Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.04

Sequence: scaffold150

Parameters: 2 7 7 80 10 50 500

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

Length: 1854615
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.30

Warning! 196055 characters in sequence are not A, C, G, or T


File 4 of 6

Found at i:760067 original size:170 final size:165

Alignment explanation

Indices: 759758--760279 Score: 677 Period size: 167 Copynumber: 3.2 Consensus size: 165 759748 AAAGAATCAT * * 759758 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCCATGTAAAACT 1 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGA-TTACTCTATATATACCTATGTAAAACT ** * * * 759823 TTAACACCCCCCA-TGTGGCCCCACCCTACCCCTAGGGATCATGATTTTCACAACTTGGAATCTA 65 TCGAC-CCCCCCATTGTGGCCCCACCCTACCCCCAGGGGTCATGATTTTCACAACTTAGAATCTA * 759887 CACTACCTGAGGATACTTCCACACAAGTTTCAGCTTTC 129 CACTACCTGAGGATGCTTCCACACAAG-TTCAGCTTTC * * ** 759925 CTGGCTGATAAGTTTCTGAGAAGAACATTTTTAAAGATTAACTCTATATATACCTATAAAAAACT 1 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATT-ACTCTATATATACCTATGTAAAACT 759990 TCGACCCCCCCCCAATTGTGGCCCCACCCTACCCCCAGGGGTCATGATTTTCACAACTTAGAATC 65 TCGA--CCCCCCC-ATTGTGGCCCCACCCTACCCCCAGGGGTCATGATTTTCACAACTTAGAATC 760055 TACACTACCTGAGGATGCTT-C-CAC-A---CAGCTTTC 127 TACACTACCTGAGGATGCTTCCACACAAGTTCAGCTTTC * * * 760088 CTGGCTGATTAGTTCCTGAGAAGAAGATTTCTAAAGATTTCTCTATAGATATATTCCTATGTAAA 1 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTACTCTAT--ATATA--CCTATGTAAA * * 760153 ACTTCGA--CCCCCATTGTGGCCCCACCCTACCCTC-GGGGTCATGATTTTCACAACTTTGAATC 62 ACTTCGACCCCCCCATTGTGGCCCCACCCTACCCCCAGGGGTCATGATTTTCACAACTTAGAATC * * 760215 TACATTACCTGAGGATGCTTCCACACAAGTGTCAGTTTTC 127 TACACTACCTGAGGATGCTTCCACACAAGT-TCAGCTTTC * * 760255 CTGGTTGATTAGTTTTTGAGAAGAA 1 CTGGCTGATTAGTTTCTGAGAAGAA 760280 NNNNNNNNNN Statistics Matches: 313, Mismatches: 26, Indels: 32 0.84 0.07 0.09 Matches are distributed among these distances: 160 46 0.15 161 22 0.07 162 14 0.04 163 44 0.14 164 5 0.02 166 17 0.05 167 88 0.28 168 9 0.03 169 3 0.01 170 65 0.21 ACGTcount: A:0.28, C:0.26, G:0.16, T:0.31 Consensus pattern (165 bp): CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTACTCTATATATACCTATGTAAAACTT CGACCCCCCCATTGTGGCCCCACCCTACCCCCAGGGGTCATGATTTTCACAACTTAGAATCTACA CTACCTGAGGATGCTTCCACACAAGTTCAGCTTTC Found at i:760226 original size:160 final size:159 Alignment explanation

Indices: 759758--760241 Score: 604 Period size: 170 Copynumber: 3.0 Consensus size: 159 759748 AAAGAATCAT * 759758 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTC--TATATATTCCCATGTAAAA 1 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTT-CTCTATATATATTCCTATGTAAAA * * * 759821 CTTTAAC-ACCCCCCA-TGTGGCCCCACCCTACCCCTAGGGATCATGATTTTCACAACTTGGAAT 65 C-TT--CGACCCCCCATTGTGGCCCCACCCTA-CCCTCGGGGTCATGATTTTCACAACTTAGAAT * 759884 CTACACTACCTGAGGATACTTCCACACAAGTTTCAGCTTTC 126 CTACACTACCTGAGGATGCTT-C-CAC-A----CAGCTTTC * * * ** 759925 CTGGCTGATAAGTTTCTGAGAAGAACATTTTTAAAGATTAACTCTATATATA--CCTATAAAAAA 1 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATT-TCTCTATATATATTCCTATGTAAAA * 759988 CTTCGACCCCCCCCCAATTGTGGCCCCACCCTACCCCCAGGGGTCATGATTTTCACAACTTAGAA 65 CTTCGA---CCCCCC-ATTGTGGCCCCACCCTACCCTC-GGGGTCATGATTTTCACAACTTAGAA 760053 TCTACACTACCTGAGGATGCTTCCACACAGCTTTC 125 TCTACACTACCTGAGGATGCTTCCACACAGCTTTC * * 760088 CTGGCTGATTAGTTCCTGAGAAGAAGATTTCTAAAGATTTCTCTATAGATATATTCCTATGTAAA 1 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTCTCTAT--ATATATTCCTATGTAAA * 760153 ACTTCGA-CCCCCATTGTGGCCCCACCCTACCCTCGGGGTCATGATTTTCACAACTTTGAATCTA 64 ACTTCGACCCCCCATTGTGGCCCCACCCTACCCTCGGGGTCATGATTTTCACAACTTAGAATCTA * 760217 CATTACCTGAGGATGCTTCCACACA 129 CACTACCTGAGGATGCTTCCACACA 760242 AGTGTCAGTT Statistics Matches: 282, Mismatches: 21, Indels: 35 0.83 0.06 0.10 Matches are distributed among these distances: 160 53 0.19 161 21 0.07 162 11 0.04 163 43 0.15 164 6 0.02 165 1 0.00 166 17 0.06 167 50 0.18 168 9 0.03 169 11 0.04 170 60 0.21 ACGTcount: A:0.28, C:0.27, G:0.15, T:0.30 Consensus pattern (159 bp): CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTCTCTATATATATTCCTATGTAAAAC TTCGACCCCCCATTGTGGCCCCACCCTACCCTCGGGGTCATGATTTTCACAACTTAGAATCTACA CTACCTGAGGATGCTTCCACACAGCTTTC Found at i:761127 original size:166 final size:166 Alignment explanation

Indices: 760619--761702 Score: 1482 Period size: 166 Copynumber: 6.5 Consensus size: 166 760609 AAAGAAACAT * * * 760619 CTGGCTGATTAGTTTCT--G-AGAAGATTTTTAAAGATTTACCCTATATATTCCTTTGTTAAATT 1 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTTAAACT * * ** 760681 TTGACCCCCCCATTGTGGCCCCACCCTA-CCCCTGGGGATCATGATTTTCACAACCATGAATCTA 66 TCGA-CCCCCCATTGTGGCCCCACCCTACCCCCAGGGG-TCATGATTTTCACAAATATGAATCTA * * 760745 CACTACCTGAGGATGCTTTCACACACGTTTCAGCTTTC 129 CACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTC * * * * * 760783 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTGTTTATTCCTATCTAAAACA 1 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTTAAACT * * * * * 760848 TCGACCTCCCATTGTGGCCCAAACCTACCCCCA-GGGTTATGATTTTCACAAATTTGAATCTACA 66 TCGACCCCCCATTGTGGCCCCACCCTACCCCCAGGGGTCATGATTTTCACAAATATGAATCTACA 760912 CTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTC 131 CTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTC * * * * 760948 CTGGCTAATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATTTAATCATATGTTAAACT 1 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTTAAACT ** * * * * * 761013 TCGACCCCCCATTGTGGCCCCATTCTACCCCCAGGGGTTATTATTTTCACAACTTTGAATCAACA 66 TCGACCCCCCATTGTGGCCCCACCCTACCCCCAGGGGTCATGATTTTCACAAATATGAATCTACA * * * 761078 CTACCTGAGGATGCTTCCAAAGAAGTTTCAGCATTGC 131 CTACCTGAGGATGCTTCCACACAAGTTTCAGC-TTTC * 761115 C-GGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTTTAACT 1 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTTAAACT * * * * 761179 TCGATCCCCCATTGTGGCCCCACCCTTCCCCCGGGGGTCATGATTTTCACAAATATGAATTTACA 66 TCGACCCCCCATTGTGGCCCCACCCTACCCCCAGGGGTCATGATTTTCACAAATATGAATCTACA * * * 761244 CTACCTGAGGATGCATCCACAAAAGTGTCAGCTTTC 131 CTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTC * * * 761280 CTCGCTGATTAGTTTCTAAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATTTTAAACT 1 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTTAAACT * * * * 761345 TCGATCCCCCATTGTGGCCCCACCCTACCCCCGGGGGCCATGATTTTCACAACTATGAATCTACA 66 TCGACCCCCCATTGTGGCCCCACCCTACCCCCAGGGGTCATGATTTTCACAAATATGAATCTACA * * 761410 CTACCTGAGGATGCTTTCACACAAGTGTCAGCTTTC 131 CTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTC * * * 761446 CTGGCCGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTATTCTATATATTCCTATGTAAAACT 1 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTTAAACT ** * * * * 761511 TCGATCCTTCC-TTGTGGCCCAACCCTACCTCC-GGGGATCATGATTTTCACAAATTTGTATCTA 66 TCGA-CCCCCCATTGTGGCCCCACCCTACCCCCAGGGG-TCATGATTTTCACAAATATGAATCTA * * * 761574 CATTACCTGATGATGCTTTCACACAAGTTTCAGCTTTC 129 CACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTC * * * 761612 CTGGCTGATTAGTTTCTGAGGAGAAGATTTTTAAAGATTTACTCTATATATTCATTTGTTAAACT 1 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTTAAACT 761677 TCGACCCCCCATTGTGGCCCCACCCT 66 TCGACCCCCCATTGTGGCCCCACCCT 761703 CAGGTGAGCT Statistics Matches: 815, Mismatches: 95, Indels: 18 0.88 0.10 0.02 Matches are distributed among these distances: 164 17 0.02 165 157 0.19 166 591 0.73 167 50 0.06 ACGTcount: A:0.26, C:0.24, G:0.16, T:0.34 Consensus pattern (166 bp): CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTTAAACT TCGACCCCCCATTGTGGCCCCACCCTACCCCCAGGGGTCATGATTTTCACAAATATGAATCTACA CTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTC Found at i:762942 original size:8 final size:8 Alignment explanation

Indices: 762931--762976 Score: 57 Period size: 8 Copynumber: 6.4 Consensus size: 8 762921 TAAAAAGTTT 762931 ACAGACGG 1 ACAGACGG 762939 ACAGACGG 1 ACAGACGG 762947 ACAGAC-G 1 ACAGACGG 762954 ---GACGG 1 ACAGACGG 762959 ACAGACGG 1 ACAGACGG 762967 AC-GACGG 1 ACAGACGG 762974 ACA 1 ACA 762977 AAATGTGATC Statistics Matches: 33, Mismatches: 0, Indels: 10 0.77 0.00 0.23 Matches are distributed among these distances: 4 3 0.09 5 1 0.03 7 8 0.24 8 21 0.64 ACGTcount: A:0.37, C:0.26, G:0.37, T:0.00 Consensus pattern (8 bp): ACAGACGG Found at i:762959 original size:4 final size:4 Alignment explanation

Indices: 762934--762975 Score: 50 Period size: 4 Copynumber: 10.8 Consensus size: 4 762924 AAAGTTTACA * * * 762934 GACG GACA GACG GACA GACG GACG GACA GACG GAC- GACG GAC 1 GACG GACG GACG GACG GACG GACG GACG GACG GACG GACG GAC 762976 AAAATGTGAT Statistics Matches: 31, Mismatches: 6, Indels: 2 0.79 0.15 0.05 Matches are distributed among these distances: 3 3 0.10 4 28 0.90 ACGTcount: A:0.33, C:0.26, G:0.40, T:0.00 Consensus pattern (4 bp): GACG Found at i:762959 original size:12 final size:12 Alignment explanation

Indices: 762942--762969 Score: 56 Period size: 12 Copynumber: 2.3 Consensus size: 12 762932 CAGACGGACA 762942 GACGGACAGACG 1 GACGGACAGACG 762954 GACGGACAGACG 1 GACGGACAGACG 762966 GACG 1 GACG 762970 ACGGACAAAA Statistics Matches: 16, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 12 16 1.00 ACGTcount: A:0.32, C:0.25, G:0.43, T:0.00 Consensus pattern (12 bp): GACGGACAGACG Found at i:767290 original size:4 final size:4 Alignment explanation

Indices: 767281--767328 Score: 60 Period size: 4 Copynumber: 12.0 Consensus size: 4 767271 AGTTGCGTCT * * * * 767281 ACAG ACAG ACGG ACAG ACGG ACAG ACAG ACAG ACGG ACAG ACGG ACAG 1 ACAG ACAG ACAG ACAG ACAG ACAG ACAG ACAG ACAG ACAG ACAG ACAG 767329 GGTGAAACCA Statistics Matches: 36, Mismatches: 8, Indels: 0 0.82 0.18 0.00 Matches are distributed among these distances: 4 36 1.00 ACGTcount: A:0.42, C:0.25, G:0.33, T:0.00 Consensus pattern (4 bp): ACAG Found at i:767297 original size:8 final size:8 Alignment explanation

Indices: 767284--767328 Score: 81 Period size: 8 Copynumber: 5.6 Consensus size: 8 767274 TGCGTCTACA 767284 GACAGACG 1 GACAGACG 767292 GACAGACG 1 GACAGACG * 767300 GACAGACA 1 GACAGACG 767308 GACAGACG 1 GACAGACG 767316 GACAGACG 1 GACAGACG 767324 GACAG 1 GACAG 767329 GGTGAAACCA Statistics Matches: 35, Mismatches: 2, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 8 35 1.00 ACGTcount: A:0.40, C:0.24, G:0.36, T:0.00 Consensus pattern (8 bp): GACAGACG Found at i:791492 original size:75 final size:75 Alignment explanation

Indices: 791370--791519 Score: 300 Period size: 75 Copynumber: 2.0 Consensus size: 75 791360 GTGGGTGGGC 791370 GGGGTGGGGGGGGTGTAGTTAGCATGTTTGAAATGTTTGTTATATTATACCTATCATATGAATTT 1 GGGGTGGGGGGGGTGTAGTTAGCATGTTTGAAATGTTTGTTATATTATACCTATCATATGAATTT 791435 TGTATTACAT 66 TGTATTACAT 791445 GGGGTGGGGGGGGTGTAGTTAGCATGTTTGAAATGTTTGTTATATTATACCTATCATATGAATTT 1 GGGGTGGGGGGGGTGTAGTTAGCATGTTTGAAATGTTTGTTATATTATACCTATCATATGAATTT 791510 TGTATTACAT 66 TGTATTACAT 791520 TTAATGATTG Statistics Matches: 75, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 75 75 1.00 ACGTcount: A:0.24, C:0.07, G:0.28, T:0.41 Consensus pattern (75 bp): GGGGTGGGGGGGGTGTAGTTAGCATGTTTGAAATGTTTGTTATATTATACCTATCATATGAATTT TGTATTACAT Found at i:799152 original size:21 final size:21 Alignment explanation

Indices: 799113--799152 Score: 62 Period size: 21 Copynumber: 1.9 Consensus size: 21 799103 TGTCTCCCGC * 799113 CTACCGCTTTTATTTAAAAAT 1 CTACCGCTTTTATTCAAAAAT * 799134 CTACCGCTTTTCTTCAAAA 1 CTACCGCTTTTATTCAAAA 799153 TACGTTCCTT Statistics Matches: 17, Mismatches: 2, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 21 17 1.00 ACGTcount: A:0.30, C:0.25, G:0.05, T:0.40 Consensus pattern (21 bp): CTACCGCTTTTATTCAAAAAT Found at i:803374 original size:13 final size:13 Alignment explanation

Indices: 803356--803380 Score: 50 Period size: 13 Copynumber: 1.9 Consensus size: 13 803346 TTGGACCACA 803356 CTTGATGCTGATG 1 CTTGATGCTGATG 803369 CTTGATGCTGAT 1 CTTGATGCTGAT 803381 CTATTACCTT 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:0.16, C:0.16, G:0.28, T:0.40 Consensus pattern (13 bp): CTTGATGCTGATG Found at i:806098 original size:2 final size:2 Alignment explanation

Indices: 806091--806165 Score: 141 Period size: 2 Copynumber: 37.5 Consensus size: 2 806081 GCCTAAACGC * 806091 CT CT CT CT CT CT CT GT CT CT CT CT CT CT CT CT CT CT CT CT CT 1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT 806133 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C 1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C 806166 CAGTAAGGTG Statistics Matches: 71, Mismatches: 2, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 2 71 1.00 ACGTcount: A:0.00, C:0.49, G:0.01, T:0.49 Consensus pattern (2 bp): CT Found at i:808212 original size:169 final size:169 Alignment explanation

Indices: 807894--808478 Score: 837 Period size: 168 Copynumber: 3.5 Consensus size: 169 807884 AAAAAGATTT * * * ** 807894 TTCCTGCATAAAAAATGTATCCCCCAATTGTGGCCCCACCCTATTCACGGGGTTCATGATTTGAA 1 TTCCTGTATAAAAAATTTATCCCCCAATTGTGGCCCCACCCTATCCACGGGGACCATGATTTGAA 807959 CAAACTTGAATCTACACTATCTGTGGAATTGCTTCCACTCAAATTTGAGCTTTCTTGGCCACATA 66 CAAACTTGAATCTACACTATCTGTGGAATTGCTTCCACTCAAATTTGAGCTTTCTTGGCCACATA * 808024 GTTTTTAACAGAATTTTTTTTCAAGATTTTCTCTATATA 131 GTTTTTAAAAGAATTTTTTTTCAAGATTTTCTCTATATA * 808063 TTCCTGTATAAAAAATTTATCCCCCAATTGTGGCCCCACCCTATCCACGGGGACCATGATTTTAA 1 TTCCTGTATAAAAAATTTATCCCCCAATTGTGGCCCCACCCTATCCACGGGGACCATGATTTGAA 808128 C-AACTTGAATCTACACTATCTGTGGAATTGCTTCCACTCAAATTTGAGCTTTCTTGGCCACATA 66 CAAACTTGAATCTACACTATCTGTGGAATTGCTTCCACTCAAATTTGAGCTTTCTTGGCCACATA 808192 GTTTTTAAAAGAATTTTTTTTCAAGATTTTCTCTATATA 131 GTTTTTAAAAGAATTTTTTTTCAAGATTTTCTCTATATA 808231 TTCCTGTATAAAAAATTTATCCCCCAATTGTGGCCCCACCCTATCCACGGGGACCATGATTTGAA 1 TTCCTGTATAAAAAATTTATCCCCCAATTGTGGCCCCACCCTATCCACGGGGACCATGATTTGAA * * * ** * ** 808296 CAAACTTGAATCTACACTATCTGAGG-A-TGCTCCCATTTTAATTTTAGCTTT-TATGGCCTGAT 66 CAAACTTGAATCTACACTATCTGTGGAATTGCTTCCACTCAAATTTGAGCTTTCT-TGGCCACAT * ** * 808358 AGTTTTTGAGAAGAA-GATTTTTAAAGATTTTCTCTATATA 130 AGTTTTT-AAAAGAATTTTTTTTCAAGATTTTCTCTATATA * * * * ** * * 808398 TTCCTATGT-AAAACTTGATCCCCCTCTTGTAGCCCCTCCCTA-CCACCGGGGACCATGA--TGA 1 TTCCTGTATAAAAAATTTATCCCCCAATTGTGGCCCCACCCTATCCA-CGGGGACCATGATTTGA 808459 ACAAACTTGAATCTACACTA 65 ACAAACTTGAATCTACACTA 808479 CCTGAGGATG Statistics Matches: 384, Mismatches: 28, Indels: 13 0.90 0.07 0.03 Matches are distributed among these distances: 164 23 0.06 165 3 0.01 166 40 0.10 167 62 0.16 168 173 0.45 169 83 0.22 ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35 Consensus pattern (169 bp): TTCCTGTATAAAAAATTTATCCCCCAATTGTGGCCCCACCCTATCCACGGGGACCATGATTTGAA CAAACTTGAATCTACACTATCTGTGGAATTGCTTCCACTCAAATTTGAGCTTTCTTGGCCACATA GTTTTTAAAAGAATTTTTTTTCAAGATTTTCTCTATATA Found at i:809056 original size:18 final size:18 Alignment explanation

Indices: 809033--809069 Score: 56 Period size: 18 Copynumber: 2.1 Consensus size: 18 809023 AATTCCAGAT * 809033 AGTGAATCCACAGTACAC 1 AGTGAATCCACAATACAC * 809051 AGTGAATTCACAATACAC 1 AGTGAATCCACAATACAC 809069 A 1 A 809070 ATCTCTCTCT Statistics Matches: 17, Mismatches: 2, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 18 17 1.00 ACGTcount: A:0.43, C:0.24, G:0.14, T:0.19 Consensus pattern (18 bp): AGTGAATCCACAATACAC Found at i:810240 original size:17 final size:16 Alignment explanation

Indices: 810218--810252 Score: 52 Period size: 17 Copynumber: 2.1 Consensus size: 16 810208 AAGAGGATCA 810218 TAATAGTTACACATTAG 1 TAATAGTTACACA-TAG * 810235 TAATAGTTTCACATAG 1 TAATAGTTACACATAG 810251 TA 1 TA 810253 CCCTAGGCTA Statistics Matches: 17, Mismatches: 1, Indels: 1 0.89 0.05 0.05 Matches are distributed among these distances: 16 5 0.29 17 12 0.71 ACGTcount: A:0.40, C:0.11, G:0.11, T:0.37 Consensus pattern (16 bp): TAATAGTTACACATAG Found at i:810474 original size:30 final size:30 Alignment explanation

Indices: 810439--810529 Score: 164 Period size: 30 Copynumber: 3.0 Consensus size: 30 810429 ATTTTGAACT * 810439 GCCGGTCAATAGACTGCGATCTATTAGACC 1 GCCGGTCAATAGACTGCGATCTATTGGACC * 810469 GCCGGTCAATAGACTTCGATCTATTGGACC 1 GCCGGTCAATAGACTGCGATCTATTGGACC 810499 GCCGGTCAATAGACTGCGATCTATTGGACC 1 GCCGGTCAATAGACTGCGATCTATTGGACC 810529 G 1 G 810530 GCAACGTATT Statistics Matches: 58, Mismatches: 3, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 30 58 1.00 ACGTcount: A:0.24, C:0.26, G:0.25, T:0.24 Consensus pattern (30 bp): GCCGGTCAATAGACTGCGATCTATTGGACC Found at i:813410 original size:162 final size:162 Alignment explanation

Indices: 813125--813574 Score: 540 Period size: 162 Copynumber: 2.8 Consensus size: 162 813115 CGGGGGCTAT * * * 813125 AACAAAGTCCTATTTAACAGGAAGTTGACGTCCGATTGGTA-ATAAAATATATACCACGATATGA 1 AACAAAGT-CTATTTAACAGGAAGTTGACGTCCGATTGGTACA-AAAATATATCCCACAATATGG * * 813189 CATGCCTAAA-AAATAGTGTGTT-AAATGTCAAGCATCTGCGATAAATAGTTGCTGAGAAATCTT 64 CATGCCTAAACAAATAGTGTTTTAAAATTTCAAGCATCTGCGATAAATAGTTGC-GAGAAATCTT * * * 813252 TGACGAAAA-TGGTTTAATAATTCTGGCTAGAAATA 128 TAACGAAAATTGGTTTAAAAATTCTGGCTA-AAACA *** 813287 AACAAAGTCATATTTAACAGGAAGTTGACGTTTTATTGGTACAAAAATATATCCCACAATATGGC 1 AACAAAGTC-TATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACAATATGGC * 813352 ATGCCTAAACAAATAGTGTTTTAAAATTTCAAGCATCTGCTATAAATAGTTG-GAGAAATCTTTA 65 ATGCCTAAACAAATAGTGTTTTAAAATTTCAAGCATCTGCGATAAATAGTTGCGAGAAATCTTTA * * * 813416 ATGAAAATTTGTTTAAAAATTTTGGCTAAAACA 130 ACGAAAATTGGTTTAAAAATTCTGGCTAAAACA * 813449 AA-AAACCTGTC-ATTTAACAGGAAGTTGATGTCCGATTGGTACAAAAATATATCCCA-AGATAT 1 AACAAA---GTCTATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACA-ATAT * * * * * 813511 GGCATGCCTAAATCAAAAAGT-TTGTTACAACTTCAAGCATATGCGATAAACAGTTGCTGAGAAA 62 GGCATGCCTAAA-CAAATAGTGTT-TTAAAATTTCAAGCATCTGCGATAAATAGTTGC-GAGAAA 813575 AATGCGACAG Statistics Matches: 250, Mismatches: 25, Indels: 23 0.84 0.08 0.08 Matches are distributed among these distances: 161 5 0.02 162 146 0.58 163 63 0.25 164 30 0.12 165 6 0.02 ACGTcount: A:0.40, C:0.14, G:0.17, T:0.30 Consensus pattern (162 bp): AACAAAGTCTATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACAATATGGCA TGCCTAAACAAATAGTGTTTTAAAATTTCAAGCATCTGCGATAAATAGTTGCGAGAAATCTTTAA CGAAAATTGGTTTAAAAATTCTGGCTAAAACA Found at i:815932 original size:185 final size:180 Alignment explanation

Indices: 815589--816082 Score: 731 Period size: 186 Copynumber: 2.7 Consensus size: 180 815579 GATAAAAAAT * * * * 815589 GTTCAAAAGCCGGTACTTTTTTCATAAATAATCAGAAATCAATATCCTAGCAATATGCACACCTC 1 GTTCAAAAGCTGGTATTTTTTTCATAAATTATCAGAAATCAAAATCCTAGCAATATGCACACCTC ** * * 815654 TGATATATGTACAATAAATCTGCAAAAGAACAACTTCCAATCTTGAAAACTGTAGGAGGAGTTTT 66 TGATATATGTACAATTGATCTGCAAAAGAACAACTTCCTATCTTGAAAACTGTAGGAGGAGTTAT ** 815719 CCGTACAATGTGGGTACCCTATATGCAATATTTTGCCAAAAAAATGACTATTTAAA 131 CCGTACAATAAGGGTACCCTATATGCAATATTTTGCC-AAAAAATGAC----T-AA * * 815775 GTTCAAAAGCTGGTATTTTTTTCATAAATTATCGGCAATCAAAATCCTAGCAATATGCACACCTC 1 GTTCAAAAGCTGGTATTTTTTTCATAAATTATCAGAAATCAAAATCCTAGCAATATGCACACCTC * 815840 TGATATATGTACAATTGATCT-CAAAAGAACAATTTCCTATCTTGAAAACTGTAGGAGGAGTTAT 66 TGATATATGTACAATTGATCTGCAAAAGAACAACTTCCTATCTTGAAAACTGTAGGAGGAGTTAT * ** 815904 CCGTACTATAAGGGTACCCTATATGCAATATTTTGCCAAAAGGTGACTAA 131 CCGTACAATAAGGGTACCCTATATGCAATATTTTGCCAAAAAATGACTAA * * 815954 GTTCAAAAGCTGGTATTTTTTTTTAATAAATTGA-CAGAAATCAAAATCTTAGCAATATGCACAC 1 GTTCAAAAGCTGGTA--TTTTTTTCATAAATT-ATCAGAAATCAAAATCCTAGCAATATGCACAC 816018 CTCTGATATATGTACAATTGATCTGCAAAAGAACAACTTCCTATCTTGAAAACTGTAGGAGGAGT 63 CTCTGATATATGTACAATTGATCTGCAAAAGAACAACTTCCTATCTTGAAAACTGTAGGAGGAGT 816083 CAGTGATTTT Statistics Matches: 283, Mismatches: 21, Indels: 12 0.90 0.07 0.04 Matches are distributed among these distances: 179 17 0.06 180 1 0.00 181 65 0.23 182 40 0.14 184 8 0.03 185 74 0.26 186 78 0.28 ACGTcount: A:0.37, C:0.17, G:0.15, T:0.31 Consensus pattern (180 bp): GTTCAAAAGCTGGTATTTTTTTCATAAATTATCAGAAATCAAAATCCTAGCAATATGCACACCTC TGATATATGTACAATTGATCTGCAAAAGAACAACTTCCTATCTTGAAAACTGTAGGAGGAGTTAT CCGTACAATAAGGGTACCCTATATGCAATATTTTGCCAAAAAATGACTAA Found at i:817534 original size:19 final size:20 Alignment explanation

Indices: 817483--817614 Score: 75 Period size: 20 Copynumber: 7.0 Consensus size: 20 817473 AACAGCAATG * 817483 ATATTATACAATATCATATC 1 ATATGATACAATATCATATC * 817503 ATATGATACAATAT-ATATT 1 ATATGATACAATATCATATC ** ** 817522 ATATGATTTAATA-CA-AAA 1 ATATGATACAATATCATATC * 817540 ATA-AAT-CAA-A--A-ATC 1 ATATGATACAATATCATATC * * * 817554 ATATTGTTACACTATCATATA 1 ATA-TGATACAATATCATATC ** 817575 ATATTTTACAATATCATATC 1 ATATGATACAATATCATATC * 817595 TTATGATACAATATCATATC 1 ATATGATACAATATCATATC 817615 TGATAAAATA Statistics Matches: 84, Mismatches: 20, Indels: 16 0.70 0.17 0.13 Matches are distributed among these distances: 14 5 0.06 15 1 0.01 16 3 0.04 17 4 0.05 18 5 0.06 19 16 0.19 20 45 0.54 21 5 0.06 ACGTcount: A:0.46, C:0.12, G:0.03, T:0.39 Consensus pattern (20 bp): ATATGATACAATATCATATC Found at i:831458 original size:14 final size:12 Alignment explanation

Indices: 831425--831452 Score: 56 Period size: 12 Copynumber: 2.3 Consensus size: 12 831415 GTGTATTCAG 831425 AATACCTTATAT 1 AATACCTTATAT 831437 AATACCTTATAT 1 AATACCTTATAT 831449 AATA 1 AATA 831453 ATCCTTGATA Statistics Matches: 16, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 12 16 1.00 ACGTcount: A:0.46, C:0.14, G:0.00, T:0.39 Consensus pattern (12 bp): AATACCTTATAT Found at i:836484 original size:160 final size:159 Alignment explanation

Indices: 836294--836615 Score: 527 Period size: 160 Copynumber: 2.0 Consensus size: 159 836284 TATATCCCGA * * * 836294 TATACATCCAAAAATGATACCTTATTTCTTATATTTACATTTGTTGCAAATTATGACAATAACAA 1 TATACATCCAAAAATGATACCTTATTTCTTATAGTTACAATTGCTGCAAATTATGACAATAACAA * * * 836359 TGCTCCATACTTTCTCTTTTGTGATGACCTAGAAAGCCGCTTCCATTAAAATGACGTAACAAAAA 66 TGCTCCATACTTTCTCTTTTGTGATGACCTAGAAAACCGCTTCAATTAAAATGACGGAACAAAAA * * 836424 ATAGTGCAATAATGTTGCAAGCATTTGAT 131 ATAGTACAACAATGTTGCAAGCATTTGAT * 836453 TATNACATCCAAAAATGATACCTTATTTCTTATAGTTACAATTGCTGCAAATTCTGACAATAACA 1 TAT-ACATCCAAAAATGATACCTTATTTCTTATAGTTACAATTGCTGCAAATTATGACAATAACA * * 836518 ATGCTCCATACTTTCTTTTTTGTGATGACCTAGAAAACCGCTTCAATTAAGATGACGGAACAAAA 65 ATGCTCCATACTTTCTCTTTTGTGATGACCTAGAAAACCGCTTCAATTAAAATGACGGAACAAAA * 836583 AATAGTACAACAATGTTGCAAGTATTTGAT 130 AATAGTACAACAATGTTGCAAGCATTTGAT 836613 TAT 1 TAT 836616 CATGATAAAT Statistics Matches: 150, Mismatches: 12, Indels: 1 0.92 0.07 0.01 Matches are distributed among these distances: 159 3 0.02 160 147 0.98 ACGTcount: A:0.36, C:0.17, G:0.12, T:0.34 Consensus pattern (159 bp): TATACATCCAAAAATGATACCTTATTTCTTATAGTTACAATTGCTGCAAATTATGACAATAACAA TGCTCCATACTTTCTCTTTTGTGATGACCTAGAAAACCGCTTCAATTAAAATGACGGAACAAAAA ATAGTACAACAATGTTGCAAGCATTTGAT Found at i:837620 original size:13 final size:13 Alignment explanation

Indices: 837602--837626 Score: 50 Period size: 13 Copynumber: 1.9 Consensus size: 13 837592 TATCATGCAC 837602 TGTATGTAAAACA 1 TGTATGTAAAACA 837615 TGTATGTAAAAC 1 TGTATGTAAAAC 837627 CTTCAATAGT 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:0.44, C:0.08, G:0.16, T:0.32 Consensus pattern (13 bp): TGTATGTAAAACA Found at i:839841 original size:16 final size:16 Alignment explanation

Indices: 839820--839855 Score: 63 Period size: 16 Copynumber: 2.2 Consensus size: 16 839810 AAGGAAAAAC 839820 TTCGAGGTTTCAAGAG 1 TTCGAGGTTTCAAGAG * 839836 TTCGAGTTTTCAAGAG 1 TTCGAGGTTTCAAGAG 839852 TTCG 1 TTCG 839856 GAATTTTCCG Statistics Matches: 19, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 16 19 1.00 ACGTcount: A:0.22, C:0.14, G:0.28, T:0.36 Consensus pattern (16 bp): TTCGAGGTTTCAAGAG Found at i:840606 original size:16 final size:16 Alignment explanation

Indices: 840568--840617 Score: 64 Period size: 16 Copynumber: 3.1 Consensus size: 16 840558 GCAGTTTGAC * * 840568 TTCGAGGAATCAAGGG 1 TTCGAGAAATCAAGAG * 840584 TTTCGAGAGATCAAGAG 1 -TTCGAGAAATCAAGAG 840601 TTCGAGAAATCAAGAG 1 TTCGAGAAATCAAGAG 840617 T 1 T 840618 AAATTTGCTA Statistics Matches: 29, Mismatches: 4, Indels: 1 0.85 0.12 0.03 Matches are distributed among these distances: 16 16 0.55 17 13 0.45 ACGTcount: A:0.36, C:0.12, G:0.30, T:0.22 Consensus pattern (16 bp): TTCGAGAAATCAAGAG Found at i:840702 original size:15 final size:15 Alignment explanation

Indices: 840665--840714 Score: 55 Period size: 15 Copynumber: 3.1 Consensus size: 15 840655 CTAGGCTCAC * 840665 TTCGAGCGATCAAGAAC 1 TTCGAGCGATC--GAAG 840682 TTCGAGCGATCGAAG 1 TTCGAGCGATCGAAG * 840697 TTCGAGCCATCGAGAG 1 TTCGAGCGATCGA-AG 840713 TT 1 TT 840715 ACCTGTATAA Statistics Matches: 30, Mismatches: 2, Indels: 3 0.86 0.06 0.09 Matches are distributed among these distances: 15 15 0.50 16 4 0.13 17 11 0.37 ACGTcount: A:0.28, C:0.22, G:0.28, T:0.22 Consensus pattern (15 bp): TTCGAGCGATCGAAG Found at i:843279 original size:2 final size:2 Alignment explanation

Indices: 843272--843306 Score: 61 Period size: 2 Copynumber: 17.5 Consensus size: 2 843262 ATAATTTTGA * 843272 AT AT AT AT AT AT AT AT GT AT AT AT AT AT AT AT AT A 1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A 843307 CTTACTTGCA Statistics Matches: 31, Mismatches: 2, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 2 31 1.00 ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49 Consensus pattern (2 bp): AT Found at i:850956 original size:2 final size:2 Alignment explanation

Indices: 850951--850985 Score: 70 Period size: 2 Copynumber: 17.5 Consensus size: 2 850941 GACATGCATG 850951 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G 1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G 850986 GACCTAAATA Statistics Matches: 33, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 33 1.00 ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00 Consensus pattern (2 bp): GA Found at i:856695 original size:2 final size:2 Alignment explanation

Indices: 856688--856727 Score: 73 Period size: 2 Copynumber: 20.5 Consensus size: 2 856678 GAGGGGGAGG 856688 GA GA GA GA GA GA G- GA GA GA GA GA GA GA GA GA GA GA GA GA G 1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G 856728 GCATGCATTT Statistics Matches: 37, Mismatches: 0, Indels: 2 0.95 0.00 0.05 Matches are distributed among these distances: 1 1 0.03 2 36 0.97 ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00 Consensus pattern (2 bp): GA Found at i:865294 original size:146 final size:146 Alignment explanation

Indices: 865028--865590 Score: 753 Period size: 146 Copynumber: 3.9 Consensus size: 146 865018 GTCTGTGCAA * 865028 TCGTGTCCGGTCCATATCTTTC-TAATGAAGAAACATTGGAAGTTCTTACTTCACACAAAGATTG 1 TCGTGTCCGGTCCATATCTTTCTTAACG-AGAAACATTGGAAGTTCTTACTTCACACAAAGATTG * * * 865092 CTTATGACCTAAGGGTGTGTCATGATCTTGACCCAAGGTCATTTGGGCAAGGTCAAGGTCACTGG 65 CTTATGAACTAAGGGTGTGTCATGACCTTGAACCAAGGTCATTTGGGCAAGGTCAAGGTCACTGG * 865157 CAGAAAAAATGCAAAAT 130 CAGAAAAAGTGCAAAAT * * * 865174 TTGTGTCCGGTCCATATCTTTTTTAACGAGAAACATTGGAAGTTCTTACTTCACACAAAGATTAC 1 TCGTGTCCGGTCCATATCTTTCTTAACGAGAAACATTGGAAGTTCTTACTTCACACAAAGATTGC * ** * 865239 TTATGAACTAAGGGTGTGTCATGACCTTGAACAAAGGTCATTCAGGCAGGGTCAAGGTCACTGGC 66 TTATGAACTAAGGGTGTGTCATGACCTTGAACCAAGGTCATTTGGGCAAGGTCAAGGTCACTGGC 865304 AGAAAAAGTGCAAAAT 131 AGAAAAAGTGCAAAAT * * 865320 TCGTGCCCGGTCCATATCTTTCTTAACAAGAAACATTGGAAGTTCTTACTTCACACAAAGATTGC 1 TCGTGTCCGGTCCATATCTTTCTTAACGAGAAACATTGGAAGTTCTTACTTCACACAAAGATTGC * * * * * 865385 TTATGACCTAAGGATGTGTCATGACCTTGACCCATGGTCATTTGGGTAAGGTCAAGGTCACTGGC 66 TTATGAACTAAGGGTGTGTCATGACCTTGAACCAAGGTCATTTGGGCAAGGTCAAGGTCACTGGC 865450 AG--AAAGTGCAAAAT 131 AGAAAAAGTGCAAAAT * * * * * * * 865464 TCATGTCCAGTCCATATCTTTCTT-ACAGACAAATATT-GAAGTTCTTAATTCACAAAAAAATAC 1 TCGTGTCCGGTCCATATCTTTCTTAAC-GAGAAACATTGGAAGTTCTTACTTCACACAAAGAT-- * * * 865527 TGCTTAT-AACCTTAGGGTGTGTCATGACCTTGAACCAAGGGTCAATTGAGG-AAGTTCAAGGTC 63 TGCTTATGAA-CTAAGGGTGTGTCATGACCTTGAACCAA-GGTCATTTG-GGCAAGGTCAAGGTC 865590 A 125 A 865591 TTGTTTCAAA Statistics Matches: 368, Mismatches: 42, Indels: 14 0.87 0.10 0.03 Matches are distributed among these distances: 143 23 0.06 144 41 0.11 145 31 0.08 146 267 0.73 147 6 0.02 ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29 Consensus pattern (146 bp): TCGTGTCCGGTCCATATCTTTCTTAACGAGAAACATTGGAAGTTCTTACTTCACACAAAGATTGC TTATGAACTAAGGGTGTGTCATGACCTTGAACCAAGGTCATTTGGGCAAGGTCAAGGTCACTGGC AGAAAAAGTGCAAAAT Found at i:892926 original size:31 final size:31 Alignment explanation

Indices: 892832--892926 Score: 154 Period size: 31 Copynumber: 3.1 Consensus size: 31 892822 ATGCGGCGGG 892832 TTGTTCCCAAAGTCAGGGTAAGTCTTCTGTC 1 TTGTTCCCAAAGTCAGGGTAAGTCTTCTGTC ** * 892863 TCATTCCCAAAGTCAGGGTAAGTCATCTGTC 1 TTGTTCCCAAAGTCAGGGTAAGTCTTCTGTC * 892894 TTGTTCCCAAAGTCAGGGTAAGTCTTGTGTC 1 TTGTTCCCAAAGTCAGGGTAAGTCTTCTGTC 892925 TT 1 TT 892927 CACCGGTCAT Statistics Matches: 57, Mismatches: 7, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 31 57 1.00 ACGTcount: A:0.21, C:0.22, G:0.22, T:0.35 Consensus pattern (31 bp): TTGTTCCCAAAGTCAGGGTAAGTCTTCTGTC Found at i:901497 original size:22 final size:22 Alignment explanation

Indices: 901458--901534 Score: 86 Period size: 22 Copynumber: 3.5 Consensus size: 22 901448 GGTGCTCTGT * * * 901458 AGGTACTCTTTAGATATACTAA 1 AGGTACACTGTAGGTATACTAA * 901480 AGGTACACTGTAGGTATACCATA 1 AGGTACACTGTAGGTATACTA-A 901503 A-GTACACTGT-GGATATACTAA 1 AGGTACACTGTAGG-TATACTAA 901524 AGGTACACTGT 1 AGGTACACTGT 901535 TAACACTGAA Statistics Matches: 47, Mismatches: 5, Indels: 6 0.81 0.09 0.10 Matches are distributed among these distances: 21 4 0.09 22 41 0.87 23 2 0.04 ACGTcount: A:0.35, C:0.16, G:0.19, T:0.30 Consensus pattern (22 bp): AGGTACACTGTAGGTATACTAA Found at i:905367 original size:35 final size:35 Alignment explanation

Indices: 905325--905394 Score: 131 Period size: 35 Copynumber: 2.0 Consensus size: 35 905315 TGTTTACAAA 905325 TTGATGAGATATTGATCTTTGTAATGACATAGATT 1 TTGATGAGATATTGATCTTTGTAATGACATAGATT * 905360 TTGATGAGTTATTGATCTTTGTAATGACATAGATT 1 TTGATGAGATATTGATCTTTGTAATGACATAGATT 905395 GTGTTTTTTT Statistics Matches: 34, Mismatches: 1, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 35 34 1.00 ACGTcount: A:0.30, C:0.06, G:0.20, T:0.44 Consensus pattern (35 bp): TTGATGAGATATTGATCTTTGTAATGACATAGATT Found at i:907618 original size:8 final size:8 Alignment explanation

Indices: 907605--907641 Score: 65 Period size: 8 Copynumber: 4.6 Consensus size: 8 907595 TGGTTTCACC 907605 CTGTCCGT 1 CTGTCCGT 907613 CTGTCCGT 1 CTGTCCGT * 907621 CTGTCTGT 1 CTGTCCGT 907629 CTGTCCGT 1 CTGTCCGT 907637 CTGTC 1 CTGTC 907642 TGTAGACGCA Statistics Matches: 27, Mismatches: 2, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 8 27 1.00 ACGTcount: A:0.00, C:0.35, G:0.24, T:0.41 Consensus pattern (8 bp): CTGTCCGT Found at i:907628 original size:4 final size:4 Alignment explanation

Indices: 907605--907644 Score: 53 Period size: 4 Copynumber: 10.0 Consensus size: 4 907595 TGGTTTCACC * * * 907605 CTGT CCGT CTGT CCGT CTGT CTGT CTGT CCGT CTGT CTGT 1 CTGT CTGT CTGT CTGT CTGT CTGT CTGT CTGT CTGT CTGT 907645 AGACGCAACT Statistics Matches: 30, Mismatches: 6, Indels: 0 0.83 0.17 0.00 Matches are distributed among these distances: 4 30 1.00 ACGTcount: A:0.00, C:0.33, G:0.25, T:0.42 Consensus pattern (4 bp): CTGT Found at i:911683 original size:10 final size:10 Alignment explanation

Indices: 911668--911712 Score: 63 Period size: 10 Copynumber: 4.5 Consensus size: 10 911658 GTGTTTGTGA 911668 AGCATTATAC 1 AGCATTATAC 911678 AGCATTATAC 1 AGCATTATAC * * 911688 AGCATTGTGC 1 AGCATTATAC * 911698 AGCATTGTAC 1 AGCATTATAC 911708 AGCAT 1 AGCAT 911713 GAACTGAGTT Statistics Matches: 32, Mismatches: 3, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 10 32 1.00 ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29 Consensus pattern (10 bp): AGCATTATAC Found at i:924048 original size:2 final size:2 Alignment explanation

Indices: 924041--924108 Score: 136 Period size: 2 Copynumber: 34.0 Consensus size: 2 924031 AATCAAAACA 924041 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 924083 TC TC TC TC TC TC TC TC TC TC TC TC TC 1 TC TC TC TC TC TC TC TC TC TC TC TC TC 924109 ATTGTCTTCA Statistics Matches: 66, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 66 1.00 ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50 Consensus pattern (2 bp): TC Found at i:924551 original size:13 final size:13 Alignment explanation

Indices: 924533--924557 Score: 50 Period size: 13 Copynumber: 1.9 Consensus size: 13 924523 GGCTGAAGCT 924533 AGCAGCCACTAAC 1 AGCAGCCACTAAC 924546 AGCAGCCACTAA 1 AGCAGCCACTAA 924558 GCCCGTAGAA Statistics Matches: 12, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 12 1.00 ACGTcount: A:0.40, C:0.36, G:0.16, T:0.08 Consensus pattern (13 bp): AGCAGCCACTAAC Found at i:927143 original size:326 final size:326 Alignment explanation

Indices: 926533--927269 Score: 1244 Period size: 326 Copynumber: 2.3 Consensus size: 326 926523 NNNNNNNNNN 926533 TTTAAAGATAAGGAAGATAATAGACCACTTTTAACCCCTATATCATTCTGAAATGCTAAAATATG 1 TTTAAAGATAAGGAAGATAATAGACCACTTTTAACCCCTATATCATTCTGAAATGCTAAAATATG 926598 ACAAATTTCGGGTGAGCTAACTGGACCCTTGCAGGGGTCATAGGTGCCCTCTATTGCTTGTTATG 66 ACAAATTTCGGGTGAGCTAACTGGACCCTTGCAGGGGTCATAGGTGCCCTCTATTGCTTGTTATG 926663 AATACCTCCTGAGGCCCTCTACCTAATCCTAGTGTTACCAAGTTCTTGTGGTCAATCTCAAGTGA 131 AATACCTCCTGAGGCCCTCTACCTAATCCTAGTGTTACCAAGTTCTTGTGGTCAATCTCAAGTGA * 926728 GATATAAAACCCTGAAATGAGCCAGAACCCCTGGGAGCCACTTGGTGGTACCACTACAGCCCAAA 196 GATATAAAACCCTGAAATGAGCCAGAACCCCTAGGAGCCACTTGGTGGTACCACTACAGCCCAAA * * * * * 926793 TTTGAAACCGGAAAATAGTAGCCCCATATGCCCCCTACACTGCCCTGTTATTCGTTTGATGCACA 261 TTTGAAACCGGAAAATAATAGCCCCATAGGCCCCCTACACTGCCCTGGTATCCGTTTAATGCACA * 926858 T 326 C 926859 TTTAAAGATAAGGAAGATAATAGACCACTTTTAACCCCTATATCATTCTGAAATGCTAAAATATG 1 TTTAAAGATAAGGAAGATAATAGACCACTTTTAACCCCTATATCATTCTGAAATGCTAAAATATG 926924 ACAAATTTCGGGTGAGCTAACTGGACCCTTGCAGGGGTCATAGGTGCCCTCTATTGCTTGTTATG 66 ACAAATTTCGGGTGAGCTAACTGGACCCTTGCAGGGGTCATAGGTGCCCTCTATTGCTTGTTATG 926989 AATACCTCCTGAGGCCCTCTACCTAATCCTAGTGTTACCAAGTTCTTGTGGTCAATCTCAAGTGA 131 AATACCTCCTGAGGCCCTCTACCTAATCCTAGTGTTACCAAGTTCTTGTGGTCAATCTCAAGTGA * 927054 GATATAAAACCCTGAAATGAGCCAGAACCCCTAGGAGCCACTTGGTGGTACCCCTACAGCCCAAA 196 GATATAAAACCCTGAAATGAGCCAGAACCCCTAGGAGCCACTTGGTGGTACCACTACAGCCCAAA * * * 927119 TTTGAGACCGGGAAATAATAGCCCCATAGGTCCCCTACACTGCCCTGGTATCCGTTTAATGCACA 261 TTTGAAACCGGAAAATAATAGCCCCATAGGCCCCCTACACTGCCCTGGTATCCGTTTAATGCACA 927184 C 326 C * * * * * * * * * * 927185 TTCAAAGATAA-AAGAGATAAT-GGCCTGCCTTTCATCCCTACAGCATTGTGAAATGCTAAAATA 1 TTTAAAGATAAGGA-AGATAATAGACC-ACTTTTAACCCCTATATCATTCTGAAATGCTAAAATA * 927248 TGACAAAGTTCGGGTGAGCTAA 64 TGACAAATTTCGGGTGAGCTAA 927270 ACCGACCCTT Statistics Matches: 387, Mismatches: 22, Indels: 4 0.94 0.05 0.01 Matches are distributed among these distances: 325 4 0.01 326 383 0.99 ACGTcount: A:0.30, C:0.24, G:0.19, T:0.27 Consensus pattern (326 bp): TTTAAAGATAAGGAAGATAATAGACCACTTTTAACCCCTATATCATTCTGAAATGCTAAAATATG ACAAATTTCGGGTGAGCTAACTGGACCCTTGCAGGGGTCATAGGTGCCCTCTATTGCTTGTTATG AATACCTCCTGAGGCCCTCTACCTAATCCTAGTGTTACCAAGTTCTTGTGGTCAATCTCAAGTGA GATATAAAACCCTGAAATGAGCCAGAACCCCTAGGAGCCACTTGGTGGTACCACTACAGCCCAAA TTTGAAACCGGAAAATAATAGCCCCATAGGCCCCCTACACTGCCCTGGTATCCGTTTAATGCACA C Found at i:927861 original size:13 final size:13 Alignment explanation

Indices: 927843--927867 Score: 50 Period size: 13 Copynumber: 1.9 Consensus size: 13 927833 TTCTACGGTC 927843 TTAGTGGCTGCTG 1 TTAGTGGCTGCTG 927856 TTAGTGGCTGCT 1 TTAGTGGCTGCT 927868 AGCTTCAGCC 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:0.08, C:0.16, G:0.36, T:0.40 Consensus pattern (13 bp): TTAGTGGCTGCTG Found at i:931965 original size:14 final size:14 Alignment explanation

Indices: 931946--931990 Score: 63 Period size: 14 Copynumber: 3.1 Consensus size: 14 931936 CCTAGATGAT 931946 AATGGACAGGTAAG 1 AATGGACAGGTAAG 931960 AATGGACAGGTAAG 1 AATGGACAGGTAAG * 931974 ATAATAGACAGGTAAG 1 --AATGGACAGGTAAG 931990 A 1 A 931991 TTTTCTGACG Statistics Matches: 28, Mismatches: 1, Indels: 4 0.85 0.03 0.12 Matches are distributed among these distances: 14 15 0.54 16 13 0.46 ACGTcount: A:0.47, C:0.07, G:0.31, T:0.16 Consensus pattern (14 bp): AATGGACAGGTAAG Found at i:931985 original size:16 final size:16 Alignment explanation

Indices: 931943--931991 Score: 75 Period size: 16 Copynumber: 3.2 Consensus size: 16 931933 TGACCTAGAT 931943 GATAATGGACAGGTAA 1 GATAATGGACAGGTAA 931959 G--AATGGACAGGTAA 1 GATAATGGACAGGTAA * 931973 GATAATAGACAGGTAA 1 GATAATGGACAGGTAA 931989 GAT 1 GAT 931992 TTTCTGACGC Statistics Matches: 30, Mismatches: 1, Indels: 4 0.86 0.03 0.11 Matches are distributed among these distances: 14 14 0.47 16 16 0.53 ACGTcount: A:0.45, C:0.06, G:0.31, T:0.18 Consensus pattern (16 bp): GATAATGGACAGGTAA Found at i:932921 original size:12 final size:12 Alignment explanation

Indices: 932904--932939 Score: 72 Period size: 12 Copynumber: 3.0 Consensus size: 12 932894 TGCAAGATTA 932904 TACTCCATATTG 1 TACTCCATATTG 932916 TACTCCATATTG 1 TACTCCATATTG 932928 TACTCCATATTG 1 TACTCCATATTG 932940 AATTTTCTTT Statistics Matches: 24, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 12 24 1.00 ACGTcount: A:0.25, C:0.25, G:0.08, T:0.42 Consensus pattern (12 bp): TACTCCATATTG Found at i:933114 original size:29 final size:29 Alignment explanation

Indices: 933068--933157 Score: 164 Period size: 29 Copynumber: 3.1 Consensus size: 29 933058 ATACACCGCA 933068 TTGTACTGTACGGAAGAGACCGTCACAAT 1 TTGTACTGTACGGAAGAGACCGTCACAAT 933097 TTGTACTGTAC-GACAGAGACCGTCACAAT 1 TTGTACTGTACGGA-AGAGACCGTCACAAT 933126 TTGTACTGTACGGAAGAGACCGTCACAAT 1 TTGTACTGTACGGAAGAGACCGTCACAAT 933155 TTG 1 TTG 933158 CATCTCCTTG Statistics Matches: 59, Mismatches: 0, Indels: 4 0.94 0.00 0.06 Matches are distributed among these distances: 28 2 0.03 29 55 0.93 30 2 0.03 ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26 Consensus pattern (29 bp): TTGTACTGTACGGAAGAGACCGTCACAAT Found at i:933737 original size:21 final size:21 Alignment explanation

Indices: 933713--933827 Score: 160 Period size: 21 Copynumber: 5.5 Consensus size: 21 933703 ATCTGCCACC * 933713 ACTTGTCAGATAGTTATGTCG 1 ACTTGTCAGATATTTATGTCG 933734 ACTTGTCAGATGA-TTATGTCG 1 ACTTGTCAGAT-ATTTATGTCG * 933755 ACTTGTCAGATATTTATGTCA 1 ACTTGTCAGATATTTATGTCG * * 933776 ACTTGTCAGATCTTTATGTCA 1 ACTTGTCAGATATTTATGTCG * * 933797 ACTTGTCAGATCTTTATGTTG 1 ACTTGTCAGATATTTATGTCG 933818 ACTTGTCAGA 1 ACTTGTCAGA 933828 AAAAAACCAT Statistics Matches: 88, Mismatches: 4, Indels: 4 0.92 0.04 0.04 Matches are distributed among these distances: 20 1 0.01 21 86 0.98 22 1 0.01 ACGTcount: A:0.24, C:0.16, G:0.19, T:0.41 Consensus pattern (21 bp): ACTTGTCAGATATTTATGTCG Found at i:933937 original size:21 final size:21 Alignment explanation

Indices: 933912--933961 Score: 64 Period size: 21 Copynumber: 2.4 Consensus size: 21 933902 TCATCATAAT * 933912 ATCTGACAAGTCGACATAAAG 1 ATCTGACAAGTCAACATAAAG * ** 933933 ATCTGACAAGTTAACATAATT 1 ATCTGACAAGTCAACATAAAG 933954 ATCTGACA 1 ATCTGACA 933962 GAAAAAATAG Statistics Matches: 25, Mismatches: 4, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 21 25 1.00 ACGTcount: A:0.42, C:0.18, G:0.14, T:0.26 Consensus pattern (21 bp): ATCTGACAAGTCAACATAAAG Found at i:934045 original size:21 final size:21 Alignment explanation

Indices: 934009--934145 Score: 188 Period size: 21 Copynumber: 6.6 Consensus size: 21 933999 CATTCATATT * 934009 ATTA-GTCGACTGGTCAAATA 1 ATTATGTCGACTTGTCAAATA * * * 934029 ATGATGTTGACTTGTCAGAT- 1 ATTATGTCGACTTGTCAAATA * * * 934049 GTTATGTTGTCTTGTCAAATA 1 ATTATGTCGACTTGTCAAATA * 934070 ATTATGTCGACTTGTCAAATG 1 ATTATGTCGACTTGTCAAATA 934091 ATTATGTCGACTTGTCAAATA 1 ATTATGTCGACTTGTCAAATA 934112 ATTATGTCGACTTGTCAAATA 1 ATTATGTCGACTTGTCAAATA 934133 ATTATGTCGACTT 1 ATTATGTCGACTT 934146 AAAAGATGCT Statistics Matches: 102, Mismatches: 13, Indels: 3 0.86 0.11 0.03 Matches are distributed among these distances: 20 19 0.19 21 83 0.81 ACGTcount: A:0.29, C:0.13, G:0.18, T:0.39 Consensus pattern (21 bp): ATTATGTCGACTTGTCAAATA Found at i:934138 original size:63 final size:62 Alignment explanation

Indices: 934009--934191 Score: 201 Period size: 63 Copynumber: 2.9 Consensus size: 62 933999 CATTCATATT * * * * * * * 934009 ATTA-GTCGACTGGTCAAATAATGATGTTGACTTGTCAGATGTTATGTTGTCTTGTCAAATA 1 ATTATGTCGACTTGTCAAATGATAATGTCGACTTGTCAGATATTATGTCGACTTGTCAAATA * * 934070 ATTATGTCGACTTGTCAAATGATTATGTCGACTTGTCAAATAATTATGTCGACTTGTCAAATA 1 ATTATGTCGACTTGTCAAATGATAATGTCGACTTGTCAGAT-ATTATGTCGACTTGTCAAATA ** * 934133 ATTATGTCGACTT-AAAAGATGCTAATGTCGACTTGTCAGAT-TCCTATGTCGACTTGTCA 1 ATTATGTCGACTTGTCAA-ATGATAATGTCGACTTGTCAGATAT--TATGTCGACTTGTCA 934192 GAAAATATTA Statistics Matches: 104, Mismatches: 13, Indels: 8 0.83 0.10 0.06 Matches are distributed among these distances: 61 5 0.05 62 33 0.32 63 66 0.63 ACGTcount: A:0.29, C:0.15, G:0.19, T:0.38 Consensus pattern (62 bp): ATTATGTCGACTTGTCAAATGATAATGTCGACTTGTCAGATATTATGTCGACTTGTCAAATA Found at i:934161 original size:42 final size:42 Alignment explanation

Indices: 934024--934188 Score: 136 Period size: 42 Copynumber: 4.0 Consensus size: 42 934014 TCGACTGGTC * * * * * * ** 934024 AAATAATGATGTTGACTTGTCAGAT-GTTATGTTGTCTTGTC 1 AAATAATAATGTCGACTTGTCAAATAATTATGTCGACTTGAA * * ** 934065 AAATAATTATGTCGACTTGTCAAATGATTATGTCGACTTGTC 1 AAATAATAATGTCGACTTGTCAAATAATTATGTCGACTTGAA * 934107 AAATAATTATGTCGACTTGTCAAATAATTATGTCGACTT-AA 1 AAATAATAATGTCGACTTGTCAAATAATTATGTCGACTTGAA ** * *** 934148 AAGATGCTAATGTCGACTTGTCAGATTCCTATGTCGACTTG 1 AA-ATAATAATGTCGACTTGTCAAATAATTATGTCGACTTG 934189 TCAGAAAATA Statistics Matches: 105, Mismatches: 16, Indels: 4 0.84 0.13 0.03 Matches are distributed among these distances: 41 24 0.23 42 81 0.77 ACGTcount: A:0.30, C:0.14, G:0.18, T:0.38 Consensus pattern (42 bp): AAATAATAATGTCGACTTGTCAAATAATTATGTCGACTTGAA Found at i:934296 original size:21 final size:21 Alignment explanation

Indices: 934270--934361 Score: 141 Period size: 21 Copynumber: 4.4 Consensus size: 21 934260 CGTGGATAAG * 934270 TGACAAGTCCACATAATTATC 1 TGACAAGTCGACATAATTATC * 934291 TGACAAGTCGACATAGTTATC 1 TGACAAGTCGACATAATTATC * 934312 TGACAAGTCGACATCAA-GATC 1 TGACAAGTCGACAT-AATTATC 934333 TGACAAGTCGACATAATTATC 1 TGACAAGTCGACATAATTATC 934354 TGACAAGT 1 TGACAAGT 934362 GGTGGCAGAT Statistics Matches: 64, Mismatches: 5, Indels: 4 0.88 0.07 0.05 Matches are distributed among these distances: 20 2 0.03 21 61 0.95 22 1 0.02 ACGTcount: A:0.37, C:0.21, G:0.16, T:0.26 Consensus pattern (21 bp): TGACAAGTCGACATAATTATC Found at i:934444 original size:21 final size:21 Alignment explanation

Indices: 934420--934513 Score: 73 Period size: 21 Copynumber: 4.5 Consensus size: 21 934410 ATCTGCCACC 934420 ACTTGTCAGATAATTATGTTA 1 ACTTGTCAGATAATTATGTTA * * * * ** 934441 ACTTCTCATATGATAATGTCG 1 ACTTGTCAGATAATTATGTTA * 934462 ACTTGTCAGATATTTAT-TTCA 1 ACTTGTCAGATAATTATGTT-A ** * * 934483 ACTTGTCAGATCTTTACGTTG 1 ACTTGTCAGATAATTATGTTA 934504 ACTTGTCAGA 1 ACTTGTCAGA 934514 AAATAACCAT Statistics Matches: 55, Mismatches: 16, Indels: 4 0.73 0.21 0.05 Matches are distributed among these distances: 20 1 0.02 21 52 0.95 22 2 0.04 ACGTcount: A:0.28, C:0.16, G:0.15, T:0.41 Consensus pattern (21 bp): ACTTGTCAGATAATTATGTTA Found at i:934628 original size:21 final size:21 Alignment explanation

Indices: 934604--934688 Score: 89 Period size: 21 Copynumber: 4.0 Consensus size: 21 934594 AATATCATAT * 934604 AAGTCGACATAAATATCTGAC 1 AAGTCAACATAAATATCTGAC * * * 934625 AAGTTAACATAATTATCTGTC 1 AAGTCAACATAAATATCTGAC * ** * 934646 AAGTCGACATAAGGAGCTGAC 1 AAGTCAACATAAATATCTGAC * 934667 AAGTTAACATAAATATCTGAC 1 AAGTCAACATAAATATCTGAC 934688 A 1 A 934689 GAAAAAATAA Statistics Matches: 49, Mismatches: 15, Indels: 0 0.77 0.23 0.00 Matches are distributed among these distances: 21 49 1.00 ACGTcount: A:0.42, C:0.16, G:0.15, T:0.26 Consensus pattern (21 bp): AAGTCAACATAAATATCTGAC Found at i:934651 original size:42 final size:42 Alignment explanation

Indices: 934604--934685 Score: 128 Period size: 42 Copynumber: 2.0 Consensus size: 42 934594 AATATCATAT * * * 934604 AAGTCGACATAAATATCTGACAAGTTAACATAATTATCTGTC 1 AAGTCGACATAAAGAGCTGACAAGTTAACATAAATATCTGTC * 934646 AAGTCGACATAAGGAGCTGACAAGTTAACATAAATATCTG 1 AAGTCGACATAAAGAGCTGACAAGTTAACATAAATATCTG 934686 ACAGAAAAAA Statistics Matches: 36, Mismatches: 4, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 42 36 1.00 ACGTcount: A:0.41, C:0.16, G:0.16, T:0.27 Consensus pattern (42 bp): AAGTCGACATAAAGAGCTGACAAGTTAACATAAATATCTGTC Found at i:934769 original size:21 final size:21 Alignment explanation

Indices: 934740--934878 Score: 145 Period size: 21 Copynumber: 6.7 Consensus size: 21 934730 CATATTGTAA * 934740 GTCGACTTGTCAGATAATGAT 1 GTCGACTTGTCAGATAATTAT * * 934761 GTTGACTTGTCAGAT-GTTAT 1 GTCGACTTGTCAGATAATTAT * * * 934781 GTCGTCTTGTCAAAAAATTAT 1 GTCGACTTGTCAGATAATTAT * 934802 GTCGACTTGTCAAATAATTAT 1 GTCGACTTGTCAGATAATTAT * *** * 934823 ATCGACTTAAAAGATGATTAT 1 GTCGACTTGTCAGATAATTAT ** 934844 GTCGACTTGTCAGATCCTTAT 1 GTCGACTTGTCAGATAATTAT 934865 GTCGACTTGTCAGA 1 GTCGACTTGTCAGA 934879 AAATATTATT Statistics Matches: 95, Mismatches: 22, Indels: 2 0.80 0.18 0.02 Matches are distributed among these distances: 20 14 0.15 21 81 0.85 ACGTcount: A:0.29, C:0.15, G:0.19, T:0.37 Consensus pattern (21 bp): GTCGACTTGTCAGATAATTAT Found at i:934999 original size:21 final size:21 Alignment explanation

Indices: 934975--935046 Score: 103 Period size: 21 Copynumber: 3.4 Consensus size: 21 934965 ACTAAAAGAA 934975 CTGACAAGT-GAACATAATTAT 1 CTGACAAGTCG-ACATAATTAT * 934996 CTGACAAGTCGACATTAA-GAT 1 CTGACAAGTCGACA-TAATTAT 935017 CTGACAAGTCGACATAATTAT 1 CTGACAAGTCGACATAATTAT 935038 CTGACAAGT 1 CTGACAAGT 935047 GGTGGCAGAT Statistics Matches: 46, Mismatches: 2, Indels: 6 0.85 0.04 0.11 Matches are distributed among these distances: 20 3 0.07 21 39 0.85 22 4 0.09 ACGTcount: A:0.39, C:0.18, G:0.17, T:0.26 Consensus pattern (21 bp): CTGACAAGTCGACATAATTAT Found at i:935021 original size:42 final size:42 Alignment explanation

Indices: 934955--935046 Score: 134 Period size: 42 Copynumber: 2.2 Consensus size: 42 934945 CATGAATAAG 934955 TGACAAGTCGACTAAAAGAACTGACAAGT-GAACATAATTATC 1 TGACAAGTCGACTAAAAGAACTGACAAGTCG-ACATAATTATC * * 934997 TGACAAGTCGAC-ATTAAGATCTGACAAGTCGACATAATTATC 1 TGACAAGTCGACTA-AAAGAACTGACAAGTCGACATAATTATC 935039 TGACAAGT 1 TGACAAGT 935047 GGTGGCAGAT Statistics Matches: 46, Mismatches: 2, Indels: 4 0.88 0.04 0.08 Matches are distributed among these distances: 41 1 0.02 42 44 0.96 43 1 0.02 ACGTcount: A:0.41, C:0.17, G:0.17, T:0.24 Consensus pattern (42 bp): TGACAAGTCGACTAAAAGAACTGACAAGTCGACATAATTATC Found at i:939000 original size:2 final size:2 Alignment explanation

Indices: 938993--939032 Score: 80 Period size: 2 Copynumber: 20.0 Consensus size: 2 938983 TATAGTTATC 938993 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG 1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG 939033 GACCAACGGC Statistics Matches: 38, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 38 1.00 ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00 Consensus pattern (2 bp): AG Found at i:955156 original size:32 final size:32 Alignment explanation

Indices: 955115--955176 Score: 115 Period size: 32 Copynumber: 1.9 Consensus size: 32 955105 TTGTTGTAGA 955115 CATAAGACTTGTTTGATATATAAAGTGTAATG 1 CATAAGACTTGTTTGATATATAAAGTGTAATG * 955147 CATAAGACTTGTTTGATATATGAAGTGTAA 1 CATAAGACTTGTTTGATATATAAAGTGTAA 955177 AATCATGCAA Statistics Matches: 29, Mismatches: 1, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 32 29 1.00 ACGTcount: A:0.37, C:0.06, G:0.19, T:0.37 Consensus pattern (32 bp): CATAAGACTTGTTTGATATATAAAGTGTAATG Found at i:955607 original size:2 final size:2 Alignment explanation

Indices: 955600--955654 Score: 110 Period size: 2 Copynumber: 27.5 Consensus size: 2 955590 AGCCTTCATT 955600 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 955642 TC TC TC TC TC TC T 1 TC TC TC TC TC TC T 955655 GTAGAAAGAG Statistics Matches: 53, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 53 1.00 ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51 Consensus pattern (2 bp): TC Found at i:957789 original size:7 final size:7 Alignment explanation

Indices: 957779--957803 Score: 50 Period size: 7 Copynumber: 3.6 Consensus size: 7 957769 TCTTATTTCA 957779 TTTTATT 1 TTTTATT 957786 TTTTATT 1 TTTTATT 957793 TTTTATT 1 TTTTATT 957800 TTTT 1 TTTT 957804 TGGTTAAAAT Statistics Matches: 18, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 7 18 1.00 ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88 Consensus pattern (7 bp): TTTTATT Found at i:968208 original size:59 final size:59 Alignment explanation

Indices: 968119--968294 Score: 258 Period size: 59 Copynumber: 3.1 Consensus size: 59 968109 AGTAAAATAC * * 968119 TTATTTTTAAGGTCTTCCGTTTCCAACGGAAGACCTTATAGTTTTCGTAC-GATTTCTTA 1 TTATTATTAAGGTCTTCCGTTTCCAACGGAAGACCTTATTGTTTTCGTACTG-TTTCTTA * 968178 TTATTATTAAGGTCTTCCGTTTCCAGCGGAAGACCTTATTGTTTTCGTACTGTTTC--- 1 TTATTATTAAGGTCTTCCGTTTCCAACGGAAGACCTTATTGTTTTCGTACTGTTTCTTA * 968234 ---TTATTAAGGTCTTCCGTTTCCAACGGAAGACCTTATTGTTTTCGTACTGTTTATTA 1 TTATTATTAAGGTCTTCCGTTTCCAACGGAAGACCTTATTGTTTTCGTACTGTTTCTTA 968290 TTATT 1 TTATT 968295 TTTTTTTTCC Statistics Matches: 105, Mismatches: 5, Indels: 14 0.85 0.04 0.11 Matches are distributed among these distances: 53 51 0.49 59 53 0.50 60 1 0.01 ACGTcount: A:0.20, C:0.18, G:0.16, T:0.45 Consensus pattern (59 bp): TTATTATTAAGGTCTTCCGTTTCCAACGGAAGACCTTATTGTTTTCGTACTGTTTCTTA Found at i:968261 original size:53 final size:53 Alignment explanation

Indices: 968125--968292 Score: 239 Period size: 53 Copynumber: 3.1 Consensus size: 53 968115 ATACTTATTT * 968125 TTAAGGTCTTCCGTTTCCAACGGAAGACCTTATAGTTTTCGTAC-GATTTCTTATTATTA 1 TTAAGGTCTTCCGTTTCCAACGGAAGACCTTATTGTTTTCGTACTG-TTTC------TTA * 968184 TTAAGGTCTTCCGTTTCCAGCGGAAGACCTTATTGTTTTCGTACTGTTTCTTA 1 TTAAGGTCTTCCGTTTCCAACGGAAGACCTTATTGTTTTCGTACTGTTTCTTA * 968237 TTAAGGTCTTCCGTTTCCAACGGAAGACCTTATTGTTTTCGTACTGTTTATTA 1 TTAAGGTCTTCCGTTTCCAACGGAAGACCTTATTGTTTTCGTACTGTTTCTTA 968290 TTA 1 TTA 968293 TTTTTTTTTT Statistics Matches: 104, Mismatches: 4, Indels: 8 0.90 0.03 0.07 Matches are distributed among these distances: 53 57 0.55 59 46 0.44 60 1 0.01 ACGTcount: A:0.21, C:0.19, G:0.17, T:0.43 Consensus pattern (53 bp): TTAAGGTCTTCCGTTTCCAACGGAAGACCTTATTGTTTTCGTACTGTTTCTTA Found at i:972644 original size:29 final size:29 Alignment explanation

Indices: 972612--972674 Score: 126 Period size: 29 Copynumber: 2.2 Consensus size: 29 972602 AACAATGGCA 972612 CACATGTAGCACAGAACAGAACGATGGTC 1 CACATGTAGCACAGAACAGAACGATGGTC 972641 CACATGTAGCACAGAACAGAACGATGGTC 1 CACATGTAGCACAGAACAGAACGATGGTC 972670 CACAT 1 CACAT 972675 CAAACAGTTT Statistics Matches: 34, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 29 34 1.00 ACGTcount: A:0.38, C:0.25, G:0.22, T:0.14 Consensus pattern (29 bp): CACATGTAGCACAGAACAGAACGATGGTC Found at i:973680 original size:14 final size:14 Alignment explanation

Indices: 973661--973702 Score: 84 Period size: 14 Copynumber: 3.0 Consensus size: 14 973651 GTAAAAGTTG 973661 CAGTGTTTGATATC 1 CAGTGTTTGATATC 973675 CAGTGTTTGATATC 1 CAGTGTTTGATATC 973689 CAGTGTTTGATATC 1 CAGTGTTTGATATC 973703 TAGAAGGATC Statistics Matches: 28, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 14 28 1.00 ACGTcount: A:0.21, C:0.14, G:0.21, T:0.43 Consensus pattern (14 bp): CAGTGTTTGATATC Found at i:979874 original size:16 final size:16 Alignment explanation

Indices: 979853--979918 Score: 105 Period size: 16 Copynumber: 4.1 Consensus size: 16 979843 ACCCTTGTGT 979853 GTCTGTCTGTCCGTCC 1 GTCTGTCTGTCCGTCC * * 979869 GTCTGTCTGTCTGTCT 1 GTCTGTCTGTCCGTCC * 979885 GTCTGTCTGTCTGTCC 1 GTCTGTCTGTCCGTCC 979901 GTCTGTCTGTCCGTCC 1 GTCTGTCTGTCCGTCC 979917 GT 1 GT 979919 AACAAAAATT Statistics Matches: 46, Mismatches: 4, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 16 46 1.00 ACGTcount: A:0.00, C:0.32, G:0.26, T:0.42 Consensus pattern (16 bp): GTCTGTCTGTCCGTCC Found at i:979918 original size:4 final size:4 Alignment explanation

Indices: 979852--979911 Score: 93 Period size: 4 Copynumber: 15.0 Consensus size: 4 979842 TACCCTTGTG * * 979852 TGTC TGTC TGTC CGTC CGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC 1 TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC * 979900 CGTC TGTC TGTC 1 TGTC TGTC TGTC 979912 CGTCCGTAAC Statistics Matches: 52, Mismatches: 4, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 4 52 1.00 ACGTcount: A:0.00, C:0.30, G:0.25, T:0.45 Consensus pattern (4 bp): TGTC Found at i:980218 original size:167 final size:167 Alignment explanation

Indices: 979942--981071 Score: 1781 Period size: 167 Copynumber: 6.8 Consensus size: 167 979932 GTCGCATTTA * 979942 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTGTTTGT-TAAGGCATGCCATA 1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTATTTGTAT-AGGCATGCCATA * 980006 TCGTGGGATATATTTTTGTACCAATCGGACACCAACTTCCTGTTAAATGACGACTTTGCTTATTT 65 TCGTGGGATATATTTTTGTACCAATCGGACGCCAACTTCCTGTTAAATGACGACTTTGCTTATTT * 980071 TTTAAGGAAAATTTTCAAACAAATTTTCGTCAAAGAAT 130 TTTAAGCAAAATTTTCAAACAAATTTTCGTCAAAGAAT * * * 980109 TCTCAGCAACTGTTTATAGCAGATGCTTGAAATTTTTACACAGTATTTGTATAGGCATGCCATAT 1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTATTTGTATAGGCATGCCATAT * * 980174 GGTGGGATATATTTTTGTACCAATCGGACGCCAACTTCCTGTTAAATGATGACTTTGCTTATTTT 66 CGTGGGATATATTTTTGTACCAATCGGACGCCAACTTCCTGTTAAATGACGACTTTGCTTATTTT * 980239 TTAACCAAAATTTTCAAACAAATTTTCGTCAAAGAAT 131 TTAAGCAAAATTTTCAAACAAATTTTCGTCAAAGAAT * * 980276 TCTCAGCAACTGTTTATCGCAGATGCTTGAAATTTTTACACAGTATTTGTATAGGCATGCCATAT 1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTATTTGTATAGGCATGCCATAT * * * 980341 GGTGGGATATATTTTTGTACCAATCAGACGTCAACTTCCTGTTAAATGACGACTTTGCTTATTTT 66 CGTGGGATATATTTTTGTACCAATCGGACGCCAACTTCCTGTTAAATGACGACTTTGCTTATTTT * * 980406 TTAAGGAAAATTTTCAAACAAATTTTCGTCAAAGATT 131 TTAAGCAAAATTTTCAAACAAATTTTCGTCAAAGAAT * * * 980443 TCTCAGCAAATATTTATTGCAGATGCTTGAAATTTTAACACACTATTTGTATAGGCATGCCATAT 1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTATTTGTATAGGCATGCCATAT * * 980508 CGTGGGATATATTTTTGTACCAATCGG-CGTCAACTTCCTGTTAAATGACGACTTTGTTTA-TTT 66 CGTGGGATATATTTTTGTACCAATCGGACGCCAACTTCCTGTTAAATGACGACTTTGCTTATTTT * * 980571 TT-AGCCAAAATTTTCAAACAAATTTCCGTCAAAGATT 131 TTAAG-CAAAATTTTCAAACAAATTTTCGTCAAAGAAT * * * 980608 TCTCAGCAACCATTTATCACAGATGCTTGAAATTTTAACACACTATTTGTATAGGCATGCCATAT 1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTATTTGTATAGGCATGCCATAT * * * * * 980673 TGTGGGATATATTTTTG-ACTCAATCGGACGTCAAACTTCCTGTGAAATGATGACTTTGTTTA-T 66 CGTGGGATATATTTTTGTAC-CAATCGGACG-CCAACTTCCTGTTAAATGACGACTTTGCTTATT * * 980736 TTTT-AGCCAAAATTTTCAAACAAATTTCCGTCAAAGATT 129 TTTTAAG-CAAAATTTTCAAACAAATTTTCGTCAAAGAAT * * * 980775 TCTCAGCAGCTATTTATCGCAGATGCTTGAAATTTCAACACAGTGTTTGT-TAAGGCATGCCATA 1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTATTTGTAT-AGGCATGCCATA * 980839 TCGTGGGATATATTTTTGTACCAATCGGATGCCAACTTCCTGTTAAATGACGACTTTGCTTATTT 65 TCGTGGGATATATTTTTGTACCAATCGGACGCCAACTTCCTGTTAAATGACGACTTTGCTTATTT * 980904 TTTAACCAAAATTTTCAAACAAATTTTCGTCAAAGAAT 130 TTTAAGCAAAATTTTCAAACAAATTTTCGTCAAAGAAT * * 980942 TCTCAGCAACTGTTTATCGCAGATGCTTGAAATTTTTACACAGTATTTGTATAGGCATGCCATAT 1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTATTTGTATAGGCATGCCATAT * 981007 CGAGGGATATATTTTTGTACCAATCGGACGCCAACTTCCTGTTAAATGACGACTTTGCTTATTTT 66 CGTGGGATATATTTTTGTACCAATCGGACGCCAACTTCCTGTTAAATGACGACTTTGCTTATTTT 981072 GCATATTCAC Statistics Matches: 896, Mismatches: 57, Indels: 20 0.92 0.06 0.02 Matches are distributed among these distances: 164 4 0.00 165 119 0.13 166 62 0.07 167 706 0.79 168 5 0.01 ACGTcount: A:0.30, C:0.18, G:0.16, T:0.37 Consensus pattern (167 bp): TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTATTTGTATAGGCATGCCATAT CGTGGGATATATTTTTGTACCAATCGGACGCCAACTTCCTGTTAAATGACGACTTTGCTTATTTT TTAAGCAAAATTTTCAAACAAATTTTCGTCAAAGAAT Found at i:980977 original size:499 final size:500 Alignment explanation

Indices: 979942--981071 Score: 1824 Period size: 499 Copynumber: 2.3 Consensus size: 500 979932 GTCGCATTTA * 979942 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTGTTTGT-TAAGGCATGCCATA 1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTATTTGTAT-AGGCATGCCATA * 980006 TCGTGGGATATATTTTTGTACCAATCGGACACCAACTTCCTGTTAAATGACGACTTTGCTTATTT 65 TCGTGGGATATATTTTTGTACCAATCGGACGCCAACTTCCTGTTAAATGACGACTTTGCTTA-TT * * ** 980071 TTTAAGGAAAATTTTCAAACAAATTTTCGTCAAAGAATTCTCAGCAACTGTTTATAGCAGATGCT 129 TTTAAGCAAAATTTTCAAACAAATTTCCGTCAAAGAATTCTCAGCAACCATTTATAGCAGATGCT * * 980136 TGAAATTTTTACACAGTATTTGTATAGGCATGCCATATGGTGGGATATATTTTTGTACCAATCGG 194 TGAAATTTTAACACACTATTTGTATAGGCATGCCATATGGTGGGATATATTTTTGTACCAATCGG * * * 980201 ACGCCAACTTCCTGTTAAATGATGACTTTGCTTATTTTTTAACCAAAATTTTCAAACAAATTTTC 259 ACGCAAACTTCCTGTGAAATGATGACTTTGCTTATTTTTTAACCAAAATTTTCAAACAAATTTCC * ** 980266 GTCAAAGAATTCTCAGCAACTGTTTATCGCAGATGCTTGAAATTTTTACACAGTATTTGTATAGG 324 GTCAAAGAATTCTCAGCAACTATTTATCGCAGATGCTTGAAATTTCAACACAGTATTTGTATAGG * * 980331 CATGCCATATGGTGGGATATATTTTTGTACCAATCAGACGTCAACTTCCTGTTAAATGACGACTT 389 CATGCCATATCGTGGGATATATTTTTGTACCAATCAGACGCCAACTTCCTGTTAAATGACGACTT ** * 980396 TGCTTATTTTTTAAGGAAAATTTTCAAACAAATTTTCGTCAAAGATT 454 TGCTTATTTTTTAACCAAAATTTTCAAACAAATTTTCGTCAAAGAAT * * * 980443 TCTCAGCAAATATTTATTGCAGATGCTTGAAATTTTAACACACTATTTGTATAGGCATGCCATAT 1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTATTTGTATAGGCATGCCATAT * * 980508 CGTGGGATATATTTTTGTACCAATCGG-CGTCAACTTCCTGTTAAATGACGACTTTGTTTATTTT 66 CGTGGGATATATTTTTGTACCAATCGGACGCCAACTTCCTGTTAAATGACGACTTTGCTTATTTT * 980572 T-AGCCAAAATTTTCAAACAAATTTCCGTCAAAGATTTCTCAGCAACCATTTATCA-CAGATGCT 131 TAAG-CAAAATTTTCAAACAAATTTCCGTCAAAGAATTCTCAGCAACCATTTAT-AGCAGATGCT * 980635 TGAAATTTTAACACACTATTTGTATAGGCATGCCATATTGTGGGATATATTTTTG-ACTCAATCG 194 TGAAATTTTAACACACTATTTGTATAGGCATGCCATATGGTGGGATATATTTTTGTAC-CAATCG * * 980699 GACGTCAAACTTCCTGTGAAATGATGACTTTGTTTA-TTTTTAGCCAAAATTTTCAAACAAATTT 258 GACG-CAAACTTCCTGTGAAATGATGACTTTGCTTATTTTTTAACCAAAATTTTCAAACAAATTT * * * 980763 CCGTCAAAGATTTCTCAGCAGCTATTTATCGCAGATGCTTGAAATTTCAACACAGTGTTTGT-TA 322 CCGTCAAAGAATTCTCAGCAACTATTTATCGCAGATGCTTGAAATTTCAACACAGTATTTGTAT- * * 980827 AGGCATGCCATATCGTGGGATATATTTTTGTACCAATCGGATGCCAACTTCCTGTTAAATGACGA 386 AGGCATGCCATATCGTGGGATATATTTTTGTACCAATCAGACGCCAACTTCCTGTTAAATGACGA 980892 CTTTGCTTATTTTTTAACCAAAATTTTCAAACAAATTTTCGTCAAAGAAT 451 CTTTGCTTATTTTTTAACCAAAATTTTCAAACAAATTTTCGTCAAAGAAT * * 980942 TCTCAGCAACTGTTTATCGCAGATGCTTGAAATTTTTACACAGTATTTGTATAGGCATGCCATAT 1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTATTTGTATAGGCATGCCATAT * 981007 CGAGGGATATATTTTTGTACCAATCGGACGCCAACTTCCTGTTAAATGACGACTTTGCTTATTTT 66 CGTGGGATATATTTTTGTACCAATCGGACGCCAACTTCCTGTTAAATGACGACTTTGCTTATTTT 981072 GCATATTCAC Statistics Matches: 581, Mismatches: 41, Indels: 15 0.91 0.06 0.02 Matches are distributed among these distances: 498 5 0.01 499 395 0.68 500 94 0.16 501 86 0.15 502 1 0.00 ACGTcount: A:0.30, C:0.18, G:0.16, T:0.37 Consensus pattern (500 bp): TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTATTTGTATAGGCATGCCATAT CGTGGGATATATTTTTGTACCAATCGGACGCCAACTTCCTGTTAAATGACGACTTTGCTTATTTT TAAGCAAAATTTTCAAACAAATTTCCGTCAAAGAATTCTCAGCAACCATTTATAGCAGATGCTTG AAATTTTAACACACTATTTGTATAGGCATGCCATATGGTGGGATATATTTTTGTACCAATCGGAC GCAAACTTCCTGTGAAATGATGACTTTGCTTATTTTTTAACCAAAATTTTCAAACAAATTTCCGT CAAAGAATTCTCAGCAACTATTTATCGCAGATGCTTGAAATTTCAACACAGTATTTGTATAGGCA TGCCATATCGTGGGATATATTTTTGTACCAATCAGACGCCAACTTCCTGTTAAATGACGACTTTG CTTATTTTTTAACCAAAATTTTCAAACAAATTTTCGTCAAAGAAT Found at i:982580 original size:18 final size:18 Alignment explanation

Indices: 982557--982594 Score: 58 Period size: 18 Copynumber: 2.1 Consensus size: 18 982547 TAAATGCATT * 982557 TGTTAAACATAATAACAA 1 TGTTAAACACAATAACAA * 982575 TGTTAAACACATTAACAA 1 TGTTAAACACAATAACAA 982593 TG 1 TG 982595 GTTCAAAGAA Statistics Matches: 18, Mismatches: 2, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 18 18 1.00 ACGTcount: A:0.50, C:0.13, G:0.08, T:0.29 Consensus pattern (18 bp): TGTTAAACACAATAACAA Found at i:985703 original size:3 final size:3 Alignment explanation

Indices: 985695--985738 Score: 54 Period size: 3 Copynumber: 15.0 Consensus size: 3 985685 GAACGTCCGC * * * 985695 CAT CAT CAT CAT CAT CAT CGT CAT CTT CAT CAA CA- CAT CAT CAT 1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT 985739 TTTCCTATTT Statistics Matches: 35, Mismatches: 5, Indels: 2 0.83 0.12 0.05 Matches are distributed among these distances: 2 2 0.06 3 33 0.94 ACGTcount: A:0.32, C:0.34, G:0.02, T:0.32 Consensus pattern (3 bp): CAT Found at i:987034 original size:27 final size:27 Alignment explanation

Indices: 986985--987037 Score: 70 Period size: 27 Copynumber: 2.0 Consensus size: 27 986975 TCACCTCAAT * 986985 TATACCATAGCGGACAGTTCTTACAAG 1 TATACCATAGCGGACAGTGCTTACAAG * ** 987012 TATACTATAGCGGTTAGTGCTTACAA 1 TATACCATAGCGGACAGTGCTTACAA 987038 TATGTCTTTG Statistics Matches: 22, Mismatches: 4, Indels: 0 0.85 0.15 0.00 Matches are distributed among these distances: 27 22 1.00 ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30 Consensus pattern (27 bp): TATACCATAGCGGACAGTGCTTACAAG Found at i:991431 original size:35 final size:35 Alignment explanation

Indices: 991385--991457 Score: 146 Period size: 35 Copynumber: 2.1 Consensus size: 35 991375 TTCAGATCTG 991385 GTAAGGAAGGGTCTGTCTGAACCCCAGTGGTACGT 1 GTAAGGAAGGGTCTGTCTGAACCCCAGTGGTACGT 991420 GTAAGGAAGGGTCTGTCTGAACCCCAGTGGTACGT 1 GTAAGGAAGGGTCTGTCTGAACCCCAGTGGTACGT 991455 GTA 1 GTA 991458 TTGTTCAGAT Statistics Matches: 38, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 35 38 1.00 ACGTcount: A:0.23, C:0.19, G:0.34, T:0.23 Consensus pattern (35 bp): GTAAGGAAGGGTCTGTCTGAACCCCAGTGGTACGT Found at i:991447 original size:86 final size:86 Alignment explanation

Indices: 991338--991508 Score: 333 Period size: 86 Copynumber: 2.0 Consensus size: 86 991328 GATCTGGTAT 991338 GGAAGGGTCCGTCTGAACCCCAGTGGTACGTGTATTGTTCAGATCTGGTAAGGAAGGGTCTGTCT 1 GGAAGGGTCCGTCTGAACCCCAGTGGTACGTGTATTGTTCAGATCTGGTAAGGAAGGGTCTGTCT 991403 GAACCCCAGTGGTACGTGTAA 66 GAACCCCAGTGGTACGTGTAA * 991424 GGAAGGGTCTGTCTGAACCCCAGTGGTACGTGTATTGTTCAGATCTGGTAAGGAAGGGTCTGTCT 1 GGAAGGGTCCGTCTGAACCCCAGTGGTACGTGTATTGTTCAGATCTGGTAAGGAAGGGTCTGTCT 991489 GAACCCCAGTGGTACGTGTA 66 GAACCCCAGTGGTACGTGTA 991509 TTGTTCAAAT Statistics Matches: 84, Mismatches: 1, Indels: 0 0.99 0.01 0.00 Matches are distributed among these distances: 86 84 1.00 ACGTcount: A:0.22, C:0.19, G:0.33, T:0.26 Consensus pattern (86 bp): GGAAGGGTCCGTCTGAACCCCAGTGGTACGTGTATTGTTCAGATCTGGTAAGGAAGGGTCTGTCT GAACCCCAGTGGTACGTGTAA Found at i:996734 original size:16 final size:16 Alignment explanation

Indices: 996705--996737 Score: 50 Period size: 16 Copynumber: 2.1 Consensus size: 16 996695 GCTCTGACCT 996705 TGATTGAATTAATAAA 1 TGATTGAATTAATAAA 996721 TGATT-AATTAAATAAA 1 TGATTGAATT-AATAAA 996737 T 1 T 996738 CGTTTCTGCG Statistics Matches: 16, Mismatches: 0, Indels: 2 0.89 0.00 0.11 Matches are distributed among these distances: 15 4 0.25 16 12 0.75 ACGTcount: A:0.52, C:0.00, G:0.09, T:0.39 Consensus pattern (16 bp): TGATTGAATTAATAAA Found at i:998030 original size:7 final size:7 Alignment explanation

Indices: 998018--998084 Score: 89 Period size: 7 Copynumber: 9.6 Consensus size: 7 998008 GAGAAGGATC 998018 ATTCGAG 1 ATTCGAG 998025 ATTCGAG 1 ATTCGAG * 998032 ATTCGAA 1 ATTCGAG * 998039 ATACGAG 1 ATTCGAG * 998046 ATTCGAA 1 ATTCGAG * 998053 ATACGAG 1 ATTCGAG 998060 ATTCGAG 1 ATTCGAG * 998067 ATTCGAA 1 ATTCGAG 998074 ATTCGAG 1 ATTCGAG 998081 ATTC 1 ATTC 998085 AATATCTAAA Statistics Matches: 50, Mismatches: 10, Indels: 0 0.83 0.17 0.00 Matches are distributed among these distances: 7 50 1.00 ACGTcount: A:0.36, C:0.15, G:0.22, T:0.27 Consensus pattern (7 bp): ATTCGAG Found at i:1000489 original size:2 final size:2 Alignment explanation

Indices: 1000482--1000533 Score: 104 Period size: 2 Copynumber: 26.0 Consensus size: 2 1000472 GCTAGGTGAT 1000482 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 1000524 GA GA GA GA GA 1 GA GA GA GA GA 1000534 NNNNNNNNNN Statistics Matches: 50, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 50 1.00 ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00 Consensus pattern (2 bp): GA Found at i:1001358 original size:7 final size:7 Alignment explanation

Indices: 1001343--1001409 Score: 89 Period size: 7 Copynumber: 9.6 Consensus size: 7 1001333 TTTAGATATT 1001343 GAATCTC 1 GAATCTC * 1001350 GAATTTC 1 GAATCTC 1001357 GAATCTC 1 GAATCTC 1001364 GAATCTC 1 GAATCTC * * 1001371 GTATTTC 1 GAATCTC 1001378 GAATCTC 1 GAATCTC * * 1001385 GTATTTC 1 GAATCTC 1001392 GAATCTC 1 GAATCTC 1001399 GAATCTC 1 GAATCTC 1001406 GAAT 1 GAAT 1001410 GATCCTTCTC Statistics Matches: 50, Mismatches: 10, Indels: 0 0.83 0.17 0.00 Matches are distributed among these distances: 7 50 1.00 ACGTcount: A:0.27, C:0.22, G:0.15, T:0.36 Consensus pattern (7 bp): GAATCTC Found at i:1001368 original size:21 final size:21 Alignment explanation

Indices: 1001343--1001409 Score: 98 Period size: 21 Copynumber: 3.2 Consensus size: 21 1001333 TTTAGATATT 1001343 GAATCTCGAATTTCGAATCTC 1 GAATCTCGAATTTCGAATCTC * 1001364 GAATCTCGTATTTCGAATCTC 1 GAATCTCGAATTTCGAATCTC * * * 1001385 GTATTTCGAATCTCGAATCTC 1 GAATCTCGAATTTCGAATCTC 1001406 GAAT 1 GAAT 1001410 GATCCTTCTC Statistics Matches: 40, Mismatches: 6, Indels: 0 0.87 0.13 0.00 Matches are distributed among these distances: 21 40 1.00 ACGTcount: A:0.27, C:0.22, G:0.15, T:0.36 Consensus pattern (21 bp): GAATCTCGAATTTCGAATCTC Found at i:1008934 original size:180 final size:180 Alignment explanation

Indices: 1008632--1009133 Score: 925 Period size: 180 Copynumber: 2.8 Consensus size: 180 1008622 NNNNNNNNNN 1008632 TAGGAAGTTGTTCTTTTGCAGATCAATTGTACATATATCAGAGGTGTGCATATTGCTAGGATTTT 1 TAGGAAGTTGTTCTTTTGCAGATCAATTGTACATATATCAGAGGTGTGCATATTGCTAGGATTTT * 1008697 GATTTCCGATAATTTATCAAAAAAATACCAGGTTTTGAACTTAGTCATTTTTTGGCAAAATATTG 66 GATTTCCGATAATTTATCAAAAAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTG * 1008762 CATATAGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTTTCAAGA 131 CATATAGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTCTCAAGA 1008812 TAGGAAGTTGTTCTTTTGCAGATCAATTGTACATATATCAGAGGTGTGCATATTGCTAGGATTTT 1 TAGGAAGTTGTTCTTTTGCAGATCAATTGTACATATATCAGAGGTGTGCATATTGCTAGGATTTT * 1008877 GATTTCCGATAATTTAT-AAAAATAATACCAGCTTTTGAACTTAGTCTTTTTTTGGCAAAATATT 66 GATTTCCGATAATTTATCAAAAA-AATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATT 1008941 GCATATAGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTCTCAAGA 130 GCATATAGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTCTCAAGA 1008992 TAGGAAGTTGTTCTTTTGCAGATCAATTGTACATATATCAGAGGTGTGCATATTGCTAGGATTTT 1 TAGGAAGTTGTTCTTTTGCAGATCAATTGTACATATATCAGAGGTGTGCATATTGCTAGGATTTT * * * 1009057 GATTTCCGATAATTTATGAAAAAAATACCAGCTTTTGAACATAGTCATTTTTTGGCAAAATGTTG 66 GATTTCCGATAATTTATCAAAAAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTG * 1009122 CATACAGGGTAC 131 CATATAGGGTAC 1009134 TCCATTTCAC Statistics Matches: 313, Mismatches: 7, Indels: 4 0.97 0.02 0.01 Matches are distributed among these distances: 179 5 0.02 180 303 0.97 181 5 0.02 ACGTcount: A:0.30, C:0.15, G:0.18, T:0.37 Consensus pattern (180 bp): TAGGAAGTTGTTCTTTTGCAGATCAATTGTACATATATCAGAGGTGTGCATATTGCTAGGATTTT GATTTCCGATAATTTATCAAAAAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTG CATATAGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTCTCAAGA Found at i:1027635 original size:16 final size:16 Alignment explanation

Indices: 1027614--1027644 Score: 53 Period size: 16 Copynumber: 1.9 Consensus size: 16 1027604 GTAATAAACT 1027614 CTCTCTCTCTCTCAAA 1 CTCTCTCTCTCTCAAA * 1027630 CTCTCTCTCTTTCAA 1 CTCTCTCTCTCTCAA 1027645 TTTGATAAGT Statistics Matches: 14, Mismatches: 1, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 16 14 1.00 ACGTcount: A:0.16, C:0.42, G:0.00, T:0.42 Consensus pattern (16 bp): CTCTCTCTCTCTCAAA Found at i:1044319 original size:19 final size:19 Alignment explanation

Indices: 1044295--1044335 Score: 64 Period size: 19 Copynumber: 2.2 Consensus size: 19 1044285 TAAGCTAAAC ** 1044295 ATTATAAACGGGATAATGA 1 ATTATAAACCAGATAATGA 1044314 ATTATAAACCAGATAATGA 1 ATTATAAACCAGATAATGA 1044333 ATT 1 ATT 1044336 GGCAGATCTT Statistics Matches: 20, Mismatches: 2, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 19 20 1.00 ACGTcount: A:0.49, C:0.07, G:0.15, T:0.29 Consensus pattern (19 bp): ATTATAAACCAGATAATGA Found at i:1056280 original size:75 final size:75 Alignment explanation

Indices: 1055934--1056251 Score: 609 Period size: 75 Copynumber: 4.2 Consensus size: 75 1055924 GAGAGTAACG * * * 1055934 TCCAGGTGTGTCTGGACACCATTAGGGAGGTGAGTTCATTGTTACAGGTGTCAGTACTAAGGTAT 1 TCCAGGTGTGTCTGGACACCATTAGGGAGGTGAGTTTATTATTACAGGTGTCAGCACTAAGGTAT 1055999 AAAGGTAATA 66 AAAGGTAATA 1056009 TCCAGGTGTGTCTGGACACCATTAGGGAGGTGAGTTTATTATTACAGGTGTCAGCACTAAGGTAT 1 TCCAGGTGTGTCTGGACACCATTAGGGAGGTGAGTTTATTATTACAGGTGTCAGCACTAAGGTAT 1056074 AAAGGTAATA 66 AAAGGTAATA 1056084 TCCAGGTGTGTCTGGACACCATTAGGGAGGTGAGTTTATTATTACAGGTGTCAGCACTAAGGTAT 1 TCCAGGTGTGTCTGGACACCATTAGGGAGGTGAGTTTATTATTACAGGTGTCAGCACTAAGGTAT 1056149 AAAGGTAATA 66 AAAGGTAATA 1056159 TCCAGGTGTGTCTGGACACCATTAGGGAGGTGAGTTTATTATTACAGGTGTCAGCACTAAGGTAT 1 TCCAGGTGTGTCTGGACACCATTAGGGAGGTGAGTTTATTATTACAGGTGTCAGCACTAAGGTAT 1056224 AAAGGTAATA 66 AAAGGTAATA 1056234 TCCAGGTGTGTCTGGACA 1 TCCAGGTGTGTCTGGACA 1056252 TCGTAAGGGA Statistics Matches: 240, Mismatches: 3, Indels: 0 0.99 0.01 0.00 Matches are distributed among these distances: 75 240 1.00 ACGTcount: A:0.28, C:0.14, G:0.29, T:0.29 Consensus pattern (75 bp): TCCAGGTGTGTCTGGACACCATTAGGGAGGTGAGTTTATTATTACAGGTGTCAGCACTAAGGTAT AAAGGTAATA Found at i:1064545 original size:13 final size:13 Alignment explanation

Indices: 1064527--1064551 Score: 50 Period size: 13 Copynumber: 1.9 Consensus size: 13 1064517 AAAAATAGTG 1064527 TCTGTGCATACAT 1 TCTGTGCATACAT 1064540 TCTGTGCATACA 1 TCTGTGCATACA 1064552 AGTACAAATT 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:0.24, C:0.24, G:0.16, T:0.36 Consensus pattern (13 bp): TCTGTGCATACAT Found at i:1065960 original size:15 final size:16 Alignment explanation

Indices: 1065930--1065978 Score: 55 Period size: 17 Copynumber: 3.1 Consensus size: 16 1065920 ACTACAGCTT * * 1065930 ACTCCACTTATATTGA 1 ACTCCGCTTATTTTGA 1065946 ACT-CGCTTATTTTGAA 1 ACTCCGCTTATTTTG-A * 1065962 ATTCCGCTTATTTTGA 1 ACTCCGCTTATTTTGA 1065978 A 1 A 1065979 ATAGGAATAA Statistics Matches: 28, Mismatches: 3, Indels: 4 0.80 0.09 0.11 Matches are distributed among these distances: 15 9 0.32 16 8 0.29 17 11 0.39 ACGTcount: A:0.27, C:0.20, G:0.10, T:0.43 Consensus pattern (16 bp): ACTCCGCTTATTTTGA Found at i:1067014 original size:30 final size:30 Alignment explanation

Indices: 1066978--1067096 Score: 193 Period size: 30 Copynumber: 4.0 Consensus size: 30 1066968 CTTTCCCAGA 1066978 TTCCTTACCTGGCCAGCACCAGCCCTCGTT 1 TTCCTTACCTGGCCAGCACCAGCCCTCGTT * 1067008 TTCCTTACCTGGCCAGCACCAGCCCCCGTT 1 TTCCTTACCTGGCCAGCACCAGCCCTCGTT * * * 1067038 TTCCTTACCTGGCCAGCACCACCCCTCATA 1 TTCCTTACCTGGCCAGCACCAGCCCTCGTT * 1067068 TTGCTTACCTGGCCAGCACCAGCCCTCGT 1 TTCCTTACCTGGCCAGCACCAGCCCTCGT 1067097 ATTCTTCCCC Statistics Matches: 81, Mismatches: 8, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 30 81 1.00 ACGTcount: A:0.15, C:0.45, G:0.16, T:0.24 Consensus pattern (30 bp): TTCCTTACCTGGCCAGCACCAGCCCTCGTT Found at i:1069866 original size:15 final size:15 Alignment explanation

Indices: 1069846--1069877 Score: 55 Period size: 15 Copynumber: 2.1 Consensus size: 15 1069836 CATTGTCTGG * 1069846 CTTCTTCTCTTCTTC 1 CTTCTTCTCTCCTTC 1069861 CTTCTTCTCTCCTTC 1 CTTCTTCTCTCCTTC 1069876 CT 1 CT 1069878 CCTCCTTAAA Statistics Matches: 16, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 15 16 1.00 ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56 Consensus pattern (15 bp): CTTCTTCTCTCCTTC Found at i:1081654 original size:16 final size:16 Alignment explanation

Indices: 1081633--1082110 Score: 381 Period size: 16 Copynumber: 29.6 Consensus size: 16 1081623 GATTGGATGA * 1081633 AGTGTGGTTTTGGTGG 1 AGTGTGGTTTAGGTGG * 1081649 ACTGTGGTTTAGGTGG 1 AGTGTGGTTTAGGTGG ** * 1081665 AGTGCAGTTT-GGATGT 1 AGTGTGGTTTAGG-TGG 1081681 AGTGTGGTTTAGGTGG 1 AGTGTGGTTTAGGTGG ** * 1081697 AGTGCAGTTTGGGT-G 1 AGTGTGGTTTAGGTGG * * 1081712 AGTGTGGATTGGGTGG 1 AGTGTGGTTTAGGTGG * * 1081728 AGTGTTGATTAGGTGG 1 AGTGTGGTTTAGGTGG * 1081744 AGTGTGGTTTGGGTGG 1 AGTGTGGTTTAGGTGG * * 1081760 AGTGTGGATTAGGAGG 1 AGTGTGGTTTAGGTGG * 1081776 AGTGTGGTTTGGGTGG 1 AGTGTGGTTTAGGTGG * * 1081792 AGTGTTGATTAGGTGG 1 AGTGTGGTTTAGGTGG * 1081808 AGTGTGGTTTAGGTGA 1 AGTGTGGTTTAGGTGG * * 1081824 AGTGTTGATTAGGAGGAGGGTGG 1 AGTG-TGGTT-----TA-GGTGG * 1081847 AGTGTGGATTAGGTGG 1 AGTGTGGTTTAGGTGG * * 1081863 AGTGTGATTTGGGTGG 1 AGTGTGGTTTAGGTGG * * 1081879 AGTGTGGATTAGGAGG 1 AGTGTGGTTTAGGTGG * 1081895 AGTGTGGTTTGGGTGG 1 AGTGTGGTTTAGGTGG * * 1081911 -GTGTTGATTAGGTGG 1 AGTGTGGTTTAGGTGG ** * 1081926 AGTGCAGTTT-GGATGT 1 AGTGTGGTTTAGG-TGG 1081942 AGTGTGGTTTAGGTGG 1 AGTGTGGTTTAGGTGG ** * 1081958 AGTGCAGTTTGGGT-G 1 AGTGTGGTTTAGGTGG * * 1081973 AGTGTGGATTGGGTGG 1 AGTGTGGTTTAGGTGG * * 1081989 AGTGTGGATTAGGAGG 1 AGTGTGGTTTAGGTGG * * 1082005 AGTGTGGATTAGGAGG 1 AGTGTGGTTTAGGTGG * 1082021 AGTGTGGTTTGGGTGG 1 AGTGTGGTTTAGGTGG * * 1082037 AGTGTGGATTAGGAGG 1 AGTGTGGTTTAGGTGG * * 1082053 AGTGTGGATTGGGTGG 1 AGTGTGGTTTAGGTGG * * 1082069 AGTGTGGATTAGGAGG 1 AGTGTGGTTTAGGTGG * * * 1082085 AGTGTTGATTGGGTGG 1 AGTGTGGTTTAGGTGG 1082101 AGTGTGGTTT 1 AGTGTGGTTT 1082111 GAATGGAGTG Statistics Matches: 367, Mismatches: 81, Indels: 28 0.77 0.17 0.06 Matches are distributed among these distances: 15 40 0.11 16 306 0.83 17 9 0.02 22 4 0.01 23 8 0.02 ACGTcount: A:0.16, C:0.01, G:0.49, T:0.34 Consensus pattern (16 bp): AGTGTGGTTTAGGTGG Found at i:1081687 original size:32 final size:32 Alignment explanation

Indices: 1081616--1082107 Score: 443 Period size: 32 Copynumber: 15.2 Consensus size: 32 1081606 AATTTTGATT * * 1081616 GAGTGTGGATT-GGATGAAGTGTGGTTTTGGTG 1 GAGTGTGGATTAGG-TGGAGTGTGGTTTGGGTG * * ** * 1081648 GACTGTGGTTTAGGTGGAGTGCAGTTTGGATG 1 GAGTGTGGATTAGGTGGAGTGTGGTTTGGGTG * * ** 1081680 TAGTGTGGTTTAGGTGGAGTGCAGTTTGGGT- 1 GAGTGTGGATTAGGTGGAGTGTGGTTTGGGTG * * * * 1081711 GAGTGTGGATTGGGTGGAGTGTTGATTAGGTG 1 GAGTGTGGATTAGGTGGAGTGTGGTTTGGGTG * * * * * 1081743 GAGTGTGGTTTGGGTGGAGTGTGGATTAGGAG 1 GAGTGTGGATTAGGTGGAGTGTGGTTTGGGTG * * * * * 1081775 GAGTGTGGTTTGGGTGGAGTGTTGATTAGGTG 1 GAGTGTGGATTAGGTGGAGTGTGGTTTGGGTG * * * * 1081807 GAGTGTGGTTTAGGTGAAGTGTTGATTAGGAGGAGGGTG 1 GAGTGTGGATTAGGTGGAGTG-TGGTT------TGGGTG * 1081846 GAGTGTGGATTAGGTGGAGTGTGATTTGGGTG 1 GAGTGTGGATTAGGTGGAGTGTGGTTTGGGTG * 1081878 GAGTGTGGATTAGGAGGAGTGTGGTTTGGGTG 1 GAGTGTGGATTAGGTGGAGTGTGGTTTGGGTG * ** * 1081910 G-GTGTTGATTAGGTGGAGTGCAGTTTGGATG 1 GAGTGTGGATTAGGTGGAGTGTGGTTTGGGTG * * ** 1081941 TAGTGTGGTTTAGGTGGAGTGCAGTTTGGGT- 1 GAGTGTGGATTAGGTGGAGTGTGGTTTGGGTG * * * * 1081972 GAGTGTGGATTGGGTGGAGTGTGGATTAGGAG 1 GAGTGTGGATTAGGTGGAGTGTGGTTTGGGTG * 1082004 GAGTGTGGATTAGGAGGAGTGTGGTTTGGGTG 1 GAGTGTGGATTAGGTGGAGTGTGGTTTGGGTG * * 1082036 GAGTGTGGATTAGGAGGAGTGTGGATTGGGTG 1 GAGTGTGGATTAGGTGGAGTGTGGTTTGGGTG * * * 1082068 GAGTGTGGATTAGGAGGAGTGTTGATTGGGTG 1 GAGTGTGGATTAGGTGGAGTGTGGTTTGGGTG 1082100 GAGTGTGG 1 GAGTGTGG 1082108 TTTGAATGGA Statistics Matches: 391, Mismatches: 58, Indels: 22 0.83 0.12 0.05 Matches are distributed among these distances: 31 72 0.18 32 287 0.73 33 4 0.01 38 5 0.01 39 23 0.06 ACGTcount: A:0.16, C:0.01, G:0.50, T:0.33 Consensus pattern (32 bp): GAGTGTGGATTAGGTGGAGTGTGGTTTGGGTG Found at i:1081850 original size:23 final size:23 Alignment explanation

Indices: 1081819--1081869 Score: 66 Period size: 23 Copynumber: 2.2 Consensus size: 23 1081809 GTGTGGTTTA * 1081819 GGTGAAGTGTTGATTAGGAGGAG 1 GGTGAAGTGTGGATTAGGAGGAG * * 1081842 GGTGGAGTGTGGATTAGGTGGAG 1 GGTGAAGTGTGGATTAGGAGGAG * 1081865 TGTGA 1 GGTGA 1081870 TTTGGGTGGA Statistics Matches: 23, Mismatches: 5, Indels: 0 0.82 0.18 0.00 Matches are distributed among these distances: 23 23 1.00 ACGTcount: A:0.22, C:0.00, G:0.51, T:0.27 Consensus pattern (23 bp): GGTGAAGTGTGGATTAGGAGGAG Found at i:1081883 original size:55 final size:55 Alignment explanation

Indices: 1081786--1081901 Score: 178 Period size: 55 Copynumber: 2.1 Consensus size: 55 1081776 AGTGTGGTTT * * * 1081786 GGGTGGAGTGTTGATTAGGTGGAGTGTGGTTTAGGTGAAGTGTTGATTAGGAGGA 1 GGGTGGAGTGTGGATTAGGTGGAGTGTGATTTAGGTGAAGTGTGGATTAGGAGGA * * 1081841 GGGTGGAGTGTGGATTAGGTGGAGTGTGATTTGGGTGGAGTGTGGATTAGGAGGA 1 GGGTGGAGTGTGGATTAGGTGGAGTGTGATTTAGGTGAAGTGTGGATTAGGAGGA * 1081896 GTGTGG 1 GGGTGG 1081902 TTTGGGTGGG Statistics Matches: 55, Mismatches: 6, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 55 55 1.00 ACGTcount: A:0.18, C:0.00, G:0.51, T:0.31 Consensus pattern (55 bp): GGGTGGAGTGTGGATTAGGTGGAGTGTGATTTAGGTGAAGTGTGGATTAGGAGGA Found at i:1082471 original size:4 final size:4 Alignment explanation

Indices: 1082462--1082542 Score: 162 Period size: 4 Copynumber: 20.2 Consensus size: 4 1082452 ATGTATAAGA 1082462 AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT 1 AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT 1082510 AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT A 1 AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT A 1082543 ATGATTAGTT Statistics Matches: 77, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 4 77 1.00 ACGTcount: A:0.51, C:0.00, G:0.25, T:0.25 Consensus pattern (4 bp): AGAT Found at i:1084948 original size:2 final size:2 Alignment explanation

Indices: 1084941--1084981 Score: 73 Period size: 2 Copynumber: 20.5 Consensus size: 2 1084931 TCCCTATTAG * 1084941 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TT TC TC TC TC T 1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T 1084982 GACGGATCAT Statistics Matches: 37, Mismatches: 2, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 2 37 1.00 ACGTcount: A:0.00, C:0.46, G:0.00, T:0.54 Consensus pattern (2 bp): TC Found at i:1088139 original size:2 final size:2 Alignment explanation

Indices: 1088134--1088172 Score: 78 Period size: 2 Copynumber: 19.5 Consensus size: 2 1088124 TTGTGTGCGT 1088134 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G 1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G 1088173 TGCATGGTTG Statistics Matches: 37, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 37 1.00 ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00 Consensus pattern (2 bp): GA Found at i:1089020 original size:2 final size:2 Alignment explanation

Indices: 1089013--1089050 Score: 76 Period size: 2 Copynumber: 19.0 Consensus size: 2 1089003 TTTCTTATAN 1089013 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG 1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG 1089051 TGCATGGTTG Statistics Matches: 36, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 36 1.00 ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00 Consensus pattern (2 bp): AG Found at i:1094963 original size:2 final size:2 Alignment explanation

Indices: 1094956--1094982 Score: 54 Period size: 2 Copynumber: 13.5 Consensus size: 2 1094946 TTGATACATA 1094956 TC TC TC TC TC TC TC TC TC TC TC TC TC T 1 TC TC TC TC TC TC TC TC TC TC TC TC TC T 1094983 GAAAGAACTT Statistics Matches: 25, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 25 1.00 ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52 Consensus pattern (2 bp): TC Found at i:1108163 original size:5 final size:5 Alignment explanation

Indices: 1108153--1108236 Score: 67 Period size: 5 Copynumber: 17.8 Consensus size: 5 1108143 CTGTAAACTG 1108153 TTTGT TTTG- TTTG- TTTGTT TTTGT TTTGT TTTG- TTT-T TTT-T TTTGT 1 TTTGT TTTGT TTTGT TTTG-T TTTGT TTTGT TTTGT TTTGT TTTGT TTTGT * * 1108199 TTT-T TTT-T TGTT-T TTTGTT TTTTT TTTGC TTTGT TTTG 1 TTTGT TTTGT T-TTGT TTTG-T TTTGT TTTGT TTTGT TTTG 1108237 AAAAAAGGGA Statistics Matches: 68, Mismatches: 4, Indels: 14 0.79 0.05 0.16 Matches are distributed among these distances: 4 26 0.38 5 34 0.50 6 8 0.12 ACGTcount: A:0.00, C:0.01, G:0.15, T:0.83 Consensus pattern (5 bp): TTTGT Found at i:1108177 original size:23 final size:22 Alignment explanation

Indices: 1108151--1108235 Score: 97 Period size: 20 Copynumber: 3.9 Consensus size: 22 1108141 CACTGTAAAC 1108151 TGTTTGTTTTGTTTGTTTGTTTT 1 TGTTTGTTTTGTTTGTTT-TTTT 1108174 TGTTTTGTTTTGTTT-TTTTTTT 1 TG-TTTGTTTTGTTTGTTTTTTT 1108196 TGTTT-TTTT-TTTGTTTTTTGT 1 TGTTTGTTTTGTTTGTTTTTT-T * 1108217 T-TTTTTTTTGCTTTGTTTT 1 TGTTTGTTTTG-TTTGTTTT 1108236 GAAAAAAGGG Statistics Matches: 56, Mismatches: 0, Indels: 12 0.82 0.00 0.18 Matches are distributed among these distances: 19 3 0.05 20 13 0.23 21 9 0.16 22 6 0.11 23 13 0.23 24 12 0.21 ACGTcount: A:0.00, C:0.01, G:0.15, T:0.84 Consensus pattern (22 bp): TGTTTGTTTTGTTTGTTTTTTT Found at i:1108190 original size:1 final size:1 Alignment explanation

Indices: 1108170--1108225 Score: 58 Period size: 1 Copynumber: 56.0 Consensus size: 1 1108160 TGTTTGTTTG * * * * * * 1108170 TTTTTGTTTTGTTTTGTTTTTTTTTTTGTTTTTTTTTTGTTTTTTGTTTTTTTTTT 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 1108226 GCTTTGTTTT Statistics Matches: 43, Mismatches: 12, Indels: 0 0.78 0.22 0.00 Matches are distributed among these distances: 1 43 1.00 ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89 Consensus pattern (1 bp): T Found at i:1108197 original size:28 final size:28 Alignment explanation

Indices: 1108153--1108236 Score: 107 Period size: 28 Copynumber: 3.0 Consensus size: 28 1108143 CTGTAAACTG * 1108153 TTTGTTTTGTTTGTTTGTTTTTGTTTTGT 1 TTTGTTTT-TTTTTTTGTTTTTGTTTTGT * 1108182 TTTGTTTTTTTTTTTGTTTTTTTTTTGT 1 TTTGTTTTTTTTTTTGTTTTTGTTTTGT * * 1108210 TTTTTGTTTTTTTTTTG-CTTTGTTTTG 1 TTTGT-TTTTTTTTTTGTTTTTGTTTTG 1108237 AAAAAAGGGA Statistics Matches: 49, Mismatches: 5, Indels: 3 0.86 0.09 0.05 Matches are distributed among these distances: 28 30 0.61 29 19 0.39 ACGTcount: A:0.00, C:0.01, G:0.15, T:0.83 Consensus pattern (28 bp): TTTGTTTTTTTTTTTGTTTTTGTTTTGT Found at i:1116345 original size:40 final size:40 Alignment explanation

Indices: 1116238--1116572 Score: 233 Period size: 40 Copynumber: 8.0 Consensus size: 40 1116228 AACACGGTGA * * * * 1116238 AAAACAGTTGATAGAGATGGTTACCTTTACACTTGAGTTAT 1 AAAACATTTGATTG-GATAGTTACCTTAACACTTGAGTTAT * ** * 1116279 AGAACATTTTGATTGGATAGCAACCTTTACACTTGAGTTAT 1 AAAACA-TTTGATTGGATAGTTACCTTAACACTTGAGTTAT * * 1116320 AAAACATTTGATTGGAAAGTTACCTTAACACTTCAGTTA- 1 AAAACATTTGATTGGATAGTTACCTTAACACTTGAGTTAT ** * * 1116359 AAGAACATTTGATTGGATAGCAACATTTACACTTCGAGTTAT 1 AA-AACATTTGATTGGATAGTTACCTTAACACTT-GAGTTAT * * * * 1116401 ATAGACCATTTTGATTGGATGGTTATCTTAACACTTGAGTTGT 1 A-A-AACA-TTTGATTGGATAGTTACCTTAACACTTGAGTTAT * * * * 1116444 AGAACATTTTATTGGATAGGTACCTTAAAACTTGAGTTAT 1 AAAACATTTGATTGGATAGTTACCTTAACACTTGAGTTAT * * 1116484 ACACATGTATAGAGCATTTTGATTGGATGGCTACCTTAACACTTGAGTTAT 1 ----A---A-A-A-CA-TTTGATTGGATAGTTACCTTAACACTTGAGTTAT * * * * 1116535 AGAACGTATGATTGGAT-GTTTACCTTTACACTTGAGTT 1 AAAACATTTGATTGGATAG-TTACCTTAACACTTGAGTT 1116573 CTAGTCGGAT Statistics Matches: 232, Mismatches: 44, Indels: 37 0.74 0.14 0.12 Matches are distributed among these distances: 39 3 0.01 40 109 0.47 41 42 0.18 42 8 0.03 43 13 0.06 44 22 0.09 47 1 0.00 48 1 0.00 49 1 0.00 50 2 0.01 51 30 0.13 ACGTcount: A:0.32, C:0.13, G:0.18, T:0.36 Consensus pattern (40 bp): AAAACATTTGATTGGATAGTTACCTTAACACTTGAGTTAT Found at i:1120283 original size:13 final size:12 Alignment explanation

Indices: 1120261--1120300 Score: 55 Period size: 11 Copynumber: 3.3 Consensus size: 12 1120251 TTCAATATTT 1120261 TTTTAATTTTTG 1 TTTTAATTTTTG 1120273 TTTTAATTTTTTG 1 TTTTAA-TTTTTG * 1120286 TTTT-GTTTTTG 1 TTTTAATTTTTG 1120297 TTTT 1 TTTT 1120301 GCATGTCTTT Statistics Matches: 26, Mismatches: 1, Indels: 3 0.87 0.03 0.10 Matches are distributed among these distances: 11 10 0.38 12 6 0.23 13 10 0.38 ACGTcount: A:0.10, C:0.00, G:0.10, T:0.80 Consensus pattern (12 bp): TTTTAATTTTTG Found at i:1122292 original size:224 final size:227 Alignment explanation

Indices: 1121914--1122351 Score: 632 Period size: 224 Copynumber: 1.9 Consensus size: 227 1121904 CAATCGGAAG * 1121914 TCAACTTCCTGTTAAATGACGACTTTGCTTATTTTTTAACCAAAAATTTCAAACAAATTTTCGTC 1 TCAACTTCCTGTTAAATGACGACTTTGCTTATTTTTTAACCAAAAATTTCAAACAAATTTCCGTC * * * 1121979 AAAGATTTCTCAGCAACTATTTATCGCAGATGATTGAAATTTTTACACAATATTTGTATAGGCAT 66 AAAGATTTCTCAGCAACTATATATCGCAGATGATTAAAATTTTAACACAATATTTGTATAGGCAT * 1122044 GCCATATTGTGGGATATATTTTTGTACCAATCAGACGTCAACTTCCTGTTAAATGACGAC-GT-T 131 GCCATATTGTGGGATATATTTTTGTACCAATCAGACGTCAACTTCCTGTTAAATAACGACTGTGT 1122107 TAGTTTTAGCCAAAATTTTTACCAATTGGACT 196 TAGTTTTAGCCAAAATTTTTACCAATTGGACT * * ** * * * 1122139 TCAACTTCCTGTTTAATGA-GTACTTTGTTTA-TTTTTAGTCAAAATTTTCTAGCAAATTTCCGT 1 TCAACTTCCTGTTAAATGACG-ACTTTGCTTATTTTTTAACCAAAAATTTCAAACAAATTTCCGT * * * * * * 1122202 CATAGATTTCTCAGCAACTATATATCGCAGATGCTTAAAATTTTAACACACTATTTTTTTGGGCA 65 CAAAGATTTCTCAGCAACTATATATCGCAGATGATTAAAATTTTAACACAATATTTGTATAGGCA * * * * 1122267 TGCCATATTGTGGGATATATTTTTGTATCAATCGGACGTCAACTTCCTGTTAAATAATGACTTTG 130 TGCCATATTGTGGGATATATTTTTGTACCAATCAGACGTCAACTTCCTGTTAAATAACGACTGTG * 1122332 TTATTTTTAGCCAAAATTTT 195 TTAGTTTTAGCCAAAATTTT 1122352 CAAACAAATT Statistics Matches: 187, Mismatches: 23, Indels: 5 0.87 0.11 0.02 Matches are distributed among these distances: 224 140 0.75 225 28 0.15 226 19 0.10 ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40 Consensus pattern (227 bp): TCAACTTCCTGTTAAATGACGACTTTGCTTATTTTTTAACCAAAAATTTCAAACAAATTTCCGTC AAAGATTTCTCAGCAACTATATATCGCAGATGATTAAAATTTTAACACAATATTTGTATAGGCAT GCCATATTGTGGGATATATTTTTGTACCAATCAGACGTCAACTTCCTGTTAAATAACGACTGTGT TAGTTTTAGCCAAAATTTTTACCAATTGGACT Found at i:1122575 original size:389 final size:386 Alignment explanation

Indices: 1121819--1122526 Score: 985 Period size: 389 Copynumber: 1.8 Consensus size: 386 1121809 GTCGCATTTA * * * * * * 1121819 TCTCAGCAACTATTTATTGCAGATGCTTGAAATTTTTACACAGTGTTTGTTAAGGCATGCCATAT 1 TCTCAGCAACTATATATCGCAGATGCTTAAAATTTTAACACACTATTTGTTAAGGCATGCCATAT * 1121884 CGTGGGATATATTTTTGTACCAATCGGAAGTCAACTTCCTGTTAAATGACGACTTTGCTTATTTT 66 CGTGGGATATATTTTTGTACCAATCGGAAGTCAACTTCCTGTTAAATAACGACTTTGCTTATTTT 1121949 TTAACCAAAAATTTCAAACAAATTTTCGTCAAAGATTTCTCAGCAACTATTTATCGCAGATGATT 131 TTAACCAAAAATTTCAAACAAATTTTCGTCAAAGATTTCTCAGCAACTATTTATCGCAGATGATT * 1122014 GAAATTTTTACACAATATTTGTATAGGCATGCCATATTGTGGGATATATTTTTGTACCAATCAGA 196 GAAATTTTTACACAATATTTGTATAGGCATGCCATATCGTGGGATATATTTTTGTACCAATCAGA * * * * 1122079 CGTCAACTTCCTGTTAAATGACGACGTTTAGTTTTAGCCAAAATTTTTACCAATTGGACTTCAAC 261 CGTCAACTTCCTGTTAAATGACGACGTTTAGTTTTAGCCAAAATTTTAACAAATTGGACCTCAAA * *** 1122144 TTCCTGTTTAATGAGTACTTTGTTTATTTTTAGTCAAAATTTTCTAGCAAATTTCCGTCATAGAT 326 TTCC---TTAATGAG-AC-TTATTTATTCGCAGTCAAAATTTTCTAGCAAATTTCCGTCATAGAT 1122209 T 386 T * ** 1122210 TCTCAGCAACTATATATCGCAGATGCTTAAAATTTTAACACACTATTTTTTTGGGCATGCCATAT 1 TCTCAGCAACTATATATCGCAGATGCTTAAAATTTTAACACACTATTTGTTAAGGCATGCCATAT * * * * 1122275 TGTGGGATATATTTTTGTATCAATCGGACGTCAACTTCCTGTTAAATAATGACTTTG-TTA-TTT 66 CGTGGGATATATTTTTGTACCAATCGGAAGTCAACTTCCTGTTAAATAACGACTTTGCTTATTTT * * * * * * 1122338 TTAGCCAAAATTTTCAAACAAATTTTTGTCAAATATTTCTCAGCAGCTATTTATCGCAGATGCTT 131 TTAACCAAAAATTTCAAACAAATTTTCGTCAAAGATTTCTCAGCAACTATTTATCGCAGATGATT * * * 1122403 GAAATTTTTACACAGTGTTTGCTA-AGGCATGCCATATCGTGGGATATATTTTTGTACCAATCGG 196 GAAATTTTTACACAATATTTG-TATAGGCATGCCATATCGTGGGATATATTTTTGTACCAATCAG 1122467 ACGTCAACTTCCTGTTAAATGA-GTACTTTGTTTA-TTTTAGCCAAAATTTTCAAACAAATT 260 ACGTCAACTTCCTGTTAAATGACG-AC---GTTTAGTTTTAGCCAAAATTTT--AACAAATT 1122527 TTCCTCAAAG Statistics Matches: 284, Mismatches: 26, Indels: 12 0.88 0.08 0.04 Matches are distributed among these distances: 388 1 0.00 389 143 0.50 390 5 0.02 391 124 0.44 392 5 0.02 393 6 0.02 ACGTcount: A:0.30, C:0.17, G:0.15, T:0.39 Consensus pattern (386 bp): TCTCAGCAACTATATATCGCAGATGCTTAAAATTTTAACACACTATTTGTTAAGGCATGCCATAT CGTGGGATATATTTTTGTACCAATCGGAAGTCAACTTCCTGTTAAATAACGACTTTGCTTATTTT TTAACCAAAAATTTCAAACAAATTTTCGTCAAAGATTTCTCAGCAACTATTTATCGCAGATGATT GAAATTTTTACACAATATTTGTATAGGCATGCCATATCGTGGGATATATTTTTGTACCAATCAGA CGTCAACTTCCTGTTAAATGACGACGTTTAGTTTTAGCCAAAATTTTAACAAATTGGACCTCAAA TTCCTTAATGAGACTTATTTATTCGCAGTCAAAATTTTCTAGCAAATTTCCGTCATAGATT Found at i:1122652 original size:165 final size:166 Alignment explanation

Indices: 1122122--1122632 Score: 726 Period size: 165 Copynumber: 3.1 Consensus size: 166 1122112 TTAGCCAAAA * * * * 1122122 TTTT-TACCAATTGGACTTCAACTTCCTGTTTAATGAGTACTTTGTTTATTTTTAGTCAAAATTT 1 TTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGAGTACTTTGTTTATTTTTAGCCAAAATTT * * * * * * 1122186 TCTAGCAAA-TTTCCGTCATAGATTTCTCAGCAACTATATATCGCAGATGCTTAAAATTTTAACA 66 TCAAACAAATTTTCC-TCAAAGATTTCTCAGCAGCTATTTATCGCAGATGCTTGAAATTTTAACA * 1122250 CACTATTTTTTTGGGCATGCCATATTGTGGGATATAT 130 CACTATTTTTTTAGGCATGCCATATTGTGGGATATAT * * 1122287 TTTTGTATCAATCGGACGTCAACTTCCTGTTAAAT-AATGACTTTG-TTATTTTTAGCCAAAATT 1 TTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGAGT-ACTTTGTTTATTTTTAGCCAAAATT ** * * 1122350 TTCAAACAAATTTTTGTCAAATATTTCTCAGCAGCTATTTATCGCAGATGCTTGAAATTTTTACA 65 TTCAAACAAATTTTCCTCAAAGATTTCTCAGCAGCTATTTATCGCAGATGCTTGAAATTTTAACA * * ** * * 1122415 CAGTGTTTGCTAAGGCATGCCATATCGTGGGATATAT 130 CACTATTTTTTTAGGCATGCCATATTGTGGGATATAT 1122452 TTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGAGTACTTTGTTTA-TTTTAGCCAAAATTT 1 TTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGAGTACTTTGTTTATTTTTAGCCAAAATTT * * 1122516 TCAAACAAATTTTCCTCAAAGATTCCTCAGCAGCTATTTATCGCAGGTGCTTGAAATTTTAACAC 66 TCAAACAAATTTTCCTCAAAGATTTCTCAGCAGCTATTTATCGCAGATGCTTGAAATTTTAACAC * 1122581 ACTATTTTTTTAGTCATGCCATATTGTGGGATATAT 131 ACTATTTTTTTAGGCATGCCATATTGTGGGATATAT * 1122617 TTCTGTACCAATCGGA 1 TTTTGTACCAATCGGA 1122633 TGCCAGCTTT Statistics Matches: 302, Mismatches: 39, Indels: 10 0.86 0.11 0.03 Matches are distributed among these distances: 165 262 0.87 166 40 0.13 ACGTcount: A:0.28, C:0.17, G:0.14, T:0.40 Consensus pattern (166 bp): TTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGAGTACTTTGTTTATTTTTAGCCAAAATTT TCAAACAAATTTTCCTCAAAGATTTCTCAGCAGCTATTTATCGCAGATGCTTGAAATTTTAACAC ACTATTTTTTTAGGCATGCCATATTGTGGGATATAT Found at i:1123276 original size:146 final size:145 Alignment explanation

Indices: 1123014--1124254 Score: 1748 Period size: 146 Copynumber: 8.5 Consensus size: 145 1123004 TAAAACTGTT * * * 1123014 GGTCATAAGCAATATTTGTGTGAAGTAAGAACATTCAATGCTTCTCCATAAGAAAGATAATGACC 1 GGTCATAAGCAATCTTTGTGTGAAGTTAGAAC-TTCAATGTTTCTCCATAAGAAAGATAATGACC * 1123079 GGACACAAATTTTGCACTTTTTCTGCCAGTGACCTTGACCTTGCCCAAATGACCTTGGGTCAAGG 65 GGACACGAATTTTGCACTTTTTCTGCCAGTGACCTTGACCTTGCCCAAATGACCTTGGGTCAAGG * 1123144 TCATGACACACCCTTT 130 TCATGACACACCCTTA * * * 1123160 GGTCCTAAGCAATATTTGTGTGAAGTTAGAACATTCAATGCTTCTCCATAAGAAAGATAATGACC 1 GGTCATAAGCAATCTTTGTGTGAAGTTAGAAC-TTCAATGTTTCTCCATAAGAAAGATAATGACC * ** * 1123225 GGACACGAATTTTGCACTATTTTC-CCCAACGACCTTGACCTTGCCCAAATGACCTTGGATCAAG 65 GGACACGAATTTTGCACT-TTTTCTGCCAGTGACCTTGACCTTGCCCAAATGACCTTGGGTCAAG 1123289 GTCATGACACACCCTTA 129 GTCATGACACACCCTTA * * * 1123306 GGTCATTAGCAATCTTTGTATGAA-TTAAGAACTTCAAATGTTTCTCCATAAGAAAGATTTATG- 1 GGTCATAAGCAATCTTTGTGTGAAGTT-AGAACTTC-AATGTTTCTCCATAAGAAAGA-TAATGA * * 1123369 CTGGACACAAATTTTGCACTTTTTCTGCCAGTGACCTTGACCTTGCCCAAATGACCTTGGGTCAA 63 CCGGACACGAATTTTGCACTTTTTCTGCCAGTGACCTTGACCTTGCCCAAATGACCTTGGGTCAA * 1123434 GGTCATGACACACCCTTT 128 GGTCATGACACACCCTTA * * * 1123452 GGTCCTAAGCAATATTTGTGTGAAGTTAGAACATTCAATGCTTCTCCATAAGAAAGATAATGACC 1 GGTCATAAGCAATCTTTGTGTGAAGTTAGAAC-TTCAATGTTTCTCCATAAGAAAGATAATGACC * ** * 1123517 GGACACGAATTTTGCACTATTTTC-CCCAACGACCTTGACCTTGCCCAAATGACCTTGGATCAAG 65 GGACACGAATTTTGCACT-TTTTCTGCCAGTGACCTTGACCTTGCCCAAATGACCTTGGGTCAAG 1123581 GTCATGACACACCCTTA 129 GTCATGACACACCCTTA * * * 1123598 GGTCATTAGCAATCTTTGTATGAA-TTAAGAACTTCAAATGTTTCTCCATAAGAAAGATTTATG- 1 GGTCATAAGCAATCTTTGTGTGAAGTT-AGAACTTC-AATGTTTCTCCATAAGAAAGA-TAATGA * * 1123661 CTGGACACAAATTTTGCACTTTTTCTGCCAGTGACCTTGACCTTGCCCAAATGACCTTGGGTCAA 63 CCGGACACGAATTTTGCACTTTTTCTGCCAGTGACCTTGACCTTGCCCAAATGACCTTGGGTCAA * 1123726 GGTCATGACACACCCTTT 128 GGTCATGACACACCCTTA * * * 1123744 GGTCCTAAGCAATATTTGTGTGAAGTTAGAACATTCAATGCTTCTCCATAAGAAAGATAATGACC 1 GGTCATAAGCAATCTTTGTGTGAAGTTAGAAC-TTCAATGTTTCTCCATAAGAAAGATAATGACC * ** * 1123809 GGACACGAATTTTGCACTATTTTC-CCCAACGACCTTGACCTTGCCCAAATGACCTTGGATCAAG 65 GGACACGAATTTTGCACT-TTTTCTGCCAGTGACCTTGACCTTGCCCAAATGACCTTGGGTCAAG 1123873 GTCATGACACACCCTTA 129 GTCATGACACACCCTTA * * * * 1123890 GGTCATTAGCAATCTTTGTATGAA-TTAAGAACTTCAAATGTTTCTCCATAAGAAAGAT-TTGGG 1 GGTCATAAGCAATCTTTGTGTGAAGTT-AGAACTTC-AATGTTTCTCCATAAGAAAGATAAT-GA * * 1123953 CCGGACACAAATTTTGCACTTTTTCTGCCAGTGACCTTGACCTTGCCCTAATGACCTTGGGTCAA 63 CCGGACACGAATTTTGCACTTTTTCTGCCAGTGACCTTGACCTTGCCCAAATGACCTTGGGTCAA * 1124018 GGTCATGACACATCCTTA 128 GGTCATGACACACCCTTA * 1124036 GGTCATAAGCAATCTTTGTGTGAAGTAAGAACTTCCAATGTTTCTCCATAAGAAAGAT-ATGGAC 1 GGTCATAAGCAATCTTTGTGTGAAGTTAGAACTT-CAATGTTTCTCCATAAGAAAGATAAT-GAC * * * ** 1124100 TGGACACGAATTTTGTATTTTTTCTGCCAGTGACCTTGACCTTGCCTGAATGACCTTGGGTCAAG 64 CGGACACGAATTTTGCACTTTTTCTGCCAGTGACCTTGACCTTGCCCAAATGACCTTGGGTCAAG * 1124165 GTCATGACACACCCCTA 129 GTCATGACACACCCTTA * 1124182 GGTCATAAGCAATCTTTGTGTGAAGTAAGAACTTCCAATGTTTCTCCATAAGAAAGAT-ATGGAC 1 GGTCATAAGCAATCTTTGTGTGAAGTTAGAACTT-CAATGTTTCTCCATAAGAAAGATAAT-GAC 1124246 CGGACACGA 64 CGGACACGA 1124255 TTGCACAGAC Statistics Matches: 984, Mismatches: 88, Indels: 46 0.88 0.08 0.04 Matches are distributed among these distances: 145 39 0.04 146 910 0.92 147 35 0.04 ACGTcount: A:0.29, C:0.23, G:0.18, T:0.30 Consensus pattern (145 bp): GGTCATAAGCAATCTTTGTGTGAAGTTAGAACTTCAATGTTTCTCCATAAGAAAGATAATGACCG GACACGAATTTTGCACTTTTTCTGCCAGTGACCTTGACCTTGCCCAAATGACCTTGGGTCAAGGT CATGACACACCCTTA Found at i:1123563 original size:292 final size:292 Alignment explanation

Indices: 1123014--1124239 Score: 2093 Period size: 292 Copynumber: 4.2 Consensus size: 292 1123004 TAAAACTGTT * * * * * * 1123014 GGTCATAAGCAATATTTGTGTGAAGTAAGAACATTC-AATGCTTCTCCATAAGAAAGA-TAATGA 1 GGTCATTAGCAATCTTTGTATGAATTAAGAAC-TTCAAATGTTTCTCCATAAGAAAGATTTATG- 1123077 CCGGACACAAATTTTGCACTTTTTCTGCCAGTGACCTTGACCTTGCCCAAATGACCTTGGGTCAA 64 CCGGACACAAATTTTGCACTTTTTCTGCCAGTGACCTTGACCTTGCCCAAATGACCTTGGGTCAA 1123142 GGTCATGACACACCCTTTGGTCCTAAGCAATATTTGTGTGAAGTTAGAACATTCAATGCTTCTCC 129 GGTCATGACACACCCTTTGGTCCTAAGCAATATTTGTGTGAAGTTAGAACATTCAATGCTTCTCC 1123207 ATAAGAAAGATAATGACCGGACACGAATTTTGCACTATTTTCCCCAACGACCTTGACCTTGCCCA 194 ATAAGAAAGATAATGACCGGACACGAATTTTGCACTATTTTCCCCAACGACCTTGACCTTGCCCA 1123272 AATGACCTTGGATCAAGGTCATGACACACCCTTA 259 AATGACCTTGGATCAAGGTCATGACACACCCTTA * 1123306 GGTCATTAGCAATCTTTGTATGAATTAAGAACTTCAAATGTTTCTCCATAAGAAAGATTTATGCT 1 GGTCATTAGCAATCTTTGTATGAATTAAGAACTTCAAATGTTTCTCCATAAGAAAGATTTATGCC 1123371 GGACACAAATTTTGCACTTTTTCTGCCAGTGACCTTGACCTTGCCCAAATGACCTTGGGTCAAGG 66 GGACACAAATTTTGCACTTTTTCTGCCAGTGACCTTGACCTTGCCCAAATGACCTTGGGTCAAGG 1123436 TCATGACACACCCTTTGGTCCTAAGCAATATTTGTGTGAAGTTAGAACATTCAATGCTTCTCCAT 131 TCATGACACACCCTTTGGTCCTAAGCAATATTTGTGTGAAGTTAGAACATTCAATGCTTCTCCAT 1123501 AAGAAAGATAATGACCGGACACGAATTTTGCACTATTTTCCCCAACGACCTTGACCTTGCCCAAA 196 AAGAAAGATAATGACCGGACACGAATTTTGCACTATTTTCCCCAACGACCTTGACCTTGCCCAAA 1123566 TGACCTTGGATCAAGGTCATGACACACCCTTA 261 TGACCTTGGATCAAGGTCATGACACACCCTTA * 1123598 GGTCATTAGCAATCTTTGTATGAATTAAGAACTTCAAATGTTTCTCCATAAGAAAGATTTATGCT 1 GGTCATTAGCAATCTTTGTATGAATTAAGAACTTCAAATGTTTCTCCATAAGAAAGATTTATGCC 1123663 GGACACAAATTTTGCACTTTTTCTGCCAGTGACCTTGACCTTGCCCAAATGACCTTGGGTCAAGG 66 GGACACAAATTTTGCACTTTTTCTGCCAGTGACCTTGACCTTGCCCAAATGACCTTGGGTCAAGG 1123728 TCATGACACACCCTTTGGTCCTAAGCAATATTTGTGTGAAGTTAGAACATTCAATGCTTCTCCAT 131 TCATGACACACCCTTTGGTCCTAAGCAATATTTGTGTGAAGTTAGAACATTCAATGCTTCTCCAT 1123793 AAGAAAGATAATGACCGGACACGAATTTTGCACTATTTTCCCCAACGACCTTGACCTTGCCCAAA 196 AAGAAAGATAATGACCGGACACGAATTTTGCACTATTTTCCCCAACGACCTTGACCTTGCCCAAA 1123858 TGACCTTGGATCAAGGTCATGACACACCCTTA 261 TGACCTTGGATCAAGGTCATGACACACCCTTA ** 1123890 GGTCATTAGCAATCTTTGTATGAATTAAGAACTTCAAATGTTTCTCCATAAGAAAGATTTGGGCC 1 GGTCATTAGCAATCTTTGTATGAATTAAGAACTTCAAATGTTTCTCCATAAGAAAGATTTATGCC * 1123955 GGACACAAATTTTGCACTTTTTCTGCCAGTGACCTTGACCTTGCCCTAATGACCTTGGGTCAAGG 66 GGACACAAATTTTGCACTTTTTCTGCCAGTGACCTTGACCTTGCCCAAATGACCTTGGGTCAAGG * * * * * * 1124020 TCATGACACATCCTTAGGTCATAAGCAATCTTTGTGTGAAGTAAGAAC-TTCCAATGTTTCTCCA 131 TCATGACACACCCTTTGGTCCTAAGCAATATTTGTGTGAAGTTAGAACATT-CAATGCTTCTCCA * * * * ** * 1124084 TAAGAAAGAT-ATGGACTGGACACGAATTTTGTA-TTTTTTCTGCCAGTGACCTTGACCTTGCCT 195 TAAGAAAGATAAT-GACCGGACACGAATTTTGCACTATTTTC-CCCAACGACCTTGACCTTGCCC * * * 1124147 GAATGACCTTGGGTCAAGGTCATGACACACCCCTA 258 AAATGACCTTGGATCAAGGTCATGACACACCCTTA * * * * 1124182 GGTCATAAGCAATCTTTGTGTGAAGTAAGAACTTCCAATGTTTCTCCATAAGAAAGAT 1 GGTCATTAGCAATCTTTGTATGAATTAAGAACTTCAAATGTTTCTCCATAAGAAAGAT 1124240 ATGGACCGGA Statistics Matches: 898, Mismatches: 31, Indels: 10 0.96 0.03 0.01 Matches are distributed among these distances: 291 13 0.01 292 881 0.98 293 4 0.00 ACGTcount: A:0.29, C:0.23, G:0.18, T:0.30 Consensus pattern (292 bp): GGTCATTAGCAATCTTTGTATGAATTAAGAACTTCAAATGTTTCTCCATAAGAAAGATTTATGCC GGACACAAATTTTGCACTTTTTCTGCCAGTGACCTTGACCTTGCCCAAATGACCTTGGGTCAAGG TCATGACACACCCTTTGGTCCTAAGCAATATTTGTGTGAAGTTAGAACATTCAATGCTTCTCCAT AAGAAAGATAATGACCGGACACGAATTTTGCACTATTTTCCCCAACGACCTTGACCTTGCCCAAA TGACCTTGGATCAAGGTCATGACACACCCTTA Found at i:1130101 original size:60 final size:60 Alignment explanation

Indices: 1130001--1130129 Score: 179 Period size: 60 Copynumber: 2.1 Consensus size: 60 1129991 GGTATTGTCA * * 1130001 ATATCGACGTTAAATATGAAAAGACTGAGTTCTGTACATATGTAAATCGATATCGATACG 1 ATATCGACGTTAAATATGAAAAGACTGAGTTCTGTACATATGCAAATCAATATCGATACG * * * * * 1130061 ATATCGACGTTAAATATGGACAG-CTGTAGTTGTGTGCATATGCAACTCAATATCGATACG 1 ATATCGACGTTAAATATGAAAAGACTG-AGTTCTGTACATATGCAAATCAATATCGATACG 1130121 ATATCGACG 1 ATATCGACG 1130130 ATATCGACAT Statistics Matches: 61, Mismatches: 7, Indels: 2 0.87 0.10 0.03 Matches are distributed among these distances: 59 3 0.05 60 58 0.95 ACGTcount: A:0.35, C:0.16, G:0.20, T:0.29 Consensus pattern (60 bp): ATATCGACGTTAAATATGAAAAGACTGAGTTCTGTACATATGCAAATCAATATCGATACG Found at i:1130209 original size:13 final size:13 Alignment explanation

Indices: 1130188--1130221 Score: 50 Period size: 13 Copynumber: 2.6 Consensus size: 13 1130178 TATTGATACG * 1130188 ATATCGACGTTAA 1 ATATGGACGTTAA 1130201 ATATGGACGTTAA 1 ATATGGACGTTAA * 1130214 ATTTGGAC 1 ATATGGAC 1130222 AGCTGTAATT Statistics Matches: 19, Mismatches: 2, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 13 19 1.00 ACGTcount: A:0.35, C:0.12, G:0.21, T:0.32 Consensus pattern (13 bp): ATATGGACGTTAA Found at i:1130314 original size:20 final size:20 Alignment explanation

Indices: 1130275--1130315 Score: 64 Period size: 20 Copynumber: 2.0 Consensus size: 20 1130265 AATCAGTGAA * 1130275 TCGATATCGATACAATATTG 1 TCGATATCGATACAACATTG * 1130295 TCGATATCGATACTACATTG 1 TCGATATCGATACAACATTG 1130315 T 1 T 1130316 GTCTTGGACA Statistics Matches: 19, Mismatches: 2, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 20 19 1.00 ACGTcount: A:0.32, C:0.17, G:0.15, T:0.37 Consensus pattern (20 bp): TCGATATCGATACAACATTG Found at i:1142995 original size:24 final size:24 Alignment explanation

Indices: 1142965--1143014 Score: 73 Period size: 24 Copynumber: 2.1 Consensus size: 24 1142955 GTAAGGCCAA * * * 1142965 TTTTTTTGTTTTGTTTTTGTTGTT 1 TTTTTTTCTTTTCTTTTTGATGTT 1142989 TTTTTTTCTTTTCTTTTTGATGTT 1 TTTTTTTCTTTTCTTTTTGATGTT 1143013 TT 1 TT 1143015 GCGTGATATA Statistics Matches: 23, Mismatches: 3, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 24 23 1.00 ACGTcount: A:0.02, C:0.04, G:0.12, T:0.82 Consensus pattern (24 bp): TTTTTTTCTTTTCTTTTTGATGTT Found at i:1143146 original size:17 final size:17 Alignment explanation

Indices: 1143124--1143156 Score: 66 Period size: 17 Copynumber: 1.9 Consensus size: 17 1143114 TCGCATAGCC 1143124 CCCTAACTCCGTCACTA 1 CCCTAACTCCGTCACTA 1143141 CCCTAACTCCGTCACT 1 CCCTAACTCCGTCACT 1143157 TTCGGGAAAC Statistics Matches: 16, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 17 16 1.00 ACGTcount: A:0.21, C:0.48, G:0.06, T:0.24 Consensus pattern (17 bp): CCCTAACTCCGTCACTA Found at i:1147332 original size:177 final size:177 Alignment explanation

Indices: 1146580--1147322 Score: 1014 Period size: 177 Copynumber: 4.2 Consensus size: 177 1146570 AAAGACTAGG ** * * * 1146580 ATGCTGAATCTGAGTCC-TAAATTTCAGATGCTGGAGGAGGTTAAGGTTGTTGGACCAGGTTAAA 1 ATGCTGAATCTGAG-CCATAGGTTTCAGATGCTGGAGGAGGTTAAGGTTTTTAGAGCAGGTTAAA * * * 1146644 GTTTTTGTTGCAGGTGCCCTTTGATAGCAATATCTAAGTTACTGCAGGTCCGTACTTCACCAAAC 65 GTTTTTGTTGCAGGTGCCCTCTGATAGCAATATCTAAGTTACTACTGGTCCGTACTTCACCAAAC * * 1146709 TTGCATGGATGGTGTGTCTTATGATACTGATGCACCAGACAGGCTTGA 130 TTCCATGGATGGTGCGTCTTATGATACTGATGCACCAGACAGGCTTGA * * * * * 1146757 GTGCTGAATCTGAGCTATAGGTTTCAGATGCTGGAGGGGGTTAAGGTTTTTGGAGCAGGTTACAG 1 ATGCTGAATCTGAGCCATAGGTTTCAGATGCTGGAGGAGGTTAAGGTTTTTAGAGCAGGTTAAAG * * 1146822 TTTTTGTTGCAGGTGCCCTTTGATAGCAATATCTAAGTTACTGCTGGTCCGTACTTCACCAAACT 66 TTTTTGTTGCAGGTGCCCTCTGATAGCAATATCTAAGTTACTACTGGTCCGTACTTCACCAAACT * * * * 1146887 TGCATGGATGGTGTGTCTTATGATACTGATGCACCAGGCAGGCTTGG 131 TCCATGGATGGTGCGTCTTATGATACTGATGCACCAGACAGGCTTGA * * * * * 1146934 GTGCTGAATCTGAGCTATAGGTTACAGATGCTGAAGGAGGTTAAGGTTTTTAGAGCTGGTTAAAG 1 ATGCTGAATCTGAGCCATAGGTTTCAGATGCTGGAGGAGGTTAAGGTTTTTAGAGCAGGTTAAAG * * * 1146999 TTTTTGTTGCAGGTGCCCTCTGAT-G-ATTATATCTTAGTTACTACTTGTCC-TAACTTCACCAG 66 TTTTTGTTGCAGGTGCCCTCTGATAGCA--ATATCTAAGTTACTACTGGTCCGT-ACTTCACCAA 1147061 ACTTCCATGGATGGTGCGTCTTATGATACTGATGCACCAGACAGGCTTGA 128 ACTTCCATGGATGGTGCGTCTTATGATACTGATGCACCAGACAGGCTTGA * * 1147111 ATGCTGAATCTGAGCCATAGGTTTCGGATGCTGGAGGAGGTTAAGGTTTTTAGAGCTGGTTAAAG 1 ATGCTGAATCTGAGCCATAGGTTTCAGATGCTGGAGGAGGTTAAGGTTTTTAGAGCAGGTTAAAG *** * * * * 1147176 TTTTTGAAACAGGTGCCCTCTGAT-G-ATTATATCTTAGTTATTACTTGTCC-TAACTTCACCAG 66 TTTTTGTTGCAGGTGCCCTCTGATAGCA--ATATCTAAGTTACTACTGGTCCGT-ACTTCACCAA * 1147238 ACTTCCATGGATGGTGCGTCTTATGATACTGATGCACCTGACAGGCTTGA 128 ACTTCCATGGATGGTGCGTCTTATGATACTGATGCACCAGACAGGCTTGA * 1147288 ATGCTGAGTCTGAGCCATAGGTTTCAGATGCTGGA 1 ATGCTGAATCTGAGCCATAGGTTTCAGATGCTGGA 1147323 TATGGTTAAG Statistics Matches: 524, Mismatches: 38, Indels: 8 0.92 0.07 0.01 Matches are distributed among these distances: 175 1 0.00 176 3 0.01 177 520 0.99 ACGTcount: A:0.23, C:0.17, G:0.27, T:0.33 Consensus pattern (177 bp): ATGCTGAATCTGAGCCATAGGTTTCAGATGCTGGAGGAGGTTAAGGTTTTTAGAGCAGGTTAAAG TTTTTGTTGCAGGTGCCCTCTGATAGCAATATCTAAGTTACTACTGGTCCGTACTTCACCAAACT TCCATGGATGGTGCGTCTTATGATACTGATGCACCAGACAGGCTTGA Found at i:1147761 original size:157 final size:157 Alignment explanation

Indices: 1147473--1147762 Score: 442 Period size: 157 Copynumber: 1.8 Consensus size: 157 1147463 GCTAAAAAAT * * 1147473 ATATCTTAGTTATTACAGGTCCTAACTTCACCAAACTTGAATGGATGGTGTGTCTTATGATACAG 1 ATATCTTAGTTATTACAGGTCCTAACTTCACCAAACTTGAATGGATGATGCGTCTTATGATACAG * * 1147538 ATGCACCTGACAGGCATGGATGTTGAATCTGAGCCATAGGTTGCGGATGCTGGAGCAGGTTAAGT 66 ATGCACCTGACAGGCATGAATGCTGAATCTGAGCCATAGGTTGCGGATGCTGGAGCAGGTTAAGT 1147603 TTTAATTGCTAGTGCCCTCTGATGATG 131 TTTAATTGCTAGTGCCCTCTGATGATG * * 1147630 ATATCTTAGTTATTACTGGT-CTGAACTTCACCAAACTTGCATGGA-GATGCGTCTTATGTATAC 1 ATATCTTAGTTATTACAGGTCCT-AACTTCACCAAACTTGAATGGATGATGCGTCTTATG-ATAC * * * * 1147693 TGATGCACCTGACAGGCTTGAATGCTGAATCTGAGCCATAGGTTTCGGATGCTGGATG-AGGTTT 64 AGATGCACCTGACAGGCATGAATGCTGAATCTGAGCCATAGGTTGCGGATGCTGGA-GCAGGTTA 1147757 AGTTTT 128 AGTTTT 1147763 TTTGGAACAG Statistics Matches: 120, Mismatches: 10, Indels: 6 0.88 0.07 0.04 Matches are distributed among these distances: 156 13 0.11 157 106 0.88 158 1 0.01 ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33 Consensus pattern (157 bp): ATATCTTAGTTATTACAGGTCCTAACTTCACCAAACTTGAATGGATGATGCGTCTTATGATACAG ATGCACCTGACAGGCATGAATGCTGAATCTGAGCCATAGGTTGCGGATGCTGGAGCAGGTTAAGT TTTAATTGCTAGTGCCCTCTGATGATG Found at i:1148160 original size:15 final size:15 Alignment explanation

Indices: 1148140--1148175 Score: 54 Period size: 15 Copynumber: 2.4 Consensus size: 15 1148130 ATACAATATT * 1148140 ATATTGTATCATACG 1 ATATTGTATAATACG * 1148155 ATATTGTATAATATG 1 ATATTGTATAATACG 1148170 ATATTG 1 ATATTG 1148176 GTTTCTGTAA Statistics Matches: 19, Mismatches: 2, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 15 19 1.00 ACGTcount: A:0.36, C:0.06, G:0.14, T:0.44 Consensus pattern (15 bp): ATATTGTATAATACG Found at i:1148297 original size:50 final size:50 Alignment explanation

Indices: 1148141--1148305 Score: 147 Period size: 50 Copynumber: 3.3 Consensus size: 50 1148131 TACAATATTA * * * * 1148141 TATTGTATCATACGATATTGTATAATATGATATTGGTTTCTGTAATTTAC 1 TATTGTATCATACGATATTGTATAATATGATATTGGTTTATATAATATAT * * ** * * * * * * 1148191 AATTATATCACGCAAAACTGTA-ATTTATGATATT-G-TAATATTATATAT 1 TATTGTATCATACGATATTGTATA-ATATGATATTGGTTTATATAATATAT * * 1148239 TATCGTATCATACGATATTGTATAATATGATATTGGTTTATATGATATAT 1 TATTGTATCATACGATATTGTATAATATGATATTGGTTTATATAATATAT * 1148289 TATTGTATCATATGATA 1 TATTGTATCATACGATA 1148306 CAATATGTAT Statistics Matches: 84, Mismatches: 27, Indels: 8 0.71 0.23 0.07 Matches are distributed among these distances: 48 30 0.36 49 4 0.05 50 50 0.60 ACGTcount: A:0.35, C:0.07, G:0.12, T:0.45 Consensus pattern (50 bp): TATTGTATCATACGATATTGTATAATATGATATTGGTTTATATAATATAT Found at i:1148406 original size:15 final size:15 Alignment explanation

Indices: 1148388--1148466 Score: 74 Period size: 15 Copynumber: 5.3 Consensus size: 15 1148378 GATACAATGT * 1148388 AATATCAAATTATAC 1 AATATCATATTATAC * 1148403 AATATCATATGATAC 1 AATATCATATTATAC 1148418 AATATCATATTAT-- 1 AATATCATATTATAC * 1148431 -GTATCAAATATTATAC 1 AATATC--ATATTATAC ** 1148447 AATATCATACAATAC 1 AATATCATATTATAC 1148462 AATAT 1 AATAT 1148467 ATCATACTGT Statistics Matches: 52, Mismatches: 7, Indels: 10 0.75 0.10 0.14 Matches are distributed among these distances: 12 4 0.08 14 7 0.13 15 37 0.71 17 4 0.08 ACGTcount: A:0.49, C:0.13, G:0.03, T:0.35 Consensus pattern (15 bp): AATATCATATTATAC Found at i:1148579 original size:20 final size:20 Alignment explanation

Indices: 1148514--1148581 Score: 75 Period size: 20 Copynumber: 3.4 Consensus size: 20 1148504 AATGTTATGA * ** 1148514 TGTATTATGTAATATGATAT 1 TGTATTATATAATACAATAT * 1148534 TGTATCATATAATACAATAT 1 TGTATTATATAATACAATAT * 1148554 TGTATTATAT-ATAATAATAT 1 TGTATTATATAAT-ACAATAT 1148574 TGTATTAT 1 TGTATTAT 1148582 GTGATCAAAT Statistics Matches: 41, Mismatches: 6, Indels: 2 0.84 0.12 0.04 Matches are distributed among these distances: 19 2 0.05 20 39 0.95 ACGTcount: A:0.40, C:0.03, G:0.09, T:0.49 Consensus pattern (20 bp): TGTATTATATAATACAATAT Found at i:1150878 original size:2 final size:2 Alignment explanation

Indices: 1150871--1150908 Score: 67 Period size: 2 Copynumber: 19.0 Consensus size: 2 1150861 ATCAATATCA * 1150871 AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT AT 1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT 1150909 GGTATTGTTG Statistics Matches: 34, Mismatches: 2, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 2 34 1.00 ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50 Consensus pattern (2 bp): AT Found at i:1152099 original size:25 final size:25 Alignment explanation

Indices: 1152061--1152259 Score: 346 Period size: 25 Copynumber: 8.0 Consensus size: 25 1152051 GTAATCTTGT * 1152061 CTCATGTACCGTACACACTAAAACA 1 CTCATGTAACGTACACACTAAAACA 1152086 CTCATGT-ACTGTACACACTAAAACA 1 CTCATGTAAC-GTACACACTAAAACA * 1152111 CTCATGTACCGTACACACTAAAACA 1 CTCATGTAACGTACACACTAAAACA * 1152136 CTCATGTAACGTACACGCTAAAACA 1 CTCATGTAACGTACACACTAAAACA * 1152161 CTCGTGTAACGTACACACTAAAACA 1 CTCATGTAACGTACACACTAAAACA 1152186 CTCATGTAACGTACACACTAAAACA 1 CTCATGTAACGTACACACTAAAACA 1152211 CTCATGTAACGTACACACTAAAACA 1 CTCATGTAACGTACACACTAAAACA 1152236 CTCATGTAACGTACACACTAAAAC 1 CTCATGTAACGTACACACTAAAAC 1152260 TTTTCCTCGT Statistics Matches: 165, Mismatches: 7, Indels: 4 0.94 0.04 0.02 Matches are distributed among these distances: 24 1 0.01 25 163 0.99 26 1 0.01 ACGTcount: A:0.41, C:0.29, G:0.09, T:0.21 Consensus pattern (25 bp): CTCATGTAACGTACACACTAAAACA Found at i:1155623 original size:43 final size:43 Alignment explanation

Indices: 1155212--1155610 Score: 690 Period size: 43 Copynumber: 9.3 Consensus size: 43 1155202 GGAACCTGAG * 1155212 TGTAGGACTCACCATATGGGTACAGCATCAGGTAAAGTATTAA 1 TGTAGGACTCACCATATGGGTACAGCATCAGGTACAGTATTAA * 1155255 TGTAAGACTCACCATATGGGTACAGCATCAGGTACAGTATTAA 1 TGTAGGACTCACCATATGGGTACAGCATCAGGTACAGTATTAA * * 1155298 TGGAGGACTCACCATATGGGTACAGCATCAGGTACAGTATTAC 1 TGTAGGACTCACCATATGGGTACAGCATCAGGTACAGTATTAA 1155341 TGTAGGACTCACCATATGGGTACAGCATCAGGTACAGTATTAA 1 TGTAGGACTCACCATATGGGTACAGCATCAGGTACAGTATTAA * 1155384 TGTAGGACTCACCATATGGGTACAGCATCAGGGACAGTATTAA 1 TGTAGGACTCACCATATGGGTACAGCATCAGGTACAGTATTAA * 1155427 TGTAGAACTCACCATATGGGTACAGCATCAGGTACAGTATTAA 1 TGTAGGACTCACCATATGGGTACAGCATCAGGTACAGTATTAA 1155470 TGTAGGACTCACCATATGGGTACAGCATCAGGTACAGTATTAA 1 TGTAGGACTCACCATATGGGTACAGCATCAGGTACAGTATTAA * * 1155513 TGTAGAACTCACCATATGGGTACAGCATCAGGTACAGTATTAT 1 TGTAGGACTCACCATATGGGTACAGCATCAGGTACAGTATTAA * ** * 1155556 TGTAGGACTCACCATATGGGTACATCATCACATACTGTATTAA 1 TGTAGGACTCACCATATGGGTACAGCATCAGGTACAGTATTAA 1155599 TGTAGGACTCAC 1 TGTAGGACTCAC 1155611 ATTATACATA Statistics Matches: 337, Mismatches: 19, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 43 337 1.00 ACGTcount: A:0.33, C:0.19, G:0.22, T:0.26 Consensus pattern (43 bp): TGTAGGACTCACCATATGGGTACAGCATCAGGTACAGTATTAA Found at i:1155701 original size:105 final size:105 Alignment explanation

Indices: 1155519--1155715 Score: 331 Period size: 105 Copynumber: 1.9 Consensus size: 105 1155509 TTAATGTAGA * * 1155519 ACTCACCATATGGGTACAGCATCAGGTACAGTATTATTGTAGGACTCACCATATGGGTACATCAT 1 ACTCACCATATGGGTACAGCATCAGGTACAGTATTAATGTAGGACTCACCATATGGGTACAGCAT * 1155584 CACATACTGTATTAATGTAGGACTCACATTATACATACAT 66 CACATACAGTATTAATGTAGGACTCACATTATACATACAT * * 1155624 ACTCACCATATGGGTACAGCATCAGGTACAGTATTAATGTAGGACTCACCATTTGGGTATAGCAT 1 ACTCACCATATGGGTACAGCATCAGGTACAGTATTAATGTAGGACTCACCATATGGGTACAGCAT ** 1155689 CAGGTACAGTATTAATGTAGGACTCAC 66 CACATACAGTATTAATGTAGGACTCAC 1155716 CATATGGGTA Statistics Matches: 85, Mismatches: 7, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 105 85 1.00 ACGTcount: A:0.32, C:0.20, G:0.19, T:0.28 Consensus pattern (105 bp): ACTCACCATATGGGTACAGCATCAGGTACAGTATTAATGTAGGACTCACCATATGGGTACAGCAT CACATACAGTATTAATGTAGGACTCACATTATACATACAT Done.