Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: D10

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: 67973905
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32

Warning! 1760000 characters in sequence are not A, C, G, or T


File 165 of 228

Found at i:49571459 original size:25 final size:24

Alignment explanation

Indices: 49571415--49571501 Score: 70 Period size: 25 Copynumber: 3.5 Consensus size: 24 49571405 TGGCTTGCAT ** * 49571415 GAGCTTCCCAATATACAGCTCGATA 1 GAGCTTCCCGTTATATAGCTCGA-A 49571440 GAGCTTCCCGTTACT-TAGCTC-ACA 1 GAGCTTCCCGTTA-TATAGCTCGA-A * * 49571464 TGAGCTTCCTGTTATATGGCTCTGAA 1 -GAGCTTCCCGTTATATAGCTC-GAA 49571490 GAGCTTCCCGTT 1 GAGCTTCCCGTT 49571502 TACATGCTCG Statistics Matches: 50, Mismatches: 7, Indels: 10 0.75 0.10 0.15 Matches are distributed among these distances: 24 3 0.06 25 44 0.88 26 2 0.04 27 1 0.02 ACGTcount: A:0.22, C:0.28, G:0.20, T:0.31 Consensus pattern (24 bp): GAGCTTCCCGTTATATAGCTCGAA Found at i:49571518 original size:25 final size:25 Alignment explanation

Indices: 49571413--49571518 Score: 65 Period size: 25 Copynumber: 4.2 Consensus size: 25 49571403 TATGGCTTGC ** * * 49571413 ATGAGCTTCCCAATATACAGCTCG- 1 ATGAGCTTCCCGTTACATAGCTCGT * ** 49571437 ATAGAGCTTCCCGTTACTTAGCTCAC 1 AT-GAGCTTCCCGTTACATAGCTCGT * * * 49571463 ATGAGCTTCCTGTTATATGGCTC-T 1 ATGAGCTTCCCGTTACATAGCTCGT * 49571487 GAAGAGCTTCCCGTTTACAT-GCTCGT 1 -ATGAGCTTCCCG-TTACATAGCTCGT 49571513 ATGAGC 1 ATGAGC 49571519 ACATATGTAT Statistics Matches: 62, Mismatches: 15, Indels: 9 0.72 0.17 0.10 Matches are distributed among these distances: 24 2 0.03 25 52 0.84 26 8 0.13 ACGTcount: A:0.23, C:0.26, G:0.20, T:0.31 Consensus pattern (25 bp): ATGAGCTTCCCGTTACATAGCTCGT Found at i:49571644 original size:21 final size:22 Alignment explanation

Indices: 49571611--49571652 Score: 52 Period size: 21 Copynumber: 2.0 Consensus size: 22 49571601 CAATGGGCAA * 49571611 AGTTCTGATATGAGA-TATTATG 1 AGTTCTGAAATGA-ACTATTATG 49571633 AGTT-TGAAATGAACTATTAT 1 AGTTCTGAAATGAACTATTAT 49571653 CCATATATAC Statistics Matches: 18, Mismatches: 1, Indels: 3 0.82 0.05 0.14 Matches are distributed among these distances: 20 1 0.06 21 13 0.72 22 4 0.22 ACGTcount: A:0.36, C:0.05, G:0.19, T:0.40 Consensus pattern (22 bp): AGTTCTGAAATGAACTATTATG Found at i:49572389 original size:42 final size:42 Alignment explanation

Indices: 49572321--49572433 Score: 154 Period size: 42 Copynumber: 2.7 Consensus size: 42 49572311 TATTTTTTTC * * * 49572321 CACACGGGCAAAGACACAGGCATGTGTCTCAGTCGTGTGTGA 1 CACACGGGCAGAGACACGGGCGTGTGTCTCAGTCGTGTGTGA * * 49572363 CACACGAGCAGAGACACGGGCGTGTGTCTCAGTCTTGTGTGA 1 CACACGGGCAGAGACACGGGCGTGTGTCTCAGTCGTGTGTGA * * 49572405 CACACGGGCAAGTGACACGGCCGTGTGTC 1 CACACGGGC-AGAGACACGGGCGTGTGTC 49572434 CCCTGTATCT Statistics Matches: 62, Mismatches: 8, Indels: 1 0.87 0.11 0.01 Matches are distributed among these distances: 42 45 0.73 43 17 0.27 ACGTcount: A:0.23, C:0.26, G:0.33, T:0.19 Consensus pattern (42 bp): CACACGGGCAGAGACACGGGCGTGTGTCTCAGTCGTGTGTGA Found at i:49587581 original size:18 final size:18 Alignment explanation

Indices: 49587558--49587595 Score: 67 Period size: 18 Copynumber: 2.1 Consensus size: 18 49587548 TGCTAGGTGC * 49587558 GTATCCTAGCCCTTATAT 1 GTATCCTAACCCTTATAT 49587576 GTATCCTAACCCTTATAT 1 GTATCCTAACCCTTATAT 49587594 GT 1 GT 49587596 TTCATTTTCT Statistics Matches: 19, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 18 19 1.00 ACGTcount: A:0.24, C:0.26, G:0.11, T:0.39 Consensus pattern (18 bp): GTATCCTAACCCTTATAT Found at i:49587871 original size:21 final size:21 Alignment explanation

Indices: 49587847--49587891 Score: 81 Period size: 21 Copynumber: 2.1 Consensus size: 21 49587837 CCCACAACCA * 49587847 GAACAACCACAACCCCCGCTG 1 GAACAACCACAACCCCCGCCG 49587868 GAACAACCACAACCCCCGCCG 1 GAACAACCACAACCCCCGCCG 49587889 GAA 1 GAA 49587892 GCTGAACTAA Statistics Matches: 23, Mismatches: 1, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 21 23 1.00 ACGTcount: A:0.36, C:0.47, G:0.16, T:0.02 Consensus pattern (21 bp): GAACAACCACAACCCCCGCCG Found at i:49591362 original size:126 final size:126 Alignment explanation

Indices: 49591133--49591416 Score: 426 Period size: 126 Copynumber: 2.3 Consensus size: 126 49591123 TAAGGCCAAA * * 49591133 CAAGAACTACTGTAGAAAAAGAGCGTCCACATGGGAGCTTTTTTCAGTAATTTTGCTGATAGTGC 1 CAAGAACTACTGTAGAAAAAGAGCGTCCACATGGGAGCTTTTTTCAGTAATTTTGCAGACAGTGC * * * 49591198 ATCCTGCTTGAAGCGTTTTTGACACTATTTTTTCAGAACCGTCTTTTCAAAATTATTTTTT 66 ATCCTACTTGAAGCGTTTTTGAAACTATTTTTTCAGAACCGTCTTCTCAAAATTATTTTTT * * * ** * * 49591259 CAAGAACCACTGTAGAAAAAGAGTGTTCATGTGGTAGCTTTTTTTAGTAATTTTGCAGACAGTGC 1 CAAGAACTACTGTAGAAAAAGAGCGTCCACATGGGAGCTTTTTTCAGTAATTTTGCAGACAGTGC * 49591324 ATCCTACTTGAAGTGTTTTTGAAACTACTTTTTT-AGAACCGTCTTCTCAAAATTATTTTTT 66 ATCCTACTTGAAGCGTTTTTGAAACTA-TTTTTTCAGAACCGTCTTCTCAAAATTATTTTTT * 49591385 CAAGAACTATTGTAGAAAAAGAGCGTCCACAT 1 CAAGAACTACTGTAGAAAAAGAGCGTCCACAT 49591417 CCTACTTCAA Statistics Matches: 138, Mismatches: 19, Indels: 2 0.87 0.12 0.01 Matches are distributed among these distances: 126 132 0.96 127 6 0.04 ACGTcount: A:0.30, C:0.17, G:0.17, T:0.37 Consensus pattern (126 bp): CAAGAACTACTGTAGAAAAAGAGCGTCCACATGGGAGCTTTTTTCAGTAATTTTGCAGACAGTGC ATCCTACTTGAAGCGTTTTTGAAACTATTTTTTCAGAACCGTCTTCTCAAAATTATTTTTT Found at i:49591484 original size:91 final size:91 Alignment explanation

Indices: 49591323--49591495 Score: 258 Period size: 91 Copynumber: 1.9 Consensus size: 91 49591313 GCAGACAGTG * * * * 49591323 CATCCTACTTGAAGTGTTTTTGAAACTACTTTTTTAGAACCGTCTTCTCAAAATTATTTTTTCAA 1 CATCCTACTTCAAGCGTTTTTGAAACTACCTTTTTAGAACCGTCTTCTCAAAATTAATTTTTCAA 49591388 GAACTATTGTAGAAAAAGAGCGTCCA 66 GAACTATTGTAGAAAAAGAGCGTCCA * * * * 49591414 CATCCTACTTCAAGCGTTTTTTACATTACCTTTTTAGAACCGTCTTCTCAAAATTAATTTTTC-T 1 CATCCTACTTCAAGCGTTTTTGAAACTACCTTTTTAGAACCGTCTTCTCAAAATTAATTTTTCAA 49591478 GAAACTATTGTAGAAAAA 66 G-AACTATTGTAGAAAAA 49591496 AAAACAAAAT Statistics Matches: 73, Mismatches: 8, Indels: 2 0.88 0.10 0.02 Matches are distributed among these distances: 90 1 0.01 91 72 0.99 ACGTcount: A:0.32, C:0.18, G:0.11, T:0.39 Consensus pattern (91 bp): CATCCTACTTCAAGCGTTTTTGAAACTACCTTTTTAGAACCGTCTTCTCAAAATTAATTTTTCAA GAACTATTGTAGAAAAAGAGCGTCCA Found at i:49591598 original size:34 final size:33 Alignment explanation

Indices: 49591557--49591683 Score: 150 Period size: 34 Copynumber: 3.8 Consensus size: 33 49591547 CACAAAATTA ** 49591557 TTTTTAAAAAAACTAAACCCTAATTTAATTAAT 1 TTTTTAAAAACTCTAAACCCTAATTTAATTAAT * 49591590 TTTCTTAAAAACTCTAAACCCTCATTTAATTAAT 1 TTT-TTAAAAACTCTAAACCCTAATTTAATTAAT * * * 49591624 TTATTT-TAAACCCTTAAAACCTAATTTAATT-AT 1 TT-TTTAAAAACTC-TAAACCCTAATTTAATTAAT * 49591657 TTTTTAAAAACTCTAAACTCTAATTTA 1 TTTTTAAAAACTCTAAACCCTAATTTA 49591684 TTTTTTAAAA Statistics Matches: 79, Mismatches: 11, Indels: 9 0.80 0.11 0.09 Matches are distributed among these distances: 32 15 0.19 33 17 0.22 34 46 0.58 35 1 0.01 ACGTcount: A:0.42, C:0.16, G:0.00, T:0.43 Consensus pattern (33 bp): TTTTTAAAAACTCTAAACCCTAATTTAATTAAT Found at i:49593211 original size:111 final size:110 Alignment explanation

Indices: 49593015--49593235 Score: 424 Period size: 111 Copynumber: 2.0 Consensus size: 110 49593005 TTAATTTATT 49593015 TCAACAAAGCCCCTTAAAATTAATTATTTAATGGTCATCATTCCTTAATTTTTTTATTAATTAAT 1 TCAACAAAGCCCCTTAAAATTAATTATTTAATGGTCATCATTCCTTAATTTTTTTATTAATTAAT 49593080 GTTCAGTGATACAAATCTGTTTCTTATTACATTTTATATAATGTA 66 GTTCAGTGATACAAATCTGTTTCTTATTACATTTTATATAATGTA * 49593125 TCAACAAAGCCCCTTAAAATTAATTATTTGATGGTCATCATTCCTTAATTTTTTTTATTAATTAA 1 TCAACAAAGCCCCTTAAAATTAATTATTTAATGGTCATCATTCCTTAA-TTTTTTTATTAATTAA 49593190 TGTTCAGTGATACAAATCTGTTTCTTATTACATTTTATATAATGTA 65 TGTTCAGTGATACAAATCTGTTTCTTATTACATTTTATATAATGTA 49593236 CAAACTGATA Statistics Matches: 109, Mismatches: 1, Indels: 1 0.98 0.01 0.01 Matches are distributed among these distances: 110 47 0.43 111 62 0.57 ACGTcount: A:0.33, C:0.14, G:0.08, T:0.46 Consensus pattern (110 bp): TCAACAAAGCCCCTTAAAATTAATTATTTAATGGTCATCATTCCTTAATTTTTTTATTAATTAAT GTTCAGTGATACAAATCTGTTTCTTATTACATTTTATATAATGTA Found at i:49593856 original size:21 final size:21 Alignment explanation

Indices: 49593832--49593900 Score: 68 Period size: 21 Copynumber: 3.3 Consensus size: 21 49593822 TTGTTGGAAA * 49593832 ATAATTATTGAGTGAAGAATG 1 ATAATTATTGAGTGATGAATG * * * ** 49593853 ATAATTGAAT-ATTGTTGAAAA 1 ATAATT-ATTGAGTGATGAATG 49593874 ATAATTATTGAGTGATGAATG 1 ATAATTATTGAGTGATGAATG 49593895 ATAATT 1 ATAATT 49593901 GTATTTCTTG Statistics Matches: 35, Mismatches: 11, Indels: 4 0.70 0.22 0.08 Matches are distributed among these distances: 20 2 0.06 21 31 0.89 22 2 0.06 ACGTcount: A:0.43, C:0.00, G:0.19, T:0.38 Consensus pattern (21 bp): ATAATTATTGAGTGATGAATG Found at i:49593879 original size:42 final size:42 Alignment explanation

Indices: 49593820--49593901 Score: 146 Period size: 42 Copynumber: 2.0 Consensus size: 42 49593810 TTTTATTATG * 49593820 TATTGTTGGAAAATAATTATTGAGTGAAGAATGATAATTGAA 1 TATTGTTGAAAAATAATTATTGAGTGAAGAATGATAATTGAA * 49593862 TATTGTTGAAAAATAATTATTGAGTGATGAATGATAATTG 1 TATTGTTGAAAAATAATTATTGAGTGAAGAATGATAATTG 49593902 TATTTCTTGG Statistics Matches: 38, Mismatches: 2, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 42 38 1.00 ACGTcount: A:0.41, C:0.00, G:0.21, T:0.38 Consensus pattern (42 bp): TATTGTTGAAAAATAATTATTGAGTGAAGAATGATAATTGAA Found at i:49599119 original size:21 final size:21 Alignment explanation

Indices: 49599093--49599164 Score: 58 Period size: 21 Copynumber: 3.4 Consensus size: 21 49599083 ATTGTAGGAA 49599093 AATAATTATTGAGTGAAGAAT 1 AATAATTATTGAGTGAAGAAT * * ** 49599114 AATAATTGAAT-ATTGTTGGAA- 1 AATAATT-ATTGAGTG-AAGAAT * 49599135 AATAATTATTGAGTGATGAAT 1 AATAATTATTGAGTGAAGAAT * 49599156 GATAATTAT 1 AATAATTAT 49599165 ATCTCTTGGT Statistics Matches: 38, Mismatches: 9, Indels: 8 0.69 0.16 0.15 Matches are distributed among these distances: 20 5 0.13 21 28 0.74 22 5 0.13 ACGTcount: A:0.44, C:0.00, G:0.18, T:0.38 Consensus pattern (21 bp): AATAATTATTGAGTGAAGAAT Found at i:49599142 original size:42 final size:42 Alignment explanation

Indices: 49599083--49599162 Score: 133 Period size: 42 Copynumber: 1.9 Consensus size: 42 49599073 CATGTAGGGG 49599083 ATTGTAGGAAAATAATTATTGAGTGAAGAATAATAATTGAAT 1 ATTGTAGGAAAATAATTATTGAGTGAAGAATAATAATTGAAT * * * 49599125 ATTGTTGGAAAATAATTATTGAGTGATGAATGATAATT 1 ATTGTAGGAAAATAATTATTGAGTGAAGAATAATAATT 49599163 ATATCTCTTG Statistics Matches: 35, Mismatches: 3, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 42 35 1.00 ACGTcount: A:0.44, C:0.00, G:0.20, T:0.36 Consensus pattern (42 bp): ATTGTAGGAAAATAATTATTGAGTGAAGAATAATAATTGAAT Found at i:49607777 original size:16 final size:16 Alignment explanation

Indices: 49607756--49607793 Score: 58 Period size: 16 Copynumber: 2.4 Consensus size: 16 49607746 TTATTTAAAA ** 49607756 AAATATTATTTATTTT 1 AAATATTATTTACATT 49607772 AAATATTATTTACATT 1 AAATATTATTTACATT 49607788 AAATAT 1 AAATAT 49607794 ATTAAATTAT Statistics Matches: 20, Mismatches: 2, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 16 20 1.00 ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53 Consensus pattern (16 bp): AAATATTATTTACATT Found at i:49608167 original size:20 final size:20 Alignment explanation

Indices: 49608122--49608167 Score: 56 Period size: 20 Copynumber: 2.3 Consensus size: 20 49608112 TTACAAAATA * * * 49608122 TCTAACAATTTATTAATTTT 1 TCTAAGAATTTACTAATATT * 49608142 TTTAAGAATTTACTAATATT 1 TCTAAGAATTTACTAATATT 49608162 TCTAAG 1 TCTAAG 49608168 GATGTTAGAA Statistics Matches: 21, Mismatches: 5, Indels: 0 0.81 0.19 0.00 Matches are distributed among these distances: 20 21 1.00 ACGTcount: A:0.37, C:0.09, G:0.04, T:0.50 Consensus pattern (20 bp): TCTAAGAATTTACTAATATT Found at i:49610588 original size:3 final size:3 Alignment explanation

Indices: 49610580--49610635 Score: 53 Period size: 3 Copynumber: 19.0 Consensus size: 3 49610570 GTAAAGTAAG * * * * 49610580 TAA TAA TAA TAA -ATA TAA TAC TAA TAA TAA TAA TAG TAG CAA TAA 1 TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA 49610625 TAA T-A TAA TAA 1 TAA TAA TAA TAA 49610636 ATAAAAGGGG Statistics Matches: 44, Mismatches: 6, Indels: 6 0.79 0.11 0.11 Matches are distributed among these distances: 2 3 0.07 3 40 0.91 4 1 0.02 ACGTcount: A:0.61, C:0.04, G:0.04, T:0.32 Consensus pattern (3 bp): TAA Found at i:49610592 original size:18 final size:18 Alignment explanation

Indices: 49610555--49610629 Score: 53 Period size: 18 Copynumber: 3.9 Consensus size: 18 49610545 AGGCACCATG * * 49610555 AGTAAATAATTAATAGTAA 1 AGTAAGTAA-TAATAATAA 49610574 AGTAAGTAATAATAATAA 1 AGTAAGTAATAATAATAA * * 49610592 ATATAATACTAATAATAATAA 1 A-GT-A-AGTAATAATAATAA * 49610613 TAGT-AGCAATAATAATA 1 -AGTAAGTAATAATAATA 49610630 TAATAAATAA Statistics Matches: 45, Mismatches: 7, Indels: 9 0.74 0.11 0.15 Matches are distributed among these distances: 18 20 0.44 19 9 0.20 20 1 0.02 21 14 0.31 22 1 0.02 ACGTcount: A:0.59, C:0.03, G:0.08, T:0.31 Consensus pattern (18 bp): AGTAAGTAATAATAATAA Found at i:49610638 original size:15 final size:15 Alignment explanation

Indices: 49610557--49610639 Score: 57 Period size: 15 Copynumber: 5.5 Consensus size: 15 49610547 GCACCATGAG * * 49610557 TAAATAATTA-ATAG 1 TAAATAATAATATAA 49610571 TAAAGTAAGTAATAATAA 1 TAAA-TAA-TAAT-ATAA 49610589 TAAAT-ATAATACTAA 1 TAAATAATAATA-TAA 49610604 T-AATAATAATAGT-A 1 TAAATAATAATA-TAA ** 49610618 GCAATAATAATATAA 1 TAAATAATAATATAA 49610633 TAAATAA 1 TAAATAA 49610640 AAGGGGTTAA Statistics Matches: 55, Mismatches: 6, Indels: 15 0.72 0.08 0.20 Matches are distributed among these distances: 14 10 0.18 15 34 0.62 16 3 0.05 17 1 0.02 18 7 0.13 ACGTcount: A:0.60, C:0.02, G:0.06, T:0.31 Consensus pattern (15 bp): TAAATAATAATATAA Found at i:49612473 original size:131 final size:132 Alignment explanation

Indices: 49612239--49613427 Score: 2009 Period size: 131 Copynumber: 9.1 Consensus size: 132 49612229 TTTTTTCAGT * * * * 49612239 CTGCTCCGCTACTACTTAGGGAGATAAGACTGGTGGCTTAAATCTACTTCACTACTGCTTAGGAA 1 CTGCTCCACTACTGCTTAGGGAGATAGGACTGGTGGCTTAAATCTGCTTCACTACTGCTTAGGAA * * * * * 49612304 GATGAGATTCGCCGTCTTCGATCTGCTCTACTACTTCTTAGGGAGATAGGATCTAACATCTTTAG 66 GATGAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACCATCTTTCG 49612369 -C 131 AC 49612370 CTGCTCCACTACTGCTTAGGGAGATAGGACTGGTGGCTTAAATCTGCTTCACTACTGCTTAGGAA 1 CTGCTCCACTACTGCTTAGGGAGATAGGACTGGTGGCTTAAATCTGCTTCACTACTGCTTAGGAA * * * * 49612435 GATGAGATTCGCCGTCTTCGATCTGCTCTACTACTTCTTAGGGAGATAGGATCTAACATCTTT-G 66 GATGAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACCATCTTTCG * 49612499 GC 131 AC 49612501 CTGCTCCACTACTGCTTAGGGAGATAGGACTGGTGGCTTAAATCTGCTTCACTACTGCTTAGGAA 1 CTGCTCCACTACTGCTTAGGGAGATAGGACTGGTGGCTTAAATCTGCTTCACTACTGCTTAGGAA * * * 49612566 GATGAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAGGGTCTAACATCTTT-G 66 GATGAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACCATCTTTCG 49612630 AC 131 AC * * 49612632 CTGCTCCACTACTACTTAGGGAGATAGGACTGGTGGCTTAAATCTGCTTCACTACTGCTGAGGAA 1 CTGCTCCACTACTGCTTAGGGAGATAGGACTGGTGGCTTAAATCTGCTTCACTACTGCTTAGGAA * * * 49612697 GATGAGATTCGCCGTCTTCGATCTGCTCCACTACTACTTAGGGAGATAGGATCTAACATCTTT-G 66 GATGAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACCATCTTTCG 49612761 AC 131 AC * * 49612763 CTGCCCCACTACTGCTTAGGGAGATAGGACTGGTGGCTTAAATTTGCTTCACTACTGCTTAGGAA 1 CTGCTCCACTACTGCTTAGGGAGATAGGACTGGTGGCTTAAATCTGCTTCACTACTGCTTAGGAA 49612828 GATGAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACCATC-TTCG 66 GATGAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACCATCTTTCG 49612892 AC 131 AC * 49612894 CTGCTCCACTACTGCTTAGGGAGATAGGACTGGTGGCTTAAATATGCTTCACTACTGCTTAGGAA 1 CTGCTCCACTACTGCTTAGGGAGATAGGACTGGTGGCTTAAATCTGCTTCACTACTGCTTAGGAA * 49612959 GATGAGATTCACCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACCATC-TTCG 66 GATGAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACCATCTTTCG 49613023 AC 131 AC * 49613025 CTGCTCCACTACTGCTTAGGGAGATAGGACTGGTGGCTTAAATCTGCTTCACTACTGTTTAGGAA 1 CTGCTCCACTACTGCTTAGGGAGATAGGACTGGTGGCTTAAATCTGCTTCACTACTGCTTAGGAA * 49613090 GATGAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATTTACCATC-TTCG 66 GATGAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACCATCTTTCG 49613154 AC 131 AC * * 49613156 CTGCTCCACTACTGCTTAGGGAGAGAGGACTGGTGGCTTAAATCTACTTCACTACTGCTTAGGAA 1 CTGCTCCACTACTGCTTAGGGAGATAGGACTGGTGGCTTAAATCTGCTTCACTACTGCTTAGGAA 49613221 GATGAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACCATC-TTCG 66 GATGAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACCATCTTTCG 49613285 AC 131 AC * 49613287 CTGCTCTACTACTGCTTAGGGAGATAGGACTGGTGGCTTAAATCTGCTTCACTACTGCTTAGGAA 1 CTGCTCCACTACTGCTTAGGGAGATAGGACTGGTGGCTTAAATCTGCTTCACTACTGCTTAGGAA * * 49613352 GATGAGATTCGCCGTCTTCGATCTACTCCACTATTGCTTAGGGAGATAAGATCTACCATC-TTCG 66 GATGAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACCATCTTTCG 49613416 AC 131 AC * 49613418 CTGTTCCACT 1 CTGCTCCACT 49613428 GTAACCTTAG Statistics Matches: 1019, Mismatches: 37, Indels: 4 0.96 0.03 0.00 Matches are distributed among these distances: 130 3 0.00 131 1016 1.00 ACGTcount: A:0.23, C:0.24, G:0.23, T:0.30 Consensus pattern (132 bp): CTGCTCCACTACTGCTTAGGGAGATAGGACTGGTGGCTTAAATCTGCTTCACTACTGCTTAGGAA GATGAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACCATCTTTCG AC Found at i:49613426 original size:44 final size:44 Alignment explanation

Indices: 49612238--49613427 Score: 870 Period size: 44 Copynumber: 27.2 Consensus size: 44 49612228 TTTTTTTCAG * * ** * ** 49612238 TCTGCTCCGCTACTACTTAGGGAGATAAGA-CTGGTGGCTTAAA 1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCCGTCTTCGA * * * * 49612281 TCTACTTCACTACTGCTTAGGAAGATGAGAT-TCGCCGTCTTCGA 1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCT-GCCGTCTTCGA * * * ** * * 49612325 TCTGCTCTACTACTTCTTAGGGAGATAGGATCTAACATCTT-TA 1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCCGTCTTCGA * * ** * ** 49612368 GCCTGCTCCACTACTGCTTAGGGAGATAGGA-CTGGTGGCTTAAA 1 -TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCCGTCTTCGA * * * 49612412 TCTGCTTCACTACTGCTTAGGAAGATGAGAT-TCGCCGTCTTCGA 1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCT-GCCGTCTTCGA * * * ** * * * 49612456 TCTGCTCTACTACTTCTTAGGGAGATAGGATCTAACATCTTTGG 1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCCGTCTTCGA * * ** * ** 49612500 CCTGCTCCACTACTGCTTAGGGAGATAGGA-CTGGTGGCTTAAA 1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCCGTCTTCGA * * * 49612543 TCTGCTTCACTACTGCTTAGGAAGATGAGAT-TCGCCGTCTTCGA 1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCT-GCCGTCTTCGA * * ** * * 49612587 TCTGCTCCACTACTGCTTAGGGAGATAGGGTCTAACATCTTTGA 1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCCGTCTTCGA * * * ** * ** 49612631 CCTGCTCCACTACTACTTAGGGAGATAGGA-CTGGTGGCTTAAA 1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCCGTCTTCGA * * * * 49612674 TCTGCTTCACTACTGCTGAGGAAGATGAGAT-TCGCCGTCTTCGA 1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCT-GCCGTCTTCGA * * ** * * 49612718 TCTGCTCCACTACTACTTAGGGAGATAGGATCTAACATCTTTGA 1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCCGTCTTCGA * * * ** * ** 49612762 CCTGCCCCACTACTGCTTAGGGAGATAGGA-CTGGTGGCTTAAA 1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCCGTCTTCGA * * * * 49612805 TTTGCTTCACTACTGCTTAGGAAGATGAGAT-TCGCCGTCTTCGA 1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCT-GCCGTCTTCGA * * 49612849 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTACCATCTTCGA 1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCCGTCTTCGA * * ** * ** 49612893 CCTGCTCCACTACTGCTTAGGGAGATAGGA-CTGGTGGCTTAAA 1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCCGTCTTCGA * * * * * 49612936 TATGCTTCACTACTGCTTAGGAAGATGAGAT-TCACCGTCTTCGA 1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCT-GCCGTCTTCGA * * 49612980 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTACCATCTTCGA 1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCCGTCTTCGA * * ** * ** 49613024 CCTGCTCCACTACTGCTTAGGGAGATAGGA-CTGGTGGCTTAAA 1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCCGTCTTCGA * * * * 49613067 TCTGCTTCACTACTGTTTAGGAAGATGAGAT-TCGCCGTCTTCGA 1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCT-GCCGTCTTCGA * * * 49613111 TCTGCTCCACTACTGCTTAGGGAGATAAGATTTACCATCTTCGA 1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCCGTCTTCGA * * * ** * ** 49613155 CCTGCTCCACTACTGCTTAGGGAGAGAGGA-CTGGTGGCTTAAA 1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCCGTCTTCGA * * * * 49613198 TCTACTTCACTACTGCTTAGGAAGATGAGAT-TCGCCGTCTTCGA 1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCT-GCCGTCTTCGA * * 49613242 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTACCATCTTCGA 1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCCGTCTTCGA * * * ** * ** 49613286 CCTGCTCTACTACTGCTTAGGGAGATAGGA-CTGGTGGCTTAAA 1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCCGTCTTCGA * * * 49613329 TCTGCTTCACTACTGCTTAGGAAGATGAGAT-TCGCCGTCTTCGA 1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCT-GCCGTCTTCGA * * * * 49613373 TCTACTCCACTATTGCTTAGGGAGATAAGATCTACCATCTTCGA 1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCCGTCTTCGA * * 49613417 CCTGTTCCACT 1 TCTGCTCCACT 49613428 GTAACCTTAG Statistics Matches: 864, Mismatches: 254, Indels: 57 0.74 0.22 0.05 Matches are distributed among these distances: 43 270 0.31 44 585 0.68 45 9 0.01 ACGTcount: A:0.23, C:0.24, G:0.23, T:0.30 Consensus pattern (44 bp): TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCCGTCTTCGA Found at i:49613474 original size:46 final size:46 Alignment explanation

Indices: 49613422--49613807 Score: 339 Period size: 46 Copynumber: 8.6 Consensus size: 46 49613412 TTCGACCTGT * * 49613422 TCCACTGTAACCTTAGGGAGATAATATCTGAAATTCTTCGGTCTAC 1 TCCACTGTAACCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTAC * 49613468 TCCACTGTAACCTCAGAGAGATAAGATCTGAAATTCTTCGGTCTAC 1 TCCACTGTAACCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTAC ** ** * 49613514 TCCACTGTAACCTCAGGGAGATAAGATCCT-TTATT-TT-AATCTGC 1 TCCACTGTAACCTCAGGGAGATAAGAT-CTGAAATTCTTCGGTCTAC * * * * * * ** * 49613558 TCCACTGTAGCTTCAGGGAGATAGGAT-T--ACTAGCTCCAATCTGC 1 TCCACTGTAACCTCAGGGAGATAAGATCTGAAAT-TCTTCGGTCTAC * 49613602 TCCACTGTAACCTCAAGGAGATAAGATCTGAAATTCTTCGGTCTAC 1 TCCACTGTAACCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTAC * * ** * 49613648 TCCACAGTAACCTCAGGGAGATAAGA-CTTGCATATTCAAC---CTGC 1 TCCACTGTAACCTCAGGGAGATAAGATC-TG-AAATTCTTCGGTCTAC * * * * * * 49613692 TCCACTGTAACTTCAGGGAGATAAGGTTTG---TGGCTTCGATCTGC 1 TCCACTGTAACCTCAGGGAGATAAGATCTGAAAT-TCTTCGGTCTAC * * * * 49613736 TCCTCTGTAATCTCATGGAGATAAGATCTGAAATTTTTCGGTCTAC 1 TCCACTGTAACCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTAC 49613782 TCCACTGTAACCTCAGGGAGATAAGA 1 TCCACTGTAACCTCAGGGAGATAAGA 49613808 CTTGCATATT Statistics Matches: 271, Mismatches: 52, Indels: 34 0.76 0.15 0.10 Matches are distributed among these distances: 40 1 0.00 41 3 0.01 42 1 0.00 43 1 0.00 44 114 0.42 45 4 0.01 46 136 0.50 47 11 0.04 ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30 Consensus pattern (46 bp): TCCACTGTAACCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTAC Found at i:49613637 original size:134 final size:132 Alignment explanation

Indices: 49613457--49614035 Score: 613 Period size: 134 Copynumber: 4.3 Consensus size: 132 49613447 ATCTGAAATT * * 49613457 CTTCGGTCTACTCCACTGTAACCTC-AGAGAGATAAGATCTGAAATTCTTCGGTCTACTCCACTG 1 CTTCGATCTGCTCCACTGTAACCTCAAG-GAGATAAGATCTGAAATTCTTCGGTCTACTCCACTG * * * 49613521 TAACCTCAGGGAGATAAGATCCTT-TAT-TTTAATCTGCTCCACTGTAGCTTCAGGGAGAT-AGG 65 TAACCTCAGGGAGATAAGA--CTTGCATATTCAA-CTGCTCCACTGTAACTTCAGGGAGATAAGG * 49613583 ATTACTAG 127 -TTA-TGG * * * 49613591 CTCCAATCTGCTCCACTGTAACCTCAAGGAGATAAGATCTGAAATTCTTCGGTCTACTCCACAGT 1 CTTCGATCTGCTCCACTGTAACCTCAAGGAGATAAGATCTGAAATTCTTCGGTCTACTCCACTGT 49613656 AACCTCAGGGAGATAAGACTTGCATATTCAACCTGCTCCACTGTAACTTCAGGGAGATAAGGTTT 66 AACCTCAGGGAGATAAGACTTGCATATTCAA-CTGCTCCACTGTAACTTCAGGGAGATAAGG-TT * 49613721 GTGG 129 ATGG * * * * 49613725 CTTCGATCTGCTCCTCTGTAATCTCATGGAGATAAGATCTGAAATTTTTCGGTCTACTCCACTGT 1 CTTCGATCTGCTCCACTGTAACCTCAAGGAGATAAGATCTGAAATTCTTCGGTCTACTCCACTGT 49613790 AACCTCAGGGAGATAAGACTTGCATATTCAACTTGC-CCTACTGTAACTTCAGGGAGATAAGGTT 66 AACCTCAGGGAGATAAGACTTGCATATTCAAC-TGCTCC-ACTGTAACTTCAGGGAGATAAGG-T 49613854 TATGG 128 TATGG * * * * ** * 49613859 CTTCGATCTGCTCCTCTGTAATCTCAGGGAAATAAGATCTGAAATTCTTCGACCTGCTCCAC--T 1 CTTCGATCTGCTCCACTGTAACCTCAAGGAGATAAGATCTGAAATTCTTCGGTCTACTCCACTGT * * * ** * * * * * * 49613922 -ACTGCTTAGGGAGATAGGA-TAGTGTCCTTGATCTTCTCCGCTGTAA-TCTCAGGGAGATAAGA 66 AAC--CTCAGGGAGATAAGACTTGCAT-ATTCAACTGCTCCACTGTAACT-TCAGGGAGATAAGG * 49613984 TCTCTGG 127 T-TATGG * * 49613991 CGTCAATCTGCTCCACTGTAACCTC-AGAGAGATAAGATCTGAAAT 1 CTTCGATCTGCTCCACTGTAACCTCAAG-GAGATAAGATCTGAAAT 49614036 ATTCACTGAT Statistics Matches: 388, Mismatches: 44, Indels: 28 0.84 0.10 0.06 Matches are distributed among these distances: 131 5 0.01 132 69 0.18 133 24 0.06 134 283 0.73 135 7 0.02 ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30 Consensus pattern (132 bp): CTTCGATCTGCTCCACTGTAACCTCAAGGAGATAAGATCTGAAATTCTTCGGTCTACTCCACTGT AACCTCAGGGAGATAAGACTTGCATATTCAACTGCTCCACTGTAACTTCAGGGAGATAAGGTTAT GG Found at i:49614017 original size:44 final size:43 Alignment explanation

Indices: 49613391--49614030 Score: 341 Period size: 44 Copynumber: 14.3 Consensus size: 43 49613381 ACTATTGCTT * * * 49613391 AGGGAGATAAGATCTACCAT-CTTCGACCTGTTCCACTGTAACCTT 1 AGGGAGATAAGATCT---ATGCTTCGATCTGCTCCACTGTAACCTC * * * * 49613436 AGGGAGATAATATCTGAAATTCTTCGGTCTACTCCACTGTAACCTC 1 AGGGAGATAAGATCT---ATGCTTCGATCTGCTCCACTGTAACCTC * * * * 49613482 AGAGAGATAAGATCTGAAATTCTTCGGTCTACTCCACTGTAACCTC 1 AGGGAGATAAGATCT---ATGCTTCGATCTGCTCCACTGTAACCTC * ** ** * * 49613528 AGGGAGATAAGATCCTTTATTTTAATCTGCTCCACTGTAGCTTC 1 AGGGAGATAAGAT-CTATGCTTCGATCTGCTCCACTGTAACCTC * * * 49613572 AGGGAGATAGGAT-TACTAGCTCCAATCTGCTCCACTGTAACCTC 1 AGGGAGATAAGATCTA-T-GCTTCGATCTGCTCCACTGTAACCTC * * * * * 49613616 AAGGAGATAAGATCTGAAATTCTTCGGTCTACTCCACAGTAACCTC 1 AGGGAGATAAGATCT---ATGCTTCGATCTGCTCCACTGTAACCTC * * * 49613662 AGGGAGATAAGA-CT-TGCATATTCAACCTGCTCCACTGTAACTTC 1 AGGGAGATAAGATCTATGC---TTCGATCTGCTCCACTGTAACCTC * * * * * 49613706 AGGGAGATAAGGTTTGTGGCTTCGATCTGCTCCTCTGTAATCTC 1 AGGGAGATAAGATCTAT-GCTTCGATCTGCTCCACTGTAACCTC * ** * * 49613750 ATGGAGATAAGATCTGAAATTTTTCGGTCTACTCCACTGTAACCTC 1 AGGGAGATAAGATCT---ATGCTTCGATCTGCTCCACTGTAACCTC * * 49613796 AGGGAGATAAGA-CT-TGCATATTC-AACTTGC-CCTACTGTAACTTC 1 AGGGAGATAAGATCTATGC---TTCGATC-TGCTCC-ACTGTAACCTC * * * * 49613840 AGGGAGATAAGGTTTATGGCTTCGATCTGCTCCTCTGTAATCTC 1 AGGGAGATAAGATCTAT-GCTTCGATCTGCTCCACTGTAACCTC * * * * 49613884 AGGGAAATAAGATCTGAAATTCTTCGACCTGCTCCAC--T-ACTGCTT 1 AGGGAGATAAGATCT---ATGCTTCGATCTGCTCCACTGTAAC--CTC * * * * * * * 49613929 AGGGAGATAGGATAGTGTCCTT-GATCTTCTCCGCTGTAATCTC 1 AGGGAGATAAGAT-CTATGCTTCGATCTGCTCCACTGTAACCTC * * * 49613972 AGGGAGATAAGATCTCTGGCGTCAATCTGCTCCACTGTAACCTC 1 AGGGAGATAAGATCTAT-GCTTCGATCTGCTCCACTGTAACCTC * 49614016 AGAGAGATAAGATCT 1 AGGGAGATAAGATCT 49614031 GAAATATTCA Statistics Matches: 454, Mismatches: 103, Indels: 77 0.72 0.16 0.12 Matches are distributed among these distances: 41 3 0.01 42 12 0.03 43 25 0.06 44 207 0.46 45 41 0.09 46 155 0.34 47 10 0.02 48 1 0.00 ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30 Consensus pattern (43 bp): AGGGAGATAAGATCTATGCTTCGATCTGCTCCACTGTAACCTC Found at i:49615271 original size:7 final size:7 Alignment explanation

Indices: 49615259--49615310 Score: 63 Period size: 7 Copynumber: 7.7 Consensus size: 7 49615249 GCCTCTCCAT 49615259 TTTTTCA 1 TTTTTCA 49615266 TTTTTCA 1 TTTTTCA * 49615273 -TTTTCT 1 TTTTTCA 49615279 TTTTTCA 1 TTTTTCA * 49615286 ATTTTCA 1 TTTTTCA * 49615293 -TTCTCA 1 TTTTTCA 49615299 TTTTTCA 1 TTTTTCA 49615306 TTTTT 1 TTTTT 49615311 TCAGAGTGCC Statistics Matches: 38, Mismatches: 5, Indels: 4 0.81 0.11 0.09 Matches are distributed among these distances: 6 10 0.26 7 28 0.74 ACGTcount: A:0.13, C:0.15, G:0.00, T:0.71 Consensus pattern (7 bp): TTTTTCA Found at i:49615283 original size:20 final size:20 Alignment explanation

Indices: 49615258--49615310 Score: 79 Period size: 20 Copynumber: 2.6 Consensus size: 20 49615248 AGCCTCTCCA * 49615258 TTTTTTCATTTTTCATTTTC 1 TTTTTTCATTTTTCATTCTC * 49615278 TTTTTTCAATTTTCATTCTC 1 TTTTTTCATTTTTCATTCTC * 49615298 ATTTTTCATTTTT 1 TTTTTTCATTTTT 49615311 TCAGAGTGCC Statistics Matches: 29, Mismatches: 4, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 20 29 1.00 ACGTcount: A:0.13, C:0.15, G:0.00, T:0.72 Consensus pattern (20 bp): TTTTTTCATTTTTCATTCTC Found at i:49620985 original size:3 final size:3 Alignment explanation

Indices: 49620977--49621032 Score: 53 Period size: 3 Copynumber: 19.0 Consensus size: 3 49620967 GTAAAGTAAG * * * * 49620977 TAA TAA TAA TAA -ATA TAA TAC TAA TAA TAA TAA TAG TAG CAA TAA 1 TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA 49621022 TAA T-A TAA TAA 1 TAA TAA TAA TAA 49621033 ATAAAAGGGG Statistics Matches: 44, Mismatches: 6, Indels: 6 0.79 0.11 0.11 Matches are distributed among these distances: 2 3 0.07 3 40 0.91 4 1 0.02 ACGTcount: A:0.61, C:0.04, G:0.04, T:0.32 Consensus pattern (3 bp): TAA Found at i:49620989 original size:18 final size:18 Alignment explanation

Indices: 49620952--49621026 Score: 53 Period size: 18 Copynumber: 3.9 Consensus size: 18 49620942 AGGCACCATG * * 49620952 AGTAAATAATTAATAGTAA 1 AGTAAGTAA-TAATAATAA 49620971 AGTAAGTAATAATAATAA 1 AGTAAGTAATAATAATAA * * 49620989 ATATAATACTAATAATAATAA 1 A-GT-A-AGTAATAATAATAA * 49621010 TAGT-AGCAATAATAATA 1 -AGTAAGTAATAATAATA 49621027 TAATAAATAA Statistics Matches: 45, Mismatches: 7, Indels: 9 0.74 0.11 0.15 Matches are distributed among these distances: 18 20 0.44 19 9 0.20 20 1 0.02 21 14 0.31 22 1 0.02 ACGTcount: A:0.59, C:0.03, G:0.08, T:0.31 Consensus pattern (18 bp): AGTAAGTAATAATAATAA Found at i:49621035 original size:15 final size:15 Alignment explanation

Indices: 49620954--49621036 Score: 57 Period size: 15 Copynumber: 5.5 Consensus size: 15 49620944 GCACCATGAG * * 49620954 TAAATAATTA-ATAG 1 TAAATAATAATATAA 49620968 TAAAGTAAGTAATAATAA 1 TAAA-TAA-TAAT-ATAA 49620986 TAAAT-ATAATACTAA 1 TAAATAATAATA-TAA 49621001 T-AATAATAATAGT-A 1 TAAATAATAATA-TAA ** 49621015 GCAATAATAATATAA 1 TAAATAATAATATAA 49621030 TAAATAA 1 TAAATAA 49621037 AAGGGGTTAA Statistics Matches: 55, Mismatches: 6, Indels: 15 0.72 0.08 0.20 Matches are distributed among these distances: 14 10 0.18 15 34 0.62 16 3 0.05 17 1 0.02 18 7 0.13 ACGTcount: A:0.60, C:0.02, G:0.06, T:0.31 Consensus pattern (15 bp): TAAATAATAATATAA Found at i:49624930 original size:90 final size:88 Alignment explanation

Indices: 49624780--49625000 Score: 284 Period size: 90 Copynumber: 2.5 Consensus size: 88 49624770 TTAAGGGTAT * * * * 49624780 AAAAAGCCCTTAAACTTTTTCAAAAAAAGCAATTAAGCCCTTCCTTTTTTTTGTATTCAATTGAG 1 AAAAAGCCCTCAAACTTTTTCAAAAAAAGCAATTAAGCCCCTGCTTTTTTTTGTACTCAATTGAG 49624845 CACTTAAACTTTCAAAATACATC 66 CACTTAAACTTTCAAAATACATC * 49624868 AAAAATGCCCTCAAACTTCTTCAAAAAAAAGCAATTAAGCCCCTGCTTTTTTTT-TCACTCAATT 1 AAAAA-GCCCTCAAACTTTTTC-AAAAAAAGCAATTAAGCCCCTGCTTTTTTTTGT-ACTCAATT * * * ** 49624932 GGGTACTTGAACTTTCAAAATGTATC 63 GAGCACTTAAACTTTCAAAATACATC * * 49624958 AAAAAGACCCTCAAAATTTTTC-AAAAAATCAATTAAGCCCCTG 1 AAAAAG-CCCTCAAACTTTTTCAAAAAAAGCAATTAAGCCCCTG 49625001 TTCTTATTAA Statistics Matches: 116, Mismatches: 13, Indels: 8 0.85 0.09 0.06 Matches are distributed among these distances: 88 25 0.22 89 16 0.14 90 75 0.65 ACGTcount: A:0.38, C:0.22, G:0.08, T:0.32 Consensus pattern (88 bp): AAAAAGCCCTCAAACTTTTTCAAAAAAAGCAATTAAGCCCCTGCTTTTTTTTGTACTCAATTGAG CACTTAAACTTTCAAAATACATC Found at i:49625033 original size:11 final size:12 Alignment explanation

Indices: 49625009--49625033 Score: 50 Period size: 12 Copynumber: 2.1 Consensus size: 12 49624999 TGTTCTTATT 49625009 AAAAATTAGAAA 1 AAAAATTAGAAA 49625021 AAAAATTAGAAA 1 AAAAATTAGAAA 49625033 A 1 A 49625034 TATTAAATTT 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:0.76, C:0.00, G:0.08, T:0.16 Consensus pattern (12 bp): AAAAATTAGAAA Found at i:49625077 original size:18 final size:19 Alignment explanation

Indices: 49625030--49625074 Score: 74 Period size: 19 Copynumber: 2.4 Consensus size: 19 49625020 AAAAAATTAG 49625030 AAAATATTAAATTTTAGAA 1 AAAATATTAAATTTTAGAA 49625049 AAAATATTAAATTTTA-ATA 1 AAAATATTAAATTTTAGA-A 49625068 AAAATAT 1 AAAATAT 49625075 AAAAAATTAT Statistics Matches: 25, Mismatches: 0, Indels: 2 0.93 0.00 0.07 Matches are distributed among these distances: 18 1 0.04 19 24 0.96 ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38 Consensus pattern (19 bp): AAAATATTAAATTTTAGAA Found at i:49625378 original size:10 final size:10 Alignment explanation

Indices: 49625363--49625429 Score: 50 Period size: 10 Copynumber: 6.9 Consensus size: 10 49625353 TTCTTACGAC 49625363 TTTATAAAAT 1 TTTATAAAAT * 49625373 TTTAT-AATT 1 TTTATAAAAT * * 49625382 TTTATTATAT 1 TTTATAAAAT * 49625392 TTT-TATATAT 1 TTTATA-AAAT 49625402 TTTAT-AAAT 1 TTTATAAAAT * * 49625411 TTTTTACAAT 1 TTTATAAAAT 49625421 TTTATAAAA 1 TTTATAAAA 49625430 AAATACAGTT Statistics Matches: 44, Mismatches: 9, Indels: 8 0.72 0.15 0.13 Matches are distributed among these distances: 9 16 0.36 10 27 0.61 11 1 0.02 ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60 Consensus pattern (10 bp): TTTATAAAAT Found at i:49625385 original size:19 final size:19 Alignment explanation

Indices: 49625363--49625429 Score: 64 Period size: 19 Copynumber: 3.5 Consensus size: 19 49625353 TTCTTACGAC 49625363 TTTATAAAATTTTATA-ATT 1 TTTATAAAATTTT-TACATT * * * 49625382 TTTATTATATTTTTATATAT 1 TTTATAAAATTTTTACAT-T * * 49625402 TTTATAAATTTTTTACAAT 1 TTTATAAAATTTTTACATT 49625421 TTTATAAAA 1 TTTATAAAA 49625430 AAATACAGTT Statistics Matches: 38, Mismatches: 8, Indels: 4 0.76 0.16 0.08 Matches are distributed among these distances: 18 2 0.05 19 22 0.58 20 14 0.37 ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60 Consensus pattern (19 bp): TTTATAAAATTTTTACATT Found at i:49625453 original size:10 final size:10 Alignment explanation

Indices: 49625438--49625483 Score: 51 Period size: 10 Copynumber: 4.6 Consensus size: 10 49625428 AAAAATACAG 49625438 TTTTTTATAT 1 TTTTTTATAT 49625448 TTTTTTACTA- 1 TTTTTTA-TAT 49625458 -TTTTTATAT 1 TTTTTTATAT * 49625467 TTTTTTCTAAT 1 TTTTTTAT-AT 49625478 TTTTTT 1 TTTTTT 49625484 TCTAATTTTT Statistics Matches: 31, Mismatches: 1, Indels: 7 0.79 0.03 0.18 Matches are distributed among these distances: 8 2 0.06 9 6 0.19 10 13 0.42 11 10 0.32 ACGTcount: A:0.17, C:0.04, G:0.00, T:0.78 Consensus pattern (10 bp): TTTTTTATAT Found at i:49625459 original size:11 final size:11 Alignment explanation

Indices: 49625438--49625493 Score: 50 Period size: 10 Copynumber: 5.4 Consensus size: 11 49625428 AAAAATACAG 49625438 TTTTTTA-TAT 1 TTTTTTACTAT 49625448 TTTTTTACTA- 1 TTTTTTACTAT 49625458 -TTTTTA-TAT 1 TTTTTTACTAT 49625467 TTTTTT-CTAAT 1 TTTTTTACT-AT * 49625478 TTTTTTTCTAAT 1 TTTTTTACT-AT 49625490 TTTT 1 TTTT 49625494 AATAGTTGAA Statistics Matches: 40, Mismatches: 0, Indels: 10 0.80 0.00 0.20 Matches are distributed among these distances: 8 2 0.05 9 6 0.15 10 13 0.32 11 10 0.25 12 9 0.22 ACGTcount: A:0.18, C:0.05, G:0.00, T:0.77 Consensus pattern (11 bp): TTTTTTACTAT Found at i:49625461 original size:19 final size:19 Alignment explanation

Indices: 49625439--49625481 Score: 70 Period size: 19 Copynumber: 2.3 Consensus size: 19 49625429 AAAATACAGT 49625439 TTTTTATATTTTTTTACT-A 1 TTTTTATATTTTTTT-CTAA 49625458 TTTTTATATTTTTTTCTAA 1 TTTTTATATTTTTTTCTAA 49625477 TTTTT 1 TTTTT 49625482 TTTCTAATTT Statistics Matches: 23, Mismatches: 0, Indels: 2 0.92 0.00 0.08 Matches are distributed among these distances: 18 2 0.09 19 21 0.91 ACGTcount: A:0.19, C:0.05, G:0.00, T:0.77 Consensus pattern (19 bp): TTTTTATATTTTTTTCTAA Found at i:49625481 original size:12 final size:12 Alignment explanation

Indices: 49625466--49625493 Score: 56 Period size: 12 Copynumber: 2.3 Consensus size: 12 49625456 TATTTTTATA 49625466 TTTTTTTCTAAT 1 TTTTTTTCTAAT 49625478 TTTTTTTCTAAT 1 TTTTTTTCTAAT 49625490 TTTT 1 TTTT 49625494 AATAGTTGAA Statistics Matches: 16, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 12 16 1.00 ACGTcount: A:0.14, C:0.07, G:0.00, T:0.79 Consensus pattern (12 bp): TTTTTTTCTAAT Found at i:49627799 original size:20 final size:18 Alignment explanation

Indices: 49627774--49627812 Score: 51 Period size: 18 Copynumber: 2.1 Consensus size: 18 49627764 GAGCTTCGGT 49627774 TTTAATAATACAACATATTA 1 TTTAAT-ATACAA-ATATTA * 49627794 TTTAATTTACAAATATTA 1 TTTAATATACAAATATTA 49627812 T 1 T 49627813 ATATATTTAA Statistics Matches: 18, Mismatches: 1, Indels: 2 0.86 0.05 0.10 Matches are distributed among these distances: 18 7 0.39 19 5 0.28 20 6 0.33 ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46 Consensus pattern (18 bp): TTTAATATACAAATATTA Found at i:49627820 original size:19 final size:19 Alignment explanation

Indices: 49627782--49627821 Score: 55 Period size: 19 Copynumber: 2.1 Consensus size: 19 49627772 GTTTTAATAA * 49627782 TACAACATATTATTTAATT 1 TACAACATATTATATAATT 49627801 TACAA-ATATTATATATATT 1 TACAACATATTATATA-ATT 49627820 TA 1 TA 49627822 AGCAATGCAT Statistics Matches: 19, Mismatches: 1, Indels: 2 0.86 0.05 0.09 Matches are distributed among these distances: 18 9 0.47 19 10 0.53 ACGTcount: A:0.45, C:0.07, G:0.00, T:0.47 Consensus pattern (19 bp): TACAACATATTATATAATT Found at i:49628166 original size:19 final size:19 Alignment explanation

Indices: 49628131--49628168 Score: 51 Period size: 19 Copynumber: 2.0 Consensus size: 19 49628121 AATATAAAAC * 49628131 TTTTAACAATAACATATTA 1 TTTTAACAAGAACATATTA 49628150 TTTTAACACAGAA-ATATTA 1 TTTTAACA-AGAACATATTA 49628169 AACTAATGAA Statistics Matches: 17, Mismatches: 1, Indels: 2 0.85 0.05 0.10 Matches are distributed among these distances: 19 14 0.82 20 3 0.18 ACGTcount: A:0.47, C:0.11, G:0.03, T:0.39 Consensus pattern (19 bp): TTTTAACAAGAACATATTA Found at i:49631211 original size:23 final size:23 Alignment explanation

Indices: 49631147--49631212 Score: 59 Period size: 23 Copynumber: 3.0 Consensus size: 23 49631137 TCGTTGGCCA * 49631147 AGTATAAATCATTT-GTAATAAA-T 1 AGTATAAATAATTTAGT--TAAATT ** 49631170 AGTAT--ATAATTTAACTAAATT 1 AGTATAAATAATTTAGTTAAATT 49631191 AGTATAAATAATTTAGTTAAAT 1 AGTATAAATAATTTAGTTAAAT 49631213 ATTTAGTAAG Statistics Matches: 34, Mismatches: 5, Indels: 8 0.72 0.11 0.17 Matches are distributed among these distances: 20 4 0.12 21 12 0.35 23 18 0.53 ACGTcount: A:0.48, C:0.03, G:0.08, T:0.41 Consensus pattern (23 bp): AGTATAAATAATTTAGTTAAATT Found at i:49631218 original size:12 final size:14 Alignment explanation

Indices: 49631189--49631220 Score: 50 Period size: 12 Copynumber: 2.4 Consensus size: 14 49631179 TTTAACTAAA 49631189 TTAGTATAAATAAT 1 TTAGTATAAATAAT 49631203 TTAGT-TAAAT-AT 1 TTAGTATAAATAAT 49631215 TTAGTA 1 TTAGTA 49631221 AGGTTAAAAT Statistics Matches: 17, Mismatches: 0, Indels: 3 0.85 0.00 0.15 Matches are distributed among these distances: 12 7 0.41 13 5 0.29 14 5 0.29 ACGTcount: A:0.44, C:0.00, G:0.09, T:0.47 Consensus pattern (14 bp): TTAGTATAAATAAT Found at i:49640505 original size:29 final size:29 Alignment explanation

Indices: 49640472--49640540 Score: 79 Period size: 29 Copynumber: 2.4 Consensus size: 29 49640462 AAACCTTATT 49640472 GTTGCGGAAAC-T-TAATTTTAAACAATTGA 1 GTTGCGGAAACATGTAA-TTTAAA-AATTGA * * * 49640501 TTTGCGAAAACATGTTATTTAAAAATTGA 1 GTTGCGGAAACATGTAATTTAAAAATTGA 49640530 GTTGCGGAAAC 1 GTTGCGGAAAC 49640541 GTAGCGTTTG Statistics Matches: 33, Mismatches: 5, Indels: 4 0.79 0.12 0.10 Matches are distributed among these distances: 29 24 0.73 30 7 0.21 31 2 0.06 ACGTcount: A:0.38, C:0.10, G:0.19, T:0.33 Consensus pattern (29 bp): GTTGCGGAAACATGTAATTTAAAAATTGA Found at i:49641279 original size:32 final size:32 Alignment explanation

Indices: 49641224--49641362 Score: 172 Period size: 32 Copynumber: 4.4 Consensus size: 32 49641214 GAATGGCTAC * * 49641224 AAGCCATAAGT-ACAGTAATATGATTGGCACA 1 AAGCCATCAGTAACAGTAATATGATCGGCACA * * 49641255 AAGCCATCAGTAGCAGTGATATGATCGGCACA 1 AAGCCATCAGTAACAGTAATATGATCGGCACA * ** * 49641287 CAGCCATCAGTAATGGTAATATGATCGGTACA 1 AAGCCATCAGTAACAGTAATATGATCGGCACA * * * 49641319 AAGCCATTAGTAACGGTAATATGACCGGCACA 1 AAGCCATCAGTAACAGTAATATGATCGGCACA 49641351 AAGCCATCAGTA 1 AAGCCATCAGTA 49641363 GCATCACAAC Statistics Matches: 91, Mismatches: 16, Indels: 1 0.84 0.15 0.01 Matches are distributed among these distances: 31 10 0.11 32 81 0.89 ACGTcount: A:0.37, C:0.20, G:0.22, T:0.21 Consensus pattern (32 bp): AAGCCATCAGTAACAGTAATATGATCGGCACA Found at i:49641565 original size:24 final size:24 Alignment explanation

Indices: 49641537--49641609 Score: 65 Period size: 24 Copynumber: 3.0 Consensus size: 24 49641527 GCTCAGAATT * * 49641537 AGTCATGCAAATCGCAGACAAATC 1 AGTCATACAAATCACAGACAAATC * * * 49641561 AGTCATACTAATTACAGACAATTC 1 AGTCATACAAATCACAGACAAATC ** * * 49641585 AGTCATTTACATCACGGACAAATC 1 AGTCATACAAATCACAGACAAATC 49641609 A 1 A 49641610 ACTATTTACA Statistics Matches: 37, Mismatches: 12, Indels: 0 0.76 0.24 0.00 Matches are distributed among these distances: 24 37 1.00 ACGTcount: A:0.41, C:0.23, G:0.12, T:0.23 Consensus pattern (24 bp): AGTCATACAAATCACAGACAAATC Found at i:49641762 original size:27 final size:27 Alignment explanation

Indices: 49641652--49641827 Score: 138 Period size: 27 Copynumber: 6.5 Consensus size: 27 49641642 TACCCTCTAG * * 49641652 GGGCATTACAGTCATTTTACCTTA-CA 1 GGGCATTACGGTCATTTTACCTTATAA * * ** 49641678 GGGTCATTGCGGTCATTTAACCTTATGG 1 GGG-CATTACGGTCATTTTACCTTATAA * * * * * 49641706 GGGTATTACAGTTATTTTACCCTACAA 1 GGGCATTACGGTCATTTTACCTTATAA * * * 49641733 GGGCATTACAGTCATTTTACCATATGA 1 GGGCATTACGGTCATTTTACCTTATAA ** ** * * 49641760 GGGTTTTTTGGTCATTTTACCCTAAAA 1 GGGCATTACGGTCATTTTACCTTATAA * * 49641787 GGGTATTACGGTCGTTTTACCTTATAA 1 GGGCATTACGGTCATTTTACCTTATAA 49641814 GGGCATTACGGTCA 1 GGGCATTACGGTCA 49641828 AACTACAACA Statistics Matches: 113, Mismatches: 35, Indels: 3 0.75 0.23 0.02 Matches are distributed among these distances: 26 3 0.03 27 107 0.95 28 3 0.03 ACGTcount: A:0.24, C:0.18, G:0.21, T:0.36 Consensus pattern (27 bp): GGGCATTACGGTCATTTTACCTTATAA Found at i:49641775 original size:81 final size:81 Alignment explanation

Indices: 49641635--49641827 Score: 194 Period size: 81 Copynumber: 2.4 Consensus size: 81 49641625 GGGGAAAAAT * * 49641635 AGTTA-TTTACCCT-CTAGGGGCATTACAGTCATTTTACCTTACAGGGTCATTGCGGTCATTTAA 1 AGTTATTTTACCCTAC-AAGGGCATTACAGTCATTTTACCATACAGGGTCATTGCGGTCATTTAA * *** 49641698 CCTTATGGGGGTATTAC 65 CCCTAAAAGGGTATTAC * * ** * 49641715 AGTTATTTTACCCTACAAGGGCATTACAGTCATTTTACCATATGAGGGT-TTTTTGGTCATTTTA 1 AGTTATTTTACCCTACAAGGGCATTACAGTCATTTTACCATA-CAGGGTCATTGCGGTCATTTAA 49641779 CCCTAAAAGGGTATTAC 65 CCCTAAAAGGGTATTAC * ** * * * 49641796 GGTCGTTTTACCTTATAAGGGCATTACGGTCA 1 AGTTATTTTACCCTACAAGGGCATTACAGTCA 49641828 AACTACAACA Statistics Matches: 93, Mismatches: 17, Indels: 5 0.81 0.15 0.04 Matches are distributed among these distances: 80 5 0.05 81 82 0.88 82 6 0.06 ACGTcount: A:0.24, C:0.19, G:0.20, T:0.37 Consensus pattern (81 bp): AGTTATTTTACCCTACAAGGGCATTACAGTCATTTTACCATACAGGGTCATTGCGGTCATTTAAC CCTAAAAGGGTATTAC Found at i:49641827 original size:54 final size:54 Alignment explanation

Indices: 49641652--49641827 Score: 165 Period size: 54 Copynumber: 3.3 Consensus size: 54 49641642 TACCCTCTAG * * * * * 49641652 GGGCATTACAGTCATTTTA-CCTTACAGGGTCATTGCGGTCATTTAACCTTATGG 1 GGGCATTACAGTCATTTTACCCTAAAAGGGT-ATTACGGTCATTTTACCTTATGA * * * * * * 49641706 GGGTATTACAGTTATTTTACCCTACAAGGGCATTACAGTCATTTTACCATATGA 1 GGGCATTACAGTCATTTTACCCTAAAAGGGTATTACGGTCATTTTACCTTATGA ** *** * * 49641760 GGGTTTTTTGGTCATTTTACCCTAAAAGGGTATTACGGTCGTTTTACCTTATAA 1 GGGCATTACAGTCATTTTACCCTAAAAGGGTATTACGGTCATTTTACCTTATGA * 49641814 GGGCATTACGGTCA 1 GGGCATTACAGTCA 49641828 AACTACAACA Statistics Matches: 95, Mismatches: 26, Indels: 2 0.77 0.21 0.02 Matches are distributed among these distances: 54 88 0.93 55 7 0.07 ACGTcount: A:0.24, C:0.18, G:0.21, T:0.36 Consensus pattern (54 bp): GGGCATTACAGTCATTTTACCCTAAAAGGGTATTACGGTCATTTTACCTTATGA Found at i:49643494 original size:51 final size:51 Alignment explanation

Indices: 49643406--49643746 Score: 288 Period size: 51 Copynumber: 6.7 Consensus size: 51 49643396 TGTCGATGAA * * * * 49643406 CACGTGTGTAGTACTGTGTGTGGAGGCTACTACGTGTATCGATAAATAATGGT 1 CACGTGTGTAGTAC--TATGTGAAGGCTACTACGTGTACCGATAAATATTGGT * * * ** 49643459 CACATGTGTAGTACTAAGTGAAGGCTACTATGTGTACCGA-AAAGCTTCGAG- 1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAATATT-G-GT * * * * * 49643510 CACGTGTGTAGTACTGTGTGAATGCTACTACGTGTATCGGTAAACTA-CGGT 1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAA-TATTGGT * * * * * * 49643561 TACATGTGTAGTACTAAGTGAAGGCTACAATGGGTACCGA-AAAGCT-TTGGT 1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAA--TATTGGT * * 49643612 CACGTATGTAGTACTATGTGAAGGCTACTACGTG-AGCCG-TAAA-ACTTGAT 1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTA-CCGATAAATA-TTGGT * * * * 49643662 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACTG-TAAA-ACTGAT 1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAATATTGGT * 49643711 CACGTATGTAGTACTATGTGAAGGCTACTACGTGTA 1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTA 49643747 TCGAATGATA Statistics Matches: 233, Mismatches: 43, Indels: 28 0.77 0.14 0.09 Matches are distributed among these distances: 49 38 0.16 50 53 0.23 51 125 0.54 52 4 0.02 53 13 0.06 ACGTcount: A:0.28, C:0.16, G:0.26, T:0.29 Consensus pattern (51 bp): CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAATATTGGT Found at i:49643584 original size:102 final size:101 Alignment explanation

Indices: 49643406--49643749 Score: 394 Period size: 102 Copynumber: 3.4 Consensus size: 101 49643396 TGTCGATGAA * * * * 49643406 CACGTGTGTAGTACTGTGTGTGGAGGCTACTACGTGTATCGATAAA-TAATGGTCACATGTGTAG 1 CACGTATGTAGTAC--TATGTGAAGGCTACTACGTGTATCGGTAAACT-ATGGTCACATGTGTAG 49643470 TACTAAGTGAAGGCTACTATGTGTACCGAAAAGCTTCGAG 63 TACTAAGTGAAGGCTACTATGTGTACCGAAAAGCTT-GAG * * * * * 49643510 CACGTGTGTAGTACTGTGTGAATGCTACTACGTGTATCGGTAAACTACGGTTACATGTGTAGTAC 1 CACGTATGTAGTACTATGTGAAGGCTACTACGTGTATCGGTAAACTATGGTCACATGTGTAGTAC * * 49643575 TAAGTGAAGGCTACAATGGGTACCGAAAAGCTTTG-G 66 TAAGTGAAGGCTACTATGTGTACCGAAAAGC-TTGAG * * * * 49643611 TCACGTATGTAGTACTATGTGAAGGCTACTACGTG-AGCCGTAAAACT-TGATCACGTGTGTAGT 1 -CACGTATGTAGTACTATGTGAAGGCTACTACGTGTATCGGT-AAACTATGGTCACATGTGTAGT * * * * * 49643674 ACTATGTGAAGGCTACTACGTGAACTGTAAAA-C-TGAT 64 ACTAAGTGAAGGCTACTATGTGTACCG-AAAAGCTTGAG 49643711 CACGTATGTAGTACTATGTGAAGGCTACTACGTGTATCG 1 CACGTATGTAGTACTATGTGAAGGCTACTACGTGTATCG 49643750 AATGATAAAA Statistics Matches: 208, Mismatches: 25, Indels: 18 0.83 0.10 0.07 Matches are distributed among these distances: 99 36 0.17 100 2 0.01 101 39 0.19 102 114 0.55 103 3 0.01 104 14 0.07 ACGTcount: A:0.28, C:0.16, G:0.26, T:0.29 Consensus pattern (101 bp): CACGTATGTAGTACTATGTGAAGGCTACTACGTGTATCGGTAAACTATGGTCACATGTGTAGTAC TAAGTGAAGGCTACTATGTGTACCGAAAAGCTTGAG Found at i:49651061 original size:36 final size:35 Alignment explanation

Indices: 49650987--49651214 Score: 175 Period size: 35 Copynumber: 6.5 Consensus size: 35 49650977 CTTAGACGTA * * 49650987 TCTATTCCAATTTTTTTAAGGTTGCCTTAG-AAGTG 1 TCTATCCCAACTTTTTTAAGGTTGCCTTAGAAAG-G * * 49651022 TCTATCCTAACTTTTTTAAGGTTGTCTTAGATAAGG 1 TCTATCCCAACTTTTTTAAGGTTGCCTTAGA-AAGG * 49651058 TCTATCCCAACTTTTTTAAGGTTGTCTTAG--A-- 1 TCTATCCCAACTTTTTTAAGGTTGCCTTAGAAAGG * * 49651089 -CGA-CCCAAATTTTTTTAAAGGTTGCCTTAGATAAGG 1 TCTATCCC-AACTTTTTT-AAGGTTGCCTTAGA-AAGG * * * * * ** 49651125 TTTATCCCAGCCTTTTTAAGTTTGTCTTAGACGGG 1 TCTATCCCAACTTTTTTAAGGTTGCCTTAGAAAGG * * * 49651160 TCTATCCCAACCTTTTTAAGATTGCCTTAG-ATGAG 1 TCTATCCCAACTTTTTTAAGGTTGCCTTAGAAAG-G * 49651195 TTTATCCCAACCTTTTTTAA 1 TCTATCCCAA-CTTTTTTAA 49651215 ATGTCGGTAT Statistics Matches: 155, Mismatches: 25, Indels: 25 0.76 0.12 0.12 Matches are distributed among these distances: 29 3 0.02 30 10 0.06 31 12 0.08 33 1 0.01 34 2 0.01 35 64 0.41 36 50 0.32 37 10 0.06 38 3 0.02 ACGTcount: A:0.24, C:0.18, G:0.15, T:0.42 Consensus pattern (35 bp): TCTATCCCAACTTTTTTAAGGTTGCCTTAGAAAGG Found at i:49651110 original size:102 final size:100 Alignment explanation

Indices: 49650995--49651190 Score: 259 Period size: 102 Copynumber: 1.9 Consensus size: 100 49650985 TATCTATTCC * * 49650995 AATTTTTTTAAGGTTGCCTTAG-AAGTGTCTATCCTAACTTTTTTAAGGTTGTCTTAGATAAGGT 1 AATTTTTTTAAGGTTGCCTTAGAAAG-GTCTATCCCAACCTTTTTAAGGTTGTCTTAGA-AAGGT * * * 49651059 CTATCCCAACTTTTTTAAGGTTGTCTTAGACGACCCA 64 CTATCCCAACCTTTTTAAGATTGCCTTAGACGACCCA * * * ** 49651096 AATTTTTTTAAAGGTTGCCTTAGATAAGGTTTATCCCAGCCTTTTTAAGTTTGTCTTAGACGGGT 1 AATTTTTTT-AAGGTTGCCTTAGA-AAGGTCTATCCCAACCTTTTTAAGGTTGTCTTAGAAAGGT 49651161 CTATCCCAACCTTTTTAAGATTGCCTTAGA 64 CTATCCCAACCTTTTTAAGATTGCCTTAGA 49651191 TGAGTTTATC Statistics Matches: 82, Mismatches: 10, Indels: 5 0.85 0.10 0.05 Matches are distributed among these distances: 101 9 0.11 102 43 0.52 103 27 0.33 104 3 0.04 ACGTcount: A:0.24, C:0.17, G:0.17, T:0.41 Consensus pattern (100 bp): AATTTTTTTAAGGTTGCCTTAGAAAGGTCTATCCCAACCTTTTTAAGGTTGTCTTAGAAAGGTCT ATCCCAACCTTTTTAAGATTGCCTTAGACGACCCA Found at i:49651125 original size:67 final size:66 Alignment explanation

Indices: 49651033--49651157 Score: 196 Period size: 67 Copynumber: 1.9 Consensus size: 66 49651023 CTATCCTAAC * * 49651033 TTTTTTAAGGTTGTCTTAGATAAGGTCTATCCCAACTTTTTTAAGGTTGTCTTAGACGACCCAAA 1 TTTTTTAAGGTTGCCTTAGATAAGGTCTATCCCAACCTTTTTAAGGTTGTCTTAGACGACCCAAA 49651098 T 66 T * * * 49651099 TTTTTTAAAGGTTGCCTTAGATAAGGTTTATCCCAGCCTTTTTAAGTTTGTCTTAGACG 1 TTTTTT-AAGGTTGCCTTAGATAAGGTCTATCCCAACCTTTTTAAGGTTGTCTTAGACG 49651158 GGTCTATCCC Statistics Matches: 53, Mismatches: 5, Indels: 1 0.90 0.08 0.02 Matches are distributed among these distances: 66 6 0.11 67 47 0.89 ACGTcount: A:0.24, C:0.16, G:0.18, T:0.42 Consensus pattern (66 bp): TTTTTTAAGGTTGCCTTAGATAAGGTCTATCCCAACCTTTTTAAGGTTGTCTTAGACGACCCAAA T Found at i:49655217 original size:18 final size:18 Alignment explanation

Indices: 49655183--49655216 Score: 52 Period size: 17 Copynumber: 1.9 Consensus size: 18 49655173 AATTGGTTAT * 49655183 TTTTATTATTTTATTTTA 1 TTTTATTATTTGATTTTA 49655201 TTTTATT-TTTGATTTT 1 TTTTATTATTTGATTTT 49655217 TGGTAAAGAT Statistics Matches: 15, Mismatches: 1, Indels: 1 0.88 0.06 0.06 Matches are distributed among these distances: 17 8 0.53 18 7 0.47 ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79 Consensus pattern (18 bp): TTTTATTATTTGATTTTA Found at i:49656107 original size:21 final size:21 Alignment explanation

Indices: 49656067--49656156 Score: 76 Period size: 21 Copynumber: 4.3 Consensus size: 21 49656057 CACGGTCTAC * 49656067 CCACACAATCGTGTAC-CTCAG 1 CCACACAAGCGTGT-CTCTCAG ** * 49656088 TTACACAAGCGTGTCTCTCAA 1 CCACACAAGCGTGTCTCTCAG * 49656109 CCACAC-AGCTGTGTCTCTTAG 1 CCACACAAGC-GTGTCTCTCAG * * 49656130 GCACACGAGCGTGTCTCTCAG 1 CCACACAAGCGTGTCTCTCAG * 49656151 ACACAC 1 CCACAC 49656157 GACCATGTAT Statistics Matches: 55, Mismatches: 11, Indels: 6 0.76 0.15 0.08 Matches are distributed among these distances: 20 4 0.07 21 48 0.87 22 3 0.05 ACGTcount: A:0.26, C:0.34, G:0.18, T:0.22 Consensus pattern (21 bp): CCACACAAGCGTGTCTCTCAG Found at i:49656157 original size:21 final size:21 Alignment explanation

Indices: 49656090--49656158 Score: 79 Period size: 21 Copynumber: 3.3 Consensus size: 21 49656080 TACCTCAGTT * 49656090 ACACAAGCGTGTCTCTCA-ACC 1 ACACGAGCGTGTCTCTCAGA-C * * 49656111 ACAC-AGCTGTGTCTCTTAGGC 1 ACACGAGC-GTGTCTCTCAGAC 49656132 ACACGAGCGTGTCTCTCAGAC 1 ACACGAGCGTGTCTCTCAGAC 49656153 ACACGA 1 ACACGA 49656159 CCATGTATTC Statistics Matches: 41, Mismatches: 4, Indels: 6 0.80 0.08 0.12 Matches are distributed among these distances: 20 3 0.07 21 35 0.85 22 3 0.07 ACGTcount: A:0.26, C:0.33, G:0.20, T:0.20 Consensus pattern (21 bp): ACACGAGCGTGTCTCTCAGAC Found at i:49656473 original size:22 final size:22 Alignment explanation

Indices: 49656423--49656476 Score: 90 Period size: 22 Copynumber: 2.5 Consensus size: 22 49656413 TGTTATGTGT * * 49656423 TTGTTTATATAAACAATTTTGG 1 TTGTTTGTGTAAACAATTTTGG 49656445 TTGTTTGTGTAAACAATTTTGG 1 TTGTTTGTGTAAACAATTTTGG 49656467 TTGTTTGTGT 1 TTGTTTGTGT 49656477 GATAGTTATT Statistics Matches: 30, Mismatches: 2, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 22 30 1.00 ACGTcount: A:0.22, C:0.04, G:0.20, T:0.54 Consensus pattern (22 bp): TTGTTTGTGTAAACAATTTTGG Found at i:49663584 original size:18 final size:18 Alignment explanation

Indices: 49663561--49663597 Score: 56 Period size: 18 Copynumber: 2.1 Consensus size: 18 49663551 CGGTTGATGG * * 49663561 TTTATTTATTCATGTAAT 1 TTTATTAATTCATCTAAT 49663579 TTTATTAATTCATCTAAT 1 TTTATTAATTCATCTAAT 49663597 T 1 T 49663598 GGACAATTAA Statistics Matches: 17, Mismatches: 2, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 18 17 1.00 ACGTcount: A:0.30, C:0.08, G:0.03, T:0.59 Consensus pattern (18 bp): TTTATTAATTCATCTAAT Found at i:49668065 original size:51 final size:51 Alignment explanation

Indices: 49667720--49668067 Score: 314 Period size: 51 Copynumber: 6.9 Consensus size: 51 49667710 CTATTATCAT * * * 49667720 TCGATACACGTTGTAGCCTTCACATAGTACTACACACGTGATCAATT-TTTA 1 TCGATTCACGTAGTAGCCTTCACATAGTACTACACACGTGA-CCATTATTTA * * * * * * 49667771 -CGGTTCACGTAATAGCCTTCACATAGTACTATACATGTGATCAAGT-TTTA 1 TCGATTCACGTAGTAGCCTTCACATAGTACTACACACGTGA-CCATTATTTA * ** * 49667821 -CGATTCACGTAGTAGCCTTCACATAGTACTACATACGTGAGTA-AAGCTTT- 1 TCGATTCACGTAGTAGCCTTCACATAGTACTACACACGTGACCATTA--TTTA * * * * * 49667871 TCGATACACATAGTAGCCTTCACTTAGTACTACACATGTGACCATCATTTA 1 TCGATTCACGTAGTAGCCTTCACATAGTACTACACACGTGACCATTATTTA * * * * * * 49667922 TCAATTCACGTAGTAGCCTTCACACAGGACTACACACGTGACCA-AAGCTTC 1 TCGATTCACGTAGTAGCCTTCACATAGTACTACACACGTGACCATTA-TTTA * * ** * * * 49667973 TCGGTACATATTGTAGCCTTCACTTAGTACTACACATGTGACCATTATTTA 1 TCGATTCACGTAGTAGCCTTCACATAGTACTACACACGTGACCATTATTTA * 49668024 TCGATTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCA 1 TCGATTCACGTAGTAGCCTTCACATAGTACTACACACGTGACCA 49668068 ACATTTTCAC Statistics Matches: 235, Mismatches: 54, Indels: 16 0.77 0.18 0.05 Matches are distributed among these distances: 49 1 0.00 50 82 0.35 51 150 0.64 52 2 0.01 ACGTcount: A:0.30, C:0.25, G:0.15, T:0.30 Consensus pattern (51 bp): TCGATTCACGTAGTAGCCTTCACATAGTACTACACACGTGACCATTATTTA Found at i:49668065 original size:102 final size:102 Alignment explanation

Indices: 49667720--49668068 Score: 445 Period size: 102 Copynumber: 3.4 Consensus size: 102 49667710 CTATTATCAT * * * * * * * * 49667720 TCGATACACGTTGTAGCCTTCACATAGTACTACACACGTGATC-AA-TTTTTACGGTTCACGTAA 1 TCGATTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTTT-CGGTACACATAG * * * * 49667783 TAGCCTTCACATAGTACTATACATGTGATCAAGT-TTTA 65 TAGCCTTCACTTAGTACTACACATGTGA-CCATTATTTA * * ** * 49667821 -CGATTCACGTAGTAGCCTTCACATAGTACTACATACGTGAGTAAAGCTTTTCGATACACATAGT 1 TCGATTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTTTCGGTACACATAGT * 49667885 AGCCTTCACTTAGTACTACACATGTGACCATCATTTA 66 AGCCTTCACTTAGTACTACACATGTGACCATTATTTA * * * * * 49667922 TCAATTCACGTAGTAGCCTTCACACAGGACTACACACGTGACCAAAGCTTCTCGGTACATATTGT 1 TCGATTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTTTCGGTACACATAGT 49667987 AGCCTTCACTTAGTACTACACATGTGACCATTATTTA 66 AGCCTTCACTTAGTACTACACATGTGACCATTATTTA 49668024 TCGATTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCAA 1 TCGATTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCAA 49668069 CATTTTCACT Statistics Matches: 216, Mismatches: 28, Indels: 7 0.86 0.11 0.03 Matches are distributed among these distances: 100 39 0.18 101 40 0.19 102 137 0.63 ACGTcount: A:0.30, C:0.25, G:0.15, T:0.30 Consensus pattern (102 bp): TCGATTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTTTCGGTACACATAGT AGCCTTCACTTAGTACTACACATGTGACCATTATTTA Found at i:49669318 original size:41 final size:41 Alignment explanation

Indices: 49669261--49669411 Score: 212 Period size: 41 Copynumber: 3.7 Consensus size: 41 49669251 TAGCAACCGC * ** * 49669261 TCGGGGAATCAGCACTTAGCAACCCCTTTTTTATCAGTGAT 1 TCGGGGAATCTGCACTTAGCAACCCCTTTTCGATCAATGAT 49669302 TCGGGGAATCTGCACTTAGCAACCCCTTTTCGATCAATGAT 1 TCGGGGAATCTGCACTTAGCAACCCCTTTTCGATCAATGAT * * 49669343 TCGGGGAATTTGCACTTGGCAACCCCTTTTCGATCAATGAT 1 TCGGGGAATCTGCACTTAGCAACCCCTTTTCGATCAATGAT * * * * 49669384 TTGGGTAATCTGCACTTAGTAACACCTT 1 TCGGGGAATCTGCACTTAGCAACCCCTT 49669412 ACATTCAATG Statistics Matches: 98, Mismatches: 12, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 41 98 1.00 ACGTcount: A:0.24, C:0.25, G:0.20, T:0.32 Consensus pattern (41 bp): TCGGGGAATCTGCACTTAGCAACCCCTTTTCGATCAATGAT Found at i:49669320 original size:67 final size:68 Alignment explanation

Indices: 49669197--49669325 Score: 170 Period size: 67 Copynumber: 1.9 Consensus size: 68 49669187 AGGATACGGT ** 49669197 GGAATCAGCACTTAGCAACCACCTTTAGAATAAATAATTTTGGGAATCAGCACTTAGCAACCGCT 1 GGAATCAGCACTTAGCAACCACCTTTAGAATAAATAATTCGGGGAATCAGCACTTAGCAACCGCT 49669262 CGG 66 CGG *** * * * * 49669265 GGAATCAGCACTTAGCAACC-CCTTTTTTATCAGTGATTCGGGGAATCTGCACTTAGCAACC 1 GGAATCAGCACTTAGCAACCACCTTTAGAATAAATAATTCGGGGAATCAGCACTTAGCAACC 49669326 CCTTTTCGAT Statistics Matches: 52, Mismatches: 9, Indels: 1 0.84 0.15 0.02 Matches are distributed among these distances: 67 32 0.62 68 20 0.38 ACGTcount: A:0.30, C:0.25, G:0.19, T:0.26 Consensus pattern (68 bp): GGAATCAGCACTTAGCAACCACCTTTAGAATAAATAATTCGGGGAATCAGCACTTAGCAACCGCT CGG Found at i:49675560 original size:9 final size:9 Alignment explanation

Indices: 49675543--49675579 Score: 56 Period size: 9 Copynumber: 4.1 Consensus size: 9 49675533 TATAGTTTGA 49675543 TATTCGAAT 1 TATTCGAAT * 49675552 TATTTGAAT 1 TATTCGAAT * 49675561 TATTCGAGT 1 TATTCGAAT 49675570 TATTCGAAT 1 TATTCGAAT 49675579 T 1 T 49675580 CAAAAACTCA Statistics Matches: 24, Mismatches: 4, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 9 24 1.00 ACGTcount: A:0.30, C:0.08, G:0.14, T:0.49 Consensus pattern (9 bp): TATTCGAAT Found at i:49677262 original size:15 final size:13 Alignment explanation

Indices: 49677244--49677277 Score: 50 Period size: 15 Copynumber: 2.5 Consensus size: 13 49677234 TCTTCTTCTC 49677244 CTTTTTCTTTTGGTT 1 CTTTTTCTTTT--TT 49677259 CTTTTTCTTTTTT 1 CTTTTTCTTTTTT 49677272 CTTTTT 1 CTTTTT 49677278 AATAACTCCG Statistics Matches: 19, Mismatches: 0, Indels: 2 0.90 0.00 0.10 Matches are distributed among these distances: 13 8 0.42 15 11 0.58 ACGTcount: A:0.00, C:0.15, G:0.06, T:0.79 Consensus pattern (13 bp): CTTTTTCTTTTTT Found at i:49680247 original size:21 final size:20 Alignment explanation

Indices: 49680227--49680277 Score: 52 Period size: 23 Copynumber: 2.5 Consensus size: 20 49680217 CCTCCATTCT 49680227 TTCTTTTTTATTATT-TTTTC 1 TTCTTTTTTATT-TTATTTTC 49680247 TCTCATTCTTTTATTTTATTTTC 1 T-TC-TT-TTTTATTTTATTTTC 49680270 -TCTTTTTT 1 TTCTTTTTT 49680278 CTTTCCCTTT Statistics Matches: 27, Mismatches: 0, Indels: 9 0.75 0.00 0.25 Matches are distributed among these distances: 19 4 0.15 20 3 0.11 21 4 0.15 22 4 0.15 23 12 0.44 ACGTcount: A:0.10, C:0.14, G:0.00, T:0.76 Consensus pattern (20 bp): TTCTTTTTTATTTTATTTTC Found at i:49681005 original size:62 final size:61 Alignment explanation

Indices: 49680851--49681015 Score: 186 Period size: 62 Copynumber: 2.7 Consensus size: 61 49680841 CTGAATTTGA * * * * 49680851 GGCACACGGGCTAGGGACACGGGCGTGTGTCTAGGTCATGTAACTCACTGTTTGTATTTCT 1 GGCACACAGGCTAGGGACACAGGCGTGTGTCTAGGCCGTGTAACTCACTGTTTGTATTTCT * * ** * * * 49680912 GGCAACACAAGCCAGGGACACCCGCGTGTGTCCAGGCCGTGTAACTTATTGTTTGTATTTCT 1 GGC-ACACAGGCTAGGGACACAGGCGTGTGTCTAGGCCGTGTAACTCACTGTTTGTATTTCT * * * 49680974 GGTCACACAGGCTAGGGACATAGGTGCGTGTCTAGGCCGTGT 1 GG-CACACAGGCTAGGGACACAGGCGTGTGTCTAGGCCGTGT 49681016 GAGGGTATTG Statistics Matches: 84, Mismatches: 18, Indels: 3 0.80 0.17 0.03 Matches are distributed among these distances: 61 3 0.04 62 80 0.95 63 1 0.01 ACGTcount: A:0.19, C:0.23, G:0.31, T:0.27 Consensus pattern (61 bp): GGCACACAGGCTAGGGACACAGGCGTGTGTCTAGGCCGTGTAACTCACTGTTTGTATTTCT Found at i:49685640 original size:23 final size:23 Alignment explanation

Indices: 49685589--49685633 Score: 65 Period size: 23 Copynumber: 2.0 Consensus size: 23 49685579 ACCAAAATAA 49685589 TAAATTATTGCAACGGTAGTGAC 1 TAAATTATTGCAACGGTAGTGAC * 49685612 TAAATTATT-CTAACGGTTGTGA 1 TAAATTATTGC-AACGGTAGTGA 49685634 TCAAATTGAA Statistics Matches: 20, Mismatches: 1, Indels: 2 0.87 0.04 0.09 Matches are distributed among these distances: 22 1 0.05 23 19 0.95 ACGTcount: A:0.33, C:0.11, G:0.20, T:0.36 Consensus pattern (23 bp): TAAATTATTGCAACGGTAGTGAC Found at i:49685834 original size:5 final size:5 Alignment explanation

Indices: 49685824--49685849 Score: 52 Period size: 5 Copynumber: 5.2 Consensus size: 5 49685814 TATCAGCGAT 49685824 GTTCA GTTCA GTTCA GTTCA GTTCA G 1 GTTCA GTTCA GTTCA GTTCA GTTCA G 49685850 CCCTTTTGTA Statistics Matches: 21, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 5 21 1.00 ACGTcount: A:0.19, C:0.19, G:0.23, T:0.38 Consensus pattern (5 bp): GTTCA Found at i:49691305 original size:9 final size:9 Alignment explanation

Indices: 49691253--49691334 Score: 58 Period size: 9 Copynumber: 8.8 Consensus size: 9 49691243 ACTATTTATG * 49691253 TATGTATAT 1 TATGTATTT * * 49691262 TAGGTATGT 1 TATGTATTT * * 49691271 TATGTAGTA 1 TATGTATTT 49691280 TAT-TATTGT 1 TATGTATT-T 49691289 TAATGTATTT 1 T-ATGTATTT * 49691299 TATGTATGT 1 TATGTATTT 49691308 TATGTAGTGTT 1 TATGTA-T-TT * 49691319 TATGTATGT 1 TATGTATTT 49691328 TATGTAT 1 TATGTAT 49691335 ATTACCATTT Statistics Matches: 57, Mismatches: 11, Indels: 10 0.73 0.14 0.13 Matches are distributed among these distances: 8 3 0.05 9 37 0.65 10 6 0.11 11 11 0.19 ACGTcount: A:0.26, C:0.00, G:0.20, T:0.55 Consensus pattern (9 bp): TATGTATTT Found at i:49691322 original size:20 final size:19 Alignment explanation

Indices: 49691225--49691334 Score: 95 Period size: 20 Copynumber: 5.8 Consensus size: 19 49691215 AATGTATATC * 49691225 ATGTATGTTATGTATATTACT 1 ATGTATGTTATGTATGTT--T * * 49691246 ATTTATG-TATGTAT-ATT 1 ATGTATGTTATGTATGTTT * * 49691263 AGGTATGTTATGTA-GTAT 1 ATGTATGTTATGTATGTTT 49691281 AT-TATTGTTAATGTAT-TTT 1 ATGTA-TGTT-ATGTATGTTT 49691300 ATGTATGTTATGTAGTGTTT 1 ATGTATGTTATGTA-TGTTT 49691320 ATGTATGTTATGTAT 1 ATGTATGTTATGTAT 49691335 ATTACCATTT Statistics Matches: 73, Mismatches: 8, Indels: 18 0.74 0.08 0.18 Matches are distributed among these distances: 17 8 0.11 18 17 0.23 19 16 0.22 20 26 0.36 21 6 0.08 ACGTcount: A:0.26, C:0.01, G:0.18, T:0.55 Consensus pattern (19 bp): ATGTATGTTATGTATGTTT Found at i:49691352 original size:50 final size:46 Alignment explanation

Indices: 49691225--49691357 Score: 128 Period size: 46 Copynumber: 2.8 Consensus size: 46 49691215 AATGTATATC * * 49691225 ATGTATGTTATGTATATTACTATTTATGTATGTATATTAGGTATGTT 1 ATGTATGTTATGTATATTAC-ATTTATTTATGTATGTTAGGTATGTT * * * 49691272 ATGTA-GTATAT-TATTGTTA-ATGTATTTTATGTATGTTATGTAGTGTTT 1 ATGTATGT-TATGTA-TATTACATTTA-TTTATGTATGTTAGGTA-TG-TT 49691320 ATGTATGTTATGTATATTACCATTTATATTATGTATGT 1 ATGTATGTTATGTATATTA-CATTTAT-TTATGTATGT 49691358 GCAGTGTTCT Statistics Matches: 69, Mismatches: 7, Indels: 17 0.74 0.08 0.18 Matches are distributed among these distances: 45 4 0.06 46 18 0.26 47 14 0.20 48 14 0.20 49 5 0.07 50 14 0.20 ACGTcount: A:0.27, C:0.02, G:0.17, T:0.54 Consensus pattern (46 bp): ATGTATGTTATGTATATTACATTTATTTATGTATGTTAGGTATGTT Found at i:49691793 original size:18 final size:18 Alignment explanation

Indices: 49691757--49691794 Score: 51 Period size: 18 Copynumber: 2.1 Consensus size: 18 49691747 GGGGAACCAC * 49691757 ATTGTAATGAAGAATTTA 1 ATTGTAATGAAGAAGTTA 49691775 ATTGTAATG-AGAGAGTTA 1 ATTGTAATGAAGA-AGTTA 49691793 AT 1 AT 49691795 AGTAGGGTTG Statistics Matches: 18, Mismatches: 1, Indels: 2 0.86 0.05 0.10 Matches are distributed among these distances: 17 3 0.17 18 15 0.83 ACGTcount: A:0.42, C:0.00, G:0.21, T:0.37 Consensus pattern (18 bp): ATTGTAATGAAGAAGTTA Found at i:49695832 original size:5 final size:5 Alignment explanation

Indices: 49695822--49695850 Score: 58 Period size: 5 Copynumber: 5.8 Consensus size: 5 49695812 GATGATAAAT 49695822 AATAA AATAA AATAA AATAA AATAA AATA 1 AATAA AATAA AATAA AATAA AATAA AATA 49695851 TCATCATTTT Statistics Matches: 24, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 5 24 1.00 ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21 Consensus pattern (5 bp): AATAA Found at i:49696811 original size:25 final size:25 Alignment explanation

Indices: 49696783--49696871 Score: 96 Period size: 25 Copynumber: 3.7 Consensus size: 25 49696773 TGGCTCGTAT * 49696783 GAGCTTCCTGATAATTGGCTCTCCG 1 GAGCTTCCCGATAATTGGCTCTCCG ** 49696808 GAGCTTCCCGATAATTGGCTCTCAT 1 GAGCTTCCCGATAATTGGCTCTCCG * * * 49696833 GAGCTT--C-TTGATTAGCTCTCCG 1 GAGCTTCCCGATAATTGGCTCTCCG 49696855 GAGCTTCCCGAT-ATTGG 1 GAGCTTCCCGATAATTGG 49696872 ATCATATGAG Statistics Matches: 51, Mismatches: 10, Indels: 7 0.75 0.15 0.10 Matches are distributed among these distances: 22 16 0.31 23 1 0.02 24 5 0.10 25 29 0.57 ACGTcount: A:0.17, C:0.27, G:0.24, T:0.33 Consensus pattern (25 bp): GAGCTTCCCGATAATTGGCTCTCCG Found at i:49696861 original size:47 final size:46 Alignment explanation

Indices: 49696800--49696892 Score: 136 Period size: 47 Copynumber: 2.0 Consensus size: 46 49696790 CTGATAATTG * 49696800 GCTCTCCGGAGCTTCCCGATAATTGGCTC-TCATGAGC-TTCTTGATTA 1 GCTCTCCGGAGCTTCCCGAT-ATTGGATCAT-ATGAGCTTTC-TGATTA 49696847 GCTCTCCGGAGCTTCCCGATATTGGATCATATGAGCTTTCTGATTA 1 GCTCTCCGGAGCTTCCCGATATTGGATCATATGAGCTTTCTGATTA 49696893 TGGTTCTTAT Statistics Matches: 43, Mismatches: 1, Indels: 5 0.88 0.02 0.10 Matches are distributed among these distances: 46 19 0.44 47 24 0.56 ACGTcount: A:0.18, C:0.26, G:0.22, T:0.34 Consensus pattern (46 bp): GCTCTCCGGAGCTTCCCGATATTGGATCATATGAGCTTTCTGATTA Found at i:49696891 original size:46 final size:47 Alignment explanation

Indices: 49696800--49696892 Score: 138 Period size: 46 Copynumber: 2.0 Consensus size: 47 49696790 CTGATAATTG * 49696800 GCTCTCCGGAGCTTCCCGATAATTGGCTCTCATGAGCTTCTTGATTA 1 GCTCTCCGGAGCTTCCCGATAATTGGATCTCATGAGCTTCTTGATTA 49696847 GCTCTCCGGAGCTTCCCGAT-ATTGGATCAT-ATGAGCTT-TCTGATTA 1 GCTCTCCGGAGCTTCCCGATAATTGGATC-TCATGAGCTTCT-TGATTA 49696893 TGGTTCTTAT Statistics Matches: 43, Mismatches: 1, Indels: 5 0.88 0.02 0.10 Matches are distributed among these distances: 45 1 0.02 46 21 0.49 47 21 0.49 ACGTcount: A:0.18, C:0.26, G:0.22, T:0.34 Consensus pattern (47 bp): GCTCTCCGGAGCTTCCCGATAATTGGATCTCATGAGCTTCTTGATTA Found at i:49700502 original size:21 final size:21 Alignment explanation

Indices: 49700478--49700517 Score: 62 Period size: 21 Copynumber: 1.9 Consensus size: 21 49700468 GAGAAAAATG * * 49700478 AAAGAGATAGCAGCGAAAACA 1 AAAGAGATAGAAGAGAAAACA 49700499 AAAGAGATAGAAGAGAAAA 1 AAAGAGATAGAAGAGAAAA 49700518 AGGTTGAAGT Statistics Matches: 17, Mismatches: 2, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 21 17 1.00 ACGTcount: A:0.62, C:0.07, G:0.25, T:0.05 Consensus pattern (21 bp): AAAGAGATAGAAGAGAAAACA Found at i:49700980 original size:29 final size:29 Alignment explanation

Indices: 49700948--49701005 Score: 73 Period size: 29 Copynumber: 2.0 Consensus size: 29 49700938 ACCAATAAAA * 49700948 GCCCTTTTTTTCAA-AATTTACCGAAATGG 1 GCCCATTTTTT-AATAATTTACCGAAATGG * * 49700977 GCCCATTTTTTAATTATTTACCGGAATGG 1 GCCCATTTTTTAATAATTTACCGAAATGG 49701006 TCATTTTTTG Statistics Matches: 25, Mismatches: 3, Indels: 2 0.83 0.10 0.07 Matches are distributed among these distances: 28 2 0.08 29 23 0.92 ACGTcount: A:0.26, C:0.19, G:0.16, T:0.40 Consensus pattern (29 bp): GCCCATTTTTTAATAATTTACCGAAATGG Found at i:49701262 original size:22 final size:23 Alignment explanation

Indices: 49701212--49701292 Score: 89 Period size: 22 Copynumber: 3.6 Consensus size: 23 49701202 TTTTCACGAA 49701212 CAAA-TCCTCTCTAATATTCCTTCT 1 CAAATTCCTCTC-AAT-TTCCTTCT * 49701236 C-AATTCCTCTCAATTTCTTTC- 1 CAAATTCCTCTCAATTTCCTTCT * 49701257 CAAATTTCTCTCAATTTCCTTCT 1 CAAATTCCTCTCAATTTCCTTCT * 49701280 AAAATT-CTCTCAA 1 CAAATTCCTCTCAA 49701293 ACTCATATTT Statistics Matches: 50, Mismatches: 4, Indels: 8 0.81 0.06 0.13 Matches are distributed among these distances: 21 1 0.02 22 31 0.62 23 10 0.20 24 8 0.16 ACGTcount: A:0.26, C:0.31, G:0.00, T:0.43 Consensus pattern (23 bp): CAAATTCCTCTCAATTTCCTTCT Found at i:49701322 original size:40 final size:41 Alignment explanation

Indices: 49701265--49701365 Score: 125 Period size: 40 Copynumber: 2.5 Consensus size: 41 49701255 TCCAAATTTC * * 49701265 TCTCAATTTCCTTCTAAAATTCTCTCAAA-CTCATATTTCAT 1 TCTCAATTTCCTTCTAAAATTATCTCAAATC-CATATTTAAT * 49701306 T-TCAATTTCCTTCTAAAATTATTTCAAATCCATATTTAAT 1 TCTCAATTTCCTTCTAAAATTATCTCAAATCCATATTTAAT * * 49701346 TCTAAATTTCCGTTTTAAAA 1 TCTCAATTTCC-TTCTAAAA 49701366 ATAATTTTAA Statistics Matches: 52, Mismatches: 5, Indels: 5 0.84 0.08 0.08 Matches are distributed among these distances: 40 35 0.67 41 10 0.19 42 7 0.13 ACGTcount: A:0.33, C:0.21, G:0.01, T:0.46 Consensus pattern (41 bp): TCTCAATTTCCTTCTAAAATTATCTCAAATCCATATTTAAT Found at i:49703188 original size:18 final size:19 Alignment explanation

Indices: 49703162--49703201 Score: 64 Period size: 18 Copynumber: 2.2 Consensus size: 19 49703152 AGGTGCGTTT * 49703162 CCTAGCCCTTATATGTA-C 1 CCTAACCCTTATATGTATC 49703180 CCTAACCCTTATATGTATC 1 CCTAACCCTTATATGTATC 49703199 CCT 1 CCT 49703202 TTTCGAGTCC Statistics Matches: 20, Mismatches: 1, Indels: 1 0.91 0.05 0.05 Matches are distributed among these distances: 18 16 0.80 19 4 0.20 ACGTcount: A:0.23, C:0.35, G:0.07, T:0.35 Consensus pattern (19 bp): CCTAACCCTTATATGTATC Found at i:49703618 original size:25 final size:25 Alignment explanation

Indices: 49703589--49703871 Score: 297 Period size: 25 Copynumber: 11.7 Consensus size: 25 49703579 TATTTAAATA * * 49703589 TTATTTGATGCAATAAAATTGAAGT 1 TTATTTGATGTAATAAAATAGAAGT 49703614 TTATTTGATGTAATAAAATAGAAGT 1 TTATTTGATGTAATAAAATAGAAGT * * * 49703639 TTATTTAATGTAATAAAATATAAAT 1 TTATTTGATGTAATAAAATAGAAGT ** * 49703664 TT-TTTCGA-GT--T-ATTTTG-A-T 1 TTATTT-GATGTAATAAAATAGAAGT 49703683 ATTATTTGATGTAATAAAATAGAAGT 1 -TTATTTGATGTAATAAAATAGAAGT * 49703709 TTATTTGATGTAATAAAATAGAAAT 1 TTATTTGATGTAATAAAATAGAAGT * 49703734 TTATTTGATGTAATAAAATATAAGT 1 TTATTTGATGTAATAAAATAGAAGT * 49703759 TTATTGGATGTAATAAAATAGAAGT 1 TTATTTGATGTAATAAAATAGAAGT * 49703784 TTATTTGATGTAATAAAATAGAAAT 1 TTATTTGATGTAATAAAATAGAAGT ** * 49703809 TT-TTTCGA-GT--T-ATTTTG-A-T 1 TTATTT-GATGTAATAAAATAGAAGT 49703828 ATTATTTGATGTAATAAAATAGAAGT 1 -TTATTTGATGTAATAAAATAGAAGT 49703854 TTATTTGATGTAATAAAA 1 TTATTTGATGTAATAAAA 49703872 ACTCTAACCT Statistics Matches: 214, Mismatches: 26, Indels: 36 0.78 0.09 0.13 Matches are distributed among these distances: 19 2 0.01 20 10 0.05 21 15 0.07 22 2 0.01 23 2 0.01 24 16 0.07 25 165 0.77 26 2 0.01 ACGTcount: A:0.42, C:0.01, G:0.14, T:0.43 Consensus pattern (25 bp): TTATTTGATGTAATAAAATAGAAGT Found at i:49703697 original size:70 final size:70 Alignment explanation

Indices: 49703614--49703871 Score: 385 Period size: 70 Copynumber: 3.6 Consensus size: 70 49703604 AAATTGAAGT * * 49703614 TTATTTGATGTAATAAAATAGAAGTTTATTTAATGTAATAAAATATAAATTTTTTCGAGTTATTT 1 TTATTTGATGTAATAAAATAGAAGTTTATTTGATGTAATAAAATAGAAATTTTTTCGAGTTATTT 49703679 TGATA 66 TGATA 49703684 TTATTTGATGTAATAAAATAGAAGTTTATTTGATGTAATAAAATAGAAATTTATTT-GATGTAAT 1 TTATTTGATGTAATAAAATAGAAGTTTATTTGATGTAATAAAATAGAAATTT-TTTCGA-GT--T *** 49703748 AAAAT-ATAA 62 ATTTTGAT-A * 49703757 GTTTATTGGATGTAATAAAATAGAAGTTTATTTGATGTAATAAAATAGAAATTTTTTCGAGTTAT 1 --TTATTTGATGTAATAAAATAGAAGTTTATTTGATGTAATAAAATAGAAATTTTTTCGAGTTAT 49703822 TTTGATA 64 TTTGATA 49703829 TTATTTGATGTAATAAAATAGAAGTTTATTTGATGTAATAAAA 1 TTATTTGATGTAATAAAATAGAAGTTTATTTGATGTAATAAAA 49703872 ACTCTAACCT Statistics Matches: 169, Mismatches: 10, Indels: 18 0.86 0.05 0.09 Matches are distributed among these distances: 70 94 0.56 71 5 0.03 72 6 0.04 73 6 0.04 74 5 0.03 75 53 0.31 ACGTcount: A:0.42, C:0.01, G:0.14, T:0.44 Consensus pattern (70 bp): TTATTTGATGTAATAAAATAGAAGTTTATTTGATGTAATAAAATAGAAATTTTTTCGAGTTATTT TGATA Found at i:49703852 original size:145 final size:146 Alignment explanation

Indices: 49703584--49703871 Score: 517 Period size: 145 Copynumber: 2.0 Consensus size: 146 49703574 TGCCGTATTT * 49703584 AAATATTATTTGATGCAATAAAATTGAAGTTTATTTGATGTAATAAAATAGAAGTTTATTTAATG 1 AAATATTATTTGATGCAATAAAATTGAAGTTTATTGGATGTAATAAAATAGAAGTTTATTTAATG * 49703649 TAATAAAATATAAATTTTTTCGAGTTATTTTGATATTATTTGATGTAATAAAATAGAAGTTTATT 66 TAATAAAATAGAAATTTTTTCGAGTTATTTTGATATTATTTGATGTAATAAAATAGAAGTTTATT 49703714 TGATGTAATAAAATAG 131 TGATGTAATAAAATAG * * 49703730 AAAT-TTATTTGATGTAATAAAATAT-AAGTTTATTGGATGTAATAAAATAGAAGTTTATTTGAT 1 AAATATTATTTGATGCAATAAAAT-TGAAGTTTATTGGATGTAATAAAATAGAAGTTTATTTAAT 49703793 GTAATAAAATAGAAATTTTTTCGAGTTATTTTGATATTATTTGATGTAATAAAATAGAAGTTTAT 65 GTAATAAAATAGAAATTTTTTCGAGTTATTTTGATATTATTTGATGTAATAAAATAGAAGTTTAT 49703858 TTGATGTAATAAAA 130 TTGATGTAATAAAA 49703872 ACTCTAACCT Statistics Matches: 137, Mismatches: 4, Indels: 3 0.95 0.03 0.02 Matches are distributed among these distances: 145 132 0.96 146 5 0.04 ACGTcount: A:0.42, C:0.01, G:0.14, T:0.43 Consensus pattern (146 bp): AAATATTATTTGATGCAATAAAATTGAAGTTTATTGGATGTAATAAAATAGAAGTTTATTTAATG TAATAAAATAGAAATTTTTTCGAGTTATTTTGATATTATTTGATGTAATAAAATAGAAGTTTATT TGATGTAATAAAATAG Found at i:49703897 original size:13 final size:13 Alignment explanation

Indices: 49703879--49703922 Score: 70 Period size: 13 Copynumber: 3.4 Consensus size: 13 49703869 AAAACTCTAA 49703879 CCTAATTAAATAC 1 CCTAATTAAATAC 49703892 CCTAATTAAATAC 1 CCTAATTAAATAC * * 49703905 CATAATTAAAAAC 1 CCTAATTAAATAC 49703918 CCTAA 1 CCTAA 49703923 CCCTAATCCT Statistics Matches: 28, Mismatches: 3, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 13 28 1.00 ACGTcount: A:0.50, C:0.23, G:0.00, T:0.27 Consensus pattern (13 bp): CCTAATTAAATAC Found at i:49703983 original size:13 final size:13 Alignment explanation

Indices: 49703948--49704053 Score: 69 Period size: 13 Copynumber: 8.5 Consensus size: 13 49703938 TAACCTAAAT * 49703948 TAATTCAAAACCT 1 TAATTCAAAACCC * 49703961 TAATCCAAAACCC 1 TAATTCAAAACCC * 49703974 TAATTAAAAACCC 1 TAATTCAAAACCC * ** 49703987 TAA-CCCTAACCC 1 TAATTCAAAACCC * * * 49703999 TAA-CCTAAA--T 1 TAATTCAAAACCC * 49704009 TAATTCAAAAACC 1 TAATTCAAAACCC 49704022 TAATT-AAATACCC 1 TAATTCAAA-ACCC * 49704035 TAATTAAAAACCC 1 TAATTCAAAACCC 49704048 TAATTC 1 TAATTC 49704054 TAGCCTAATT Statistics Matches: 72, Mismatches: 16, Indels: 10 0.73 0.16 0.10 Matches are distributed among these distances: 10 3 0.04 11 4 0.06 12 15 0.21 13 47 0.65 14 3 0.04 ACGTcount: A:0.47, C:0.27, G:0.00, T:0.25 Consensus pattern (13 bp): TAATTCAAAACCC Found at i:49703995 original size:61 final size:61 Alignment explanation

Indices: 49703921--49704050 Score: 210 Period size: 61 Copynumber: 2.1 Consensus size: 61 49703911 TAAAAACCCT * 49703921 AACCCTAATCCTAACCCTAACCTAAATTAATTC-AAAACCTTAATCCAAA-ACCCTAATTAAA 1 AACCCTAACCCTAACCCTAACCTAAATTAATTCAAAAACC-TAAT-CAAATACCCTAATTAAA * 49703982 AACCCTAACCCTAACCCTAACCTAAATTAATTCAAAAACCTAATTAAATACCCTAATTAAA 1 AACCCTAACCCTAACCCTAACCTAAATTAATTCAAAAACCTAATCAAATACCCTAATTAAA 49704043 AACCCTAA 1 AACCCTAA 49704051 TTCTAGCCTA Statistics Matches: 65, Mismatches: 2, Indels: 4 0.92 0.03 0.06 Matches are distributed among these distances: 60 3 0.05 61 56 0.86 62 6 0.09 ACGTcount: A:0.47, C:0.29, G:0.00, T:0.24 Consensus pattern (61 bp): AACCCTAACCCTAACCCTAACCTAAATTAATTCAAAAACCTAATCAAATACCCTAATTAAA Found at i:49704047 original size:55 final size:58 Alignment explanation

Indices: 49703930--49704075 Score: 160 Period size: 61 Copynumber: 2.5 Consensus size: 58 49703920 TAACCCTAAT 49703930 CCTAACCCTAACCTAAATTAATTC-AAAACCTTAATCCAAAACCCTAATTAAAAACCCTAAC 1 CCTAACCCTAACCTAAATTAATTCAAAAACCTTAATCCAAAACCCTAATT-AAAA--C-AAC * 49703991 CCTAACCCTAACCTAAATTAATTCAAAAACC-TAAT-TAAATACCCTAATT-AAA-AAC 1 CCTAACCCTAACCTAAATTAATTCAAAAACCTTAATCCAAA-ACCCTAATTAAAACAAC ** * * 49704046 CCTAATTCTAGCCTAATTTAATT-AAAAACC 1 CCTAACCCTAACCTAAATTAATTCAAAAACC 49704076 CTAAAAACCC Statistics Matches: 78, Mismatches: 5, Indels: 11 0.83 0.05 0.12 Matches are distributed among these distances: 54 7 0.09 55 22 0.28 59 3 0.04 60 3 0.04 61 37 0.47 62 6 0.08 ACGTcount: A:0.46, C:0.27, G:0.01, T:0.26 Consensus pattern (58 bp): CCTAACCCTAACCTAAATTAATTCAAAAACCTTAATCCAAAACCCTAATTAAAACAAC Found at i:49704070 original size:29 final size:27 Alignment explanation

Indices: 49704035--49704675 Score: 353 Period size: 33 Copynumber: 22.6 Consensus size: 27 49704025 TTAAATACCC * 49704035 TAATTAAAAACCCTAATTCTAGCCTAATT 1 TAATTAAAAACCCTAA-CCTA-CCTAATT 49704064 TAATTAAAAACCCTAAAAACCCTAATCCTAATT 1 TAATTAAAAACCCT---AA-CCT-A-CCTAATT ** 49704097 TAATTAAAAACCCTAACCTA---AACCC 1 TAATTAAAAACCCTAACCTACCTAA-TT * * 49704122 TAATTAAATACCTTAACCCTAACCTAATT 1 TAATTAAAAACCCTAA-CCT-ACCTAATT 49704151 TAATTAAAAACCCTAA--T-CCTAATT 1 TAATTAAAAACCCTAACCTACCTAATT ** 49704175 TAATTAAAAACCCTAACCTA---AACCC 1 TAATTAAAAACCCTAACCTACCTAA-TT * * 49704200 T-ATTAAATACTCTAACCCTAACCTAATT 1 TAATTAAAAACCCTAA-CCT-ACCTAATT 49704228 TAATTAAAAACCCTAAAAACCCTAATCCTAATT 1 TAATTAAAAACCCT---AA-CCT-A-CCTAATT ** 49704261 TAATTAAAAACCCTAACCTA---AACCC 1 TAATTAAAAACCCTAACCTACCTAA-TT * 49704286 TAATTAAATACCCTAACCCTAACCTAATT 1 TAATTAAAAACCCTAA-CCT-ACCTAATT 49704315 TAATTAAAAACCCTAAAAACCCTAATCCTAATT 1 TAATTAAAAACCCT---AA-CCT-A-CCTAATT * 49704348 TAATTAAAAACCCTAACCTA---AACCT 1 TAATTAAAAACCCTAACCTACCTAA-TT * * 49704373 TAATTAAATACCCTAACCCTATCTAATT 1 TAATTAAAAACCCTAA-CCTACCTAATT 49704401 TAATTAAAAACCCTAAAAACCTTAATCCTAATT 1 TAATTAAAAACCCT---AACC-T-A-CCTAATT ** 49704434 TAATTAAAAACCCTAACCTA---AACCC 1 TAATTAAAAACCCTAACCTACCTAA-TT * * 49704459 TAATTAAATACCCTAACCCTAATCTAATT 1 TAATTAAAAACCCTAA-CCT-ACCTAATT 49704488 TAATTAAAAACCCTAAAAACCCTTATCCTAATT 1 TAATTAAAAACCCT---AA-CC-TA-CCTAATT ** 49704521 TAATTAAAAACCCTAACCTA---AACCC 1 TAATTAAAAACCCTAACCTACCTAA-TT * 49704546 TAATTAAATACCCTAACCCTAACCTAATT 1 TAATTAAAAACCCTAA-CCT-ACCTAATT 49704575 TAATTAAAAACCCTAAAAACCCTAATCCTAATT 1 TAATTAAAAACCCT---AA-CCT-A-CCTAATT * 49704608 TAATTAAAGACCCTAACCCTAACCTAATT 1 TAATTAAAAACCCTAA-CCT-ACCTAATT * * 49704637 TAATTCAAAACCTTAACCTA---AA-T 1 TAATTAAAAACCCTAACCTACCTAATT * 49704660 TATTTAAAAACCCTAA 1 TAATTAAAAACCCTAA 49704676 ACTAAGTTAA Statistics Matches: 496, Mismatches: 50, Indels: 138 0.73 0.07 0.20 Matches are distributed among these distances: 23 14 0.03 24 49 0.10 25 79 0.16 26 19 0.04 27 5 0.01 28 24 0.05 29 113 0.23 30 30 0.06 31 3 0.01 32 35 0.07 33 125 0.25 ACGTcount: A:0.45, C:0.26, G:0.00, T:0.29 Consensus pattern (27 bp): TAATTAAAAACCCTAACCTACCTAATT Found at i:49704106 original size:24 final size:23 Alignment explanation

Indices: 49704077--49704243 Score: 136 Period size: 24 Copynumber: 6.5 Consensus size: 23 49704067 TTAAAAACCC 49704077 TAAAAACCCTAATCCTAATTTAAT 1 TAAAAACCCTAA-CCTAATTTAAT ** 49704101 TAAAAACCCTAACCTAAACCCTAAT 1 TAAAAACCCTAACCT-AA-TTTAAT 49704126 TAAATACCTTAACCCTAACCTAATTTAAT 1 T-AA-A----AACCCTAACCTAATTTAAT 49704155 TAAAAACCCTAATCCTAATTTAAT 1 TAAAAACCCTAA-CCTAATTTAAT * 49704179 TAAAAACCCTAACCTAAACCCTATTAAA 1 TAAAAACCCTAACCT-AA---T-TTAAT ** 49704207 TACTCTAACCCTAACCTAATTTAAT 1 TA--AAAACCCTAACCTAATTTAAT 49704232 TAAAAACCCTAA 1 TAAAAACCCTAA 49704244 AAACCCTAAT Statistics Matches: 117, Mismatches: 10, Indels: 33 0.73 0.06 0.21 Matches are distributed among these distances: 23 22 0.19 24 39 0.33 25 11 0.09 26 3 0.03 27 3 0.03 28 8 0.07 29 7 0.06 30 13 0.11 31 11 0.09 ACGTcount: A:0.46, C:0.26, G:0.00, T:0.29 Consensus pattern (23 bp): TAAAAACCCTAACCTAATTTAAT Found at i:49704106 original size:87 final size:87 Alignment explanation

Indices: 49703974--49704676 Score: 1026 Period size: 87 Copynumber: 8.2 Consensus size: 87 49703964 TCCAAAACCC * * * 49703974 TAATTAAAAACCCTAACCCTAACCCTAA-CCTAAATTAATTCAAAAA-CCTAA-TTAAATACCCT 1 TAATTAAAAACCCTAA---AAACCCTAATCCTAATTTAATT-AAAAACCCTAACCT-AA-ACCCT * ** * 49704036 AATTAAAAACCCTAATTCTAGCCTAATT 60 AATTAAATACCCTAACCCTAACCTAATT 49704064 TAATTAAAAACCCTAAAAACCCTAATCCTAATTTAATTAAAAACCCTAACCTAAACCCTAATTAA 1 TAATTAAAAACCCTAAAAACCCTAATCCTAATTTAATTAAAAACCCTAACCTAAACCCTAATTAA * 49704129 ATACCTTAACCCTAACCTAATT 66 ATACCCTAACCCTAACCTAATT 49704151 TAA-T--------TAAAAACCCTAATCCTAATTTAATTAAAAACCCTAACCTAAACCCT-ATTAA 1 TAATTAAAAACCCTAAAAACCCTAATCCTAATTTAATTAAAAACCCTAACCTAAACCCTAATTAA * 49704206 ATACTCTAACCCTAACCTAATT 66 ATACCCTAACCCTAACCTAATT 49704228 TAATTAAAAACCCTAAAAACCCTAATCCTAATTTAATTAAAAACCCTAACCTAAACCCTAATTAA 1 TAATTAAAAACCCTAAAAACCCTAATCCTAATTTAATTAAAAACCCTAACCTAAACCCTAATTAA 49704293 ATACCCTAACCCTAACCTAATT 66 ATACCCTAACCCTAACCTAATT * 49704315 TAATTAAAAACCCTAAAAACCCTAATCCTAATTTAATTAAAAACCCTAACCTAAACCTTAATTAA 1 TAATTAAAAACCCTAAAAACCCTAATCCTAATTTAATTAAAAACCCTAACCTAAACCCTAATTAA * 49704380 ATACCCTAACCCT-ATCTAATT 66 ATACCCTAACCCTAACCTAATT * 49704401 TAATTAAAAACCCTAAAAACCTTAATCCTAATTTAATTAAAAACCCTAACCTAAACCCTAATTAA 1 TAATTAAAAACCCTAAAAACCCTAATCCTAATTTAATTAAAAACCCTAACCTAAACCCTAATTAA * 49704466 ATACCCTAACCCTAATCTAATT 66 ATACCCTAACCCTAACCTAATT * 49704488 TAATTAAAAACCCTAAAAACCCTTATCCTAATTTAATTAAAAACCCTAACCTAAACCCTAATTAA 1 TAATTAAAAACCCTAAAAACCCTAATCCTAATTTAATTAAAAACCCTAACCTAAACCCTAATTAA 49704553 ATACCCTAACCCTAACCTAATT 66 ATACCCTAACCCTAACCTAATT * * 49704575 TAATTAAAAACCCTAAAAACCCTAATCCTAATTTAATTAAAGACCCTAACCCT-AA-CCTAATTT 1 TAATTAAAAACCCTAAAAACCCTAATCCTAATTTAATTAAAAACCCTAA-CCTAAACCCTAATTA * ** * * 49704638 AAT-TCAAAACCTTAACCTAAAT 65 AATACCCTAACCCTAACCTAATT * 49704660 TATTTAAAAACCCTAAA 1 TAATTAAAAACCCTAAA 49704677 CTAAGTTAAC Statistics Matches: 571, Mismatches: 27, Indels: 35 0.90 0.04 0.06 Matches are distributed among these distances: 77 28 0.05 78 47 0.08 85 30 0.05 86 140 0.25 87 288 0.50 88 21 0.04 89 1 0.00 90 16 0.03 ACGTcount: A:0.46, C:0.26, G:0.00, T:0.28 Consensus pattern (87 bp): TAATTAAAAACCCTAAAAACCCTAATCCTAATTTAATTAAAAACCCTAACCTAAACCCTAATTAA ATACCCTAACCCTAACCTAATT Found at i:49704117 original size:38 final size:39 Alignment explanation

Indices: 49704022--49704125 Score: 91 Period size: 33 Copynumber: 2.8 Consensus size: 39 49704012 TTCAAAAACC * * 49704022 TAATTAAATACCCTAA-TTAAAAACCCTAATTCTAGCCTAATT 1 TAATTAAAAACCCTAACCTAAAAACCCTAA---TA-CCTAATT 49704064 TAATTAAAAA--C---CCTAAAAACCCTAAT-CCTAATT 1 TAATTAAAAACCCTAACCTAAAAACCCTAATACCTAATT 49704097 TAATTAAAAACCCTAACCT--AAACCCTAAT 1 TAATTAAAAACCCTAACCTAAAAACCCTAAT 49704126 TAAATACCTT Statistics Matches: 54, Mismatches: 2, Indels: 18 0.73 0.03 0.24 Matches are distributed among these distances: 33 17 0.31 35 2 0.04 36 10 0.19 38 15 0.28 40 1 0.02 42 9 0.17 ACGTcount: A:0.46, C:0.24, G:0.01, T:0.29 Consensus pattern (39 bp): TAATTAAAAACCCTAACCTAAAAACCCTAATACCTAATT Found at i:49704281 original size:38 final size:31 Alignment explanation

Indices: 49704213--49704648 Score: 395 Period size: 33 Copynumber: 14.9 Consensus size: 31 49704203 TAAATACTCT 49704213 AACCCTAA-CCTAATTTAATTAAAAACCCTAAA 1 AACCCTAATCCTAATTTAATTAAAAACCCT--A 49704245 AACCCTAATCCTAATTTAATTAAAAACCCT- 1 AACCCTAATCCTAATTTAATTAAAAACCCTA * * * 49704275 AA-CCTAAACC----CTAATTAAATACCCT- 1 AACCCTAATCCTAATTTAATTAAAAACCCTA 49704300 AACCCTAA-CCTAATTTAATTAAAAACCCTAAA 1 AACCCTAATCCTAATTTAATTAAAAACCCT--A 49704332 AACCCTAATCCTAATTTAATTAAAAACCCT- 1 AACCCTAATCCTAATTTAATTAAAAACCCTA * * 49704362 AA-CCTAAACC----TTAATTAAATACCCT- 1 AACCCTAATCCTAATTTAATTAAAAACCCTA 49704387 AACCCT-AT-CTAATTTAATTAAAAACCCTAAA 1 AACCCTAATCCTAATTTAATTAAAAACCCT--A * 49704418 AACCTTAATCCTAATTTAATTAAAAACCCT- 1 AACCCTAATCCTAATTTAATTAAAAACCCTA * * * 49704448 AA-CCTAAACC----CTAATTAAATACCCT- 1 AACCCTAATCCTAATTTAATTAAAAACCCTA 49704473 AACCCTAAT-CTAATTTAATTAAAAACCCTAAA 1 AACCCTAATCCTAATTTAATTAAAAACCCT--A * 49704505 AACCCTTATCCTAATTTAATTAAAAACCCT- 1 AACCCTAATCCTAATTTAATTAAAAACCCTA * * * 49704535 AA-CCTAAACC----CTAATTAAATACCCT- 1 AACCCTAATCCTAATTTAATTAAAAACCCTA 49704560 AACCCTAA-CCTAATTTAATTAAAAACCCTAAA 1 AACCCTAATCCTAATTTAATTAAAAACCCT--A * 49704592 AACCCTAATCCTAATTTAATTAAAGACCCT- 1 AACCCTAATCCTAATTTAATTAAAAACCCTA * 49704622 AACCCTAA-CCTAATTTAATTCAAAACC 1 AACCCTAATCCTAATTTAATTAAAAACC 49704649 TTAACCTAAA Statistics Matches: 339, Mismatches: 27, Indels: 79 0.76 0.06 0.18 Matches are distributed among these distances: 24 1 0.00 25 67 0.20 26 18 0.05 28 14 0.04 29 82 0.24 30 16 0.05 31 5 0.01 32 34 0.10 33 102 0.30 ACGTcount: A:0.45, C:0.27, G:0.00, T:0.28 Consensus pattern (31 bp): AACCCTAATCCTAATTTAATTAAAAACCCTA Found at i:49704309 original size:25 final size:24 Alignment explanation

Indices: 49704241--49704574 Score: 89 Period size: 25 Copynumber: 12.0 Consensus size: 24 49704231 TTAAAAACCC ** 49704241 TAAAAACCCTAATCCT-AATTTAAT 1 TAAAAACCCTAA-CCTAAACCTAAT 49704265 TAAAAACCCTAACCTAAACCCTAAT 1 TAAAAACCCTAACCTAAA-CCTAAT * 49704290 TAAATACCCTAACCCT-AACCTAATTTAAT 1 TAAAAACCCTAA-CCTAAACC-----TAAT * 49704319 TAAAAACCCTAAAAACCCTAATCCTAATTTAAT 1 TAAAAACCCT---AA-CCTAAACCT-----AAT 49704352 TAAAAACCCTAACCTAAACCTTAAT 1 TAAAAACCCTAACCTAAACC-TAAT * ** 49704377 TAAATACCCTAACCCTATCTAATTTAAT 1 TAAAAACCCTAA-CCTA---AACCTAAT * 49704405 TAAAAACCCTAAAAACCTTAATCCTAATTTAAT 1 TAAAAACCCT---AACC-TAAACCT-----AAT 49704438 TAAAAACCCTAACCTAAACCCTAAT 1 TAAAAACCCTAACCTAAA-CCTAAT * ** 49704463 TAAATACCCTAACCCTAATCTAATTTAAT 1 TAAAAACCCTAA-CCT-A---AACCTAAT * * 49704492 TAAAAACCCTAAAAACCCTTATCCTAATTTAAT 1 TAAAAACCCT---AA-CCTAAACC-----TAAT 49704525 TAAAAACCCTAACCTAAACCCTAAT 1 TAAAAACCCTAACCTAAA-CCTAAT * 49704550 TAAATACCCTAACCCT-AACCTAAT 1 TAAAAACCCTAA-CCTAAACCTAAT 49704574 T 1 T 49704575 TAATTAAAAA Statistics Matches: 238, Mismatches: 25, Indels: 94 0.67 0.07 0.26 Matches are distributed among these distances: 23 3 0.01 24 23 0.10 25 62 0.26 26 13 0.05 27 1 0.00 28 17 0.07 29 42 0.18 30 18 0.08 31 4 0.02 32 12 0.05 33 43 0.18 ACGTcount: A:0.45, C:0.27, G:0.00, T:0.28 Consensus pattern (24 bp): TAAAAACCCTAACCTAAACCTAAT Found at i:49704362 original size:173 final size:174 Alignment explanation

Indices: 49703974--49704676 Score: 1026 Period size: 173 Copynumber: 4.1 Consensus size: 174 49703964 TCCAAAACCC * * * 49703974 TAATTAAAAACCCTAACCCTAACCCTAA-CCTAAATTAATTCAAAAA-CCTAA-TTAAATACCCT 1 TAATTAAAAACCCTAA---AAACCCTAATCCTAATTTAATT-AAAAACCCTAACCT-AA-ACCCT * ** * 49704036 AATTAAAAACCCTAATTCTAGCCTAATTTAATTAAAAACCCTAAAAACCCTAATCCTAATTTAAT 60 AATTAAATACCCTAACCCTAACCTAATTTAATTAAAAACCCTAAAAACCCTAATCCTAATTTAAT * 49704101 TAAAAACCCTAACCTAAACCCTAATTAAATACCTTAACCCTAACCTAATT 125 TAAAAACCCTAACCTAAACCCTAATTAAATACCCTAACCCTAACCTAATT 49704151 TAA-T--------TAAAAACCCTAATCCTAATTTAATTAAAAACCCTAACCTAAACCCT-ATTAA 1 TAATTAAAAACCCTAAAAACCCTAATCCTAATTTAATTAAAAACCCTAACCTAAACCCTAATTAA * 49704206 ATACTCTAACCCTAACCTAATTTAATTAAAAACCCTAAAAACCCTAATCCTAATTTAATTAAAAA 66 ATACCCTAACCCTAACCTAATTTAATTAAAAACCCTAAAAACCCTAATCCTAATTTAATTAAAAA 49704271 CCCTAACCTAAACCCTAATTAAATACCCTAACCCTAACCTAATT 131 CCCTAACCTAAACCCTAATTAAATACCCTAACCCTAACCTAATT * 49704315 TAATTAAAAACCCTAAAAACCCTAATCCTAATTTAATTAAAAACCCTAACCTAAACCTTAATTAA 1 TAATTAAAAACCCTAAAAACCCTAATCCTAATTTAATTAAAAACCCTAACCTAAACCCTAATTAA * * 49704380 ATACCCTAACCCT-ATCTAATTTAATTAAAAACCCTAAAAACCTTAATCCTAATTTAATTAAAAA 66 ATACCCTAACCCTAACCTAATTTAATTAAAAACCCTAAAAACCCTAATCCTAATTTAATTAAAAA * 49704444 CCCTAACCTAAACCCTAATTAAATACCCTAACCCTAATCTAATT 131 CCCTAACCTAAACCCTAATTAAATACCCTAACCCTAACCTAATT * 49704488 TAATTAAAAACCCTAAAAACCCTTATCCTAATTTAATTAAAAACCCTAACCTAAACCCTAATTAA 1 TAATTAAAAACCCTAAAAACCCTAATCCTAATTTAATTAAAAACCCTAACCTAAACCCTAATTAA * 49704553 ATACCCTAACCCTAACCTAATTTAATTAAAAACCCTAAAAACCCTAATCCTAATTTAATTAAAGA 66 ATACCCTAACCCTAACCTAATTTAATTAAAAACCCTAAAAACCCTAATCCTAATTTAATTAAAAA * * ** * * 49704618 CCCTAACCCT-AA-CCTAATTTAAT-TCAAAACCTTAACCTAAAT 131 CCCTAA-CCTAAACCCTAATTAAATACCCTAACCCTAACCTAATT * 49704660 TATTTAAAAACCCTAAA 1 TAATTAAAAACCCTAAA 49704677 CTAAGTTAAC Statistics Matches: 484, Mismatches: 27, Indels: 35 0.89 0.05 0.06 Matches are distributed among these distances: 164 111 0.23 165 19 0.04 166 18 0.04 167 1 0.00 168 3 0.01 172 29 0.06 173 223 0.46 174 73 0.15 175 3 0.01 176 1 0.00 177 3 0.01 ACGTcount: A:0.46, C:0.26, G:0.00, T:0.28 Consensus pattern (174 bp): TAATTAAAAACCCTAAAAACCCTAATCCTAATTTAATTAAAAACCCTAACCTAAACCCTAATTAA ATACCCTAACCCTAACCTAATTTAATTAAAAACCCTAAAAACCCTAATCCTAATTTAATTAAAAA CCCTAACCTAAACCCTAATTAAATACCCTAACCCTAACCTAATT Found at i:49704648 original size:23 final size:23 Alignment explanation

Indices: 49704622--49704685 Score: 74 Period size: 23 Copynumber: 2.8 Consensus size: 23 49704612 TAAAGACCCT * * 49704622 AACCCTAACCTAATTTAATTCAA 1 AACCCTAACCTAAATTAATTAAA * * 49704645 AACCTTAACCTAAATTATTTAAA 1 AACCCTAACCTAAATTAATTAAA * * 49704668 AACCCTAAACTAAGTTAA 1 AACCCTAACCTAAATTAA 49704686 CAATGTTACA Statistics Matches: 33, Mismatches: 8, Indels: 0 0.80 0.20 0.00 Matches are distributed among these distances: 23 33 1.00 ACGTcount: A:0.47, C:0.22, G:0.02, T:0.30 Consensus pattern (23 bp): AACCCTAACCTAAATTAATTAAA Found at i:49704838 original size:116 final size:116 Alignment explanation

Indices: 49704682--49704906 Score: 337 Period size: 116 Copynumber: 1.9 Consensus size: 116 49704672 CTAAACTAAG ** 49704682 TTAACAATGTTACATTCATGTAATGTTAGATTTGGAAAAATGTTTTGACTGGTACTAACAATTAA 1 TTAACAATGTTACATTCACATAATGTTAGATTTGGAAAAATGTTTTGACTGGTACTAACAATTAA * * 49704747 T-AATTT-TACATAATTTGATAGTTTTACTAACCATTAACACAATTTGTTGAC 66 TAAATTTATAC-T-ATTTGATAATTTTACTAACAATTAACACAATTTGTTGAC * * * 49704798 TTAATAATTTTACATTCACATAATGTTAGATTTGGTAAAATGTTTTGACTGGTACTAACAATTAA 1 TTAACAATGTTACATTCACATAATGTTAGATTTGGAAAAATGTTTTGACTGGTACTAACAATTAA * * 49704863 TAAATTTATACTATTTGATAATTTTAGTAACAATTAATACAATT 66 TAAATTTATACTATTTGATAATTTTACTAACAATTAACACAATT 49704907 ATCAATTAAT Statistics Matches: 98, Mismatches: 9, Indels: 4 0.88 0.08 0.04 Matches are distributed among these distances: 116 89 0.91 117 6 0.06 118 3 0.03 ACGTcount: A:0.38, C:0.10, G:0.11, T:0.42 Consensus pattern (116 bp): TTAACAATGTTACATTCACATAATGTTAGATTTGGAAAAATGTTTTGACTGGTACTAACAATTAA TAAATTTATACTATTTGATAATTTTACTAACAATTAACACAATTTGTTGAC Found at i:49708229 original size:126 final size:125 Alignment explanation

Indices: 49707934--49708286 Score: 526 Period size: 126 Copynumber: 2.8 Consensus size: 125 49707924 CCCAAACATG * * * 49707934 CTACTGTAGCAAAATCGCGTCCACGACGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC 1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTAC * * * * *** * 49707999 TAGAAGTGATTTTACACTATTTGCTTAGAAACATCAACTCAAAATTATTTTTTCCGGGAC 66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAAATTATTTCTTCCGGGAC * * 49708059 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATATCACAAATTTTTCTCAAATAGCATCCTAC 1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTAC * * * 49708124 TACAAGCGATTTTATACTATTTGCTCAAAAACGTCAAAAAAATAATTATTTCTTCCGTGAC 66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAA-AATTATTTCTTCCGGGAC * * 49708185 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGGGATTTCATAAATTCTTCTCAAATAGCATCCTAC 1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTAC * 49708250 TAGAAGCGATTTTATACTATTTGATCAGAAACGTCAA 66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAA 49708287 CTCGAAATTA Statistics Matches: 204, Mismatches: 23, Indels: 1 0.89 0.10 0.00 Matches are distributed among these distances: 125 93 0.46 126 111 0.54 ACGTcount: A:0.32, C:0.23, G:0.16, T:0.29 Consensus pattern (125 bp): CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTAC TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAAATTATTTCTTCCGGGAC Found at i:49711053 original size:39 final size:39 Alignment explanation

Indices: 49710999--49711078 Score: 151 Period size: 39 Copynumber: 2.1 Consensus size: 39 49710989 GTATAATTTA 49710999 GAACTTTTGTTTGCATTCCTCATCCTCATCTTAGCTTTG 1 GAACTTTTGTTTGCATTCCTCATCCTCATCTTAGCTTTG * 49711038 GAACTTTTGTTTGCATTCCTCATCCTTATCTTAGCTTTG 1 GAACTTTTGTTTGCATTCCTCATCCTCATCTTAGCTTTG 49711077 GA 1 GA 49711079 CTTCTCATTT Statistics Matches: 40, Mismatches: 1, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 39 40 1.00 ACGTcount: A:0.16, C:0.24, G:0.14, T:0.46 Consensus pattern (39 bp): GAACTTTTGTTTGCATTCCTCATCCTCATCTTAGCTTTG Found at i:49712568 original size:16 final size:16 Alignment explanation

Indices: 49712547--49712578 Score: 55 Period size: 16 Copynumber: 2.0 Consensus size: 16 49712537 GCGAGGAATG 49712547 GCTTAGTAGGAGCCTA 1 GCTTAGTAGGAGCCTA * 49712563 GCTTAGTAGGTGCCTA 1 GCTTAGTAGGAGCCTA 49712579 AATAGGTACC Statistics Matches: 15, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 16 15 1.00 ACGTcount: A:0.22, C:0.19, G:0.31, T:0.28 Consensus pattern (16 bp): GCTTAGTAGGAGCCTA Found at i:49713029 original size:22 final size:22 Alignment explanation

Indices: 49713004--49713050 Score: 67 Period size: 22 Copynumber: 2.1 Consensus size: 22 49712994 TCAGCTCTAT * * 49713004 CTTCCTTTCCATATCTCTTAAC 1 CTTCCTTTACATATCTCTCAAC * 49713026 CTTCCTTTATATATCTCTCAAC 1 CTTCCTTTACATATCTCTCAAC 49713048 CTT 1 CTT 49713051 GGCTCTTTGT Statistics Matches: 22, Mismatches: 3, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 22 22 1.00 ACGTcount: A:0.19, C:0.34, G:0.00, T:0.47 Consensus pattern (22 bp): CTTCCTTTACATATCTCTCAAC Found at i:49720011 original size:12 final size:12 Alignment explanation

Indices: 49719994--49720018 Score: 50 Period size: 12 Copynumber: 2.1 Consensus size: 12 49719984 TTATATGTTC 49719994 TTTAAATTTTTT 1 TTTAAATTTTTT 49720006 TTTAAATTTTTT 1 TTTAAATTTTTT 49720018 T 1 T 49720019 AAAATTTTCT 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:0.00, G:0.00, T:0.76 Consensus pattern (12 bp): TTTAAATTTTTT Found at i:49722642 original size:10 final size:10 Alignment explanation

Indices: 49722627--49722685 Score: 57 Period size: 10 Copynumber: 5.8 Consensus size: 10 49722617 TGCCCCTAAT 49722627 TTATAAAAAA 1 TTATAAAAAA 49722637 TTATAAAAAA 1 TTATAAAAAA * 49722647 TTATAAAATA 1 TTATAAAAAA * 49722657 -TATAGAAATA 1 TTATA-AAAAA * * 49722667 TAGAAAAAAAA 1 T-TATAAAAAA 49722678 TTATAAAA 1 TTATAAAA 49722686 TTCTATAAAG Statistics Matches: 40, Mismatches: 6, Indels: 6 0.77 0.12 0.12 Matches are distributed among these distances: 9 4 0.10 10 29 0.73 11 5 0.12 12 2 0.05 ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29 Consensus pattern (10 bp): TTATAAAAAA Found at i:49722706 original size:21 final size:20 Alignment explanation

Indices: 49722682--49722754 Score: 55 Period size: 20 Copynumber: 3.7 Consensus size: 20 49722672 AAAAAATTAT * 49722682 AAAATTCTATAAAGTCGTAA 1 AAAATTCTATAAAATCGTAA * * 49722702 GAAAATTATAAAAAAT-GTAA 1 -AAAATTCTATAAAATCGTAA * 49722722 AGAAA-TCTA-AAATTCGTAAA 1 A-AAATTCTATAAAATCGT-AA 49722742 AAAATT-TATAAAA 1 AAAATTCTATAAAA 49722755 GTTATCGTAC Statistics Matches: 41, Mismatches: 6, Indels: 11 0.71 0.10 0.19 Matches are distributed among these distances: 18 4 0.10 19 11 0.27 20 14 0.34 21 12 0.29 ACGTcount: A:0.59, C:0.05, G:0.08, T:0.27 Consensus pattern (20 bp): AAAATTCTATAAAATCGTAA Found at i:49723285 original size:87 final size:84 Alignment explanation

Indices: 49723159--49723385 Score: 255 Period size: 87 Copynumber: 2.7 Consensus size: 84 49723149 TAACGGTTAA * * * * 49723159 AGGGCATTTTTGATACATTTTGATAGTTTAAGTACCCAATTGAGTGTAAAAAAAAGCAGGGGCCT 1 AGGGCCTTTTTGATGCATTTTGAAAGTTCAAGTACCCAATTGAGTG-AAAAAAAA--A-GGGCCT * * 49723224 AATTACTTATGT-TGAAAAAGTTT 62 AATGACTT-TGTCTGAAAAAATTT * * 49723247 -GGGCCTTTTTGATGCATTTTGAAAGTTCAAGTACCCAATTGAGTG-AAAAAAAAGGGCTTTATG 1 AGGGCCTTTTTGATGCATTTTGAAAGTTCAAGTACCCAATTGAGTGAAAAAAAAAGGGCCTAATG * * 49723310 GCTTTTTCTGAAAAAATTT 66 ACTTTGTCTGAAAAAATTT * 49723329 GAGGGCCTCTTTT-ATGCATTTTGAAAGTTCAAGTATCCAATTGAGTGCAAAAAAAAA 1 -AGGGCCT-TTTTGATGCATTTTGAAAGTTCAAGTACCCAATTGAGTG-AAAAAAAAA 49723386 ACTTAATTGT Statistics Matches: 122, Mismatches: 11, Indels: 14 0.83 0.07 0.10 Matches are distributed among these distances: 81 2 0.02 82 20 0.16 83 1 0.01 84 39 0.32 85 11 0.09 86 8 0.07 87 41 0.34 ACGTcount: A:0.34, C:0.12, G:0.20, T:0.33 Consensus pattern (84 bp): AGGGCCTTTTTGATGCATTTTGAAAGTTCAAGTACCCAATTGAGTGAAAAAAAAAGGGCCTAATG ACTTTGTCTGAAAAAATTT Found at i:49723400 original size:84 final size:83 Alignment explanation

Indices: 49723159--49723414 Score: 241 Period size: 84 Copynumber: 3.0 Consensus size: 83 49723149 TAACGGTTAA * * * * * * 49723159 AGGGCATTTTTGATACATTTTGATAGTTTAAGTACCCAATTGAGTGTAAAAAAAAGCAGGGGCCT 1 AGGGCCTTTTTGATGCATTTTGAAAGTTCAAGTACCCAATTGAGTG-AAAAAAAAG-A---ACTT ** * * 49723224 AATTACTTATGTTGAAAAAGT-T- 61 AATGGCTT-TTTTGAAAAAATATG * ** * 49723246 TGGGCCTTTTTGATGCATTTTGAAAGTTCAAGTACCCAATTGAGTGAAAAAAAAGGGCTTTATGG 1 AGGGCCTTTTTGATGCATTTTGAAAGTTCAAGTACCCAATTGAGTGAAAAAAAAGAACTTAATGG * 49723311 CTTTTTCTGAAAAAATTTG 66 CTTTTT-TGAAAAAATATG * 49723330 AGGGCCTCTTTT-ATGCATTTTGAAAGTTCAAGTATCCAATTGAGTGCAAAAAAAA-AACTTAAT 1 AGGGCCT-TTTTGATGCATTTTGAAAGTTCAAGTACCCAATTGAGTG-AAAAAAAAGAACTTAAT * * 49723393 TGTTTTTTTGAAAAAATATG 64 GGCTTTTTTGAAAAAATATG 49723413 AG 1 AG 49723415 AACTTTTTAC Statistics Matches: 144, Mismatches: 20, Indels: 14 0.81 0.11 0.08 Matches are distributed among these distances: 81 2 0.01 82 16 0.11 83 14 0.10 84 50 0.35 85 12 0.08 86 9 0.06 87 41 0.28 ACGTcount: A:0.35, C:0.11, G:0.20, T:0.35 Consensus pattern (83 bp): AGGGCCTTTTTGATGCATTTTGAAAGTTCAAGTACCCAATTGAGTGAAAAAAAAGAACTTAATGG CTTTTTTGAAAAAATATG Found at i:49725314 original size:247 final size:247 Alignment explanation

Indices: 49724521--49725399 Score: 1286 Period size: 247 Copynumber: 3.6 Consensus size: 247 49724511 AAATAATAAT * * * 49724521 AATAACATACAATAGATAATGAACTTATGGTTTGAAACTAGTTAACAATAACACATGAAATATGT 1 AATAACATACAATAGATAATGAAATTATGGTTTGAAACTAATTAATAATAACACATGAAATATGT *** * * * * * 49724586 ACGATGTTAAAATTGAAAATTTTAGGTTAAAAATGGTTATCATGGCGTTGGCATCAATCTTGAGT 66 ACGATGTTAAAA-TGAAAAAAATAGATTAAAATTGTTTATCATGGTGTTGTCATCAATCTTGAGT * 49724651 GGATGTCGAGTTAACTTATGACACCAACTCAATCAAATACATTAATATATACTAGAATCCCTATC 130 GGATGTCGAGTTAACTTATGACACCAACTCAATCAAATACATTAATATATACTAGAATTCCTATC * 49724716 ACATGTGTATGCGTGT--AAAAACAAAAATTTGTGAACACAAATGTGTGTTTAAA 195 ACATGCGTATGCGTGTGGAAAAA-AAAAATTT-TGAACACAAATGTGTGTTTAAA * * 49724769 AATAGCATACAATAGATAATGAAACTTATGGTTTGAAAATAATTAATAATAACACATGAAATATG 1 AATAACATACAATAGATAATGAAA-TTATGGTTTGAAACTAATTAATAATAACACATGAAATATG 49724834 TACGATGTTAAAATGAAAAAAATAGATTAAAATTGTTTATCATGGTGTTGTCATCAATCTTGAGT 65 TACGATGTTAAAATGAAAAAAATAGATTAAAATTGTTTATCATGGTGTTGTCATCAATCTTGAGT * 49724899 GGATGTCGAGTTAAGTTATGACACCAACTCAATCAAATACATTAATATATACTAGAATT--TATC 130 GGATGTCGAGTTAACTTATGACACCAACTCAATCAAATACATTAATATATACTAGAATTCCTATC * * * * 49724962 ACATGCGTATGTGGGTGGAAACAACAAATTTTGAACACAAATGTGTGTTTAAA 195 ACATGCGTATGCGTGTGGAAAAAAAAAATTTTGAACACAAATGTGTGTTTAAA 49725015 AATAACATACAATAGATAATGAAATGTATGGTTTGAAACTAATTAATAATAACACATGAAATATG 1 AATAACATACAATAGATAATGAAAT-TATGGTTTGAAACTAATTAATAATAACACATGAAATATG * * * 49725080 TATGATGTTAAAATGAAAAAAA-A-ATTAAAATTTTTTTATCATGATGTTGTCATCAATCTTGAG 65 TACGATGTTAAAATGAAAAAAATAGATTAAAA-TTGTTTATCATGGTGTTGTCATCAATCTTGAG * ** * 49725143 TTGATGTCGAGTTAACTTATGTTACCAACTCAATCAAACACATTAATATATACTAGAATTCCTAT 129 TGGATGTCGAGTTAACTTATGACACCAACTCAATCAAATACATTAATATATACTAGAATTCCTAT * * * * * * 49725208 CACACGCATATGCGTGTGGATATAAAAAATTTTGAACACAAATCTGTGTTCAAA 194 CACATGCGTATGCGTGTGGAAAAAAAAAATTTTGAACACAAATGTGTGTTTAAA * * 49725262 TATAACATACAATAGATAACGAAATATATGGTTTGAAACTAATTAATAATAACACATGAAATATG 1 AATAACATACAATAGATAATGAAAT-TATGGTTTGAAACTAATTAATAATAACACATGAAATATG * * * * 49725327 TACAATGTTAAAAT-AAAAAAATAGATTAAAATTGTTTAACATGGTTTTGTCATCAATCTTAAGT 65 TACGATGTTAAAATGAAAAAAATAGATTAAAATTGTTTATCATGGTGTTGTCATCAATCTTGAGT * 49725391 TGATGTCGA 130 GGATGTCGA 49725400 TTATACACAC Statistics Matches: 573, Mismatches: 49, Indels: 19 0.89 0.08 0.03 Matches are distributed among these distances: 244 7 0.01 245 87 0.15 246 128 0.22 247 167 0.29 248 134 0.23 249 50 0.09 ACGTcount: A:0.42, C:0.11, G:0.14, T:0.32 Consensus pattern (247 bp): AATAACATACAATAGATAATGAAATTATGGTTTGAAACTAATTAATAATAACACATGAAATATGT ACGATGTTAAAATGAAAAAAATAGATTAAAATTGTTTATCATGGTGTTGTCATCAATCTTGAGTG GATGTCGAGTTAACTTATGACACCAACTCAATCAAATACATTAATATATACTAGAATTCCTATCA CATGCGTATGCGTGTGGAAAAAAAAAATTTTGAACACAAATGTGTGTTTAAA Found at i:49728368 original size:25 final size:26 Alignment explanation

Indices: 49728314--49728368 Score: 69 Period size: 25 Copynumber: 2.2 Consensus size: 26 49728304 GAGCTATTAA * 49728314 CGGGAAGCTCGTAAGAACCATATAAT 1 CGGGAAGCTCGTAAGAACCAAATAAT * * 49728340 -GGGAAGCTGGTGAGAACCAAAT-AT 1 CGGGAAGCTCGTAAGAACCAAATAAT 49728364 CGGGA 1 CGGGA 49728369 TACTTATGAG Statistics Matches: 25, Mismatches: 3, Indels: 3 0.81 0.10 0.10 Matches are distributed among these distances: 24 2 0.08 25 23 0.92 ACGTcount: A:0.36, C:0.16, G:0.31, T:0.16 Consensus pattern (26 bp): CGGGAAGCTCGTAAGAACCAAATAAT Found at i:49737049 original size:49 final size:50 Alignment explanation

Indices: 49736988--49737152 Score: 142 Period size: 49 Copynumber: 3.3 Consensus size: 50 49736978 AAGCTGATCT * 49736988 GAGCAATATAACGGGAAGCTCACAAAGAGCCAATAACGGGTAGCTCCAAA 1 GAGCAATATAACGGGAAGCTCACAAAGAGCCAATAACGGGAAGCTCCAAA * * * * * * * 49737038 GAGCAAT-TAACGGGAAGCAC-CAGATAGCCATATAACAGGCAG-TTCAAGC 1 GAGCAATATAACGGGAAGCTCACAAAGAGCCA-ATAACGGGAAGCTCCAA-A * ** * 49737087 GAGC-A-CTAACGGGAAGCTCACAAAGAGCCTTTAATCGGGAAGCTCACGAA 1 GAGCAATATAACGGGAAGCTCACAAAGAGCCAATAA-CGGGAAGCTC-CAAA * 49737137 GAGCCATATAACGGGA 1 GAGCAATATAACGGGA 49737153 CGCTTATAAG Statistics Matches: 88, Mismatches: 18, Indels: 16 0.72 0.15 0.13 Matches are distributed among these distances: 48 28 0.32 49 37 0.42 50 12 0.14 51 3 0.03 52 8 0.09 ACGTcount: A:0.39, C:0.22, G:0.25, T:0.13 Consensus pattern (50 bp): GAGCAATATAACGGGAAGCTCACAAAGAGCCAATAACGGGAAGCTCCAAA Found at i:49737151 original size:26 final size:26 Alignment explanation

Indices: 49736988--49737152 Score: 139 Period size: 24 Copynumber: 6.6 Consensus size: 26 49736978 AAGCTGATCT * 49736988 GAGCAATATAACGGGAAGCTCACAAA 1 GAGCCATATAACGGGAAGCTCACAAA * 49737014 GAGCCA-ATAACGGGTAGCTC-CAAA 1 GAGCCATATAACGGGAAGCTCACAAA * * * 49737038 GAGCAAT-TAACGGGAAGCAC-CAGA 1 GAGCCATATAACGGGAAGCTCACAAA * * * * ** 49737062 TAGCCATATAACAGGCAGTTCA-AGC 1 GAGCCATATAACGGGAAGCTCACAAA * 49737087 GAG-CA-CTAACGGGAAGCTCACAAA 1 GAGCCATATAACGGGAAGCTCACAAA * * 49737111 GAGCC-TTTAATCGGGAAGCTCACGAA 1 GAGCCATATAA-CGGGAAGCTCACAAA 49737137 GAGCCATATAACGGGA 1 GAGCCATATAACGGGA 49737153 CGCTTATAAG Statistics Matches: 108, Mismatches: 23, Indels: 16 0.73 0.16 0.11 Matches are distributed among these distances: 23 11 0.10 24 34 0.31 25 30 0.28 26 29 0.27 27 4 0.04 ACGTcount: A:0.39, C:0.22, G:0.25, T:0.13 Consensus pattern (26 bp): GAGCCATATAACGGGAAGCTCACAAA Found at i:49741120 original size:19 final size:20 Alignment explanation

Indices: 49741088--49741131 Score: 63 Period size: 19 Copynumber: 2.2 Consensus size: 20 49741078 TATTTTTATC * * 49741088 ATAAAAAATCATTAAAAATT 1 ATAAAAAATAATTAAAAATA 49741108 ATAAAAAA-AATTAAAAATA 1 ATAAAAAATAATTAAAAATA 49741127 ATAAA 1 ATAAA 49741132 TTTGATATAA Statistics Matches: 22, Mismatches: 2, Indels: 1 0.88 0.08 0.04 Matches are distributed among these distances: 19 14 0.64 20 8 0.36 ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25 Consensus pattern (20 bp): ATAAAAAATAATTAAAAATA Found at i:49741266 original size:10 final size:10 Alignment explanation

Indices: 49741253--49741327 Score: 66 Period size: 10 Copynumber: 7.7 Consensus size: 10 49741243 ATTTAAAGTT 49741253 TTATAAAAAA 1 TTATAAAAAA * 49741263 TTATAAAAAC 1 TTATAAAAAA 49741273 TTAT-AAAAA 1 TTATAAAAAA 49741282 -TATAAAAAA 1 TTATAAAAAA * ** 49741291 TT-CAAAATT 1 TTATAAAAAA * 49741300 TTCTAAAAAA 1 TTATAAAAAA * 49741310 ATATAAAAAAA 1 TTAT-AAAAAA 49741321 TTATAAA 1 TTATAAA 49741328 TCACAAAACA Statistics Matches: 50, Mismatches: 11, Indels: 8 0.72 0.16 0.12 Matches are distributed among these distances: 8 3 0.06 9 15 0.30 10 23 0.46 11 9 0.18 ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31 Consensus pattern (10 bp): TTATAAAAAA Found at i:49741276 original size:20 final size:18 Alignment explanation

Indices: 49741253--49741289 Score: 56 Period size: 18 Copynumber: 1.9 Consensus size: 18 49741243 ATTTAAAGTT 49741253 TTATAAAAAATTATAAAAAC 1 TTAT-AAAAA-TATAAAAAC 49741273 TTATAAAAATATAAAAA 1 TTATAAAAATATAAAAA 49741290 ATTCAAAATT Statistics Matches: 17, Mismatches: 0, Indels: 2 0.89 0.00 0.11 Matches are distributed among these distances: 18 8 0.47 19 5 0.29 20 4 0.24 ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30 Consensus pattern (18 bp): TTATAAAAATATAAAAAC Found at i:49741285 original size:49 final size:47 Alignment explanation

Indices: 49741158--49741327 Score: 159 Period size: 49 Copynumber: 3.5 Consensus size: 47 49741148 CGAACTTACA * * 49741158 AAAAAATTATAAAAATTATTAAAACATCAT-CAAAATTTATAGTTATTAT 1 AAAAAATTATAAAAATTA-TAAAACAT-ATAAAAAATTTAAAGTT-TTAT 49741207 AAAAAAATTAT-AAAATTA-ACAAAGCATATAAAACATATTTAAAGTTTTAT 1 -AAAAAATTATAAAAATTATA-AAA-CATATAAAA-A-ATTTAAAGTTTTAT * * * 49741257 AAAAAATTATAAAAACTTATAAAA-ATATAAAAAATTCAAAATTTTCT 1 AAAAAATTATAAAAA-TTATAAAACATATAAAAAATTTAAAGTTTTAT * 49741304 AAAAAAATATAAAAAAATTATAAA 1 -AAAAAAT-TATAAAAATTATAAA 49741328 TCACAAAACA Statistics Matches: 104, Mismatches: 6, Indels: 22 0.79 0.05 0.17 Matches are distributed among these distances: 47 12 0.12 48 20 0.19 49 37 0.36 50 19 0.18 51 15 0.14 52 1 0.01 ACGTcount: A:0.61, C:0.05, G:0.02, T:0.32 Consensus pattern (47 bp): AAAAAATTATAAAAATTATAAAACATATAAAAAATTTAAAGTTTTAT Found at i:49743839 original size:19 final size:21 Alignment explanation

Indices: 49743810--49743850 Score: 59 Period size: 20 Copynumber: 2.0 Consensus size: 21 49743800 GTCCCTTGGA 49743810 ACCCAAAAATTATA-GTTTTG 1 ACCCAAAAATTATATGTTTTG * 49743830 ACCC-AAAATTTTATGTTTTG 1 ACCCAAAAATTATATGTTTTG 49743850 A 1 A 49743851 TCAATTTAGT Statistics Matches: 19, Mismatches: 1, Indels: 2 0.86 0.05 0.09 Matches are distributed among these distances: 19 8 0.42 20 11 0.58 ACGTcount: A:0.37, C:0.15, G:0.10, T:0.39 Consensus pattern (21 bp): ACCCAAAAATTATATGTTTTG Found at i:49745208 original size:52 final size:52 Alignment explanation

Indices: 49745102--49745273 Score: 214 Period size: 50 Copynumber: 3.4 Consensus size: 52 49745092 ATGATGCTTA * * * 49745102 AATGCATGATTTAA-TTAA-GATGCAAAC-TAAA-TGAACA-AATGAGTTACTT 1 AATGCATGACTTAATTTAATGATGCAAACTTAAACT-AACATGA-GAGTTACAT 49745151 AATGCATGACTTAATTTAATGATGCAAACTTAAACTAACATGAGAGTTACAT 1 AATGCATGACTTAATTTAATGATGCAAACTTAAACTAACATGAGAGTTACAT * * 49745203 AATGCATGTCATAATTT-ATGATGCAAACTT-AACTAACATGAGAGTTACAT 1 AATGCATGACTTAATTTAATGATGCAAACTTAAACTAACATGAGAGTTACAT * * 49745253 AATGCATGACTTTATTAAATG 1 AATGCATGACTTAATTTAATG 49745274 CAGAACACAT Statistics Matches: 108, Mismatches: 9, Indels: 10 0.85 0.07 0.08 Matches are distributed among these distances: 49 13 0.12 50 37 0.34 51 25 0.23 52 31 0.29 53 2 0.02 ACGTcount: A:0.42, C:0.12, G:0.14, T:0.32 Consensus pattern (52 bp): AATGCATGACTTAATTTAATGATGCAAACTTAAACTAACATGAGAGTTACAT Found at i:49747499 original size:19 final size:18 Alignment explanation

Indices: 49747462--49747497 Score: 56 Period size: 18 Copynumber: 2.1 Consensus size: 18 49747452 AAAAATTGTC * 49747462 TTGTGTCGTTTTCATATA 1 TTGTGTCCTTTTCATATA 49747480 TTGTGTCCTTTT-ATATA 1 TTGTGTCCTTTTCATATA 49747497 T 1 T 49747498 ATATATATAT Statistics Matches: 17, Mismatches: 1, Indels: 1 0.89 0.05 0.05 Matches are distributed among these distances: 17 6 0.35 18 11 0.65 ACGTcount: A:0.17, C:0.11, G:0.14, T:0.58 Consensus pattern (18 bp): TTGTGTCCTTTTCATATA Found at i:49750134 original size:40 final size:40 Alignment explanation

Indices: 49750079--49750160 Score: 155 Period size: 40 Copynumber: 2.0 Consensus size: 40 49750069 TGTTGAGGAG 49750079 ATTGCTTCAAACCGTACAAAGACTTTTGTAAGAGACAAAC 1 ATTGCTTCAAACCGTACAAAGACTTTTGTAAGAGACAAAC * 49750119 ATTGCTTCAAACCGTATAAAGACTTTTGTAAGAGACAAAC 1 ATTGCTTCAAACCGTACAAAGACTTTTGTAAGAGACAAAC 49750159 AT 1 AT 49750161 AATATTCTTT Statistics Matches: 41, Mismatches: 1, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 40 41 1.00 ACGTcount: A:0.40, C:0.18, G:0.15, T:0.27 Consensus pattern (40 bp): ATTGCTTCAAACCGTACAAAGACTTTTGTAAGAGACAAAC Found at i:49753551 original size:25 final size:25 Alignment explanation

Indices: 49753503--49753551 Score: 64 Period size: 25 Copynumber: 2.0 Consensus size: 25 49753493 CTAGGTTAAT * * 49753503 TAGAGTTTAAGTGGGAAAGTAAAAA 1 TAGAGTTTAACTAGGAAAGTAAAAA 49753528 TAGAGTTTAACTAGGAGAAG-AAAA 1 TAGAGTTTAACTAGGA-AAGTAAAA 49753552 GCCAAAATAA Statistics Matches: 21, Mismatches: 2, Indels: 2 0.84 0.08 0.08 Matches are distributed among these distances: 25 18 0.86 26 3 0.14 ACGTcount: A:0.49, C:0.02, G:0.27, T:0.22 Consensus pattern (25 bp): TAGAGTTTAACTAGGAAAGTAAAAA Done.