Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.04

Sequence: scaffold1188

Parameters: 2 7 7 80 10 50 500

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500

Length: 1075576
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.29

Warning! 121203 characters in sequence are not A, C, G, or T


File 4 of 3

Found at i:737485 original size:62 final size:62

Alignment explanation

Indices: 737388--737695 Score: 351 Period size: 54 Copynumber: 5.4 Consensus size: 62 737378 CGTGTTGTGT * * 737388 GTTAGCGCGGA-GGCGTGTTGTGCAAAGTTGCGTTAGCGCGACGGCGTGTTGTGCAAAATTGC 1 GTTAGCGC-GACGGCGTGTTGTGCAAAGTTGTGTTAGCGCGACGGCGTGTTGTGCAAAGTTGC * 737450 GTTAGCGCGACGGCGTGTTGTGCAAAGTTGTGTTAGCGCGACGGCGTGTTATGCAAAGTTGC 1 GTTAGCGCGACGGCGTGTTGTGCAAAGTTGTGTTAGCGCGACGGCGTGTTGTGCAAAGTTGC * 737512 GTTAGTGCGACGGCGTG-T-T-----G-TGTGTTAGCGCGACGGCGTGTTGT-----G-T-- 1 GTTAGCGCGACGGCGTGTTGTGCAAAGTTGTGTTAGCGCGACGGCGTGTTGTGCAAAGTTGC * * 737558 GTTAGCGCGACGGCGTGTTGTGCAAAGTTGCGTTAGCGCGACGGCGTATTGTGCAAAGTTGC 1 GTTAGCGCGACGGCGTGTTGTGCAAAGTTGTGTTAGCGCGACGGCGTGTTGTGCAAAGTTGC * * 737620 GTTAGCGCGACGGCGTG-T-T-----G-TGTGTTAGCACGACGGCGTGTTATGCAAAGTTGC 1 GTTAGCGCGACGGCGTGTTGTGCAAAGTTGTGTTAGCGCGACGGCGTGTTGTGCAAAGTTGC * 737674 GTTAGAGCGACGGCGTGTTGTG 1 GTTAGCGCGACGGCGTGTTGTG 737696 TGTTAGCGCG Statistics Matches: 213, Mismatches: 13, Indels: 45 0.79 0.05 0.17 Matches are distributed among these distances: 46 16 0.08 47 1 0.00 48 2 0.01 49 1 0.00 53 1 0.00 54 91 0.43 55 3 0.01 56 1 0.00 59 1 0.00 60 3 0.01 61 4 0.02 62 89 0.42 ACGTcount: A:0.16, C:0.18, G:0.39, T:0.28 Consensus pattern (62 bp): GTTAGCGCGACGGCGTGTTGTGCAAAGTTGTGTTAGCGCGACGGCGTGTTGTGCAAAGTTGC Found at i:737500 original size:16 final size:16 Alignment explanation

Indices: 737450--737500 Score: 50 Period size: 16 Copynumber: 3.2 Consensus size: 16 737440 GCAAAATTGC 737450 GTTAGCGCGACGGCGT 1 GTTAGCGCGACGGCGT * * * ** 737466 GTT-GTGCAAAGTTGT 1 GTTAGCGCGACGGCGT 737481 GTTAGCGCGACGGCGT 1 GTTAGCGCGACGGCGT 737497 GTTA 1 GTTA 737501 TGCAAAGTTG Statistics Matches: 24, Mismatches: 10, Indels: 2 0.67 0.28 0.06 Matches are distributed among these distances: 15 10 0.42 16 14 0.58 ACGTcount: A:0.16, C:0.18, G:0.39, T:0.27 Consensus pattern (16 bp): GTTAGCGCGACGGCGT Found at i:737538 original size:23 final size:23 Alignment explanation

Indices: 737512--737579 Score: 127 Period size: 23 Copynumber: 3.0 Consensus size: 23 737502 GCAAAGTTGC * 737512 GTTAGTGCGACGGCGTGTTGTGT 1 GTTAGCGCGACGGCGTGTTGTGT 737535 GTTAGCGCGACGGCGTGTTGTGT 1 GTTAGCGCGACGGCGTGTTGTGT 737558 GTTAGCGCGACGGCGTGTTGTG 1 GTTAGCGCGACGGCGTGTTGTG 737580 CAAAGTTGCG Statistics Matches: 44, Mismatches: 1, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 23 44 1.00 ACGTcount: A:0.09, C:0.16, G:0.44, T:0.31 Consensus pattern (23 bp): GTTAGCGCGACGGCGTGTTGTGT Found at i:737646 original size:255 final size:255 Alignment explanation

Indices: 737195--737695 Score: 905 Period size: 255 Copynumber: 2.0 Consensus size: 255 737185 NNNNNNNTGT * ** 737195 GTTAGCGCGACGGCGTGTTGTGCAAAGTTGCGTTAGCGCGACGGCGTGTTGTGCAAAGTTTTGTT 1 GTTAGCGCGACGGCGTGTTGTGCAAAGTTGCGTTAGCGCGACGGCGTGTTATGCAAAGTTGCGTT 737260 AGCGCGACGGCGTGTTGTGTGTTAGCGCGACGGCGTGTTGTGTGTTAGCGCGACGGCGTGTTGTG 66 AGCGCGACGGCGTGTTGTGTGTTAGCGCGACGGCGTGTTGTGTGTTAGCGCGACGGCGTGTTGTG * 737325 CAAAGTTGCGTTAGCGCGACGGCGTGTTGTGCAAAGTTGCGTTAGCGCGACGGCGTGTTGTGTGT 131 CAAAGTTGCGTTAGCGCGACGGCGTATTGTGCAAAGTTGCGTTAGCGCGACGGCGTGTTGTGTGT * * * 737390 TAGCGCGGA-GGCGTGTTGTGCAAAGTTGCGTTAGCGCGACGGCGTGTTGTGCAAAATTGC 196 TAGCAC-GACGGCGTGTTATGCAAAGTTGCGTTAGAGCGACGGCGTGTTGTGCAAAATTGC * 737450 GTTAGCGCGACGGCGTGTTGTGCAAAGTTGTGTTAGCGCGACGGCGTGTTATGCAAAGTTGCGTT 1 GTTAGCGCGACGGCGTGTTGTGCAAAGTTGCGTTAGCGCGACGGCGTGTTATGCAAAGTTGCGTT * 737515 AGTGCGACGGCGTGTTGTGTGTTAGCGCGACGGCGTGTTGTGTGTTAGCGCGACGGCGTGTTGTG 66 AGCGCGACGGCGTGTTGTGTGTTAGCGCGACGGCGTGTTGTGTGTTAGCGCGACGGCGTGTTGTG 737580 CAAAGTTGCGTTAGCGCGACGGCGTATTGTGCAAAGTTGCGTTAGCGCGACGGCGTGTTGTGTGT 131 CAAAGTTGCGTTAGCGCGACGGCGTATTGTGCAAAGTTGCGTTAGCGCGACGGCGTGTTGTGTGT 737645 TAGCACGACGGCGTGTTATGCAAAGTTGCGTTAGAGCGACGGCGTGTTGTG 196 TAGCACGACGGCGTGTTATGCAAAGTTGCGTTAGAGCGACGGCGTGTTGTG 737696 TGTTAGCGCG Statistics Matches: 236, Mismatches: 9, Indels: 2 0.96 0.04 0.01 Matches are distributed among these distances: 254 2 0.01 255 234 0.99 ACGTcount: A:0.15, C:0.18, G:0.39, T:0.28 Consensus pattern (255 bp): GTTAGCGCGACGGCGTGTTGTGCAAAGTTGCGTTAGCGCGACGGCGTGTTATGCAAAGTTGCGTT AGCGCGACGGCGTGTTGTGTGTTAGCGCGACGGCGTGTTGTGTGTTAGCGCGACGGCGTGTTGTG CAAAGTTGCGTTAGCGCGACGGCGTATTGTGCAAAGTTGCGTTAGCGCGACGGCGTGTTGTGTGT TAGCACGACGGCGTGTTATGCAAAGTTGCGTTAGAGCGACGGCGTGTTGTGCAAAATTGC Found at i:740538 original size:434 final size:434 Alignment explanation

Indices: 739662--740658 Score: 1357 Period size: 434 Copynumber: 2.3 Consensus size: 434 739652 TCCAACTAAT * * * * * * * 739662 TCAAGAAAAAGGGGCTGGGCCGTTTATTTAGGGGCCAAGAGAGTCTTAAACTCTATTACGAATAA 1 TCAAGAAAAAGGGGCTGGCCCCTTTAATTAGGGGCCAAGACACTCGTAAACTCTATTACAAATAA * * * 739727 CTTAAAAACGATAAAGATATTGTAAT-CTATTATAGAAGCAAAGTTGTTGATAATACCAATATCT 66 CTTAAAAACGATAAAGATTTTGTAATGC-ATTATAGAAGCAAAGTTGTTGATCATAACAATATCT ** * * * 739791 ATTTTAAAAAATCATTGCCACGCCCCTTTATTACGTAATAGGGATTTTTAGGGGCCAAAGTACTT 130 ATTCAAAAAAATCAATGCCACGCCCATTTATTACGTAATAGGGATTTATAGGGGCCAAAGTACTT * * 739856 AAACTTTGACGCAATATATCTAAAGAAGTAGACATATTTTGTTAGACATCACAGAAGAGAAAATG 195 AAACTTTGACGCAATATATCTAAAGAAGGAGACATATTTCGTTAGACAT--CAGAAGAGAAAATG 739921 ATTGCAGTAATGATTTAAATCGATTCAACTTATCAAAACACCAATATATGTCCCCATAAGGGATC 258 ATTGCAGTAATGATTTAAATCGATTCAACTTATCAAAACACCAATATATGTCCCCATAAGGGATC 739986 TACAGGGCTGGCCCCTAAAATATTCAAACATTTGTATCTCAAAAATGAACAACAATTTTAGATGG 323 TACAGGGCTGGCCCCTAAAATATTCAAACATTTGTATCTCAAAAATGAACAACAATTTTAGATGG * * * * 740051 GTTTAAGAACAAAAAATATTTGTATTCTTAAGACCTTTTCAAAGAAA 388 CTGTAAGAACAAAAAATATTAGTATTCGTAAGACCTTTTCAAAGAAA * 740098 TCAAGAAAAAGGGGCTGGCCCTTTTAATTAGGGGCCAAGACACTCGTAAACTCTATTACAAATAA 1 TCAAGAAAAAGGGGCTGGCCCCTTTAATTAGGGGCCAAGACACTCGTAAACTCTATTACAAATAA * * 740163 CTTAAAAATGATAAAGATTTTGTAATGCATTATAGAAGAAAAGTTGTTGATCATAACAATATCTA 66 CTTAAAAACGATAAAGATTTTGTAATGCATTATAGAAGCAAAGTTGTTGATCATAACAATATCTA * * 740228 -TCAAAGAAAATCAATGCCACGCCCATTTATTGCGTAATTAGGGATTTATAGGGGCTAAAGTACT 131 TTCAAA-AAAATCAATGCCACGCCCATTTATTACGTAA-TAGGGATTTATAGGGGCCAAAGTACT * * * 740292 TAAACTTTGGCGCAATATATCTAGAA-AAGGAGACATATTTCGTTA-AGCAT-TGTAGAGAAAAT 194 TAAACTTTGACGCAATATATCTA-AAGAAGGAGACATATTTCGTTAGA-CATCAGAAGAGAAAAT * * * * * * 740354 GTTTGCATTGATGATTTTAATCGATTCCA-TTAAT-AAAAGCACC-ATAGTCTGTCCCCATTAA- 257 GATTGCAGTAATGATTTAAATCGATTCAACTT-ATCAAAA-CACCAATA-TATGTCCCCA-TAAG * * 740415 GGATCTAGAGGGCTGGCCCCTAAAATATTCAATCATTTGTATCTCAAAAATGAACAACAATTTTA 318 GGATCTACAGGGCTGGCCCCTAAAATATTCAAACATTTGTATCTCAAAAATGAACAACAATTTTA ** * * * * 740480 GATGGCTGTAAGAACAAAAAA-AGTTAGTATTCGTGGGATCTTTTGAATGAAC 383 GATGGCTGTAAGAACAAAAAATA-TTAGTATTCGTAAGACCTTTTCAAAGAAA * * * * * 740532 TCAAGAAAAAGGGGCAGGCCCCTTTAATTAGGGGCCAAGACACTCGTAAAGTCTCTTACACATAC 1 TCAAGAAAAAGGGGCTGGCCCCTTTAATTAGGGGCCAAGACACTCGTAAACTCTATTACAAATAA * * * 740597 CTTAAAAACGATGAAGATTTTGTAATGCATTATAGAAGCAAATTTGTTGATCGTAACAATAT 66 CTTAAAAACGATAAAGATTTTGTAATGCATTATAGAAGCAAAGTTGTTGATCATAACAATAT 740659 TAGTTTGTAA Statistics Matches: 498, Mismatches: 53, Indels: 22 0.87 0.09 0.04 Matches are distributed among these distances: 433 10 0.02 434 268 0.54 435 6 0.01 436 145 0.29 437 67 0.13 438 2 0.00 ACGTcount: A:0.38, C:0.15, G:0.17, T:0.29 Consensus pattern (434 bp): TCAAGAAAAAGGGGCTGGCCCCTTTAATTAGGGGCCAAGACACTCGTAAACTCTATTACAAATAA CTTAAAAACGATAAAGATTTTGTAATGCATTATAGAAGCAAAGTTGTTGATCATAACAATATCTA TTCAAAAAAATCAATGCCACGCCCATTTATTACGTAATAGGGATTTATAGGGGCCAAAGTACTTA AACTTTGACGCAATATATCTAAAGAAGGAGACATATTTCGTTAGACATCAGAAGAGAAAATGATT GCAGTAATGATTTAAATCGATTCAACTTATCAAAACACCAATATATGTCCCCATAAGGGATCTAC AGGGCTGGCCCCTAAAATATTCAAACATTTGTATCTCAAAAATGAACAACAATTTTAGATGGCTG TAAGAACAAAAAATATTAGTATTCGTAAGACCTTTTCAAAGAAA Found at i:746912 original size:12 final size:12 Alignment explanation

Indices: 746882--746915 Score: 50 Period size: 12 Copynumber: 2.8 Consensus size: 12 746872 GTTGCCCTGT * * 746882 TCCGTCCGTTCG 1 TCCGTCTGTCCG 746894 TCCGTCTGTCCG 1 TCCGTCTGTCCG 746906 TCCGTCTGTC 1 TCCGTCTGTC 746916 ACGTTTCACT Statistics Matches: 20, Mismatches: 2, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 12 20 1.00 ACGTcount: A:0.00, C:0.41, G:0.24, T:0.35 Consensus pattern (12 bp): TCCGTCTGTCCG Found at i:747698 original size:169 final size:164 Alignment explanation

Indices: 747451--747849 Score: 518 Period size: 169 Copynumber: 2.4 Consensus size: 164 747441 AGTAGCTATG * * * * * 747451 TCATCTCTTGGGATATAATTAGGG-CTGTCCTATAGATGTGCAATAAGGTTTTAAAAATTAAAAT 1 TCATATCTTGGGATATGA-TAGGGACTGTTCTATAGATGTGCATTAAGGTTTTAAAAATTTAAAT * ******* * 747515 TTCATCCAGGGAGTCAAATAGTGGCAGAAAATTGACGTTTATCACTCAAACACCCCCCCCCCCCC 65 TTCATCCAGGGAGTCAAATAGTAGCAGAAAATTGACGTTTATCACT-AAA-A----AAAAAAACA 747580 GAGA-CCCAGAACTCCTCTTATGATTTAAT-GGATAGACACA 124 GAGATCCCAGAACTCCTCTTATGATTTAATAGG-TAGACACA * 747620 TCATATCTTGGGATATGATAGGGACTGTTCTATAGATGTGCATTAAGGATTTAAAAATTTAAATT 1 TCATATCTTGGGATATGATAGGGACTGTTCTATAGATGTGCATTAAGGTTTTAAAAATTTAAATT 747685 TCATCCAGGGAGTCAAATAGTAGCAGAAAATTGACGTTTATCACTAAAAAAAAAAACAGAGATCC 66 TCATCCAGGGAGTCAAATAGTAGCAGAAAATTGACGTTTATCACTAAAAAAAAAAACAGAGATCC * 747750 CAGAACTCCTCTTCTGATTTAATAGGTAGACACA 131 CAGAACTCCTCTTATGATTTAATAGGTAGACACA * * * 747784 TCATATCCTGGGTTATGATAGGGACTGTTCTATAGATGTGCATTACGGTTTTGAAAAA-TTAAAT 1 TCATATCTTGGGATATGATAGGGACTGTTCTATAGATGTGCATTAAGGTTTT-AAAAATTTAAAT 747848 TT 65 TT 747850 AACCCTGGGG Statistics Matches: 206, Mismatches: 20, Indels: 13 0.86 0.08 0.05 Matches are distributed among these distances: 163 5 0.02 164 88 0.43 165 7 0.03 167 1 0.00 168 8 0.04 169 97 0.47 ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30 Consensus pattern (164 bp): TCATATCTTGGGATATGATAGGGACTGTTCTATAGATGTGCATTAAGGTTTTAAAAATTTAAATT TCATCCAGGGAGTCAAATAGTAGCAGAAAATTGACGTTTATCACTAAAAAAAAAAACAGAGATCC CAGAACTCCTCTTATGATTTAATAGGTAGACACA Found at i:747848 original size:164 final size:165 Alignment explanation

Indices: 747459--747849 Score: 513 Period size: 164 Copynumber: 2.3 Consensus size: 165 747449 TGTCATCTCT * * * 747459 TGGGATATAATTAGGG-CTGTCCTATAGATGTGCAATAAGGTTTTAAAAATTAAAATTTCATCCA 1 TGGGATATGA-TAGGGACTGTTCTATAGATGTGCATTAAGGTTTTAAAAATT-AAATTTCATCCA * ******* * 747523 GGGAGTCAAATAGTGGCAGAAAATTGACGTTTATCACTCAAACACCCCCCCCCCCCCGAGACCCA 64 GGGAGTCAAATAGTAGCAGAAAATTGACGTTTATCACTCAAACA---CAAAAAAACAGAGACCCA * 747588 GAACTCCTCTTATGATTTAATGGATAGACACATCATATCT 126 GAACTCCTCTTATGATTTAATGGATAGACACATCATATCC * 747628 TGGGATATGATAGGGACTGTTCTATAGATGTGCATTAAGGATTTAAAAATTTAAATTTCATCCAG 1 TGGGATATGATAGGGACTGTTCTATAGATGTGCATTAAGGTTTTAAAAA-TTAAATTTCATCCAG 747693 GGAGTCAAATAGTAGCAGAAAATTGACGTTTATCACT-AAA-A-AAAAAAACAGAGATCCCAGAA 65 GGAGTCAAATAGTAGCAGAAAATTGACGTTTATCACTCAAACACAAAAAAACAGAGA-CCCAGAA * 747755 CTCCTCTTCTGATTTAATAGG-TAGACACATCATATCC 129 CTCCTCTTATGATTTAAT-GGATAGACACATCATATCC * * 747792 TGGGTTATGATAGGGACTGTTCTATAGATGTGCATTACGGTTTTGAAAAATTAAATTT 1 TGGGATATGATAGGGACTGTTCTATAGATGTGCATTAAGGTTTT-AAAAATTAAATTT 747850 AACCCTGGGG Statistics Matches: 199, Mismatches: 18, Indels: 15 0.86 0.08 0.06 Matches are distributed among these distances: 163 5 0.03 164 88 0.44 165 7 0.04 167 1 0.01 168 8 0.04 169 88 0.44 170 2 0.01 ACGTcount: A:0.35, C:0.17, G:0.18, T:0.30 Consensus pattern (165 bp): TGGGATATGATAGGGACTGTTCTATAGATGTGCATTAAGGTTTTAAAAATTAAATTTCATCCAGG GAGTCAAATAGTAGCAGAAAATTGACGTTTATCACTCAAACACAAAAAAACAGAGACCCAGAACT CCTCTTATGATTTAATGGATAGACACATCATATCC Found at i:754071 original size:161 final size:161 Alignment explanation

Indices: 753797--754124 Score: 426 Period size: 161 Copynumber: 2.0 Consensus size: 161 753787 GGTCCACCAA * * * * * 753797 CAGTTTCCGTTCATTTTCTTCATATAGGATAAACATATTGAAATGAAATTTGGTATACAGGTTCA 1 CAGTTTCCGCTCATTTTCTTCACAGAGGATAAACATATTGAAATGAAATTTAGCATACAGGTTCA * * 753862 TCCGGATAATATCTAGGTCAAATTCGATACTGGGTACGATCGAGCAATTTTCGACACAGTT-TTG 66 TCAGGATAATATCTAGGTCAAATTCGATACTGGGTACGATCAAGCAATTTTCGACACAGTTATT- * ** 753926 GCCCTTGGACGTAGAAAAATTCCAGTTATTTG 130 GCCCTTGGACGTAGAAAAAATCCAAATATTTG ** * * 753958 CAGTTTCCGCTCATTTTCTTTGCAGAGGATGAACATATTGAAATGAAATTTAGCATACAGGTTTA 1 CAGTTTCCGCTCATTTTCTTCACAGAGGATAAACATATTGAAATGAAATTTAGCATACAGGTTCA * * * * * 754023 TCAGGATAATATTTAGGTCAAGTTCGATATTGGGTAC-AGTCAAGCAATTTTTGACAGAGTTATT 66 TCAGGATAATATCTAGGTCAAATTCGATACTGGGTACGA-TCAAGCAATTTTCGACACAGTTATT * * * 754087 GCCCTTGGACTTCGAAAAAATCCAAATATTTT 130 GCCCTTGGACGTAGAAAAAATCCAAATATTTG 754119 CAGTTT 1 CAGTTT 754125 ACTTACATTT Statistics Matches: 143, Mismatches: 22, Indels: 4 0.85 0.13 0.02 Matches are distributed among these distances: 160 1 0.01 161 140 0.98 162 2 0.01 ACGTcount: A:0.30, C:0.16, G:0.19, T:0.35 Consensus pattern (161 bp): CAGTTTCCGCTCATTTTCTTCACAGAGGATAAACATATTGAAATGAAATTTAGCATACAGGTTCA TCAGGATAATATCTAGGTCAAATTCGATACTGGGTACGATCAAGCAATTTTCGACACAGTTATTG CCCTTGGACGTAGAAAAAATCCAAATATTTG Found at i:776777 original size:31 final size:32 Alignment explanation

Indices: 776741--776811 Score: 108 Period size: 31 Copynumber: 2.2 Consensus size: 32 776731 AAACACCCAT 776741 GGGTCATTTTTGTACGCAGAATAATGACC-GG 1 GGGTCATTTTTGTACGCAGAATAATGACCGGG * * * 776772 GGGTCATTTTTTTGCGTAGAATAATGACCGGG 1 GGGTCATTTTTGTACGCAGAATAATGACCGGG 776804 GGGTCATT 1 GGGTCATT 776812 ATTCTACGTC Statistics Matches: 36, Mismatches: 3, Indels: 1 0.90 0.08 0.03 Matches are distributed among these distances: 31 26 0.72 32 10 0.28 ACGTcount: A:0.23, C:0.14, G:0.31, T:0.32 Consensus pattern (32 bp): GGGTCATTTTTGTACGCAGAATAATGACCGGG Found at i:776829 original size:31 final size:31 Alignment explanation

Indices: 776741--776829 Score: 101 Period size: 31 Copynumber: 2.9 Consensus size: 31 776731 AAACACCCAT * 776741 GGGTCATTTTTGTACG-CAGAATAATGACCGG 1 GGGTCATTTTTCTACGTC-GAATAATGACCGG * * * 776772 GGGTCATTTTTTTGCGTAGAATAATGACCGGG 1 GGGTCATTTTTCTACGTCGAATAATGACC-GG * 776804 GGGTCATTATTCTACGTCGAA-AATGA 1 GGGTCATTTTTCTACGTCGAATAATGA 776830 TCCCCGGTCA Statistics Matches: 49, Mismatches: 7, Indels: 4 0.82 0.12 0.07 Matches are distributed among these distances: 31 30 0.61 32 19 0.39 ACGTcount: A:0.26, C:0.15, G:0.28, T:0.31 Consensus pattern (31 bp): GGGTCATTTTTCTACGTCGAATAATGACCGG Found at i:778225 original size:207 final size:206 Alignment explanation

Indices: 777870--778282 Score: 817 Period size: 207 Copynumber: 2.0 Consensus size: 206 777860 ATGAGGGTAA 777870 GCAAAATCATTGCCATATTTGATGCTTTTGGTGGGCAAAACCGTGCTTTTTAAAATAAAAATTAA 1 GCAAAATCATTGCCATATTTGATGCTTTTGGTGGGCAAAACCGTGCTTTTTAAAATAAAAATTAA 777935 CAAGTGTCTGTCTTGTATTAAGACCTAGTAAATCGAACCGTTTTCAAGGAACGTTCTGCATAGAA 66 CAAGTGTCTGTCTTGTATTAAGACCTAGTAAATCGAACCGTTTTCAAGGAACGTTCTGCATAGAA 778000 TAGTGTAGTCTGTTTCACTATTGATGCTTTTACTAGGTCAGGCGCGGATCGAAAATTAATCCTTA 131 TAGTGTAGTCTGTTTCACTATTGATGCTTTTACTAGGTCAGGCGCGGATCGAAAATTAATCCTTA 778065 GGAGGTTCGCT 196 GGAGGTTCGCT 778076 NGCAAAATCATTGCCATATTTGATGCTTTTGGTGGGCAAAACCGTGCTTTTTAAAATAAAAATTA 1 -GCAAAATCATTGCCATATTTGATGCTTTTGGTGGGCAAAACCGTGCTTTTTAAAATAAAAATTA 778141 ACAAGTGTCTGTCTTGTATTAAGACCTAGTAAATCGAACCGTTTTCAAGGAACGTTCTGCATAGA 65 ACAAGTGTCTGTCTTGTATTAAGACCTAGTAAATCGAACCGTTTTCAAGGAACGTTCTGCATAGA 778206 ATAGTGTAGTCTGTTTCACTATTGATGCTTTTACTAGGTCAGGCGCGGATCGAAAATTAATCCTT 130 ATAGTGTAGTCTGTTTCACTATTGATGCTTTTACTAGGTCAGGCGCGGATCGAAAATTAATCCTT 778271 AGGAGGTTCGCT 195 AGGAGGTTCGCT 778283 ACTAAGCATG Statistics Matches: 206, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 207 206 1.00 ACGTcount: A:0.29, C:0.16, G:0.21, T:0.33 Consensus pattern (206 bp): GCAAAATCATTGCCATATTTGATGCTTTTGGTGGGCAAAACCGTGCTTTTTAAAATAAAAATTAA CAAGTGTCTGTCTTGTATTAAGACCTAGTAAATCGAACCGTTTTCAAGGAACGTTCTGCATAGAA TAGTGTAGTCTGTTTCACTATTGATGCTTTTACTAGGTCAGGCGCGGATCGAAAATTAATCCTTA GGAGGTTCGCT Found at i:787395 original size:16 final size:16 Alignment explanation

Indices: 787374--787421 Score: 87 Period size: 16 Copynumber: 3.0 Consensus size: 16 787364 AACTGAAGTG 787374 GGACAGACAGACGGAC 1 GGACAGACAGACGGAC 787390 GGACAGACAGACGGAC 1 GGACAGACAGACGGAC * 787406 GGACGGACAGACGGAC 1 GGACAGACAGACGGAC 787422 TGACGGACGC Statistics Matches: 31, Mismatches: 1, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 16 31 1.00 ACGTcount: A:0.35, C:0.25, G:0.40, T:0.00 Consensus pattern (16 bp): GGACAGACAGACGGAC Found at i:787400 original size:20 final size:20 Alignment explanation

Indices: 787375--787430 Score: 85 Period size: 20 Copynumber: 2.8 Consensus size: 20 787365 ACTGAAGTGG 787375 GACAGACAGACGGACGGACA 1 GACAGACAGACGGACGGACA * 787395 GACAGACGGACGGACGGACA 1 GACAGACAGACGGACGGACA * * 787415 GACGGACTGACGGACG 1 GACAGACAGACGGACG 787431 CAGAGGAAAG Statistics Matches: 33, Mismatches: 3, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 20 33 1.00 ACGTcount: A:0.34, C:0.25, G:0.39, T:0.02 Consensus pattern (20 bp): GACAGACAGACGGACGGACA Found at i:787426 original size:16 final size:16 Alignment explanation

Indices: 787374--787429 Score: 85 Period size: 16 Copynumber: 3.5 Consensus size: 16 787364 AACTGAAGTG * 787374 GGACAGACAGACGGAC 1 GGACGGACAGACGGAC * 787390 GGACAGACAGACGGAC 1 GGACGGACAGACGGAC 787406 GGACGGACAGACGGAC 1 GGACGGACAGACGGAC * 787422 TGACGGAC 1 GGACGGAC 787430 GCAGAGGAAA Statistics Matches: 38, Mismatches: 2, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 16 38 1.00 ACGTcount: A:0.34, C:0.25, G:0.39, T:0.02 Consensus pattern (16 bp): GGACGGACAGACGGAC Found at i:787430 original size:4 final size:4 Alignment explanation

Indices: 787383--787430 Score: 60 Period size: 4 Copynumber: 12.0 Consensus size: 4 787373 GGGACAGACA * * * * 787383 GACG GACG GACA GACA GACG GACG GACG GACA GACG GACT GACG GACG 1 GACG GACG GACG GACG GACG GACG GACG GACG GACG GACG GACG GACG 787431 CAGAGGAAAG Statistics Matches: 38, Mismatches: 6, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 4 38 1.00 ACGTcount: A:0.31, C:0.25, G:0.42, T:0.02 Consensus pattern (4 bp): GACG Found at i:793932 original size:16 final size:16 Alignment explanation

Indices: 793911--793958 Score: 87 Period size: 16 Copynumber: 3.0 Consensus size: 16 793901 AACTGAAGTG 793911 GGACAGACAGACGGAC 1 GGACAGACAGACGGAC 793927 GGACAGACAGACGGAC 1 GGACAGACAGACGGAC * 793943 GGACGGACAGACGGAC 1 GGACAGACAGACGGAC 793959 TGACGGACGC Statistics Matches: 31, Mismatches: 1, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 16 31 1.00 ACGTcount: A:0.35, C:0.25, G:0.40, T:0.00 Consensus pattern (16 bp): GGACAGACAGACGGAC Found at i:793937 original size:20 final size:20 Alignment explanation

Indices: 793912--793967 Score: 85 Period size: 20 Copynumber: 2.8 Consensus size: 20 793902 ACTGAAGTGG 793912 GACAGACAGACGGACGGACA 1 GACAGACAGACGGACGGACA * 793932 GACAGACGGACGGACGGACA 1 GACAGACAGACGGACGGACA * * 793952 GACGGACTGACGGACG 1 GACAGACAGACGGACG 793968 CAGAGGAAAG Statistics Matches: 33, Mismatches: 3, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 20 33 1.00 ACGTcount: A:0.34, C:0.25, G:0.39, T:0.02 Consensus pattern (20 bp): GACAGACAGACGGACGGACA Found at i:793963 original size:16 final size:16 Alignment explanation

Indices: 793911--793966 Score: 85 Period size: 16 Copynumber: 3.5 Consensus size: 16 793901 AACTGAAGTG * 793911 GGACAGACAGACGGAC 1 GGACGGACAGACGGAC * 793927 GGACAGACAGACGGAC 1 GGACGGACAGACGGAC 793943 GGACGGACAGACGGAC 1 GGACGGACAGACGGAC * 793959 TGACGGAC 1 GGACGGAC 793967 GCAGAGGAAA Statistics Matches: 38, Mismatches: 2, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 16 38 1.00 ACGTcount: A:0.34, C:0.25, G:0.39, T:0.02 Consensus pattern (16 bp): GGACGGACAGACGGAC Found at i:793967 original size:4 final size:4 Alignment explanation

Indices: 793920--793967 Score: 60 Period size: 4 Copynumber: 12.0 Consensus size: 4 793910 GGGACAGACA * * * * 793920 GACG GACG GACA GACA GACG GACG GACG GACA GACG GACT GACG GACG 1 GACG GACG GACG GACG GACG GACG GACG GACG GACG GACG GACG GACG 793968 CAGAGGAAAG Statistics Matches: 38, Mismatches: 6, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 4 38 1.00 ACGTcount: A:0.31, C:0.25, G:0.42, T:0.02 Consensus pattern (4 bp): GACG Found at i:802111 original size:123 final size:124 Alignment explanation

Indices: 801973--802236 Score: 469 Period size: 124 Copynumber: 2.1 Consensus size: 124 801963 AAATTATGCA * * 801973 TAATTAATCTTAGGCAACATGTTCTAGTCACAAAAATGGA-C-GGTATTAACGTAGGCTAACACA 1 TAATTAATCTTAGGCAACATGTTCTAGTCACAAAAAT-AACCAGATATTAACGTAGGCTAACACA * 802036 TGTTAGAGGTTTTTCAATACCAATTATATGACACTGAGATACACTATCTCATGTCGTAAT 65 TGTTAGAGGTTTTTCAATACCAATTATATGACACTGAGATACACTATCACATGTCGTAAT * 802096 TAATTAATCTTAGGCAACATGTTCTAGTCACAAAAATAACCAGATATTTACGTAGGCTAACACAT 1 TAATTAATCTTAGGCAACATGTTCTAGTCACAAAAATAACCAGATATTAACGTAGGCTAACACAT 802161 GTTAGAGGTTTTTCAATACCAATTATATGACACTGAGATACACTATCACATGTCGTAAT 66 GTTAGAGGTTTTTCAATACCAATTATATGACACTGAGATACACTATCACATGTCGTAAT 802220 TAATTAATCTTAGGCAA 1 TAATTAATCTTAGGCAA 802237 AAGTAAAAAA Statistics Matches: 135, Mismatches: 4, Indels: 3 0.95 0.03 0.02 Matches are distributed among these distances: 122 1 0.01 123 38 0.28 124 96 0.71 ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32 Consensus pattern (124 bp): TAATTAATCTTAGGCAACATGTTCTAGTCACAAAAATAACCAGATATTAACGTAGGCTAACACAT GTTAGAGGTTTTTCAATACCAATTATATGACACTGAGATACACTATCACATGTCGTAAT Found at i:805332 original size:10 final size:10 Alignment explanation

Indices: 805317--805342 Score: 52 Period size: 10 Copynumber: 2.6 Consensus size: 10 805307 GATTTATTTA 805317 AAAAAAAAAG 1 AAAAAAAAAG 805327 AAAAAAAAAG 1 AAAAAAAAAG 805337 AAAAAA 1 AAAAAA 805343 GATTATCAAC Statistics Matches: 16, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 10 16 1.00 ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00 Consensus pattern (10 bp): AAAAAAAAAG Found at i:811164 original size:21 final size:21 Alignment explanation

Indices: 811138--811225 Score: 88 Period size: 21 Copynumber: 4.2 Consensus size: 21 811128 TTTTTCTGTC 811138 AAATATGTCGACATGCAAGAT 1 AAATATGTCGACATGCAAGAT * * 811159 AAATATGTTGTCATGCAAGAT 1 AAATATGTCGACATGCAAGAT ** * * 811180 AGTTATGTCAACATGCAACAT 1 AAATATGTCGACATGCAAGAT * * * 811201 AACTATGTTGACATGCACGA- 1 AAATATGTCGACATGCAAGAT 811221 AAATA 1 AAATA 811226 GCAATCAAAT Statistics Matches: 52, Mismatches: 15, Indels: 1 0.76 0.22 0.01 Matches are distributed among these distances: 20 4 0.08 21 48 0.92 ACGTcount: A:0.41, C:0.15, G:0.17, T:0.27 Consensus pattern (21 bp): AAATATGTCGACATGCAAGAT Found at i:811319 original size:21 final size:21 Alignment explanation

Indices: 811295--811388 Score: 82 Period size: 21 Copynumber: 4.5 Consensus size: 21 811285 GCTAAATGCT * 811295 ACTTATTTATGTCGACATTCA 1 ACTTATTTATGTCAACATTCA 811316 ACTTATTTATGTCAACATT-A 1 ACTTATTTATGTCAACATTCA ** ** ** * 811336 GAGATAAATATGTTGACATACA 1 -ACTTATTTATGTCAACATTCA * 811358 ACTTATTTATGTCAACATGCA 1 ACTTATTTATGTCAACATTCA * 811379 ACTTAGTTAT 1 ACTTATTTAT 811389 TTGATAGAAA Statistics Matches: 55, Mismatches: 16, Indels: 4 0.73 0.21 0.05 Matches are distributed among these distances: 20 1 0.02 21 53 0.96 22 1 0.02 ACGTcount: A:0.35, C:0.15, G:0.11, T:0.39 Consensus pattern (21 bp): ACTTATTTATGTCAACATTCA Found at i:823323 original size:21 final size:21 Alignment explanation

Indices: 823257--823313 Score: 89 Period size: 21 Copynumber: 2.7 Consensus size: 21 823247 GAGGGAATTT 823257 TACAGATTAAAT-TGTAAACTA 1 TACAGATT-AATGTGTAAACTA * 823278 TACAGTTTAATGTGTAAACTA 1 TACAGATTAATGTGTAAACTA 823299 TACAGATTAATGTGT 1 TACAGATTAATGTGT 823314 TAATAATACA Statistics Matches: 33, Mismatches: 2, Indels: 2 0.89 0.05 0.05 Matches are distributed among these distances: 20 3 0.09 21 30 0.91 ACGTcount: A:0.40, C:0.09, G:0.14, T:0.37 Consensus pattern (21 bp): TACAGATTAATGTGTAAACTA Found at i:834976 original size:2 final size:2 Alignment explanation

Indices: 834971--835004 Score: 68 Period size: 2 Copynumber: 17.0 Consensus size: 2 834961 AAAAATAATA 834971 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 835005 AGTAGGACGT Statistics Matches: 32, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 32 1.00 ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50 Consensus pattern (2 bp): TC Found at i:836899 original size:29 final size:29 Alignment explanation

Indices: 836857--836917 Score: 113 Period size: 29 Copynumber: 2.1 Consensus size: 29 836847 TGATCTTAAA * 836857 CAATGTGAAGGTTCTTACATTTGCCTCAT 1 CAATGTGAAGGTTCTTACATTCGCCTCAT 836886 CAATGTGAAGGTTCTTACATTCGCCTCAT 1 CAATGTGAAGGTTCTTACATTCGCCTCAT 836915 CAA 1 CAA 836918 AGATCTCAAA Statistics Matches: 31, Mismatches: 1, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 29 31 1.00 ACGTcount: A:0.26, C:0.23, G:0.16, T:0.34 Consensus pattern (29 bp): CAATGTGAAGGTTCTTACATTCGCCTCAT Found at i:837269 original size:15 final size:15 Alignment explanation

Indices: 837249--837278 Score: 60 Period size: 15 Copynumber: 2.0 Consensus size: 15 837239 ACCTTTCTCG 837249 TTGTAGTCCTCGTCT 1 TTGTAGTCCTCGTCT 837264 TTGTAGTCCTCGTCT 1 TTGTAGTCCTCGTCT 837279 AAATAGTTGT Statistics Matches: 15, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 15 15 1.00 ACGTcount: A:0.07, C:0.27, G:0.20, T:0.47 Consensus pattern (15 bp): TTGTAGTCCTCGTCT Found at i:840121 original size:70 final size:70 Alignment explanation

Indices: 840037--840213 Score: 318 Period size: 70 Copynumber: 2.5 Consensus size: 70 840027 AGACACTAAA 840037 GACCACAGGATTTGGTGCCTGATTCCGTAGCCCGTCATCATCTGTGTCACCTACCTGTTCAGACA 1 GACCACAGGATTTGGTGCCTGATTCCGTAGCCCGTCATCATCTGTGTCACCTACCTGTTCAGACA 840102 ACATG 66 ACATG * 840107 GACCACAGGATTTGGTGCCTGATTCTGTAGCCCGTCATCATCTGTGTCACCTACCTGTTCAGACA 1 GACCACAGGATTTGGTGCCTGATTCCGTAGCCCGTCATCATCTGTGTCACCTACCTGTTCAGACA 840172 ACATG 66 ACATG * ** 840177 GACCACAGGATCTGGTGTGTGATTCCGTAGCCCGTCA 1 GACCACAGGATTTGGTGCCTGATTCCGTAGCCCGTCA 840214 ATCCTTGGCT Statistics Matches: 102, Mismatches: 5, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 70 102 1.00 ACGTcount: A:0.21, C:0.29, G:0.23, T:0.27 Consensus pattern (70 bp): GACCACAGGATTTGGTGCCTGATTCCGTAGCCCGTCATCATCTGTGTCACCTACCTGTTCAGACA ACATG Found at i:845769 original size:16 final size:16 Alignment explanation

Indices: 845748--845780 Score: 66 Period size: 16 Copynumber: 2.1 Consensus size: 16 845738 TAACAGATCA 845748 ATACGGAAGCCCTGGG 1 ATACGGAAGCCCTGGG 845764 ATACGGAAGCCCTGGG 1 ATACGGAAGCCCTGGG 845780 A 1 A 845781 GGACATTGAC Statistics Matches: 17, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 16 17 1.00 ACGTcount: A:0.27, C:0.24, G:0.36, T:0.12 Consensus pattern (16 bp): ATACGGAAGCCCTGGG Found at i:856230 original size:1 final size:1 Alignment explanation

Indices: 856226--856324 Score: 72 Period size: 1 Copynumber: 99.0 Consensus size: 1 856216 ATTGTTGTTG * * * * * * * * * 856226 TTTTTGTTTTTTGTTTTTTTTTTGTTTTTTTTTTTTTTGTTTTGTTTGTTTTGTTTTGTTTTGTT 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT * * * ** 856291 TTTTGTTTTTTTGTTTTGTTTTGGTTTTTTTTTT 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 856325 GGGGGGGGGT Statistics Matches: 72, Mismatches: 26, Indels: 0 0.73 0.27 0.00 Matches are distributed among these distances: 1 72 1.00 ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86 Consensus pattern (1 bp): T Found at i:856242 original size:5 final size:5 Alignment explanation

Indices: 856217--856322 Score: 98 Period size: 5 Copynumber: 21.4 Consensus size: 5 856207 GAGGGGGTTA * * 856217 TTGTT GTTGTTT TTGTT TT-TT GTT-TT TT-TT TTGTT TTTTT TTTTT 1 TTGTT -TTG-TT TTGTT TTGTT -TTGTT TTGTT TTGTT TTGTT TTGTT * 856262 TTGTT TTG-T TTGTT TTGTT TTGTT TTGTT TT-TT GTTTTT TTGTT TTGTT 1 TTGTT TTGTT TTGTT TTGTT TTGTT TTGTT TTGTT -TTGTT TTGTT TTGTT 856311 TTGGTT TT-TT TT 1 TT-GTT TTGTT TT 856323 TTGGGGGGGG Statistics Matches: 90, Mismatches: 3, Indels: 16 0.83 0.03 0.15 Matches are distributed among these distances: 4 18 0.20 5 57 0.63 6 13 0.14 7 2 0.02 ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84 Consensus pattern (5 bp): TTGTT Found at i:856257 original size:20 final size:20 Alignment explanation

Indices: 856232--856325 Score: 99 Period size: 19 Copynumber: 4.9 Consensus size: 20 856222 GTTGTTTTTG 856232 TTTTTTGTTTTTTTTTTGTT 1 TTTTTTGTTTTTTTTTTGTT 856252 TTTTTT-TTTTTTGTTTTGTT 1 TTTTTTGTTTTTT-TTTTGTT * * 856272 TGTTTTG-TTTTGTTTTG-- 1 TTTTTTGTTTTTTTTTTGTT * 856289 TTTTTTGTTTTTTTGTT-TT 1 TTTTTTGTTTTTTTTTTGTT * * 856308 GTTTTGGTTTTTTTTTTG 1 TTTTTTGTTTTTTTTTTG 856326 GGGGGGGGTG Statistics Matches: 60, Mismatches: 8, Indels: 12 0.75 0.10 0.15 Matches are distributed among these distances: 17 6 0.10 18 7 0.12 19 25 0.42 20 22 0.37 ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85 Consensus pattern (20 bp): TTTTTTGTTTTTTTTTTGTT Found at i:856266 original size:39 final size:38 Alignment explanation

Indices: 856227--856325 Score: 139 Period size: 39 Copynumber: 2.6 Consensus size: 38 856217 TTGTTGTTGT * 856227 TTTTGTTTTTTGTTTTTTTTTTGTTTTTTTTTTTTTTG 1 TTTTGTTTTTTGTTTTTTTTTTGTTTTTTGTTTTTTTG * 856265 TTTTGTTTGTTT-TGTTTTGTTTTGTTTTTTGTTTTTTTG 1 TTTTGTTT-TTTGT-TTTTTTTTTGTTTTTTGTTTTTTTG * 856304 TTTTG-TTTTGGTTTTTTTTTTG 1 TTTTGTTTTTTGTTTTTTTTTTG 856326 GGGGGGGGTG Statistics Matches: 54, Mismatches: 4, Indels: 7 0.83 0.06 0.11 Matches are distributed among these distances: 37 11 0.20 38 12 0.22 39 31 0.57 ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85 Consensus pattern (38 bp): TTTTGTTTTTTGTTTTTTTTTTGTTTTTTGTTTTTTTG Found at i:856325 original size:30 final size:30 Alignment explanation

Indices: 856217--856325 Score: 147 Period size: 30 Copynumber: 3.7 Consensus size: 30 856207 GAGGGGGTTA 856217 TTGTTGTTGTTTTTGTTTTTTG-TTTTTT-TT 1 TTGTT-TTG-TTTTGTTTTTTGTTTTTTTGTT 856247 TTGTTTT-TTTT-TTTTTTGTTTTGTTTGTT 1 TTGTTTTGTTTTGTTTTTTGTTTT-TTTGTT 856276 TTGTTTTGTTTTGTTTTTTGTTTTTTTGTT 1 TTGTTTTGTTTTGTTTTTTGTTTTTTTGTT 856306 TTGTTTTGGTTTT-TTTTTTG 1 TTGTTTT-GTTTTGTTTTTTG 856326 GGGGGGGGTG Statistics Matches: 73, Mismatches: 0, Indels: 12 0.86 0.00 0.14 Matches are distributed among these distances: 26 7 0.10 27 7 0.10 28 3 0.04 29 11 0.15 30 29 0.40 31 16 0.22 ACGTcount: A:0.00, C:0.00, G:0.17, T:0.83 Consensus pattern (30 bp): TTGTTTTGTTTTGTTTTTTGTTTTTTTGTT Found at i:859435 original size:14 final size:14 Alignment explanation

Indices: 859416--859446 Score: 62 Period size: 14 Copynumber: 2.2 Consensus size: 14 859406 AGTGTTAATA 859416 AGATAATTAACAGT 1 AGATAATTAACAGT 859430 AGATAATTAACAGT 1 AGATAATTAACAGT 859444 AGA 1 AGA 859447 AAACACGCAC Statistics Matches: 17, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 14 17 1.00 ACGTcount: A:0.52, C:0.06, G:0.16, T:0.26 Consensus pattern (14 bp): AGATAATTAACAGT Found at i:866627 original size:39 final size:39 Alignment explanation

Indices: 866573--866653 Score: 153 Period size: 39 Copynumber: 2.1 Consensus size: 39 866563 ATAAATTAAG * 866573 AATTCCTTGCCCGTGATAGAGGTACAATGGGACTCGGTT 1 AATTCCTTGCCCGTGATAAAGGTACAATGGGACTCGGTT 866612 AATTCCTTGCCCGTGATAAAGGTACAATGGGACTCGGTT 1 AATTCCTTGCCCGTGATAAAGGTACAATGGGACTCGGTT 866651 AAT 1 AAT 866654 CTTTTAAGAT Statistics Matches: 41, Mismatches: 1, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 39 41 1.00 ACGTcount: A:0.26, C:0.20, G:0.26, T:0.28 Consensus pattern (39 bp): AATTCCTTGCCCGTGATAAAGGTACAATGGGACTCGGTT Found at i:883450 original size:2 final size:2 Alignment explanation

Indices: 883443--883502 Score: 93 Period size: 2 Copynumber: 30.0 Consensus size: 2 883433 CTCTGGAAGA * * * 883443 TC TC TC TC TC TT TC TC TT TC TC TT TC TC TC TC TC TC TC TC TC 1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 883485 TC TC TC TC TC TC TC TC TC 1 TC TC TC TC TC TC TC TC TC 883503 ATATACACAT Statistics Matches: 52, Mismatches: 6, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 2 52 1.00 ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55 Consensus pattern (2 bp): TC Found at i:890855 original size:2 final size:2 Alignment explanation

Indices: 890850--890904 Score: 101 Period size: 2 Copynumber: 27.5 Consensus size: 2 890840 AGGGGGGGGG * 890850 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA NA GA 1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 890892 GA GA GA GA GA GA G 1 GA GA GA GA GA GA G 890905 GTGGGGGATT Statistics Matches: 51, Mismatches: 2, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 2 51 1.00 ACGTcount: A:0.49, C:0.00, G:0.49, T:0.00 Consensus pattern (2 bp): GA Found at i:892535 original size:2 final size:2 Alignment explanation

Indices: 892528--892580 Score: 106 Period size: 2 Copynumber: 26.5 Consensus size: 2 892518 NNNNNNGAGG 892528 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 892570 GA GA GA GA GA G 1 GA GA GA GA GA G 892581 GTGGGGGATT Statistics Matches: 51, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 51 1.00 ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00 Consensus pattern (2 bp): GA Found at i:904082 original size:2 final size:2 Alignment explanation

Indices: 904075--904120 Score: 92 Period size: 2 Copynumber: 23.0 Consensus size: 2 904065 TTCAATTTAT 904075 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 904117 TC TC 1 TC TC 904121 ATTAAAACCC Statistics Matches: 44, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 44 1.00 ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50 Consensus pattern (2 bp): TC Found at i:911219 original size:19 final size:19 Alignment explanation

Indices: 911195--911233 Score: 78 Period size: 19 Copynumber: 2.1 Consensus size: 19 911185 ATTAGAACTA 911195 TTTCCAGTTTTCCAAGTTG 1 TTTCCAGTTTTCCAAGTTG 911214 TTTCCAGTTTTCCAAGTTG 1 TTTCCAGTTTTCCAAGTTG 911233 T 1 T 911234 AAGACAAAGT Statistics Matches: 20, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 19 20 1.00 ACGTcount: A:0.15, C:0.21, G:0.15, T:0.49 Consensus pattern (19 bp): TTTCCAGTTTTCCAAGTTG Found at i:925389 original size:19 final size:21 Alignment explanation

Indices: 925353--925391 Score: 55 Period size: 20 Copynumber: 2.0 Consensus size: 21 925343 TTTTGTTATT 925353 CTGTGTTTTTAACAACAATAG 1 CTGTGTTTTTAACAACAATAG * 925374 CTGT-TTTTTGAC-ACAATA 1 CTGTGTTTTTAACAACAATA 925392 CCTGAGGGTG Statistics Matches: 17, Mismatches: 1, Indels: 2 0.85 0.05 0.10 Matches are distributed among these distances: 19 6 0.35 20 7 0.41 21 4 0.24 ACGTcount: A:0.31, C:0.15, G:0.13, T:0.41 Consensus pattern (21 bp): CTGTGTTTTTAACAACAATAG Found at i:928443 original size:2 final size:2 Alignment explanation

Indices: 928436--928474 Score: 55 Period size: 2 Copynumber: 20.5 Consensus size: 2 928426 ATTTATAATA * 928436 CT CT CT CT CT CT CT CT CT C- CT CT CT CT -T TT CT CT CT CT C 1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C 928475 ATTTTGAAAA Statistics Matches: 34, Mismatches: 1, Indels: 4 0.87 0.03 0.10 Matches are distributed among these distances: 1 2 0.06 2 32 0.94 ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51 Consensus pattern (2 bp): CT Found at i:948410 original size:2 final size:2 Alignment explanation

Indices: 948403--948429 Score: 54 Period size: 2 Copynumber: 13.5 Consensus size: 2 948393 NNNNNNNNNN 948403 TA TA TA TA TA TA TA TA TA TA TA TA TA T 1 TA TA TA TA TA TA TA TA TA TA TA TA TA T 948430 CGTTTATCCT Statistics Matches: 25, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 25 1.00 ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52 Consensus pattern (2 bp): TA Found at i:948742 original size:21 final size:21 Alignment explanation

Indices: 948717--948808 Score: 87 Period size: 21 Copynumber: 4.4 Consensus size: 21 948707 ATATGCCATC * 948717 ACTTGTCAGATAATTTTGTCG 1 ACTTGTCAGATAATTATGTCG * * 948738 ACTTGTCTGAT-CTTGATGTCG 1 ACTTGTCAGATAATT-ATGTCG * * 948759 ACTTTTCAGATAATTATGTTG 1 ACTTGTCAGATAATTATGTCG * ** * 948780 ACTTGTCAGTTCTTTAAGTCG 1 ACTTGTCAGATAATTATGTCG 948801 ACTTGTCA 1 ACTTGTCA 948809 CTTATTCACG Statistics Matches: 56, Mismatches: 13, Indels: 4 0.77 0.18 0.05 Matches are distributed among these distances: 20 2 0.04 21 52 0.93 22 2 0.04 ACGTcount: A:0.22, C:0.16, G:0.18, T:0.43 Consensus pattern (21 bp): ACTTGTCAGATAATTATGTCG Found at i:948783 original size:42 final size:42 Alignment explanation

Indices: 948717--948808 Score: 121 Period size: 42 Copynumber: 2.2 Consensus size: 42 948707 ATATGCCATC * * * 948717 ACTTGTCAGATAATTTTGTCGACTTGTCTGATCTTGATGTCG 1 ACTTGTCAGATAATTATGTCGACTTGTCAGATCTTGAAGTCG * * * * 948759 ACTTTTCAGATAATTATGTTGACTTGTCAGTTCTTTAAGTCG 1 ACTTGTCAGATAATTATGTCGACTTGTCAGATCTTGAAGTCG 948801 ACTTGTCA 1 ACTTGTCA 948809 CTTATTCACG Statistics Matches: 42, Mismatches: 8, Indels: 0 0.84 0.16 0.00 Matches are distributed among these distances: 42 42 1.00 ACGTcount: A:0.22, C:0.16, G:0.18, T:0.43 Consensus pattern (42 bp): ACTTGTCAGATAATTATGTCGACTTGTCAGATCTTGAAGTCG Found at i:948920 original size:21 final size:21 Alignment explanation

Indices: 948895--949022 Score: 91 Period size: 21 Copynumber: 6.1 Consensus size: 21 948885 CTGACTAGTG ** 948895 GACATAATCATCTTTTAAGTC 1 GACATAATCATCTTACAAGTC * 948916 GACATAATTAT-TTGACAAGTC 1 GACATAATCATCTT-ACAAGTC * * 948937 GACTTAATCATCTGACAAGTC 1 GACATAATCATCTTACAAGTC * * 948958 GACATAATTAT-TTGACAAGAC 1 GACATAATCATCTT-ACAAGTC * * * 948979 GATATAA-CATCTGAAAAGTC 1 GACATAATCATCTTACAAGTC * * * * 948999 AACATCATTATCTGACAAGTC 1 GACATAATCATCTTACAAGTC 949020 GAC 1 GAC 949023 TTATAATATG Statistics Matches: 81, Mismatches: 21, Indels: 10 0.72 0.19 0.09 Matches are distributed among these distances: 20 14 0.17 21 66 0.81 22 1 0.01 ACGTcount: A:0.38, C:0.19, G:0.13, T:0.30 Consensus pattern (21 bp): GACATAATCATCTTACAAGTC Found at i:948945 original size:42 final size:42 Alignment explanation

Indices: 948911--949025 Score: 162 Period size: 41 Copynumber: 2.8 Consensus size: 42 948901 ATCATCTTTT * 948911 AAGTCGACATAATTATTTGACAAGTCGACTTAATCATCTGAC 1 AAGTCGACATAATTATTTGACAAGTCGACTTAATCATCTGAA * 948953 AAGTCGACATAATTATTTGACAAGACGA-TATAA-CATCTGAA 1 AAGTCGACATAATTATTTGACAAGTCGACT-TAATCATCTGAA * * * 948994 AAGTCAACATCATTATCTGACAAGTCGACTTA 1 AAGTCGACATAATTATTTGACAAGTCGACTTA 949026 TAATATGAAT Statistics Matches: 65, Mismatches: 6, Indels: 5 0.86 0.08 0.07 Matches are distributed among these distances: 41 34 0.52 42 31 0.48 ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29 Consensus pattern (42 bp): AAGTCGACATAATTATTTGACAAGTCGACTTAATCATCTGAA Found at i:949098 original size:21 final size:21 Alignment explanation

Indices: 949073--949139 Score: 89 Period size: 21 Copynumber: 3.2 Consensus size: 21 949063 TTATTTTTTC 949073 TGTCAGATAATTATGTTAACT 1 TGTCAGATAATTATGTTAACT ** ** 949094 TGTCAGATCTTTATGTCGACT 1 TGTCAGATAATTATGTTAACT * 949115 TGTCAAATAATTATGTTAACT 1 TGTCAGATAATTATGTTAACT 949136 TGTC 1 TGTC 949140 TGATCCTTAT Statistics Matches: 37, Mismatches: 9, Indels: 0 0.80 0.20 0.00 Matches are distributed among these distances: 21 37 1.00 ACGTcount: A:0.28, C:0.13, G:0.15, T:0.43 Consensus pattern (21 bp): TGTCAGATAATTATGTTAACT Found at i:949119 original size:42 final size:43 Alignment explanation

Indices: 949073--949167 Score: 140 Period size: 42 Copynumber: 2.3 Consensus size: 43 949063 TTATTTTTTC * * 949073 TGTCAGATAATTATGTTAACTTGTCAGATCTTTATGTCGA-CT 1 TGTCAGATAATTATGTTAACTTGTCAGATCCTTATGACGACCT * * 949115 TGTCAAATAATTATGTTAACTTGTCTGATCCTTATGACGACCT 1 TGTCAGATAATTATGTTAACTTGTCAGATCCTTATGACGACCT 949158 T-TCAGATAAT 1 TGTCAGATAAT 949168 ATGAAGCCAA Statistics Matches: 47, Mismatches: 5, Indels: 2 0.87 0.09 0.04 Matches are distributed among these distances: 42 44 0.94 43 3 0.06 ACGTcount: A:0.28, C:0.16, G:0.15, T:0.41 Consensus pattern (43 bp): TGTCAGATAATTATGTTAACTTGTCAGATCCTTATGACGACCT Found at i:949149 original size:21 final size:21 Alignment explanation

Indices: 949073--949150 Score: 84 Period size: 21 Copynumber: 3.7 Consensus size: 21 949063 TTATTTTTTC * 949073 TGTCAGATAATTATGTTAACT 1 TGTCAGATCATTATGTTAACT * ** 949094 TGTCAGATCTTTATGTCGACT 1 TGTCAGATCATTATGTTAACT * * 949115 TGTCAAATAATTATGTTAACT 1 TGTCAGATCATTATGTTAACT * * 949136 TGTCTGATCCTTATG 1 TGTCAGATCATTATG 949151 ACGACCTTTC Statistics Matches: 44, Mismatches: 13, Indels: 0 0.77 0.23 0.00 Matches are distributed among these distances: 21 44 1.00 ACGTcount: A:0.27, C:0.14, G:0.15, T:0.44 Consensus pattern (21 bp): TGTCAGATCATTATGTTAACT Found at i:949274 original size:21 final size:21 Alignment explanation

Indices: 949249--949342 Score: 127 Period size: 21 Copynumber: 4.5 Consensus size: 21 949239 ATGGTTATTT * * * 949249 TCTGACATGTCAACATAAAGA 1 TCTGACAAGTCGACATAAATA * 949270 TCTGACAAGTTGACATAAATA 1 TCTGACAAGTCGACATAAATA 949291 TCTGACAAGTCGACAT-AATCA 1 TCTGACAAGTCGACATAAAT-A * 949312 TCTGACAAGTCGACATAATTA 1 TCTGACAAGTCGACATAAATA 949333 TCTGACAAGT 1 TCTGACAAGT 949343 GGTGGCAGAT Statistics Matches: 65, Mismatches: 6, Indels: 4 0.87 0.08 0.05 Matches are distributed among these distances: 20 3 0.05 21 60 0.92 22 2 0.03 ACGTcount: A:0.39, C:0.19, G:0.15, T:0.27 Consensus pattern (21 bp): TCTGACAAGTCGACATAAATA Found at i:949553 original size:22 final size:23 Alignment explanation

Indices: 949506--949554 Score: 64 Period size: 22 Copynumber: 2.2 Consensus size: 23 949496 CAGAATTATT * * 949506 TTTTCCTTGACTGCATTTTTACA 1 TTTTCCTTGACTGCAGTTTTAAA * 949529 TTTTCCTTTACT-CAGTTTTAAA 1 TTTTCCTTGACTGCAGTTTTAAA 949551 TTTT 1 TTTT 949555 TTTGTACCAC Statistics Matches: 23, Mismatches: 3, Indels: 1 0.85 0.11 0.04 Matches are distributed among these distances: 22 12 0.52 23 11 0.48 ACGTcount: A:0.18, C:0.18, G:0.06, T:0.57 Consensus pattern (23 bp): TTTTCCTTGACTGCAGTTTTAAA Found at i:949555 original size:23 final size:24 Alignment explanation

Indices: 949505--949555 Score: 61 Period size: 23 Copynumber: 2.2 Consensus size: 24 949495 TCAGAATTAT * * 949505 TTTTTCCTTGACTGCATTTTTACA 1 TTTTTCCTTGACTGCAGTTTTAAA * 949529 -TTTTCCTTTACT-CAGTTTTAAA 1 TTTTTCCTTGACTGCAGTTTTAAA 949551 TTTTT 1 TTTTT 949556 TTGTACCACT Statistics Matches: 23, Mismatches: 3, Indels: 3 0.79 0.10 0.10 Matches are distributed among these distances: 22 8 0.35 23 15 0.65 ACGTcount: A:0.18, C:0.18, G:0.06, T:0.59 Consensus pattern (24 bp): TTTTTCCTTGACTGCAGTTTTAAA Found at i:953654 original size:2 final size:2 Alignment explanation

Indices: 953647--953686 Score: 80 Period size: 2 Copynumber: 20.0 Consensus size: 2 953637 GCTCTCGTTT 953647 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 953687 CTATGGATAG Statistics Matches: 38, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 38 1.00 ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00 Consensus pattern (2 bp): GA Found at i:957259 original size:21 final size:21 Alignment explanation

Indices: 957235--957293 Score: 64 Period size: 21 Copynumber: 2.8 Consensus size: 21 957225 ATCTCGTTAT * 957235 TTCTTGTTATTACGAGATGTC 1 TTCTTGTAATTACGAGATGTC * * * * 957256 TTCTCGTAATAACGAGATTTT 1 TTCTTGTAATTACGAGATGTC * 957277 TTCTTGTCATTACGAGA 1 TTCTTGTAATTACGAGA 957294 AAAAATATTT Statistics Matches: 30, Mismatches: 8, Indels: 0 0.79 0.21 0.00 Matches are distributed among these distances: 21 30 1.00 ACGTcount: A:0.24, C:0.15, G:0.17, T:0.44 Consensus pattern (21 bp): TTCTTGTAATTACGAGATGTC Found at i:958139 original size:2 final size:2 Alignment explanation

Indices: 958132--958175 Score: 88 Period size: 2 Copynumber: 22.0 Consensus size: 2 958122 ACTCCCCATT 958132 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 958174 TC 1 TC 958176 AAAATTACAC Statistics Matches: 42, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 42 1.00 ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50 Consensus pattern (2 bp): TC Found at i:958960 original size:12 final size:12 Alignment explanation

Indices: 958943--958967 Score: 50 Period size: 12 Copynumber: 2.1 Consensus size: 12 958933 AGTACCGCTG 958943 TATTTAATTCTT 1 TATTTAATTCTT 958955 TATTTAATTCTT 1 TATTTAATTCTT 958967 T 1 T 958968 TAAAAAAGGT 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:0.08, G:0.00, T:0.68 Consensus pattern (12 bp): TATTTAATTCTT Found at i:961244 original size:13 final size:13 Alignment explanation

Indices: 961226--961250 Score: 50 Period size: 13 Copynumber: 1.9 Consensus size: 13 961216 GGCTGAAGCT 961226 AGCAGCCACTAAC 1 AGCAGCCACTAAC 961239 AGCAGCCACTAA 1 AGCAGCCACTAA 961251 GCCCGTAGAA 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:0.36, G:0.16, T:0.08 Consensus pattern (13 bp): AGCAGCCACTAAC Found at i:962544 original size:326 final size:326 Alignment explanation

Indices: 961947--962612 Score: 1269 Period size: 326 Copynumber: 2.0 Consensus size: 326 961937 AAGGGTCGGT 961947 TTAGCTCACCCGAACTTTGTCATATTTTAGCATTTCACAATGATATAGGGGTTAAAAGTGGTCCA 1 TTAGCTCACCCGAACTTTGTCATATTTTAGCATTTCACAATGATATAGGGGTTAAAAGTGGTCCA 962012 TTATCTTCCTTATCTTTGAAGTGTGCATCAAACGAATAACAGGGTAGTGTAGGGGGCATATGGGG 66 TTATCTTCCTTATCTTTGAAGTGTGCATCAAACGAATAACAGGGTAGTGTAGGGGGCATATGGGG 962077 CTATTATTTCCCGGTCTCAGATTTGGGCTGTAGGGGTACCACCAAGTGGCTCCCAAGGGTTCTGG 131 CTATTATTTCCCGGTCTCAGATTTGGGCTGTAGGGGTACCACCAAGTGGCTCCCAAGGGTTCTGG 962142 CTCATTTCAGGGATTTATATCTCACTTGAGATTGGCCACAAGAACTTACAAACACTTGGATTAGG 196 CTCATTTCAGGGATTTATATCTCACTTGAGATTGGCCACAAGAACTTACAAACACTTGGATTAGG * 962207 TAGAAGACCTCAAGAGGTATTCATAATAAGCATTAGAGGGCACATATGAGCCCTACAAGGGTTAG 261 TAGAAGACCTCAAGAGGTATTCATAATAAGCATTAGAGGGCACATATGACCCCTACAAGGGTTAG 962272 G 326 G * 962273 TTAGCTCACCCGAACTTTGTCATATTTTAGCATTTCACATTGATATAGGGGTTAAAAGTGGTCCA 1 TTAGCTCACCCGAACTTTGTCATATTTTAGCATTTCACAATGATATAGGGGTTAAAAGTGGTCCA 962338 TTATCTTCCTTATCTTTGAAGTGTGCATCAAACGAATAACAGGGTAGTGTAGGGGGCATATGGGG 66 TTATCTTCCTTATCTTTGAAGTGTGCATCAAACGAATAACAGGGTAGTGTAGGGGGCATATGGGG * 962403 CTATTATTTCCCGGTCTCAGATTTGGGCTGTAGGGGTACCACCAAGTGGCTCCCAGGGGTTCTGG 131 CTATTATTTCCCGGTCTCAGATTTGGGCTGTAGGGGTACCACCAAGTGGCTCCCAAGGGTTCTGG 962468 CTCATTTCAGGGATTTATATCTCACTTGAGATTGGCCACAAGAACTTACAAACACTTGGATTAGG 196 CTCATTTCAGGGATTTATATCTCACTTGAGATTGGCCACAAGAACTTACAAACACTTGGATTAGG * * * 962533 TAGAGGACCTCAAGAGGTATTCATAATAAGCGTTAGAGGGCACATATGACCCCTACAATGGTTAG 261 TAGAAGACCTCAAGAGGTATTCATAATAAGCATTAGAGGGCACATATGACCCCTACAAGGGTTAG 962598 G 326 G * 962599 TTAGCACACCCGAA 1 TTAGCTCACCCGAA 962613 GTGTAGGGGG Statistics Matches: 333, Mismatches: 7, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 326 333 1.00 ACGTcount: A:0.27, C:0.19, G:0.24, T:0.29 Consensus pattern (326 bp): TTAGCTCACCCGAACTTTGTCATATTTTAGCATTTCACAATGATATAGGGGTTAAAAGTGGTCCA TTATCTTCCTTATCTTTGAAGTGTGCATCAAACGAATAACAGGGTAGTGTAGGGGGCATATGGGG CTATTATTTCCCGGTCTCAGATTTGGGCTGTAGGGGTACCACCAAGTGGCTCCCAAGGGTTCTGG CTCATTTCAGGGATTTATATCTCACTTGAGATTGGCCACAAGAACTTACAAACACTTGGATTAGG TAGAAGACCTCAAGAGGTATTCATAATAAGCATTAGAGGGCACATATGACCCCTACAAGGGTTAG G Found at i:969873 original size:2 final size:2 Alignment explanation

Indices: 969868--969902 Score: 70 Period size: 2 Copynumber: 17.5 Consensus size: 2 969858 GTGTGTGTGT 969868 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G 1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G 969903 GGATTTGTTT Statistics Matches: 33, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 33 1.00 ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00 Consensus pattern (2 bp): GA Found at i:972481 original size:22 final size:22 Alignment explanation

Indices: 972453--972495 Score: 68 Period size: 22 Copynumber: 2.0 Consensus size: 22 972443 CCCGAAACAA ** 972453 CTTGTTTCTTCGCTACGATAGC 1 CTTGTTTCTTCAATACGATAGC 972475 CTTGTTTCTTCAATACGATAG 1 CTTGTTTCTTCAATACGATAG 972496 AACATGCACT Statistics Matches: 19, Mismatches: 2, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 22 19 1.00 ACGTcount: A:0.19, C:0.23, G:0.16, T:0.42 Consensus pattern (22 bp): CTTGTTTCTTCAATACGATAGC Found at i:982596 original size:12 final size:12 Alignment explanation

Indices: 982579--982605 Score: 54 Period size: 12 Copynumber: 2.2 Consensus size: 12 982569 ATTAATTTAT 982579 GTTATATTTTCA 1 GTTATATTTTCA 982591 GTTATATTTTCA 1 GTTATATTTTCA 982603 GTT 1 GTT 982606 GTTCTTTTTC Statistics Matches: 15, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 12 15 1.00 ACGTcount: A:0.22, C:0.07, G:0.11, T:0.59 Consensus pattern (12 bp): GTTATATTTTCA Found at i:987432 original size:2 final size:2 Alignment explanation

Indices: 987425--987476 Score: 104 Period size: 2 Copynumber: 26.0 Consensus size: 2 987415 CAAATAAAAC 987425 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 987467 GA GA GA GA GA 1 GA GA GA GA GA 987477 TATTTCTCGT Statistics Matches: 50, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 50 1.00 ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00 Consensus pattern (2 bp): GA Found at i:988446 original size:1 final size:1 Alignment explanation

Indices: 988435--988471 Score: 65 Period size: 1 Copynumber: 37.0 Consensus size: 1 988425 AATATTTTCA * 988435 CCCCTCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 988472 GGTAGGTTTC Statistics Matches: 34, Mismatches: 2, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 1 34 1.00 ACGTcount: A:0.00, C:0.97, G:0.00, T:0.03 Consensus pattern (1 bp): C Found at i:989559 original size:170 final size:169 Alignment explanation

Indices: 988872--989611 Score: 1001 Period size: 168 Copynumber: 4.4 Consensus size: 169 988862 CCCACCATGT * * * 988872 CCTGAACCCCAGACCCAGGGGCCATGAATTTCACAA-TTTAGGTAAAGGAG-TT-AGTGGACATC 1 CCTGAACCCCTGACCCAGGGGTCATGAATTTCACAATTTTA-GTAGAGG-GCTTCA-TGGACATC * * * ** ** * * * * * 988934 ATAACCATGTATTCA-GTTTTTTGCCCACATGTGTGAGAGTAGAGAAGAAGATTTTTTAAGATTT 63 ATAATCATGCATTTAGGTTTTTAACAAATATATATGGGAGTAGAGAAGAAGATTTTCTAAGATTT * * 988998 AAAACATTTTTACTAAATGGCCATATTGAG-CCCACCCTAGAG 128 AATACATTTTTACTATATGGCCATATTG-GCCCCACCCTAGAG *** 989040 CCTGAACCCCT-AAAAAGGGGTCATGAATTTCACAATTTTAGTAGA-GGCTTTCATGGACATCAT 1 CCTGAACCCCTGACCCAGGGGTCATGAATTTCACAATTTTAGTAGAGGGC-TTCATGGACATCAT * 989103 AATCATGCATTTAGTTTTTTAACAAATATATATGGGAGTAGAGAAGAAGATTTTCTAAGATTTAA 65 AATCATGCATTTAGGTTTTTAACAAATATATATGGGAGTAGAGAAGAAGATTTTCTAAGATTTAA * 989168 TACAGTTTTACTATATGGCCATATTGGCCCCACCCTAGAG 130 TACATTTTTACTATATGGCCATATTGGCCCCACCCTAGAG * * 989208 CCTGAACCCCTGACCCAGGGGTCATGAATTTCACAATTTTGGTAGAGGGCCTCATGGACATCATA 1 CCTGAACCCCTGACCCAGGGGTCATGAATTTCACAATTTTAGTAGAGGGCTTCATGGACATCATA * * * * 989273 ACCAAGCATTTA-GTTATTAACAAATATATATGGGAGTAGAGAAGAAGATTTTCTAAGATTAAAT 66 ATCATGCATTTAGGTTTTTAACAAATATATATGGGAGTAGAGAAGAAGATTTTCTAAGATTTAAT * 989337 ACATTTTTACTATATGGCCATATTGGCCCCATCCTAGAG 131 ACATTTTTACTATATGGCCATATTGGCCCCACCCTAGAG * * * 989376 CCTGAAACCCTGACCCAGGGGTCATGAATTTCACAATTTAAATAGAGGGCTTCATGGACATCATA 1 CCTGAACCCCTGACCCAGGGGTCATGAATTTCACAATTTTAGTAGAGGGCTTCATGGACATCATA * * 989441 ATCATGCATTTAGGTTTTTAAAAATATATATATGGTAGTAGAGAAGAAGATTTTCTAAGATTTAA 66 ATCATGCATTTAGGTTTTTAACAA-ATATATATGGGAGTAGAGAAGAAGATTTTCTAAGATTTAA 989506 TACATTTTTACTATATGGCCATATTGGCCCCACCCTAGAG 130 TACATTTTTACTATATGGCCATATTGGCCCCACCCTAGAG * * ** * * * 989546 CCAGAACCCCTGACCCAGCGACCATGAATTTCACAATTTTGGTAGAAGGCTTCATTGACATCATA 1 CCTGAACCCCTGACCCAGGGGTCATGAATTTCACAATTTTAGTAGAGGGCTTCATGGACATCATA 989611 A 66 A 989612 CTATGCAACC Statistics Matches: 506, Mismatches: 56, Indels: 18 0.87 0.10 0.03 Matches are distributed among these distances: 165 1 0.00 166 1 0.00 167 47 0.09 168 258 0.51 169 63 0.12 170 136 0.27 ACGTcount: A:0.33, C:0.19, G:0.19, T:0.30 Consensus pattern (169 bp): CCTGAACCCCTGACCCAGGGGTCATGAATTTCACAATTTTAGTAGAGGGCTTCATGGACATCATA ATCATGCATTTAGGTTTTTAACAAATATATATGGGAGTAGAGAAGAAGATTTTCTAAGATTTAAT ACATTTTTACTATATGGCCATATTGGCCCCACCCTAGAG Found at i:989577 original size:338 final size:336 Alignment explanation

Indices: 988875--989612 Score: 1043 Period size: 338 Copynumber: 2.2 Consensus size: 336 988865 ACCATGTCCT * * * * ** * 988875 GAACCCCAGACCCAGGGGCCATGAATTTCACAATTTAGGTA-AAGGAGTTAGTGGACATCATAAC 1 GAACCCCTGACCCAGCGACCATGAATTTCACAATTTTGGTAGAAGGCCTCA-TGGACATCATAAC * * * * ** ** * * * * * 988939 CATGTATTCAGTTTTTTGCCCACATGTGTGAGAGTAGAGAAGAAGATTTTTTAAGATTTAAAACA 65 CAAGCATTTAGTTATTAACAAATATATATGGGAGTAGAGAAGAAGATTTTCTAAGATTTAAAACA * 989004 TTTTTACTAAATGGCCATATTGAGCCCACCCTAGAGCCTGAACCCCTAAAAAGGGGTCATGAATT 130 TTTTTACTAAATGGCCATATTGAGCCCACCCTAGAGCCTGAAACCCTAAAAAGGGGTCATGAATT * * * * 989069 TCACAATTTTAGTAGAGGCTTTCATGGACATCATAATCATGCATTTAGTTTTTTAACAAATATAT 195 TCACAATTTAAATAGAGGCTTTCATGGACATCATAATCATGCATTTAGGTTTTTAAAAAATATAT 989134 ATGGGAGTAGAGAAGAAGATTTTCTAAGATTTAATACAGTTTTACTATATGGCCATATTGGCCCC 260 ATGGGAGTAGAGAAGAAGATTTTCTAAGATTTAATACAGTTTTACTATATGGCCATATTGGCCCC * 989199 ACCCTAGAGCCT 325 ACCCTAGAGCCA * ** * 989211 GAACCCCTGACCCAGGGGTCATGAATTTCACAATTTTGGTAGAGGGCCTCATGGACATCATAACC 1 GAACCCCTGACCCAGCGACCATGAATTTCACAATTTTGGTAGAAGGCCTCATGGACATCATAACC 989276 AAGCATTTAGTTATTAACAAATATATATGGGAGTAGAGAAGAAGATTTTCTAAGA-TTAAATACA 66 AAGCATTTAGTTATTAACAAATATATATGGGAGTAGAGAAGAAGATTTTCTAAGATTTAAA-ACA * * *** 989340 TTTTTACTATATGGCCATATTG-GCCCCATCCTAGAGCCTGAAACCCTGACCCAGGGGTCATGAA 130 TTTTTACTAAATGGCCATATTGAG-CCCACCCTAGAGCCTGAAACCCT-AAAAAGGGGTCATGAA 989404 TTTCACAATTTAAATAGAGGGC-TTCATGGACATCATAATCATGCATTTAGGTTTTTAAAAATAT 193 TTTCACAATTTAAATAGA-GGCTTTCATGGACATCATAATCATGCATTTAGGTTTTTAAAAA-AT * * 989468 ATATATGGTAGTAGAGAAGAAGATTTTCTAAGATTTAATACATTTTTACTATATGGCCATATTGG 256 ATATATGGGAGTAGAGAAGAAGATTTTCTAAGATTTAATACAGTTTTACTATATGGCCATATTGG 989533 CCCCACCCTAGAGCCA 321 CCCCACCCTAGAGCCA * * 989549 GAACCCCTGACCCAGCGACCATGAATTTCACAATTTTGGTAGAAGGCTTCATTGACATCATAAC 1 GAACCCCTGACCCAGCGACCATGAATTTCACAATTTTGGTAGAAGGCCTCATGGACATCATAAC 989613 TATGCAACCA Statistics Matches: 357, Mismatches: 39, Indels: 10 0.88 0.10 0.02 Matches are distributed among these distances: 335 6 0.02 336 139 0.39 337 71 0.20 338 141 0.39 ACGTcount: A:0.33, C:0.19, G:0.19, T:0.30 Consensus pattern (336 bp): GAACCCCTGACCCAGCGACCATGAATTTCACAATTTTGGTAGAAGGCCTCATGGACATCATAACC AAGCATTTAGTTATTAACAAATATATATGGGAGTAGAGAAGAAGATTTTCTAAGATTTAAAACAT TTTTACTAAATGGCCATATTGAGCCCACCCTAGAGCCTGAAACCCTAAAAAGGGGTCATGAATTT CACAATTTAAATAGAGGCTTTCATGGACATCATAATCATGCATTTAGGTTTTTAAAAAATATATA TGGGAGTAGAGAAGAAGATTTTCTAAGATTTAATACAGTTTTACTATATGGCCATATTGGCCCCA CCCTAGAGCCA Found at i:1024974 original size:20 final size:20 Alignment explanation

Indices: 1024901--1025013 Score: 65 Period size: 20 Copynumber: 5.6 Consensus size: 20 1024891 CTGAGAAACC * 1024901 ATACAAATTAAACATTAT-ACA 1 ATACAAATGAAA-ATT-TGACA * * 1024922 ATACAAATGGAAA-TTGTATA 1 ATACAAATGAAAATTTG-ACA ** * 1024942 ATACAAACAAAAATTTGACC 1 ATACAAATGAAAATTTGACA 1024962 ATACAAATGAAAATATT--CA 1 ATACAAATGAAAAT-TTGACA * 1024981 ATATAAATGTAAAATTAT-ACA 1 ATACAAATG-AAAATT-TGACA * 1025002 ATAAAAATGAAA 1 ATACAAATGAAA 1025014 TGTATACAAT Statistics Matches: 72, Mismatches: 13, Indels: 15 0.72 0.13 0.15 Matches are distributed among these distances: 18 1 0.01 19 11 0.15 20 35 0.49 21 25 0.35 ACGTcount: A:0.58, C:0.10, G:0.06, T:0.27 Consensus pattern (20 bp): ATACAAATGAAAATTTGACA Found at i:1025014 original size:19 final size:19 Alignment explanation

Indices: 1024966--1025024 Score: 64 Period size: 21 Copynumber: 2.9 Consensus size: 19 1024956 TTGACCATAC * * * 1024966 AAATGAAAATATTCAATAT 1 AAATGAAATTATACAATAA 1024985 AAATGTAAAATTATACAATAA 1 AAATG--AAATTATACAATAA 1025006 AAATGAAATGTATACAATA 1 AAATGAAAT-TATACAATA 1025025 CTAAAGAGAA Statistics Matches: 34, Mismatches: 3, Indels: 5 0.81 0.07 0.12 Matches are distributed among these distances: 19 9 0.26 20 9 0.26 21 16 0.47 ACGTcount: A:0.59, C:0.05, G:0.07, T:0.29 Consensus pattern (19 bp): AAATGAAATTATACAATAA Found at i:1028177 original size:36 final size:36 Alignment explanation

Indices: 1028124--1029827 Score: 2053 Period size: 36 Copynumber: 47.1 Consensus size: 36 1028114 AGGCCTGTGC * * * 1028124 TGCATGTTATTGCTCGCTTCTTCTGTACGGACAGAA 1 TGCATGTTATTGGTCGCTTCTACTGTACGTACAGAA * * * 1028160 TGCTTGTTATTGGTCGCTTCTTCTGTACGTACATAA 1 TGCATGTTATTGGTCGCTTCTACTGTACGTACAGAA * * * 1028196 TGCATGTTAATGGTCGCTTCTTCTGTACGTACATAA 1 TGCATGTTATTGGTCGCTTCTACTGTACGTACAGAA * * 1028232 TGCATGTTATTGGTCGCTTCTCCTGTACGTACATAA 1 TGCATGTTATTGGTCGCTTCTACTGTACGTACAGAA * 1028268 TGCATGTTATTGGTCGCTTCTCCTGTACGTACAGAA 1 TGCATGTTATTGGTCGCTTCTACTGTACGTACAGAA * * ** * * 1028304 TGCATGTTAATGGTCGCTTCTTCTGTATATACTGAT 1 TGCATGTTATTGGTCGCTTCTACTGTACGTACAGAA * ** * * 1028340 TGCACGTTAACGGTCGTTTCTCCTGTACGTACAGAA 1 TGCATGTTATTGGTCGCTTCTACTGTACGTACAGAA * * * * 1028376 TGCATGTTTCATATGAATTG-TTCGCTTCT-TCCGTACAGAA 1 TGCATG-TT-AT-TG-GTCGCTT--CTACTGTACGTACAGAA * * * 1028416 TACTTGGTATTGGTCGCTTCTACTGTACGTACAGAA 1 TGCATGTTATTGGTCGCTTCTACTGTACGTACAGAA * * * * 1028452 TGCACGTTAATGGTCGCTTCTTCTGTATGTACAGAA 1 TGCATGTTATTGGTCGCTTCTACTGTACGTACAGAA ** ** * * 1028488 TGCACATTAACGGTAGCTTCTCCTGTACGTACAGAA 1 TGCATGTTATTGGTCGCTTCTACTGTACGTACAGAA * * * * 1028524 TGCATGTTTCATATGTATTG-TTCGCTTCT-TCCGTACAGAA 1 TGCATG-TT-AT-TG-GTCGCTT--CTACTGTACGTACAGAA * * * 1028564 TACTTGTTATTGGTCGCTTCTACTGTTCGTACAGAA 1 TGCATGTTATTGGTCGCTTCTACTGTACGTACAGAA * * * 1028600 TGCACGTTAACT-GTCGCTTCTTCTGTACGTACAGAA 1 TGCATGTT-ATTGGTCGCTTCTACTGTACGTACAGAA * * 1028636 TGCATGGTATTGGTCGCTTCTCCTGTACGTACAGAA 1 TGCATGTTATTGGTCGCTTCTACTGTACGTACAGAA * * * 1028672 TGCACGTTAACT-GTCGCATCTACTGTACGTACAGAA 1 TGCATGTT-ATTGGTCGCTTCTACTGTACGTACAGAA * 1028708 TGCATGGTATTGGTCGCTTCTACTGTACGTACAGAA 1 TGCATGTTATTGGTCGCTTCTACTGTACGTACAGAA * 1028744 TGCTTGTTATTGGTCGCTTCTACTGTACGTACAGAA 1 TGCATGTTATTGGTCGCTTCTACTGTACGTACAGAA * * 1028780 TGCATGTTAACT-GTTGCTTCTACTGTACGTACAGAA 1 TGCATGTT-ATTGGTCGCTTCTACTGTACGTACAGAA * 1028816 TGCATGGTATTGGTCGCTTCTACTGTACGTACAGAA 1 TGCATGTTATTGGTCGCTTCTACTGTACGTACAGAA * * * * 1028852 TGCTTGTTATT-TTCG-TCTCAATATCATCTATG-A-A-AA 1 TGCATGTTATTGGTCGCT-TC--TA-C-TGTACGTACAGAA * 1028888 -GCATCGTTAACT-GTCGCTTCTACTGTACGTACAGAA 1 TGCAT-GTT-ATTGGTCGCTTCTACTGTACGTACAGAA * 1028924 TGCATGGTATTGGTCGCTTCTACTGTACGTACAGAA 1 TGCATGTTATTGGTCGCTTCTACTGTACGTACAGAA * * 1028960 TGCTTGTTATTGGTCGCTTCTACTGTACTTACAGAA 1 TGCATGTTATTGGTCGCTTCTACTGTACGTACAGAA * * 1028996 TGCATGTTAATGGTCGCTTCTACTGTACGTACAGAT 1 TGCATGTTATTGGTCGCTTCTACTGTACGTACAGAA * * 1029032 TGCTTGTTATTGGTCGCTTCTACTGTACGTACAGAT 1 TGCATGTTATTGGTCGCTTCTACTGTACGTACAGAA * 1029068 TGCATGTT-TACGGTCGCTTCTACTGTACGTACAGAA 1 TGCATGTTAT-TGGTCGCTTCTACTGTACGTACAGAA * 1029104 TGCATGTT-TACGGTCGCTTCTACTGTACGTACAGAA 1 TGCATGTTAT-TGGTCGCTTCTACTGTACGTACAGAA * 1029140 TGCTTGTTATTGGTCGCTTCTACTGTACGTACAGAA 1 TGCATGTTATTGGTCGCTTCTACTGTACGTACAGAA * 1029176 TGCTTGTTATTGGTCGCTTCTACTGTACGTACAGAA 1 TGCATGTTATTGGTCGCTTCTACTGTACGTACAGAA * 1029212 TGCATGTT-TACGGTCGCTTCTACTGTACGTACAGAA 1 TGCATGTTAT-TGGTCGCTTCTACTGTACGTACAGAA * * 1029248 TGCATGTT-TACGGTCGCTTCTACTGTACGTACAGAT 1 TGCATGTTAT-TGGTCGCTTCTACTGTACGTACAGAA * 1029284 TGCTTGTTATTGGTCGCTTCTACTGTACGTACAGAA 1 TGCATGTTATTGGTCGCTTCTACTGTACGTACAGAA * ** * 1029320 TGCACGTTAACGGTCGCTTCTACTGTACGTACAGAT 1 TGCATGTTATTGGTCGCTTCTACTGTACGTACAGAA * 1029356 TGCTTGTTATTGGTCGCTTCTACTGTACGTACAGAA 1 TGCATGTTATTGGTCGCTTCTACTGTACGTACAGAA ** 1029392 TGCATGTTAACGGTCGCTTCTACTGTACGTACAGAA 1 TGCATGTTATTGGTCGCTTCTACTGTACGTACAGAA * 1029428 TGCTTGTTATTGGTCGCTTCTACTGTACGTACAGAA 1 TGCATGTTATTGGTCGCTTCTACTGTACGTACAGAA * 1029464 TGCATGTTAATGGTCGCTTCTACTGTACGTACAGAA 1 TGCATGTTATTGGTCGCTTCTACTGTACGTACAGAA * * 1029500 TGCTTGTTAATGGTCGCTTCTACTGTACGTACAGAA 1 TGCATGTTATTGGTCGCTTCTACTGTACGTACAGAA * 1029536 TGCATGTTAATGGTCGCTTCTACTGTACGTACAGAA 1 TGCATGTTATTGGTCGCTTCTACTGTACGTACAGAA * 1029572 TGCTTGTTATTGGTCGCTTCTACTGTACGTACAGAA 1 TGCATGTTATTGGTCGCTTCTACTGTACGTACAGAA ** * 1029608 TGCATGTTAACGGTCGCTTCTACTGTTCGTACAGAA 1 TGCATGTTATTGGTCGCTTCTACTGTACGTACAGAA * * 1029644 TGCACGTTAACT-GTCGCTTCTACTGTACGTACAGAA 1 TGCATGTT-ATTGGTCGCTTCTACTGTACGTACAGAA * * 1029680 TGCATGTTAATGGTCGCTTCTACTGTACGCACAGAA 1 TGCATGTTATTGGTCGCTTCTACTGTACGTACAGAA * * 1029716 TGCTTGTTATTCGTCGCTTCTACTGTACGTACAGAA 1 TGCATGTTATTGGTCGCTTCTACTGTACGTACAGAA * * * * * 1029752 TGCACGTTAACT-GTTGCTTCTTCTGTATGTACAGAA 1 TGCATGTT-ATTGGTCGCTTCTACTGTACGTACAGAA 1029788 TGCATGTTATTGGTCGCTTCTACTGTACGTACAGAA 1 TGCATGTTATTGGTCGCTTCTACTGTACGTACAGAA 1029824 TGCA 1 TGCA 1029828 ACATCAGTCA Statistics Matches: 1455, Mismatches: 170, Indels: 86 0.85 0.10 0.05 Matches are distributed among these distances: 33 4 0.00 34 3 0.00 35 33 0.02 36 1316 0.90 37 37 0.03 38 9 0.01 39 13 0.01 40 32 0.02 41 8 0.01 ACGTcount: A:0.22, C:0.21, G:0.21, T:0.36 Consensus pattern (36 bp): TGCATGTTATTGGTCGCTTCTACTGTACGTACAGAA Found at i:1030729 original size:1 final size:1 Alignment explanation

Indices: 1030723--1030747 Score: 50 Period size: 1 Copynumber: 25.0 Consensus size: 1 1030713 TATTTTGCCA 1030723 CCCCCCCCCCCCCCCCCCCCCCCCC 1 CCCCCCCCCCCCCCCCCCCCCCCCC 1030748 TCCTGTCCGC Statistics Matches: 24, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 1 24 1.00 ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00 Consensus pattern (1 bp): C Found at i:1049030 original size:2 final size:2 Alignment explanation

Indices: 1049023--1049050 Score: 56 Period size: 2 Copynumber: 14.0 Consensus size: 2 1049013 TGTGTTAATC 1049023 AT AT AT AT AT AT AT AT AT AT AT AT AT AT 1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT 1049051 GATTTTTTTT Statistics Matches: 26, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 26 1.00 ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50 Consensus pattern (2 bp): AT Found at i:1067518 original size:2 final size:2 Alignment explanation

Indices: 1067511--1067563 Score: 106 Period size: 2 Copynumber: 26.5 Consensus size: 2 1067501 NNNNNNNNNN 1067511 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT 1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT 1067553 CT CT CT CT CT C 1 CT CT CT CT CT C 1067564 CACACACACA Statistics Matches: 51, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 51 1.00 ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49 Consensus pattern (2 bp): CT Found at i:1067569 original size:2 final size:2 Alignment explanation

Indices: 1067564--1067594 Score: 62 Period size: 2 Copynumber: 15.5 Consensus size: 2 1067554 TCTCTCTCTC 1067564 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA C 1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA C 1067595 TAAAACTCAT Statistics Matches: 29, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 29 1.00 ACGTcount: A:0.48, C:0.52, G:0.00, T:0.00 Consensus pattern (2 bp): CA Found at i:1070641 original size:2 final size:2 Alignment explanation

Indices: 1070636--1070681 Score: 92 Period size: 2 Copynumber: 23.0 Consensus size: 2 1070626 AAAAACACAC 1070636 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT 1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT 1070678 GT GT 1 GT GT 1070682 TTTAAAACCA Statistics Matches: 44, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 44 1.00 ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50 Consensus pattern (2 bp): GT Found at i:1074530 original size:2 final size:2 Alignment explanation

Indices: 1074523--1074551 Score: 58 Period size: 2 Copynumber: 14.5 Consensus size: 2 1074513 AGAGACTCGC 1074523 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A 1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A 1074552 TGTCTCAAAA Statistics Matches: 27, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 27 1.00 ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00 Consensus pattern (2 bp): AG Done.