Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: A05

Parameters: 2 7 7 80 10 50 1000

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000

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

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


File 130 of 318

Found at i:40227105 original size:48 final size:49

Alignment explanation

Indices: 40227014--40227112 Score: 146 Period size: 48 Copynumber: 2.0 Consensus size: 49 40227004 ATAAAATTAA ** 40227014 AATTAAAATTGCATAAATGAAAAAAAATATTAAATTGTATTGAAAAATT 1 AATTAAAATTGCATAAATGAAAAAAAATATTAAATACTATTGAAAAATT * * * 40227063 AATTAAAATTGCATAAAT-TAAAAAGATATTAAATACTATTGAAATATT 1 AATTAAAATTGCATAAATGAAAAAAAATATTAAATACTATTGAAAAATT 40227111 AA 1 AA 40227113 AATTATCACT Statistics Matches: 45, Mismatches: 5, Indels: 1 0.88 0.10 0.02 Matches are distributed among these distances: 48 27 0.60 49 18 0.40 ACGTcount: A:0.57, C:0.03, G:0.07, T:0.33 Consensus pattern (49 bp): AATTAAAATTGCATAAATGAAAAAAAATATTAAATACTATTGAAAAATT Found at i:40235523 original size:206 final size:206 Alignment explanation

Indices: 40234980--40235536 Score: 907 Period size: 207 Copynumber: 2.7 Consensus size: 206 40234970 GCAGATCTGG * 40234980 CTGAAGCAAAATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCT 1 CTGAAGC-AGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCT * 40235045 GATTTGGCTTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAG 65 GATTTGGTTTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAG * * ** 40235110 AGAACAAATCAAAGTTTGGCGTCTCCATATTCGACAGAGAGCAGACACATAGCAGATCTGGCCTT 130 AGAACAAATCGAAGTTTGGCATCTCCATATTCGACAGAGAGCAGACACATAGCAGATCTAACCTT * * 40235175 CAGATGTTTATA 195 CAGATGATTAGA * * 40235187 CTGAAGTAAGATCCAAGATGATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCT 1 CTGAAG-CAGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCT ** 40235252 GATTTGGTTTTCACGTGCTTACGATGAAAAAAATCTAAGATGATTTGGCATCTCTGTATTGTCAG 65 GATTTGGTTTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAG * * 40235317 AGAACAAATCGAAGTTTGGCATCTCCATATTCGACGGAGGGCAGACACATAGCAGATCTAACCTT 130 AGAACAAATCGAAGTTTGGCATCTCCATATTCGACAGAGAGCAGACACATAGCAGATCTAACCTT 40235382 CAGATGATTAGA 195 CAGATGATTAGA * * 40235394 CTGAAGCAGATCCAAGATGGTTTGGTATCCTTGTGCTTACAAGGAGCAAATCGAAGACATAGCTG 1 CTGAAGCAGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCTG ** ** * 40235459 ATTTGGTTTTTGCGTGCTTACCCTGAAGCAAATCTAAGATAATTTGGCATCTCTGTATTGTCAGA 66 ATTTGGTTTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGA 40235524 GAACAAATCGAAG 131 GAACAAATCGAAG 40235537 AAGCAGATTT Statistics Matches: 324, Mismatches: 25, Indels: 3 0.92 0.07 0.01 Matches are distributed among these distances: 206 126 0.39 207 198 0.61 ACGTcount: A:0.32, C:0.18, G:0.22, T:0.28 Consensus pattern (206 bp): CTGAAGCAGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCTG ATTTGGTTTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGA GAACAAATCGAAGTTTGGCATCTCCATATTCGACAGAGAGCAGACACATAGCAGATCTAACCTTC AGATGATTAGA Found at i:40239729 original size:44 final size:44 Alignment explanation

Indices: 40239664--40240077 Score: 261 Period size: 44 Copynumber: 9.5 Consensus size: 44 40239654 CAGCCTGTTA * 40239664 CCCTACTGCTTTGGGGGTTAAGGCCCTTCGTCTTCGATCTCTTT 1 CCCTACTGCTTAGGGGGTTAAGGCCCTTCGTCTTCGATCTCTTT * * ** *** * 40239708 CCCTGCTGCTTAGGGCGTTAA-GATCTAT-AAATTC-AGC-CTGTT 1 CCCTACTGCTTAGGGGGTTAAGGCCCT-TCGTCTTCGATCTCT-TT * 40239750 ACCCTACTGCTTAGGGGGTTAAGGCCCTTCATCTTCGATCTCTTT 1 -CCCTACTGCTTAGGGGGTTAAGGCCCTTCGTCTTCGATCTCTTT ** * * * * * 40239795 CCCTACTGCTTAGGGGGTTAA-GATC-T-GTAAATT-TAGCATGTTA 1 CCCTACTGCTTAGGGGGTTAAGGCCCTTCGT--CTTCGATC-TCTTT * 40239838 CCCTACTGCTTAGGGGGTTAAGGCCCTTCGTCTTCGATCTATTT 1 CCCTACTGCTTAGGGGGTTAAGGCCCTTCGTCTTCGATCTCTTT * ** * * 40239882 CCCTACTGCTTAGGGGGCTAA-GATC-T-GTAAATTC-AGC-CTGTT 1 CCCTACTGCTTAGGGGGTTAAGGCCCTTCGT--CTTCGATCTCT-TT * * 40239924 ACCCTACTGCTTAGGGGCTTAAGGCCCTTCGTCTTCGATCTGTTT 1 -CCCTACTGCTTAGGGGGTTAAGGCCCTTCGTCTTCGATCTCTTT * * *** * * 40239969 CCCTACTGCTTAGGGAGCTAA-AATC-T-GTAAATTC-AGC-CTGTT 1 CCCTACTGCTTAGGGGGTTAAGGCCCTTCGT--CTTCGATCTCT-TT * 40240011 ACCCTACTACTTAGGGGGTTAAGGCCCTTCGTCTTCGATCTCTTT 1 -CCCTACTGCTTAGGGGGTTAAGGCCCTTCGTCTTCGATCTCTTT * * 40240056 CCCTACTACTTAGGGGGCTAAG 1 CCCTACTGCTTAGGGGGTTAAG 40240078 ATCTGTAAAT Statistics Matches: 276, Mismatches: 62, Indels: 64 0.69 0.15 0.16 Matches are distributed among these distances: 41 9 0.03 42 17 0.06 43 100 0.36 44 122 0.44 45 17 0.06 46 11 0.04 ACGTcount: A:0.18, C:0.26, G:0.22, T:0.34 Consensus pattern (44 bp): CCCTACTGCTTAGGGGGTTAAGGCCCTTCGTCTTCGATCTCTTT Found at i:40239775 original size:87 final size:87 Alignment explanation

Indices: 40239621--40240111 Score: 793 Period size: 87 Copynumber: 5.6 Consensus size: 87 40239611 CAGCCTGTTA * * * * * 40239621 CCCTACTACTTAGAGGGTTAAGATTTGTAAATTCAGCCTGTTACCCTACTGCTTTGGGGGTTAAG 1 CCCTACTGCTTAGGGGGCTAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAG 40239686 GCCCTTCGTCTTCGATCTCTTT 66 GCCCTTCGTCTTCGATCTCTTT * * * * 40239708 CCCTGCTGCTTAGGGCGTTAAGATCTATAAATTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAG 1 CCCTACTGCTTAGGGGGCTAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAG * 40239773 GCCCTTCATCTTCGATCTCTTT 66 GCCCTTCGTCTTCGATCTCTTT * * * 40239795 CCCTACTGCTTAGGGGGTTAAGATCTGTAAATTTAGCATGTTACCCTACTGCTTAGGGGGTTAAG 1 CCCTACTGCTTAGGGGGCTAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAG * 40239860 GCCCTTCGTCTTCGATCTATTT 66 GCCCTTCGTCTTCGATCTCTTT * 40239882 CCCTACTGCTTAGGGGGCTAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGCTTAAG 1 CCCTACTGCTTAGGGGGCTAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAG * 40239947 GCCCTTCGTCTTCGATCTGTTT 66 GCCCTTCGTCTTCGATCTCTTT * * * 40239969 CCCTACTGCTTAGGGAGCTAAAATCTGTAAATTCAGCCTGTTACCCTACTACTTAGGGGGTTAAG 1 CCCTACTGCTTAGGGGGCTAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAG 40240034 GCCCTTCGTCTTCGATCTCTTT 66 GCCCTTCGTCTTCGATCTCTTT * * 40240056 CCCTACTACTTAGGGGGCTAAGATCTGTAAATTCAGCTTGTTACCCTACTGCTTAG 1 CCCTACTGCTTAGGGGGCTAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAG 40240112 AGGGCTGTTA Statistics Matches: 374, Mismatches: 30, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 87 374 1.00 ACGTcount: A:0.19, C:0.25, G:0.21, T:0.34 Consensus pattern (87 bp): CCCTACTGCTTAGGGGGCTAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAG GCCCTTCGTCTTCGATCTCTTT Found at i:40240085 original size:261 final size:271 Alignment explanation

Indices: 40239621--40240251 Score: 879 Period size: 261 Copynumber: 2.3 Consensus size: 271 40239611 CAGCCTGTTA * * * * * 40239621 CCCTACTACTTAGAGGGTTAAGATTTGTAAATTCAGCCTGTTACCCTACTGCTTTGGGGGTTAAG 1 CCCTACTGCTTAGGGGGCTAAGATCTGTAAATTCAGCCTGTTACCCTACTGC-TTAGGGGTTAAG * * * * * 40239686 GCCCTTCGTCTTCGATCTCTTTCCCTGCTGCTTAGGGCGTTAAGATCTATAAATTCAGCCTGTTA 65 GCCCTTCGTCTTCGATCTGTTTCCCTACTGCTTAGGGAGCTAAAATCTATAAATTCAGCCTGTTA * * * 40239751 CCCTACTGCTTAGGGGGTTAAGGCCCTTCATCTTCGATCTCTTTCCCTACTGCTTAGGGGGTTAA 130 CCCTACTACTTAGGGGGTTAAGGCCCTTCATCTTCGATCTCTTTCCCTACTACTTAGGGGGCTAA * * 40239816 GATCTGT-AA-A-T-TTA-GC-A-TG-TT-A-C-CCTACTGCTTAGGGGGTTAAGGCCCTTCGTC 195 GATCTGTAAATACTGTTACCCTACTGCTTAAGCTCCTACTACTTAGGGGGTTAAGGCCCTTCGTC 40239870 TTCGATCTATTT 260 TTCGATCTATTT 40239882 CCCTACTGCTTAGGGGGCTAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGCTTAAG 1 CCCTACTGCTTAGGGGGCTAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGG-TTAAG * 40239947 GCCCTTCGTCTTCGATCTGTTTCCCTACTGCTTAGGGAGCTAAAATCTGTAAATTCAGCCTGTTA 65 GCCCTTCGTCTTCGATCTGTTTCCCTACTGCTTAGGGAGCTAAAATCTATAAATTCAGCCTGTTA * 40240012 CCCTACTACTTAGGGGGTTAAGGCCCTTCGTCTTCGATCTCTTTCCCTACTACTTAGGGGGCTAA 130 CCCTACTACTTAGGGGGTTAAGGCCCTTCATCTTCGATCTCTTTCCCTACTACTTAGGGGGCTAA 40240077 GATCTGTAAATTCAGCTTGTTACCCTACTGCTTAGAGGGCTGTTACCCTACTACTTAGGGGGTTA 195 GATCTGTAAA-T-A-C-TGTTACCCTACTGCTTA-A--GC---T--CCTACTACTTAGGGGGTTA * 40240142 AGGCCCTTCGTCTTCGATCTCTTT 248 AGGCCCTTCGTCTTCGATCTATTT * 40240166 CCCTACTGTTTAGGGGGCTAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAAGGGGTTAAG 1 CCCTACTGCTTAGGGGGCTAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTT-AGGGGTTAAG 40240231 GCCCTTCGTCTTCGATCTGTT 65 GCCCTTCGTCTTCGATCTGTT 40240252 ACACCATTCT Statistics Matches: 326, Mismatches: 19, Indels: 27 0.88 0.05 0.07 Matches are distributed among these distances: 260 6 0.02 261 180 0.55 262 2 0.01 265 1 0.00 268 1 0.00 269 3 0.01 270 1 0.00 271 1 0.00 272 2 0.01 273 2 0.01 275 1 0.00 278 1 0.00 284 120 0.37 285 5 0.02 ACGTcount: A:0.19, C:0.25, G:0.22, T:0.34 Consensus pattern (271 bp): CCCTACTGCTTAGGGGGCTAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGTTAAGG CCCTTCGTCTTCGATCTGTTTCCCTACTGCTTAGGGAGCTAAAATCTATAAATTCAGCCTGTTAC CCTACTACTTAGGGGGTTAAGGCCCTTCATCTTCGATCTCTTTCCCTACTACTTAGGGGGCTAAG ATCTGTAAATACTGTTACCCTACTGCTTAAGCTCCTACTACTTAGGGGGTTAAGGCCCTTCGTCT TCGATCTATTT Found at i:40240199 original size:110 final size:109 Alignment explanation

Indices: 40240006--40240224 Score: 402 Period size: 110 Copynumber: 2.0 Consensus size: 109 40239996 TAAATTCAGC 40240006 CTGTTACCCTACTACTTAGGGGGTTAAGGCCCTTCGTCTTCGATCTCTTTCCCTACTACTTAGGG 1 CTGTTACCCTACTACTTAGGGGGTTAAGGCCCTTCGTCTTCGATCTCTTTCCCTACTACTTAGGG * 40240071 GGCTAAGATCTGTAAATTCAGCTTGTTACCCTACTGCTTAGAGGG 66 GGCTAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTA-AGGG ** 40240116 CTGTTACCCTACTACTTAGGGGGTTAAGGCCCTTCGTCTTCGATCTCTTTCCCTACTGTTTAGGG 1 CTGTTACCCTACTACTTAGGGGGTTAAGGCCCTTCGTCTTCGATCTCTTTCCCTACTACTTAGGG 40240181 GGCTAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAAGGG 66 GGCTAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAAGGG 40240225 GTTAAGGCCC Statistics Matches: 106, Mismatches: 3, Indels: 1 0.96 0.03 0.01 Matches are distributed among these distances: 109 4 0.04 110 102 0.96 ACGTcount: A:0.19, C:0.26, G:0.22, T:0.34 Consensus pattern (109 bp): CTGTTACCCTACTACTTAGGGGGTTAAGGCCCTTCGTCTTCGATCTCTTTCCCTACTACTTAGGG GGCTAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAAGGG Found at i:40240251 original size:44 final size:44 Alignment explanation

Indices: 40240116--40240253 Score: 131 Period size: 44 Copynumber: 3.2 Consensus size: 44 40240106 GCTTAGAGGG * 40240116 CTGTTACCCTACTACTTAGGGGGTTAAGGCCCTTCGTCTTCGAT 1 CTGTTACCCTACTGCTTAGGGGGTTAAGGCCCTTCGTCTTCGAT * * * * ** * * 40240160 CTCTTTCCCTACTGTTTAGGGGGCTAA-GATC-T-GTAAATTC-AGC 1 CTGTTACCCTACTGCTTAGGGGGTTAAGGCCCTTCGT--CTTCGA-T * 40240203 CTGTTACCCTACTGCTTAAGGGGTTAAGGCCCTTCGTCTTCGAT 1 CTGTTACCCTACTGCTTAGGGGGTTAAGGCCCTTCGTCTTCGAT 40240247 CTGTTAC 1 CTGTTAC 40240254 ACCATTCTTT Statistics Matches: 69, Mismatches: 18, Indels: 14 0.68 0.18 0.14 Matches are distributed among these distances: 41 2 0.03 42 2 0.03 43 27 0.39 44 34 0.49 45 2 0.03 46 2 0.03 ACGTcount: A:0.17, C:0.26, G:0.22, T:0.35 Consensus pattern (44 bp): CTGTTACCCTACTGCTTAGGGGGTTAAGGCCCTTCGTCTTCGAT Found at i:40240286 original size:87 final size:87 Alignment explanation

Indices: 40240116--40240279 Score: 206 Period size: 87 Copynumber: 1.9 Consensus size: 87 40240106 GCTTAGAGGG * * * * 40240116 CTGTTACCCTACTACTTAGGGGGTTAAGGCCCTTCGTCTTCGATCTCTTTCCCTACTGTTTAGGG 1 CTGTTACCCTACTACTTAAGGGGTTAAGGCCCTTCGTCTTCGATCTCTTACCCTACTCTTTAGAG ** * 40240181 GGCTAAGATCTGTAAATTCAGC 66 AACTAAGACCTGTAAATTCAGC * * * 40240203 CTGTTACCCTACTGCTTAAGGGGTTAAGGCCCTTCGTCTTCGATCTGTTACACC-ATTCTTTAGA 1 CTGTTACCCTACTACTTAAGGGGTTAAGGCCCTTCGTCTTCGATCTCTTAC-CCTACTCTTTAGA * 40240267 GAAC-ATGACCTGT 65 GAACTAAGACCTGT 40240280 TGAATTCGTT Statistics Matches: 65, Mismatches: 11, Indels: 3 0.82 0.14 0.04 Matches are distributed among these distances: 86 7 0.11 87 56 0.86 88 2 0.03 ACGTcount: A:0.20, C:0.26, G:0.21, T:0.34 Consensus pattern (87 bp): CTGTTACCCTACTACTTAAGGGGTTAAGGCCCTTCGTCTTCGATCTCTTACCCTACTCTTTAGAG AACTAAGACCTGTAAATTCAGC Found at i:40240982 original size:14 final size:14 Alignment explanation

Indices: 40240963--40240991 Score: 58 Period size: 14 Copynumber: 2.1 Consensus size: 14 40240953 TGTTAATTCA 40240963 GAGAAGACAAAACT 1 GAGAAGACAAAACT 40240977 GAGAAGACAAAACT 1 GAGAAGACAAAACT 40240991 G 1 G 40240992 CCGCATGCCC Statistics Matches: 15, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 14 15 1.00 ACGTcount: A:0.55, C:0.14, G:0.24, T:0.07 Consensus pattern (14 bp): GAGAAGACAAAACT Found at i:40248339 original size:19 final size:20 Alignment explanation

Indices: 40248315--40248357 Score: 61 Period size: 19 Copynumber: 2.2 Consensus size: 20 40248305 GGTCTTTTCG * * 40248315 TGAAATTTAATGCACATG-A 1 TGAAATGTAATGCAAATGAA 40248334 TGAAATGTAATGCAAATGAA 1 TGAAATGTAATGCAAATGAA 40248354 TGAA 1 TGAA 40248358 TGCAAAAAGA Statistics Matches: 21, Mismatches: 2, Indels: 1 0.88 0.08 0.04 Matches are distributed among these distances: 19 16 0.76 20 5 0.24 ACGTcount: A:0.47, C:0.07, G:0.19, T:0.28 Consensus pattern (20 bp): TGAAATGTAATGCAAATGAA Found at i:40254892 original size:5 final size:5 Alignment explanation

Indices: 40254884--40254935 Score: 54 Period size: 5 Copynumber: 10.4 Consensus size: 5 40254874 AAATTACACA * * 40254884 TATAT TATA- TATTT TATAT TATTAT T-TACT TATAT TTTAT TATAT TATAT 1 TATAT TATAT TATAT TATAT TA-TAT TATA-T TATAT TATAT TATAT TATAT 40254934 TA 1 TA 40254936 CTTCATATTT Statistics Matches: 39, Mismatches: 4, Indels: 8 0.76 0.08 0.16 Matches are distributed among these distances: 4 5 0.13 5 28 0.72 6 6 0.15 ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63 Consensus pattern (5 bp): TATAT Found at i:40254921 original size:23 final size:24 Alignment explanation

Indices: 40254884--40255049 Score: 92 Period size: 23 Copynumber: 7.3 Consensus size: 24 40254874 AAATTACACA 40254884 TATATTA--TATATTTTATATTAT 1 TATATTACTTATATTTTATATTAT 40254906 TAT-TTACTTATATTTTAT-TATAT 1 TATATTACTTATATTTTATAT-TAT * 40254929 TATATTACTTCATATTTTTCTATTAT 1 TATATTACTT-ATA-TTTTATATTAT * * * 40254955 CATATTAATATATATTTTA-A-CA- 1 TATATTACT-TATATTTTATATTAT * 40254977 TATATCA-TTAT-TTATTAT-TTAT 1 TATATTACTTATATT-TTATATTAT * 40254999 TATATTA--TAT-TTTT-TATCA- 1 TATATTACTTATATTTTATATTAT * * * 40255018 CATAATATTTATATTTTTATATTAT 1 TATATTACTTATA-TTTTATATTAT 40255043 TATATTA 1 TATATTA 40255050 TTTTACATTT Statistics Matches: 110, Mismatches: 15, Indels: 35 0.69 0.09 0.22 Matches are distributed among these distances: 19 8 0.07 20 10 0.09 21 13 0.12 22 15 0.14 23 21 0.19 24 11 0.10 25 12 0.11 26 18 0.16 27 2 0.02 ACGTcount: A:0.34, C:0.05, G:0.00, T:0.60 Consensus pattern (24 bp): TATATTACTTATATTTTATATTAT Found at i:40255008 original size:41 final size:41 Alignment explanation

Indices: 40254884--40255118 Score: 126 Period size: 44 Copynumber: 5.7 Consensus size: 41 40254874 AAATTACACA 40254884 TATATTATATATTTT---ATAT-TATTATTTACTTATATTTTAT 1 TATATTATATATTTTAACATATATATTATTTA-TTATA--TTAT * * 40254924 TATATTATAT-TACTT--CATAT-T-TT-TCTATTATCA-TAT 1 TATATTATATAT-TTTAACATATATATTATTTATTAT-ATTAT 40254960 TA-A-TATATATTTTAACATATATCATTATTTATTAT-TTAT 1 TATATTATATATTTTAACATATAT-ATTATTTATTATATTAT * * 40254999 TATATTATATTTTTTATCACATA-ATATTTATATTTTTATATTAT 1 TATATTATATATTTTA--ACATATATA-TTAT-TTATTATATTAT * 40255043 TATATTATTTTACATTTTAACA-ATATATTATTTCA-TATTATTAT 1 TATATTA---TATATTTTAACATATATATTATTT-ATTA-TATTAT ** * 40255087 TATCCATTATATATTTTTTCATGTATATTATT 1 TAT--ATTATATATTTTAACATATATATTATT 40255119 ATTCACATTA Statistics Matches: 155, Mismatches: 13, Indels: 50 0.71 0.06 0.23 Matches are distributed among these distances: 34 7 0.05 35 2 0.01 36 10 0.06 37 1 0.01 38 4 0.03 39 12 0.08 40 22 0.14 41 16 0.10 42 6 0.04 43 24 0.15 44 34 0.22 45 6 0.04 46 4 0.03 47 7 0.05 ACGTcount: A:0.34, C:0.06, G:0.00, T:0.60 Consensus pattern (41 bp): TATATTATATATTTTAACATATATATTATTTATTATATTAT Found at i:40255119 original size:31 final size:32 Alignment explanation

Indices: 40255065--40255142 Score: 94 Period size: 30 Copynumber: 2.6 Consensus size: 32 40255055 CATTTTAACA 40255065 ATATATTATTTCATATTATTATTA-TC-CATT 1 ATATATTATTTCATATTATTATTATTCACATT * * 40255095 ATATATTTTTTCATGTATATTATTATTCACATT 1 ATATATTATTTCATAT-TATTATTATTCACATT 40255128 AT-T-TT-TTTCATATTA 1 ATATATTATTTCATATTA 40255143 AATTGATATT Statistics Matches: 42, Mismatches: 3, Indels: 7 0.81 0.06 0.13 Matches are distributed among these distances: 29 2 0.05 30 21 0.50 31 10 0.24 32 3 0.07 33 6 0.14 ACGTcount: A:0.31, C:0.09, G:0.01, T:0.59 Consensus pattern (32 bp): ATATATTATTTCATATTATTATTATTCACATT Found at i:40261822 original size:101 final size:102 Alignment explanation

Indices: 40261660--40261873 Score: 340 Period size: 101 Copynumber: 2.1 Consensus size: 102 40261650 ACTTCTGATC * * * 40261660 AGTGACAAGTGATAAGTGGTAGCCTCAGCTACACTTATCTGATCAGTGATAAGTGACAAGTGATA 1 AGTGATAAATGATAAGTGGTAGCCTCAGCTACACTTATCTGATCAGTGACAAGTGACAAGTGATA 40261725 AGTAGTAGCTTTAGCTACACTTATCTGATCAGTGACA 66 AGTAGTAGCTTTAGCTACACTTATCTGATCAGTGACA ** * * 40261762 AGTGATAAATGATAAGTGGTAGTGT-AGCTACACTTGTCTGATCAGTGACAAGTGATAAGTGATA 1 AGTGATAAATGATAAGTGGTAGCCTCAGCTACACTTATCTGATCAGTGACAAGTGACAAGTGATA * * 40261826 AGTGGTAGCTTTAGCTACACTTATCTGATCAGTGATA 66 AGTAGTAGCTTTAGCTACACTTATCTGATCAGTGACA 40261863 AGTGATAAATG 1 AGTGATAAATG 40261874 TGATCAGTGT Statistics Matches: 103, Mismatches: 9, Indels: 1 0.91 0.08 0.01 Matches are distributed among these distances: 101 82 0.80 102 21 0.20 ACGTcount: A:0.33, C:0.14, G:0.24, T:0.30 Consensus pattern (102 bp): AGTGATAAATGATAAGTGGTAGCCTCAGCTACACTTATCTGATCAGTGACAAGTGACAAGTGATA AGTAGTAGCTTTAGCTACACTTATCTGATCAGTGACA Found at i:40261868 original size:51 final size:51 Alignment explanation

Indices: 40261655--40261870 Score: 326 Period size: 51 Copynumber: 4.3 Consensus size: 51 40261645 TGAGTACTTC * * * * 40261655 TGATCAGTGACAAGTGATAAGTGGTAGCCTCAGCTACACTTATCTGATCAG 1 TGATAAGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAG * * 40261706 TGATAAGTGACAAGTGATAAGTAGTAGCTTTAGCTACACTTATCTGATCAG 1 TGATAAGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAG * * * * 40261757 TGACAAGTGATAAATGATAAGTGGTAG-TGTAGCTACACTTGTCTGATCAG 1 TGATAAGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAG * 40261807 TGACAAGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAG 1 TGATAAGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAG 40261858 TGATAAGTGATAA 1 TGATAAGTGATAA 40261871 ATGTGATCAG Statistics Matches: 150, Mismatches: 14, Indels: 2 0.90 0.08 0.01 Matches are distributed among these distances: 50 47 0.31 51 103 0.69 ACGTcount: A:0.32, C:0.14, G:0.24, T:0.30 Consensus pattern (51 bp): TGATAAGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAG Found at i:40268846 original size:21 final size:21 Alignment explanation

Indices: 40268820--40268860 Score: 73 Period size: 21 Copynumber: 2.0 Consensus size: 21 40268810 AGACGAGCAA * 40268820 TACTCCAAAGCAGGTGGAGTG 1 TACTCCAAAACAGGTGGAGTG 40268841 TACTCCAAAACAGGTGGAGT 1 TACTCCAAAACAGGTGGAGT 40268861 TTGAGCAGAT Statistics Matches: 19, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 21 19 1.00 ACGTcount: A:0.32, C:0.20, G:0.29, T:0.20 Consensus pattern (21 bp): TACTCCAAAACAGGTGGAGTG Found at i:40272228 original size:14 final size:14 Alignment explanation

Indices: 40272209--40272235 Score: 54 Period size: 14 Copynumber: 1.9 Consensus size: 14 40272199 TAATGACCTT 40272209 AATTGAGAATGCCC 1 AATTGAGAATGCCC 40272223 AATTGAGAATGCC 1 AATTGAGAATGCC 40272236 TAGAGAATAG Statistics Matches: 13, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 14 13 1.00 ACGTcount: A:0.37, C:0.19, G:0.22, T:0.22 Consensus pattern (14 bp): AATTGAGAATGCCC Found at i:40274651 original size:40 final size:40 Alignment explanation

Indices: 40274569--40274651 Score: 105 Period size: 40 Copynumber: 2.1 Consensus size: 40 40274559 TTCATGCACA * * * * * 40274569 CAAGAATTCATGCACATAATTTGTCCGGGTAAAGTACGTG 1 CAAGAATCCATGCACATAATTTGCCCGGCTAAAATACATG 40274609 CAAGAATCCATGCACATAAGTTT-CCCGGCTAAAATACATG 1 CAAGAATCCATGCACATAA-TTTGCCCGGCTAAAATACATG 40274649 CAA 1 CAA 40274652 CAGGAGATGT Statistics Matches: 37, Mismatches: 5, Indels: 2 0.84 0.11 0.05 Matches are distributed among these distances: 40 34 0.92 41 3 0.08 ACGTcount: A:0.36, C:0.22, G:0.18, T:0.24 Consensus pattern (40 bp): CAAGAATCCATGCACATAATTTGCCCGGCTAAAATACATG Found at i:40276685 original size:12 final size:13 Alignment explanation

Indices: 40276667--40276715 Score: 57 Period size: 14 Copynumber: 3.8 Consensus size: 13 40276657 AAAAAATATG 40276667 ATATTTAATAATA 1 ATATTTAATAATA 40276680 AT-TTTAA-AATA 1 ATATTTAATAATA * 40276691 GTATTTAATATATA 1 ATATTTAATA-ATA * 40276705 ATATATAATAA 1 ATATTTAATAA 40276716 AAAAATTATA Statistics Matches: 30, Mismatches: 3, Indels: 6 0.77 0.08 0.15 Matches are distributed among these distances: 11 5 0.17 12 10 0.33 13 4 0.13 14 11 0.37 ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45 Consensus pattern (13 bp): ATATTTAATAATA Found at i:40276714 original size:24 final size:24 Alignment explanation

Indices: 40276659--40276712 Score: 63 Period size: 26 Copynumber: 2.1 Consensus size: 24 40276649 TACTTATAAA * 40276659 AAAATATGATATTTAATAATAATTTT 1 AAAATA-G-TATTTAATAATAATTAT 40276685 AAAATAGTATTTAATATATAATATAT 1 AAAATAGTATTTAATA-ATAAT-TAT 40276711 AA 1 AA 40276713 TAAAAAAATT Statistics Matches: 25, Mismatches: 1, Indels: 4 0.83 0.03 0.13 Matches are distributed among these distances: 24 9 0.36 25 6 0.24 26 10 0.40 ACGTcount: A:0.54, C:0.00, G:0.04, T:0.43 Consensus pattern (24 bp): AAAATAGTATTTAATAATAATTAT Found at i:40277052 original size:22 final size:21 Alignment explanation

Indices: 40276995--40277081 Score: 79 Period size: 22 Copynumber: 4.0 Consensus size: 21 40276985 AACTTTTGAT * 40276995 AATA-ATAATATAGATAAAA-A 1 AATACATAATA-ATATAAAATA * * 40277015 AATATATAATAGTATAAAATA 1 AATACATAATAATATAAAATA 40277036 AATGACATAATAATATAAAATA 1 AAT-ACATAATAATATAAAATA * 40277058 AATATAATATATAATATGAAAATA 1 AATA-CATA-ATAATAT-AAAATA 40277082 TATATGTAAA Statistics Matches: 56, Mismatches: 5, Indels: 8 0.81 0.07 0.12 Matches are distributed among these distances: 20 10 0.18 21 11 0.20 22 22 0.39 23 7 0.12 24 6 0.11 ACGTcount: A:0.64, C:0.01, G:0.05, T:0.30 Consensus pattern (21 bp): AATACATAATAATATAAAATA Found at i:40277137 original size:45 final size:41 Alignment explanation

Indices: 40276995--40277160 Score: 109 Period size: 45 Copynumber: 3.8 Consensus size: 41 40276985 AACTTTTGAT * * * * * 40276995 AATAATAATATAGATAAAAAAATATATAATAGTAT-AAAATA 1 AATAATAAAATA-ATATAAATATATAAAATAATATGAAAATA * * * 40277036 AATGACATAATAATATAAAATAAATATAATATATAATATGAAAATA 1 AATAATAAAATAATAT-AAAT--ATATAA-A-ATAATATGAAAATA * * 40277082 TATATGTAAAAATAATATATAATATATATAAATAATATGAATAATA 1 AATA-AT-AAAATAATATA-AATATATA-AAATAATATGAA-AATA * 40277128 AATAATAAAATAATTATATAATATATAATATAA 1 AATAATAAAATAA-TATA-AATATATAAAATAA 40277161 GAATAAGATT Statistics Matches: 97, Mismatches: 16, Indels: 21 0.72 0.12 0.16 Matches are distributed among these distances: 40 3 0.03 41 11 0.11 43 5 0.05 44 13 0.13 45 30 0.31 46 21 0.22 47 2 0.02 48 12 0.12 ACGTcount: A:0.63, C:0.01, G:0.04, T:0.33 Consensus pattern (41 bp): AATAATAAAATAATATAAATATATAAAATAATATGAAAATA Found at i:40277188 original size:52 final size:50 Alignment explanation

Indices: 40277093--40277208 Score: 119 Period size: 52 Copynumber: 2.3 Consensus size: 50 40277083 ATATGTAAAA * * * 40277093 ATAATATATAATATATATAAATAATATGAATAATAAATAATAAAATAATTAT 1 ATAATATATAATATATATAAATAAGATGAAAAATAAACAATAAAA-AATT-T * * 40277145 ATAATATATAATATA-A-GAATAAGATTAAAAATAAAACAGATAAAAAATTT 1 ATAATATATAATATATATAAATAAGATGAAAAAT-AAACA-ATAAAAAATTT * 40277195 ATATTTATATAATA 1 ATA-ATATATAATA 40277209 ACAACAGAAA Statistics Matches: 55, Mismatches: 6, Indels: 7 0.81 0.09 0.10 Matches are distributed among these distances: 50 16 0.29 51 18 0.33 52 21 0.38 ACGTcount: A:0.61, C:0.01, G:0.03, T:0.34 Consensus pattern (50 bp): ATAATATATAATATATATAAATAAGATGAAAAATAAACAATAAAAAATTT Found at i:40289293 original size:25 final size:26 Alignment explanation

Indices: 40289260--40289320 Score: 74 Period size: 25 Copynumber: 2.4 Consensus size: 26 40289250 TATTATTTTG 40289260 AAAT-TTAAAATATATAAAATCTA-AA 1 AAATATTAAAATATAT-AAATCTACAA * * 40289285 AAA-ATTAAAATTTATAAATTTACAA 1 AAATATTAAAATATATAAATCTACAA 40289310 AAATATTAAAA 1 AAATATTAAAA 40289321 ATAATTTTTG Statistics Matches: 31, Mismatches: 2, Indels: 5 0.82 0.05 0.13 Matches are distributed among these distances: 24 6 0.19 25 18 0.58 26 7 0.23 ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33 Consensus pattern (26 bp): AAATATTAAAATATATAAATCTACAA Found at i:40289521 original size:26 final size:24 Alignment explanation

Indices: 40289492--40289540 Score: 62 Period size: 24 Copynumber: 2.0 Consensus size: 24 40289482 AAAATCTGAT 40289492 ATTTTATAATATTTTACATTTTATAC 1 ATTTT-TAATATTTT-CATTTTATAC * * 40289518 ATTTTTTATATTTTTATTTTATA 1 ATTTTTAATATTTTCATTTTATA 40289541 TAAATTATAT Statistics Matches: 21, Mismatches: 2, Indels: 2 0.84 0.08 0.08 Matches are distributed among these distances: 24 8 0.38 25 8 0.38 26 5 0.24 ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65 Consensus pattern (24 bp): ATTTTTAATATTTTCATTTTATAC Found at i:40289530 original size:18 final size:17 Alignment explanation

Indices: 40289490--40289531 Score: 57 Period size: 18 Copynumber: 2.4 Consensus size: 17 40289480 ATAAAATCTG 40289490 ATATTTTATAATATTTT 1 ATATTTTATAATATTTT * * 40289507 ACATTTTATACATTTTTT 1 ATATTTTATA-ATATTTT 40289525 ATATTTT 1 ATATTTT 40289532 TATTTTATAT Statistics Matches: 21, Mismatches: 3, Indels: 1 0.84 0.12 0.04 Matches are distributed among these distances: 17 9 0.43 18 12 0.57 ACGTcount: A:0.31, C:0.05, G:0.00, T:0.64 Consensus pattern (17 bp): ATATTTTATAATATTTT Found at i:40292723 original size:40 final size:40 Alignment explanation

Indices: 40292687--40292765 Score: 124 Period size: 39 Copynumber: 2.0 Consensus size: 40 40292677 CACTAAAGAT * 40292687 TGAGCATTAGTGGCGTTTTT-AAAAAAATGCCGCTAAAAA 1 TGAGCATTAGCGGCGTTTTTCAAAAAAATGCCGCTAAAAA * * 40292726 TGAGCATTAGCGGCGTTTTTCAAAAAAACGCCGCAAAAAA 1 TGAGCATTAGCGGCGTTTTTCAAAAAAATGCCGCTAAAAA 40292766 CCTTAGCCCA Statistics Matches: 36, Mismatches: 3, Indels: 1 0.90 0.08 0.03 Matches are distributed among these distances: 39 19 0.53 40 17 0.47 ACGTcount: A:0.39, C:0.16, G:0.20, T:0.24 Consensus pattern (40 bp): TGAGCATTAGCGGCGTTTTTCAAAAAAATGCCGCTAAAAA Found at i:40292741 original size:39 final size:39 Alignment explanation

Indices: 40292612--40292765 Score: 139 Period size: 40 Copynumber: 3.8 Consensus size: 39 40292602 AGCGGCACTT ** * * 40292612 TTAGCGGCGTTTGGACAAAAAACGCCGGTAAAAATCAAGCA 1 TTAGCGGCGTTTTTA-AAAAAACGCCGCTAAAAAT-GAGCA * ** * * * 40292653 TTAGCGGCGCTTTCT-GGAAATCGCCACTAAAGATTGAGCA 1 TTAGCGGCG-TTTTTAAAAAAACGCCGCTAAA-AATGAGCA * * 40292693 TTAGTGGCGTTTTTAAAAAAATGCCGCTAAAAATGAGCA 1 TTAGCGGCGTTTTTAAAAAAACGCCGCTAAAAATGAGCA * 40292732 TTAGCGGCGTTTTTCAAAAAAACGCCGCAAAAAA 1 TTAGCGGCGTTTTT-AAAAAAACGCCGCTAAAAA 40292766 CCTTAGCCCA Statistics Matches: 89, Mismatches: 20, Indels: 9 0.75 0.17 0.08 Matches are distributed among these distances: 39 24 0.27 40 51 0.57 41 11 0.12 42 3 0.03 ACGTcount: A:0.36, C:0.19, G:0.22, T:0.23 Consensus pattern (39 bp): TTAGCGGCGTTTTTAAAAAAACGCCGCTAAAAATGAGCA Found at i:40292857 original size:40 final size:40 Alignment explanation

Indices: 40292804--40292902 Score: 130 Period size: 40 Copynumber: 2.5 Consensus size: 40 40292794 ATTTCGTGGC * * 40292804 TTTGAAAAACGCCGCTAATGCCT-GGGTCTTTAGCGGC-TT 1 TTTGAAAAGCGCCGCTAATG-CTAGGGGCTTTAGCGGCGTT * 40292843 TTTGGAAAAGCGCCGCTAATGGTAGGGGCTTTAGCGGCGTT 1 TTT-GAAAAGCGCCGCTAATGCTAGGGGCTTTAGCGGCGTT 40292884 TTTGATAAAGCGCCGCTAA 1 TTTGA-AAAGCGCCGCTAA 40292903 AAACATTTTA Statistics Matches: 53, Mismatches: 3, Indels: 6 0.85 0.05 0.10 Matches are distributed among these distances: 39 4 0.08 40 31 0.58 41 18 0.34 ACGTcount: A:0.22, C:0.20, G:0.29, T:0.28 Consensus pattern (40 bp): TTTGAAAAGCGCCGCTAATGCTAGGGGCTTTAGCGGCGTT Found at i:40293154 original size:15 final size:14 Alignment explanation

Indices: 40293143--40293176 Score: 50 Period size: 14 Copynumber: 2.4 Consensus size: 14 40293133 GAGTATGTAT 40293143 TTAAGGATTATGGA 1 TTAAGGATTATGGA * * 40293157 TTAGGGATTATGGT 1 TTAAGGATTATGGA 40293171 TTAAGG 1 TTAAGG 40293177 GTTGAGATTT Statistics Matches: 17, Mismatches: 3, Indels: 0 0.85 0.15 0.00 Matches are distributed among these distances: 14 17 1.00 ACGTcount: A:0.29, C:0.00, G:0.32, T:0.38 Consensus pattern (14 bp): TTAAGGATTATGGA Found at i:40293230 original size:22 final size:22 Alignment explanation

Indices: 40293168--40293251 Score: 73 Period size: 22 Copynumber: 3.9 Consensus size: 22 40293158 TAGGGATTAT * * * 40293168 GGTTTAAGGGTTGAGATTTAA- 1 GGTTTAGGGGTTAAGAGTTAAG * * 40293189 GGTTTAGGGGTT-AGTGGTTAGG 1 GGTTTAGGGGTTAAG-AGTTAAG 40293211 GGTTTAGGGGTTAAGAGTTAAG 1 GGTTTAGGGGTTAAGAGTTAAG * * * 40293233 GATTTAGGGTTTATGAGTT 1 GGTTTAGGGGTTAAGAGTT 40293252 CATGGGTCAA Statistics Matches: 51, Mismatches: 9, Indels: 5 0.78 0.14 0.08 Matches are distributed among these distances: 20 2 0.04 21 14 0.27 22 33 0.65 23 2 0.04 ACGTcount: A:0.23, C:0.00, G:0.39, T:0.38 Consensus pattern (22 bp): GGTTTAGGGGTTAAGAGTTAAG Found at i:40293321 original size:23 final size:23 Alignment explanation

Indices: 40293281--40293334 Score: 74 Period size: 22 Copynumber: 2.3 Consensus size: 23 40293271 TTGGGTTTAG * 40293281 ATTAATTATTTTTTAATTTAT-T 1 ATTAAATATTTTTTAATTTATAT * 40293303 TTTAAATATTTTTTAAATTTATAT 1 ATTAAATATTTTTT-AATTTATAT 40293327 ATTAAATA 1 ATTAAATA 40293335 ATTTCATATA Statistics Matches: 27, Mismatches: 3, Indels: 2 0.84 0.09 0.06 Matches are distributed among these distances: 22 12 0.44 23 7 0.26 24 8 0.30 ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61 Consensus pattern (23 bp): ATTAAATATTTTTTAATTTATAT Found at i:40293556 original size:21 final size:21 Alignment explanation

Indices: 40293532--40293572 Score: 73 Period size: 21 Copynumber: 2.0 Consensus size: 21 40293522 GATTTAAGGT 40293532 TTAGGGATTAAGAGTTAGGGG 1 TTAGGGATTAAGAGTTAGGGG * 40293553 TTAGGGGTTAAGAGTTAGGG 1 TTAGGGATTAAGAGTTAGGG 40293573 ATTTAGGGTT Statistics Matches: 19, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 21 19 1.00 ACGTcount: A:0.27, C:0.00, G:0.44, T:0.29 Consensus pattern (21 bp): TTAGGGATTAAGAGTTAGGGG Found at i:40293581 original size:21 final size:20 Alignment explanation

Indices: 40293529--40293582 Score: 72 Period size: 21 Copynumber: 2.5 Consensus size: 20 40293519 TAGGATTTAA 40293529 GGTTTAGGGATTAAGAGTTAG 1 GGTTTAGGG-TTAAGAGTTAG * 40293550 GGGTTAGGGGTTAAGAGTTAG 1 GGTTTA-GGGTTAAGAGTTAG 40293571 GGATTTAGGGTT 1 GG-TTTAGGGTT 40293583 TCAATGGTCG Statistics Matches: 29, Mismatches: 2, Indels: 4 0.83 0.06 0.11 Matches are distributed among these distances: 21 23 0.79 22 6 0.21 ACGTcount: A:0.24, C:0.00, G:0.43, T:0.33 Consensus pattern (20 bp): GGTTTAGGGTTAAGAGTTAG Found at i:40298175 original size:43 final size:43 Alignment explanation

Indices: 40298128--40298373 Score: 278 Period size: 43 Copynumber: 5.7 Consensus size: 43 40298118 ATGGCACTTT * * * * * 40298128 TAGCGGCGTTTGCGAAAAAAACGTCGCTAAAAGTCATGATCTA 1 TAGCGGCGTTTGTGAAAAAAGCGCCGCTAAAGGTCCTGATCTA * * * * 40298171 TAGCGGCATTTATAAAAAAAGCGCCGCTAAAGGTCTTGATCTA 1 TAGCGGCGTTTGTGAAAAAAGCGCCGCTAAAGGTCCTGATCTA * * 40298214 TAGCGGCGTTTGTG-TAAAAGTGCCGCTAAAGGTCCTGATCTA 1 TAGCGGCGTTTGTGAAAAAAGCGCCGCTAAAGGTCCTGATCTA * ** * * * 40298256 TAGCGGCATTTGTGGGAAAAGTGTCGCTAAAGGTTCTGATCTA 1 TAGCGGCGTTTGTGAAAAAAGCGCCGCTAAAGGTCCTGATCTA ** * * 40298299 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGGTCTT 1 TAGCGGCGTTTGTGAAAAAAGCGCCGCTAAAGGTCCTGATCTA ** 40298342 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAG 1 TAGCGGCGTTTGTGAAAAAAGCGCCGCTAAAG 40298374 TTAGCGACGC Statistics Matches: 178, Mismatches: 24, Indels: 2 0.87 0.12 0.01 Matches are distributed among these distances: 42 38 0.21 43 140 0.79 ACGTcount: A:0.27, C:0.18, G:0.29, T:0.26 Consensus pattern (43 bp): TAGCGGCGTTTGTGAAAAAAGCGCCGCTAAAGGTCCTGATCTA Found at i:40298253 original size:85 final size:86 Alignment explanation

Indices: 40298128--40298373 Score: 307 Period size: 85 Copynumber: 2.9 Consensus size: 86 40298118 ATGGCACTTT * ** * * * * * *** 40298128 TAGCGGCGTTTGCGAAAAAAACGTCGCTAAAAGTCATGATCTATAGCGGCATTTATAAAAAAAGC 1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGATCTATAGCGGCATTTGTGGGAAAAGC 40298193 GCCGCTAAAGG-TCTTGATCTA 66 GCCGCTAAAGGTTC-TGATCTA * * * 40298214 TAGCGGCGTTTGT-GTAAAAGTGCCGCTAAAGGTCCTGATCTATAGCGGCATTTGTGGGAAAAGT 1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGATCTATAGCGGCATTTGTGGGAAAAGC * 40298278 GTCGCTAAAGGTTCTGATCTA 66 GCCGCTAAAGGTTCTGATCTA * * * 40298299 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGGTCTTTAGCGGCGTTTGTGGGAAAAGC 1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGATCTATAGCGGCATTTGTGGGAAAAGC 40298364 GCCGCTAAAG 66 GCCGCTAAAG 40298374 TTAGCGACGC Statistics Matches: 137, Mismatches: 21, Indels: 4 0.85 0.13 0.02 Matches are distributed among these distances: 85 69 0.50 86 68 0.50 ACGTcount: A:0.27, C:0.18, G:0.29, T:0.26 Consensus pattern (86 bp): TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGATCTATAGCGGCATTTGTGGGAAAAGC GCCGCTAAAGGTTCTGATCTA Found at i:40298473 original size:22 final size:22 Alignment explanation

Indices: 40298445--40298487 Score: 77 Period size: 22 Copynumber: 2.0 Consensus size: 22 40298435 CAGTGGCGCT * 40298445 AAAAAGCGCCGCTAAAGGCCTA 1 AAAAAGCGCCGCTAAAAGCCTA 40298467 AAAAAGCGCCGCTAAAAGCCT 1 AAAAAGCGCCGCTAAAAGCCT 40298488 GTTTTGGTGT Statistics Matches: 20, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 22 20 1.00 ACGTcount: A:0.42, C:0.28, G:0.21, T:0.09 Consensus pattern (22 bp): AAAAAGCGCCGCTAAAAGCCTA Found at i:40303838 original size:43 final size:44 Alignment explanation

Indices: 40303741--40303893 Score: 145 Period size: 43 Copynumber: 3.5 Consensus size: 44 40303731 ATCGATATGT * * * 40303741 GATTATATGTAAGACCATGTTTGGGACATTGGCAT-TGTATTGA 1 GATTACATGTAAGACCATGTCTGGGACATTGGCATCTGTAATGA * 40303784 GATTACATGTAAGACCATGTCTGGGACATTGGCATCAT-TAAT-C 1 GATTACATGTAAGACCATGTCTGGGACATTGGCATC-TGTAATGA *** * * * 40303827 GATTTTGTGTAAGACCCTGTCTGGGACAGTGGCATC-G-ATATGT 1 GATTACATGTAAGACCATGTCTGGGACATTGGCATCTGTA-ATGA * * 40303870 GATAACATGTAAGACCATATCTGG 1 GATTACATGTAAGACCATGTCTGG 40303894 AATATGATAT Statistics Matches: 89, Mismatches: 16, Indels: 10 0.77 0.14 0.09 Matches are distributed among these distances: 41 1 0.01 42 2 0.02 43 82 0.92 44 3 0.03 45 1 0.01 ACGTcount: A:0.28, C:0.15, G:0.25, T:0.32 Consensus pattern (44 bp): GATTACATGTAAGACCATGTCTGGGACATTGGCATCTGTAATGA Found at i:40308159 original size:42 final size:42 Alignment explanation

Indices: 40308111--40308228 Score: 139 Period size: 43 Copynumber: 2.8 Consensus size: 42 40308101 TTAGGGTTAT * * 40308111 TGAGACTTCGTGTAAGACCATATTTGGGATATGACATCGATA 1 TGAGACTTCGTGTAAGACCATATCTGGGATATGACATCAATA * * * * 40308153 TGAGACTTCGTATAAGACCATAGCTGGGCTATTGGCATCAATA 1 TGAGACTTCGTGTAAGACCATATCTGGGATA-TGACATCAATA * * 40308196 TGAGA-TCCCATGTAAGACCATATCTGGGATATG 1 TGAGACT-TCGTGTAAGACCATATCTGGGATATG 40308229 GCATTGGTAT Statistics Matches: 63, Mismatches: 11, Indels: 4 0.81 0.14 0.05 Matches are distributed among these distances: 42 30 0.48 43 33 0.52 ACGTcount: A:0.31, C:0.17, G:0.24, T:0.29 Consensus pattern (42 bp): TGAGACTTCGTGTAAGACCATATCTGGGATATGACATCAATA Found at i:40309033 original size:47 final size:46 Alignment explanation

Indices: 40308974--40309066 Score: 159 Period size: 47 Copynumber: 2.0 Consensus size: 46 40308964 TATGTGAACG * 40308974 GAAGGGTGACAAAATGGCTTGGTAAATAGCCTTATTTTATGTGCATA 1 GAAGGGTGACAAAATGGCTTGGTAAATAGCCTTATTTT-TGTCCATA * 40309021 GAAGGGTGACAAAATGGCTTGGTAAATAGCCTTGTTTTTGTCCATA 1 GAAGGGTGACAAAATGGCTTGGTAAATAGCCTTATTTTTGTCCATA 40309067 TGGGTAGACA Statistics Matches: 44, Mismatches: 2, Indels: 1 0.94 0.04 0.02 Matches are distributed among these distances: 46 7 0.16 47 37 0.84 ACGTcount: A:0.30, C:0.12, G:0.26, T:0.32 Consensus pattern (46 bp): GAAGGGTGACAAAATGGCTTGGTAAATAGCCTTATTTTTGTCCATA Found at i:40328662 original size:18 final size:17 Alignment explanation

Indices: 40328626--40328668 Score: 50 Period size: 18 Copynumber: 2.5 Consensus size: 17 40328616 AGGCCAAGTT * 40328626 GGGCATGTAGGCTACAC 1 GGGCATGTAGGCCACAC * 40328643 GGGCATGTGGGACCACAC 1 GGGCATGTAGG-CCACAC * 40328661 GGCCATGT 1 GGGCATGT 40328669 CACACGGGCA Statistics Matches: 22, Mismatches: 3, Indels: 1 0.85 0.12 0.04 Matches are distributed among these distances: 17 10 0.45 18 12 0.55 ACGTcount: A:0.21, C:0.26, G:0.37, T:0.16 Consensus pattern (17 bp): GGGCATGTAGGCCACAC Found at i:40336290 original size:37 final size:37 Alignment explanation

Indices: 40336193--40336290 Score: 151 Period size: 37 Copynumber: 2.6 Consensus size: 37 40336183 AGCGCTATAT * * * 40336193 AAATTGACACCTAGTGTCTCATCAGTTAAACGGAAGC 1 AAATTGACACCCAGTGCCTCATCGGTTAAACGGAAGC * * 40336230 AAATTGATACCCAGTGCCTCATCGGTTAAACTGAAGC 1 AAATTGACACCCAGTGCCTCATCGGTTAAACGGAAGC 40336267 AAATTGACACCCAGTGCCTCATCG 1 AAATTGACACCCAGTGCCTCATCG 40336291 AATTCACGTT Statistics Matches: 55, Mismatches: 6, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 37 55 1.00 ACGTcount: A:0.33, C:0.26, G:0.18, T:0.23 Consensus pattern (37 bp): AAATTGACACCCAGTGCCTCATCGGTTAAACGGAAGC Found at i:40341645 original size:80 final size:80 Alignment explanation

Indices: 40341543--40341719 Score: 239 Period size: 80 Copynumber: 2.2 Consensus size: 80 40341533 AATACATCTG * * 40341543 AAACACACGAAAAAAAGCCTCATAAGAGTTGATCCAATCGAAACACCCCAAACAGAAACTCATAA 1 AAACACACCAAAAAAAGCCTCATAAGAGCTGATCCAATCGAAACACCCCAAACAGAAACTCATAA * 40341608 GGGCTGATCCAACAA 66 GAGCTGATCCAACAA * * * * 40341623 AAACACACCAAACAAAAG-CTCATGAGAGCTGATCCAATCGAAACACGCCAAATAGAAGCTCATA 1 AAACACACCAAA-AAAAGCCTCATAAGAGCTGATCCAATCGAAACACCCCAAACAGAAACTCATA ** 40341687 AGAGCTGATCCAACCG 65 AGAGCTGATCCAACAA * * 40341703 AAACACGCCAAATAAAG 1 AAACACACCAAAAAAAG 40341720 AGTATAACAC Statistics Matches: 85, Mismatches: 11, Indels: 3 0.86 0.11 0.03 Matches are distributed among these distances: 79 4 0.05 80 76 0.89 81 5 0.06 ACGTcount: A:0.47, C:0.27, G:0.15, T:0.12 Consensus pattern (80 bp): AAACACACCAAAAAAAGCCTCATAAGAGCTGATCCAATCGAAACACCCCAAACAGAAACTCATAA GAGCTGATCCAACAA Found at i:40341715 original size:40 final size:40 Alignment explanation

Indices: 40341503--40341716 Score: 205 Period size: 40 Copynumber: 5.3 Consensus size: 40 40341493 TAGATCAACT * * * * * * * 40341503 AAACAGACCAGATAGAAGCTCGTAAGAGCTAATACATCTG 1 AAACACACCAAATAGAAGCTCATAAGAGCTGATCCAACCG * * * * 40341543 AAACACACGAAA-AAAAGCCTCATAAGAGTTGATCCAATCG 1 AAACACACCAAATAGAAG-CTCATAAGAGCTGATCCAACCG * * * * ** 40341583 AAACACCCCAAACAGAAACTCATAAGGGCTGATCCAACAA 1 AAACACACCAAATAGAAGCTCATAAGAGCTGATCCAACCG * * * * 40341623 AAACACACCAAACAAAAGCTCATGAGAGCTGATCCAATCG 1 AAACACACCAAATAGAAGCTCATAAGAGCTGATCCAACCG * 40341663 AAACACGCCAAATAGAAGCTCATAAGAGCTGATCCAACCG 1 AAACACACCAAATAGAAGCTCATAAGAGCTGATCCAACCG * 40341703 AAACACGCCAAATA 1 AAACACACCAAATA 40341717 AAGAGTATAA Statistics Matches: 139, Mismatches: 33, Indels: 4 0.79 0.19 0.02 Matches are distributed among these distances: 39 4 0.03 40 132 0.95 41 3 0.02 ACGTcount: A:0.46, C:0.26, G:0.15, T:0.13 Consensus pattern (40 bp): AAACACACCAAATAGAAGCTCATAAGAGCTGATCCAACCG Found at i:40343250 original size:23 final size:23 Alignment explanation

Indices: 40343168--40343254 Score: 92 Period size: 21 Copynumber: 4.0 Consensus size: 23 40343158 CCTGATCAGT * 40343168 ATACGACACATAAAGTGCCT-AA 1 ATACGACACACAAAGTGCCTGAA * * 40343190 A-ACGACACACGAGGTGCCTG-- 1 ATACGACACACAAAGTGCCTGAA * * 40343210 ATACGACACACGAGGTGCCTGAA 1 ATACGACACACAAAGTGCCTGAA * 40343233 ATACGACACATAAAGTGCCTGA 1 ATACGACACACAAAGTGCCTGA 40343255 TCAGTAAAGC Statistics Matches: 55, Mismatches: 6, Indels: 7 0.81 0.09 0.10 Matches are distributed among these distances: 20 1 0.02 21 34 0.62 22 1 0.02 23 19 0.35 ACGTcount: A:0.38, C:0.25, G:0.22, T:0.15 Consensus pattern (23 bp): ATACGACACACAAAGTGCCTGAA Found at i:40351078 original size:21 final size:21 Alignment explanation

Indices: 40351052--40351134 Score: 76 Period size: 21 Copynumber: 3.9 Consensus size: 21 40351042 TGATCAGTAT * 40351052 ACGACACATAAAGTGCCTAAA 1 ACGACACACAAAGTGCCTAAA * * * * 40351073 ACGACACACGAGGTGCCTGAT 1 ACGACACACAAAGTGCCTAAA * * 40351094 ACGACACACGAGGTGCCTAAAA 1 ACGACACACAAAGTGCCT-AAA * 40351116 TACGACACATAAAGTGCCT 1 -ACGACACACAAAGTGCCT 40351135 GATCAGTAAA Statistics Matches: 50, Mismatches: 10, Indels: 2 0.81 0.16 0.03 Matches are distributed among these distances: 21 34 0.68 22 1 0.02 23 15 0.30 ACGTcount: A:0.39, C:0.27, G:0.20, T:0.14 Consensus pattern (21 bp): ACGACACACAAAGTGCCTAAA Found at i:40351118 original size:23 final size:22 Alignment explanation

Indices: 40351050--40351124 Score: 91 Period size: 21 Copynumber: 3.5 Consensus size: 22 40351040 CCTGATCAGT ** * 40351050 ATACGACACATAAAGTGCCTAA 1 ATACGACACACGAGGTGCCTAA * 40351072 A-ACGACACACGAGGTGCCT-G 1 ATACGACACACGAGGTGCCTAA 40351092 ATACGACACACGAGGTGCCTAAA 1 ATACGACACACGAGGTGCCT-AA 40351115 ATACGACACA 1 ATACGACACA 40351125 TAAAGTGCCT Statistics Matches: 45, Mismatches: 5, Indels: 5 0.82 0.09 0.09 Matches are distributed among these distances: 20 1 0.02 21 33 0.73 22 1 0.02 23 10 0.22 ACGTcount: A:0.40, C:0.27, G:0.20, T:0.13 Consensus pattern (22 bp): ATACGACACACGAGGTGCCTAA Found at i:40355223 original size:86 final size:85 Alignment explanation

Indices: 40355120--40355281 Score: 227 Period size: 86 Copynumber: 1.9 Consensus size: 85 40355110 ACGTTTATTA * * ** 40355120 AAAAAACGTCGCTAAAAGTGCTGGCTTTTAGCGACGTTTGTTAAAAAAGCACAGCTAAAAGTGCA 1 AAAAAACGCCGCTAAAAGTGCTGCCTTTTAGCGACGTTTCCTAAAAAAGCACAGCTAAAAGT-CA 40355185 -GGCTTTTTAGCGTCGTTTGCT 65 TGGC-TTTTAGCGTCGTTTGCT * * * * 40355206 AAAAAATGCCGCTAAAAGTGCTGCCTTTTAGCGGCGTTTCCTAAAAAAGCGCCGCTAAAAGTCAT 1 AAAAAACGCCGCTAAAAGTGCTGCCTTTTAGCGACGTTTCCTAAAAAAGCACAGCTAAAAGTCAT 40355271 GGCTTTTAGCG 66 GGCTTTTAGCG 40355282 GCGCTTTTCC Statistics Matches: 67, Mismatches: 8, Indels: 3 0.86 0.10 0.04 Matches are distributed among these distances: 85 10 0.15 86 57 0.85 ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27 Consensus pattern (85 bp): AAAAAACGCCGCTAAAAGTGCTGCCTTTTAGCGACGTTTCCTAAAAAAGCACAGCTAAAAGTCAT GGCTTTTAGCGTCGTTTGCT Found at i:40355282 original size:43 final size:43 Alignment explanation

Indices: 40355118--40355284 Score: 203 Period size: 43 Copynumber: 3.9 Consensus size: 43 40355108 AAACGTTTAT * * * * 40355118 TAAAAAAACGTCGCTAAAAGTGCTGGCTTTTAGCGACGTTTGT 1 TAAAAAAGCGCCGCTAAAAGTGCTGGCTTTTAGCGGCGTTTGC * * * * 40355161 TAAAAAAGCACAGCTAAAAGTGCAGGCTTTTTAGCGTCGTTTGC 1 TAAAAAAGCGCCGCTAAAAGTGCTGGC-TTTTAGCGGCGTTTGC * * * 40355205 TAAAAAA-TGCCGCTAAAAGTGCTGCCTTTTAGCGGCGTTTCC 1 TAAAAAAGCGCCGCTAAAAGTGCTGGCTTTTAGCGGCGTTTGC 40355247 TAAAAAAGCGCCGCTAAAAGT-CATGGCTTTTAGCGGCG 1 TAAAAAAGCGCCGCTAAAAGTGC-TGGCTTTTAGCGGCG 40355285 CTTTTCCCAC Statistics Matches: 105, Mismatches: 16, Indels: 6 0.83 0.13 0.05 Matches are distributed among these distances: 42 22 0.21 43 62 0.59 44 21 0.20 ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27 Consensus pattern (43 bp): TAAAAAAGCGCCGCTAAAAGTGCTGGCTTTTAGCGGCGTTTGC Found at i:40355303 original size:86 final size:86 Alignment explanation

Indices: 40355120--40355306 Score: 225 Period size: 86 Copynumber: 2.2 Consensus size: 86 40355110 ACGTTTATTA * * ** 40355120 AAAAAACGTCGCTAAAAGTGCTGGCTTTTAGCGACGTTTGTTAAAAAAGCACAGCTAAAAGTGCA 1 AAAAAACGCCGCTAAAAGTGCTGCCTTTTAGCGACGTTTCCTAAAAAAGCACAGCTAAAAGTGCA * * 40355185 GGCTTTTTAGCGTCGTTTGCT 66 GGCTTTTTAGCGGCGTTTGCC * * * * 40355206 AAAAAATGCCGCTAAAAGTGCTGCCTTTTAGCGGCGTTTCCTAAAAAAGCGCCGCTAAAAGT-CA 1 AAAAAACGCCGCTAAAAGTGCTGCCTTTTAGCGACGTTTCCTAAAAAAGCACAGCTAAAAGTGCA * 40355270 TGGC-TTTTAGCGGCGCTTTTCC 66 -GGCTTTTTAGCGGCG-TTTGCC * * 40355292 CACAAACGCCGCTAA 1 AAAAAACGCCGCTAA 40355307 TTTTGACAGA Statistics Matches: 85, Mismatches: 14, Indels: 4 0.83 0.14 0.04 Matches are distributed among these distances: 85 12 0.14 86 73 0.86 ACGTcount: A:0.29, C:0.22, G:0.22, T:0.26 Consensus pattern (86 bp): AAAAAACGCCGCTAAAAGTGCTGCCTTTTAGCGACGTTTCCTAAAAAAGCACAGCTAAAAGTGCA GGCTTTTTAGCGGCGTTTGCC Found at i:40361323 original size:9 final size:9 Alignment explanation

Indices: 40361311--40361369 Score: 82 Period size: 9 Copynumber: 6.6 Consensus size: 9 40361301 TCCGTCAGTT * 40361311 GTTATGTAC 1 GTTATGTAA * 40361320 GTTATGTGA 1 GTTATGTAA 40361329 GTTATGTAA 1 GTTATGTAA * 40361338 ATTATGTAA 1 GTTATGTAA * 40361347 GTTATGTGA 1 GTTATGTAA 40361356 GTTATGTAA 1 GTTATGTAA 40361365 GTTAT 1 GTTAT 40361370 TTTTTAAGAT Statistics Matches: 43, Mismatches: 7, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 9 43 1.00 ACGTcount: A:0.29, C:0.02, G:0.24, T:0.46 Consensus pattern (9 bp): GTTATGTAA Found at i:40361343 original size:27 final size:27 Alignment explanation

Indices: 40361312--40361369 Score: 98 Period size: 27 Copynumber: 2.1 Consensus size: 27 40361302 CCGTCAGTTG * 40361312 TTATGTACGTTATGTGAGTTATGTAAA 1 TTATGTAAGTTATGTGAGTTATGTAAA * 40361339 TTATGTAAGTTATGTGAGTTATGTAAG 1 TTATGTAAGTTATGTGAGTTATGTAAA 40361366 TTAT 1 TTAT 40361370 TTTTTAAGAT Statistics Matches: 29, Mismatches: 2, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 27 29 1.00 ACGTcount: A:0.29, C:0.02, G:0.22, T:0.47 Consensus pattern (27 bp): TTATGTAAGTTATGTGAGTTATGTAAA Found at i:40363883 original size:25 final size:25 Alignment explanation

Indices: 40363855--40363919 Score: 76 Period size: 25 Copynumber: 2.6 Consensus size: 25 40363845 GAGAAGCAGC * 40363855 AGAGGGATGCCGACGGAGATGTAAA 1 AGAGGGATGCCGACGGAGAAGTAAA * * ** 40363880 AGAGGGATGCCAATGGAGAAGTAGC 1 AGAGGGATGCCGACGGAGAAGTAAA * 40363905 AGAGGGCTGCCGACG 1 AGAGGGATGCCGACG 40363920 ATGATGCAGA Statistics Matches: 32, Mismatches: 8, Indels: 0 0.80 0.20 0.00 Matches are distributed among these distances: 25 32 1.00 ACGTcount: A:0.32, C:0.15, G:0.42, T:0.11 Consensus pattern (25 bp): AGAGGGATGCCGACGGAGAAGTAAA Found at i:40365935 original size:19 final size:19 Alignment explanation

Indices: 40365911--40365949 Score: 69 Period size: 19 Copynumber: 2.1 Consensus size: 19 40365901 GAAAGGCTGA * 40365911 GAAAGAAAAGGGAATTGGG 1 GAAAGAAAAGGGAATCGGG 40365930 GAAAGAAAAGGGAATCGGG 1 GAAAGAAAAGGGAATCGGG 40365949 G 1 G 40365950 GAGAGAAATA Statistics Matches: 19, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 19 19 1.00 ACGTcount: A:0.46, C:0.03, G:0.44, T:0.08 Consensus pattern (19 bp): GAAAGAAAAGGGAATCGGG Found at i:40365956 original size:20 final size:19 Alignment explanation

Indices: 40365911--40365957 Score: 67 Period size: 19 Copynumber: 2.4 Consensus size: 19 40365901 GAAAGGCTGA * 40365911 GAAAGAAAAGGGAATTGGG 1 GAAAGAAAAGGGAATGGGG 40365930 GAAAGAAAAGGGAATCGGGG 1 GAAAGAAAAGGGAAT-GGGG * 40365950 GAGAGAAA 1 GAAAGAAA 40365958 TAGAAGTACA Statistics Matches: 25, Mismatches: 2, Indels: 1 0.89 0.07 0.04 Matches are distributed among these distances: 19 15 0.60 20 10 0.40 ACGTcount: A:0.49, C:0.02, G:0.43, T:0.06 Consensus pattern (19 bp): GAAAGAAAAGGGAATGGGG Found at i:40366015 original size:16 final size:19 Alignment explanation

Indices: 40365984--40366020 Score: 53 Period size: 17 Copynumber: 2.1 Consensus size: 19 40365974 GAATGGCTGA 40365984 GAAAGAAAGTGGAATT-GG 1 GAAAGAAAGTGGAATTAGG 40366002 GAAAG-AAG-GGAATTAGG 1 GAAAGAAAGTGGAATTAGG 40366019 GA 1 GA 40366021 GGGGAGAGAA Statistics Matches: 18, Mismatches: 0, Indels: 3 0.86 0.00 0.14 Matches are distributed among these distances: 16 6 0.33 17 7 0.39 18 5 0.28 ACGTcount: A:0.46, C:0.00, G:0.41, T:0.14 Consensus pattern (19 bp): GAAAGAAAGTGGAATTAGG Found at i:40366224 original size:22 final size:20 Alignment explanation

Indices: 40366197--40366253 Score: 62 Period size: 22 Copynumber: 2.6 Consensus size: 20 40366187 ATGTTTGATT 40366197 TTTTATAATTTTTATATTGAA 1 TTTTATAATTTTTATATT-AA 40366218 TTATTAT-ATCTTTTATATTAA 1 TT-TTATAAT-TTTTATATTAA 40366239 TTTTAAATAATTTTT 1 TTTT--ATAATTTTT 40366254 TTTAAAATTT Statistics Matches: 31, Mismatches: 0, Indels: 9 0.77 0.00 0.22 Matches are distributed among these distances: 20 2 0.06 21 8 0.26 22 19 0.61 23 2 0.06 ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63 Consensus pattern (20 bp): TTTTATAATTTTTATATTAA Found at i:40366682 original size:7 final size:7 Alignment explanation

Indices: 40366581--40366726 Score: 53 Period size: 7 Copynumber: 20.6 Consensus size: 7 40366571 TTTTATCTCC * 40366581 TAAACCC 1 TAAACCA * 40366588 TAAATCA 1 TAAACCA 40366595 TACAA-CA 1 TA-AACCA * * 40366602 TAACCCT 1 TAAACCA 40366609 TAAACCCA 1 TAAA-CCA * 40366617 TAACCCA 1 TAAACCA * * 40366624 TAACCCC 1 TAAACCA * * 40366631 TAATCCC 1 TAAACCA 40366638 TAACACC- 1 TAA-ACCA * 40366645 TAAACCT 1 TAAACCA * 40366652 TAAACCC 1 TAAACCA * * * 40366659 CAACCCT 1 TAAACCA 40366666 TAAACCA 1 TAAACCA * 40366673 TAAACTA 1 TAAACCA * 40366680 TAAATCA 1 TAAACCA * 40366687 TAATCCA 1 TAAACCA 40366694 TAAACCCA 1 TAAA-CCA * 40366702 TAATCCA 1 TAAACCA ** 40366709 TAATTCA 1 TAAACCA * 40366716 TAAACCT 1 TAAACCA 40366723 TAAA 1 TAAA 40366727 ATAGTAACTC Statistics Matches: 105, Mismatches: 28, Indels: 12 0.72 0.19 0.08 Matches are distributed among these distances: 6 4 0.04 7 86 0.82 8 15 0.14 ACGTcount: A:0.45, C:0.33, G:0.00, T:0.22 Consensus pattern (7 bp): TAAACCA Found at i:40366726 original size:29 final size:28 Alignment explanation

Indices: 40366663--40366726 Score: 74 Period size: 29 Copynumber: 2.2 Consensus size: 28 40366653 AAACCCCAAC * * 40366663 CCTTAAACCATAAACTATAAATCATAAT 1 CCTTAAACCATAAACCATAAATCATAAA * * * 40366691 CCATAAACCCATAATCCATAATTCATAAA 1 CCTTAAA-CCATAAACCATAAATCATAAA 40366720 CCTTAAA 1 CCTTAAA 40366727 ATAGTAACTC Statistics Matches: 29, Mismatches: 6, Indels: 1 0.81 0.17 0.03 Matches are distributed among these distances: 28 6 0.21 29 23 0.79 ACGTcount: A:0.48, C:0.25, G:0.00, T:0.27 Consensus pattern (28 bp): CCTTAAACCATAAACCATAAATCATAAA Found at i:40367037 original size:24 final size:24 Alignment explanation

Indices: 40367009--40367058 Score: 82 Period size: 24 Copynumber: 2.1 Consensus size: 24 40366999 ACCAAAATAA * 40367009 AAATTAATTTTTATATAGACTTTT 1 AAATTAATTTTTATATAAACTTTT * 40367033 AAATTAATTTTTTTATAAACTTTT 1 AAATTAATTTTTATATAAACTTTT 40367057 AA 1 AA 40367059 TAAATATACG Statistics Matches: 24, Mismatches: 2, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 24 24 1.00 ACGTcount: A:0.40, C:0.04, G:0.02, T:0.54 Consensus pattern (24 bp): AAATTAATTTTTATATAAACTTTT Found at i:40367613 original size:16 final size:16 Alignment explanation

Indices: 40367580--40367615 Score: 54 Period size: 16 Copynumber: 2.2 Consensus size: 16 40367570 CTTGTTAGGA ** 40367580 TTTAGGGGTTTACTAT 1 TTTAGGGGTTTAAGAT 40367596 TTTAGGGGTTTAAGAT 1 TTTAGGGGTTTAAGAT 40367612 TTTA 1 TTTA 40367616 AGAGTTATAT Statistics Matches: 18, Mismatches: 2, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 16 18 1.00 ACGTcount: A:0.22, C:0.03, G:0.25, T:0.50 Consensus pattern (16 bp): TTTAGGGGTTTAAGAT Found at i:40367673 original size:41 final size:41 Alignment explanation

Indices: 40367628--40367900 Score: 371 Period size: 41 Copynumber: 6.8 Consensus size: 41 40367618 AGTTATATGA * * 40367628 CTTTTAGCGGTGTTTTACCAAAAGCGTCGCTAATGCTCTGT 1 CTTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGT * * * * 40367669 CTTTTAGTGGCGTTTTACCAAAAGTGTCGCTACTGCTCTGT 1 CTTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGT * 40367710 CTTTTAGCAGCGTTTTACCAAAAGCGCCGCTAATGCTCTGT 1 CTTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGT * 40367751 CTTTTAGCGGCGTTTTACCAAAAGCGCCGCT-ACGTCTCTGT 1 CTTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATG-CTCTGT * * * 40367792 CTTTTAGTGGCGTTTTACCAAAAGCACTGCTAATGCTCTGT 1 CTTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGT * 40367833 CTTTTA---GCG--TT-CCAAAAGCGCCGCTAGTGCTCTGT 1 CTTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGT * 40367868 CTTTTAGCGGCGTTTTACTAAAAGCGCCGCTAA 1 CTTTTAGCGGCGTTTTACCAAAAGCGCCGCTAA 40367901 AGCCCTATTT Statistics Matches: 204, Mismatches: 20, Indels: 16 0.85 0.08 0.07 Matches are distributed among these distances: 35 27 0.13 36 2 0.01 38 6 0.03 40 4 0.02 41 163 0.80 42 2 0.01 ACGTcount: A:0.20, C:0.25, G:0.21, T:0.34 Consensus pattern (41 bp): CTTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGT Found at i:40379015 original size:49 final size:47 Alignment explanation

Indices: 40378931--40379435 Score: 803 Period size: 47 Copynumber: 10.6 Consensus size: 47 40378921 TATTTGAATA * * 40378931 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG 1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG 40378978 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG 1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATG * * 40379027 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG 1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG 40379074 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG 1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATG 40379123 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG 1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATG * * 40379172 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG 1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG 40379219 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG 1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATG * 40379268 AATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATG 1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG 40379315 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG 1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG * * * * * * 40379362 AATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATG 1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG * * 40379409 GATGTGAAAGTGTATAAATGTGATAAG 1 AATGTGAAAGTGTATATATGTGATAAG 40379436 TCCCGAAGGG Statistics Matches: 430, Mismatches: 22, Indels: 12 0.93 0.05 0.03 Matches are distributed among these distances: 47 246 0.57 49 184 0.43 ACGTcount: A:0.33, C:0.08, G:0.30, T:0.29 Consensus pattern (47 bp): AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG Found at i:40379039 original size:96 final size:94 Alignment explanation

Indices: 40378931--40379435 Score: 803 Period size: 96 Copynumber: 5.3 Consensus size: 94 40378921 TATTTGAATA * * 40378931 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATA 1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATA 40378996 TATGTGATAAGGCCTAATGGCCGATGTGATG 64 TATGTGATAAGGCCTAATGGCCGATGTGATG * * 40379027 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATA 1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATA 40379092 TATGTGATAAGGCCTAATGGCCGATGTGATG 64 TATGTGATAAGGCCTAATGGCCGATGTGATG 40379123 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA 1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA * * 40379188 TATGTGATAAGGCCGAATGGCCAATGTGATG 64 TATGTGATAAGGCCTAATGGCCGATGTGATG 40379219 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA 1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA * 40379284 TATGTGATAAGGCCTAATAGCCGATGTGATG 64 TATGTGATAAGGCCTAATGGCCGATGTGATG 40379315 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA 1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA * * * * * * 40379380 TGTGACAGGGCCGAGTGGCCAACGTGATG 66 TGTGATAAGGCCTAATGGCCGATGTGATG * * 40379409 GATGTGAAAGTGTATAAATGTGATAAG 1 AATGTGAAAGTGTATATATGTGATAAG 40379436 TCCCGAAGGG Statistics Matches: 391, Mismatches: 16, Indels: 6 0.95 0.04 0.01 Matches are distributed among these distances: 94 100 0.26 96 246 0.63 98 45 0.12 ACGTcount: A:0.33, C:0.08, G:0.30, T:0.29 Consensus pattern (94 bp): AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA TGTGATAAGGCCTAATGGCCGATGTGATG Found at i:40390409 original size:20 final size:20 Alignment explanation

Indices: 40390386--40390446 Score: 81 Period size: 20 Copynumber: 3.1 Consensus size: 20 40390376 ATTTTTTATA 40390386 TTTTA-AATTTATTATAATTT 1 TTTTACAATTT-TTATAATTT * 40390406 TTTTACAATTTTTATAAATT 1 TTTTACAATTTTTATAATTT * 40390426 TTTAACAATTTTT-TAATTT 1 TTTTACAATTTTTATAATTT 40390445 TT 1 TT 40390447 AAACAACTTA Statistics Matches: 37, Mismatches: 3, Indels: 3 0.86 0.07 0.07 Matches are distributed among these distances: 19 7 0.19 20 25 0.68 21 5 0.14 ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64 Consensus pattern (20 bp): TTTTACAATTTTTATAATTT Found at i:40390417 original size:10 final size:9 Alignment explanation

Indices: 40390386--40390551 Score: 63 Period size: 10 Copynumber: 17.6 Consensus size: 9 40390376 ATTTTTTATA 40390386 TTTTAAATT 1 TTTTAAATT * 40390395 TATTATAATTT 1 T-TT-TAAATT 40390406 TTTTACAATT 1 TTTTA-AATT 40390416 TTTATAAATT 1 TTT-TAAATT * 40390426 TTTAACAATT 1 TTTTA-AATT 40390436 TTTT-AA-T 1 TTTTAAATT ** 40390443 TTTTAAACA 1 TTTTAAATT ** 40390452 ACTTAAATT 1 TTTTAAATT * 40390461 TTTTATATAT 1 TTTTAAAT-T * 40390471 TTTTAAATAAA 1 TTTTAAAT--T 40390482 TTTTAAATT 1 TTTTAAATT * 40390491 TTCTAAATAAT 1 TTTTAAAT--T * 40390502 TTTGGAAATT 1 TTT-TAAATT * 40390512 TTAT-AA-T 1 TTTTAAATT 40390519 TTTTACAATT 1 TTTTA-AATT ** 40390529 TTTTTCA-T 1 TTTTAAATT 40390537 TTTTAAATAT 1 TTTTAAAT-T 40390547 TTTTA 1 TTTTA 40390552 TGATTTTCGA Statistics Matches: 115, Mismatches: 25, Indels: 33 0.66 0.14 0.19 Matches are distributed among these distances: 7 9 0.08 8 12 0.10 9 24 0.21 10 46 0.40 11 20 0.17 12 4 0.03 ACGTcount: A:0.36, C:0.04, G:0.01, T:0.58 Consensus pattern (9 bp): TTTTAAATT Found at i:40390451 original size:19 final size:19 Alignment explanation

Indices: 40390391--40390558 Score: 77 Period size: 20 Copynumber: 8.8 Consensus size: 19 40390381 TTATATTTTA * 40390391 AATTTATTATAATTTTTTTAC 1 AATTT-TTATAA-TTTTTAAC 40390412 AATTTTTATAAATTTTTAAC 1 AATTTTTAT-AATTTTTAAC 40390432 AATTTTT-TAATTTTTAAAC 1 AATTTTTATAATTTTT-AAC * * * 40390451 AA--CTTA-AATTTTTTAT 1 AATTTTTATAATTTTTAAC * 40390467 ATATTTTTAAATAAATTTT-A- 1 A-ATTTTT--ATAATTTTTAAC ** 40390487 AATTTTCTAAATAATTTTGGA- 1 AATTTT-T--ATAATTTTTAAC 40390508 AA-TTTTATAATTTTT-AC 1 AATTTTTATAATTTTTAAC * * 40390525 AATTTTTTTCATTTTTAA- 1 AATTTTTATAATTTTTAAC * 40390543 ATATTTTTATGATTTT 1 A-ATTTTTATAATTTT 40390559 CGAATGATTT Statistics Matches: 119, Mismatches: 13, Indels: 32 0.73 0.08 0.20 Matches are distributed among these distances: 16 3 0.03 17 20 0.17 18 19 0.16 19 27 0.23 20 32 0.27 21 12 0.10 22 6 0.05 ACGTcount: A:0.36, C:0.04, G:0.02, T:0.58 Consensus pattern (19 bp): AATTTTTATAATTTTTAAC Found at i:40398089 original size:3 final size:3 Alignment explanation

Indices: 40398081--40398122 Score: 84 Period size: 3 Copynumber: 14.0 Consensus size: 3 40398071 AATTGAGCAT 40398081 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA 1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA 40398123 AACCTTAATG Statistics Matches: 39, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 3 39 1.00 ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33 Consensus pattern (3 bp): TAA Found at i:40403444 original size:21 final size:21 Alignment explanation

Indices: 40403418--40403459 Score: 84 Period size: 21 Copynumber: 2.0 Consensus size: 21 40403408 AGACACGGGC 40403418 ATGTGTCTTAGCTGTGTGTGA 1 ATGTGTCTTAGCTGTGTGTGA 40403439 ATGTGTCTTAGCTGTGTGTGA 1 ATGTGTCTTAGCTGTGTGTGA 40403460 CACACGGCCT Statistics Matches: 21, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 21 21 1.00 ACGTcount: A:0.14, C:0.10, G:0.33, T:0.43 Consensus pattern (21 bp): ATGTGTCTTAGCTGTGTGTGA Found at i:40409824 original size:94 final size:94 Alignment explanation

Indices: 40409659--40409830 Score: 211 Period size: 94 Copynumber: 1.8 Consensus size: 94 40409649 AATGTTTAAA * * * * ** 40409659 TGTAAGACCATAGCTGGGCTATGACATTTTAGTGAAAAGACCATAATTGGGATATGGCACCGTGA 1 TGTAAGACCATAGCTGGGCTATGACATCTGAGTGAAAAGACCATAACTAGGATATGGCACCACGA 40409724 ACGTAAGACCATGGCAGTATATGTATATG 66 ACGTAAGACCATGGCAGTATATGTATATG * * * ** 40409753 TGTAAGACCATAGCTGGGCTATGGCATCCTGA-TGATAAGACCATAACTAGGTTATGGCATTACG 1 TGTAAGACCATAGCTGGGCTATGACAT-CTGAGTGAAAAGACCATAACTAGGATATGGCACCACG ** 40409817 AGTGTAAGACCATG 65 AACGTAAGACCATG 40409831 TCAGCGGCAT Statistics Matches: 64, Mismatches: 13, Indels: 2 0.81 0.16 0.03 Matches are distributed among these distances: 94 62 0.97 95 2 0.03 ACGTcount: A:0.32, C:0.16, G:0.26, T:0.26 Consensus pattern (94 bp): TGTAAGACCATAGCTGGGCTATGACATCTGAGTGAAAAGACCATAACTAGGATATGGCACCACGA ACGTAAGACCATGGCAGTATATGTATATG Found at i:40409825 original size:33 final size:33 Alignment explanation

Indices: 40409752--40409829 Score: 88 Period size: 33 Copynumber: 2.4 Consensus size: 33 40409742 ATATGTATAT * * * 40409752 GTGTAAGACCATAGCTGGGCTATGGCATCCTGA 1 GTGTAAGACCATAACTAGGCTATGGCATACTGA * 40409785 -TGATAAGACCATAACTAGGTTATGGCATTAC-GA 1 GTG-TAAGACCATAACTAGGCTATGGCA-TACTGA 40409818 GTGTAAGACCAT 1 GTGTAAGACCAT 40409830 GTCAGCGGCA Statistics Matches: 38, Mismatches: 4, Indels: 6 0.79 0.08 0.12 Matches are distributed among these distances: 32 2 0.05 33 32 0.84 34 4 0.11 ACGTcount: A:0.31, C:0.18, G:0.26, T:0.26 Consensus pattern (33 bp): GTGTAAGACCATAACTAGGCTATGGCATACTGA Found at i:40411609 original size:18 final size:18 Alignment explanation

Indices: 40411588--40411651 Score: 76 Period size: 18 Copynumber: 3.6 Consensus size: 18 40411578 TAGCAATTGG * 40411588 TTATTCAGTAACGGTCAA 1 TTATTCAGTAACAGTCAA * * 40411606 TTATTCGGTAACAGTCAG 1 TTATTCAGTAACAGTCAA * 40411624 TCT-TTCAGTAATAGTCAA 1 T-TATTCAGTAACAGTCAA 40411642 TTATTCAGTA 1 TTATTCAGTA 40411652 CATTTATTTA Statistics Matches: 38, Mismatches: 6, Indels: 4 0.79 0.12 0.08 Matches are distributed among these distances: 17 1 0.03 18 36 0.95 19 1 0.03 ACGTcount: A:0.31, C:0.16, G:0.16, T:0.38 Consensus pattern (18 bp): TTATTCAGTAACAGTCAA Found at i:40411774 original size:6 final size:6 Alignment explanation

Indices: 40411763--40411797 Score: 52 Period size: 6 Copynumber: 5.8 Consensus size: 6 40411753 TACACTGTAT * * 40411763 CAGTAA CAGTAA CGGTAA CAGTAA CAGTAG CAGTA 1 CAGTAA CAGTAA CAGTAA CAGTAA CAGTAA CAGTA 40411798 CACAAAGTAC Statistics Matches: 26, Mismatches: 3, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 6 26 1.00 ACGTcount: A:0.43, C:0.17, G:0.23, T:0.17 Consensus pattern (6 bp): CAGTAA Found at i:40412068 original size:18 final size:19 Alignment explanation

Indices: 40412045--40412081 Score: 58 Period size: 19 Copynumber: 2.0 Consensus size: 19 40412035 TAAGCTAATC * 40412045 ATATATAT-TTTCAGTTCA 1 ATATATATATTTCAATTCA 40412063 ATATATATATTTCAATTCA 1 ATATATATATTTCAATTCA 40412082 CTTTACATTA Statistics Matches: 17, Mismatches: 1, Indels: 1 0.89 0.05 0.05 Matches are distributed among these distances: 18 8 0.47 19 9 0.53 ACGTcount: A:0.38, C:0.11, G:0.03, T:0.49 Consensus pattern (19 bp): ATATATATATTTCAATTCA Found at i:40414506 original size:50 final size:51 Alignment explanation

Indices: 40414429--40414557 Score: 206 Period size: 50 Copynumber: 2.5 Consensus size: 51 40414419 GACCATGGCA * * 40414429 ACAAGTGATAAGTAATAGCTTCGGCTACACTTATCTGATCAAGGACAAGTG 1 ACAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATG * 40414480 A-AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAATGACAAATG 1 ACAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATG * * 40414530 ACAAGTGAGAAGTGGTAGCTTCGGCTAC 1 ACAAGTGATAAGTGATAGCTTCGGCTAC 40414558 CTGATCAGTG Statistics Matches: 72, Mismatches: 5, Indels: 2 0.91 0.06 0.03 Matches are distributed among these distances: 50 47 0.65 51 25 0.35 ACGTcount: A:0.34, C:0.17, G:0.23, T:0.26 Consensus pattern (51 bp): ACAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATG Found at i:40414574 original size:31 final size:31 Alignment explanation

Indices: 40414533--40414681 Score: 244 Period size: 31 Copynumber: 4.8 Consensus size: 31 40414523 ACAAATGACA * 40414533 AGTGAGAAGTGGTAGCTTCGGCTACCTGATC 1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC * 40414564 AGTGAAAAGTGGTAGCTTCTGCTACCTGATC 1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC * 40414595 AGTGAAAAGTGGTAGCTCCGGCTACCTGATC 1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC * * 40414626 AGTGAAAAATGGTAGCTCCGGCTACCTGATC 1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC * 40414657 AGTGAATAGTGGTAGCTTCGGCTAC 1 AGTGAAAAGTGGTAGCTTCGGCTAC 40414682 AAGTGACAAG Statistics Matches: 110, Mismatches: 8, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 31 110 1.00 ACGTcount: A:0.26, C:0.20, G:0.29, T:0.26 Consensus pattern (31 bp): AGTGAAAAGTGGTAGCTTCGGCTACCTGATC Found at i:40414852 original size:48 final size:48 Alignment explanation

Indices: 40414781--40414885 Score: 167 Period size: 49 Copynumber: 2.2 Consensus size: 48 40414771 GCATCAGTGA * 40414781 GATATGTGATTCGTGTAAAACCATAGCT-GACTATGGCATCGATATGT 1 GATATGTGATTCGTGTAAAACCATAGCTGGACTATGGCATCGATATAT * 40414828 GATATGTGATTACGTGTAAGACCATAGCTGGACTATGGCATCGATATAT 1 GATATGTGATT-CGTGTAAAACCATAGCTGGACTATGGCATCGATATAT 40414877 GAATATGTG 1 G-ATATGTG 40414886 TAAGACCATA Statistics Matches: 53, Mismatches: 2, Indels: 3 0.91 0.03 0.05 Matches are distributed among these distances: 47 11 0.21 48 16 0.30 49 19 0.36 50 7 0.13 ACGTcount: A:0.30, C:0.13, G:0.25, T:0.31 Consensus pattern (48 bp): GATATGTGATTCGTGTAAAACCATAGCTGGACTATGGCATCGATATAT Found at i:40414887 original size:42 final size:43 Alignment explanation

Indices: 40414793--40414955 Score: 163 Period size: 42 Copynumber: 3.7 Consensus size: 43 40414783 TATGTGATTC * * 40414793 GTGTAAAACCATAGCT-GACTATGGCATCGATATGTGATATG-TGATT 1 GTGTAAGACCATAGCTGGACTATGGCATCG--AT-T-ATATGAAGA-T * 40414839 ACGTGTAAGACCATAGCTGGACTATGGCATCGA-TATATGAATAT 1 --GTGTAAGACCATAGCTGGACTATGGCATCGATTATATGAAGAT ** * 40414883 GTGTAAGACCATAGCTGGGTTATGGCATC-ATTATGTGAAGAT 1 GTGTAAGACCATAGCTGGACTATGGCATCGATTATATGAAGAT * * 40414925 GTGTAAGACCATAGTTGAACTATGGCATCGA 1 GTGTAAGACCATAGCTGGACTATGGCATCGA 40414956 GAAAACGAAG Statistics Matches: 100, Mismatches: 11, Indels: 13 0.81 0.09 0.10 Matches are distributed among these distances: 41 1 0.01 42 61 0.61 43 1 0.01 44 6 0.06 45 2 0.02 47 1 0.01 48 15 0.15 49 13 0.13 ACGTcount: A:0.31, C:0.14, G:0.25, T:0.29 Consensus pattern (43 bp): GTGTAAGACCATAGCTGGACTATGGCATCGATTATATGAAGAT Found at i:40416239 original size:20 final size:18 Alignment explanation

Indices: 40416203--40416247 Score: 65 Period size: 19 Copynumber: 2.4 Consensus size: 18 40416193 AAACATTCAA 40416203 TTTTCCCTTTCTTCTTTC 1 TTTTCCCTTTCTTCTTTC 40416221 TTTTCTCCTTTCTTTCTTTC 1 TTTTC-CCTTTC-TTCTTTC 40416241 -TTTCCCT 1 TTTTCCCT 40416248 GCTTTTCGTT Statistics Matches: 25, Mismatches: 0, Indels: 4 0.86 0.00 0.14 Matches are distributed among these distances: 18 8 0.32 19 10 0.40 20 7 0.28 ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67 Consensus pattern (18 bp): TTTTCCCTTTCTTCTTTC Found at i:40418539 original size:26 final size:26 Alignment explanation

Indices: 40418510--40418619 Score: 184 Period size: 26 Copynumber: 4.2 Consensus size: 26 40418500 TGGTACAAAT * 40418510 TGATAATAGGTTAGGTAAATGTTCAA 1 TGATAATAGGTTAGGTAAATGTTCCA 40418536 TGATAATAGGTTAGGTAAATGTTCCA 1 TGATAATAGGTTAGGTAAATGTTCCA * 40418562 TGATAATGGGTTAGGTAAATGTTCCA 1 TGATAATAGGTTAGGTAAATGTTCCA * * 40418588 TGATAATGGGTTAGGTAAATGTTTCA 1 TGATAATAGGTTAGGTAAATGTTCCA 40418614 TGATAA 1 TGATAA 40418620 GAATTTCATG Statistics Matches: 81, Mismatches: 3, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 26 81 1.00 ACGTcount: A:0.35, C:0.05, G:0.25, T:0.35 Consensus pattern (26 bp): TGATAATAGGTTAGGTAAATGTTCCA Found at i:40420101 original size:28 final size:26 Alignment explanation

Indices: 40420070--40420134 Score: 69 Period size: 27 Copynumber: 2.4 Consensus size: 26 40420060 AATTACTATA 40420070 ATACCCCTATGTATGGAAAATT-CCTGTT 1 ATACCCCTA-G-ATGGAAAATTACC-GTT * * 40420098 ATACCCCCTAGGTGTAAAATTACCGTT 1 ATA-CCCCTAGATGGAAAATTACCGTT 40420125 ATACCCCTAG 1 ATACCCCTAG 40420135 GGTTAATTTT Statistics Matches: 33, Mismatches: 2, Indels: 6 0.80 0.05 0.15 Matches are distributed among these distances: 26 7 0.21 27 14 0.42 28 6 0.18 29 6 0.18 ACGTcount: A:0.29, C:0.26, G:0.14, T:0.31 Consensus pattern (26 bp): ATACCCCTAGATGGAAAATTACCGTT Found at i:40420279 original size:27 final size:26 Alignment explanation

Indices: 40420238--40420323 Score: 91 Period size: 27 Copynumber: 3.2 Consensus size: 26 40420228 GAGGAAGCGT * * 40420238 TCTGGTGGCTATGCCACAAATATCTGA 1 TCTGGTGGCTCTGCCAC-ATTATCTGA 40420265 TCTGGTGGCTCTGCCACGATTATCTGTA 1 TCTGGTGGCTCTGCCAC-ATTATCTG-A * * * * 40420293 TTTGGTGACTCTGTCACATTATCTGT 1 TCTGGTGGCTCTGCCACATTATCTGA 40420319 TCTGG 1 TCTGG 40420324 CAGTCATGCT Statistics Matches: 50, Mismatches: 8, Indels: 3 0.82 0.13 0.05 Matches are distributed among these distances: 26 4 0.08 27 31 0.62 28 15 0.30 ACGTcount: A:0.17, C:0.22, G:0.23, T:0.37 Consensus pattern (26 bp): TCTGGTGGCTCTGCCACATTATCTGA Found at i:40424031 original size:26 final size:26 Alignment explanation

Indices: 40424000--40424107 Score: 189 Period size: 26 Copynumber: 4.2 Consensus size: 26 40423990 TGAAATGCCC * 40424000 ATCATGGAACATTTACCTAAACCATT 1 ATCATGGAACATTTACCTAACCCATT 40424026 ATCATGGAACATTTACCTAACCCATT 1 ATCATGGAACATTTACCTAACCCATT * * 40424052 ATCATGGAATATTTACCTAATCCATT 1 ATCATGGAACATTTACCTAACCCATT 40424078 ATCATGGAACATTTACCTAACCCATT 1 ATCATGGAACATTTACCTAACCCATT 40424104 ATCA 1 ATCA 40424108 ATTTGTACCA Statistics Matches: 77, Mismatches: 5, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 26 77 1.00 ACGTcount: A:0.36, C:0.24, G:0.07, T:0.32 Consensus pattern (26 bp): ATCATGGAACATTTACCTAACCCATT Found at i:40428581 original size:27 final size:27 Alignment explanation

Indices: 40428551--40428728 Score: 205 Period size: 27 Copynumber: 6.6 Consensus size: 27 40428541 ATATTGAGTC * * * * 40428551 CGCACACTCAGTGCTATATAATCAACT 1 CGCACACTTAGTGCTACATAGTCAAAT * * 40428578 CGCACACTTAGTGCTACGTAATCAAAT 1 CGCACACTTAGTGCTACATAGTCAAAT 40428605 CGCACACTTAGTGCTACATAGTCAAACT 1 CGCACACTTAGTGCTACATAGTCAAA-T ** * * 40428633 CGCACACTTAGTGCCGCATGGTCAATT 1 CGCACACTTAGTGCTACATAGTCAAAT * ** 40428660 CGCACACTTAGTGC-ATCATATTCATTT 1 CGCACACTTAGTGCTA-CATAGTCAAAT * 40428687 CGCACACTTAGTGCAACATAGTCAAAT 1 CGCACACTTAGTGCTACATAGTCAAAT 40428714 CGCACACTTAGTGCT 1 CGCACACTTAGTGCT 40428729 GTACAATTTA Statistics Matches: 130, Mismatches: 18, Indels: 6 0.84 0.12 0.04 Matches are distributed among these distances: 27 106 0.82 28 24 0.18 ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27 Consensus pattern (27 bp): CGCACACTTAGTGCTACATAGTCAAAT Found at i:40428690 original size:82 final size:81 Alignment explanation

Indices: 40428572--40428727 Score: 233 Period size: 82 Copynumber: 1.9 Consensus size: 81 40428562 TGCTATATAA * * 40428572 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA 1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA 40428637 CACTTAGTGCCGCATGG 65 CACTTAGTGCCGCATGG * * ** 40428654 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA 1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA 40428718 CACTTAGTGC 65 CACTTAGTGC 40428728 TGTACAATTT Statistics Matches: 67, Mismatches: 6, Indels: 3 0.88 0.08 0.04 Matches are distributed among these distances: 81 16 0.24 82 51 0.76 ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27 Consensus pattern (81 bp): TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC ACTTAGTGCCGCATGG Found at i:40434316 original size:26 final size:26 Alignment explanation

Indices: 40434280--40434388 Score: 168 Period size: 26 Copynumber: 4.2 Consensus size: 26 40434270 ATGAAAGGCC 40434280 TATCATGGAACATTTACCTAAACCAT 1 TATCATGGAACATTTACCTAAACCAT 40434306 TATCATGGAACATTTACCT-AACTCAT 1 TATCATGGAACATTTACCTAAAC-CAT * 40434332 TATCATGGAATATTTACCTAATA-CAT 1 TATCATGGAACATTTACCTAA-ACCAT * 40434358 TATCATGGAACATTTACCTAACCCAT 1 TATCATGGAACATTTACCTAAACCAT 40434384 TATCA 1 TATCA 40434389 ATTTGTACCA Statistics Matches: 76, Mismatches: 3, Indels: 8 0.87 0.03 0.09 Matches are distributed among these distances: 25 3 0.04 26 71 0.93 27 1 0.01 28 1 0.01 ACGTcount: A:0.37, C:0.22, G:0.07, T:0.34 Consensus pattern (26 bp): TATCATGGAACATTTACCTAAACCAT Found at i:40435038 original size:11 final size:11 Alignment explanation

Indices: 40435024--40435064 Score: 55 Period size: 11 Copynumber: 3.7 Consensus size: 11 40435014 TGTTTTCTCC 40435024 CTATTTTGCTA 1 CTATTTTGCTA * 40435035 CTATTTTACTA 1 CTATTTTGCTA * * 40435046 TTATGTTGCTA 1 CTATTTTGCTA 40435057 CTATTTTG 1 CTATTTTG 40435065 TTGTTATTGT Statistics Matches: 24, Mismatches: 6, Indels: 0 0.80 0.20 0.00 Matches are distributed among these distances: 11 24 1.00 ACGTcount: A:0.20, C:0.15, G:0.10, T:0.56 Consensus pattern (11 bp): CTATTTTGCTA Found at i:40436705 original size:13 final size:13 Alignment explanation

Indices: 40436689--40436713 Score: 50 Period size: 13 Copynumber: 1.9 Consensus size: 13 40436679 AATATTAAAT 40436689 AATAATATTTACG 1 AATAATATTTACG 40436702 AATAATATTTAC 1 AATAATATTTAC 40436714 ATACTTACTC Statistics Matches: 12, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 12 1.00 ACGTcount: A:0.48, C:0.08, G:0.04, T:0.40 Consensus pattern (13 bp): AATAATATTTACG Found at i:40436942 original size:19 final size:18 Alignment explanation

Indices: 40436892--40436945 Score: 63 Period size: 20 Copynumber: 2.8 Consensus size: 18 40436882 TATGAAAAAT 40436892 AATATTTATTTTAATTATAA 1 AATATTTA-TTT-ATTATAA * 40436912 AATATATAATTTATTATAAA 1 AATAT-TTATTTATTAT-AA 40436932 AATATTTATTTATT 1 AATATTTATTTATT 40436946 TTTAACATAT Statistics Matches: 30, Mismatches: 2, Indels: 5 0.81 0.05 0.14 Matches are distributed among these distances: 19 13 0.43 20 15 0.50 21 2 0.07 ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54 Consensus pattern (18 bp): AATATTTATTTATTATAA Found at i:40445236 original size:22 final size:23 Alignment explanation

Indices: 40445183--40445237 Score: 62 Period size: 22 Copynumber: 2.5 Consensus size: 23 40445173 ACACTTCAAT 40445183 AATATAAATAATATAAAATGTGA 1 AATATAAATAATATAAAATGTGA * 40445206 AAT-TTAATAATAT-AAATAGT-A 1 AATATAAATAATATAAAAT-GTGA * 40445227 TATATAAATAA 1 AATATAAATAA 40445238 AATTATTACT Statistics Matches: 27, Mismatches: 3, Indels: 5 0.77 0.09 0.14 Matches are distributed among these distances: 21 7 0.26 22 17 0.63 23 3 0.11 ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35 Consensus pattern (23 bp): AATATAAATAATATAAAATGTGA Found at i:40448862 original size:63 final size:63 Alignment explanation

Indices: 40448756--40448881 Score: 198 Period size: 63 Copynumber: 2.0 Consensus size: 63 40448746 TCCCTTTGGT *** * 40448756 TATGCACTAGTTGATGGTCTGAGAGTCAATCGATTGTAGAAGTTGGGTAGAATCCGTCTAAAA 1 TATGCACTAGTTGATGGTCTGAGAGTCAATCGACCATAGAAGTTGGGTAGAATCCGACTAAAA * * 40448819 TATGCACTAGTTGATGGTCTGAGAGTCAATCGACCATATAAGTTGGGTAGAATCTGACTAAAA 1 TATGCACTAGTTGATGGTCTGAGAGTCAATCGACCATAGAAGTTGGGTAGAATCCGACTAAAA 40448882 CAGAAAGGAC Statistics Matches: 57, Mismatches: 6, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 63 57 1.00 ACGTcount: A:0.32, C:0.13, G:0.25, T:0.29 Consensus pattern (63 bp): TATGCACTAGTTGATGGTCTGAGAGTCAATCGACCATAGAAGTTGGGTAGAATCCGACTAAAA Found at i:40450147 original size:19 final size:19 Alignment explanation

Indices: 40450123--40450171 Score: 64 Period size: 20 Copynumber: 2.5 Consensus size: 19 40450113 TAGCTGTAGC 40450123 CGTAAAAGGCT-GCTATAGA 1 CGTAAAAGGCTAGCTATA-A * 40450142 CGTAAAAGGTTAGCTATAA 1 CGTAAAAGGCTAGCTATAA 40450161 CTGTAAAAGGC 1 C-GTAAAAGGC 40450172 AAGTTTGCGC Statistics Matches: 26, Mismatches: 2, Indels: 3 0.84 0.06 0.10 Matches are distributed among these distances: 19 12 0.46 20 14 0.54 ACGTcount: A:0.39, C:0.14, G:0.24, T:0.22 Consensus pattern (19 bp): CGTAAAAGGCTAGCTATAA Found at i:40450159 original size:20 final size:20 Alignment explanation

Indices: 40450111--40450171 Score: 72 Period size: 19 Copynumber: 3.1 Consensus size: 20 40450101 AGTTGAATAA * * 40450111 GCTAGCTGTAGCCGTAAAAG 1 GCTAGCTATAGACGTAAAAG 40450131 GCT-GCTATAGACGTAAAAG 1 GCTAGCTATAGACGTAAAAG * 40450150 GTTAGCTATA-ACTGTAAAAG 1 GCTAGCTATAGAC-GTAAAAG 40450170 GC 1 GC 40450172 AAGTTTGCGC Statistics Matches: 35, Mismatches: 4, Indels: 4 0.81 0.09 0.09 Matches are distributed among these distances: 19 18 0.51 20 17 0.49 ACGTcount: A:0.34, C:0.16, G:0.26, T:0.23 Consensus pattern (20 bp): GCTAGCTATAGACGTAAAAG Found at i:40458006 original size:19 final size:19 Alignment explanation

Indices: 40457982--40458018 Score: 74 Period size: 19 Copynumber: 1.9 Consensus size: 19 40457972 ATCACTATCA 40457982 CCACTGTAATCAAATTTGT 1 CCACTGTAATCAAATTTGT 40458001 CCACTGTAATCAAATTTG 1 CCACTGTAATCAAATTTG 40458019 AATAATTCGA Statistics Matches: 18, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 19 18 1.00 ACGTcount: A:0.32, C:0.22, G:0.11, T:0.35 Consensus pattern (19 bp): CCACTGTAATCAAATTTGT Found at i:40458058 original size:18 final size:18 Alignment explanation

Indices: 40458013--40458067 Score: 65 Period size: 18 Copynumber: 3.0 Consensus size: 18 40458003 ACTGTAATCA * 40458013 AATTTGAATAATTCGAGTT 1 AATTCGAATAATTCGA-TT * * 40458032 GACTCGAATAATTCGATT 1 AATTCGAATAATTCGATT * 40458050 AATTCGAATAACTCGATT 1 AATTCGAATAATTCGATT 40458068 CGTCTAACTC Statistics Matches: 30, Mismatches: 6, Indels: 1 0.81 0.16 0.03 Matches are distributed among these distances: 18 17 0.57 19 13 0.43 ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36 Consensus pattern (18 bp): AATTCGAATAATTCGATT Found at i:40460730 original size:124 final size:124 Alignment explanation

Indices: 40460501--40460962 Score: 504 Period size: 124 Copynumber: 3.8 Consensus size: 124 40460491 AACCTTGGTC * * * * * 40460501 TCTGCTCATAATTTGGCAATATGCCTCTCATTCGACTCAATGTAAGAGGTGAGTTGATCAATCAT 1 TCTGCTCGTAATTTGGCAACATGCCTCTCATTCGACTCATTATAGGAGGTGAGTTGATCAATCAT * * * 40460566 TCGTTCTTGAATGCTTGTGGGAATAGACTTGGGGCTTGAGCTAGTGAGCACTCATTGAG 66 TCGTTCTTGAATGCTTGTGGGAATAGCCTTGGGACCTGAGCTAGTGAGCACTCATTGAG 40460625 TCTGCTCGTAATTTGGCAACATGCCTCTCATTCGACTCATTATAGGAGGTGAGTTGATCAATCAT 1 TCTGCTCGTAATTTGGCAACATGCCTCTCATTCGACTCATTATAGGAGGTGAGTTGATCAATCAT * * * * ** * 40460690 TCGTTCTTGAATACTTGTGGGAGTAGCCTTTGGACCTGAGCTAGTGGGCTTTCCTTGAG 66 TCGTTCTTGAATGCTTGTGGGAATAGCCTTGGGACCTGAGCTAGTGAGCACTCATTGAG * * * * * * * 40460749 TCTGCTCGTAATCTGGAAACATGCCTCTTATTCTACTCATTATAGAAGGTGAGTAGATTAATCAT 1 TCTGCTCGTAATTTGGCAACATGCCTCTCATTCGACTCATTATAGGAGGTGAGTTGATCAATCAT * * 40460814 TCGTTCTTGAATGCTTGTGGGAATAGCCTT-GG----G-GC-------CACTCCTTAAG 66 TCGTTCTTGAATGCTTGTGGGAATAGCCTTGGGACCTGAGCTAGTGAGCACTCATTGAG * * * * * * * 40460860 GCT-ATCGTAATTTGGAAACATGCCTCTCATTTGAATCACTT-TAAGAGGTGAGTTGACCAATCA 1 TCTGCTCGTAATTTGGCAACATGCCTCTCATTCGACTCA-TTATAGGAGGTGAGTTGATCAATCA * * * 40460923 TTCATTCTTGAATGCCTGTGGGAATAGCCTTGGGGCCTGA 65 TTCGTTCTTGAATGCTTGTGGGAATAGCCTTGGGACCTGA 40460963 AGTAATGGGC Statistics Matches: 290, Mismatches: 41, Indels: 22 0.82 0.12 0.06 Matches are distributed among these distances: 110 75 0.26 111 14 0.05 115 1 0.00 118 2 0.01 119 1 0.00 123 2 0.01 124 195 0.67 ACGTcount: A:0.23, C:0.19, G:0.24, T:0.34 Consensus pattern (124 bp): TCTGCTCGTAATTTGGCAACATGCCTCTCATTCGACTCATTATAGGAGGTGAGTTGATCAATCAT TCGTTCTTGAATGCTTGTGGGAATAGCCTTGGGACCTGAGCTAGTGAGCACTCATTGAG Found at i:40460947 original size:110 final size:110 Alignment explanation

Indices: 40460754--40460959 Score: 292 Period size: 110 Copynumber: 1.9 Consensus size: 110 40460744 TTGAGTCTGC * * ** * 40460754 TCGTAATCTGGAAACATGCCTCTTATTCTACTCATTATAGAAGGTGAGTAGATTAATCATTCGTT 1 TCGTAATCTGGAAACATGCCTCTCATTCTAATCATTATAGAAGGTGAGTAGACCAATCATTCATT * 40460819 CTTGAATGCTTGTGGGAATAGCCTTGGGGCCACTCCTTAAGGCTA 66 CTTGAATGCCTGTGGGAATAGCCTTGGGGCCACTCCTTAAGGCTA * * 40460864 TCGTAATTTGGAAACATGCCTCTCATT-TGAATCACTT-TA-AGAGGTGAGTTGACCAATCATTC 1 TCGTAATCTGGAAACATGCCTCTCATTCT-AATCA-TTATAGA-AGGTGAGTAGACCAATCATTC 40460926 ATTCTTGAATGCCTGTGGGAATAGCCTTGGGGCC 63 ATTCTTGAATGCCTGTGGGAATAGCCTTGGGGCC 40460960 TGAAGTAATG Statistics Matches: 85, Mismatches: 8, Indels: 6 0.86 0.08 0.06 Matches are distributed among these distances: 109 2 0.02 110 81 0.95 111 2 0.02 ACGTcount: A:0.25, C:0.19, G:0.22, T:0.33 Consensus pattern (110 bp): TCGTAATCTGGAAACATGCCTCTCATTCTAATCATTATAGAAGGTGAGTAGACCAATCATTCATT CTTGAATGCCTGTGGGAATAGCCTTGGGGCCACTCCTTAAGGCTA Found at i:40465385 original size:29 final size:29 Alignment explanation

Indices: 40465342--40465429 Score: 104 Period size: 29 Copynumber: 3.0 Consensus size: 29 40465332 GTACATAGTA * * 40465342 CCTGATAATTATAACACTGGCACAAAGTG 1 CCTGATAACTGTAACACTGGCACAAAGTG * * 40465371 CCTGATAACTGTAACACTAGCACAAAGTA 1 CCTGATAACTGTAACACTGGCACAAAGTG * * * 40465400 CCTAATAACTGTAATCACCGGCACATAGTG 1 CCTGATAACTGTAA-CACTGGCACAAAGTG 40465430 TCTCATAAAC Statistics Matches: 49, Mismatches: 9, Indels: 1 0.83 0.15 0.02 Matches are distributed among these distances: 29 38 0.78 30 11 0.22 ACGTcount: A:0.38, C:0.24, G:0.16, T:0.23 Consensus pattern (29 bp): CCTGATAACTGTAACACTGGCACAAAGTG Found at i:40469459 original size:24 final size:24 Alignment explanation

Indices: 40469432--40469535 Score: 86 Period size: 24 Copynumber: 4.3 Consensus size: 24 40469422 TGGCTCTTCG * * 40469432 GAGCTACCTGTTATTGGCTCGCAT 1 GAGCTTCCTGTTATAGGCTCGCAT ** 40469456 GAGCTTCCTGATT-TAGGCTCTTAT 1 GAGCTTCCTG-TTATAGGCTCGCAT * * 40469480 GAGCTTCCTGTTATA-GCCCGAAT 1 GAGCTTCCTGTTATAGGCTCGCAT * * * * 40469503 AAGCTTCCTGTTACATGGCTCACTT 1 GAGCTTCCTGTTATA-GGCTCGCAT 40469528 GAGCTTCC 1 GAGCTTCC 40469536 CATTAAATGG Statistics Matches: 62, Mismatches: 14, Indels: 7 0.75 0.17 0.08 Matches are distributed among these distances: 23 20 0.32 24 29 0.47 25 13 0.21 ACGTcount: A:0.18, C:0.26, G:0.21, T:0.35 Consensus pattern (24 bp): GAGCTTCCTGTTATAGGCTCGCAT Found at i:40477251 original size:35 final size:35 Alignment explanation

Indices: 40477205--40477274 Score: 140 Period size: 35 Copynumber: 2.0 Consensus size: 35 40477195 GCCTGAAGAC 40477205 CCAATTGGGCAAAGAGAATCACATTAGTTGTCGAA 1 CCAATTGGGCAAAGAGAATCACATTAGTTGTCGAA 40477240 CCAATTGGGCAAAGAGAATCACATTAGTTGTCGAA 1 CCAATTGGGCAAAGAGAATCACATTAGTTGTCGAA 40477275 ATGATGACAG Statistics Matches: 35, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 35 35 1.00 ACGTcount: A:0.37, C:0.17, G:0.23, T:0.23 Consensus pattern (35 bp): CCAATTGGGCAAAGAGAATCACATTAGTTGTCGAA Found at i:40490616 original size:38 final size:38 Alignment explanation

Indices: 40490505--40490623 Score: 159 Period size: 38 Copynumber: 3.1 Consensus size: 38 40490495 ATTTGATGTG * * 40490505 TATCCGGGCTTAAAGACCCGCAGGCTTCA-TGCTGGTAATA 1 TATCCGGG-TTAAA-TCCCGCAGGCTT-AGTGCTGGTATTA * 40490545 TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTATTA 1 TATCCGGGTTAAATCCCGCAGGCTTAGTGCTGGTATTA * * 40490583 TATCCGGGTTAAATCCCGCAGGCCTAGTACTGGTATTA 1 TATCCGGGTTAAATCCCGCAGGCTTAGTGCTGGTATTA 40490621 TAT 1 TAT 40490624 TCAGGCCTTT Statistics Matches: 72, Mismatches: 6, Indels: 4 0.88 0.07 0.05 Matches are distributed among these distances: 38 59 0.82 39 5 0.07 40 8 0.11 ACGTcount: A:0.23, C:0.24, G:0.24, T:0.29 Consensus pattern (38 bp): TATCCGGGTTAAATCCCGCAGGCTTAGTGCTGGTATTA Found at i:40490676 original size:45 final size:45 Alignment explanation

Indices: 40490620--40490751 Score: 148 Period size: 45 Copynumber: 3.0 Consensus size: 45 40490610 TACTGGTATT * * * 40490620 ATATTCAGGCCTTTGAGCCTAGCAGGCTATTATGCCGGTGAGAT- 1 ATATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGACATG * * 40490664 ACTATTCGGGCCTTTGAGCCTAGTAGGCTATAATGTCGGTGACATG 1 A-TATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGACATG * * * 40490710 ATA-TCGAGCC-TTGAGCCTAGCAGGCGA-AATACCGGTGA-ATG 1 ATATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGACATG 40490751 A 1 A 40490752 ATAAAAGTCT Statistics Matches: 76, Mismatches: 10, Indels: 7 0.82 0.11 0.08 Matches are distributed among these distances: 41 4 0.05 42 9 0.12 43 15 0.20 44 7 0.09 45 40 0.53 46 1 0.01 ACGTcount: A:0.25, C:0.20, G:0.28, T:0.27 Consensus pattern (45 bp): ATATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGACATG Found at i:40491863 original size:34 final size:35 Alignment explanation

Indices: 40491817--40491894 Score: 99 Period size: 34 Copynumber: 2.3 Consensus size: 35 40491807 ATCTCAATAC * 40491817 AGTATCAATATGT-TGTAGGGCCTTAGCCCATCA-A 1 AGTATCAGTATGTAT-TAGGGCCTTAGCCCATCACA * * 40491851 AGTATCAGTATGTATTAGGGCTTTAGCTCATCACA 1 AGTATCAGTATGTATTAGGGCCTTAGCCCATCACA 40491886 A-TATCAGTA 1 AGTATCAGTA 40491895 GCAGTCATGC Statistics Matches: 39, Mismatches: 3, Indels: 4 0.85 0.07 0.09 Matches are distributed among these distances: 34 36 0.92 35 3 0.08 ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32 Consensus pattern (35 bp): AGTATCAGTATGTATTAGGGCCTTAGCCCATCACA Found at i:40493548 original size:22 final size:22 Alignment explanation

Indices: 40493520--40493570 Score: 102 Period size: 22 Copynumber: 2.3 Consensus size: 22 40493510 CACAATGAAT 40493520 AATGTGACTAATTATTAAGCTA 1 AATGTGACTAATTATTAAGCTA 40493542 AATGTGACTAATTATTAAGCTA 1 AATGTGACTAATTATTAAGCTA 40493564 AATGTGA 1 AATGTGA 40493571 TGTTATAGAT Statistics Matches: 29, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 22 29 1.00 ACGTcount: A:0.41, C:0.08, G:0.16, T:0.35 Consensus pattern (22 bp): AATGTGACTAATTATTAAGCTA Found at i:40498827 original size:26 final size:26 Alignment explanation

Indices: 40498791--40498844 Score: 99 Period size: 26 Copynumber: 2.1 Consensus size: 26 40498781 CCCTAGCCAC 40498791 CAATATAACTCACGAAGGTCTTGGTA 1 CAATATAACTCACGAAGGTCTTGGTA * 40498817 CAATATAACTCATGAAGGTCTTGGTA 1 CAATATAACTCACGAAGGTCTTGGTA 40498843 CA 1 CA 40498845 TCTTATTTCC Statistics Matches: 27, Mismatches: 1, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 26 27 1.00 ACGTcount: A:0.35, C:0.19, G:0.19, T:0.28 Consensus pattern (26 bp): CAATATAACTCACGAAGGTCTTGGTA Found at i:40502333 original size:25 final size:23 Alignment explanation

Indices: 40502303--40502358 Score: 58 Period size: 25 Copynumber: 2.3 Consensus size: 23 40502293 TTAACTATAG 40502303 TTTTCAGTATGTACTAACTAGAGTA 1 TTTTCAGTA--TACTAACTAGAGTA * 40502328 TTTTCACAGTATACTAACTATAGTA 1 TTTT--CAGTATACTAACTAGAGTA * 40502353 GTTTCA 1 TTTTCA 40502359 AAATAGCATA Statistics Matches: 27, Mismatches: 2, Indels: 6 0.77 0.06 0.17 Matches are distributed among these distances: 23 2 0.07 25 20 0.74 27 5 0.19 ACGTcount: A:0.32, C:0.14, G:0.12, T:0.41 Consensus pattern (23 bp): TTTTCAGTATACTAACTAGAGTA Found at i:40511159 original size:19 final size:19 Alignment explanation

Indices: 40511122--40511221 Score: 168 Period size: 19 Copynumber: 5.3 Consensus size: 19 40511112 CAAGATTACA 40511122 ATATCATATCTTCAAGATTGC 1 ATATCATATC-T-AAGATTGC 40511143 ATATCATATCTAAGATTGC 1 ATATCATATCTAAGATTGC 40511162 ATATCATATCTAAGATTG- 1 ATATCATATCTAAGATTGC 40511180 -TATCATATCTAAGATTGC 1 ATATCATATCTAAGATTGC 40511198 ATATCATATCTAAGATTGC 1 ATATCATATCTAAGATTGC 40511217 ATATC 1 ATATC 40511222 CCTAAAGATT Statistics Matches: 77, Mismatches: 0, Indels: 6 0.93 0.00 0.07 Matches are distributed among these distances: 17 17 0.22 19 49 0.64 20 1 0.01 21 10 0.13 ACGTcount: A:0.36, C:0.16, G:0.10, T:0.38 Consensus pattern (19 bp): ATATCATATCTAAGATTGC Found at i:40511190 original size:36 final size:37 Alignment explanation

Indices: 40511113--40511221 Score: 157 Period size: 36 Copynumber: 2.8 Consensus size: 37 40511103 TTAAATCTCC * 40511113 AAGATTACAATATCATATCTTCAAGATTGCATATCATATCT 1 AAGATTGC-ATATCATATC-T-AAGATTG-ATATCATATCT 40511154 AAGATTGCATATCATATCTAAGATTG-TATCATATCT 1 AAGATTGCATATCATATCTAAGATTGATATCATATCT 40511190 AAGATTGCATATCATATCTAAGATTGCATATC 1 AAGATTGCATATCATATCTAAGATTG-ATATC 40511222 CCTAAAGATT Statistics Matches: 65, Mismatches: 1, Indels: 7 0.89 0.01 0.10 Matches are distributed among these distances: 36 36 0.55 38 11 0.17 39 1 0.02 40 10 0.15 41 7 0.11 ACGTcount: A:0.38, C:0.16, G:0.10, T:0.37 Consensus pattern (37 bp): AAGATTGCATATCATATCTAAGATTGATATCATATCT Found at i:40511452 original size:28 final size:29 Alignment explanation

Indices: 40511420--40511492 Score: 103 Period size: 28 Copynumber: 2.6 Consensus size: 29 40511410 GATTAGGCCT * 40511420 AATGGGCCATATGAATGTGATTGGGCCCG 1 AATGGGCCATATGAATGAGATTGGGCCCG * 40511449 -ATGGGCCATATGAATGAGATTGGGCCTG 1 AATGGGCCATATGAATGAGATTGGGCCCG * * 40511477 AAGGGGCCAAATGAAT 1 AATGGGCCATATGAAT 40511493 AAGTATGGAT Statistics Matches: 39, Mismatches: 4, Indels: 2 0.87 0.09 0.04 Matches are distributed among these distances: 28 26 0.67 29 13 0.33 ACGTcount: A:0.29, C:0.15, G:0.34, T:0.22 Consensus pattern (29 bp): AATGGGCCATATGAATGAGATTGGGCCCG Found at i:40520347 original size:16 final size:16 Alignment explanation

Indices: 40520326--40520362 Score: 56 Period size: 16 Copynumber: 2.3 Consensus size: 16 40520316 CGGTAAATTT * 40520326 TGAAATGCCGAAAAGC 1 TGAAATACCGAAAAGC 40520342 TGAAATACCGAAAAGC 1 TGAAATACCGAAAAGC * 40520358 CGAAA 1 TGAAA 40520363 GTTTGGCTAA Statistics Matches: 19, Mismatches: 2, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 16 19 1.00 ACGTcount: A:0.49, C:0.19, G:0.22, T:0.11 Consensus pattern (16 bp): TGAAATACCGAAAAGC Found at i:40520589 original size:28 final size:28 Alignment explanation

Indices: 40520556--40520675 Score: 150 Period size: 28 Copynumber: 4.2 Consensus size: 28 40520546 ATTGCATGAC * 40520556 TATGAATGTGATTGGGCCTGACGGGCCA 1 TATGAATGTGATTGGGCCTGATGGGCCA * * 40520584 TATGAAAGTGATTGGGCCTAATGGGCCA 1 TATGAATGTGATTGGGCCTGATGGGCCA * * 40520612 TATGAATTTGATTGGGCCCGATGGGCCA 1 TATGAATGTGATTGGGCCTGATGGGCCA * * * 40520640 TACGAATGAGATTGGGCCTGAAAGGGCCA 1 TATGAATGTGATTGGGCCTG-ATGGGCCA * 40520669 AATGAAT 1 TATGAAT 40520676 AAGTATGGAT Statistics Matches: 77, Mismatches: 14, Indels: 1 0.84 0.15 0.01 Matches are distributed among these distances: 28 65 0.84 29 12 0.16 ACGTcount: A:0.28, C:0.16, G:0.33, T:0.24 Consensus pattern (28 bp): TATGAATGTGATTGGGCCTGATGGGCCA Found at i:40521977 original size:26 final size:26 Alignment explanation

Indices: 40521948--40522001 Score: 108 Period size: 26 Copynumber: 2.1 Consensus size: 26 40521938 TTGGTATAGG 40521948 TATGTTTTGACCATGTTTAAAATACT 1 TATGTTTTGACCATGTTTAAAATACT 40521974 TATGTTTTGACCATGTTTAAAATACT 1 TATGTTTTGACCATGTTTAAAATACT 40522000 TA 1 TA 40522002 GATAGGTGAA Statistics Matches: 28, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 26 28 1.00 ACGTcount: A:0.31, C:0.11, G:0.11, T:0.46 Consensus pattern (26 bp): TATGTTTTGACCATGTTTAAAATACT Found at i:40545152 original size:24 final size:25 Alignment explanation

Indices: 40545125--40545178 Score: 58 Period size: 24 Copynumber: 2.2 Consensus size: 25 40545115 TAGACAAGTC 40545125 ACATTTTCG-TATAATATTTTAACA 1 ACATTTTCGTTATAATATTTTAACA * * * * 40545149 ACA-TCTCGTTATCATATTTTTACT 1 ACATTTTCGTTATAATATTTTAACA 40545173 ACATTT 1 ACATTT 40545179 CCCTTTTTTA Statistics Matches: 23, Mismatches: 5, Indels: 3 0.74 0.16 0.10 Matches are distributed among these distances: 23 4 0.17 24 18 0.78 25 1 0.04 ACGTcount: A:0.31, C:0.17, G:0.04, T:0.48 Consensus pattern (25 bp): ACATTTTCGTTATAATATTTTAACA Found at i:40548507 original size:11 final size:11 Alignment explanation

Indices: 40548491--40548526 Score: 54 Period size: 11 Copynumber: 3.1 Consensus size: 11 40548481 GATTGGTTAG 40548491 AATATTTTATT 1 AATATTTTATT 40548502 AATATTTTATCAT 1 AATATTTTAT--T 40548515 AATATTTTATT 1 AATATTTTATT 40548526 A 1 A 40548527 TAAGAATTTG Statistics Matches: 23, Mismatches: 0, Indels: 4 0.85 0.00 0.15 Matches are distributed among these distances: 11 12 0.52 13 11 0.48 ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58 Consensus pattern (11 bp): AATATTTTATT Found at i:40548519 original size:13 final size:12 Alignment explanation

Indices: 40548491--40548529 Score: 53 Period size: 13 Copynumber: 3.2 Consensus size: 12 40548481 GATTGGTTAG 40548491 AATATTTTAT-T 1 AATATTTTATAT 40548502 AATATTTTATCAT 1 AATATTTTAT-AT 40548515 AATATTTTATTAT 1 AATATTTTA-TAT 40548528 AA 1 AA 40548530 GAATTTGTAT Statistics Matches: 25, Mismatches: 0, Indels: 4 0.86 0.00 0.14 Matches are distributed among these distances: 11 10 0.40 13 14 0.56 14 1 0.04 ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56 Consensus pattern (12 bp): AATATTTTATAT Found at i:40551816 original size:48 final size:48 Alignment explanation

Indices: 40551660--40551875 Score: 269 Period size: 48 Copynumber: 4.5 Consensus size: 48 40551650 TATGTGTGCT * * * * 40551660 AGTGTAAGACATGTCTGGGACATGCATTGGCCAC-A-TTATGA-GAGCC 1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATAT-ACAAGCC * * 40551706 AGTATAAGACATGTTTGGGACATGCATCGGCCTCGAGATATATACAAGCC 1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAG--ATATACAAGCC 40551756 AGTGTAAGACATGTCTGGGACATGCATCGGCC-CTGAGATATACAAGCC 1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTC-GAGATATACAAGCC * * * 40551804 AGTGTAAGACATGTCTGGGACATGCATCAGCCTCGAAATATACAAGCT 1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATATACAAGCC * * 40551852 AGTGTAAGACCTGTCTAGGACATG 1 AGTGTAAGACATGTCTGGGACATG 40551876 GCATTAGCTT Statistics Matches: 150, Mismatches: 13, Indels: 12 0.86 0.07 0.07 Matches are distributed among these distances: 46 30 0.20 47 1 0.01 48 76 0.51 49 3 0.02 50 40 0.27 ACGTcount: A:0.31, C:0.20, G:0.26, T:0.23 Consensus pattern (48 bp): AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATATACAAGCC Found at i:40551955 original size:49 final size:49 Alignment explanation

Indices: 40551660--40552067 Score: 233 Period size: 48 Copynumber: 8.5 Consensus size: 49 40551650 TATGTGTGCT * * * * * * 40551660 AGTGTAAGACATGTCTGGGACAT-GCATTGGCCAC-AT-TATGAGAGCC 1 AGTGTAAGACCTGTCTGGGACATGGCATCGACCTCGATAGATGAAAGCC * * * * * 40551706 AGTATAAGACATGTTTGGGACAT-GCATCGGCCTCGAGATATAT-ACAAGCC 1 AGTGTAAGACCTGTCTGGGACATGGCATCGACCTC--GATAGATGA-AAGCC * * * * 40551756 AGTGTAAGACATGTCTGGGACAT-GCATCGGCC-CTGAGATAT-ACAAGCC 1 AGTGTAAGACCTGTCTGGGACATGGCATCGACCTC-GATAGATGA-AAGCC * * * * 40551804 AGTGTAAGACATGTCTGGGACAT-GCATC-AGCCTCGAAATAT-ACAAGCT 1 AGTGTAAGACCTGTCTGGGACATGGCATCGA-CCTCGATAGATGA-AAGCC * * * * * * * 40551852 AGTGTAAGACCTGTCTAGGACATGGCAT-TAGCTTG-TTG-TG--TGTC 1 AGTGTAAGACCTGTCTGGGACATGGCATCGACCTCGATAGATGAAAGCC * 40551896 AGTGTAAGACCTGTCTGGGACATGGCATCGACAC-CGATAGATGAGAGCC 1 AGTGTAAGACCTGTCTGGGACATGGCATCGAC-CTCGATAGATGAAAGCC * * * * * * ** 40551945 AGTGTAAGACCTATCTGGGACATGACATTGGCCTTGATATATGAAATTC 1 AGTGTAAGACCTGTCTGGGACATGGCATCGACCTCGATAGATGAAAGCC * * ** 40551994 AGTGTAAGACCTGTCTGGGACATGGCATCGACTTTGAT-G-TGCTAGCC 1 AGTGTAAGACCTGTCTGGGACATGGCATCGACCTCGATAGATGAAAGCC * * 40552041 AGTGTAAGACCATGTTTGGAACATGGC 1 AGTGTAAGACC-TGTCTGGGACATGGC 40552068 GTCGGCATCT Statistics Matches: 294, Mismatches: 50, Indels: 34 0.78 0.13 0.09 Matches are distributed among these distances: 44 28 0.10 45 2 0.01 46 34 0.12 47 17 0.06 48 93 0.32 49 83 0.28 50 37 0.13 ACGTcount: A:0.28, C:0.20, G:0.27, T:0.25 Consensus pattern (49 bp): AGTGTAAGACCTGTCTGGGACATGGCATCGACCTCGATAGATGAAAGCC Found at i:40552010 original size:98 final size:97 Alignment explanation

Indices: 40551660--40552025 Score: 319 Period size: 98 Copynumber: 3.8 Consensus size: 97 40551650 TATGTGTGCT * ** * ** * * * 40551660 AGTGTAAGACATGTCTGGGACATGCATTGGCC-ACAT-TATGAGAGCCAGTATAAGACATGTTTG 1 AGTGTAAGACCTGTCTGGGACATGCATTGGCCTTGATATATGAAATTCAGTGTAAGACCTGTCTG * * 40551723 GGACAT-GCATCGGCCTCGAGATATATACAAGCC 66 GGACATGGCATCGACCTCGA-A-AGATACAAGCC * * * * ** * 40551756 AGTGTAAGACATGTCTGGGACATGCATCGGCCCTGAGATAT-ACAAGCCAGTGTAAGACATGTCT 1 AGTGTAAGACCTGTCTGGGACATGCATTGGCCTTGATATATGA-AATTCAGTGTAAGACCTGTCT * * 40551820 GGGACAT-GCATC-AGCCTCGAAATATACAAGCT 65 GGGACATGGCATCGA-CCTCGAAAGATACAAGCC * * * 40551852 AGTGTAAGACCTGTCTAGGACATGGCATTAG-CTTG-T-TGTG---TGTCAGTGTAAGACCTGTC 1 AGTGTAAGACCTGTCTGGGACAT-GCATTGGCCTTGATATATGAAAT-TCAGTGTAAGACCTGTC * * 40551911 TGGGACATGGCATCGACAC-CGATAGATGA-GAGCC 64 TGGGACATGGCATCGAC-CTCGAAAGAT-ACAAGCC * 40551945 AGTGTAAGACCTATCTGGGACATGACATTGGCCTTGATATATGAAATTCAGTGTAAGACCTGTCT 1 AGTGTAAGACCTGTCTGGGACATG-CATTGGCCTTGATATATGAAATTCAGTGTAAGACCTGTCT 40552010 GGGACATGGCATCGAC 65 GGGACATGGCATCGAC 40552026 TTTGATGTGC Statistics Matches: 225, Mismatches: 27, Indels: 34 0.79 0.09 0.12 Matches are distributed among these distances: 92 24 0.11 93 41 0.18 94 9 0.04 95 1 0.00 96 68 0.30 97 8 0.04 98 73 0.32 99 1 0.00 ACGTcount: A:0.29, C:0.20, G:0.27, T:0.25 Consensus pattern (97 bp): AGTGTAAGACCTGTCTGGGACATGCATTGGCCTTGATATATGAAATTCAGTGTAAGACCTGTCTG GGACATGGCATCGACCTCGAAAGATACAAGCC Found at i:40554745 original size:22 final size:22 Alignment explanation

Indices: 40554720--40554761 Score: 66 Period size: 22 Copynumber: 1.9 Consensus size: 22 40554710 ATGATTATGG * 40554720 TTGCTCATACAAGCTAACATAT 1 TTGCTCACACAAGCTAACATAT * 40554742 TTGCTCACACAAGCTGACAT 1 TTGCTCACACAAGCTAACAT 40554762 TATAACCTCT Statistics Matches: 18, Mismatches: 2, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 22 18 1.00 ACGTcount: A:0.33, C:0.26, G:0.12, T:0.29 Consensus pattern (22 bp): TTGCTCACACAAGCTAACATAT Done.