534 --TTCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT 1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT 84152577 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA 1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA 84152614 TGCTCAACCA Statistics Matches: 110, Mismatches: 11, Indels: 18 0.79 0.08 0.13 Matches are distributed among these distances: 42 2 0.02 43 4 0.04 44 1 0.01 45 2 0.02 46 64 0.58 47 29 0.26 48 2 0.02 49 1 0.01 50 3 0.03 51 2 0.02 ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22 Consensus pattern (46 bp): CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT Found at i:84165049 original size:21 final size:20 Alignment explanation

Indices: 84165024--84165064 Score: 55 Period size: 21 Copynumber: 1.9 Consensus size: 20 84165014 TTAAAAACAC 84165024 AAAAATAAATATTAAAACAAA 1 AAAAAT-AATATTAAAACAAA * 84165045 TAAAAATGATATTAAAACAA 1 -AAAAATAATATTAAAACAA 84165065 TTATTAAAAC Statistics Matches: 18, Mismatches: 1, Indels: 1 0.90 0.05 0.05 Matches are distributed among these distances: 21 12 0.67 22 6 0.33 ACGTcount: A:0.71, C:0.05, G:0.02, T:0.22 Consensus pattern (20 bp): AAAAATAATATTAAAACAAA Found at i:84167433 original size:13 final size:13 Alignment explanation

Indices: 84167415--84167439 Score: 50 Period size: 13 Copynumber: 1.9 Consensus size: 13 84167405 TATATTATAT 84167415 GTGTGAAAATTTC 1 GTGTGAAAATTTC 84167428 GTGTGAAAATTT 1 GTGTGAAAATTT 84167440 TATCGTTTGT Statistics Matches: 12, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 12 1.00 ACGTcount: A:0.32, C:0.04, G:0.24, T:0.40 Consensus pattern (13 bp): GTGTGAAAATTTC Found at i:84168918 original size:42 final size:41 Alignment explanation

Indices: 84168863--84168975 Score: 106 Period size: 42 Copynumber: 2.7 Consensus size: 41 84168853 CAATATTGAT * * 84168863 GCCTCTGTCCCAGACAAGGTCTTACACGAA-ATCAGATACGAT 1 GCCTGTGTCCCAGACAAGGTCTTACACGAATATCA-AT-CGAG * * * 84168905 TCC-GATGTCCCAGACATA-GTCTTATACGTAATCTCAATCGAG 1 GCCTG-TGTCCCAGACA-AGGTCTTACACG-AATATCAATCGAG * 84168947 GCCTGTGTCCCAGACACGGTCTTACACGA 1 GCCTGTGTCCCAGACAAGGTCTTACACGA 84168976 TGTCTCAGAC Statistics Matches: 57, Mismatches: 8, Indels: 13 0.73 0.10 0.17 Matches are distributed among these distances: 41 1 0.02 42 47 0.82 43 6 0.11 44 3 0.05 ACGTcount: A:0.27, C:0.29, G:0.19, T:0.24 Consensus pattern (41 bp): GCCTGTGTCCCAGACAAGGTCTTACACGAATATCAATCGAG Found at i:84176127 original size:43 final size:43 Alignment explanation

Indices: 84176066--84176215 Score: 155 Period size: 43 Copynumber: 3.5 Consensus size: 43 84176056 CAATGCTGGC * * * 84176066 GTCCCGGACATGGTCTTACATGTAACTCAATATCGATGCCTCT 1 GTCCCAGACATGGTCTTACACGTAACTCAATATCGATGCCTAT * * * 84176109 GTCCCAGACAAGGTCTTACACG-AAATCAGATA-CGATGCCGAT 1 GTCCCAGACATGGTCTTACACGTAACTCA-ATATCGATGCCTAT * * * 84176151 GTCCCAGACATGGTCTTATACGTAAATCTC-A-ATCGAGGCCTGT 1 GTCCCAGACATGGTCTTACACGT-AA-CTCAATATCGATGCCTAT * 84176194 GTCCCAGACACGGTCTTACACG 1 GTCCCAGACATGGTCTTACACG 84176216 ATGTCTCAGA Statistics Matches: 88, Mismatches: 14, Indels: 10 0.79 0.12 0.09 Matches are distributed among these distances: 42 34 0.39 43 50 0.57 44 2 0.02 45 2 0.02 ACGTcount: A:0.27, C:0.28, G:0.21, T:0.25 Consensus pattern (43 bp): GTCCCAGACATGGTCTTACACGTAACTCAATATCGATGCCTAT Found at i:84178328 original size:56 final size:56 Alignment explanation

Indices: 84178242--84178375 Score: 196 Period size: 56 Copynumber: 2.4 Consensus size: 56 84178232 CATGGAATCA * * * * * 84178242 ATATATGTATACGAGTAAAACCACGTTTAATACGTTGGCATCGATATGTGATTTCG 1 ATATATGTGTGCGAGTAAGACCACGTTTAATACGTTGGCATCGATATATGACTTCG * 84178298 ATATATGTGTGCGAGTAAGACCACGTTTAATACGTTGGCATCGATTTATGACTTCG 1 ATATATGTGTGCGAGTAAGACCACGTTTAATACGTTGGCATCGATATATGACTTCG ** 84178354 ATATATGTGTGTAAGTAAGACC 1 ATATATGTGTGCGAGTAAGACC 84178376 CTGTCTGGGA Statistics Matches: 70, Mismatches: 8, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 56 70 1.00 ACGTcount: A:0.31, C:0.14, G:0.22, T:0.34 Consensus pattern (56 bp): ATATATGTGTGCGAGTAAGACCACGTTTAATACGTTGGCATCGATATATGACTTCG Found at i:84186048 original size:36 final size:37 Alignment explanation

Indices: 84186001--84186073 Score: 121 Period size: 37 Copynumber: 2.0 Consensus size: 37 84185991 TACGTATGAT 84186001 CACTTATCAC-TTGTCCCTTGATCAGATAAGTGTAGC 1 CACTTATCACTTTGTCCCTTGATCAGATAAGTGTAGC ** 84186037 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC 1 CACTTATCACTTTGTCCCTTGATCAGATAAGTGTAGC 84186074 TAAAGCTATC Statistics Matches: 34, Mismatches: 2, Indels: 1 0.92 0.05 0.03 Matches are distributed among these distances: 36 10 0.29 37 24 0.71 ACGTcount: A:0.25, C:0.22, G:0.16, T:0.37 Consensus pattern (37 bp): CACTTATCACTTTGTCCCTTGATCAGATAAGTGTAGC Found at i:84186089 original size:46 final size:46 Alignment explanation

Indices: 84186037--84186207 Score: 225 Period size: 46 Copynumber: 3.6 Consensus size: 46 84186027 TAAGTGTAGC * ** 84186037 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGCTAAAGCTAT 1 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCCGAAGCTAT * 84186083 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTAT 1 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCCGAAGCTAT * 84186129 CACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT 1 CACTTATCAC---T---TTGTCTCTTGATCAGATAAGTGTAGCCGAAGCTAT * * 84186181 CACTTATCACTTTATCACTTGATCAGA 1 CACTTATCACTTTGTCTCTTGATCAGA 84186208 AGTACTCAAA Statistics Matches: 112, Mismatches: 7, Indels: 12 0.85 0.05 0.09 Matches are distributed among these distances: 46 67 0.60 49 2 0.02 52 43 0.38 ACGTcount: A:0.28, C:0.22, G:0.14, T:0.36 Consensus pattern (46 bp): CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCCGAAGCTAT Found at i:84186156 original size:52 final size:52 Alignment explanation

Indices: 84186080--84186201 Score: 199 Period size: 52 Copynumber: 2.3 Consensus size: 52 84186070 TAGCTAAAGC * * 84186080 TATCACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACT 1 TATCACTTTTCAC-TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT * 84186133 TATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT 1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT 84186185 TATCACTTTATCACTTG 1 TATCACTTT-TCACTTG 84186202 ATCAGAAGTA Statistics Matches: 65, Mismatches: 3, Indels: 2 0.93 0.04 0.03 Matches are distributed among these distances: 52 46 0.71 53 19 0.29 ACGTcount: A:0.27, C:0.23, G:0.13, T:0.37 Consensus pattern (52 bp): TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT Found at i:84189388 original size:49 final size:49 Alignment explanation

Indices: 84189333--84189527 Score: 309 Period size: 49 Copynumber: 4.0 Consensus size: 49 84189323 TTCGTTTTCT * * * 84189333 CGATGCCATAGTCCAACTATGGTCTTACACGTAATCACAAATCACATAC 1 CGATGCCATAGCCCAGCTATGGTCTTACACGGAATCACAAATCACATAC * * * 84189382 CGATGCCATAGCCCAGCTATGGTCTTACACGGAGTCACATATCACTTAC 1 CGATGCCATAGCCCAGCTATGGTCTTACACGGAATCACAAATCACATAC * * 84189431 CGATGCCATAGCCCAGCTATGGTCTTACACGGAATCACATATCACTTAC 1 CGATGCCATAGCCCAGCTATGGTCTTACACGGAATCACAAATCACATAC 84189480 CGATGCCATAGCCCAGCTATGGTCTTACACGGAATCACATAATCACAT 1 CGATGCCATAGCCCAGCTATGGTCTTACACGGAATCACA-AATCACAT 84189528 GTTCACATGT Statistics Matches: 136, Mismatches: 9, Indels: 1 0.93 0.06 0.01 Matches are distributed among these distances: 49 130 0.96 50 6 0.04 ACGTcount: A:0.30, C:0.30, G:0.16, T:0.24 Consensus pattern (49 bp): CGATGCCATAGCCCAGCTATGGTCTTACACGGAATCACAAATCACATAC Found at i:84190698 original size:36 final size:37 Alignment explanation

Indices: 84190651--84190723 Score: 121 Period size: 37 Copynumber: 2.0 Consensus size: 37 84190641 TACGTATGAT 84190651 CACTTATCAC-TTGTCCCTTGATCAGATAAGTGTAGC 1 CACTTATCACTTTGTCCCTTGATCAGATAAGTGTAGC ** 84190687 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC 1 CACTTATCACTTTGTCCCTTGATCAGATAAGTGTAGC 84190724 TAAAGCTATC Statistics Matches: 34, Mismatches: 2, Indels: 1 0.92 0.05 0.03 Matches are distributed among these distances: 36 10 0.29 37 24 0.71 ACGTcount: A:0.25, C:0.22, G:0.16, T:0.37 Consensus pattern (37 bp): CACTTATCACTTTGTCCCTTGATCAGATAAGTGTAGC Found at i:84190739 original size:46 final size:46 Alignment explanation

Indices: 84190687--84190857 Score: 225 Period size: 46 Copynumber: 3.6 Consensus size: 46 84190677 TAAGTGTAGC * ** 84190687 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGCTAAAGCTAT 1 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCCGAAGCTAT * 84190733 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTAT 1 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCCGAAGCTAT * 84190779 CACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT 1 CACTTATCAC---T---TTGTCTCTTGATCAGATAAGTGTAGCCGAAGCTAT * * 84190831 CACTTATCACTTTATCACTTGATCAGA 1 CACTTATCACTTTGTCTCTTGATCAGA 84190858 AGTACTCAAA Statistics Matches: 112, Mismatches: 7, Indels: 12 0.85 0.05 0.09 Matches are distributed among these distances: 46 67 0.60 49 2 0.02 52 43 0.38 ACGTcount: A:0.28, C:0.22, G:0.14, T:0.36 Consensus pattern (46 bp): CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCCGAAGCTAT Found at i:84190806 original size:52 final size:52 Alignment explanation

Indices: 84190730--84190851 Score: 199 Period size: 52 Copynumber: 2.3 Consensus size: 52 84190720 TAGCTAAAGC * * 84190730 TATCACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACT 1 TATCACTTTTCAC-TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT * 84190783 TATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT 1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT 84190835 TATCACTTTATCACTTG 1 TATCACTTT-TCACTTG 84190852 ATCAGAAGTA Statistics Matches: 65, Mismatches: 3, Indels: 2 0.93 0.04 0.03 Matches are distributed among these distances: 52 46 0.71 53 19 0.29 ACGTcount: A:0.27, C:0.23, G:0.13, T:0.37 Consensus pattern (52 bp): TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT Found at i:84200793 original size:42 final size:43 Alignment explanation

Indices: 84200743--84200824 Score: 105 Period size: 43 Copynumber: 1.9 Consensus size: 43 84200733 TAGGACCATC ** * * 84200743 TCTGGGACATCGGCATC-ATATCT-AATTTCGTGTAAGACCCTA 1 TCTGGGACAGAGGCATCGATAT-TGAATTACATGTAAGACCCTA 84200785 TCTGGGACAGAGGCATCGATATTGAATTACATGTAAGACC 1 TCTGGGACAGAGGCATCGATATTGAATTACATGTAAGACC 84200825 ACGTCAGAGA Statistics Matches: 34, Mismatches: 4, Indels: 3 0.83 0.10 0.07 Matches are distributed among these distances: 42 16 0.47 43 18 0.53 ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28 Consensus pattern (43 bp): TCTGGGACAGAGGCATCGATATTGAATTACATGTAAGACCCTA Found at i:84211855 original size:28 final size:28 Alignment explanation

Indices: 84211792--84212001 Score: 341 Period size: 28 Copynumber: 7.5 Consensus size: 28 84211782 ATATTAAGTC * * 84211792 CGCACACTCAGTGCTATATAATC-AACT 1 CGCACACTTAGTGCTACATAATCAAACT * 84211819 CGCACACTTAGTGCTATATAATCAAACT 1 CGCACACTTAGTGCTACATAATCAAACT 84211847 CGCACACTTAGTGCTACATAATCAAACT 1 CGCACACTTAGTGCTACATAATCAAACT * * 84211875 CGCACACCTAGTGCTACATAATCAAATT 1 CGCACACTTAGTGCTACATAATCAAACT * 84211903 CGCACACTTAGTGCTACATAATCAAGCT 1 CGCACACTTAGTGCTACATAATCAAACT * 84211931 CGCACACTTAGTGCTACATAATCAAGCT 1 CGCACACTTAGTGCTACATAATCAAACT * 84211959 CGCACACTTAGTGCTACATAATCAAGCT 1 CGCACACTTAGTGCTACATAATCAAACT 84211987 CGCACACTTAGTGCT 1 CGCACACTTAGTGCT 84212002 GTACAATTTA Statistics Matches: 175, Mismatches: 7, Indels: 1 0.96 0.04 0.01 Matches are distributed among these distances: 27 22 0.13 28 153 0.87 ACGTcount: A:0.33, C:0.29, G:0.13, T:0.26 Consensus pattern (28 bp): CGCACACTTAGTGCTACATAATCAAACT Found at i:84220147 original size:28 final size:28 Alignment explanation

Indices: 84220084--84220293 Score: 341 Period size: 28 Copynumber: 7.5 Consensus size: 28 84220074 ATATTAAGTC * * 84220084 CGCACACTCAGTGCTATATAATC-AACT 1 CGCACACTTAGTGCTACATAATCAAACT * 84220111 CGCACACTTAGTGCTATATAATCAAACT 1 CGCACACTTAGTGCTACATAATCAAACT 84220139 CGCACACTTAGTGCTACATAATCAAACT 1 CGCACACTTAGTGCTACATAATCAAACT * * 84220167 CGCACACCTAGTGCTACATAATCAAATT 1 CGCACACTTAGTGCTACATAATCAAACT * 84220195 CGCACACTTAGTGCTACATAATCAAGCT 1 CGCACACTTAGTGCTACATAATCAAACT * 84220223 CGCACACTTAGTGCTACATAATCAAGCT 1 CGCACACTTAGTGCTACATAATCAAACT * 84220251 CGCACACTTAGTGCTACATAATCAAGCT 1 CGCACACTTAGTGCTACATAATCAAACT 84220279 CGCACACTTAGTGCT 1 CGCACACTTAGTGCT 84220294 GTACAATTTA Statistics Matches: 175, Mismatches: 7, Indels: 1 0.96 0.04 0.01 Matches are distributed among these distances: 27 22 0.13 28 153 0.87 ACGTcount: A:0.33, C:0.29, G:0.13, T:0.26 Consensus pattern (28 bp): CGCACACTTAGTGCTACATAATCAAACT Found at i:84227617 original size:47 final size:47 Alignment explanation

Indices: 84227554--84227989 Score: 683 Period size: 47 Copynumber: 9.3 Consensus size: 47 84227544 CCCTTCGGGA * * 84227554 CTTATCACATTTATACACTTTCACATCCATCACATTGGCCATTCGGC 1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC * * * * * * 84227601 CTTATCACATATATACACCTTCACATCCATCACATCGACCATTAGGT 1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC * * 84227648 CTTATCTCATATATACACTTTCACATTCATCACATTGGCCATTAGGC 1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC * * * 84227695 CTTATCACATATATACACTTTCACATTCATCACGTTGGCCACTCGGT 1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC * * 84227742 CTTATCACATATATACACTTTCACATTCATCACGTTGGCCACTCGGC 1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC 84227789 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC 1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC * * 84227836 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC 1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC * 84227883 CTTATCACATATACACACTTTCACATTCATCACATTGGCCATTCGGC 1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC * * * 84227930 CTTATCACATATATACACTTTCACATTCATCACGTCGGCCATTAGGC 1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC 84227977 CTTATCACATATA 1 CTTATCACATATA 84227990 CACAACTTGT Statistics Matches: 360, Mismatches: 29, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 47 360 1.00 ACGTcount: A:0.28, C:0.30, G:0.09, T:0.33 Consensus pattern (47 bp): CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC Found at i:84232448 original size:40 final size:40 Alignment explanation

Indices: 84232388--84232571 Score: 235 Period size: 40 Copynumber: 4.6 Consensus size: 40 84232378 TATTCGAATG * * 84232388 ATATCCGGGCTAAGTCCCGAAGGCTTTTATGCTAGTGACT 1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGACT * * * * * 84232428 ATATCCGGACTGAGATCCGAAGGCATTTGTGCGAGTTG-CT 1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAG-TGACT * * * 84232468 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGATT 1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGACT * * * 84232508 ATATCTGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACC 1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGACT 84232548 ATATCCGGGCTAAGACCCGAAGGC 1 ATATCCGGGCTAAGACCCGAAGGC 84232572 CTTGTGCGAG Statistics Matches: 121, Mismatches: 21, Indels: 4 0.83 0.14 0.03 Matches are distributed among these distances: 39 1 0.01 40 118 0.98 41 2 0.02 ACGTcount: A:0.24, C:0.23, G:0.27, T:0.26 Consensus pattern (40 bp): ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGACT Found at i:84238840 original size:18 final size:18 Alignment explanation

Indices: 84238803--84238840 Score: 51 Period size: 18 Copynumber: 2.1 Consensus size: 18 84238793 AAAAAATCAC * 84238803 ATTTTTTATATTTAATAT 1 ATTTTTTATATTTAAAAT 84238821 ATTTTTTA-ATTTCAAAAT 1 ATTTTTTATATTT-AAAAT 84238839 AT 1 AT 84238841 ATTGTGGCAA Statistics Matches: 18, Mismatches: 1, Indels: 2 0.86 0.05 0.10 Matches are distributed among these distances: 17 4 0.22 18 14 0.78 ACGTcount: A:0.37, C:0.03, G:0.00, T:0.61 Consensus pattern (18 bp): ATTTTTTATATTTAAAAT Found at i:84241251 original size:46 final size:45 Alignment explanation

Indices: 84241155--84241251 Score: 117 Period size: 45 Copynumber: 2.2 Consensus size: 45 84241145 CATTTTCATT * 84241155 TCCATTT-A-AGAAAACCACATTCATTTCCAAATGATTCCATTTC 1 TCCATTTCAGAGAAAACCACAATCATTTCCAAATGATTCCATTTC * ** * 84241198 TCCATTTCAGAGAAAACCATAATCATTTCTGAATGTTTTCCATTTC 1 TCCATTTCAGAGAAAACCACAATCATTTCCAAATG-ATTCCATTTC * 84241244 TCTATTTC 1 TCCATTTC 84241252 TATTCATTCT Statistics Matches: 45, Mismatches: 6, Indels: 3 0.83 0.11 0.06 Matches are distributed among these distances: 43 7 0.16 44 1 0.02 45 21 0.47 46 16 0.36 ACGTcount: A:0.31, C:0.24, G:0.06, T:0.39 Consensus pattern (45 bp): TCCATTTCAGAGAAAACCACAATCATTTCCAAATGATTCCATTTC Found at i:84246616 original size:24 final size:24 Alignment explanation

Indices: 84246566--84246637 Score: 74 Period size: 23 Copynumber: 3.0 Consensus size: 24 84246556 TAATACAATA * * * * 84246566 AATTATAATTTTTTGAGATAA-TA 1 AATTATAATTTTTTTAAAAAATTT 84246589 AATTATAATTTTTTTAAAAAATTT 1 AATTATAATTTTTTTAAAAAATTT * * 84246613 AATTAAAATTATTTTAAAACAATTT 1 AATTATAATTTTTTTAAAA-AATTT 84246638 TAAAATTAAT Statistics Matches: 41, Mismatches: 6, Indels: 2 0.84 0.12 0.04 Matches are distributed among these distances: 23 18 0.44 24 18 0.44 25 5 0.12 ACGTcount: A:0.47, C:0.01, G:0.03, T:0.49 Consensus pattern (24 bp): AATTATAATTTTTTTAAAAAATTT Found at i:84246689 original size:17 final size:18 Alignment explanation

Indices: 84246656--84246692 Score: 58 Period size: 17 Copynumber: 2.1 Consensus size: 18 84246646 ATGACCTTAA * 84246656 AATTATAAAGGATAAAAT 1 AATTATAAAGAATAAAAT 84246674 AATTAT-AAGAATAAAAT 1 AATTATAAAGAATAAAAT 84246691 AA 1 AA 84246693 CTGTTGTAAA Statistics Matches: 18, Mismatches: 1, Indels: 1 0.90 0.05 0.05 Matches are distributed among these distances: 17 12 0.67 18 6 0.33 ACGTcount: A:0.65, C:0.00, G:0.08, T:0.27 Consensus pattern (18 bp): AATTATAAAGAATAAAAT Found at i:84271579 original size:17 final size:17 Alignment explanation

Indices: 84271559--84271610 Score: 61 Period size: 17 Copynumber: 3.0 Consensus size: 17 84271549 GTTAAGAAAA 84271559 TAATTTAATTAATAAAT 1 TAATTTAATTAATAAAT * 84271576 TAATTTAGTTAATTAAAT 1 TAATTTAATTAA-TAAAT * 84271594 TGA-TTAATTAAATAAAT 1 TAATTTAATT-AATAAAT 84271611 AATATTTTGG Statistics Matches: 30, Mismatches: 3, Indels: 4 0.81 0.08 0.11 Matches are distributed among these distances: 17 21 0.70 18 9 0.30 ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46 Consensus pattern (17 bp): TAATTTAATTAATAAAT Found at i:84273339 original size:6 final size:6 Alignment explanation

Indices: 84273330--84273367 Score: 76 Period size: 6 Copynumber: 6.3 Consensus size: 6 84273320 TCAAAATCAC 84273330 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TT 1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TT 84273368 GTATTTCTAT Statistics Matches: 32, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 6 32 1.00 ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84 Consensus pattern (6 bp): TTTCTT Found at i:84276204 original size:7 final size:7 Alignment explanation

Indices: 84276192--84276226 Score: 70 Period size: 7 Copynumber: 5.0 Consensus size: 7 84276182 AGAGATATAG 84276192 GTGGCAA 1 GTGGCAA 84276199 GTGGCAA 1 GTGGCAA 84276206 GTGGCAA 1 GTGGCAA 84276213 GTGGCAA 1 GTGGCAA 84276220 GTGGCAA 1 GTGGCAA 84276227 TGAAAAGGGT Statistics Matches: 28, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 7 28 1.00 ACGTcount: A:0.29, C:0.14, G:0.43, T:0.14 Consensus pattern (7 bp): GTGGCAA Found at i:84276592 original size:3 final size:3 Alignment explanation

Indices: 84276584--84276618 Score: 61 Period size: 3 Copynumber: 11.7 Consensus size: 3 84276574 ATAGATTAAG * 84276584 ATT ATT ATT ACT ATT ATT ATT ATT ATT ATT ATT AT 1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT 84276619 AGTATAACAA Statistics Matches: 30, Mismatches: 2, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 3 30 1.00 ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63 Consensus pattern (3 bp): ATT Found at i:84287443 original size:40 final size:40 Alignment explanation

Indices: 84287366--84287623 Score: 405 Period size: 40 Copynumber: 6.5 Consensus size: 40 84287356 AAACCAAGTA * * 84287366 CCTTCGGGATTTAG-CCGGATATAGCT-ACTCGCTCAAATG 1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG * 84287405 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG 1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG * 84287445 CCTTCGGGACCTAGCCCGGATATAGTAACTCGCACAAATG 1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG * 84287485 CCTTCGGGACTTAGCCCGAATATAGTAACTCGCACAAATG 1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG 84287525 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG 1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG * * * 84287565 CCTTCGGGACTTAGCCTGGA-ATTAGTCACTAGCACAAATG 1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG 84287605 CCTTCGGGACTTAGCCCGG 1 CCTTCGGGACTTAGCCCGG 84287624 TTATCATCCG Statistics Matches: 204, Mismatches: 12, Indels: 5 0.92 0.05 0.02 Matches are distributed among these distances: 39 15 0.07 40 189 0.93 ACGTcount: A:0.26, C:0.28, G:0.23, T:0.24 Consensus pattern (40 bp): CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG Found at i:84296809 original size:27 final size:27 Alignment explanation

Indices: 84296779--84296956 Score: 171 Period size: 27 Copynumber: 6.6 Consensus size: 27 84296769 ATATTGAGCC * * 84296779 CGCACACTCAGTGCTATATAATCAACT 1 CGCACACTTAGTGCTACATAATCAACT ** * * 84296806 CGCACACTTAGTGCTATGTAACCAAAT 1 CGCACACTTAGTGCTACATAATCAACT * 84296833 CGCACACTTAGTGCTACATAGTCAAACT 1 CGCACACTTAGTGCTACATAATC-AACT ** * * 84296861 CGCACACTTAGTGCCGCATGATCAATT 1 CGCACACTTAGTGCTACATAATCAACT * ** 84296888 CGCACACTTAGTGC-ATCATATTCATTT 1 CGCACACTTAGTGCTA-CATAATCAACT * * 84296915 CGCACACTTAGTGCAACATAGTCGAA-T 1 CGCACACTTAGTGCTACATAATC-AACT 84296942 CGCACACTTAGTGCT 1 CGCACACTTAGTGCT 84296957 GTACAATTTA Statistics Matches: 126, Mismatches: 21, Indels: 8 0.81 0.14 0.05 Matches are distributed among these distances: 27 102 0.81 28 24 0.19 ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27 Consensus pattern (27 bp): CGCACACTTAGTGCTACATAATCAACT Found at i:84298815 original size:40 final size:40 Alignment explanation

Indices: 84298738--84298955 Score: 334 Period size: 40 Copynumber: 5.5 Consensus size: 40 84298728 AAACCAAGTA * * 84298738 CCTTCGGGATTTAG-CCGGATATAGCT-ACTCGCTCAAATG 1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG * 84298777 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG 1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG * 84298817 CCTTCGGGACCTAGCCCGGATATAGTAACTCGCACAAATG 1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG 84298857 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG 1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG * * * 84298897 CCTTCGGGACTTAGCCCGGA-ATTAGTCACTAGCATAAATG 1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG 84298937 CCTTCGGGACTTAGCCCGG 1 CCTTCGGGACTTAGCCCGG 84298956 TTATCATCCG Statistics Matches: 167, Mismatches: 9, Indels: 5 0.92 0.05 0.03 Matches are distributed among these distances: 39 15 0.09 40 152 0.91 ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24 Consensus pattern (40 bp): CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG Found at i:84301718 original size:30 final size:31 Alignment explanation

Indices: 84301692--84301750 Score: 84 Period size: 30 Copynumber: 1.9 Consensus size: 31 84301682 GTAAATACTC * * * 84301692 AAAATTTGAGGGATTAA-AGTGCAAATATAA 1 AAAATTTGAAGGACTAATAGTACAAATATAA 84301722 AAAATTTGAAGGACTAATAGTACAAATAT 1 AAAATTTGAAGGACTAATAGTACAAATAT 84301751 TTTAAGGGTG Statistics Matches: 25, Mismatches: 3, Indels: 1 0.86 0.10 0.03 Matches are distributed among these distances: 30 15 0.60 31 10 0.40 ACGTcount: A:0.51, C:0.05, G:0.17, T:0.27 Consensus pattern (31 bp): AAAATTTGAAGGACTAATAGTACAAATATAA Found at i:84311767 original size:40 final size:40 Alignment explanation

Indices: 84311717--84311801 Score: 116 Period size: 40 Copynumber: 2.1 Consensus size: 40 84311707 TAATTTTTTT * * * 84311717 GCGGTATTTTTTAAAAAACGCCGCTAATGCTAGATCTATA 1 GCGGCATTTTTCAAAAAACACCGCTAATGCTAGATCTATA ** * 84311757 GCGGCATTTTTCAAAAGGCACCGCTAATGCTCGATCTATA 1 GCGGCATTTTTCAAAAAACACCGCTAATGCTAGATCTATA 84311797 GCGGC 1 GCGGC 84311802 GATAGCAGCG Statistics Matches: 39, Mismatches: 6, Indels: 0 0.87 0.13 0.00 Matches are distributed among these distances: 40 39 1.00 ACGTcount: A:0.28, C:0.22, G:0.21, T:0.28 Consensus pattern (40 bp): GCGGCATTTTTCAAAAAACACCGCTAATGCTAGATCTATA Found at i:84311969 original size:22 final size:22 Alignment explanation

Indices: 84311937--84311981 Score: 81 Period size: 22 Copynumber: 2.0 Consensus size: 22 84311927 GTTTTTCATG * 84311937 AAACGCTGCTAATGCTCGATCT 1 AAACGCCGCTAATGCTCGATCT 84311959 AAACGCCGCTAATGCTCGATCT 1 AAACGCCGCTAATGCTCGATCT 84311981 A 1 A 84311982 TAGTGGCGTT Statistics Matches: 22, Mismatches: 1, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 22 22 1.00 ACGTcount: A:0.29, C:0.29, G:0.18, T:0.24 Consensus pattern (22 bp): AAACGCCGCTAATGCTCGATCT Found at i:84312706 original size:40 final size:40 Alignment explanation

Indices: 84312651--84312730 Score: 160 Period size: 40 Copynumber: 2.0 Consensus size: 40 84312641 TTATTAAGTT 84312651 TATTTTTTACATTTCACTAACGAGCTCCAAGTAACGATTC 1 TATTTTTTACATTTCACTAACGAGCTCCAAGTAACGATTC 84312691 TATTTTTTACATTTCACTAACGAGCTCCAAGTAACGATTC 1 TATTTTTTACATTTCACTAACGAGCTCCAAGTAACGATTC 84312731 GATGATTGGT Statistics Matches: 40, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 40 40 1.00 ACGTcount: A:0.30, C:0.23, G:0.10, T:0.38 Consensus pattern (40 bp): TATTTTTTACATTTCACTAACGAGCTCCAAGTAACGATTC Found at i:84318888 original size:111 final size:111 Alignment explanation

Indices: 84318694--84319255 Score: 1092 Period size: 111 Copynumber: 5.1 Consensus size: 111 84318684 AGCCTTTAAC * 84318694 TTTTGTTGCTTTTAATAATTTGTGAACATTTCTCTTAAACAAAATAGTGAGCTGTGAGTATCACA 1 TTTTGTTGCTTTTAATAATTTTTGAACATTTCTCTTAAACAAAATAGTGAGCTGTGAGTATCACA 84318759 TGTAGTCTTCTAGGTTCTGCTTTCAGCTGATTGTTAATTTTTTTCT 66 TGTAGTCTTCTAGGTTCTGCTTTCAGCTGATTGTTAATTTTTTTCT * 84318805 TTTTGTTGCTTTTAATAATTTGTGAACATTTCTCTTAAACAAAATAGTGAGCTGTGAGTATCACA 1 TTTTGTTGCTTTTAATAATTTTTGAACATTTCTCTTAAACAAAATAGTGAGCTGTGAGTATCACA 84318870 TGTAGTCTTCTAGGTTCTGCTTTCAGCTGATTGTTAA-TTTTTTCT 66 TGTAGTCTTCTAGGTTCTGCTTTCAGCTGATTGTTAATTTTTTTCT 84318915 TTTTGTTGCTTTTAATAATTTTTGAACATTTCTCTTAAAC-AAATAGTGAGCTGTGAGTATCACA 1 TTTTGTTGCTTTTAATAATTTTTGAACATTTCTCTTAAACAAAATAGTGAGCTGTGAGTATCACA 84318979 TGTAGTCTTCTAGGTTCTGCTTTCAGCTGATTGTTAATTTTTTTCT 66 TGTAGTCTTCTAGGTTCTGCTTTCAGCTGATTGTTAATTTTTTTCT 84319025 TTTTGTTGCTTTTAATAATTTTTGAACATTTCTCTTAAACAAAATAGTGAGCTGTGAGTATCACA 1 TTTTGTTGCTTTTAATAATTTTTGAACATTTCTCTTAAACAAAATAGTGAGCTGTGAGTATCACA 84319090 TGTAGTCTTCTAGGTTCTGCTTTCAGCTGATTGTTAATTTTTTTCT 66 TGTAGTCTTCTAGGTTCTGCTTTCAGCTGATTGTTAATTTTTTTCT 84319136 TTTTGTTGCTTTTAATAATTTTTGAACATTTCTCTTAAACAAAATAGTGAGCTGTGAGTATCACA 1 TTTTGTTGCTTTTAATAATTTTTGAACATTTCTCTTAAACAAAATAGTGAGCTGTGAGTATCACA 84319201 TGTAGTCTTCTAGGTTCTGCTTTCAGCTGATTGTTAATTTTTTTCT 66 TGTAGTCTTCTAGGTTCTGCTTTCAGCTGATTGTTAATTTTTTTCT 84319247 TTTTGTTGC 1 TTTTGTTGC 84319256 ATCCCATTGG Statistics Matches: 448, Mismatches: 1, Indels: 4 0.99 0.00 0.01 Matches are distributed among these distances: 109 61 0.14 110 95 0.21 111 292 0.65 ACGTcount: A:0.23, C:0.14, G:0.16, T:0.48 Consensus pattern (111 bp): TTTTGTTGCTTTTAATAATTTTTGAACATTTCTCTTAAACAAAATAGTGAGCTGTGAGTATCACA TGTAGTCTTCTAGGTTCTGCTTTCAGCTGATTGTTAATTTTTTTCT Found at i:84319077 original size:220 final size:222 Alignment explanation

Indices: 84318694--84319255 Score: 1092 Period size: 220 Copynumber: 2.5 Consensus size: 222 84318684 AGCCTTTAAC * 84318694 TTTTGTTGCTTTTAATAATTTGTGAACATTTCTCTTAAACAAAATAGTGAGCTGTGAGTATCACA 1 TTTTGTTGCTTTTAATAATTTTTGAACATTTCTCTTAAACAAAATAGTGAGCTGTGAGTATCACA 84318759 TGTAGTCTTCTAGGTTCTGCTTTCAGCTGATTGTTAATTTTTTTCTTTTTGTTGCTTTTAATAAT 66 TGTAGTCTTCTAGGTTCTGCTTTCAGCTGATTGTTAATTTTTTTCTTTTTGTTGCTTTTAATAAT 84318824 TTGTGAACATTTCTCTTAAACAAAATAGTGAGCTGTGAGTATCACATGTAGTCTTCTAGGTTCTG 131 TTGTGAACATTTCTCTTAAACAAAATAGTGAGCTGTGAGTATCACATGTAGTCTTCTAGGTTCTG 84318889 CTTTCAGCTGATTGTTAA-TTTTTTCT 196 CTTTCAGCTGATTGTTAATTTTTTTCT 84318915 TTTTGTTGCTTTTAATAATTTTTGAACATTTCTCTTAAAC-AAATAGTGAGCTGTGAGTATCACA 1 TTTTGTTGCTTTTAATAATTTTTGAACATTTCTCTTAAACAAAATAGTGAGCTGTGAGTATCACA 84318979 TGTAGTCTTCTAGGTTCTGCTTTCAGCTGATTGTTAATTTTTTTCTTTTTGTTGCTTTTAATAAT 66 TGTAGTCTTCTAGGTTCTGCTTTCAGCTGATTGTTAATTTTTTTCTTTTTGTTGCTTTTAATAAT * 84319044 TTTTGAACATTTCTCTTAAACAAAATAGTGAGCTGTGAGTATCACATGTAGTCTTCTAGGTTCTG 131 TTGTGAACATTTCTCTTAAACAAAATAGTGAGCTGTGAGTATCACATGTAGTCTTCTAGGTTCTG 84319109 CTTTCAGCTGATTGTTAATTTTTTTCT 196 CTTTCAGCTGATTGTTAATTTTTTTCT 84319136 TTTTGTTGCTTTTAATAATTTTTGAACATTTCTCTTAAACAAAATAGTGAGCTGTGAGTATCACA 1 TTTTGTTGCTTTTAATAATTTTTGAACATTTCTCTTAAACAAAATAGTGAGCTGTGAGTATCACA 84319201 TGTAGTCTTCTAGGTTCTGCTTTCAGCTGATTGTTAATTTTTTTCTTTTTGTTGC 66 TGTAGTCTTCTAGGTTCTGCTTTCAGCTGATTGTTAATTTTTTTCTTTTTGTTGC 84319256 ATCCCATTGG Statistics Matches: 337, Mismatches: 2, Indels: 3 0.99 0.01 0.01 Matches are distributed among these distances: 220 171 0.51 221 87 0.26 222 79 0.23 ACGTcount: A:0.23, C:0.14, G:0.16, T:0.48 Consensus pattern (222 bp): TTTTGTTGCTTTTAATAATTTTTGAACATTTCTCTTAAACAAAATAGTGAGCTGTGAGTATCACA TGTAGTCTTCTAGGTTCTGCTTTCAGCTGATTGTTAATTTTTTTCTTTTTGTTGCTTTTAATAAT TTGTGAACATTTCTCTTAAACAAAATAGTGAGCTGTGAGTATCACATGTAGTCTTCTAGGTTCTG CTTTCAGCTGATTGTTAATTTTTTTCT Found at i:84320580 original size:16 final size:16 Alignment explanation

Indices: 84320555--84320592 Score: 51 Period size: 16 Copynumber: 2.4 Consensus size: 16 84320545 TTTTATTGGA 84320555 ATAATATTTTAGTTAAT 1 ATAAT-TTTTAGTTAAT * 84320572 ATAATTTTTATTTAAT 1 ATAATTTTTAGTTAAT 84320588 A-AATT 1 ATAATT 84320593 CTAATTAATA Statistics Matches: 20, Mismatches: 1, Indels: 2 0.87 0.04 0.09 Matches are distributed among these distances: 15 4 0.20 16 11 0.55 17 5 0.25 ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55 Consensus pattern (16 bp): ATAATTTTTAGTTAAT Found at i:84325065 original size:20 final size:20 Alignment explanation

Indices: 84325003--84325066 Score: 53 Period size: 20 Copynumber: 3.2 Consensus size: 20 84324993 ATTATAAAAA * 84325003 ATAAAAATCAATAAAA--GTT 1 ATAAAAATC-ATAAAATTTTT * * 84325022 ATAAAAATCATTAAATTTTA 1 ATAAAAATCATAAAATTTTT * 84325042 ATAAAAAT-GTAAAATTATTT 1 ATAAAAATCATAAAATT-TTT 84325062 ATAAA 1 ATAAA 84325067 TTATTAAAAA Statistics Matches: 36, Mismatches: 6, Indels: 5 0.77 0.13 0.11 Matches are distributed among these distances: 18 5 0.14 19 15 0.42 20 16 0.44 ACGTcount: A:0.59, C:0.03, G:0.03, T:0.34 Consensus pattern (20 bp): ATAAAAATCATAAAATTTTT Found at i:84332271 original size:49 final size:52 Alignment explanation

Indices: 84332190--84332297 Score: 141 Period size: 49 Copynumber: 2.1 Consensus size: 52 84332180 TATAGTGTTT * * 84332190 CAGGTGTGTTTTGAGGGAGGATGTAAAGCCTACGGGCTTGACACTTGGTGCC 1 CAGGTGTGTTTTGAGAGAGGATGTAAAGCCTACGGGCTTGACACTTAGTGCC * * * * 84332242 GAGGTGTGTTTTG-GAG-GGATGT-TAGCCTACGGGTTTGGCACTTAGTGCC 1 CAGGTGTGTTTTGAGAGAGGATGTAAAGCCTACGGGCTTGACACTTAGTGCC 84332291 CAGGTGT 1 CAGGTGT 84332298 ATTCTCAGTT Statistics Matches: 49, Mismatches: 7, Indels: 3 0.83 0.12 0.05 Matches are distributed among these distances: 49 29 0.59 50 6 0.12 51 2 0.04 52 12 0.24 ACGTcount: A:0.17, C:0.16, G:0.38, T:0.30 Consensus pattern (52 bp): CAGGTGTGTTTTGAGAGAGGATGTAAAGCCTACGGGCTTGACACTTAGTGCC Found at i:84333160 original size:21 final size:21 Alignment explanation

Indices: 84333121--84333162 Score: 59 Period size: 21 Copynumber: 2.0 Consensus size: 21 84333111 TTTAAAGCAA * 84333121 GTATCGATACTTTGGCATTTG 1 GTATCGATACTTTGCCATTTG 84333142 GTATCGATAC-TTGACCATTTG 1 GTATCGATACTTTG-CCATTTG 84333163 AATAGTTTTC Statistics Matches: 19, Mismatches: 1, Indels: 2 0.86 0.05 0.09 Matches are distributed among these distances: 20 3 0.16 21 16 0.84 ACGTcount: A:0.21, C:0.17, G:0.21, T:0.40 Consensus pattern (21 bp): GTATCGATACTTTGCCATTTG Found at i:84333219 original size:18 final size:18 Alignment explanation

Indices: 84333191--84333226 Score: 56 Period size: 18 Copynumber: 2.0 Consensus size: 18 84333181 CAAAATGCTA 84333191 ATTTGGTATCGAT-TTTT 1 ATTTGGTATCGATATTTT 84333208 ATTTGAGTATCGATATTTT 1 ATTTG-GTATCGATATTTT 84333227 TTCATAAAAT Statistics Matches: 17, Mismatches: 0, Indels: 2 0.89 0.00 0.11 Matches are distributed among these distances: 17 5 0.29 18 8 0.47 19 4 0.24 ACGTcount: A:0.22, C:0.06, G:0.17, T:0.56 Consensus pattern (18 bp): ATTTGGTATCGATATTTT Found at i:84337410 original size:48 final size:48 Alignment explanation

Indices: 84337335--84337572 Score: 262 Period size: 48 Copynumber: 5.0 Consensus size: 48 84337325 AGGGTAAATA * * * * * 84337335 GCCGATGCCATGTTCTAGACATGGTCTTACACTGGCTCACATGTCGAG 1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATCAAG * * * * * * 84337383 GCCAATGCCATGTCCCAGACATGGTCTTATACTAGCTCTCTTCTCAAT 1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATCAAG * ** * * 84337431 GCCGATGCCATTTCTTAGACATGGTCTTACACTAGCACACATATCAAC 1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATCAAG * * ** 84337479 GCCGATGCCATGTCCCAGATATGGTCTTACACTAGCTCTCATAAT-GTG 1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACAT-ATCAAG * * 84337527 GTCGATGCCATGTCCCAGACATGGTCTTACACTAGCACACATATCA 1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATCA 84337573 CCCAAATGTT Statistics Matches: 154, Mismatches: 34, Indels: 4 0.80 0.18 0.02 Matches are distributed among these distances: 47 2 0.01 48 150 0.97 49 2 0.01 ACGTcount: A:0.25, C:0.29, G:0.18, T:0.28 Consensus pattern (48 bp): GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATCAAG Found at i:84337503 original size:96 final size:94 Alignment explanation

Indices: 84337335--84337572 Score: 291 Period size: 96 Copynumber: 2.5 Consensus size: 94 84337325 AGGGTAAATA * * * * * 84337335 GCCGATGCCATGTTCTAGACATGGTCTTACACTGGCTCACATGTCGAGGCCAATGCCATGTCCCA 1 GCCGATGCCAT-TTCTAGACATGGTCTTACACTAGCACACATATCAACGCCAATGCCATGTCCCA * * 84337400 GACATGGTCTTATACTAGCTCTCTTCTCAA-T- 65 GACATGGTCTTACACTAGCTCTC--AT-AAGTG * 84337431 GCCGATGCCATTTCTTAGACATGGTCTTACACTAGCACACATATCAACGCCGATGCCATGTCCCA 1 GCCGATGCCATTTC-TAGACATGGTCTTACACTAGCACACATATCAACGCCAATGCCATGTCCCA * 84337496 GATATGGTCTTACACTAGCTCTCATAATGTG 65 GACATGGTCTTACACTAGCTCTCATAA-GTG * * * 84337527 GTCGATGCCATGTCCCAGACATGGTCTTACACTAGCACACATATCA 1 GCCGATGCCAT-TTCTAGACATGGTCTTACACTAGCACACATATCA 84337573 CCCAAATGTT Statistics Matches: 125, Mismatches: 12, Indels: 10 0.85 0.08 0.07 Matches are distributed among these distances: 93 2 0.02 94 1 0.01 95 4 0.03 96 116 0.93 97 2 0.02 ACGTcount: A:0.25, C:0.29, G:0.18, T:0.28 Consensus pattern (94 bp): GCCGATGCCATTTCTAGACATGGTCTTACACTAGCACACATATCAACGCCAATGCCATGTCCCAG ACATGGTCTTACACTAGCTCTCATAAGTG Found at i:84343980 original size:26 final size:26 Alignment explanation

Indices: 84343944--84343999 Score: 103 Period size: 26 Copynumber: 2.2 Consensus size: 26 84343934 CATAAAAGAG 84343944 TTAATTTTATTGTTGGATTCTATTAA 1 TTAATTTTATTGTTGGATTCTATTAA * 84343970 TTAATTTTATTGTTGGATTCTGTTAA 1 TTAATTTTATTGTTGGATTCTATTAA 84343996 TTAA 1 TTAA 84344000 ATGAAATTAA Statistics Matches: 29, Mismatches: 1, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 26 29 1.00 ACGTcount: A:0.27, C:0.04, G:0.12, T:0.57 Consensus pattern (26 bp): TTAATTTTATTGTTGGATTCTATTAA Found at i:84348872 original size:36 final size:36 Alignment explanation

Indices: 84348825--84348896 Score: 144 Period size: 36 Copynumber: 2.0 Consensus size: 36 84348815 TCCATATTCG 84348825 GATGAACTAGTAATAATTTCAATTCATGAGACAAAC 1 GATGAACTAGTAATAATTTCAATTCATGAGACAAAC 84348861 GATGAACTAGTAATAATTTCAATTCATGAGACAAAC 1 GATGAACTAGTAATAATTTCAATTCATGAGACAAAC 84348897 TTTAGAATAA Statistics Matches: 36, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 36 36 1.00 ACGTcount: A:0.44, C:0.14, G:0.14, T:0.28 Consensus pattern (36 bp): GATGAACTAGTAATAATTTCAATTCATGAGACAAAC Found at i:84350217 original size:19 final size:20 Alignment explanation

Indices: 84350193--84350230 Score: 53 Period size: 19 Copynumber: 1.9 Consensus size: 20 84350183 GGTACCACCA 84350193 AAACAT-ATATCA-CATCTTT 1 AAACATCAT-TCATCATCTTT 84350212 AAACATCATTCATCATCTT 1 AAACATCATTCATCATCTT 84350231 ACCACCTTAT Statistics Matches: 17, Mismatches: 0, Indels: 3 0.85 0.00 0.15 Matches are distributed among these distances: 19 9 0.53 20 8 0.47 ACGTcount: A:0.39, C:0.24, G:0.00, T:0.37 Consensus pattern (20 bp): AAACATCATTCATCATCTTT Found at i:84350570 original size:93 final size:93 Alignment explanation

Indices: 84350460--84350630 Score: 279 Period size: 93 Copynumber: 1.8 Consensus size: 93 84350450 GCCCCTAAGT * * 84350460 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAATGAACTCAGACTCAACTCAA 1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAATGAACTCAGACTCAACTCAA * 84350525 CGAGTTCGGATGCCTAGTTACATCTCAC 66 CGAGCTCGGATGCCTAGTTACATCTCAC * * * * 84350553 GAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCAA 1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAATGAACTCAGACTCAACTCAA 84350618 CGAGCTCGGATGC 66 CGAGCTCGGATGC 84350631 TCAACCATCC Statistics Matches: 71, Mismatches: 7, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 93 71 1.00 ACGTcount: A:0.29, C:0.29, G:0.20, T:0.21 Consensus pattern (93 bp): GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAATGAACTCAGACTCAACTCAA CGAGCTCGGATGCCTAGTTACATCTCAC Found at i:84350627 original size:46 final size:46 Alignment explanation

Indices: 84350455--84350627 Score: 190 Period size: 46 Copynumber: 3.7 Consensus size: 46 84350445 AACCCGCCCC * * * 84350455 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA 1 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTTGCATCCA * * * * * 84350501 TAAATGAACTCAGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT-C- 1 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGA---C-ATTTGCATCCA * * * 84350549 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA 1 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTTGCATCCA 84350594 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGA 1 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGA 84350628 TGCTCAACCA Statistics Matches: 104, Mismatches: 16, Indels: 14 0.78 0.12 0.10 Matches are distributed among these distances: 43 6 0.06 44 2 0.02 45 2 0.02 46 58 0.56 47 28 0.27 48 2 0.02 49 2 0.02 50 4 0.04 ACGTcount: A:0.30, C:0.28, G:0.20, T:0.21 Consensus pattern (46 bp): TAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTTGCATCCA Found at i:84353814 original size:15 final size:15 Alignment explanation

Indices: 84353791--84353830 Score: 55 Period size: 15 Copynumber: 2.7 Consensus size: 15 84353781 TTTACATTTA 84353791 ATATTTATTAATATT- 1 ATATTTATTAA-ATTG * 84353806 ATTTTTATTAAATTG 1 ATATTTATTAAATTG 84353821 ATATTTATTA 1 ATATTTATTA 84353831 TGAAATAAAT Statistics Matches: 22, Mismatches: 2, Indels: 2 0.85 0.08 0.08 Matches are distributed among these distances: 14 3 0.14 15 19 0.86 ACGTcount: A:0.38, C:0.00, G:0.03, T:0.60 Consensus pattern (15 bp): ATATTTATTAAATTG Done.