Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Chr10 129486693 

Parameters: 2 7 7 80 10 50 1000

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

Length: 129486693
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32

Warning! 305 characters in sequence are not A, C, G, or T


File 159 of 444

Found at i:43593201 original size:94 final size:92

Alignment explanation

Indices: 43593055--43593228 Score: 242 Period size: 94 Copynumber: 1.9 Consensus size: 92 43593045 ACATTACGTA * ** * 43593055 GCCGATGCATGTCCCAGACATGTATTACACTAGCTTACGTCTTGAGGCTGATGCCTGTCCCAGAC 1 GCCGATGCATGTCCCAGACATGTATTACACTAGCTTACATAATGAGGCTGATGCATGTCCCAGAC 43593120 ATGTCTTACACTAGCACTCGTCTCAAT 66 ATGTCTTACACTAGCACTCGTCTCAAT * * * * 43593147 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCT-CATAATGTGGCTGATGCATGTCTCA 1 GCCGATG-CATGTCCCAGACAT-GTATTACACTAGCT-TACATAATGAGGCTGATGCATGTCCCA 43593211 GACATGTCTTACACTAGC 63 GACATGTCTTACACTAGC 43593229 TCACACAAGT Statistics Matches: 71, Mismatches: 8, Indels: 4 0.86 0.10 0.05 Matches are distributed among these distances: 92 7 0.10 93 14 0.20 94 49 0.69 95 1 0.01 ACGTcount: A:0.22, C:0.29, G:0.21, T:0.28 Consensus pattern (92 bp): GCCGATGCATGTCCCAGACATGTATTACACTAGCTTACATAATGAGGCTGATGCATGTCCCAGAC ATGTCTTACACTAGCACTCGTCTCAAT Found at i:43597328 original size:29 final size:29 Alignment explanation

Indices: 43597304--43597397 Score: 152 Period size: 29 Copynumber: 3.2 Consensus size: 29 43597294 TCGCACACCC * * 43597304 AGTGCCGTATTTTTCCAGCATGCACACTT 1 AGTGCCATATATTTCCAGCATGCACACTT * 43597333 AGTGCCATATATTTCTAGCATGCACACTT 1 AGTGCCATATATTTCCAGCATGCACACTT * 43597362 AGTGCCATATATTTCCAGCACGCACACTT 1 AGTGCCATATATTTCCAGCATGCACACTT 43597391 AGTGCCA 1 AGTGCCA 43597398 ATCTCGTCAC Statistics Matches: 60, Mismatches: 5, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 29 60 1.00 ACGTcount: A:0.26, C:0.28, G:0.16, T:0.31 Consensus pattern (29 bp): AGTGCCATATATTTCCAGCATGCACACTT Found at i:43597329 original size:58 final size:58 Alignment explanation

Indices: 43597266--43597397 Score: 158 Period size: 58 Copynumber: 2.3 Consensus size: 58 43597256 GATTTAAGCC * * * * 43597266 CGCACACATAGTGCCATACCCTTCGAGC-TCGCACACCCAGTGCCGTATTTTTCCAGCA 1 CGCACACTTAGTGCCATACACTTCGAGCAT-GCACACCCAGTGCCATATATTTCCAGCA * * * * ** 43597324 TGCACACTTAGTGCCATATATTTCTAGCATGCACACTTAGTGCCATATATTTCCAGCA 1 CGCACACTTAGTGCCATACACTTCGAGCATGCACACCCAGTGCCATATATTTCCAGCA 43597382 CGCACACTTAGTGCCA 1 CGCACACTTAGTGCCA 43597398 ATCTCGTCAC Statistics Matches: 62, Mismatches: 11, Indels: 2 0.83 0.15 0.03 Matches are distributed among these distances: 58 61 0.98 59 1 0.02 ACGTcount: A:0.25, C:0.33, G:0.16, T:0.27 Consensus pattern (58 bp): CGCACACTTAGTGCCATACACTTCGAGCATGCACACCCAGTGCCATATATTTCCAGCA Found at i:43610004 original size:40 final size:39 Alignment explanation

Indices: 43609836--43610006 Score: 159 Period size: 40 Copynumber: 4.3 Consensus size: 39 43609826 AGAAATTGAA * * 43609836 TGATATCCGGGCTAAGCCCCGAAGACAATTATGCTG-AAAT- 1 TGATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCAAATG * * * * * 43609876 TTATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTAG 1 TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAAT-G * * 43609916 CT-ATATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTG 1 -TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAA-ATG * * 43609956 TTAAATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG 1 TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAAT-G 43609996 TGATATCCGGG 1 TGATATCCGGG 43610007 TAAAGTCCCG Statistics Matches: 107, Mismatches: 17, Indels: 14 0.78 0.12 0.10 Matches are distributed among these distances: 37 2 0.02 38 4 0.04 39 4 0.04 40 95 0.89 41 2 0.02 ACGTcount: A:0.28, C:0.22, G:0.26, T:0.24 Consensus pattern (39 bp): TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATG Found at i:43614993 original size:34 final size:34 Alignment explanation

Indices: 43614950--43615020 Score: 142 Period size: 34 Copynumber: 2.1 Consensus size: 34 43614940 GAGTACGAAG 43614950 ATGTACAATGATTTGAAACGTCGGTTTTGGTGGC 1 ATGTACAATGATTTGAAACGTCGGTTTTGGTGGC 43614984 ATGTACAATGATTTGAAACGTCGGTTTTGGTGGC 1 ATGTACAATGATTTGAAACGTCGGTTTTGGTGGC 43615018 ATG 1 ATG 43615021 GTATGAAGCG Statistics Matches: 37, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 34 37 1.00 ACGTcount: A:0.24, C:0.11, G:0.30, T:0.35 Consensus pattern (34 bp): ATGTACAATGATTTGAAACGTCGGTTTTGGTGGC Found at i:43618605 original size:30 final size:30 Alignment explanation

Indices: 43618571--43618668 Score: 74 Period size: 30 Copynumber: 3.2 Consensus size: 30 43618561 AAGAGAGCTA 43618571 CGTGAAAGATAAATGTAGCTAGGTCGCATG 1 CGTGAAAGATAAATGTAGCTAGGTCGCATG ** * * * * * 43618601 CGTGATCCGGACACCATGTAGACAAGAG-AGC-TA 1 CGTGA--AAGATA-AATGTAG-CTAG-GTCGCATG 43618634 CGTGAAAGATAAATGTAGCTAGGTCGCATG 1 CGTGAAAGATAAATGTAGCTAGGTCGCATG 43618664 CGTGA 1 CGTGA 43618669 TTCCAAGTGA Statistics Matches: 47, Mismatches: 14, Indels: 14 0.63 0.19 0.19 Matches are distributed among these distances: 28 1 0.02 29 5 0.11 30 17 0.36 31 3 0.06 32 3 0.06 33 12 0.26 34 5 0.11 35 1 0.02 ACGTcount: A:0.33, C:0.17, G:0.30, T:0.20 Consensus pattern (30 bp): CGTGAAAGATAAATGTAGCTAGGTCGCATG Found at i:43618636 original size:63 final size:65 Alignment explanation

Indices: 43618551--43618706 Score: 244 Period size: 63 Copynumber: 2.3 Consensus size: 65 43618541 GAGATGTATC 43618551 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGA-TCC-GGACA 1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAGGACA 43618614 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA 1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCC------ 43618679 AGGACA 60 AGGACA 43618685 CCATGTAGACAAGAGAGCTACG 1 CCATGTAGACAAGAGAGCTACG 43618707 AGACAAATCG Statistics Matches: 85, Mismatches: 0, Indels: 8 0.91 0.00 0.09 Matches are distributed among these distances: 63 55 0.65 64 3 0.04 71 27 0.32 ACGTcount: A:0.35, C:0.19, G:0.28, T:0.19 Consensus pattern (65 bp): CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAGGACA Found at i:43629510 original size:41 final size:39 Alignment explanation

Indices: 43629476--43629629 Score: 125 Period size: 38 Copynumber: 3.9 Consensus size: 39 43629466 GAATCCAGTC * 43629476 ACCAGCACAAAACCTGCGGGACTTTAAGCTCGAATATAAT 1 ACCAGCACAAAACCTGCGGGA-TTTAAGCTCGAATACAAT * * * * 43629516 ACCAGCACTAAGCCTGCGGGATTTAA-C-CCAGATATAAT 1 ACCAGCACAAAACCTGCGGGATTTAAGCTCGA-ATACAAT * * * * * 43629554 ACCAGCACGAAGCCTGCGGGATTTAACCT-GGATATAAT 1 ACCAGCACAAAACCTGCGGGATTTAAGCTCGAATACAAT * * * * * 43629592 ACCAGCACATAGCCTGCGGGTCTTTAAGCCCGGATACA 1 ACCAGCACAAAACCTGCGGG-ATTTAAGCTCGAATACA 43629630 CATCAAATAT Statistics Matches: 97, Mismatches: 12, Indels: 10 0.82 0.10 0.08 Matches are distributed among these distances: 37 2 0.02 38 58 0.60 39 12 0.12 40 25 0.26 ACGTcount: A:0.32, C:0.27, G:0.21, T:0.20 Consensus pattern (39 bp): ACCAGCACAAAACCTGCGGGATTTAAGCTCGAATACAAT Found at i:43629560 original size:38 final size:36 Alignment explanation

Indices: 43629476--43629611 Score: 164 Period size: 38 Copynumber: 3.5 Consensus size: 36 43629466 GAATCCAGTC * * 43629476 ACCAGCACAAAACCTGCGGGACTTTAAGCTCGAATATAAT 1 ACCAGCAC-AAGCCTGCGGGA-TTTAA-CCCG-ATATAAT 43629516 ACCAGCACTAAGCCTGCGGGATTTAACCCAGATATAAT 1 ACCAGCAC-AAGCCTGCGGGATTTAACCC-GATATAAT * 43629554 ACCAGCACGAAGCCTGCGGGATTTAACCTGGATATAAT 1 ACCAGCAC-AAGCCTGCGGGATTTAACC-CGATATAAT 43629592 ACCAGCACATAGCCTGCGGG 1 ACCAGCACA-AGCCTGCGGG 43629612 TCTTTAAGCC Statistics Matches: 88, Mismatches: 5, Indels: 8 0.87 0.05 0.08 Matches are distributed among these distances: 37 1 0.01 38 62 0.70 39 6 0.07 40 19 0.22 ACGTcount: A:0.33, C:0.26, G:0.21, T:0.19 Consensus pattern (36 bp): ACCAGCACAAGCCTGCGGGATTTAACCCGATATAAT Found at i:43641081 original size:28 final size:27 Alignment explanation

Indices: 43641018--43641087 Score: 131 Period size: 27 Copynumber: 2.6 Consensus size: 27 43641008 ATAGTGAGTC 43641018 CGCACACTTAGTGCTATATAATCAACT 1 CGCACACTTAGTGCTATATAATCAACT 43641045 CGCACACTTAGTGCTATATAATCAAACT 1 CGCACACTTAGTGCTATATAATC-AACT 43641073 CGCACACTTAGTGCT 1 CGCACACTTAGTGCT 43641088 GTACAAATTT Statistics Matches: 42, Mismatches: 0, Indels: 1 0.98 0.00 0.02 Matches are distributed among these distances: 27 23 0.55 28 19 0.45 ACGTcount: A:0.31, C:0.27, G:0.13, T:0.29 Consensus pattern (27 bp): CGCACACTTAGTGCTATATAATCAACT Found at i:43643572 original size:14 final size:15 Alignment explanation

Indices: 43643553--43643582 Score: 53 Period size: 14 Copynumber: 2.1 Consensus size: 15 43643543 CCCGACTAGG 43643553 GTCACACTAGG-GCT 1 GTCACACTAGGAGCT 43643567 GTCACACTAGGAGCT 1 GTCACACTAGGAGCT 43643582 G 1 G 43643583 ATTGGGGTGA Statistics Matches: 15, Mismatches: 0, Indels: 1 0.94 0.00 0.06 Matches are distributed among these distances: 14 11 0.73 15 4 0.27 ACGTcount: A:0.23, C:0.27, G:0.30, T:0.20 Consensus pattern (15 bp): GTCACACTAGGAGCT Found at i:43644886 original size:28 final size:28 Alignment explanation

Indices: 43644826--43644891 Score: 98 Period size: 28 Copynumber: 2.4 Consensus size: 28 43644816 GATTTACTAG * 43644826 AATACCCCTATGTATGCAAAATTACCAT 1 AATACCCCTATGTATGCAAAATGACCAT * 43644854 TATACCCCTATGTATGCAAAATGACC-T 1 AATACCCCTATGTATGCAAAATGACCAT 43644881 CAATACCCCTA 1 -AATACCCCTA 43644892 GGGTTAATTT Statistics Matches: 34, Mismatches: 3, Indels: 2 0.87 0.08 0.05 Matches are distributed among these distances: 27 1 0.03 28 33 0.97 ACGTcount: A:0.36, C:0.29, G:0.08, T:0.27 Consensus pattern (28 bp): AATACCCCTATGTATGCAAAATGACCAT Found at i:43645056 original size:27 final size:27 Alignment explanation

Indices: 43644997--43645086 Score: 101 Period size: 28 Copynumber: 3.2 Consensus size: 27 43644987 AGGAAGCGTC 43644997 CTGGTGGCTA-TGCCACAAATTATCTGTT 1 CTGGTGGC-ACTGCCACAAA-TATCTGTT * * 43645025 CTGGTGGCCCTGCCACATATATCTGTT 1 CTGGTGGCACTGCCACAAATATCTGTT * * 43645052 TTGGTGGCACTGCTACAACATATCTGTAT 1 CTGGTGGCACTGCCACAA-ATATCTGT-T 43645081 CTGGTG 1 CTGGTG 43645087 ACTCTATCAC Statistics Matches: 52, Mismatches: 7, Indels: 5 0.81 0.11 0.08 Matches are distributed among these distances: 27 22 0.42 28 24 0.46 29 6 0.12 ACGTcount: A:0.19, C:0.23, G:0.23, T:0.34 Consensus pattern (27 bp): CTGGTGGCACTGCCACAAATATCTGTT Found at i:43645579 original size:18 final size:18 Alignment explanation

Indices: 43645540--43645580 Score: 55 Period size: 18 Copynumber: 2.3 Consensus size: 18 43645530 TAATAAGGCC * * 43645540 TTTTAATTATTTTTATGG 1 TTTTAATTACTTTTATGA * 43645558 TTTTAATTACTTTTATTA 1 TTTTAATTACTTTTATGA 43645576 TTTTA 1 TTTTA 43645581 TTTTACTATG Statistics Matches: 20, Mismatches: 3, Indels: 0 0.87 0.13 0.00 Matches are distributed among these distances: 18 20 1.00 ACGTcount: A:0.24, C:0.02, G:0.05, T:0.68 Consensus pattern (18 bp): TTTTAATTACTTTTATGA Found at i:43646199 original size:11 final size:10 Alignment explanation

Indices: 43646171--43646204 Score: 50 Period size: 10 Copynumber: 3.3 Consensus size: 10 43646161 AGCCTGTAAG 43646171 TATTCTGAAT 1 TATTCTGAAT * 43646181 TTTTCTGAAT 1 TATTCTGAAT 43646191 ATATTCTGAAT 1 -TATTCTGAAT 43646202 TAT 1 TAT 43646205 CTGTCTGTAC Statistics Matches: 21, Mismatches: 2, Indels: 2 0.84 0.08 0.08 Matches are distributed among these distances: 10 12 0.57 11 9 0.43 ACGTcount: A:0.29, C:0.09, G:0.09, T:0.53 Consensus pattern (10 bp): TATTCTGAAT Found at i:43649378 original size:40 final size:39 Alignment explanation

Indices: 43649334--43649564 Score: 313 Period size: 40 Copynumber: 5.8 Consensus size: 39 43649324 GGATATAGCT * * 43649334 ACTCGCTCAAATGCCTTCGGGACATAGCCCGG-TTAGGGTA 1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTA--GTA * 43649374 ACTCGCACAATTGCCTTCGGGACTTAGCCCGGATTTAGTA 1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGA-TTAGTA 43649414 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA 1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGA-TTAGTA 43649454 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA 1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGA-TTAGTA * * * 43649494 ACTCGTACAAATGCCTTCGGGACTT-GCCCGGAACTAGTC 1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGG-ATTAGTA * * * 43649533 ACTAGCGCAGATGCCTTCGGGACTTAGCCCGG 1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGG 43649565 TTATCATCCA Statistics Matches: 176, Mismatches: 11, Indels: 8 0.90 0.06 0.04 Matches are distributed among these distances: 39 31 0.18 40 142 0.81 42 3 0.02 ACGTcount: A:0.23, C:0.29, G:0.25, T:0.24 Consensus pattern (39 bp): ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTAGTA Found at i:43656073 original size:28 final size:28 Alignment explanation

Indices: 43656041--43656105 Score: 105 Period size: 28 Copynumber: 2.3 Consensus size: 28 43656031 ATTTACTAGA * 43656041 ATACCCCTATGTATGCAAAATTACCAT-T 1 ATACCCCTATGTATGCAAAATGACC-TCT 43656069 ATACCCCTATGTATGCAAAATGACCTCT 1 ATACCCCTATGTATGCAAAATGACCTCT 43656097 ATACCCCTA 1 ATACCCCTA 43656106 GGGTTAATTT Statistics Matches: 35, Mismatches: 1, Indels: 2 0.92 0.03 0.05 Matches are distributed among these distances: 27 1 0.03 28 34 0.97 ACGTcount: A:0.34, C:0.29, G:0.08, T:0.29 Consensus pattern (28 bp): ATACCCCTATGTATGCAAAATGACCTCT Found at i:43656255 original size:28 final size:27 Alignment explanation

Indices: 43656221--43656297 Score: 84 Period size: 27 Copynumber: 2.7 Consensus size: 27 43656211 CTGGTGGCTA 43656221 TGCCACAAATTATCTGTTCTGATGGC-C 1 TGCCACAAA-TATCTGTTCTGATGGCAC * * * 43656248 TTGCCACATATATCTATTCTGGTGGCAC 1 -TGCCACAAATATCTGTTCTGATGGCAC 43656276 TGCCACAACATATCTGTATCTG 1 TGCCACAA-ATATCTGT-TCTG 43656298 GTGACTCTGT Statistics Matches: 41, Mismatches: 5, Indels: 5 0.80 0.10 0.10 Matches are distributed among these distances: 27 21 0.51 28 16 0.39 29 4 0.10 ACGTcount: A:0.23, C:0.26, G:0.17, T:0.34 Consensus pattern (27 bp): TGCCACAAATATCTGTTCTGATGGCAC Found at i:43656273 original size:27 final size:27 Alignment explanation

Indices: 43656211--43656300 Score: 94 Period size: 28 Copynumber: 3.2 Consensus size: 27 43656201 AGGAAGCGTC 43656211 CTGGTGG-CTATGCCACAAATTATCTGTT 1 CTGGTGGCCT-TGCCACAAA-TATCTGTT * * * 43656239 CTGATGGCCTTGCCACATATATCTATT 1 CTGGTGGCCTTGCCACAAATATCTGTT 43656266 CTGGTGGCAC-TGCCACAACATATCTGTAT 1 CTGGTGGC-CTTGCCACAA-ATATCTGT-T 43656295 CTGGTG 1 CTGGTG 43656301 ACTCTGTCAC Statistics Matches: 52, Mismatches: 6, Indels: 7 0.80 0.09 0.11 Matches are distributed among these distances: 27 21 0.40 28 22 0.42 29 9 0.17 ACGTcount: A:0.21, C:0.24, G:0.21, T:0.33 Consensus pattern (27 bp): CTGGTGGCCTTGCCACAAATATCTGTT Found at i:43656311 original size:29 final size:28 Alignment explanation

Indices: 43656249--43656311 Score: 65 Period size: 29 Copynumber: 2.2 Consensus size: 28 43656239 CTGATGGCCT * * 43656249 TGCCAC-ATATATCTATTCTGGTGGCAC 1 TGCCACAACATATCTATTCTGGTGACAC * * 43656276 TGCCACAACATATCTGTATCTGGTGACTC 1 TGCCACAACATATCTAT-TCTGGTGACAC * 43656305 TGTCACA 1 TGCCACA 43656312 TTTTCTGTAT Statistics Matches: 29, Mismatches: 5, Indels: 2 0.81 0.14 0.06 Matches are distributed among these distances: 27 6 0.21 28 8 0.28 29 15 0.52 ACGTcount: A:0.24, C:0.27, G:0.17, T:0.32 Consensus pattern (28 bp): TGCCACAACATATCTATTCTGGTGACAC Found at i:43656791 original size:18 final size:18 Alignment explanation

Indices: 43656752--43656792 Score: 55 Period size: 18 Copynumber: 2.3 Consensus size: 18 43656742 TAATAAGGCC * * 43656752 TTTTAATTATTTTTATGG 1 TTTTAATTACTTTTATGA * 43656770 TTTTAATTACTTTTATTA 1 TTTTAATTACTTTTATGA 43656788 TTTTA 1 TTTTA 43656793 TTTTACGATG Statistics Matches: 20, Mismatches: 3, Indels: 0 0.87 0.13 0.00 Matches are distributed among these distances: 18 20 1.00 ACGTcount: A:0.24, C:0.02, G:0.05, T:0.68 Consensus pattern (18 bp): TTTTAATTACTTTTATGA Found at i:43657412 original size:11 final size:10 Alignment explanation

Indices: 43657384--43657417 Score: 50 Period size: 10 Copynumber: 3.3 Consensus size: 10 43657374 AGCCTGTAAG 43657384 TATTCTGAAT 1 TATTCTGAAT * 43657394 TTTTCTGAAT 1 TATTCTGAAT 43657404 ATATTCTGAAT 1 -TATTCTGAAT 43657415 TAT 1 TAT 43657418 CTGTCTGTAC Statistics Matches: 21, Mismatches: 2, Indels: 2 0.84 0.08 0.08 Matches are distributed among these distances: 10 12 0.57 11 9 0.43 ACGTcount: A:0.29, C:0.09, G:0.09, T:0.53 Consensus pattern (10 bp): TATTCTGAAT Found at i:43662421 original size:40 final size:40 Alignment explanation

Indices: 43662336--43662486 Score: 134 Period size: 40 Copynumber: 3.8 Consensus size: 40 43662326 AATTGAATGA * * * 43662336 TATCCGGGCTAA-ATCCCGAAGACAATTATGCTG-GAAATTA- 1 TATCCGGGCTAAGA-CCCGAAGGCAATTGTGC-GAGACA-TAC * * * 43662376 TATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGC-TAC 1 TATCCGGGCTAAGACCCGAAGGCAATTGTGC--GAGACATAC * 43662417 -ATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGACATTC 1 TATCCGGGCTAAGACCCGAAGGCAATT-GTGCGAGACATAC * 43662456 TATCCGGGCTAAGACCCGAAGGCATTTGTGC 1 TATCCGGGCTAAGACCCGAAGGCAATTGTGC 43662487 ACATTATATC Statistics Matches: 92, Mismatches: 11, Indels: 16 0.77 0.09 0.13 Matches are distributed among these distances: 38 3 0.03 39 5 0.05 40 79 0.86 41 4 0.04 42 1 0.01 ACGTcount: A:0.27, C:0.24, G:0.26, T:0.23 Consensus pattern (40 bp): TATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGACATAC Found at i:43670393 original size:40 final size:40 Alignment explanation

Indices: 43670327--43670477 Score: 146 Period size: 40 Copynumber: 3.8 Consensus size: 40 43670317 AAATTGAATG * * * 43670327 ATATCCGGGCTAA-TCCCGAAGACAATTATGCTGGAAATT 1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGAAATT * * **** 43670366 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT 1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGAAATT * * 43670406 ACATCCGGGCTAAGACCCGAAGGC-ATTCGTGC-GAGACATT 1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-GAAATT * * 43670446 CTATCCGGGCTAAGACCCGAAGGCATTTGTGC 1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGC 43670478 ACATTTATAT Statistics Matches: 89, Mismatches: 19, Indels: 7 0.77 0.17 0.06 Matches are distributed among these distances: 39 15 0.17 40 72 0.81 41 2 0.02 ACGTcount: A:0.27, C:0.24, G:0.26, T:0.23 Consensus pattern (40 bp): ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGAAATT Found at i:43676301 original size:93 final size:93 Alignment explanation

Indices: 43676142--43676313 Score: 290 Period size: 93 Copynumber: 1.8 Consensus size: 93 43676132 GCCCATAAGT * * * 43676142 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATGAGTGAACTCGGACTCAACTCAA 1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA 43676207 CGAGTTCAGATGCTTAGTTACATCTGAC 66 CGAGTTCAGATGCTTAGTTACATCTGAC * * 43676235 GAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCAA 1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA * 43676300 CGAGTTCGGATGCT 66 CGAGTTCAGATGCT 43676314 CAACCATCCT Statistics Matches: 73, Mismatches: 6, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 93 73 1.00 ACGTcount: A:0.28, C:0.27, G:0.22, T:0.23 Consensus pattern (93 bp): GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA CGAGTTCAGATGCTTAGTTACATCTGAC Found at i:43676309 original size:46 final size:46 Alignment explanation

Indices: 43676134--43676309 Score: 205 Period size: 46 Copynumber: 3.8 Consensus size: 46 43676124 TGTAACCCGC * * * * 43676134 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT 1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT * * * * 43676180 CCATGAGTGAACTCGGACTCAACTCAACGAGTTCAGATGCTTAGTTACAT 1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA--C--ATTTGCAT * * 43676230 -C-TGA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT 1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT 43676273 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA 1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA 43676310 TGCTCAACCA Statistics Matches: 109, Mismatches: 14, Indels: 14 0.80 0.10 0.10 Matches are distributed among these distances: 43 6 0.06 44 1 0.01 45 3 0.03 46 62 0.57 47 28 0.26 48 4 0.04 49 1 0.01 50 4 0.04 ACGTcount: A:0.29, C:0.27, G:0.22, T:0.22 Consensus pattern (46 bp): CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT Found at i:43678701 original size:15 final size:15 Alignment explanation

Indices: 43678672--43678721 Score: 66 Period size: 15 Copynumber: 3.4 Consensus size: 15 43678662 CAAAGATAAC * 43678672 AAGAAAACC-GAATA 1 AAGAAATCCAGAATA 43678686 AAGAAATCCAGAATA 1 AAGAAATCCAGAATA * * 43678701 AAGAGATCCAGGATA 1 AAGAAATCCAGAATA 43678716 AAGAAA 1 AAGAAA 43678722 CCCAAGATAC Statistics Matches: 31, Mismatches: 4, Indels: 1 0.86 0.11 0.03 Matches are distributed among these distances: 14 8 0.26 15 23 0.74 ACGTcount: A:0.60, C:0.12, G:0.18, T:0.10 Consensus pattern (15 bp): AAGAAATCCAGAATA Found at i:43678730 original size:15 final size:15 Alignment explanation

Indices: 43678683--43678730 Score: 53 Period size: 15 Copynumber: 3.2 Consensus size: 15 43678673 AGAAAACCGA 43678683 ATAAAGAAATCC-AG 1 ATAAAGAAATCCAAG * * 43678697 AATAAAGAGATCCAGG 1 -ATAAAGAAATCCAAG * 43678713 ATAAAGAAACCCAAG 1 ATAAAGAAATCCAAG 43678728 ATA 1 ATA 43678731 CGATACTATG Statistics Matches: 27, Mismatches: 5, Indels: 2 0.79 0.15 0.06 Matches are distributed among these distances: 15 26 0.96 16 1 0.04 ACGTcount: A:0.56, C:0.15, G:0.17, T:0.12 Consensus pattern (15 bp): ATAAAGAAATCCAAG Found at i:43681736 original size:46 final size:46 Alignment explanation

Indices: 43681644--43681772 Score: 179 Period size: 46 Copynumber: 2.8 Consensus size: 46 43681634 TGTAACCCGC * * * * 43681644 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCAGGCGTTCGCAT 1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCAGACATTCGCAT * * * 43681690 CCATGAGTGAACTCGGACTCAACTCAATGAGTTC-GAACATTTGCAT 1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCAG-ACATTCGCAT 43681736 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCAGA 1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCAGA 43681773 TGCTCAACCA Statistics Matches: 72, Mismatches: 9, Indels: 4 0.85 0.11 0.05 Matches are distributed among these distances: 45 1 0.01 46 70 0.97 47 1 0.01 ACGTcount: A:0.31, C:0.28, G:0.20, T:0.21 Consensus pattern (46 bp): CCATAAGTGAACTCGGACTCAACTCAACGAGTTCAGACATTCGCAT Found at i:43681791 original size:46 final size:45 Alignment explanation

Indices: 43681652--43681791 Score: 117 Period size: 46 Copynumber: 3.0 Consensus size: 45 43681642 GCCCATAAGC * ** * 43681652 GAACTCGGACTCAACTCAACGAGCTCAGGCGTTC-GCATCCATGAGT 1 GAACTCGGACTCAACTCAACGAGTTCAGATGTTCACCATCC-T-AGT * * * 43681698 GAACTCGGACTCAACTCAATGAGTTCGAACAT-TTGCATCCAT--AAGT 1 GAACTCGGACTCAACTCAACGAGTTC--AGATGTT-CA-CCATCCTAGT * 43681744 GAACTCGGACTCAACTCAACGAGTTCAGATGCTCAACCATCCTAGT 1 GAACTCGGACTCAACTCAACGAGTTCAGATGTTC-ACCATCCTAGT 43681790 GA 1 GA 43681792 CATGTCACTT Statistics Matches: 74, Mismatches: 11, Indels: 18 0.72 0.11 0.17 Matches are distributed among these distances: 44 8 0.11 45 2 0.03 46 57 0.77 47 2 0.03 48 2 0.03 50 3 0.04 ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22 Consensus pattern (45 bp): GAACTCGGACTCAACTCAACGAGTTCAGATGTTCACCATCCTAGT Found at i:43686051 original size:43 final size:43 Alignment explanation

Indices: 43685985--43686070 Score: 115 Period size: 43 Copynumber: 2.0 Consensus size: 43 43685975 AAATCGTACA * 43685985 ATGCCAACGTCCCAGACGTGGTCTTACAT-GTAACCACATATCG 1 ATGCCAACGTCCCAGACGTGGTCTTAC-TCGTAAACACATATCG 43686028 ATGCC-ACTGTCCCAGACAG-GGTCTTACTCGTAAACACATATCG 1 ATGCCAAC-GTCCCAGAC-GTGGTCTTACTCGTAAACACATATCG 43686071 GAATCACATA Statistics Matches: 39, Mismatches: 1, Indels: 6 0.85 0.02 0.13 Matches are distributed among these distances: 42 3 0.08 43 35 0.90 44 1 0.03 ACGTcount: A:0.28, C:0.30, G:0.19, T:0.23 Consensus pattern (43 bp): ATGCCAACGTCCCAGACGTGGTCTTACTCGTAAACACATATCG Found at i:43692249 original size:38 final size:38 Alignment explanation

Indices: 43692171--43692340 Score: 232 Period size: 38 Copynumber: 4.4 Consensus size: 38 43692161 GAATCCAGTC * * * * 43692171 ACCAGCACAAAACCTGCGGGAATTTAAGCTCGAATATAAT 1 ACCAGCACAAAGCCTGTGGG-ATTTAA-CCCGGATATAAT * 43692211 ACCAGCACTAAGCCTGTGGGATTTAACCCGGATATAAT 1 ACCAGCACAAAGCCTGTGGGATTTAACCCGGATATAAT * * * 43692249 ACCAGCACGAAGCCTGTGGGATTTAACTCGGATATATT 1 ACCAGCACAAAGCCTGTGGGATTTAACCCGGATATAAT * 43692287 ACCAGCACAAAGCCTGTGGGATTTAACCCAGATATAAT 1 ACCAGCACAAAGCCTGTGGGATTTAACCCGGATATAAT * 43692325 ACCAGCACATAGCCTG 1 ACCAGCACAAAGCCTG 43692341 CGGGTCTTTA Statistics Matches: 117, Mismatches: 13, Indels: 2 0.89 0.10 0.02 Matches are distributed among these distances: 38 94 0.80 39 6 0.05 40 17 0.15 ACGTcount: A:0.34, C:0.24, G:0.20, T:0.22 Consensus pattern (38 bp): ACCAGCACAAAGCCTGTGGGATTTAACCCGGATATAAT Found at i:43692290 original size:76 final size:77 Alignment explanation

Indices: 43692171--43692360 Score: 258 Period size: 76 Copynumber: 2.5 Consensus size: 77 43692161 GAATCCAGTC * * 43692171 ACCAGCACAAAACCTGCGGGAATTTAAGCTCGAATATAATACCAGCACTAAGCCTGTGGGATTTA 1 ACCAGCAC-AAGCCTGCGGGAATTTAAGCTCGAATATAATACCAGCACAAAGCCTGTGGGATTTA * 43692236 ACCCGGATATAAT 65 ACCCAGATATAAT * * * 43692249 ACCAGCACGAAGCCTGTGGG-ATTTAA-CTCGGATATATTACCAGCACAAAGCCTGTGGGATTTA 1 ACCAGCAC-AAGCCTGCGGGAATTTAAGCTCGAATATAATACCAGCACAAAGCCTGTGGGATTTA 43692312 ACCCAGATATAAT 65 ACCCAGATATAAT ** * 43692325 ACCAGCACATAGCCTGCGGGTCTTTAAGCCCGAATA 1 ACCAGCACA-AGCCTGCGGGAATTTAAGCTCGAATA 43692361 CACATCAAAT Statistics Matches: 98, Mismatches: 11, Indels: 6 0.85 0.10 0.05 Matches are distributed among these distances: 75 1 0.01 76 63 0.64 77 11 0.11 78 23 0.23 ACGTcount: A:0.33, C:0.24, G:0.21, T:0.22 Consensus pattern (77 bp): ACCAGCACAAGCCTGCGGGAATTTAAGCTCGAATATAATACCAGCACAAAGCCTGTGGGATTTAA CCCAGATATAAT Found at i:43712248 original size:32 final size:32 Alignment explanation

Indices: 43712184--43712246 Score: 83 Period size: 33 Copynumber: 1.9 Consensus size: 32 43712174 ATTAGAAAAA * 43712184 CATTTTATATTTATAATTAATGTTTTGAAAATT 1 CATTTTATATTTATAATTAATATTTT-AAAATT 43712217 CATTTT-TATTTATAATTTAATATTTATAAA 1 CATTTTATATTTATAA-TTAATATTT-TAAA 43712247 TTTTTAATAT Statistics Matches: 27, Mismatches: 1, Indels: 4 0.84 0.03 0.12 Matches are distributed among these distances: 32 9 0.33 33 17 0.63 34 1 0.04 ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56 Consensus pattern (32 bp): CATTTTATATTTATAATTAATATTTTAAAATT Found at i:43712252 original size:17 final size:19 Alignment explanation

Indices: 43712232--43712278 Score: 62 Period size: 20 Copynumber: 2.5 Consensus size: 19 43712222 TTATTTATAA 43712232 TTTAATAT-TTATA-AATT 1 TTTAATATATTATATAATT 43712249 TTTAATATAATTATATAATT 1 TTTAATAT-ATTATATAATT * 43712269 TTTAAAATAT 1 TTTAATATAT 43712279 ATTTTTAAAA Statistics Matches: 26, Mismatches: 1, Indels: 4 0.84 0.03 0.13 Matches are distributed among these distances: 17 8 0.31 19 7 0.27 20 11 0.42 ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55 Consensus pattern (19 bp): TTTAATATATTATATAATT Found at i:43715159 original size:28 final size:28 Alignment explanation

Indices: 43715113--43715190 Score: 88 Period size: 28 Copynumber: 2.8 Consensus size: 28 43715103 CACAAAACAC * * 43715113 AATATTTTATTCAACATAATATTGACA-T 1 AATATTTTATTTAAAATAATATTGA-ATT 43715141 AATATTTTATTTAAAATAATATTGAATT 1 AATATTTTATTTAAAATAATATTGAATT * * * 43715169 AA-ATTATGTTTAATATAATATT 1 AATATTTTATTTAAAATAATATT 43715191 TAACCAAATT Statistics Matches: 44, Mismatches: 5, Indels: 3 0.85 0.10 0.06 Matches are distributed among these distances: 27 18 0.41 28 26 0.59 ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47 Consensus pattern (28 bp): AATATTTTATTTAAAATAATATTGAATT Found at i:43716877 original size:40 final size:40 Alignment explanation

Indices: 43716831--43717013 Score: 244 Period size: 40 Copynumber: 4.6 Consensus size: 40 43716821 CTCGCACAAG * * 43716831 GCCTTCGGGTCTTAGCCCGGATATGGTCACTAGCATAAAT 1 GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAAT * * * 43716871 GCCTTCGGGACTTAGTCCGGATATAGTCGCTAGCACAAAT 1 GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAAT * 43716911 GCCTTCGGGTCTTAGCCCGGATATAG-CAACTCGCACAAAT 1 GCCTTCGGGTCTTAGCCCGGATATAGTC-ACTAGCACAAAT * * * * 43716951 GCCTTCGGATCTTAGTCCGGATATAGTCACTAGCATAAAA 1 GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAAT * 43716991 GCCTTCGGGACTTAG-CCGGATAT 1 GCCTTCGGGTCTTAGCCCGGATAT 43717014 CATTCGAATA Statistics Matches: 125, Mismatches: 16, Indels: 5 0.86 0.11 0.03 Matches are distributed among these distances: 39 9 0.07 40 115 0.92 41 1 0.01 ACGTcount: A:0.25, C:0.26, G:0.24, T:0.26 Consensus pattern (40 bp): GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAAT Found at i:43724977 original size:40 final size:40 Alignment explanation

Indices: 43724894--43725112 Score: 259 Period size: 40 Copynumber: 5.5 Consensus size: 40 43724884 ACCCAAGTAT ** * * 43724894 CTTCGGGAT-TTAG-CCGGATATAACCACTCGCAC-AAGGC 1 CTTCGGG-TCTTAGCCCGGATATAGTCACTAGCACAAATGC * * 43724932 CTTCGGGTCTTAGCCCGGATATGGTCACTAGCATAAATGC 1 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATGC * * 43724972 CTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAATGC 1 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATGC * 43725012 CTTCGGGTCTTAGCCC-GATATAG-CAACTCGCACAAATGC 1 CTTCGGGTCTTAGCCCGGATATAGTC-ACTAGCACAAATGC * * * * 43725051 CTTCGGATCTTAGTCCGGATATAGTCACTAGCATAAAAGC 1 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATGC * 43725091 CTTCGGGACTTAGCCCGGATAT 1 CTTCGGGTCTTAGCCCGGATAT 43725113 CATTCGAATA Statistics Matches: 154, Mismatches: 21, Indels: 10 0.83 0.11 0.05 Matches are distributed among these distances: 37 1 0.01 38 12 0.08 39 48 0.31 40 92 0.60 41 1 0.01 ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25 Consensus pattern (40 bp): CTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATGC Found at i:43725032 original size:79 final size:79 Alignment explanation

Indices: 43724894--43725112 Score: 266 Period size: 79 Copynumber: 2.8 Consensus size: 79 43724884 ACCCAAGTAT * ** * * * 43724894 CTTCGGGATTTAGCCGGATATAACCACTCGCAC-AAGGCCTTCGGGTCTTAGCCCGGATATGGTC 1 CTTCGGGACTTAGCCGGATATAGTCACTAGCACAAAAGCCTTCGGGTCTTAGCCCGGATATAG-C * 43724958 -ACTAGCATAAATGC 65 AACTAGCACAAATGC * * 43724972 CTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAATGCCTTCGGGTCTTAGCCC-GATATAGC 1 CTTCGGGACTTAG-CCGGATATAGTCACTAGCACAAAAGCCTTCGGGTCTTAGCCCGGATATAGC * 43725036 AACTCGCACAAATGC 65 AACTAGCACAAATGC * * 43725051 CTTC-GGATCTTAGTCCGGATATAGTCACTAGCATAAAAGCCTTCGGGACTTAGCCCGGATAT 1 CTTCGGGA-CTTAG-CCGGATATAGTCACTAGCACAAAAGCCTTCGGGTCTTAGCCCGGATAT 43725113 CATTCGAATA Statistics Matches: 122, Mismatches: 14, Indels: 8 0.85 0.10 0.06 Matches are distributed among these distances: 78 16 0.13 79 81 0.66 80 25 0.20 ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25 Consensus pattern (79 bp): CTTCGGGACTTAGCCGGATATAGTCACTAGCACAAAAGCCTTCGGGTCTTAGCCCGGATATAGCA ACTAGCACAAATGC Found at i:43725104 original size:119 final size:118 Alignment explanation

Indices: 43724894--43725112 Score: 341 Period size: 119 Copynumber: 1.8 Consensus size: 118 43724884 ACCCAAGTAT * * * * 43724894 CTTCGGGATTTAGCCGGATATAACCACTCGCACAAGGCCTTCGGGTCTTAGCCCGGATATGGTCA 1 CTTCGGGATTTAGCCCGATATAACAACTCGCACAAGGCCTTCGGATCTTAGCCCGGATATAGTCA * 43724959 CTAGCATAAATGCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAATGC 66 CTAGCATAAAAGCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAATGC * * * 43725012 CTTCGGG-TCTTAGCCCGATATAGCAACTCGCACAAATGCCTTCGGATCTTAGTCCGGATATAGT 1 CTTCGGGAT-TTAGCCCGATATAACAACTCGCAC-AAGGCCTTCGGATCTTAGCCCGGATATAGT 43725076 CACTAGCATAAAAGCCTTCGGGACTTAGCCCGGATAT 64 CACTAGCATAAAAGCCTTCGGGACTTAGCCCGGATAT 43725113 CATTCGAATA Statistics Matches: 91, Mismatches: 8, Indels: 3 0.89 0.08 0.03 Matches are distributed among these distances: 117 1 0.01 118 28 0.31 119 62 0.68 ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25 Consensus pattern (118 bp): CTTCGGGATTTAGCCCGATATAACAACTCGCACAAGGCCTTCGGATCTTAGCCCGGATATAGTCA CTAGCATAAAAGCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAATGC Found at i:43729714 original size:95 final size:95 Alignment explanation

Indices: 43729546--43729748 Score: 271 Period size: 95 Copynumber: 2.1 Consensus size: 95 43729536 GGAGGAAGTG * * 43729546 TACGGCCTGTAGTAATCCTGTATAAGGCTTTCAGCCTTTCTGCGATACTTATGGCTTATAGCCAT 1 TACGGCCTGTAGCAATCCTGTATAAGGCTTTCAGCCTTTCTGCAATACTTATGGCTTATAGCCAT * * 43729611 GCTGTTAACTAGCAGCGTTGCTGCGATATT 66 GCTATTAACTAGCAGCGTTGCTACGATATT ** * * * * 43729641 TACGGCCTGTAGCCGTCCTGTATAAGGCTTTTAGCCTTTTTGTAATACTTATGGCTTATAGCCGT 1 TACGGCCTGTAGCAATCCTGTATAAGGCTTTCAGCCTTTCTGCAATACTTATGGCTTATAGCCAT * * * 43729706 TCTATTAACTGGTAGCGTTGCTACGATATT 66 GCTATTAACTAGCAGCGTTGCTACGATATT * * 43729736 TATGGCCTTTAGC 1 TACGGCCTGTAGC 43729749 TTTCCTATCT Statistics Matches: 93, Mismatches: 15, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 95 93 1.00 ACGTcount: A:0.20, C:0.21, G:0.22, T:0.37 Consensus pattern (95 bp): TACGGCCTGTAGCAATCCTGTATAAGGCTTTCAGCCTTTCTGCAATACTTATGGCTTATAGCCAT GCTATTAACTAGCAGCGTTGCTACGATATT Found at i:43729950 original size:27 final size:27 Alignment explanation

Indices: 43729919--43729971 Score: 81 Period size: 27 Copynumber: 2.0 Consensus size: 27 43729909 GCATCTGATA * 43729919 CTGATTCTG-TACTGGGCTTAGGCCCAC 1 CTGATTCTGTTAATGGGC-TAGGCCCAC 43729946 CTGATTCTGTTAATGGGCTAGGCCCA 1 CTGATTCTGTTAATGGGCTAGGCCCA 43729972 ACTATTACTA Statistics Matches: 24, Mismatches: 1, Indels: 2 0.89 0.04 0.07 Matches are distributed among these distances: 27 17 0.71 28 7 0.29 ACGTcount: A:0.17, C:0.26, G:0.26, T:0.30 Consensus pattern (27 bp): CTGATTCTGTTAATGGGCTAGGCCCAC Found at i:43732266 original size:10 final size:9 Alignment explanation

Indices: 43732251--43732286 Score: 54 Period size: 9 Copynumber: 3.9 Consensus size: 9 43732241 GGGACTGTTC 43732251 TGGGCCTCGA 1 TGGGCC-CGA 43732261 TGGGCCCGA 1 TGGGCCCGA * 43732270 TAGGCCCGA 1 TGGGCCCGA 43732279 TGGGCCCG 1 TGGGCCCG 43732287 TAGGCCCGCT Statistics Matches: 24, Mismatches: 2, Indels: 1 0.89 0.07 0.04 Matches are distributed among these distances: 9 18 0.75 10 6 0.25 ACGTcount: A:0.11, C:0.33, G:0.42, T:0.14 Consensus pattern (9 bp): TGGGCCCGA Found at i:43732292 original size:17 final size:18 Alignment explanation

Indices: 43732253--43732294 Score: 68 Period size: 18 Copynumber: 2.3 Consensus size: 18 43732243 GACTGTTCTG 43732253 GGCCTCGATGGGCCCGATA 1 GGCC-CGATGGGCCCGATA 43732272 GGCCCGATGGGCCCG-TA 1 GGCCCGATGGGCCCGATA 43732289 GGCCCG 1 GGCCCG 43732295 CTTGTGTAAA Statistics Matches: 23, Mismatches: 0, Indels: 2 0.92 0.00 0.08 Matches are distributed among these distances: 17 8 0.35 18 11 0.48 19 4 0.17 ACGTcount: A:0.12, C:0.36, G:0.40, T:0.12 Consensus pattern (18 bp): GGCCCGATGGGCCCGATA Found at i:43732294 original size:8 final size:9 Alignment explanation

Indices: 43732253--43732294 Score: 50 Period size: 9 Copynumber: 4.7 Consensus size: 9 43732243 GACTGTTCTG * 43732253 GGCCTCGATG 1 GGCC-CGATA 43732263 GGCCCGATA 1 GGCCCGATA * 43732272 GGCCCGATG 1 GGCCCGATA 43732281 GGCCCG-TA 1 GGCCCGATA 43732289 GGCCCG 1 GGCCCG 43732295 CTTGTGTAAA Statistics Matches: 29, Mismatches: 3, Indels: 2 0.85 0.09 0.06 Matches are distributed among these distances: 8 7 0.24 9 18 0.62 10 4 0.14 ACGTcount: A:0.12, C:0.36, G:0.40, T:0.12 Consensus pattern (9 bp): GGCCCGATA Found at i:43739558 original size:18 final size:18 Alignment explanation

Indices: 43739535--43739571 Score: 65 Period size: 18 Copynumber: 2.1 Consensus size: 18 43739525 ACAGGGTACG * 43739535 AGGCATTGCCGGACTTAA 1 AGGCATTACCGGACTTAA 43739553 AGGCATTACCGGACTTAA 1 AGGCATTACCGGACTTAA 43739571 A 1 A 43739572 CACAAGGAAA Statistics Matches: 18, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 18 18 1.00 ACGTcount: A:0.32, C:0.22, G:0.24, T:0.22 Consensus pattern (18 bp): AGGCATTACCGGACTTAA Found at i:43741569 original size:43 final size:43 Alignment explanation

Indices: 43741507--43741597 Score: 130 Period size: 43 Copynumber: 2.1 Consensus size: 43 43741497 TACTGTACCA * * * * 43741507 ATGCC-ATATCCCAGATATGGTCTTACATGTAATCTCGTATTG 1 ATGCCAATAGCCCAGATATGGTCTTACACGAAATCTCATATTG * 43741549 ATGCCAATAGCCCAGCTATGGTCTTACACGAAATCTCATATTG 1 ATGCCAATAGCCCAGATATGGTCTTACACGAAATCTCATATTG 43741592 ATGCCA 1 ATGCCA 43741598 TGTGACACCC Statistics Matches: 43, Mismatches: 5, Indels: 1 0.88 0.10 0.02 Matches are distributed among these distances: 42 5 0.12 43 38 0.88 ACGTcount: A:0.29, C:0.24, G:0.16, T:0.31 Consensus pattern (43 bp): ATGCCAATAGCCCAGATATGGTCTTACACGAAATCTCATATTG Found at i:43742854 original size:47 final size:47 Alignment explanation

Indices: 43742767--43743131 Score: 509 Period size: 47 Copynumber: 7.8 Consensus size: 47 43742757 CCCTTCGGAA * * * * * 43742767 CTTATCACATTTATACACTTTCACATCCATCACGTCGGCCACTCGGC 1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC * * * 43742814 CCTACCGCATATATACACTTTCACATTCATCACATTGGCCATTCGGC 1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC * * * * 43742861 CTTATCACTTATATACACTTTCACGTTCATCACATCGGCCATTAGGC 1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC * * * 43742908 CTTATCACATATATACGCTTCCACATTCATCACATGGGCCATTCGGC 1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC * 43742955 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC 1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC * * 43743002 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC 1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC * * 43743049 CTTATCACACATATGCA-TGTTCACATTCATCACATTGGCCATTCGGC 1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC * 43743096 CTTATCACATATATGCA-TGTTCACATTCATCACATT 1 CTTATCACATATATACACT-TTCACATTCATCACATT 43743132 AAATCCTAAA Statistics Matches: 286, Mismatches: 31, Indels: 2 0.90 0.10 0.01 Matches are distributed among these distances: 46 1 0.00 47 285 1.00 ACGTcount: A:0.27, C:0.31, G:0.10, T:0.32 Consensus pattern (47 bp): CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC Found at i:43745658 original size:22 final size:20 Alignment explanation

Indices: 43745618--43745658 Score: 55 Period size: 20 Copynumber: 1.9 Consensus size: 20 43745608 AGTCCTATTA * 43745618 ACTAAATTCACATGCAATTG 1 ACTAAATTCACATGAAATTG 43745638 ACTAAATTCAAACATGAAATT 1 ACTAAATTC--ACATGAAATT 43745659 TTCACACATG Statistics Matches: 18, Mismatches: 1, Indels: 2 0.86 0.05 0.10 Matches are distributed among these distances: 20 9 0.50 22 9 0.50 ACGTcount: A:0.46, C:0.17, G:0.07, T:0.29 Consensus pattern (20 bp): ACTAAATTCACATGAAATTG Found at i:43747797 original size:22 final size:22 Alignment explanation

Indices: 43747772--43747894 Score: 70 Period size: 22 Copynumber: 5.3 Consensus size: 22 43747762 ATATGTATAT 43747772 ATGTGATAAGGCCGAATGGCCA 1 ATGTGATAAGGCCGAATGGCCA * * *** 43747794 ATGTGATGAATG-TGAAAGTGTATA 1 ATGTGAT-AAGGCCG-AA-TGGCCA 43747818 TATGTGATAAGGCCGAATGGCCA 1 -ATGTGATAAGGCCGAATGGCCA * * *** 43747841 ATGTGATGAATG-TGAAAGTGTATA 1 ATGTGAT-AAGGCCG-AA-TGGCCA 43747865 TATGTGATAAGGCCGAATGGCCA 1 -ATGTGATAAGGCCGAATGGCCA 43747888 ATGTGAT 1 ATGTGAT 43747895 GAATGTAAAA Statistics Matches: 71, Mismatches: 20, Indels: 20 0.64 0.18 0.18 Matches are distributed among these distances: 22 23 0.32 23 16 0.23 24 16 0.23 25 16 0.23 ACGTcount: A:0.33, C:0.10, G:0.30, T:0.27 Consensus pattern (22 bp): ATGTGATAAGGCCGAATGGCCA Found at i:43747819 original size:47 final size:47 Alignment explanation

Indices: 43747765--43748016 Score: 450 Period size: 47 Copynumber: 5.4 Consensus size: 47 43747755 GTACAAGATA 43747765 TGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAG 1 TGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAG 43747812 TGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAG 1 TGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAG * 43747859 TGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTAAAAG 1 TGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAG * * * 43747906 TGTATATATGAGATAAGACCTAATGGCCAATGTGATGAATGTGAAAG 1 TGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAG * 43747953 TGTATATATGTGATAAGGCCGAATGGCCAATGTGATGGATGTGAAAG 1 TGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAG * 43748000 TGTATAAATGTGATAAG 1 TGTATATATGTGATAAG 43748017 TCCCGAAGGG Statistics Matches: 195, Mismatches: 10, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 47 195 1.00 ACGTcount: A:0.35, C:0.08, G:0.29, T:0.28 Consensus pattern (47 bp): TGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAG Found at i:43750980 original size:13 final size:13 Alignment explanation

Indices: 43750962--43751007 Score: 51 Period size: 13 Copynumber: 3.5 Consensus size: 13 43750952 CCAAACGTCA 43750962 AAATTTTTGAACG 1 AAATTTTTGAACG * 43750975 AAATTTTCATG--CA 1 AAATTTT--TGAACG 43750988 AAATTTTTGAACG 1 AAATTTTTGAACG 43751001 AAATTTT 1 AAATTTT 43751008 CATGAAATCA Statistics Matches: 27, Mismatches: 2, Indels: 8 0.73 0.05 0.22 Matches are distributed among these distances: 11 2 0.07 13 23 0.85 15 2 0.07 ACGTcount: A:0.39, C:0.09, G:0.11, T:0.41 Consensus pattern (13 bp): AAATTTTTGAACG Found at i:43750989 original size:26 final size:26 Alignment explanation

Indices: 43750960--43751011 Score: 104 Period size: 26 Copynumber: 2.0 Consensus size: 26 43750950 GCCCAAACGT 43750960 CAAAATTTTTGAACGAAATTTTCATG 1 CAAAATTTTTGAACGAAATTTTCATG 43750986 CAAAATTTTTGAACGAAATTTTCATG 1 CAAAATTTTTGAACGAAATTTTCATG 43751012 AAATCATTCC Statistics Matches: 26, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 26 26 1.00 ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38 Consensus pattern (26 bp): CAAAATTTTTGAACGAAATTTTCATG Found at i:43757362 original size:71 final size:67 Alignment explanation

Indices: 43757243--43757460 Score: 245 Period size: 67 Copynumber: 3.3 Consensus size: 67 43757233 CACTTAGTAC * * * 43757243 CACTCATGCGACCTAGC--CGATTTA--TCT--CGTAGCTCTCTTGTCTACATGGTGTCCTTCAC 1 CACTCATGCGACCTAGCTAC-ATTTATCTCTCACGTAGCTCTCTTGTCTACATGG-ATACATC-C * 43757302 TTGGAAT 63 --CGAAT * 43757309 CACTCATGCGACCTAGCTACATTTATCTCTCACGTAGCTCTCTTGTCTACATGGATACATCCCGT 1 CACTCATGCGACCTAGCTACATTTATCTCTCACGTAGCTCTCTTGTCTACATGGATACATCCCGA 43757374 AT 66 AT * * * 43757376 CACACATGTGACCTAGCTACATTTATCTCTCACGTAGCTCTCTTGTCTACA--GATACATCCCGT 1 CACTCATGCGACCTAGCTACATTTATCTCTCACGTAGCTCTCTTGTCTACATGGATACATCCCGA 43757439 AT 66 AT * * 43757441 CACACATGTGACCTAGCTAC 1 CACTCATGCGACCTAGCTAC 43757461 TATATAGTAT Statistics Matches: 139, Mismatches: 7, Indels: 13 0.87 0.04 0.08 Matches are distributed among these distances: 65 34 0.24 66 17 0.12 67 57 0.41 68 1 0.01 69 4 0.03 70 4 0.03 71 22 0.16 ACGTcount: A:0.22, C:0.31, G:0.15, T:0.32 Consensus pattern (67 bp): CACTCATGCGACCTAGCTACATTTATCTCTCACGTAGCTCTCTTGTCTACATGGATACATCCCGA AT Found at i:43757392 original size:67 final size:65 Alignment explanation

Indices: 43757307--43757460 Score: 272 Period size: 67 Copynumber: 2.3 Consensus size: 65 43757297 TTCACTTGGA * * 43757307 ATCACTCATGCGACCTAGCTACATTTATCTCTCACGTAGCTCTCTTGTCTACATGGATACATCCC 1 ATCACACATGTGACCTAGCTACATTTATCTCTCACGTAGCTCTCTTGTCTACA--GATACATCCC 43757372 GT 64 GT 43757374 ATCACACATGTGACCTAGCTACATTTATCTCTCACGTAGCTCTCTTGTCTACAGATACATCCCGT 1 ATCACACATGTGACCTAGCTACATTTATCTCTCACGTAGCTCTCTTGTCTACAGATACATCCCGT 43757439 ATCACACATGTGACCTAGCTAC 1 ATCACACATGTGACCTAGCTAC 43757461 TATATAGTAT Statistics Matches: 85, Mismatches: 2, Indels: 2 0.96 0.02 0.02 Matches are distributed among these distances: 65 34 0.40 67 51 0.60 ACGTcount: A:0.25, C:0.31, G:0.13, T:0.31 Consensus pattern (65 bp): ATCACACATGTGACCTAGCTACATTTATCTCTCACGTAGCTCTCTTGTCTACAGATACATCCCGT Found at i:43765078 original size:39 final size:40 Alignment explanation

Indices: 43765031--43765236 Score: 222 Period size: 40 Copynumber: 5.2 Consensus size: 40 43765021 TCTTCGGAAT * * * 43765031 TTAG-CCGGATATAACCACAAGCACAATTGCCTTC-GGTC 1 TTAGCCCGGATATAATCACTAGCACAAATGCCTTCGGGTC * * ** * * 43765069 TTAACCCGGATTTGGTAACTTGCACAAATGCCTTCGGGTC 1 TTAGCCCGGATATAATCACTAGCACAAATGCCTTCGGGTC * * 43765109 TTAGCCCGGATATAA-CAACTCGCACGAATGCCTTC-GGTC 1 TTAGCCCGGATATAATC-ACTAGCACAAATGCCTTCGGGTC * * * 43765148 TTAGCCCGAATATAATCACTAGCATAAATGCCTTCGGGAC 1 TTAGCCCGGATATAATCACTAGCACAAATGCCTTCGGGTC * * * 43765188 TTAGCCCGGATATAATCACTAGCATAAATGCCTTTGGGAC 1 TTAGCCCGGATATAATCACTAGCACAAATGCCTTCGGGTC 43765228 TTAGCCCGG 1 TTAGCCCGG 43765237 GTATCATTCA Statistics Matches: 140, Mismatches: 23, Indels: 8 0.82 0.13 0.05 Matches are distributed among these distances: 38 3 0.02 39 55 0.39 40 82 0.59 ACGTcount: A:0.27, C:0.27, G:0.20, T:0.26 Consensus pattern (40 bp): TTAGCCCGGATATAATCACTAGCACAAATGCCTTCGGGTC Found at i:43765124 original size:79 final size:78 Alignment explanation

Indices: 43765022--43765221 Score: 222 Period size: 79 Copynumber: 2.5 Consensus size: 78 43765012 AACCGAGCTT * * * * * ** 43765022 CTTCGGAATTTAG-CCGGATATAACCACAAGCACAATTGCCTTCGGTCTTAACCCGGATTTGGTA 1 CTTCGGGACTTAGCCCGGATATAACCACTAGCACAA-TGCCTTCGGTCTTAACCCGAATATAATA * 43765086 ACTTGCACAAATGC 65 ACTAGCACAAATGC * * * * * 43765100 CTTCGGGTCTTAGCCCGGATATAACAACTCGCACGAATGCCTTCGGTCTTAGCCCGAATATAATC 1 CTTCGGGACTTAGCCCGGATATAACCACTAGCAC-AATGCCTTCGGTCTTAACCCGAATATAATA * 43765165 ACTAGCATAAATGC 65 ACTAGCACAAATGC * * 43765179 CTTCGGGACTTAGCCCGGATATAATCACTAGCATAAATGCCTT 1 CTTCGGGACTTAGCCCGGATATAACCACTAGCA-CAATGCCTT 43765222 TGGGACTTAG Statistics Matches: 100, Mismatches: 19, Indels: 5 0.81 0.15 0.04 Matches are distributed among these distances: 78 10 0.10 79 88 0.88 80 2 0.02 ACGTcount: A:0.28, C:0.27, G:0.19, T:0.27 Consensus pattern (78 bp): CTTCGGGACTTAGCCCGGATATAACCACTAGCACAATGCCTTCGGTCTTAACCCGAATATAATAA CTAGCACAAATGC Found at i:43767412 original size:28 final size:29 Alignment explanation

Indices: 43767352--43767509 Score: 212 Period size: 29 Copynumber: 5.5 Consensus size: 29 43767342 CCTCCGAGCT ** * * * 43767352 CGCACACCCAGTGCCGTATTTTTCCAGCT 1 CGCACACTTAGTGCCATATATTTCCAGCA * * * 43767381 TGCACACATAGTGTCATAT-TTTCCAGCA 1 CGCACACTTAGTGCCATATATTTCCAGCA * * 43767409 TGCACACTTAGTGCCTTATATTT-CAGCA 1 CGCACACTTAGTGCCATATATTTCCAGCA 43767437 CGCACACTTAGTGCCATATATTTCCAGCA 1 CGCACACTTAGTGCCATATATTTCCAGCA 43767466 CGCACACTTAGTGCCATATATTTCCAGCA 1 CGCACACTTAGTGCCATATATTTCCAGCA 43767495 CGCACACTTAGTGCC 1 CGCACACTTAGTGCC 43767510 GATCTCGTCA Statistics Matches: 116, Mismatches: 11, Indels: 4 0.89 0.08 0.03 Matches are distributed among these distances: 28 50 0.43 29 66 0.57 ACGTcount: A:0.25, C:0.31, G:0.15, T:0.29 Consensus pattern (29 bp): CGCACACTTAGTGCCATATATTTCCAGCA Found at i:43767461 original size:57 final size:57 Alignment explanation

Indices: 43767294--43767509 Score: 213 Period size: 57 Copynumber: 3.8 Consensus size: 57 43767284 TACTCGATTT * * ** *** * 43767294 CGCACACTTAGTGCCACGTA-ATTT-AAGCCCGCACACACAGTGCCATACCCTCCGAGCT 1 CGCACACTTAGTGCCA--TATATTTCCAGCACGCACACTTAGTGCCATATTTTCC-AGCA ** * * ** * * 43767352 CGCACACCCAGTGCCGTATTTTTCCAGCTTGCACACATAGTGTCATATTTTCCAGCA 1 CGCACACTTAGTGCCATATATTTCCAGCACGCACACTTAGTGCCATATTTTCCAGCA * * 43767409 TGCACACTTAGTGCCTTATATTT-CAGCACGCACACTTAGTGCCATATATTTCCAGCA 1 CGCACACTTAGTGCCATATATTTCCAGCACGCACACTTAGTGCCATAT-TTTCCAGCA 43767466 CGCACACTTAGTGCCATATATTTCCAGCACGCACACTTAGTGCC 1 CGCACACTTAGTGCCATATATTTCCAGCACGCACACTTAGTGCC 43767510 GATCTCGTCA Statistics Matches: 130, Mismatches: 24, Indels: 8 0.80 0.15 0.05 Matches are distributed among these distances: 56 22 0.17 57 54 0.42 58 54 0.42 ACGTcount: A:0.25, C:0.33, G:0.16, T:0.26 Consensus pattern (57 bp): CGCACACTTAGTGCCATATATTTCCAGCACGCACACTTAGTGCCATATTTTCCAGCA Found at i:43775263 original size:29 final size:29 Alignment explanation

Indices: 43775229--43775389 Score: 216 Period size: 29 Copynumber: 5.6 Consensus size: 29 43775219 CCCTCGAGCT ** * * * 43775229 CGCACACCCAGTGCCGTATTTTTCCAGCT 1 CGCACACTTAGTGCCATATATTTCCAGCA * * * * 43775258 TGCACACATAGTGTCATATTTTTCCAGCA 1 CGCACACTTAGTGCCATATATTTCCAGCA * * 43775287 TGCACACTTAGTGCCTTATATTT-CAGCA 1 CGCACACTTAGTGCCATATATTTCCAGCA 43775315 CGCACACTTAGTGCCATATATTTCCAGCA 1 CGCACACTTAGTGCCATATATTTCCAGCA 43775344 CGCACACTTAGTGCCATATATTTCCAGCA 1 CGCACACTTAGTGCCATATATTTCCAGCA 43775373 CGCACACTTAGTGCCAT 1 CGCACACTTAGTGCCAT 43775390 CTCGTCACCG Statistics Matches: 119, Mismatches: 12, Indels: 2 0.89 0.09 0.02 Matches are distributed among these distances: 28 26 0.22 29 93 0.78 ACGTcount: A:0.25, C:0.30, G:0.15, T:0.30 Consensus pattern (29 bp): CGCACACTTAGTGCCATATATTTCCAGCA Found at i:43775292 original size:86 final size:84 Alignment explanation

Indices: 43775201--43775389 Score: 207 Period size: 86 Copynumber: 2.2 Consensus size: 84 43775191 AATTTAAGCC ** * * * ** 43775201 CGCACACACAGTGCCATACCCTCGAGCTCGCACACCCAGTGCCGTATTTTTCCAGCTTGCACACA 1 CGCACACTTAGTGCCATA-CCTC-AGCACGCACACCCAGTGCCATATATTTCCAGCACGCACACA * * 43775266 TAGTGTCATATTTTTCCAGCA 64 TAGTGCCATATATTTCCAGCA * ** ** * 43775287 TGCACACTTAGTGCCTTATATTTCAGCACGCACACTTAGTGCCATATATTTCCAGCACGCACACT 1 CGCACACTTAGTGCC--ATACCTCAGCACGCACACCCAGTGCCATATATTTCCAGCACGCACACA 43775352 TAGTGCCATATATTTCCAGCA 64 TAGTGCCATATATTTCCAGCA 43775373 CGCACACTTAGTGCCAT 1 CGCACACTTAGTGCCAT 43775390 CTCGTCACCG Statistics Matches: 85, Mismatches: 16, Indels: 6 0.79 0.15 0.06 Matches are distributed among these distances: 84 2 0.02 86 78 0.92 87 2 0.02 88 3 0.04 ACGTcount: A:0.25, C:0.32, G:0.15, T:0.28 Consensus pattern (84 bp): CGCACACTTAGTGCCATACCTCAGCACGCACACCCAGTGCCATATATTTCCAGCACGCACACATA GTGCCATATATTTCCAGCA Found at i:43775320 original size:57 final size:58 Alignment explanation

Indices: 43775229--43775389 Score: 216 Period size: 57 Copynumber: 2.8 Consensus size: 58 43775219 CCCTCGAGCT ** * * ** * * * 43775229 CGCACACCCAGTGCCGTATTTTTCCAGCTTGCACACATAGTGTCATATTTTTCCAGCA 1 CGCACACTTAGTGCCATATATTTCCAGCACGCACACTTAGTGCCATATATTTCCAGCA * * 43775287 TGCACACTTAGTGCCTTATATTT-CAGCACGCACACTTAGTGCCATATATTTCCAGCA 1 CGCACACTTAGTGCCATATATTTCCAGCACGCACACTTAGTGCCATATATTTCCAGCA 43775344 CGCACACTTAGTGCCATATATTTCCAGCACGCACACTTAGTGCCAT 1 CGCACACTTAGTGCCATATATTTCCAGCACGCACACTTAGTGCCAT 43775390 CTCGTCACCG Statistics Matches: 90, Mismatches: 12, Indels: 2 0.87 0.12 0.02 Matches are distributed among these distances: 57 50 0.56 58 40 0.44 ACGTcount: A:0.25, C:0.30, G:0.15, T:0.30 Consensus pattern (58 bp): CGCACACTTAGTGCCATATATTTCCAGCACGCACACTTAGTGCCATATATTTCCAGCA Found at i:43782371 original size:40 final size:40 Alignment explanation

Indices: 43782327--43782511 Score: 227 Period size: 40 Copynumber: 4.7 Consensus size: 40 43782317 GCTACTCGTT * 43782327 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA 1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA * 43782367 CAAATGCCTTCGGGACTTAACCCGGATTTAGT-ACTCGCA 1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA 43782406 CAAATGCCTTCGGGACTTCA-CCCGGATTTAGTAACTCGCA 1 CAAATGCCTTCGGGACTT-AGCCCGGATTTAGTAACTCGCA ** * * * * 43782446 CAAATGCCTTC-GGATCTTATTCTGGATATAGTCACTTAGCA 1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA 43782487 CAAA-GCCTTCGGGACTTAGCCCGGA 1 CAAATGCCTTCGGGACTTAGCCCGGA 43782512 CATCATTCGA Statistics Matches: 128, Mismatches: 10, Indels: 14 0.84 0.07 0.09 Matches are distributed among these distances: 39 41 0.32 40 74 0.58 41 13 0.10 ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25 Consensus pattern (40 bp): CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA Found at i:43782438 original size:79 final size:79 Alignment explanation

Indices: 43782304--43782511 Score: 255 Period size: 79 Copynumber: 2.6 Consensus size: 79 43782294 CCTACGGAGT ** * 43782304 TTAACCGGATATAGCTACTCGTTCAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCAC 1 TTAACCGGATATAG-TACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTATAGTAACTCGCAC 43782368 AAATGCCTTCGGGA-C 65 AAATGCCTTC-GGATC * 43782383 TTAACCCGGATTTAGTACTCGCACAAATGCCTTCGGGACTTCA-CCCGGATT-TAGTAACTCGCA 1 TTAA-CCGGATATAGTACTCGCACAAATGCCTTCGGGACTT-AGCCCGGATTATAGTAACTCGCA 43782446 CAAATGCCTTCGGATC 64 CAAATGCCTTCGGATC * * * 43782462 TTATTCTGGATATAGTCACTTAGCACAAA-GCCTTCGGGACTTAGCCCGGA 1 TTA-ACCGGATATAGT-AC-TCGCACAAATGCCTTCGGGACTTAGCCCGGA 43782512 CATCATTCGA Statistics Matches: 113, Mismatches: 8, Indels: 15 0.83 0.06 0.11 Matches are distributed among these distances: 78 3 0.03 79 69 0.61 80 33 0.29 81 8 0.07 ACGTcount: A:0.26, C:0.27, G:0.21, T:0.26 Consensus pattern (79 bp): TTAACCGGATATAGTACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTATAGTAACTCGCACA AATGCCTTCGGATC Found at i:43784392 original size:29 final size:29 Alignment explanation

Indices: 43784359--43784461 Score: 197 Period size: 29 Copynumber: 3.6 Consensus size: 29 43784349 GTGACGAGAT 43784359 TGGCACTAAGTGTGCGTGCTGGAAATATA 1 TGGCACTAAGTGTGCGTGCTGGAAATATA 43784388 TGGCACTAAGTGTGCGTGCTGGAAATATA 1 TGGCACTAAGTGTGCGTGCTGGAAATATA * 43784417 TGGCACTAAGTGTGCATGCTGGAAATATA 1 TGGCACTAAGTGTGCGTGCTGGAAATATA 43784446 TGGCACTAAGTGTGCG 1 TGGCACTAAGTGTGCG 43784462 AGCTCGAAGG Statistics Matches: 72, Mismatches: 2, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 29 72 1.00 ACGTcount: A:0.27, C:0.15, G:0.31, T:0.27 Consensus pattern (29 bp): TGGCACTAAGTGTGCGTGCTGGAAATATA Found at i:43784489 original size:58 final size:58 Alignment explanation

Indices: 43784359--43784481 Score: 183 Period size: 58 Copynumber: 2.1 Consensus size: 58 43784349 GTGACGAGAT * * * * * 43784359 TGGCACTAAGTGTGCGTGCTGGAAATATATGGCACTAAGTGTGCGTGCTGGAAATATA 1 TGGCACTAAGTGTGCATGCTGGAAATATATGGCACTAAGTGTGCGAGCTCGAAAGACA * * 43784417 TGGCACTAAGTGTGCATGCTGGAAATATATGGCACTAAGTGTGCGAGCTCGAAGGGCA 1 TGGCACTAAGTGTGCATGCTGGAAATATATGGCACTAAGTGTGCGAGCTCGAAAGACA 43784475 TGGCACT 1 TGGCACT 43784482 GTGTGTGCGG Statistics Matches: 58, Mismatches: 7, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 58 58 1.00 ACGTcount: A:0.27, C:0.16, G:0.32, T:0.25 Consensus pattern (58 bp): TGGCACTAAGTGTGCATGCTGGAAATATATGGCACTAAGTGTGCGAGCTCGAAAGACA Found at i:43790575 original size:40 final size:40 Alignment explanation

Indices: 43790531--43790716 Score: 218 Period size: 40 Copynumber: 4.7 Consensus size: 40 43790521 GCTACTCGTT * 43790531 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCACA 1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCACA * * * 43790571 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAGCTCGCA 1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACA * 43790611 CAAATGCCTTCGGGACTTCA-CCCGGATTTAGTAACTCGCA 1 CAAATGCCTTCGGGACTT-AGCCCGGATTTAGTAACTCACA * * * * 43790651 CAAATGCCTTC-GGATCTTAGTCCGGATATAGTCACTTAGCA 1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAACTCA-CA * 43790692 CAAA-GCCTTCGAGACTTAGCCCGGA 1 CAAATGCCTTCGGGACTTAGCCCGGA 43790717 CATCATTCGA Statistics Matches: 128, Mismatches: 12, Indels: 12 0.84 0.08 0.08 Matches are distributed among these distances: 39 4 0.03 40 113 0.88 41 11 0.09 ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24 Consensus pattern (40 bp): CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACA Found at i:43796511 original size:31 final size:31 Alignment explanation

Indices: 43796473--43796533 Score: 122 Period size: 31 Copynumber: 2.0 Consensus size: 31 43796463 AAACTGTCAC 43796473 ACGCCCGTGTAGATGGGTCGTGTGGATTCAA 1 ACGCCCGTGTAGATGGGTCGTGTGGATTCAA 43796504 ACGCCCGTGTAGATGGGTCGTGTGGATTCA 1 ACGCCCGTGTAGATGGGTCGTGTGGATTCA 43796534 CACACCTGTG Statistics Matches: 30, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 31 30 1.00 ACGTcount: A:0.18, C:0.20, G:0.36, T:0.26 Consensus pattern (31 bp): ACGCCCGTGTAGATGGGTCGTGTGGATTCAA Found at i:43806822 original size:25 final size:26 Alignment explanation

Indices: 43806751--43806847 Score: 135 Period size: 26 Copynumber: 3.8 Consensus size: 26 43806741 GAGGAAGTGC * 43806751 AAAAGGGCTTATGTCCCAGTTTATTG 1 AAAAGGGCTTATGCCCCAGTTTATTG 43806777 AAAAGGGCTTATGCCCCAGTTTATTG 1 AAAAGGGCTTATGCCCCAGTTTATTG * *** 43806803 AAAAGGCCTT-TGCCCCAGTTTACCA 1 AAAAGGGCTTATGCCCCAGTTTATTG 43806828 AAAAGGGCTT-TGCCCCAGTT 1 AAAAGGGCTTATGCCCCAGTT 43806848 ATTAAAGAGG Statistics Matches: 65, Mismatches: 6, Indels: 1 0.90 0.08 0.01 Matches are distributed among these distances: 25 31 0.48 26 34 0.52 ACGTcount: A:0.27, C:0.23, G:0.22, T:0.29 Consensus pattern (26 bp): AAAAGGGCTTATGCCCCAGTTTATTG Found at i:43812054 original size:17 final size:18 Alignment explanation

Indices: 43812012--43812060 Score: 50 Period size: 17 Copynumber: 2.8 Consensus size: 18 43812002 AGTTGAAAAG 43812012 GAGCATGATTGTCATACTT 1 GAGCATGA-TGTCATACTT * 43812031 G-GCCATGATG-CATTCTT 1 GAG-CATGATGTCATACTT 43812048 GAGCATGAT-TCAT 1 GAGCATGATGTCAT 43812061 GCTTCTTGCA Statistics Matches: 26, Mismatches: 1, Indels: 8 0.74 0.03 0.23 Matches are distributed among these distances: 17 16 0.62 18 4 0.15 19 6 0.23 ACGTcount: A:0.24, C:0.18, G:0.22, T:0.35 Consensus pattern (18 bp): GAGCATGATGTCATACTT Found at i:43812949 original size:40 final size:40 Alignment explanation

Indices: 43812883--43813033 Score: 155 Period size: 40 Copynumber: 3.8 Consensus size: 40 43812873 AAATTGAATG * * * 43812883 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT 1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT * * *** 43812922 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT 1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT * * 43812962 ACATCCGGGCTAAGACCCGAAGGC-ATTCGTGC-GAGTTATT 1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-GTAATT * * 43813002 CTATCCGGGCTAAGACCCGAAGGCATTTGTGC 1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGC 43813034 ACTTGATTAT Statistics Matches: 91, Mismatches: 17, Indels: 7 0.79 0.15 0.06 Matches are distributed among these distances: 39 16 0.18 40 73 0.80 41 2 0.02 ACGTcount: A:0.26, C:0.23, G:0.27, T:0.23 Consensus pattern (40 bp): ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT Found at i:43813047 original size:40 final size:40 Alignment explanation

Indices: 43812919--43813049 Score: 149 Period size: 40 Copynumber: 3.3 Consensus size: 40 43812909 TATGCTGGAA * * * * 43812919 ATTATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTG 1 ATTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGATTG ** * * 43812959 GCTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTT- 1 ATTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-TTG * 43812999 ATTCTATCCGGGCTAAGACCCGAAGGCATTTGTGC-ACTTG 1 ATTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-TTG 43813039 ATTATATCCGG 1 ATTATATCCGG 43813050 TTATATTCCG Statistics Matches: 74, Mismatches: 15, Indels: 4 0.80 0.16 0.04 Matches are distributed among these distances: 39 3 0.04 40 70 0.95 41 1 0.01 ACGTcount: A:0.24, C:0.23, G:0.27, T:0.26 Consensus pattern (40 bp): ATTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGATTG Found at i:43820070 original size:17 final size:18 Alignment explanation

Indices: 43820028--43820076 Score: 50 Period size: 17 Copynumber: 2.8 Consensus size: 18 43820018 AGTTGAAAAG 43820028 GAGCATGATTGTCATACTT 1 GAGCATGA-TGTCATACTT * 43820047 G-GCCATGATG-CATTCTT 1 GAG-CATGATGTCATACTT 43820064 GAGCATGAT-TCAT 1 GAGCATGATGTCAT 43820077 GCTTCTTGCA Statistics Matches: 26, Mismatches: 1, Indels: 8 0.74 0.03 0.23 Matches are distributed among these distances: 17 16 0.62 18 4 0.15 19 6 0.23 ACGTcount: A:0.24, C:0.18, G:0.22, T:0.35 Consensus pattern (18 bp): GAGCATGATGTCATACTT Found at i:43820957 original size:40 final size:40 Alignment explanation

Indices: 43820892--43821041 Score: 146 Period size: 40 Copynumber: 3.8 Consensus size: 40 43820882 AAATTGAATG * * * 43820892 ATATCCGGGCTAAG--CCGAAGACAATTATGCTGGAAATT 1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT * * *** 43820930 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT 1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT * * 43820970 ACATCCGGGCTAAGACCCGAAGGC-ATTCGTGC-GAGTTATT 1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-GTAATT * * 43821010 CTATCCGGGCTAAGACCCGAAGGCATTTGTGC 1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGC 43821042 ACTTGATTAT Statistics Matches: 90, Mismatches: 17, Indels: 8 0.78 0.15 0.07 Matches are distributed among these distances: 38 13 0.14 39 3 0.03 40 72 0.80 41 2 0.02 ACGTcount: A:0.27, C:0.23, G:0.27, T:0.23 Consensus pattern (40 bp): ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT Found at i:43821055 original size:40 final size:40 Alignment explanation

Indices: 43820927--43821057 Score: 149 Period size: 40 Copynumber: 3.3 Consensus size: 40 43820917 TATGCTGGAA * * * * 43820927 ATTATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTG 1 ATTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGATTG ** * * 43820967 GCTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTT- 1 ATTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-TTG * 43821007 ATTCTATCCGGGCTAAGACCCGAAGGCATTTGTGC-ACTTG 1 ATTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-TTG 43821047 ATTATATCCGG 1 ATTATATCCGG 43821058 TTATATTCCG Statistics Matches: 74, Mismatches: 15, Indels: 4 0.80 0.16 0.04 Matches are distributed among these distances: 39 3 0.04 40 70 0.95 41 1 0.01 ACGTcount: A:0.24, C:0.23, G:0.27, T:0.26 Consensus pattern (40 bp): ATTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGATTG Found at i:43822286 original size:28 final size:28 Alignment explanation

Indices: 43822221--43822321 Score: 114 Period size: 28 Copynumber: 3.5 Consensus size: 28 43822211 ATAGTGAATC * 43822221 CGCACACTTAGTGCTATATGTATTC-AACT 1 CGCACACTTAGTGCTATA--TAATCAAACT 43822250 CGCACACTTAGTGCTATATAATCAAACT 1 CGCACACTTAGTGCTATATAATCAAACT * * * * 43822278 CGCACACTTAGTGCTGTACAATTTTAAACC 1 CGCACACTTAGTGCTATATAA--TCAAACT 43822308 CGCACACTTAGTGC 1 CGCACACTTAGTGC 43822322 CAATCTTGTC Statistics Matches: 64, Mismatches: 5, Indels: 5 0.86 0.07 0.07 Matches are distributed among these distances: 27 4 0.06 28 23 0.36 29 18 0.28 30 19 0.30 ACGTcount: A:0.30, C:0.27, G:0.14, T:0.30 Consensus pattern (28 bp): CGCACACTTAGTGCTATATAATCAAACT Found at i:43830124 original size:28 final size:28 Alignment explanation

Indices: 43830059--43830159 Score: 114 Period size: 28 Copynumber: 3.5 Consensus size: 28 43830049 ATAGTGAATC * 43830059 CGCACACTTAGTGCTATATGTATTC-AACT 1 CGCACACTTAGTGCTATA--TAATCAAACT 43830088 CGCACACTTAGTGCTATATAATCAAACT 1 CGCACACTTAGTGCTATATAATCAAACT * * * * 43830116 CGCACACTTAGTGCTGTACAATTTTAAACC 1 CGCACACTTAGTGCTATATAA--TCAAACT 43830146 CGCACACTTAGTGC 1 CGCACACTTAGTGC 43830160 CAATCTTGTC Statistics Matches: 64, Mismatches: 5, Indels: 5 0.86 0.07 0.07 Matches are distributed among these distances: 27 4 0.06 28 23 0.36 29 18 0.28 30 19 0.30 ACGTcount: A:0.30, C:0.27, G:0.14, T:0.30 Consensus pattern (28 bp): CGCACACTTAGTGCTATATAATCAAACT Found at i:43847881 original size:2 final size:2 Alignment explanation

Indices: 43847874--43847905 Score: 64 Period size: 2 Copynumber: 16.0 Consensus size: 2 43847864 ACATTCGGAC 43847874 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT 1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT 43847906 GCATGTGTGA Statistics Matches: 30, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 30 1.00 ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50 Consensus pattern (2 bp): AT Found at i:43848373 original size:29 final size:29 Alignment explanation

Indices: 43848338--43848408 Score: 99 Period size: 29 Copynumber: 2.4 Consensus size: 29 43848328 GTTGTGAGAT * * 43848338 TGGCACTAAGTGTGCGGGCTTGAAA-TGCA 1 TGGCACTAAGTGTGCGAG-TTGAAAGTACA * 43848367 TGGCACTAAGTGTGCGAGTTTAAAGTACA 1 TGGCACTAAGTGTGCGAGTTGAAAGTACA 43848396 TGGCACTAAGTGT 1 TGGCACTAAGTGT 43848409 TCGTGGTTGA Statistics Matches: 38, Mismatches: 3, Indels: 2 0.88 0.07 0.05 Matches are distributed among these distances: 28 5 0.13 29 33 0.87 ACGTcount: A:0.27, C:0.15, G:0.31, T:0.27 Consensus pattern (29 bp): TGGCACTAAGTGTGCGAGTTGAAAGTACA Found at i:43850253 original size:31 final size:31 Alignment explanation

Indices: 43850210--43850281 Score: 117 Period size: 31 Copynumber: 2.3 Consensus size: 31 43850200 AAAGTGTCAC * 43850210 ACGCCCGCGTAGATGGATCGTGTGGATTCAA 1 ACGCCCGTGTAGATGGATCGTGTGGATTCAA * * 43850241 ACGCCCGTGTAGATGGGTCGTGTGGATTCAC 1 ACGCCCGTGTAGATGGATCGTGTGGATTCAA 43850272 ACGCCCGTGT 1 ACGCCCGTGT 43850282 GGCTTGGGGC Statistics Matches: 38, Mismatches: 3, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 31 38 1.00 ACGTcount: A:0.18, C:0.25, G:0.33, T:0.24 Consensus pattern (31 bp): ACGCCCGTGTAGATGGATCGTGTGGATTCAA Found at i:43853521 original size:28 final size:28 Alignment explanation

Indices: 43853489--43853546 Score: 66 Period size: 29 Copynumber: 2.0 Consensus size: 28 43853479 AATTTTGATG 43853489 AAATAGAGCTTATTG-A-GCTAAATTGTGA 1 AAATA-AGCTT-TTGAAGGCTAAATTGTGA * 43853517 AAATAAGGTTTTGAAGGGCTAAATTGTGA 1 AAATAAGCTTTTGAA-GGCTAAATTGTGA 43853546 A 1 A 43853547 TTAAATATGT Statistics Matches: 26, Mismatches: 1, Indels: 5 0.81 0.03 0.16 Matches are distributed among these distances: 26 3 0.12 27 5 0.19 28 5 0.19 29 13 0.50 ACGTcount: A:0.40, C:0.05, G:0.24, T:0.31 Consensus pattern (28 bp): AAATAAGCTTTTGAAGGCTAAATTGTGA Found at i:43854064 original size:43 final size:44 Alignment explanation

Indices: 43854008--43854093 Score: 102 Period size: 43 Copynumber: 2.0 Consensus size: 44 43853998 TTGATTTGTT * * * 43854008 ATTTTGTGCAAGACCATGTTTGGGACATAGGCCTCGAT-TTGAG 1 ATTTTGTGCAAGACCATATTTGGAACAGAGGCCTCGATATTGAG ** * * 43854051 ATTTTGTTTAAGACCCTATTTGGAACAGAGGCTTCGATATTGA 1 ATTTTGTGCAAGACCATATTTGGAACAGAGGCCTCGATATTGA 43854094 ATTACATGTA Statistics Matches: 35, Mismatches: 7, Indels: 1 0.81 0.16 0.02 Matches are distributed among these distances: 43 31 0.89 44 4 0.11 ACGTcount: A:0.26, C:0.15, G:0.24, T:0.35 Consensus pattern (44 bp): ATTTTGTGCAAGACCATATTTGGAACAGAGGCCTCGATATTGAG Found at i:43859439 original size:8 final size:9 Alignment explanation

Indices: 43859419--43859448 Score: 51 Period size: 9 Copynumber: 3.3 Consensus size: 9 43859409 TAGGGTGGCA * 43859419 TTTTTCTCT 1 TTTTTTTCT 43859428 TTTTTTTCT 1 TTTTTTTCT 43859437 TTTTTTTCT 1 TTTTTTTCT 43859446 TTT 1 TTT 43859449 CACTTGTGTC Statistics Matches: 20, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 9 20 1.00 ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87 Consensus pattern (9 bp): TTTTTTTCT Found at i:43860351 original size:20 final size:21 Alignment explanation

Indices: 43860313--43860352 Score: 64 Period size: 21 Copynumber: 2.0 Consensus size: 21 43860303 GCATTACGGT * 43860313 AAGTTGGGCCTCGATGGGCTG 1 AAGTTGGGCCTCAATGGGCTG 43860334 AAGTTGGGCC-CAATGGGCT 1 AAGTTGGGCCTCAATGGGCT 43860353 TTCAGGCCCA Statistics Matches: 18, Mismatches: 1, Indels: 1 0.90 0.05 0.05 Matches are distributed among these distances: 20 8 0.44 21 10 0.56 ACGTcount: A:0.17, C:0.20, G:0.40, T:0.23 Consensus pattern (21 bp): AAGTTGGGCCTCAATGGGCTG Found at i:43860731 original size:20 final size:20 Alignment explanation

Indices: 43860716--43860772 Score: 96 Period size: 20 Copynumber: 2.9 Consensus size: 20 43860706 ACATGATTAA * 43860716 TATGATTTGCACATGATATG 1 TATGATATGCACATGATATG * 43860736 TATGATATGCGCATGATATG 1 TATGATATGCACATGATATG 43860756 TATGATATGCACATGAT 1 TATGATATGCACATGAT 43860773 GTATTTATAA Statistics Matches: 34, Mismatches: 3, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 20 34 1.00 ACGTcount: A:0.32, C:0.11, G:0.21, T:0.37 Consensus pattern (20 bp): TATGATATGCACATGATATG Found at i:43860862 original size:26 final size:25 Alignment explanation

Indices: 43860822--43860918 Score: 133 Period size: 26 Copynumber: 3.8 Consensus size: 25 43860812 GAGGAAGTGC 43860822 AAAAGGGCTTGTGCCCCAGTTTATTG 1 AAAAGGGCTT-TGCCCCAGTTTATTG * 43860848 AAAAGGGCTTATGCCCTAGTTTATTG 1 AAAAGGGCTT-TGCCCCAGTTTATTG ** 43860874 AAATA-GGCTTTGCCCCAGTTTACCG 1 AAA-AGGGCTTTGCCCCAGTTTATTG 43860899 AAAAGGGCTTTGCCCCAGTT 1 AAAAGGGCTTTGCCCCAGTT 43860919 ATTAAAGAGG Statistics Matches: 64, Mismatches: 5, Indels: 5 0.86 0.07 0.07 Matches are distributed among these distances: 24 1 0.02 25 30 0.47 26 32 0.50 27 1 0.02 ACGTcount: A:0.25, C:0.22, G:0.24, T:0.30 Consensus pattern (25 bp): AAAAGGGCTTTGCCCCAGTTTATTG Found at i:43860904 original size:51 final size:49 Alignment explanation

Indices: 43860823--43860930 Score: 139 Period size: 51 Copynumber: 2.2 Consensus size: 49 43860813 AGGAAGTGCA ** * 43860823 AAAG-GGCTTGTGCCCCAGTTTATTGAAAAGGGCTTATGCCCTAGTTTATT 1 AAAGAGGCTTGTGCCCCAGTTTACCGAAAAGGGCTT-TGCCCCAG-TTATT * 43860873 GAAATAGGCTT-TGCCCCAGTTTACCGAAAAGGGCTTTGCCCCAGTTATT 1 -AAAGAGGCTTGTGCCCCAGTTTACCGAAAAGGGCTTTGCCCCAGTTATT 43860922 AAAGAGGCT 1 AAAGAGGCT 43860931 AGGCCTCCAG Statistics Matches: 51, Mismatches: 5, Indels: 5 0.84 0.08 0.08 Matches are distributed among these distances: 48 8 0.16 49 5 0.10 50 7 0.14 51 26 0.51 52 5 0.10 ACGTcount: A:0.26, C:0.20, G:0.24, T:0.30 Consensus pattern (49 bp): AAAGAGGCTTGTGCCCCAGTTTACCGAAAAGGGCTTTGCCCCAGTTATT Found at i:43868831 original size:20 final size:20 Alignment explanation

Indices: 43868806--43868872 Score: 100 Period size: 20 Copynumber: 3.4 Consensus size: 20 43868796 ATTTTGATAT * 43868806 ACATGAT-TGATATGATTTGC 1 ACATGATATG-TATGATATGC 43868826 ACATGATATGTATGATATGC 1 ACATGATATGTATGATATGC * 43868846 GCATGATATGTATGATATGC 1 ACATGATATGTATGATATGC 43868866 ACATGAT 1 ACATGAT 43868873 GTATTCATAA Statistics Matches: 43, Mismatches: 3, Indels: 2 0.90 0.06 0.04 Matches are distributed among these distances: 20 41 0.95 21 2 0.05 ACGTcount: A:0.33, C:0.10, G:0.21, T:0.36 Consensus pattern (20 bp): ACATGATATGTATGATATGC Found at i:43868950 original size:25 final size:27 Alignment explanation

Indices: 43868922--43869042 Score: 189 Period size: 27 Copynumber: 4.7 Consensus size: 27 43868912 GAGGAAGTGC 43868922 AAAAGGGCTTATG-CCCAGTTTATTGA 1 AAAAGGGCTTATGCCCCAGTTTATTGA 43868948 AAAAGGGCTTATGCCCCAGTTTATTGA 1 AAAAGGGCTTATGCCCCAGTTTATTGA 43868975 AAAAGGGCTTATGCCCCAGTTTATTG- 1 AAAAGGGCTTATGCCCCAGTTTATTGA ** 43869001 AAAAGGGCTT-TGCCCCAGTTTACCG- 1 AAAAGGGCTTATGCCCCAGTTTATTGA 43869026 AAAAGGGCTT-TGCCCCA 1 AAAAGGGCTTATGCCCCA 43869043 ATTATTAAAG Statistics Matches: 92, Mismatches: 2, Indels: 3 0.95 0.02 0.03 Matches are distributed among these distances: 25 30 0.33 26 23 0.25 27 39 0.42 ACGTcount: A:0.28, C:0.21, G:0.23, T:0.27 Consensus pattern (27 bp): AAAAGGGCTTATGCCCCAGTTTATTGA Found at i:43875368 original size:49 final size:49 Alignment explanation

Indices: 43875308--43875806 Score: 862 Period size: 49 Copynumber: 10.3 Consensus size: 49 43875298 TACTTGATAG * 43875308 TATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTGTA 1 TATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTGTA * 43875357 TATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA 1 TATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTGTA * 43875406 TATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTGTA 1 TATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTGTA * * 43875455 TATATGTGATAAGGCCTAATGGTCGATGTGATGAATGTGAAAGTGTATA 1 TATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTGTA 43875504 TATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTGTA 1 TATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTGTA 43875553 TATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTGTA 1 TATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTGTA 43875602 TATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA--GTGTA 1 TATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTGTA * 43875649 TATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA 1 TATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTGTA * ** 43875698 TATATGTGACAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGCATA 1 TATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTGTA * * 43875747 TATATGTGACAAGGCCTAATGGCCAATGTGATGAATGTGAAA--GTGTA 1 TATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTGTA * 43875794 TAAATGTGATAAG 1 TATATGTGATAAG 43875807 TCCCGAAGGG Statistics Matches: 431, Mismatches: 17, Indels: 6 0.95 0.04 0.01 Matches are distributed among these distances: 47 61 0.14 49 370 0.86 ACGTcount: A:0.33, C:0.08, G:0.29, T:0.30 Consensus pattern (49 bp): TATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTGTA Found at i:43880684 original size:20 final size:20 Alignment explanation

Indices: 43880659--43880705 Score: 60 Period size: 20 Copynumber: 2.4 Consensus size: 20 43880649 ATTTTGATAT * 43880659 ACATGAT-TGACATGATTTGC 1 ACATGATATG-CATGATATGC * 43880679 ACATGATATGTATGATATGC 1 ACATGATATGCATGATATGC 43880699 ACATGAT 1 ACATGAT 43880706 GTATTCATAA Statistics Matches: 24, Mismatches: 2, Indels: 2 0.86 0.07 0.07 Matches are distributed among these distances: 20 22 0.92 21 2 0.08 ACGTcount: A:0.34, C:0.13, G:0.19, T:0.34 Consensus pattern (20 bp): ACATGATATGCATGATATGC Found at i:43880856 original size:52 final size:52 Alignment explanation

Indices: 43880757--43880900 Score: 206 Period size: 51 Copynumber: 2.8 Consensus size: 52 43880747 GGAAGTCCAG * 43880757 AAGGGCTTA-GCCCCAGTTTATTGAAAAAGGGCTTATGCCCCAGTTTATTGAAA 1 AAGGGCTTATGCCCCAGTTTATTG-AAAAGGGCTTATGCCCCAATTTATTG-AA * * 43880810 AAGGG-TTATGCCTCAGTTTATTGAAAAGGGCTTATGCCCTAATTTATTGAA 1 AAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTATGCCCCAATTTATTGAA * 43880861 AAGGGCTT-TGCCCCAGTTTATCGAAAAGGGCTT-TGCCCCA 1 AAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTATGCCCCA 43880901 GTTATTAAAG Statistics Matches: 83, Mismatches: 6, Indels: 7 0.86 0.06 0.07 Matches are distributed among these distances: 50 6 0.07 51 30 0.36 52 29 0.35 53 18 0.22 ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30 Consensus pattern (52 bp): AAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTATGCCCCAATTTATTGAA Found at i:43880880 original size:25 final size:26 Alignment explanation

Indices: 43880757--43880903 Score: 212 Period size: 26 Copynumber: 5.7 Consensus size: 26 43880747 GGAAGTCCAG 43880757 AAGGGCTTA-GCCCCAGTTTATTGAAA 1 AAGGGCTTATGCCCCAGTTTATTG-AA 43880783 AAGGGCTTATGCCCCAGTTTATTGAAA 1 AAGGGCTTATGCCCCAGTTTATTG-AA * 43880810 AAGGG-TTATGCCTCAGTTTATTGAA 1 AAGGGCTTATGCCCCAGTTTATTGAA * * 43880835 AAGGGCTTATGCCCTAATTTATTGAA 1 AAGGGCTTATGCCCCAGTTTATTGAA * 43880861 AAGGGCTT-TGCCCCAGTTTATCGAA 1 AAGGGCTTATGCCCCAGTTTATTGAA 43880886 AAGGGCTT-TGCCCCAGTT 1 AAGGGCTTATGCCCCAGTT 43880904 ATTAAAGAGG Statistics Matches: 112, Mismatches: 7, Indels: 5 0.90 0.06 0.04 Matches are distributed among these distances: 25 39 0.35 26 51 0.46 27 22 0.20 ACGTcount: A:0.27, C:0.19, G:0.23, T:0.31 Consensus pattern (26 bp): AAGGGCTTATGCCCCAGTTTATTGAA Found at i:43886908 original size:93 final size:93 Alignment explanation

Indices: 43886749--43886920 Score: 254 Period size: 93 Copynumber: 1.8 Consensus size: 93 43886739 CGCCCATAAG * * * * * 43886749 CGAACTCGGACTCAAATCAACAAGCTCGGGCGTTCACATCCATAGGTGAACTCGGACTCAACTCA 1 CGAACTCGGACTCAAATCAACAAGCTCAGACATTCACATCCATAAGTGAACTCAGACTCAACTCA * 43886814 ACGAGTTCGGATGCCTAGTTACATTTCA 66 ACGAGCTCGGATGCCTAGTTACATTTCA * * * * 43886842 CGAACTCGGACTCAACTCAACGAGTTCAGACATTCGCATCCATAAGTGAACTCAGACTCAACTCA 1 CGAACTCGGACTCAAATCAACAAGCTCAGACATTCACATCCATAAGTGAACTCAGACTCAACTCA 43886907 ACGAGCTCGGATGC 66 ACGAGCTCGGATGC 43886921 TCAACATCCT Statistics Matches: 69, Mismatches: 10, Indels: 0 0.87 0.13 0.00 Matches are distributed among these distances: 93 69 1.00 ACGTcount: A:0.30, C:0.29, G:0.20, T:0.21 Consensus pattern (93 bp): CGAACTCGGACTCAAATCAACAAGCTCAGACATTCACATCCATAAGTGAACTCAGACTCAACTCA ACGAGCTCGGATGCCTAGTTACATTTCA Found at i:43888486 original size:27 final size:26 Alignment explanation

Indices: 43888456--43888638 Score: 181 Period size: 27 Copynumber: 6.9 Consensus size: 26 43888446 AAGACCCGGT * 43888456 TTGTAAAATTACCGAAATACCCCCAGA 1 TTGTAAAATTATCGAAATA-CCCCAGA 43888483 TTGTAAAATTATCGAAATACCCCA-A 1 TTGTAAAATTATCGAAATACCCCAGA 43888508 TTTGTAAAATTATCGAAATACCCCAGA 1 -TTGTAAAATTATCGAAATACCCCAGA ** * * 43888535 TTACAAAATTA-CTGAAATAACCCTAGT 1 TTGTAAAATTATC-GAAAT-ACCCCAGA * * ** 43888562 TTGTAAAATTACCAAAATACCCTTGTA 1 TTGTAAAATTATCGAAATACCCCAG-A * ** 43888589 TTGTAAAATTATCGGAATACCCTTGCA 1 TTGTAAAATTATCGAAATACCCCAG-A * 43888616 GTGTAAAATTATCGAAATACCCC 1 TTGTAAAATTATCGAAATACCCC 43888639 TATAGGATAA Statistics Matches: 133, Mismatches: 17, Indels: 12 0.82 0.10 0.07 Matches are distributed among these distances: 25 2 0.02 26 49 0.37 27 81 0.61 28 1 0.01 ACGTcount: A:0.40, C:0.20, G:0.10, T:0.29 Consensus pattern (26 bp): TTGTAAAATTATCGAAATACCCCAGA Found at i:43888565 original size:53 final size:52 Alignment explanation

Indices: 43888454--43888638 Score: 178 Period size: 53 Copynumber: 3.5 Consensus size: 52 43888444 TTAAGACCCG ** 43888454 GTTTGTAAAATTACCGAAATACCCCCAGATTGTAAAATTATCGAAATACCCCA 1 GTTTGTAAAATTACCGAAATA-CCCCAGATTACAAAATTATCGAAATACCCCA * * * 43888507 ATTTGTAAAATTATCGAAATACCCCAGATTACAAAATTA-CTGAAATAACCCTA 1 GTTTGTAAAATTACCGAAATACCCCAGATTACAAAATTATC-GAAAT-ACCCCA * ** ** * 43888560 GTTTGTAAAATTACCAAAATACCCTTGTATTGTAAAATTATCGGAATACCCTTGCA 1 GTTTGTAAAATTACCGAAATACCCCAG-ATTACAAAATTATCGAAATACCC---CA * 43888616 G--TGTAAAATTATCGAAATACCCC 1 GTTTGTAAAATTACCGAAATACCCC 43888639 TATAGGATAA Statistics Matches: 108, Mismatches: 17, Indels: 13 0.78 0.12 0.09 Matches are distributed among these distances: 51 1 0.01 52 21 0.19 53 50 0.46 54 33 0.31 55 1 0.01 56 2 0.02 ACGTcount: A:0.40, C:0.20, G:0.11, T:0.29 Consensus pattern (52 bp): GTTTGTAAAATTACCGAAATACCCCAGATTACAAAATTATCGAAATACCCCA Found at i:43892829 original size:27 final size:27 Alignment explanation

Indices: 43892798--43892924 Score: 188 Period size: 27 Copynumber: 4.7 Consensus size: 27 43892788 CCCTAGTTTT * 43892798 TAAAATTACTAAAATACCCTCAGA-TTG 1 TAAAATTACCAAAATACCCTC-GATTTG 43892825 TAAAATTACCAAAATACCCTCGATTTG 1 TAAAATTACCAAAATACCCTCGATTTG * 43892852 TAAAATTACCAAAATACCC-C-ATATTA 1 TAAAATTACCAAAATACCCTCGAT-TTG 43892878 TAAAATTACCAAAATACCCTCGATTTG 1 TAAAATTACCAAAATACCCTCGATTTG * 43892905 TAAAATTATCAAAATACCCT 1 TAAAATTACCAAAATACCCT 43892925 TGTAGTGTAA Statistics Matches: 92, Mismatches: 4, Indels: 8 0.88 0.04 0.08 Matches are distributed among these distances: 25 2 0.02 26 24 0.26 27 64 0.70 28 2 0.02 ACGTcount: A:0.45, C:0.21, G:0.05, T:0.29 Consensus pattern (27 bp): TAAAATTACCAAAATACCCTCGATTTG Found at i:43892888 original size:53 final size:54 Alignment explanation

Indices: 43892798--43892924 Score: 211 Period size: 53 Copynumber: 2.4 Consensus size: 54 43892788 CCCTAGTTTT * * 43892798 TAAAATTACTAAAATACCCTCAGATTGTAAAATTACCAAAATACCCTCGATTTG 1 TAAAATTACCAAAATACCCTCAGATTATAAAATTACCAAAATACCCTCGATTTG * 43892852 TAAAATTACCAAAATACCC-CATATTATAAAATTACCAAAATACCCTCGATTTG 1 TAAAATTACCAAAATACCCTCAGATTATAAAATTACCAAAATACCCTCGATTTG * 43892905 TAAAATTATCAAAATACCCT 1 TAAAATTACCAAAATACCCT 43892925 TGTAGTGTAA Statistics Matches: 68, Mismatches: 4, Indels: 2 0.92 0.05 0.03 Matches are distributed among these distances: 53 50 0.74 54 18 0.26 ACGTcount: A:0.45, C:0.21, G:0.05, T:0.29 Consensus pattern (54 bp): TAAAATTACCAAAATACCCTCAGATTATAAAATTACCAAAATACCCTCGATTTG Found at i:43892933 original size:27 final size:26 Alignment explanation

Indices: 43892798--43892977 Score: 182 Period size: 27 Copynumber: 6.7 Consensus size: 26 43892788 CCCTAGTTTT * 43892798 TAAAATTACTAAAATACCCTCAGATTG 1 TAAAATTACCAAAATACCCTC-GATTG 43892825 TAAAATTACCAAAATACCCTCGATTTG 1 TAAAATTACCAAAATACCCTCGA-TTG * * 43892852 TAAAATTACCAAAATACCC-CATATTA 1 TAAAATTACCAAAATACCCTC-GATTG 43892878 TAAAATTACCAAAATACCCTCGATTTG 1 TAAAATTACCAAAATACCCTCGA-TTG * * * 43892905 TAAAATTATCAAAATACCCTTGTAGTG 1 TAAAATTACCAAAATACCCTCG-ATTG *** * * * 43892932 TAAAATTATTGAAGTACCCTTGTAGTG 1 TAAAATTACCAAAATACCCTCG-ATTG * 43892959 TAAAATTACCGAAATACCC 1 TAAAATTACCAAAATACCC 43892978 CAGTTGGGTA Statistics Matches: 134, Mismatches: 14, Indels: 10 0.85 0.09 0.06 Matches are distributed among these distances: 26 25 0.19 27 108 0.81 28 1 0.01 ACGTcount: A:0.42, C:0.19, G:0.08, T:0.30 Consensus pattern (26 bp): TAAAATTACCAAAATACCCTCGATTG Found at i:43892950 original size:80 final size:81 Alignment explanation

Indices: 43892798--43892977 Score: 204 Period size: 80 Copynumber: 2.2 Consensus size: 81 43892788 CCCTAGTTTT * * 43892798 TAAAATTACTAAAATACCCTCAGATTGTAAAATTACCAAAATACCCTCGATTTGTAAAATTACCA 1 TAAAATTACCAAAATACCCTCAGATTGTAAAATTACCAAAATACCCTCGATGTGTAAAATTACCA * 43892863 AAATACCC-CATATTA 66 AAATACCCTCATAGTA * * * 43892878 TAAAATTACCAAAATACCCTC-GATTTGTAAAATTATCAAAATACCCTTG-TAGTGTAAAATTAT 1 TAAAATTACCAAAATACCCTCAGA-TTGTAAAATTACCAAAATACCCTCGAT-GTGTAAAATTAC ** * ** * 43892941 TGAAGTACCCTTGTAGTG 64 CAAAATACCCTCATAGTA * 43892959 TAAAATTACCGAAATACCC 1 TAAAATTACCAAAATACCC 43892978 CAGTTGGGTA Statistics Matches: 84, Mismatches: 13, Indels: 5 0.82 0.13 0.05 Matches are distributed among these distances: 79 3 0.04 80 60 0.71 81 21 0.25 ACGTcount: A:0.42, C:0.19, G:0.08, T:0.30 Consensus pattern (81 bp): TAAAATTACCAAAATACCCTCAGATTGTAAAATTACCAAAATACCCTCGATGTGTAAAATTACCA AAATACCCTCATAGTA Found at i:43892988 original size:27 final size:26 Alignment explanation

Indices: 43892787--43892991 Score: 146 Period size: 27 Copynumber: 7.7 Consensus size: 26 43892777 GGTCGTTAAG * * * 43892787 ACCCTAGTTTTTAAAATTACTAAAAT 1 ACCCCAGTTTGTAAAATTACCAAAAT * 43892813 ACCCTCAGATTGTAAAATTACCAAAAT 1 ACCC-CAGTTTGTAAAATTACCAAAAT 43892840 ACCCTC-GATTTGTAAAATTACCAAAAT 1 ACCC-CAG-TTTGTAAAATTACCAAAAT * 43892867 ACCCCA-TATTATAAAATTACCAAAAT 1 ACCCCAGT-TTGTAAAATTACCAAAAT * 43892893 ACCCTC-GATTTGTAAAATTATCAAAAT 1 ACCC-CAG-TTTGTAAAATTACCAAAAT ** * *** * 43892920 ACCCTTGTAGTGTAAAATTATTGAAGT 1 ACCCCAGT-TTGTAAAATTACCAAAAT ** * * 43892947 ACCCTTGTAGTGTAAAATTACCGAAAT 1 ACCCCAGT-TTGTAAAATTACCAAAAT * 43892974 ACCCCAGTTGGGTAAAAT 1 ACCCCAGTT-TGTAAAAT 43892992 GACTGTTTTA Statistics Matches: 149, Mismatches: 20, Indels: 19 0.79 0.11 0.10 Matches are distributed among these distances: 25 1 0.01 26 28 0.19 27 119 0.80 28 1 0.01 ACGTcount: A:0.40, C:0.19, G:0.10, T:0.31 Consensus pattern (26 bp): ACCCCAGTTTGTAAAATTACCAAAAT Found at i:43898163 original size:42 final size:42 Alignment explanation

Indices: 43898013--43898164 Score: 157 Period size: 42 Copynumber: 3.6 Consensus size: 42 43898003 TGAGTTTACC * * * * * 43898013 TGTAAGACCATATCTGGGATATGACATCGTTGTGATATTTCA 1 TGTAAGACCATATCTGGGATATGGCATCGATATGAGATTCCA * * * * * 43898055 TGTAAGACCAT-GCTGGGACATGGAATCGATATGAGA-ACCG 1 TGTAAGACCATATCTGGGATATGGCATCGATATGAGATTCCA * 43898095 TGTAAGACCATCA-CTGGGCTATTGGCATCGATATGAGATTCCA 1 TGTAAGACCAT-ATCTGGGATA-TGGCATCGATATGAGATTCCA * 43898138 CGTAAGACCATATCTGGGATATGGCAT 1 TGTAAGACCATATCTGGGATATGGCAT 43898165 TGGTACAATT Statistics Matches: 88, Mismatches: 17, Indels: 10 0.77 0.15 0.09 Matches are distributed among these distances: 40 12 0.14 41 24 0.27 42 33 0.38 43 19 0.22 ACGTcount: A:0.30, C:0.18, G:0.25, T:0.28 Consensus pattern (42 bp): TGTAAGACCATATCTGGGATATGGCATCGATATGAGATTCCA Found at i:43901886 original size:40 final size:39 Alignment explanation

Indices: 43901820--43901970 Score: 153 Period size: 40 Copynumber: 3.8 Consensus size: 39 43901810 AAATTGAATG * * * 43901820 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT 1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGC-GGTAATT * * *** 43901859 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCAAGTGGCT 1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGC-GGTAATT * 43901899 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTCATT 1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCG-GTAATT * * 43901939 CTATCCGGGCTAAGACCCGAAGGCATTTGTGC 1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGC 43901971 ACATGGTTAT Statistics Matches: 92, Mismatches: 16, Indels: 7 0.80 0.14 0.06 Matches are distributed among these distances: 39 16 0.17 40 74 0.80 41 2 0.02 ACGTcount: A:0.27, C:0.23, G:0.27, T:0.23 Consensus pattern (39 bp): ATATCCGGGCTAAGACCCGAAGGCAATTGTGCGGTAATT Found at i:43901984 original size:40 final size:39 Alignment explanation

Indices: 43901857--43901986 Score: 161 Period size: 40 Copynumber: 3.3 Consensus size: 39 43901847 ATGCTGGAAA * * 43901857 TTATATCCGGGTTAAGACCCGAAGGCAATTGTGCAAGTGG 1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCAA-TGG * * * ** 43901897 CTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCA 1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGC-AATGG * 43901937 TTCTATCCGGGCTAAGACCCGAAGGCATTTGTGCACATGG 1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCA-ATGG 43901977 TTATATCCGG 1 TTATATCCGG 43901987 TTATATTCCG Statistics Matches: 74, Mismatches: 14, Indels: 4 0.80 0.15 0.04 Matches are distributed among these distances: 39 1 0.01 40 72 0.97 41 1 0.01 ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25 Consensus pattern (39 bp): TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCAATGG Found at i:43910335 original size:49 final size:49 Alignment explanation

Indices: 43910279--43910493 Score: 367 Period size: 49 Copynumber: 4.4 Consensus size: 49 43910269 TACATATATG * * * 43910279 TGTGATAAGGCCGAATGGCCAATGCGATGAATGTGAAAGTGTATGTATA 1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATGTATA 43910328 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATGTATA 1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATGTATA * * 43910377 TGTGATGAGGCCTAATGGCCGATGTGGTGAATGTGAAAGTGTATGTATA 1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATGTATA * * 43910426 TGTGATGAGGCCTAATGGCCGATGTGGTGAATGTGAAAGTGTATGTATA 1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATGTATA 43910475 TGTGATAAGGCCTAATGGC 1 TGTGATAAGGCCTAATGGC 43910494 TAATGTAAAA Statistics Matches: 160, Mismatches: 6, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 49 160 1.00 ACGTcount: A:0.29, C:0.09, G:0.33, T:0.29 Consensus pattern (49 bp): TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATGTATA Found at i:43910652 original size:37 final size:37 Alignment explanation

Indices: 43910595--43910715 Score: 217 Period size: 37 Copynumber: 3.3 Consensus size: 37 43910585 GGAATATGTT * 43910595 CCGGGTGAGA-CCGATGACTACGTGTGGAGATTATGA 1 CCGGGTAAGACCCGATGACTACGTGTGGAGATTATGA 43910631 CCGGGTAAGACCCGATGACTACGTGTGGAGATTATGA 1 CCGGGTAAGACCCGATGACTACGTGTGGAGATTATGA * 43910668 CCGGGTAAGACCCGATGACTACGTGTGGAGATTATGT 1 CCGGGTAAGACCCGATGACTACGTGTGGAGATTATGA 43910705 CCGGGTAAGAC 1 CCGGGTAAGAC 43910716 TTCTTTTATA Statistics Matches: 82, Mismatches: 2, Indels: 1 0.96 0.02 0.01 Matches are distributed among these distances: 36 9 0.11 37 73 0.89 ACGTcount: A:0.26, C:0.19, G:0.34, T:0.21 Consensus pattern (37 bp): CCGGGTAAGACCCGATGACTACGTGTGGAGATTATGA Found at i:43912810 original size:29 final size:29 Alignment explanation

Indices: 43912768--43912931 Score: 310 Period size: 29 Copynumber: 5.7 Consensus size: 29 43912758 GCGAATGATT 43912768 GAGGCACTATGTGTGCGAGATCAGTAATC 1 GAGGCACTATGTGTGCGAGATCAGTAATC 43912797 GAGGCACTATGTGTGCGAGATCAGTAATC 1 GAGGCACTATGTGTGCGAGATCAGTAATC 43912826 GAGGCACTATGTGTGCGAGATCAGTAATC 1 GAGGCACTATGTGTGCGAGATCAGTAATC 43912855 GAGGCACTATGTGTGCGAGATCAGTAATC 1 GAGGCACTATGTGTGCGAGATCAGTAATC * 43912884 GAGGCACTATGTGTGCGAGATCAGTAATT 1 GAGGCACTATGTGTGCGAGATCAGTAATC * 43912913 GAGGCACTGTGTGTGCGAG 1 GAGGCACTATGTGTGCGAG 43912932 TTTTTCAACA Statistics Matches: 133, Mismatches: 2, Indels: 0 0.99 0.01 0.00 Matches are distributed among these distances: 29 133 1.00 ACGTcount: A:0.26, C:0.16, G:0.33, T:0.24 Consensus pattern (29 bp): GAGGCACTATGTGTGCGAGATCAGTAATC Found at i:43913511 original size:40 final size:41 Alignment explanation

Indices: 43913413--43913511 Score: 114 Period size: 41 Copynumber: 2.4 Consensus size: 41 43913403 TTCGAATGGT * ** * * 43913413 ATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGTTACTAA 1 ATCCGGGCTATGTCCCGAAGGCAATTGTGCGAAGTAACTAA 43913454 ATCCGGGCTAAT-TCCCGAAGGCAATTGTGCGAA-TAACTATA 1 ATCCGGGCT-ATGTCCCGAAGGCAATTGTGCGAAGTAACTA-A 43913495 A-CCGGGCTATGTCCCGA 1 ATCCGGGCTATGTCCCGA 43913512 GGACAATCGA Statistics Matches: 50, Mismatches: 5, Indels: 7 0.81 0.08 0.11 Matches are distributed among these distances: 39 2 0.04 40 18 0.36 41 29 0.58 42 1 0.02 ACGTcount: A:0.26, C:0.24, G:0.24, T:0.25 Consensus pattern (41 bp): ATCCGGGCTATGTCCCGAAGGCAATTGTGCGAAGTAACTAA Found at i:43916287 original size:49 final size:49 Alignment explanation

Indices: 43916231--43916445 Score: 376 Period size: 49 Copynumber: 4.4 Consensus size: 49 43916221 TACATATATG * * * 43916231 TGTGATAAGGCCGAATGGCCAATGCGATGAATGTGAAAGTGTATGTATA 1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATGTATA 43916280 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATGTATA 1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATGTATA * * 43916329 TGTGATGAGGCCTAATGGCCGATGTGGTGAATGTGAAAGTGTATGTATA 1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATGTATA * 43916378 TGTGATAAGGCCTAATGGCCGATGTGGTGAATGTGAAAGTGTATGTATA 1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATGTATA 43916427 TGTGATAAGGCCTAATGGC 1 TGTGATAAGGCCTAATGGC 43916446 TAATGTAAAA Statistics Matches: 160, Mismatches: 6, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 49 160 1.00 ACGTcount: A:0.29, C:0.09, G:0.32, T:0.29 Consensus pattern (49 bp): TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATGTATA Found at i:43916597 original size:37 final size:37 Alignment explanation

Indices: 43916547--43916668 Score: 226 Period size: 37 Copynumber: 3.3 Consensus size: 37 43916537 GGAATATGTT * 43916547 CCGGGTGAGACCCGATGACTACGTGTGGAGATTATGA 1 CCGGGTAAGACCCGATGACTACGTGTGGAGATTATGA 43916584 CCGGGTAAGACCCGATGACTACGTGTGGAGATTATGA 1 CCGGGTAAGACCCGATGACTACGTGTGGAGATTATGA * 43916621 CCGGGTAAGACCCGATGACTACGTGTGGAGATTATGT 1 CCGGGTAAGACCCGATGACTACGTGTGGAGATTATGA 43916658 CCGGGTAAGAC 1 CCGGGTAAGAC 43916669 TTCTTTATAA Statistics Matches: 83, Mismatches: 2, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 37 83 1.00 ACGTcount: A:0.25, C:0.20, G:0.34, T:0.21 Consensus pattern (37 bp): CCGGGTAAGACCCGATGACTACGTGTGGAGATTATGA Found at i:43918060 original size:40 final size:40 Alignment explanation

Indices: 43917933--43918062 Score: 174 Period size: 40 Copynumber: 3.2 Consensus size: 40 43917923 ATGCTGGAAA * * 43917933 TTATATCCGGGTTAAGACCCGAAGGCAATT-GTGCTAGTGG 1 TTATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTGG * * * 43917973 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCG 1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGG * 43918013 TTCTATCCGGGCTAAGACCCGAAGGCATTCGTGC-ACGTGG 1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGA-GTGG 43918053 TTATATCCGG 1 TTATATCCGG 43918063 TTGTATTCCG Statistics Matches: 78, Mismatches: 10, Indels: 4 0.85 0.11 0.04 Matches are distributed among these distances: 39 4 0.05 40 74 0.95 ACGTcount: A:0.22, C:0.25, G:0.29, T:0.24 Consensus pattern (40 bp): TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGG Found at i:43925271 original size:40 final size:40 Alignment explanation

Indices: 43925144--43925273 Score: 167 Period size: 40 Copynumber: 3.2 Consensus size: 40 43925134 ATGCTGGAAA * 43925144 TTATATCCGGGTTAAGACCCGAAGGCAATT-GTGC-TAGTGG 1 TTATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCAT-GTGG * * * 43925184 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGA-GTCG 1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGC-ATGTGG * 43925224 TTCTATCCGGGCTAAGACCCGAAGGCATTCGTGCATGTGG 1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCATGTGG 43925264 TTATATCCGG 1 TTATATCCGG 43925274 TTGTATTCCG Statistics Matches: 77, Mismatches: 9, Indels: 8 0.82 0.10 0.09 Matches are distributed among these distances: 39 4 0.05 40 73 0.95 ACGTcount: A:0.22, C:0.24, G:0.29, T:0.25 Consensus pattern (40 bp): TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCATGTGG Found at i:43928062 original size:27 final size:27 Alignment explanation

Indices: 43928032--43928085 Score: 65 Period size: 27 Copynumber: 2.0 Consensus size: 27 43928022 GCTGCCAGAG * 43928032 ACAGT-AATTGTGGCAAAGCCACCAGTA 1 ACAGTGAA-TGTGACAAAGCCACCAGTA * * 43928059 ACAGTGAATGTGACATAGTCACCAGTA 1 ACAGTGAATGTGACAAAGCCACCAGTA 43928086 CAGAACTTCC Statistics Matches: 23, Mismatches: 3, Indels: 2 0.82 0.11 0.07 Matches are distributed among these distances: 27 21 0.91 28 2 0.09 ACGTcount: A:0.37, C:0.20, G:0.22, T:0.20 Consensus pattern (27 bp): ACAGTGAATGTGACAAAGCCACCAGTA Found at i:43928290 original size:27 final size:27 Alignment explanation

Indices: 43928226--43928278 Score: 79 Period size: 27 Copynumber: 2.0 Consensus size: 27 43928216 GGGCATAATC * 43928226 GTCATTTTACCATACAGGGGTATTACA 1 GTCATTTTACCATACAGGGGCATTACA * * 43928253 GTCACTTTACCCTACAGGGGCATTAC 1 GTCATTTTACCATACAGGGGCATTAC 43928279 GCTCTTTTTA Statistics Matches: 23, Mismatches: 3, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 27 23 1.00 ACGTcount: A:0.26, C:0.25, G:0.19, T:0.30 Consensus pattern (27 bp): GTCATTTTACCATACAGGGGCATTACA Found at i:43928476 original size:54 final size:54 Alignment explanation

Indices: 43928323--43928617 Score: 245 Period size: 54 Copynumber: 5.4 Consensus size: 54 43928313 TCGCCTACAA * * * ** * * 43928323 GGGTGTTTTGGTAAATCTACAAACCAAAGGTATTTCAGTAATTTTGA-AAACCAA 1 GGGTATTTTGGTAATTTTACAAATTAAAGGTATTTCAGTAATTTT-ACAAATCAG * * * * * * * * * 43928377 TGGTACTTCT-ATAATTTTTAGAAAGTCAAGGGTATTTCCGTAATTTTATAAATTAG 1 GGGTA-TTTTGGTAA-TTTTACAAA-TTAAAGGTATTTCAGTAATTTTACAAATCAG * * * 43928433 GGGTATTTTTGTAATTTTCCAAATTAAAGGTATTTCAGTAATTTTCCAAATCAG 1 GGGTATTTTGGTAATTTTACAAATTAAAGGTATTTCAGTAATTTTACAAATCAG * * * 43928487 GGGTATTTTGGTAATTTTACAAATTAAGGGTTTTTCAGTAATTTTACAAGTC-G 1 GGGTATTTTGGTAATTTTACAAATTAAAGGTATTTCAGTAATTTTACAAATCAG * * * ** * * * * 43928540 AGGGTATTTCGATAATTTTATAGGTTGAGGGTATTTCAGTAATTTCACAAAACAG 1 -GGGTATTTTGGTAATTTTACAAATTAAAGGTATTTCAGTAATTTTACAAATCAG 43928595 GGGTATTTTGGTAATTTTACAAA 1 GGGTATTTTGGTAATTTTACAAA 43928618 CCAGGGGTAT Statistics Matches: 189, Mismatches: 45, Indels: 14 0.76 0.18 0.06 Matches are distributed among these distances: 53 1 0.01 54 137 0.72 55 21 0.11 56 30 0.16 ACGTcount: A:0.32, C:0.09, G:0.19, T:0.40 Consensus pattern (54 bp): GGGTATTTTGGTAATTTTACAAATTAAAGGTATTTCAGTAATTTTACAAATCAG Found at i:43928532 original size:27 final size:27 Alignment explanation

Indices: 43928351--43928617 Score: 180 Period size: 27 Copynumber: 9.8 Consensus size: 27 43928341 ACAAACCAAA ** * 43928351 GGTATTTCAGTAATTTTGA-AAACCAAT 1 GGTATTTCAGTAATTTT-ACAAATTAAG * * * 43928378 GGTACTTCTA-TAATTTTTAGAAAGTCAAG 1 GGTATTTC-AGTAA-TTTTACAAA-TTAAG * * * 43928407 GGTATTTCCGTAATTTTATAAATTAGG 1 GGTATTTCAGTAATTTTACAAATTAAG ** * * 43928434 GGTATTTTTGTAATTTTCCAAATTAAA 1 GGTATTTCAGTAATTTTACAAATTAAG * * * 43928461 GGTATTTCAGTAATTTTCCAAATCAGG 1 GGTATTTCAGTAATTTTACAAATTAAG ** 43928488 GGTATTTTGGTAATTTTACAAATTAAG 1 GGTATTTCAGTAATTTTACAAATTAAG * * ** 43928515 GGTTTTTCAGTAATTTTACAAGTCGAG 1 GGTATTTCAGTAATTTTACAAATTAAG * ** * 43928542 GGTATTTC-GATAATTTTATAGGTTGAG 1 GGTATTTCAG-TAATTTTACAAATTAAG * ** * 43928569 GGTATTTCAGTAATTTCACAAAACAGG 1 GGTATTTCAGTAATTTTACAAATTAAG ** 43928596 GGTATTTTGGTAATTTTACAAA 1 GGTATTTCAGTAATTTTACAAA 43928618 CCAGGGGTAT Statistics Matches: 188, Mismatches: 45, Indels: 14 0.76 0.18 0.06 Matches are distributed among these distances: 26 1 0.01 27 157 0.84 28 17 0.09 29 13 0.07 ACGTcount: A:0.32, C:0.09, G:0.18, T:0.41 Consensus pattern (27 bp): GGTATTTCAGTAATTTTACAAATTAAG Found at i:43928655 original size:27 final size:27 Alignment explanation

Indices: 43928578--43928639 Score: 70 Period size: 27 Copynumber: 2.3 Consensus size: 27 43928568 GGGTATTTCA * * ** 43928578 GTAATTTCACAAAACAGGGGTATTTTG 1 GTAATTTTACAAACCAGAAGTATTTTG ** 43928605 GTAATTTTACAAACCAGGGGTATTTTG 1 GTAATTTTACAAACCAGAAGTATTTTG 43928632 GTAATTTT 1 GTAATTTT 43928640 GTAAATCATA Statistics Matches: 33, Mismatches: 2, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 27 33 1.00 ACGTcount: A:0.31, C:0.10, G:0.21, T:0.39 Consensus pattern (27 bp): GTAATTTTACAAACCAGAAGTATTTTG Found at i:43928726 original size:27 final size:26 Alignment explanation

Indices: 43928653--43928728 Score: 98 Period size: 27 Copynumber: 2.8 Consensus size: 26 43928643 AATCATAAGT * 43928653 ATTCAGTAATTCTACCGTACAAGGGCA 1 ATTCAGTAATTCTACC-TACAGGGGCA * 43928680 TTTCAGTAATTCTACACTACAGGGGCA 1 ATTCAGTAATTCTAC-CTACAGGGGCA * 43928707 ATTCAGTAATACTAGCCTACAG 1 ATTCAGTAATTCTA-CCTACAG 43928729 ATATAAGATT Statistics Matches: 43, Mismatches: 4, Indels: 4 0.84 0.08 0.08 Matches are distributed among these distances: 27 41 0.95 28 2 0.05 ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28 Consensus pattern (26 bp): ATTCAGTAATTCTACCTACAGGGGCA Found at i:43930794 original size:33 final size:33 Alignment explanation

Indices: 43930742--43930851 Score: 166 Period size: 33 Copynumber: 3.3 Consensus size: 33 43930732 AGTGAATAAC * 43930742 ACAGTATCAGTACAGTCTGGGCCAAAGCCCTAT 1 ACAGTATCAGTACAGTCTGGGCCTAAGCCCTAT * * * 43930775 TCAGTATCAATACAATCTGGGCCTAAGCCCTAT 1 ACAGTATCAGTACAGTCTGGGCCTAAGCCCTAT * 43930808 ACAGTATCAGTACAGTCTGGACCTAAGCCCTAT 1 ACAGTATCAGTACAGTCTGGGCCTAAGCCCTAT * 43930841 ACAGTAGCAGT 1 ACAGTATCAGT 43930852 GTAGGCCTAA Statistics Matches: 68, Mismatches: 9, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 33 68 1.00 ACGTcount: A:0.31, C:0.26, G:0.19, T:0.24 Consensus pattern (33 bp): ACAGTATCAGTACAGTCTGGGCCTAAGCCCTAT Found at i:43931276 original size:27 final size:26 Alignment explanation

Indices: 43931246--43931307 Score: 61 Period size: 27 Copynumber: 2.3 Consensus size: 26 43931236 CATTTTTCCA 43931246 TACAAGGGTATTACAGTCACTTTACCC 1 TACAAGGGTATTACAGTCACTTTA-CC * * * * * 43931273 TACAGGGGCATTATAGTGATTTTACC 1 TACAAGGGTATTACAGTCACTTTACC * 43931299 TATAAGGGT 1 TACAAGGGT 43931308 GTTTTGGTAA Statistics Matches: 27, Mismatches: 8, Indels: 1 0.75 0.22 0.03 Matches are distributed among these distances: 26 8 0.30 27 19 0.70 ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32 Consensus pattern (26 bp): TACAAGGGTATTACAGTCACTTTACC Done.