Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Chr04 ID=Chr04-JGI_221_v2.0

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: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33

Warning! 912357 characters in sequence are not A, C, G, or T


File 128 of 198

Found at i:40864201 original size:44 final size:44

Alignment explanation

Indices: 40864151--40864244 Score: 134 Period size: 44 Copynumber: 2.1 Consensus size: 44 40864141 AATTCTTGCG * ** 40864151 TCCTTCTTGCCCAATTTCTTGAATTCCCAAATCTGTAAATCGCC 1 TCCTTCTTGCCCAATTTCTTGAAATCCCAAATCCCTAAATCGCC * ** 40864195 TCCTTCTTGCCGAATTTCTTGAAATCTGAAATCCCTAAATCGCC 1 TCCTTCTTGCCCAATTTCTTGAAATCCCAAATCCCTAAATCGCC 40864239 TCCTTC 1 TCCTTC 40864245 CTCCTTCCAG Statistics Matches: 44, Mismatches: 6, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 44 44 1.00 ACGTcount: A:0.22, C:0.32, G:0.10, T:0.36 Consensus pattern (44 bp): TCCTTCTTGCCCAATTTCTTGAAATCCCAAATCCCTAAATCGCC Found at i:40865966 original size:35 final size:35 Alignment explanation

Indices: 40865879--40865959 Score: 144 Period size: 35 Copynumber: 2.3 Consensus size: 35 40865869 TAAAGTTATA * * 40865879 TTTTAAATATTTTATTTTATTTTAATCACGAATTT 1 TTTTAAATATTTTATTTTATTTGAATCACGAATAT 40865914 TTTTAAATATTTTATTTTATTTGAATCACGAATAT 1 TTTTAAATATTTTATTTTATTTGAATCACGAATAT 40865949 TTTTAAATATT 1 TTTTAAATATT 40865960 AAATTTTTTT Statistics Matches: 44, Mismatches: 2, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 35 44 1.00 ACGTcount: A:0.33, C:0.05, G:0.04, T:0.58 Consensus pattern (35 bp): TTTTAAATATTTTATTTTATTTGAATCACGAATAT Found at i:40866009 original size:18 final size:17 Alignment explanation

Indices: 40865978--40866033 Score: 78 Period size: 16 Copynumber: 3.3 Consensus size: 17 40865968 TTAAAGTTCA 40865978 AATTTCATAACTTACGT 1 AATTTCATAACTTACGT * * 40865995 AATTTACATATCTTACAT 1 AATTT-CATAACTTACGT 40866013 AA-TTCATAACTTACGT 1 AATTTCATAACTTACGT 40866029 AATTT 1 AATTT 40866034 AAATTTATAA Statistics Matches: 33, Mismatches: 4, Indels: 4 0.80 0.10 0.10 Matches are distributed among these distances: 16 12 0.36 17 9 0.27 18 12 0.36 ACGTcount: A:0.38, C:0.16, G:0.04, T:0.43 Consensus pattern (17 bp): AATTTCATAACTTACGT Found at i:40866053 original size:29 final size:33 Alignment explanation

Indices: 40865983--40866055 Score: 100 Period size: 34 Copynumber: 2.3 Consensus size: 33 40865973 GTTCAAATTT * 40865983 CATAACTTACGTAATTTACATATCTTACATAATT 1 CATAACTTACGTAATTTACATATCTTA-ATAATA 40866017 CATAACTTACGTAATTTA-A-AT-TT-ATAATA 1 CATAACTTACGTAATTTACATATCTTAATAATA 40866046 CATAACTTAC 1 CATAACTTAC 40866056 ATAACTTATT Statistics Matches: 38, Mismatches: 1, Indels: 5 0.86 0.02 0.11 Matches are distributed among these distances: 29 15 0.39 31 2 0.05 32 2 0.05 33 1 0.03 34 18 0.47 ACGTcount: A:0.41, C:0.16, G:0.03, T:0.40 Consensus pattern (33 bp): CATAACTTACGTAATTTACATATCTTAATAATA Found at i:40866105 original size:19 final size:19 Alignment explanation

Indices: 40866083--40866120 Score: 67 Period size: 19 Copynumber: 2.0 Consensus size: 19 40866073 ATATATAGTT 40866083 TTTATATATATATTTAAAA 1 TTTATATATATATTTAAAA * 40866102 TTTATATATATTTTTAAAA 1 TTTATATATATATTTAAAA 40866121 ATTGATACAT Statistics Matches: 18, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 19 18 1.00 ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55 Consensus pattern (19 bp): TTTATATATATATTTAAAA Found at i:40866175 original size:23 final size:22 Alignment explanation

Indices: 40866125--40866325 Score: 65 Period size: 24 Copynumber: 9.3 Consensus size: 22 40866115 TTAAAAATTG 40866125 ATACATTACATAACTTACATAAC 1 ATACA-TACATAACTTACATAAC * 40866148 CTACATACATAAGCTTACAT--- 1 ATACATACATAA-CTTACATAAC * 40866168 ATA-ATACATAACTTATATAAC 1 ATACATACATAACTTACATAAC * * * * 40866189 TTAAATTTAGCA-ATCATATCATAAC 1 ATACA--TA-CATAACTTA-CATAAC * * 40866214 TTACATACATAA-TTA-GT-A- 1 ATACATACATAACTTACATAAC * * 40866232 AT-CATATCACAATTTACATAACC 1 ATACATA-CATAACTTACATAA-C * 40866255 A-ACATA-ATGACTTACATAATAAC 1 ATACATACATAACTTAC---ATAAC * * 40866278 CTACATA-ATAACTTACATAATA 1 ATACATACATAACTTACATAA-C 40866300 ATACATA-ATAA--TACATAAC 1 ATACATACATAACTTACATAAC 40866319 ATACATA 1 ATACATA 40866326 AATTAAATAA Statistics Matches: 134, Mismatches: 22, Indels: 48 0.66 0.11 0.24 Matches are distributed among these distances: 17 4 0.03 18 11 0.08 19 19 0.14 20 11 0.08 21 13 0.10 22 22 0.16 23 20 0.15 24 23 0.17 25 11 0.08 ACGTcount: A:0.48, C:0.18, G:0.02, T:0.31 Consensus pattern (22 bp): ATACATACATAACTTACATAAC Found at i:40866212 original size:34 final size:31 Alignment explanation

Indices: 40866142--40866251 Score: 89 Period size: 31 Copynumber: 3.4 Consensus size: 31 40866132 ACATAACTTA * * 40866142 CATAACCTACATACATAAGCTTA-CATATAATA- 1 CATAACTTACATACATAA--TTAGCA-ATCATAT * * 40866174 CATAACTTATATAACTTAAATTTAGCAATCATAT 1 CATAACTTACAT-ACAT-AA-TTAGCAATCATAT * 40866208 CATAACTTACATACATAATTAGTAATCATAT 1 CATAACTTACATACATAATTAGCAATCATAT * * 40866239 CACAATTTACATA 1 CATAACTTACATA 40866252 ACCAACATAA Statistics Matches: 64, Mismatches: 10, Indels: 9 0.77 0.12 0.11 Matches are distributed among these distances: 31 23 0.36 32 12 0.19 33 14 0.22 34 15 0.23 ACGTcount: A:0.45, C:0.18, G:0.03, T:0.34 Consensus pattern (31 bp): CATAACTTACATACATAATTAGCAATCATAT Found at i:40866273 original size:12 final size:12 Alignment explanation

Indices: 40866256--40866310 Score: 78 Period size: 12 Copynumber: 4.8 Consensus size: 12 40866246 TACATAACCA * 40866256 ACATAATGACTT 1 ACATAATAACTT * 40866268 ACATAATAACCT 1 ACATAATAACTT 40866280 ACATAATAACTT 1 ACATAATAACTT 40866292 ACATAATAA--T 1 ACATAATAACTT 40866302 ACATAATAA 1 ACATAATAA 40866311 TACATAACAT Statistics Matches: 40, Mismatches: 3, Indels: 2 0.89 0.07 0.04 Matches are distributed among these distances: 10 10 0.25 12 30 0.75 ACGTcount: A:0.53, C:0.16, G:0.02, T:0.29 Consensus pattern (12 bp): ACATAATAACTT Found at i:40866283 original size:24 final size:24 Alignment explanation

Indices: 40866249--40866317 Score: 92 Period size: 24 Copynumber: 3.0 Consensus size: 24 40866239 CACAATTTAC * * 40866249 ATAACCAACATAATGACTTACATA 1 ATAACCTACATAATAACTTACATA 40866273 ATAACCTACATAATAACTTACATA 1 ATAACCTACATAATAACTTACATA 40866297 ATAA--TACATAATAA--TACATA 1 ATAACCTACATAATAACTTACATA 40866317 A 1 A 40866318 CATACATAAA Statistics Matches: 43, Mismatches: 2, Indels: 4 0.88 0.04 0.08 Matches are distributed among these distances: 20 7 0.16 22 10 0.23 24 26 0.60 ACGTcount: A:0.54, C:0.17, G:0.01, T:0.28 Consensus pattern (24 bp): ATAACCTACATAATAACTTACATA Found at i:40866306 original size:10 final size:10 Alignment explanation

Indices: 40866267--40866326 Score: 68 Period size: 12 Copynumber: 5.7 Consensus size: 10 40866257 CATAATGACT 40866267 TACATAATAA 1 TACATAATAA 40866277 CCTACATAATAA 1 --TACATAATAA 40866289 CTTACATAATAA 1 --TACATAATAA 40866301 TACATAATAA 1 TACATAATAA * 40866311 TACATAA-CA 1 TACATAATAA 40866320 TACATAA 1 TACATAA 40866327 ATTAAATAAG Statistics Matches: 46, Mismatches: 2, Indels: 3 0.90 0.04 0.06 Matches are distributed among these distances: 9 8 0.17 10 17 0.37 12 21 0.46 ACGTcount: A:0.55, C:0.17, G:0.00, T:0.28 Consensus pattern (10 bp): TACATAATAA Found at i:40866310 original size:34 final size:34 Alignment explanation

Indices: 40866267--40866411 Score: 91 Period size: 34 Copynumber: 4.2 Consensus size: 34 40866257 CATAATGACT 40866267 TACATAATAACCTACATAATAACTTACATAATAA 1 TACATAATAACCTACATAATAACTTACATAATAA * * * 40866301 TACATAATAA--TACATAACATACATAAATTAAATAA 1 TACATAATAACCTACATAATA-ACTTACA-T-AATAA ** * * * * 40866336 GTTACATAATACACAAAAACAAAAACTTACATAA-AT 1 --TACATAATA-ACCTACATAATAACTTACATAATAA * ** 40866372 TACATAATATCCTACATCCCT-ACTTACATAATAA 1 TACATAATAACCTACAT-AATAACTTACATAATAA 40866406 TACATA 1 TACATA 40866412 CCGTACATAA Statistics Matches: 82, Mismatches: 19, Indels: 20 0.68 0.16 0.17 Matches are distributed among these distances: 32 8 0.10 33 18 0.22 34 27 0.33 35 5 0.06 36 1 0.01 37 11 0.13 38 2 0.02 39 5 0.06 40 5 0.06 ACGTcount: A:0.53, C:0.18, G:0.01, T:0.28 Consensus pattern (34 bp): TACATAATAACCTACATAATAACTTACATAATAA Found at i:40866376 original size:9 final size:9 Alignment explanation

Indices: 40866285--40866378 Score: 52 Period size: 9 Copynumber: 10.4 Consensus size: 9 40866275 AACCTACATA * 40866285 ATAACTTAC 1 ATAAATTAC * 40866294 ATAATAATAC 1 ATAA-ATTAC * 40866304 ATAATAATAC 1 ATAA-ATTAC 40866314 ATAACA-TAC 1 ATAA-ATTAC * 40866323 ATAAATTAA 1 ATAAATTAC * 40866332 ATAAGTTAC 1 ATAAATTAC 40866341 AT-AA-TAC 1 ATAAATTAC * * 40866348 ACAAA-AAC 1 ATAAATTAC * 40866356 AAAAACTTAC 1 ATAAA-TTAC 40866366 ATAAATTAC 1 ATAAATTAC 40866375 ATAA 1 ATAA 40866379 TATCCTACAT Statistics Matches: 68, Mismatches: 12, Indels: 10 0.76 0.13 0.11 Matches are distributed among these distances: 7 4 0.06 8 10 0.15 9 30 0.44 10 24 0.35 ACGTcount: A:0.59, C:0.14, G:0.01, T:0.27 Consensus pattern (9 bp): ATAAATTAC Found at i:40866411 original size:95 final size:95 Alignment explanation

Indices: 40866301--40866707 Score: 595 Period size: 95 Copynumber: 4.5 Consensus size: 95 40866291 TACATAATAA * * 40866301 TACATAATAATACATAACATACATAAATTAAATAAGTTACATAATACACAAAAACAAAAACTTAC 1 TACATAATAATACATACCGTACATAAATTAAATAAGTTACATAATACACAAAAACAAAAACTTAC * 40866366 ATAAATTACATAATATCCTACATCCCTACT 66 ATAACTTACATAATATCCTACATCCCTACT * 40866396 TACATAATAATACATACCGTACATAAATTAAATAAGTTACATAATGCACAAAAACAAAAACTTAC 1 TACATAATAATACATACCGTACATAAATTAAATAAGTTACATAATACACAAAAACAAAAACTTAC 40866461 ATAACTTACATAATATCCTACATCCCTACT 66 ATAACTTACATAATATCCTACATCCCTACT * 40866491 TACATAATAATACATACCGTACATAAATTAAATAAGTAACATAATACACAAAAAC----A---A- 1 TACATAATAATACATACCGTACATAAATTAAATAAGTTACATAATACACAAAAACAAAAACTTAC 40866548 A-AACTTACATAATATCCTACATCCCTACT 66 ATAACTTACATAATATCCTACATCCCTACT * 40866577 TACATAATAATACATACCGTACATAAATTAAATAAGTTACATAATAAACAAAAACAAAAACTTAC 1 TACATAATAATACATACCGTACATAAATTAAATAAGTTACATAATACACAAAAACAAAAACTTAC 40866642 ATAACTTACAT-A-A---T--A-----ACT 66 ATAACTTACATAATATCCTACATCCCTACT * * 40866660 TACATAATAATGCATACCCTACATAAATTAAATAAGTTACATAATACA 1 TACATAATAATACATACCGTACATAAATTAAATAAGTTACATAATACA 40866708 TTGAAGAGTT Statistics Matches: 292, Mismatches: 11, Indels: 30 0.88 0.03 0.09 Matches are distributed among these distances: 83 48 0.16 86 81 0.28 87 1 0.00 88 2 0.01 90 2 0.01 91 1 0.00 93 2 0.01 94 2 0.01 95 153 0.52 ACGTcount: A:0.52, C:0.19, G:0.02, T:0.27 Consensus pattern (95 bp): TACATAATAATACATACCGTACATAAATTAAATAAGTTACATAATACACAAAAACAAAAACTTAC ATAACTTACATAATATCCTACATCCCTACT Found at i:40866419 original size:52 final size:52 Alignment explanation

Indices: 40866363--40866525 Score: 164 Period size: 52 Copynumber: 3.3 Consensus size: 52 40866353 AACAAAAACT * 40866363 TACATAAATTACATAATATCCTACATCCCTACTTACATAATAATACATACCG 1 TACATAAATTAAATAATATCCTACATCCCTACTTACATAATAATACATACCG * ** * * * * * 40866415 TACATAAATTAAATAA-GT--TACAT-AATGC--ACA-AA-AACA-AAAACT 1 TACATAAATTAAATAATATCCTACATCCCTACTTACATAATAATACATACCG * * 40866458 TACATAACTTACATAATATCCTACATCCCTACTTACATAATAATACATACCG 1 TACATAAATTAAATAATATCCTACATCCCTACTTACATAATAATACATACCG 40866510 TACATAAATTAAATAA 1 TACATAAATTAAATAA 40866526 GTAACATAAT Statistics Matches: 81, Mismatches: 21, Indels: 18 0.68 0.17 0.15 Matches are distributed among these distances: 43 17 0.21 44 4 0.05 45 2 0.02 46 8 0.10 47 2 0.02 48 2 0.02 49 8 0.10 50 2 0.02 51 4 0.05 52 32 0.40 ACGTcount: A:0.48, C:0.21, G:0.02, T:0.29 Consensus pattern (52 bp): TACATAAATTAAATAATATCCTACATCCCTACTTACATAATAATACATACCG Found at i:40866506 original size:181 final size:178 Alignment explanation

Indices: 40866285--40866707 Score: 572 Period size: 181 Copynumber: 2.4 Consensus size: 178 40866275 AACCTACATA 40866285 ATAACTTACATAATAA--TACATAATAATACATAACATACATAAATTAAATAAGTTACATAATAC 1 ATAACTTACATAATAACCTACATAATAATACATAACATACATAAATTAAATAAGTTACATAATAC 40866348 ACA-AA-A-ACAAAAACTTACATAAA-TTACATAATATCCTACATCCCTACTTACATAATAATAC 66 ACATAATACACAAAAAC--A-A-AAACTTACATAATATCCTACATCCCTACTTACATAATAATAC ** 40866409 ATACCGTACATAAATTAAATAAGTTACATAATGCACAAAAACAAAAACTTAC 127 ATACCGTACATAAATTAAATAAGTTACATAATAAACAAAAACAAAAACTTAC * ** * * *** * * * 40866461 ATAACTTACATAATATCCTACATCCCTACTTACATAATAATACATACCGTACATAAATTAAATAA 1 ATAACTTACATAATAACCTACAT-AATA-ATACATAA-CATACATAAATTAAATAAGTTACATAA 40866526 GTA-ACATAATACACAAAAACAAAAACTTACATAATATCCTACATCCCTACTTACATAATAATAC 63 -TACACATAATACACAAAAACAAAAACTTACATAATATCCTACATCCCTACTTACATAATAATAC 40866590 ATACCGTACATAAATTAAATAAGTTACATAATAAACAAAAACAAAAACTTAC 127 ATACCGTACATAAATTAAATAAGTTACATAATAAACAAAAACAAAAACTTAC * * * * 40866642 ATAACTTACATAATAACTTACATAATAATGCATACCCTACATAAATTAAATAAGTTACATAATAC 1 ATAACTTACATAATAACCTACATAATAATACATAACATACATAAATTAAATAAGTTACATAATAC 40866707 A 66 A 40866708 TTGAAGAGTT Statistics Matches: 208, Mismatches: 28, Indels: 20 0.81 0.11 0.08 Matches are distributed among these distances: 176 15 0.07 177 2 0.01 178 25 0.12 179 7 0.03 180 12 0.06 181 133 0.64 182 5 0.02 183 1 0.00 184 8 0.04 ACGTcount: A:0.52, C:0.19, G:0.02, T:0.27 Consensus pattern (178 bp): ATAACTTACATAATAACCTACATAATAATACATAACATACATAAATTAAATAAGTTACATAATAC ACATAATACACAAAAACAAAAACTTACATAATATCCTACATCCCTACTTACATAATAATACATAC CGTACATAAATTAAATAAGTTACATAATAAACAAAAACAAAAACTTAC Found at i:40866618 original size:37 final size:37 Alignment explanation

Indices: 40866576--40866705 Score: 109 Period size: 37 Copynumber: 3.3 Consensus size: 37 40866566 ACATCCCTAC * 40866576 TTACATAATAATACATACCGTACATAAATTAAATAAG 1 TTACATAATAATACATACCCTACATAAATTAAATAAG * * * * 40866613 TTACATAATAA-ACAAAAACAAAAACTTACATAACTTACATAATAAC 1 TTACATAATAATAC--ATAC-----CCTACATAAATT--A-AATAAG * 40866659 TTACATAATAATGCATACCCTACATAAATTAAATAAG 1 TTACATAATAATACATACCCTACATAAATTAAATAAG 40866696 TTACATAATA 1 TTACATAATA 40866706 CATTGAAGAG Statistics Matches: 73, Mismatches: 9, Indels: 22 0.70 0.09 0.21 Matches are distributed among these distances: 36 2 0.03 37 26 0.36 38 4 0.05 40 10 0.14 43 10 0.14 45 4 0.05 46 16 0.22 47 1 0.01 ACGTcount: A:0.53, C:0.15, G:0.03, T:0.28 Consensus pattern (37 bp): TTACATAATAATACATACCCTACATAAATTAAATAAG Found at i:40866659 original size:12 final size:12 Alignment explanation

Indices: 40866642--40866669 Score: 56 Period size: 12 Copynumber: 2.3 Consensus size: 12 40866632 AAAAACTTAC 40866642 ATAACTTACATA 1 ATAACTTACATA 40866654 ATAACTTACATA 1 ATAACTTACATA 40866666 ATAA 1 ATAA 40866670 TGCATACCCT Statistics Matches: 16, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 12 16 1.00 ACGTcount: A:0.54, C:0.14, G:0.00, T:0.32 Consensus pattern (12 bp): ATAACTTACATA Found at i:40870610 original size:21 final size:21 Alignment explanation

Indices: 40870584--40870652 Score: 93 Period size: 21 Copynumber: 3.3 Consensus size: 21 40870574 CAACAACTTA ** * 40870584 AAGCAGAGGCGGCAGCGAGGG 1 AAGCAGAGGCCACAGCGAGAG * * 40870605 AAGCAGATGCTACAGCGAGAG 1 AAGCAGAGGCCACAGCGAGAG 40870626 AAGCAGAGGCCACAGCGAGAG 1 AAGCAGAGGCCACAGCGAGAG 40870647 AAGCAG 1 AAGCAG 40870653 CGATAGAAGC Statistics Matches: 42, Mismatches: 6, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 21 42 1.00 ACGTcount: A:0.36, C:0.20, G:0.41, T:0.03 Consensus pattern (21 bp): AAGCAGAGGCCACAGCGAGAG Found at i:40871192 original size:43 final size:42 Alignment explanation

Indices: 40871091--40871231 Score: 144 Period size: 42 Copynumber: 3.3 Consensus size: 42 40871081 TTTGTGAAAT * * * * 40871091 AAGCGCCGCTAAATAACACTACTATTAGCGGCGTTTTTGAAC 1 AAGCGCCGCTAAAGAACATTACTTTTAGCGGCGTTTTTCAAC * * 40871133 AAGCGCCGCTATAGAACATTACTTTTAGCGGCGTTTTCTC-CC 1 AAGCGCCGCTAAAGAACATTACTTTTAGCGGCGTTTT-TCAAC * * 40871175 AAAGCGCCGCTAAAGAACATGA-TCTTTAGCGGCGTTTTTTC-AT 1 -AAGCGCCGCTAAAGAACATTACT-TTTAGCGGCG-TTTTTCAAC * 40871218 AAGCGCCGCAAAAG 1 AAGCGCCGCTAAAG 40871232 TTAGCGACGT Statistics Matches: 84, Mismatches: 11, Indels: 8 0.82 0.11 0.08 Matches are distributed among these distances: 42 48 0.57 43 32 0.38 44 4 0.05 ACGTcount: A:0.28, C:0.25, G:0.21, T:0.26 Consensus pattern (42 bp): AAGCGCCGCTAAAGAACATTACTTTTAGCGGCGTTTTTCAAC Found at i:40871378 original size:16 final size:16 Alignment explanation

Indices: 40871343--40871385 Score: 59 Period size: 16 Copynumber: 2.7 Consensus size: 16 40871333 TGGTGTAGTG * ** 40871343 TCTATTCTATTACAGT 1 TCTATTCCATTACAAC 40871359 TCTATTCCATTACAAC 1 TCTATTCCATTACAAC 40871375 TCTATTCCATT 1 TCTATTCCATT 40871386 CCTCCAACAA Statistics Matches: 24, Mismatches: 3, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 16 24 1.00 ACGTcount: A:0.26, C:0.26, G:0.02, T:0.47 Consensus pattern (16 bp): TCTATTCCATTACAAC Found at i:40875870 original size:13 final size:13 Alignment explanation

Indices: 40875852--40875882 Score: 53 Period size: 13 Copynumber: 2.4 Consensus size: 13 40875842 GGCTCAACCC 40875852 ATATATATTAAAT 1 ATATATATTAAAT * 40875865 ATATATATTTAAT 1 ATATATATTAAAT 40875878 ATATA 1 ATATA 40875883 ATTCGGGCTA Statistics Matches: 17, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 13 17 1.00 ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48 Consensus pattern (13 bp): ATATATATTAAAT Found at i:40877058 original size:19 final size:19 Alignment explanation

Indices: 40876999--40877059 Score: 61 Period size: 19 Copynumber: 3.1 Consensus size: 19 40876989 ATTTTCGAGG * * 40876999 ATATACAATCTTA-AATAT 1 ATATGCAATCTTAGAAGAT * 40877017 GATATGCATTCTTAGATATGAT 1 -ATATGCAATCTTAGA-A-GAT 40877039 ATATGCAATCTTAGAAGAT 1 ATATGCAATCTTAGAAGAT 40877058 AT 1 AT 40877060 GATTTTGTAA Statistics Matches: 35, Mismatches: 4, Indels: 6 0.78 0.09 0.13 Matches are distributed among these distances: 19 16 0.46 20 2 0.06 21 15 0.43 22 2 0.06 ACGTcount: A:0.41, C:0.10, G:0.11, T:0.38 Consensus pattern (19 bp): ATATGCAATCTTAGAAGAT Found at i:40878119 original size:25 final size:23 Alignment explanation

Indices: 40878052--40878131 Score: 74 Period size: 21 Copynumber: 3.3 Consensus size: 23 40878042 AATCATTATT * 40878052 TTTTATGTATATATGT-AA-TTA 1 TTTTATATATATATGTAAATTTA 40878073 TTTTATATATATATGTACAAATTTA 1 TTTTATATATATATGT--AAATTTA * * 40878098 TTATATATATGTATATGTAAATATA 1 TT-T-TATATATATATGTAAATTTA 40878123 TTGTTATAT 1 TT-TTATAT 40878132 TTTTTAAAAT Statistics Matches: 49, Mismatches: 4, Indels: 9 0.79 0.06 0.15 Matches are distributed among these distances: 21 15 0.31 24 7 0.14 25 14 0.29 26 1 0.02 27 12 0.24 ACGTcount: A:0.38, C:0.01, G:0.07, T:0.54 Consensus pattern (23 bp): TTTTATATATATATGTAAATTTA Found at i:40879660 original size:29 final size:30 Alignment explanation

Indices: 40879601--40879658 Score: 89 Period size: 30 Copynumber: 1.9 Consensus size: 30 40879591 TCCGAGCCTT * 40879601 GGGGCAAAAATGTAATTATGTAAAAGTTTA 1 GGGGCAAAAATGTAATTATGAAAAAGTTTA * * 40879631 GGGGCAAAATTGTAATTTTGAAAAAGTT 1 GGGGCAAAAATGTAATTATGAAAAAGTT 40879659 AGAGTCAAGG Statistics Matches: 25, Mismatches: 3, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 30 25 1.00 ACGTcount: A:0.41, C:0.03, G:0.24, T:0.31 Consensus pattern (30 bp): GGGGCAAAAATGTAATTATGAAAAAGTTTA Found at i:40879888 original size:13 final size:13 Alignment explanation

Indices: 40879870--40879901 Score: 55 Period size: 13 Copynumber: 2.5 Consensus size: 13 40879860 TTTCCAGCAA 40879870 TTATGAATTTATT 1 TTATGAATTTATT 40879883 TTATGAATTTATT 1 TTATGAATTTATT * 40879896 TGATGA 1 TTATGA 40879902 TGATCCAAGC Statistics Matches: 18, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 13 18 1.00 ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56 Consensus pattern (13 bp): TTATGAATTTATT Found at i:40880107 original size:50 final size:50 Alignment explanation

Indices: 40879996--40880244 Score: 318 Period size: 50 Copynumber: 4.8 Consensus size: 50 40879986 ATTTGGGTAA * 40879996 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATG 1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CC----GA-CATG * * 40880052 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG 1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGACATG * * * 40880102 AGAGGTCCCATGTAAGACCATGTTTGGGTCATGGCATTGGCACCGAGATG 1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGACATG * * * * 40880152 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACCAACATG 1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGACATG ** * 40880202 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA 1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA 40880245 TGTTATTATC Statistics Matches: 173, Mismatches: 19, Indels: 7 0.87 0.10 0.04 Matches are distributed among these distances: 50 95 0.55 51 36 0.21 55 2 0.01 56 40 0.23 ACGTcount: A:0.27, C:0.22, G:0.29, T:0.22 Consensus pattern (50 bp): AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGACATG Found at i:40889293 original size:2 final size:2 Alignment explanation

Indices: 40889286--40889325 Score: 80 Period size: 2 Copynumber: 20.0 Consensus size: 2 40889276 CCCAAGCTGA 40889286 AT AT AT AT 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 AT AT AT AT 40889326 GTCAGTTTAC Statistics Matches: 38, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 38 1.00 ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50 Consensus pattern (2 bp): AT Found at i:40898123 original size:5 final size:6 Alignment explanation

Indices: 40898106--40898130 Score: 50 Period size: 6 Copynumber: 4.2 Consensus size: 6 40898096 GCTATTGGCC 40898106 TCTTTT TCTTTT TCTTTT TCTTTT T 1 TCTTTT TCTTTT TCTTTT TCTTTT T 40898131 GATTCTTGAA Statistics Matches: 19, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 6 19 1.00 ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84 Consensus pattern (6 bp): TCTTTT Found at i:40900607 original size:14 final size:13 Alignment explanation

Indices: 40900588--40900621 Score: 52 Period size: 14 Copynumber: 2.6 Consensus size: 13 40900578 TATATAATTT 40900588 TATATTAATATTAA 1 TATATTAATA-TAA 40900602 TATATTAATATAA 1 TATATTAATATAA 40900615 -ATATTAA 1 TATATTAA 40900622 AATATTATTA Statistics Matches: 20, Mismatches: 0, Indels: 2 0.91 0.00 0.09 Matches are distributed among these distances: 12 7 0.35 13 3 0.15 14 10 0.50 ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47 Consensus pattern (13 bp): TATATTAATATAA Found at i:40900617 original size:20 final size:20 Alignment explanation

Indices: 40900589--40900628 Score: 62 Period size: 20 Copynumber: 2.0 Consensus size: 20 40900579 ATATAATTTT * * 40900589 ATATTAATATTAATATATTA 1 ATATAAATATTAAAATATTA 40900609 ATATAAATATTAAAATATTA 1 ATATAAATATTAAAATATTA 40900629 TTAAAATGTA Statistics Matches: 18, Mismatches: 2, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 20 18 1.00 ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45 Consensus pattern (20 bp): ATATAAATATTAAAATATTA Found at i:40900649 original size:38 final size:44 Alignment explanation

Indices: 40900606--40900710 Score: 116 Period size: 45 Copynumber: 2.5 Consensus size: 44 40900596 TATTAATATA * 40900606 TTAATA-TAAATATTAAAATAT-TAT-TA-A-AA-TGTATACTT 1 TTAATATTAAATATTAAAATATATATCTATATAATTGTATAATT * 40900644 TTAATATTAATATAATAAAATATAATATCTATATAATTGTATAATT 1 TTAATATTAA-ATATTAAAATAT-ATATCTATATAATTGTATAATT 40900690 TT-ATATTAAATATATAAAATA 1 TTAATATTAAATAT-TAAAATA 40900711 ATAAAATATT Statistics Matches: 55, Mismatches: 3, Indels: 11 0.80 0.04 0.16 Matches are distributed among these distances: 38 6 0.11 39 3 0.05 40 11 0.20 42 3 0.05 43 2 0.04 44 4 0.07 45 16 0.29 46 10 0.18 ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45 Consensus pattern (44 bp): TTAATATTAAATATTAAAATATATATCTATATAATTGTATAATT Found at i:40900774 original size:20 final size:20 Alignment explanation

Indices: 40900749--40900790 Score: 68 Period size: 20 Copynumber: 2.1 Consensus size: 20 40900739 AATAATAAAA 40900749 TATATATTTT-TATTAACATT 1 TATATATTTTATATTAA-ATT 40900769 TATATATTTTATATTAAATT 1 TATATATTTTATATTAAATT 40900789 TA 1 TA 40900791 AATAAAAATA Statistics Matches: 21, Mismatches: 0, Indels: 2 0.91 0.00 0.09 Matches are distributed among these distances: 20 15 0.71 21 6 0.29 ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60 Consensus pattern (20 bp): TATATATTTTATATTAAATT Found at i:40912303 original size:18 final size:17 Alignment explanation

Indices: 40912280--40912313 Score: 59 Period size: 17 Copynumber: 1.9 Consensus size: 17 40912270 ACCCGACCCA 40912280 TTTTTAAATTAAAATTAT 1 TTTTTAAA-TAAAATTAT 40912298 TTTTTAAATAAAATTA 1 TTTTTAAATAAAATTA 40912314 AAACTAATTG Statistics Matches: 16, Mismatches: 0, Indels: 1 0.94 0.00 0.06 Matches are distributed among these distances: 17 8 0.50 18 8 0.50 ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53 Consensus pattern (17 bp): TTTTTAAATAAAATTAT Found at i:40912347 original size:16 final size:16 Alignment explanation

Indices: 40912312--40912350 Score: 51 Period size: 16 Copynumber: 2.4 Consensus size: 16 40912302 TAAATAAAAT * * * 40912312 TAAAACTAATTGTTAT 1 TAAAATTAATTGGTAG 40912328 TAAAATTAATTGGTAG 1 TAAAATTAATTGGTAG 40912344 TAAAATT 1 TAAAATT 40912351 TTGAAATTAT Statistics Matches: 20, Mismatches: 3, Indels: 0 0.87 0.13 0.00 Matches are distributed among these distances: 16 20 1.00 ACGTcount: A:0.46, C:0.03, G:0.10, T:0.41 Consensus pattern (16 bp): TAAAATTAATTGGTAG Found at i:40912436 original size:9 final size:9 Alignment explanation

Indices: 40912424--40912466 Score: 72 Period size: 9 Copynumber: 5.0 Consensus size: 9 40912414 TTTATCAAAT 40912424 TATTAATTG 1 TATTAATTG 40912433 TATTAATTG 1 TATTAATTG 40912442 --TTAATTG 1 TATTAATTG 40912449 TATTAATTG 1 TATTAATTG 40912458 TATTAATTG 1 TATTAATTG 40912467 CTAATTTGCT Statistics Matches: 32, Mismatches: 0, Indels: 4 0.89 0.00 0.11 Matches are distributed among these distances: 7 7 0.22 9 25 0.78 ACGTcount: A:0.33, C:0.00, G:0.12, T:0.56 Consensus pattern (9 bp): TATTAATTG Found at i:40912440 original size:16 final size:16 Alignment explanation

Indices: 40912421--40912466 Score: 65 Period size: 16 Copynumber: 2.8 Consensus size: 16 40912411 AAATTTATCA 40912421 AATTATTAATTGTATT 1 AATTATTAATTGTATT * 40912437 AATTGTTAATTGTATT 1 AATTATTAATTGTATT 40912453 AATTGTATTAATTG 1 AA-T-TATTAATTG 40912467 CTAATTTGCT Statistics Matches: 26, Mismatches: 2, Indels: 2 0.87 0.07 0.07 Matches are distributed among these distances: 16 17 0.65 17 1 0.04 18 8 0.31 ACGTcount: A:0.35, C:0.00, G:0.11, T:0.54 Consensus pattern (16 bp): AATTATTAATTGTATT Found at i:40912452 original size:25 final size:25 Alignment explanation

Indices: 40912424--40912472 Score: 89 Period size: 25 Copynumber: 2.0 Consensus size: 25 40912414 TTTATCAAAT * 40912424 TATTAATTGTATTAATTGTTAATTG 1 TATTAATTGTATTAATTGCTAATTG 40912449 TATTAATTGTATTAATTGCTAATT 1 TATTAATTGTATTAATTGCTAATT 40912473 TGCTATAACA Statistics Matches: 23, Mismatches: 1, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 25 23 1.00 ACGTcount: A:0.33, C:0.02, G:0.10, T:0.55 Consensus pattern (25 bp): TATTAATTGTATTAATTGCTAATTG Found at i:40912472 original size:16 final size:16 Alignment explanation

Indices: 40912421--40912458 Score: 67 Period size: 16 Copynumber: 2.4 Consensus size: 16 40912411 AAATTTATCA * 40912421 AATTATTAATTGTATT 1 AATTGTTAATTGTATT 40912437 AATTGTTAATTGTATT 1 AATTGTTAATTGTATT 40912453 AATTGT 1 AATTGT 40912459 ATTAATTGCT Statistics Matches: 21, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 16 21 1.00 ACGTcount: A:0.34, C:0.00, G:0.11, T:0.55 Consensus pattern (16 bp): AATTGTTAATTGTATT Found at i:40916061 original size:14 final size:14 Alignment explanation

Indices: 40916044--40916071 Score: 56 Period size: 14 Copynumber: 2.0 Consensus size: 14 40916034 CTCACATTTC 40916044 TTTTCTTTTCTCCA 1 TTTTCTTTTCTCCA 40916058 TTTTCTTTTCTCCA 1 TTTTCTTTTCTCCA 40916072 GATTTCTGCT Statistics Matches: 14, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 14 14 1.00 ACGTcount: A:0.07, C:0.29, G:0.00, T:0.64 Consensus pattern (14 bp): TTTTCTTTTCTCCA Found at i:40916062 original size:19 final size:18 Alignment explanation

Indices: 40916024--40916068 Score: 58 Period size: 19 Copynumber: 2.5 Consensus size: 18 40916014 TACGATACGC 40916024 TTCTTTTC-TTCTCACAT 1 TTCTTTTCTTTCTCACAT 40916041 TTCTTTTCTTTTCTC-CATT 1 TTCTTTTC-TTTCTCACA-T 40916060 TTCTTTTCT 1 TTCTTTTCT 40916069 CCAGATTTCT Statistics Matches: 25, Mismatches: 0, Indels: 5 0.83 0.00 0.17 Matches are distributed among these distances: 17 8 0.32 18 3 0.12 19 14 0.56 ACGTcount: A:0.07, C:0.27, G:0.00, T:0.67 Consensus pattern (18 bp): TTCTTTTCTTTCTCACAT Found at i:40916141 original size:6 final size:6 Alignment explanation

Indices: 40916132--40916173 Score: 59 Period size: 6 Copynumber: 7.2 Consensus size: 6 40916122 GTAAAATCGA * * 40916132 TTTTGA TTTTG- TTTTGC TTTTGC TTTTGC TTTTGC TTGTGC T 1 TTTTGC TTTTGC TTTTGC TTTTGC TTTTGC TTTTGC TTTTGC T 40916174 CAAATTTGGA Statistics Matches: 34, Mismatches: 1, Indels: 2 0.92 0.03 0.05 Matches are distributed among these distances: 5 5 0.15 6 29 0.85 ACGTcount: A:0.02, C:0.12, G:0.19, T:0.67 Consensus pattern (6 bp): TTTTGC Found at i:40919011 original size:15 final size:15 Alignment explanation

Indices: 40918987--40919027 Score: 50 Period size: 15 Copynumber: 2.8 Consensus size: 15 40918977 AAGCTCTGTG 40918987 ATAT-TTTAATTATA 1 ATATATTTAATTATA * 40919001 ATATATTTAATAATA 1 ATATATTTAATTATA 40919016 AT-TATGTTAATT 1 ATATAT-TTAATT 40919028 TATATTTTAT Statistics Matches: 23, Mismatches: 2, Indels: 3 0.82 0.07 0.11 Matches are distributed among these distances: 14 7 0.30 15 16 0.70 ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54 Consensus pattern (15 bp): ATATATTTAATTATA Found at i:40919131 original size:15 final size:15 Alignment explanation

Indices: 40919096--40919147 Score: 56 Period size: 15 Copynumber: 3.6 Consensus size: 15 40919086 TTAAGAATTT * 40919096 TATTAAATTAT-ATA 1 TATTTAATTATAATA 40919110 T-TTTAATTATAATA 1 TATTTAATTATAATA * 40919124 TATTTAATAATAAT- 1 TATTTAATTATAATA 40919138 TATGTTAATT 1 TAT-TTAATT 40919148 TATATTTTAT Statistics Matches: 32, Mismatches: 3, Indels: 5 0.80 0.08 0.12 Matches are distributed among these distances: 13 8 0.25 14 8 0.25 15 16 0.50 ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54 Consensus pattern (15 bp): TATTTAATTATAATA Found at i:40919200 original size:120 final size:120 Alignment explanation

Indices: 40918987--40919381 Score: 745 Period size: 120 Copynumber: 3.3 Consensus size: 120 40918977 AAGCTCTGTG 40918987 ATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTATAGTATCATATATTA 1 ATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTATAGTATCATATATTA * 40919052 TGATTTGAGTAATTTCATATAAGAATATTGATTATTAAGAATTTTATTAAATTAT 66 TGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATTAT 40919107 ATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTATAGTATCATATATTA 1 ATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTATAGTATCATATATTA * * 40919172 TGATTTGAGTAAATTCATGTAAGAATATTGGTTATTAAGAATTTTATTAAATTAT 66 TGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATTAT 40919227 ATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTATAGTATCATATATTA 1 ATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTATAGTATCATATATTA * 40919292 TGATTTGAGTAATATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTAT 66 TGATTTGAGTAA-ATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATTAT 40919348 ATATTTTAATTATAATATATTTAATAATAATTAT 1 ATATTTTAATTATAATATATTTAATAATAATTAT 40919382 ATTTAAATAT Statistics Matches: 268, Mismatches: 6, Indels: 1 0.97 0.02 0.00 Matches are distributed among these distances: 120 194 0.72 121 74 0.28 ACGTcount: A:0.42, C:0.02, G:0.06, T:0.51 Consensus pattern (120 bp): ATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTATAGTATCATATATTA TGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATTAT Found at i:40919251 original size:15 final size:15 Alignment explanation

Indices: 40919216--40919387 Score: 60 Period size: 15 Copynumber: 11.5 Consensus size: 15 40919206 TTAAGAATTT * 40919216 TATTAAATTAT-ATA 1 TATTTAATTATAATA 40919230 T-TTTAATTATAATA 1 TATTTAATTATAATA * 40919244 TATTTAATAATAAT- 1 TATTTAATTATAATA 40919258 TATGTTAATT-T-ATA 1 TAT-TTAATTATAATA * * 40919272 T-TTTATAGTATCATA 1 TATTTA-ATTATAATA * * 40919287 TATTATGATT-TGAGTA 1 TATT-TAATTAT-AATA * * 40919303 -ATATTCA-TATAAGA 1 TAT-TTAATTATAATA * 40919317 -ATATTAATTATTAAGA 1 TAT-TTAATTA-TAATA * * 40919333 -ATTTTATTAAATTATA 1 TATTTAATT--ATAATA 40919349 TATTTTAATTATAATA 1 TA-TTTAATTATAATA * 40919365 TATTTAATAATAATTA 1 TATTTAATTATAA-TA 40919381 TATTTAA 1 TATTTAA 40919388 ATATGATTAA Statistics Matches: 121, Mismatches: 18, Indels: 36 0.69 0.10 0.21 Matches are distributed among these distances: 12 3 0.02 13 13 0.11 14 20 0.17 15 43 0.36 16 33 0.27 17 3 0.02 18 6 0.05 ACGTcount: A:0.44, C:0.01, G:0.04, T:0.51 Consensus pattern (15 bp): TATTTAATTATAATA Found at i:40919396 original size:16 final size:16 Alignment explanation

Indices: 40919347--40919387 Score: 57 Period size: 16 Copynumber: 2.6 Consensus size: 16 40919337 TATTAAATTA * 40919347 TATATTTTAATTATAA- 1 TATA-TTTAATAATAAT 40919363 TATATTTAATAATAAT 1 TATATTTAATAATAAT 40919379 TATATTTAA 1 TATATTTAA 40919388 ATATGATTAA Statistics Matches: 23, Mismatches: 1, Indels: 2 0.88 0.04 0.08 Matches are distributed among these distances: 15 10 0.43 16 13 0.57 ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54 Consensus pattern (16 bp): TATATTTAATAATAAT Found at i:40919558 original size:39 final size:40 Alignment explanation

Indices: 40919515--40919619 Score: 113 Period size: 44 Copynumber: 2.5 Consensus size: 40 40919505 TTCAATTATG 40919515 CTATTACACCTCTATTCCATTCAACCAAACACAAGA-TTA 1 CTATTACACCTCTATTCCATTCAACCAAACACAAGATTTA * *** * 40919554 CTATTACGCCTCTATTCCATTACATTCAACCAAACAGTTGATTTG 1 CTATTACACCTCTATT-C----CATTCAACCAAACACAAGATTTA 40919599 CTATTACACCTCTATTCCATT 1 CTATTACACCTCTATTCCATT 40919620 ACACCTCTAA Statistics Matches: 54, Mismatches: 6, Indels: 11 0.76 0.08 0.15 Matches are distributed among these distances: 39 15 0.28 40 5 0.09 44 17 0.31 45 17 0.31 ACGTcount: A:0.31, C:0.30, G:0.05, T:0.34 Consensus pattern (40 bp): CTATTACACCTCTATTCCATTCAACCAAACACAAGATTTA Found at i:40919613 original size:45 final size:44 Alignment explanation

Indices: 40919513--40919622 Score: 131 Period size: 45 Copynumber: 2.6 Consensus size: 44 40919503 TTTTCAATTA 40919513 TGCTATTACACCTCTATT-C----CATTCAACCAAACACAAGAT 1 TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGAT * * *** 40919552 TACTATTACGCCTCTATTCCATTACATTCAACCAAACAGTTGATT 1 TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGA-T 40919597 TGCTATTACACCTCTATTCCATTACA 1 TGCTATTACACCTCTATTCCATTACA 40919623 CCTCTAATCC Statistics Matches: 58, Mismatches: 7, Indels: 6 0.82 0.10 0.08 Matches are distributed among these distances: 39 16 0.28 40 1 0.02 44 16 0.28 45 25 0.43 ACGTcount: A:0.32, C:0.29, G:0.05, T:0.34 Consensus pattern (44 bp): TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGAT Found at i:40919622 original size:16 final size:16 Alignment explanation

Indices: 40919601--40919638 Score: 58 Period size: 16 Copynumber: 2.4 Consensus size: 16 40919591 TTGATTTGCT * 40919601 ATTACACCTCTATTCC 1 ATTACACCTCTAATCC 40919617 ATTACACCTCTAATCC 1 ATTACACCTCTAATCC * 40919633 AATACA 1 ATTACA 40919639 GCGAACCAAA Statistics Matches: 20, Mismatches: 2, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 16 20 1.00 ACGTcount: A:0.34, C:0.34, G:0.00, T:0.32 Consensus pattern (16 bp): ATTACACCTCTAATCC Found at i:40919777 original size:21 final size:21 Alignment explanation

Indices: 40919751--40919794 Score: 52 Period size: 21 Copynumber: 2.0 Consensus size: 21 40919741 GAATCTGTTC 40919751 TATATAATAATATAATAATATAT 1 TATATAAT-AT-TAATAATATAT * * 40919774 TATATATTATTTATAATATAT 1 TATATAATATTAATAATATAT 40919795 ACAACAATCA Statistics Matches: 19, Mismatches: 2, Indels: 2 0.83 0.09 0.09 Matches are distributed among these distances: 21 10 0.53 22 2 0.11 23 7 0.37 ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50 Consensus pattern (21 bp): TATATAATATTAATAATATAT Found at i:40920238 original size:23 final size:23 Alignment explanation

Indices: 40920207--40920285 Score: 67 Period size: 23 Copynumber: 3.4 Consensus size: 23 40920197 ATCAGTCTTT 40920207 TAAATTAATAACTTTAATTTGCTA 1 TAAA-TAATAACTTTAATTTGCTA ** 40920231 TAAATAATATA-TAGAATTT--TA 1 TAAATAATA-ACTTTAATTTGCTA * 40920252 -AATTAATAACTCTTTAATTTGCTA 1 TAAATAATAA--CTTTAATTTGCTA 40920276 TAAATAATAA 1 TAAATAATAA 40920286 AAATTGTACT Statistics Matches: 42, Mismatches: 6, Indels: 13 0.69 0.10 0.21 Matches are distributed among these distances: 19 1 0.02 20 7 0.17 21 2 0.05 22 6 0.14 23 11 0.26 24 7 0.17 25 8 0.19 ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43 Consensus pattern (23 bp): TAAATAATAACTTTAATTTGCTA Found at i:40921288 original size:2 final size:2 Alignment explanation

Indices: 40921281--40921312 Score: 64 Period size: 2 Copynumber: 16.0 Consensus size: 2 40921271 ATGGAAGGGA 40921281 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 40921313 TTCAACAACA 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:40922787 original size:31 final size:33 Alignment explanation

Indices: 40922752--40922821 Score: 90 Period size: 31 Copynumber: 2.1 Consensus size: 33 40922742 TTTTCTAAAT * 40922752 GGGCCTAAATTTTTGCCC-AA-TCCCATATTTC 1 GGGCCTAAATTTTTACCCGAACTCCCATATTTC * 40922783 GGGCCTATATTTTTACCCGAACCCTCCCATATTTC 1 GGGCCTAAATTTTTACCCGAA--CTCCCATATTTC 40922818 GGGC 1 GGGC 40922822 GGGCCGTCGG Statistics Matches: 33, Mismatches: 2, Indels: 4 0.85 0.05 0.10 Matches are distributed among these distances: 31 16 0.48 32 2 0.06 35 15 0.45 ACGTcount: A:0.20, C:0.31, G:0.16, T:0.33 Consensus pattern (33 bp): GGGCCTAAATTTTTACCCGAACTCCCATATTTC Found at i:40927556 original size:24 final size:25 Alignment explanation

Indices: 40927492--40927562 Score: 81 Period size: 25 Copynumber: 2.9 Consensus size: 25 40927482 GAAGCTTGCA * * * * 40927492 AGAGCCATATAATGGGAAGCTCGTG 1 AGAGCCAAATAACGGGATGCTCATG * 40927517 AGAGCCAAATATCGGGATGCTCATG 1 AGAGCCAAATAACGGGATGCTCATG * 40927542 AGAG-CTAATAACGGGATGCTC 1 AGAGCCAAATAACGGGATGCTC 40927563 TTTCGAGCTG Statistics Matches: 39, Mismatches: 7, Indels: 1 0.83 0.15 0.02 Matches are distributed among these distances: 24 15 0.38 25 24 0.62 ACGTcount: A:0.32, C:0.18, G:0.30, T:0.20 Consensus pattern (25 bp): AGAGCCAAATAACGGGATGCTCATG Found at i:40931435 original size:44 final size:45 Alignment explanation

Indices: 40931362--40931448 Score: 158 Period size: 44 Copynumber: 2.0 Consensus size: 45 40931352 CTATTTTTAG 40931362 TTTCTCACTTAAACTCTGATTAGTATAGGTTATTTTAATATTAAT 1 TTTCTCACTTAAACTCTGATTAGTATAGGTTATTTTAATATTAAT * 40931407 TTTC-CACTTAAACTCTGATTAGTGTAGGTTATTTTAATATTA 1 TTTCTCACTTAAACTCTGATTAGTATAGGTTATTTTAATATTA 40931449 TTTGACCTAC Statistics Matches: 41, Mismatches: 1, Indels: 1 0.95 0.02 0.02 Matches are distributed among these distances: 44 37 0.90 45 4 0.10 ACGTcount: A:0.30, C:0.11, G:0.10, T:0.48 Consensus pattern (45 bp): TTTCTCACTTAAACTCTGATTAGTATAGGTTATTTTAATATTAAT Found at i:40933506 original size:11 final size:11 Alignment explanation

Indices: 40933490--40933523 Score: 52 Period size: 11 Copynumber: 3.1 Consensus size: 11 40933480 AAAATTGATG 40933490 AATAATGACAA 1 AATAATGACAA 40933501 AATAATGA-AA 1 AATAATGACAA 40933511 ATATAATGACAA 1 A-ATAATGACAA 40933523 A 1 A 40933524 CTTTGTAATT Statistics Matches: 21, Mismatches: 0, Indels: 3 0.88 0.00 0.12 Matches are distributed among these distances: 10 3 0.14 11 15 0.71 12 3 0.14 ACGTcount: A:0.65, C:0.06, G:0.09, T:0.21 Consensus pattern (11 bp): AATAATGACAA Found at i:40938261 original size:4 final size:4 Alignment explanation

Indices: 40938252--40938277 Score: 52 Period size: 4 Copynumber: 6.5 Consensus size: 4 40938242 AGAAACGCAC 40938252 AATA AATA AATA AATA AATA AATA AA 1 AATA AATA AATA AATA AATA AATA AA 40938278 CCAAAAATGG Statistics Matches: 22, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 4 22 1.00 ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23 Consensus pattern (4 bp): AATA Found at i:40939060 original size:45 final size:44 Alignment explanation

Indices: 40939026--40939365 Score: 116 Period size: 44 Copynumber: 7.8 Consensus size: 44 40939016 TTCGCTGTTG * * * 40939026 TCAATCTGC-CCTACTGCAACTTCAGGGGGATAAGACTTGCTTTC 1 TCAATCTGCTCC-ACTACAACCTCAGGGAGATAAGACTTGCTTTC * * * * 40939070 TCAGTCTGCTCCACTACAACCTCAGGGAGATAAGACCTG--ATG 1 TCAATCTGCTCCACTACAACCTCAGGGAGATAAGACTTGCTTTC * * ** * * * 40939112 T-GATCTACTCTGC-GCAACTTCAGAGAGATAAGATCTAT--TATT- 1 TCAATCTGCTCCACTACAACCTCAGGGAGATAAGA-CT-TGCT-TTC ** * * ** * 40939154 TCAATCCACTCCACTGCAACTTCAGGGAGATAAGA-TTTATTAC 1 TCAATCTGCTCCACTACAACCTCAGGGAGATAAGACTTGCTTTC * * * * * * 40939197 TTTAATCCGCTCCACTACAACTTCAGGGAGATAGGA-TT-ATTGGC 1 -TCAATCTGCTCCACTACAACCTCAGGGAGATAAGACTTGCTT-TC * * * * 40939241 TTCAATTTGCTCCACTGCAACCTCAAGGAGATAAGATTATCGGC--T- 1 -TCAATCTGCTCCACTACAACCTCAGGGAGATAAGACT-T--GCTTTC * * * 40939286 TCAATCTACTCCACTGCAACCTCAGGGAGATAAGATTTGC-TTC 1 TCAATCTGCTCCACTACAACCTCAGGGAGATAAGACTTGCTTTC ** * ** * 40939329 TTCGGTCTGCTCCGCTGGAACCTCAGGGAAATAAGAC 1 -TCAATCTGCTCCACTACAACCTCAGGGAGATAAGAC 40939366 CTGATGCGAT Statistics Matches: 229, Mismatches: 47, Indels: 40 0.72 0.15 0.13 Matches are distributed among these distances: 40 17 0.07 41 11 0.05 42 7 0.03 43 14 0.06 44 176 0.77 45 3 0.01 46 1 0.00 ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28 Consensus pattern (44 bp): TCAATCTGCTCCACTACAACCTCAGGGAGATAAGACTTGCTTTC Found at i:40939177 original size:44 final size:43 Alignment explanation

Indices: 40939125--40939451 Score: 228 Period size: 44 Copynumber: 7.5 Consensus size: 43 40939115 TCTACTCTGC * * 40939125 GCAACTTCAGAGAGATAAGATCTATTATTTCAATCCACTCCACT 1 GCAACTTCAGGGAGATAAGAT-TATTACTTCAATCCACTCCACT * * 40939169 GCAACTTCAGGGAGATAAGATTTATTACTTTAATCCGCTCCACT 1 GCAACTTCAGGGAGATAAGA-TTATTACTTCAATCCACTCCACT * * * *** 40939213 ACAACTTCAGGGAGATAGGATTATTGGCTTCAATTTGCTCCACT 1 GCAACTTCAGGGAGATAAGATTATT-ACTTCAATCCACTCCACT * * ** * 40939257 GCAACCTCAAGGAGATAAGATTATCGGCTTCAATCTACTCCACT 1 GCAACTTCAGGGAGATAAGATTAT-TACTTCAATCCACTCCACT * * ** ** * 40939301 GCAACCTCAGGGAGATAAGATT-TGCTTCTTCGGTCTGCTCCGCT 1 GCAACTTCAGGGAGATAAGATTAT--TACTTCAATCCACTCCACT * * * ** * * * * * 40939345 GGAACCTCAGGGAAATAAGA-CCTGA-TGCGATCTACTCTACT 1 GCAACTTCAGGGAGATAAGATTATTACTTCAATCCACTCCACT * * * * 40939386 ACAACTTCAGAGAGATAAGATCTATTACTTTAATCCGCTCCACT 1 GCAACTTCAGGGAGATAAGAT-TATTACTTCAATCCACTCCACT * * 40939430 ACAACTTCAGGGAGATAGGATT 1 GCAACTTCAGGGAGATAAGATT 40939452 TGTGGCTTAA Statistics Matches: 225, Mismatches: 50, Indels: 17 0.77 0.17 0.06 Matches are distributed among these distances: 41 26 0.12 43 9 0.04 44 189 0.84 45 1 0.00 ACGTcount: A:0.30, C:0.24, G:0.18, T:0.28 Consensus pattern (43 bp): GCAACTTCAGGGAGATAAGATTATTACTTCAATCCACTCCACT Found at i:40940205 original size:25 final size:25 Alignment explanation

Indices: 40940177--40940225 Score: 64 Period size: 25 Copynumber: 2.0 Consensus size: 25 40940167 ATTTTTCGGC * 40940177 TTTT-CTTCTCCCAGTTAAACTCTAT 1 TTTTACTT-TCCCACTTAAACTCTAT * 40940202 TTTTAGTTTCCCACTTAAACTCTA 1 TTTTACTTTCCCACTTAAACTCTA 40940226 AAAAGTGTAG Statistics Matches: 21, Mismatches: 2, Indels: 2 0.84 0.08 0.08 Matches are distributed among these distances: 25 19 0.90 26 2 0.10 ACGTcount: A:0.22, C:0.27, G:0.04, T:0.47 Consensus pattern (25 bp): TTTTACTTTCCCACTTAAACTCTAT Found at i:40940267 original size:44 final size:44 Alignment explanation

Indices: 40940204--40940294 Score: 155 Period size: 44 Copynumber: 2.1 Consensus size: 44 40940194 AACTCTATTT 40940204 TTAGTTTCCCACTTAAACTCTAAAAAGTGTAGGTTATTTTAATA 1 TTAGTTTCCCACTTAAACTCTAAAAAGTGTAGGTTATTTTAATA * ** 40940248 TTAGTTTCCCACTTAAACTCTGATTAGTGTAGGTTATTTTAATA 1 TTAGTTTCCCACTTAAACTCTAAAAAGTGTAGGTTATTTTAATA 40940292 TTA 1 TTA 40940295 TTTTACCTAC Statistics Matches: 44, Mismatches: 3, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 44 44 1.00 ACGTcount: A:0.31, C:0.13, G:0.12, T:0.44 Consensus pattern (44 bp): TTAGTTTCCCACTTAAACTCTAAAAAGTGTAGGTTATTTTAATA Found at i:40942606 original size:19 final size:17 Alignment explanation

Indices: 40942573--40942605 Score: 66 Period size: 17 Copynumber: 1.9 Consensus size: 17 40942563 ATATATTTTA 40942573 TTTTTAATCAAATATAC 1 TTTTTAATCAAATATAC 40942590 TTTTTAATCAAATATA 1 TTTTTAATCAAATATA 40942606 TATATTAAAT Statistics Matches: 16, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 17 16 1.00 ACGTcount: A:0.42, C:0.09, G:0.00, T:0.48 Consensus pattern (17 bp): TTTTTAATCAAATATAC Found at i:40943148 original size:31 final size:29 Alignment explanation

Indices: 40943112--40943197 Score: 79 Period size: 28 Copynumber: 2.9 Consensus size: 29 40943102 CATCCAACTA 40943112 TCATTTTTTAATTTGGTCACGTAATTATTG 1 TCATTTTTTAATTTGGTCAC-TAATTATTG * ** 40943142 TTCATTTTCTT-TTTTGGTCACCCA-T-TTG 1 -TCATTTT-TTAATTTGGTCACTAATTATTG 40943170 TCAATTTTTTAATTTGGTCACCTAATTA 1 TC-ATTTTTTAATTTGGTCA-CTAATTA 40943198 ATTGAGATTG Statistics Matches: 43, Mismatches: 6, Indels: 12 0.70 0.10 0.20 Matches are distributed among these distances: 27 4 0.09 28 16 0.37 29 3 0.07 30 2 0.05 31 16 0.37 32 2 0.05 ACGTcount: A:0.21, C:0.15, G:0.10, T:0.53 Consensus pattern (29 bp): TCATTTTTTAATTTGGTCACTAATTATTG Found at i:40945072 original size:14 final size:14 Alignment explanation

Indices: 40945053--40945079 Score: 54 Period size: 14 Copynumber: 1.9 Consensus size: 14 40945043 TCTCAAACCT 40945053 AATGATATATGTAG 1 AATGATATATGTAG 40945067 AATGATATATGTA 1 AATGATATATGTA 40945080 TCGATTTCTT Statistics Matches: 13, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 14 13 1.00 ACGTcount: A:0.44, C:0.00, G:0.19, T:0.37 Consensus pattern (14 bp): AATGATATATGTAG Found at i:40946462 original size:14 final size:14 Alignment explanation

Indices: 40946443--40946470 Score: 56 Period size: 14 Copynumber: 2.0 Consensus size: 14 40946433 TTTATATGTA 40946443 ATAAAAACACGTAT 1 ATAAAAACACGTAT 40946457 ATAAAAACACGTAT 1 ATAAAAACACGTAT 40946471 GTATATATGA Statistics Matches: 14, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 14 14 1.00 ACGTcount: A:0.57, C:0.14, G:0.07, T:0.21 Consensus pattern (14 bp): ATAAAAACACGTAT Found at i:40946767 original size:3 final size:3 Alignment explanation

Indices: 40946759--40946861 Score: 188 Period size: 3 Copynumber: 33.7 Consensus size: 3 40946749 GATTAAATGC 40946759 AAT AAT AAT AAT AAT AAT AAT AAT GCAAT AAT AAT AAT AAT AAT AAT 1 AAT AAT AAT AAT AAT AAT AAT AAT --AAT AAT AAT AAT AAT AAT AAT 40946806 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT 1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT 40946854 AAT AAT AA 1 AAT AAT AA 40946862 ACTAAATAAA Statistics Matches: 98, Mismatches: 0, Indels: 4 0.96 0.00 0.04 Matches are distributed among these distances: 3 95 0.97 5 3 0.03 ACGTcount: A:0.66, C:0.01, G:0.01, T:0.32 Consensus pattern (3 bp): AAT Found at i:40952896 original size:9 final size:9 Alignment explanation

Indices: 40952882--40952925 Score: 74 Period size: 9 Copynumber: 5.1 Consensus size: 9 40952872 TTTTGTTATA 40952882 ACAATTAAT 1 ACAATTAAT 40952891 ACAATTAAT 1 ACAATTAAT 40952900 ACAATT-A- 1 ACAATTAAT 40952907 ACAATTAAT 1 ACAATTAAT 40952916 ACAATTAAT 1 ACAATTAAT 40952925 A 1 A 40952926 ATTTGATAAT Statistics Matches: 33, Mismatches: 0, Indels: 4 0.89 0.00 0.11 Matches are distributed among these distances: 7 6 0.18 8 2 0.06 9 25 0.76 ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32 Consensus pattern (9 bp): ACAATTAAT Found at i:40952912 original size:16 final size:16 Alignment explanation

Indices: 40952891--40952928 Score: 67 Period size: 16 Copynumber: 2.4 Consensus size: 16 40952881 AACAATTAAT 40952891 ACAATTAATACAATTA 1 ACAATTAATACAATTA 40952907 ACAATTAATACAATTA 1 ACAATTAATACAATTA * 40952923 ATAATT 1 ACAATT 40952929 TGATAATTTT Statistics Matches: 21, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 16 21 1.00 ACGTcount: A:0.55, C:0.11, G:0.00, T:0.34 Consensus pattern (16 bp): ACAATTAATACAATTA Found at i:40957401 original size:32 final size:31 Alignment explanation

Indices: 40957337--40957401 Score: 78 Period size: 32 Copynumber: 2.1 Consensus size: 31 40957327 TTATATAAAT * * 40957337 AAAAATTATAAAAGAATTATTTAAAATATAA 1 AAAAATAATAAAAGAATTATGTAAAATATAA * 40957368 AAAAATAATTAAAAGAA-TATGTAAGAATGTAA 1 AAAAATAA-TAAAAGAATTATGTAA-AATATAA 40957400 AA 1 AA 40957402 TTTTTTAAAA Statistics Matches: 29, Mismatches: 3, Indels: 3 0.83 0.09 0.09 Matches are distributed among these distances: 31 13 0.45 32 16 0.55 ACGTcount: A:0.65, C:0.00, G:0.08, T:0.28 Consensus pattern (31 bp): AAAAATAATAAAAGAATTATGTAAAATATAA Found at i:40958827 original size:20 final size:20 Alignment explanation

Indices: 40958786--40958838 Score: 54 Period size: 20 Copynumber: 2.6 Consensus size: 20 40958776 TATTTTTACT * ** 40958786 ATTTTT-ATATTTTTTTCTA 1 ATTTTTAATATTTTATTAAA 40958805 ATTTTTAATATTTTATTAAA 1 ATTTTTAATATTTTATTAAA * 40958825 ATTTAATAATATTT 1 ATTT-TTAATATTT 40958839 ATAGCTTTTA Statistics Matches: 28, Mismatches: 4, Indels: 2 0.82 0.12 0.06 Matches are distributed among these distances: 19 6 0.21 20 14 0.50 21 8 0.29 ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64 Consensus pattern (20 bp): ATTTTTAATATTTTATTAAA Found at i:40959037 original size:89 final size:89 Alignment explanation

Indices: 40958886--40959060 Score: 237 Period size: 89 Copynumber: 2.0 Consensus size: 89 40958876 TAATAAAAGC * * * * 40958886 AGGGGCTTAATTGCTTTTCTTGAAAAAGTTTGAGAGTCTTTTTGATGTATTTTGAAAGTTCAAGT 1 AGGGGCTTAATTACTTTTCTTGAAAAAGTTTGAGAGTCTTTTTAATGCATTTTAAAAGTTCAAGT * 40958951 AC-CTAATTGAGTGAAAAAAAAAAT 66 ACTC-AAATGAGTGAAAAAAAAAAT * * * 40958975 AGGGGCTTAATTACTTTTTTTG-AAAAGATTTGAGGGTTTTTTTAATGCATTTTAAAAGTTCAAG 1 AGGGGCTTAATTACTTTTCTTGAAAAAG-TTTGAGAGTCTTTTTAATGCATTTTAAAAGTTCAAG * 40959039 TACTCAAATGAGTGTAAAAAAA 65 TACTCAAATGAGTGAAAAAAAA 40959061 CAAGCAGAAA Statistics Matches: 75, Mismatches: 9, Indels: 4 0.85 0.10 0.05 Matches are distributed among these distances: 88 5 0.07 89 69 0.92 90 1 0.01 ACGTcount: A:0.35, C:0.07, G:0.19, T:0.38 Consensus pattern (89 bp): AGGGGCTTAATTACTTTTCTTGAAAAAGTTTGAGAGTCTTTTTAATGCATTTTAAAAGTTCAAGT ACTCAAATGAGTGAAAAAAAAAAT Found at i:40959083 original size:89 final size:87 Alignment explanation

Indices: 40958891--40959084 Score: 194 Period size: 89 Copynumber: 2.2 Consensus size: 87 40958881 AAAGCAGGGG * * * * 40958891 CTTAATTGCTTTTCTTGAAAAAGTTTGAGAGTCTTTTTGATGTATTTTGAAAGTTCAAGTACCTA 1 CTTAATT-ATTTT-TTGAAAAAGTTTGAGAGTCTTTTTAATGCATTTTAAAAGTTCAAGTACCTA * * *** 40958956 ATTGAGTGAAAAAAAAAATAGGGG 64 AATGAGTGAAAAAAAAAACAGAAA * * 40958980 CTTAATTACTTTTTTTG-AAAAGATTTGAGGGTTTTTTTAATGCATTTTAAAAGTTCAAGTA-CT 1 CTTAATTA--TTTTTTGAAAAAG-TTTGAGAGTCTTTTTAATGCATTTTAAAAGTTCAAGTACCT * 40959043 CAAATGAGTGTAAAAAAACAAGCAGAAA 63 -AAATGAGTG-AAAAAAA-AAACAGAAA 40959071 CTTAATTATTTTTT 1 CTTAATTATTTTTT 40959085 TGGGAGAGTT Statistics Matches: 87, Mismatches: 12, Indels: 12 0.78 0.11 0.11 Matches are distributed among these distances: 88 7 0.08 89 57 0.66 90 11 0.13 91 12 0.14 ACGTcount: A:0.36, C:0.08, G:0.16, T:0.39 Consensus pattern (87 bp): CTTAATTATTTTTTGAAAAAGTTTGAGAGTCTTTTTAATGCATTTTAAAAGTTCAAGTACCTAAA TGAGTGAAAAAAAAAACAGAAA Found at i:40959451 original size:21 final size:19 Alignment explanation

Indices: 40959427--40959476 Score: 50 Period size: 21 Copynumber: 2.6 Consensus size: 19 40959417 TACCTATTAT 40959427 TTACTTATTTATTCTTTATAA 1 TTAC-TATTTATTCTTT-TAA * 40959448 TTACGTAATT-TTCTTTTAA 1 TTAC-TATTTATTCTTTTAA 40959467 TTA-TATTTAT 1 TTACTATTTAT 40959477 CTAGTTCCAC Statistics Matches: 25, Mismatches: 3, Indels: 5 0.76 0.09 0.15 Matches are distributed among these distances: 17 4 0.16 18 1 0.04 19 6 0.24 20 6 0.24 21 8 0.32 ACGTcount: A:0.28, C:0.08, G:0.02, T:0.62 Consensus pattern (19 bp): TTACTATTTATTCTTTTAA Found at i:40962291 original size:15 final size:15 Alignment explanation

Indices: 40962273--40962310 Score: 51 Period size: 15 Copynumber: 2.5 Consensus size: 15 40962263 CATCCACCAA * 40962273 TCATTCATTCA-TTTT 1 TCATTC-TTCACTTAT 40962288 TCATTCTTCACTTAT 1 TCATTCTTCACTTAT 40962303 TCATTCTT 1 TCATTCTT 40962311 ATTCTTTTCA Statistics Matches: 21, Mismatches: 1, Indels: 2 0.88 0.04 0.08 Matches are distributed among these distances: 14 4 0.19 15 17 0.81 ACGTcount: A:0.18, C:0.24, G:0.00, T:0.58 Consensus pattern (15 bp): TCATTCTTCACTTAT Found at i:40964787 original size:131 final size:129 Alignment explanation

Indices: 40964536--40965259 Score: 490 Period size: 131 Copynumber: 5.7 Consensus size: 129 40964526 ATTCAGGATC * * * * * * 40964536 GTAAATC-AATAAACTTAGGCTGTGATCATAAATCAATGAGACTTAATAATATCAATTGCGATAT 1 GTAAATCAAATGAACTTAGGCTGTGATCGTAAATCAACGAGCCCTAATAATATCAACTGCGATAT * * * * * * 40964600 TAAATTAACTAGTTGTTTAGAGTAGTGGCA-AG-AAATCAATTAACTTAGAGGAGATTGCTCATG 66 TAAATCAGCTAGATGTTTGGAGTAG-CG-ATAGTAAATCAACTAACTTAGA-GAGATTG-TCATG 40964663 ATA 127 ATA * 40964666 GTAAATCAAATGAACTTAGGTTGTGATCGTAAATCAACGAGCCCTAATAATATCAACTGCGATAT 1 GTAAATCAAATGAACTTAGGCTGTGATCGTAAATCAACGAGCCCTAATAATATCAACTGCGATAT * * * 40964731 TAAATCAGCTAGCTGTTTGGAGTAGCGATAGTAAATCAACTAACTCAGAGATGATTGTTCGTGAT 66 TAAATCAGCTAGATGTTTGGAGTAGCGATAGTAAATCAACTAACTTAGAGA-GATTG-TCATGAT 40964796 A 129 A * ** * * * 40964797 GTAAATCAAATGAACTTAGGTTGTGATATTAAATCAGCGAGCCTTAATAATATCAACT-CTGACA 1 GTAAATCAAATGAACTTAGGCTGTGATCGTAAATCAACGAGCCCTAATAATATCAACTGC-GATA * * * * 40964861 TTAAATCAGCTAGATGTTTGGAATAGCGATAGTAAATCAGCTAACTTAGAAAAAAAATT-TCATG 65 TTAAATCAGCTAGATGTTTGGAGTAGCGATAGTAAATCAACTAACTTAG---AGAGATTGTCATG 40964925 ATA 127 ATA * * * * 40964928 GTAATTCAAATGAATTTAGGCTGTGATCGTAAATCAGC-AACCCTTAATAATATCAACT---ATG 1 GTAAATCAAATGAACTTAGGCTGTGATCGTAAATCAACGAGCCC-TAATAATATCAACTGCGAT- * * * * * * * * * 40964989 A-T--ATC-G---GA-G-TAGCGA-TAG-TA-AAT-CAGCTAACTTA--GAGA-AAATTTTTCAT 64 ATTAAATCAGCTAGATGTTTG-GAGTAGCGATAGTAAATC-AACTAACTTAGAGAGA-TTGTCAT 40965038 GATA 126 GATA * * * * * * * * * * 40965042 GTAAATCAAATGAACTTAGGTTGTGACCATAAATTAGCAAGTCTTAATAATATCAGCTGTGATAT 1 GTAAATCAAATGAACTTAGGCTGTGATCGTAAATCAACGAGCCCTAATAATATCAACTGCGATAT * * * * * * * * 40965107 TAAATTAGCGAGTTGTTTGGAGTAACGATAATAAATTAGCTAACTTAGAGAAAATTGTTCATGAT 66 TAAATCAGCTAGATGTTTGGAGTAGCGATAGTAAATCAACTAACTTAGAG-AGATTG-TCATGAT * 40965172 G 129 A * * * ** * ** * 40965173 GTAAATCAAATAAACTTAGGTTGTGATCATAAATCAGTGAGCCTTAATAATATCAGTTGCGATCT 1 GTAAATCAAATGAACTTAGGCTGTGATCGTAAATCAACGAGCCCTAATAATATCAACTGCGATAT * * * 40965238 TAAATCAACGAGCTGTTTGGAG 66 TAAATCAGCTAGATGTTTGGAG 40965260 CAATGATAGA Statistics Matches: 479, Mismatches: 79, Indels: 71 0.76 0.13 0.11 Matches are distributed among these distances: 112 3 0.01 113 3 0.01 114 53 0.11 115 2 0.00 116 3 0.01 117 5 0.01 118 6 0.01 119 3 0.01 120 6 0.01 121 3 0.01 122 2 0.00 123 1 0.00 124 3 0.01 125 5 0.01 126 4 0.01 127 7 0.01 128 3 0.01 129 5 0.01 130 18 0.04 131 339 0.71 133 3 0.01 134 2 0.00 ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31 Consensus pattern (129 bp): GTAAATCAAATGAACTTAGGCTGTGATCGTAAATCAACGAGCCCTAATAATATCAACTGCGATAT TAAATCAGCTAGATGTTTGGAGTAGCGATAGTAAATCAACTAACTTAGAGAGATTGTCATGATA Found at i:40965088 original size:114 final size:114 Alignment explanation

Indices: 40964884--40965106 Score: 329 Period size: 114 Copynumber: 2.0 Consensus size: 114 40964874 ATGTTTGGAA * * 40964884 TAGCGATAGTAAATCAGCTAACTTAGAAAAAAAATTTCATGATAGTAATTCAAATGAATTTAGGC 1 TAGCGATAGTAAATCAGCTAACTTAGAAAAAAAATTTCATGATAGTAAATCAAATGAACTTAGGC * * 40964949 TGTGATCGTAAATCAGCAACCCTTAATAATATCAACTATGATATCGGAG 66 TGTGACCATAAATCAGCAACCCTTAATAATATCAACTATGATATCGGAG * ** * 40964998 TAGCGATAGTAAATCAGCTAACTTAGAGAAAATTTTTCATGATAGTAAATCAAATGAACTTAGGT 1 TAGCGATAGTAAATCAGCTAACTTAGAAAAAAAATTTCATGATAGTAAATCAAATGAACTTAGGC * ** * * 40965063 TGTGACCATAAATTAGCAAGTCTTAATAATATCAGCTGTGATAT 66 TGTGACCATAAATCAGCAACCCTTAATAATATCAACTATGATAT 40965107 TAAATTAGCG Statistics Matches: 96, Mismatches: 13, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 114 96 1.00 ACGTcount: A:0.40, C:0.13, G:0.16, T:0.30 Consensus pattern (114 bp): TAGCGATAGTAAATCAGCTAACTTAGAAAAAAAATTTCATGATAGTAAATCAAATGAACTTAGGC TGTGACCATAAATCAGCAACCCTTAATAATATCAACTATGATATCGGAG Found at i:40965200 original size:245 final size:245 Alignment explanation

Indices: 40964749--40965227 Score: 647 Period size: 245 Copynumber: 2.0 Consensus size: 245 40964739 CTAGCTGTTT ** * 40964749 GGAGTAGCGATAGTAAATCAACTAACTCAGAGATGATTGTTCGTGATAGTAAATCAAATGAACTT 1 GGAGTAGCGATAGTAAATCAACTAACTCAGAGAAAATTGTTCATGATAGTAAATCAAATGAACTT * * * 40964814 AGGTTGTGATATTAAATCAGCGAGCCTTAATAATATCAACTCTGACATTAAATCAGCTAGATGTT 66 AGGTTGTGACATTAAATCAGCAAGCCTTAATAATATCAACTCTGACATTAAATCAGCGAGATGTT * * * * * 40964879 TGGAATAGCGATAGTAAATCAGCTAACTTAGAAAAAAAATTTCATGATAGTAATTCAAATGAATT 131 TGGAATAACGATAATAAATCAGCTAACTTAGAAAAAAAATTTCATGATAGTAAATCAAATAAACT * 40964944 TAGGCTGTGATCGTAAATCAGCAACCCTTAATAATATCAACTATGATATC 196 TAGGCTGTGATCATAAATCAGCAACCCTTAATAATATCAACTATGATATC * * * 40964994 GGAGTAGCGATAGTAAATCAGCTAACTTAGAGAAAATTTTTCATGATAGTAAATCAAATGAACTT 1 GGAGTAGCGATAGTAAATCAACTAACTCAGAGAAAATTGTTCATGATAGTAAATCAAATGAACTT * * * * * * * 40965059 AGGTTGTGACCA-TAAATTAGCAAGTCTTAATAATATCAGCTGTGATATTAAATTAGCGAGTTGT 66 AGGTTGTGA-CATTAAATCAGCAAGCCTTAATAATATCAACTCTGACATTAAATCAGCGAGATGT * * * * * 40965123 TTGGAGTAACGATAATAAATTAGCTAACTTAG-AGAAAATTGTTCATGATGGTAAATCAAATAAA 130 TTGGAATAACGATAATAAATCAGCTAACTTAGAAAAAAAAT-TTCATGATAGTAAATCAAATAAA * ** * 40965187 CTTAGGTTGTGATCATAAATCAGTGAGCCTTAATAATATCA 194 CTTAGGCTGTGATCATAAATCAGCAACCCTTAATAATATCA 40965228 GTTGCGATCT Statistics Matches: 201, Mismatches: 31, Indels: 4 0.85 0.13 0.02 Matches are distributed among these distances: 244 6 0.03 245 194 0.97 246 1 0.00 ACGTcount: A:0.39, C:0.12, G:0.18, T:0.31 Consensus pattern (245 bp): GGAGTAGCGATAGTAAATCAACTAACTCAGAGAAAATTGTTCATGATAGTAAATCAAATGAACTT AGGTTGTGACATTAAATCAGCAAGCCTTAATAATATCAACTCTGACATTAAATCAGCGAGATGTT TGGAATAACGATAATAAATCAGCTAACTTAGAAAAAAAATTTCATGATAGTAAATCAAATAAACT TAGGCTGTGATCATAAATCAGCAACCCTTAATAATATCAACTATGATATC Found at i:40970491 original size:26 final size:26 Alignment explanation

Indices: 40970462--40970532 Score: 106 Period size: 26 Copynumber: 2.7 Consensus size: 26 40970452 TTTTATAATG ** 40970462 TTGCTCACACGAGCTGTGAAATGGTT 1 TTGCTCACACGAGCTGTGAAATGGGC * 40970488 TTGCTCACATGAGCTGTGAAATGGGC 1 TTGCTCACACGAGCTGTGAAATGGGC * 40970514 CTGCTCACACGAGCTGTGA 1 TTGCTCACACGAGCTGTGA 40970533 GTCAGAATGT Statistics Matches: 40, Mismatches: 5, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 26 40 1.00 ACGTcount: A:0.23, C:0.23, G:0.28, T:0.27 Consensus pattern (26 bp): TTGCTCACACGAGCTGTGAAATGGGC Found at i:40981259 original size:35 final size:35 Alignment explanation

Indices: 40981212--40981287 Score: 118 Period size: 35 Copynumber: 2.2 Consensus size: 35 40981202 AAAACATCTA 40981212 ATTTT-TCATTAGAACAATATTTTGATTTTTTAGT 1 ATTTTATCATTAGAACAATATTTTGATTTTTTAGT * * * 40981246 ATTTTATCTTTAGAATAATTTTTTGATTTTTTAGT 1 ATTTTATCATTAGAACAATATTTTGATTTTTTAGT 40981281 ATTTTAT 1 ATTTTAT 40981288 TTTTTTATCT Statistics Matches: 38, Mismatches: 3, Indels: 1 0.90 0.07 0.02 Matches are distributed among these distances: 34 5 0.13 35 33 0.87 ACGTcount: A:0.28, C:0.04, G:0.08, T:0.61 Consensus pattern (35 bp): ATTTTATCATTAGAACAATATTTTGATTTTTTAGT Found at i:40991642 original size:3 final size:3 Alignment explanation

Indices: 40991636--40991689 Score: 99 Period size: 3 Copynumber: 18.0 Consensus size: 3 40991626 AAGAAGAAGA * 40991636 AGG AGG AGG AGA AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG 1 AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG 40991684 AGG AGG 1 AGG AGG 40991690 TGCCGGAAAA Statistics Matches: 49, Mismatches: 2, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 3 49 1.00 ACGTcount: A:0.35, C:0.00, G:0.65, T:0.00 Consensus pattern (3 bp): AGG Found at i:40991922 original size:39 final size:39 Alignment explanation

Indices: 40991874--40992026 Score: 123 Period size: 39 Copynumber: 3.8 Consensus size: 39 40991864 GTTTAGTTAT * 40991874 TAATAATTATTGTTACTTAGTATTATTGTTAGTAAAAAAC 1 TAAT-ATTATTGTTAGTTAGTATTATTGTTAGTAAAAAAC * * * 40991914 TAATATTATTATTATGGTTAGTTATTA-AGATTAGTAAAAACC 1 TAATATTATTGTTA--GTTAG-TATTATTG-TTAGTAAAAAAC * * **** 40991956 TACTTATTATT-TTAGTTAGTATGATTGTTAGT-TTTTAC 1 TA-ATATTATTGTTAGTTAGTATTATTGTTAGTAAAAAAC * 40991994 ATTATATTATTGTTAGTTAGTATTATTGTTAGT 1 -TAATATTATTGTTAGTTAGTATTATTGTTAGT 40992027 TAGTATTATT Statistics Matches: 90, Mismatches: 15, Indels: 17 0.74 0.12 0.14 Matches are distributed among these distances: 38 8 0.09 39 39 0.43 40 10 0.11 41 5 0.06 42 21 0.23 43 7 0.08 ACGTcount: A:0.33, C:0.04, G:0.12, T:0.50 Consensus pattern (39 bp): TAATATTATTGTTAGTTAGTATTATTGTTAGTAAAAAAC Found at i:40992019 original size:16 final size:16 Alignment explanation

Indices: 40991998--40992036 Score: 78 Period size: 16 Copynumber: 2.4 Consensus size: 16 40991988 TTTTACATTA 40991998 TATTATTGTTAGTTAG 1 TATTATTGTTAGTTAG 40992014 TATTATTGTTAGTTAG 1 TATTATTGTTAGTTAG 40992030 TATTATT 1 TATTATT 40992037 TTGAGTATAA Statistics Matches: 23, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 16 23 1.00 ACGTcount: A:0.26, C:0.00, G:0.15, T:0.59 Consensus pattern (16 bp): TATTATTGTTAGTTAG Found at i:40997531 original size:154 final size:153 Alignment explanation

Indices: 40997245--40998009 Score: 1007 Period size: 154 Copynumber: 5.0 Consensus size: 153 40997235 CTTCAAAAAA * * * 40997245 AAATTAGTAAAAAACCCTTATTTCGGCCATTTGTTCGTATTTTTTTCCCGAATTTTATTACTTTT 1 AAATTAGAAAAAAACCCTTATTTCGGCCCTTTGTTCGTATTTTTTTCCCGAATTTTATTACTTTA * 40997310 AAAAAATATACTATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAGATTTA 66 AAAAAATATACTATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTTA * 40997375 TTATTTTAGTGTGTTTTTTAAAT 131 TTAATTTAGTGTGTTTTTTAAAT * * 40997398 AAATTA-AAAAAAACCCCTTATTTC-TCCCTTTGCTCGTATTTTTTTCCCGAATTTTATTACTTT 1 AAATTAGAAAAAAA-CCCTTATTTCGGCCCTTTGTTCGTATTTTTTTCCCGAATTTTATTACTTT * * * * 40997461 CAATAAAAATATATTATTTTCGT-ATTTTATCATTTTACTTTATTTTAGTAAATTATGTTTGAAA 65 -AA-AAAAATATACTATTTTC-TAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAA * * * * * 40997525 TGTATTAATTAATTTTATTTTTT---T 127 TTTATTAATTTAGTGTGTTTTTTAAAT * * * 40997549 AAATTTAGTAAAAAACTCTTATTTCGGACCTTTGTTCGTA-TTTTTTCCCGAATTTTATTACTTT 1 AAA-TTAGAAAAAAACCCTTATTTCGGCCCTTTGTTCGTATTTTTTTCCCGAATTTTATTACTTT * * 40997613 GAAAAAATATACTATTTTATAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTT 65 AAAAAAATATACTATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTT 40997678 ATTAATTTAGTGTGTTTTTTAAAT 130 ATTAATTTAGTGTGTTTTTTAAAT * ** * 40997702 ATATTTA-AAAAAAACCCTTATTTCGGCCCTTTACTCGTA-TTTTTTCTCGAATTTTATTACTTT 1 A-AATTAGAAAAAAACCCTTATTTCGGCCCTTTGTTCGTATTTTTTTCCCGAATTTTATTACTTT * * 40997765 CAATAAAAATATATTATTTTCGT-ATTTTATAATTTTACATTATTTTAGTACATTATGTTTGAAA 65 -AA-AAAAATATACTATTTTC-TAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAA * * * * 40997829 TGTATTAA-TTATTTCTGTTTTTTTAA- 127 TTTATTAATTTA-GTGTGTTTTTTAAAT * * * * * 40997855 AATTTAGTAAAAAACCCTTACTTCGGCCATTTGTTCGTATTTTTTTCTCCGCATTTTATTACTTT 1 AAATTAGAAAAAAACCCTTATTTCGGCCCTTTGTTCGTATTTTTTTC-CCGAATTTTATTACTTT 40997920 AAAAAAATAT-CATATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATT 65 AAAAAAATATAC-TATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATT 40997984 TATTAATTTAGTGTGTTTTTTAAAT 129 TATTAATTTAGTGTGTTTTTTAAAT 40998009 A 1 A 40998010 TACAATTCTT Statistics Matches: 529, Mismatches: 60, Indels: 45 0.83 0.09 0.07 Matches are distributed among these distances: 149 1 0.00 150 71 0.13 151 5 0.01 152 134 0.25 153 144 0.27 154 157 0.30 155 17 0.03 ACGTcount: A:0.30, C:0.10, G:0.07, T:0.52 Consensus pattern (153 bp): AAATTAGAAAAAAACCCTTATTTCGGCCCTTTGTTCGTATTTTTTTCCCGAATTTTATTACTTTA AAAAAATATACTATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTTA TTAATTTAGTGTGTTTTTTAAAT Found at i:40997802 original size:304 final size:307 Alignment explanation

Indices: 40997243--40998011 Score: 1284 Period size: 304 Copynumber: 2.5 Consensus size: 307 40997233 AACTTCAAAA * 40997243 AAAAATTAGTAAAAAACCCTTATTTCGGCCATTTGTTCGTATTTTTTTCCCGAATTTTATTACTT 1 AAAATTTAGTAAAAAACCCTTATTTCGGCCATTTGTTCGTATTTTTTTCCCGAATTTTATTACTT * * 40997308 TTAAAAAATATACTATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAGATT 66 TAAAAAAATATACTATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATT * * * 40997373 TATTATTTTAGTGTGTTTTTTAAATA-AATTAAAAAAAACCCCTTATTTCTCCCTTTGCTCGTAT 131 TATTAATTTAGTGTGTTTTTTAAATATAATTAAAAAAAACCCCTTATTTCGCCCTTTACTCGTAT * * 40997437 TTTTTTCCCGAATTTTATTACTTTCAATAAAAATATATTATTTTCGTATTTTATCATTTTACTTT 196 TTTTTTCCCGAATTTTATTACTTTCAATAAAAATATATTATTTTCGTATTTTATAATTTTACATT 40997502 ATTTTAGTAAATTATGTTTGAAATGTATTAATTAATTT-TATTTTTTT 261 ATTTTAGTAAATTATGTTTGAAATGTATTAATT-ATTTCTATTTTTTT * 40997549 -AAATTTAGTAAAAAACTCTTATTTCGGACC-TTTGTTCGTA-TTTTTTCCCGAATTTTATTACT 1 AAAATTTAGTAAAAAACCCTTATTTCGG-CCATTTGTTCGTATTTTTTTCCCGAATTTTATTACT * * 40997611 TTGAAAAAATATACTATTTTATAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAAT 65 TTAAAAAAATATACTATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAAT * 40997676 TTATTAATTTAGTGTGTTTTTTAAATATATTTAAAAAAAA-CCCTTATTTCGGCCCTTTACTCGT 130 TTATTAATTTAGTGTGTTTTTTAAATATAATTAAAAAAAACCCCTTATTTC-GCCCTTTACTCGT * 40997740 A-TTTTTTCTCGAATTTTATTACTTTCAATAAAAATATATTATTTTCGTATTTTATAATTTTACA 194 ATTTTTTTCCCGAATTTTATTACTTTCAATAAAAATATATTATTTTCGTATTTTATAATTTTACA * * 40997804 TTATTTTAGTACATTATGTTTGAAATGTATTAATTATTTCTGTTTTTTT 259 TTATTTTAGTAAATTATGTTTGAAATGTATTAATTATTTCTATTTTTTT * * 40997853 AAAATTTAGTAAAAAACCCTTACTTCGGCCATTTGTTCGTATTTTTTTCTCCGCATTTTATTACT 1 AAAATTTAGTAAAAAACCCTTATTTCGGCCATTTGTTCGTATTTTTTTC-CCGAATTTTATTACT 40997918 TTAAAAAAATAT-CATATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAA 65 TTAAAAAAATATAC-TATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAA 40997982 TTTATTAATTTAGTGTGTTTTTTAAATATA 129 TTTATTAATTTAGTGTGTTTTTTAAATATA 40998012 CAATTCTTTT Statistics Matches: 435, Mismatches: 19, Indels: 17 0.92 0.04 0.04 Matches are distributed among these distances: 303 4 0.01 304 224 0.51 305 93 0.21 306 10 0.02 307 104 0.24 ACGTcount: A:0.31, C:0.10, G:0.07, T:0.52 Consensus pattern (307 bp): AAAATTTAGTAAAAAACCCTTATTTCGGCCATTTGTTCGTATTTTTTTCCCGAATTTTATTACTT TAAAAAAATATACTATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATT TATTAATTTAGTGTGTTTTTTAAATATAATTAAAAAAAACCCCTTATTTCGCCCTTTACTCGTAT TTTTTTCCCGAATTTTATTACTTTCAATAAAAATATATTATTTTCGTATTTTATAATTTTACATT ATTTTAGTAAATTATGTTTGAAATGTATTAATTATTTCTATTTTTTT Found at i:40998400 original size:4 final size:4 Alignment explanation

Indices: 40998378--40998504 Score: 82 Period size: 4 Copynumber: 29.2 Consensus size: 4 40998368 TTCCCTCTTC * 40998378 TTCT TCTCT TT-T TTTT TTCT TTCT TCTCAT TTCCTT TTCT TTCT TTC- 1 TTCT T-TCT TTCT TTCT TTCT TTCT T-TC-T TT-C-T TTCT TTCT TTCT 40998425 TT-T TTCT TTCT TCTCCT TTCATT TTCT TTCT TTCT TTCT TCTCCT TTCCTT 1 TTCT TTCT TTCT T-T-CT TTC--T TTCT TTCT TTCT TTCT T-T-CT TT-C-T * 40998476 TTCT TTCT TT-T TCTTT TTCT TTCT TTCT T 1 TTCT TTCT TTCT T-TCT TTCT TTCT TTCT T 40998505 CTCCTTTCCC Statistics Matches: 104, Mismatches: 3, Indels: 32 0.75 0.02 0.23 Matches are distributed among these distances: 3 9 0.09 4 59 0.57 5 17 0.16 6 19 0.18 ACGTcount: A:0.02, C:0.26, G:0.00, T:0.72 Consensus pattern (4 bp): TTCT Found at i:40998420 original size:24 final size:20 Alignment explanation

Indices: 40998378--40998507 Score: 99 Period size: 20 Copynumber: 6.4 Consensus size: 20 40998368 TTCCCTCTTC 40998378 TTCTTCTCTTTTTTTTTTCT 1 TTCTTCTCTTTTTTTTTTCT * ** 40998398 TTCTTCTCATTTCCTTTTCT 1 TTCTTCTCTTTTTTTTTTCT 40998418 TTCTT-TCTTTTTCTTTCTTC- 1 TTCTTCTCTTTTT-TTT-TTCT * 40998438 TCCTT-TCATTTTCTTTCTTTCT 1 TTCTTCTC-TTTT-TTT-TTTCT * ** 40998460 TTCTTCTCCTTTCCTTTTCT 1 TTCTTCTCTTTTTTTTTTCT 40998480 TTCTT-T-TTCTTTTTCTTTCT 1 TTCTTCTCTT-TTTTT-TTTCT 40998500 TTCTTCTC 1 TTCTTCTC 40998508 CTTTCCCTCT Statistics Matches: 85, Mismatches: 14, Indels: 20 0.71 0.12 0.17 Matches are distributed among these distances: 18 1 0.01 19 9 0.11 20 50 0.59 21 14 0.16 22 9 0.11 23 2 0.02 ACGTcount: A:0.02, C:0.27, G:0.00, T:0.72 Consensus pattern (20 bp): TTCTTCTCTTTTTTTTTTCT Found at i:40998426 original size:44 final size:42 Alignment explanation

Indices: 40998343--40998507 Score: 121 Period size: 44 Copynumber: 4.0 Consensus size: 42 40998333 CCTTTACTTC * ** 40998343 TTTTTTTTTCTTTCTGTTTCCTTCCTTCCCTCTTC-TTCTTCTCT 1 TTTTTTTTTCTTTC--TTTCTTTCCTTTTCT-TTCTTTCTTCTCT 40998387 TTTTTTTTTCTTTCTTCTCATTTCCTTTTCTTTCTTTC-T-T-T 1 TTTTTTTTTCTTTCTT-TC-TTTCCTTTTCTTTCTTTCTTCTCT * * * * * 40998428 TTCTTTCTTC-TCCTTTCATTTTC-TTTCTTTCTTTCTTCTCC 1 TTTTTTTTTCTTTCTTTC-TTTCCTTTTCTTTCTTTCTTCTCT ** * 40998469 TTTCCTTTTCTTTC-TT-TTTCTTTTTCTTTCTTTCTTCTC 1 TTTTTTTTTCTTTCTTTCTTTCCTTTTCTTTCTTTCTTCTC 40998508 CTTTCCCTCT Statistics Matches: 98, Mismatches: 15, Indels: 20 0.74 0.11 0.15 Matches are distributed among these distances: 38 12 0.12 39 11 0.11 40 22 0.22 41 17 0.17 42 5 0.05 43 6 0.06 44 25 0.26 ACGTcount: A:0.01, C:0.28, G:0.01, T:0.70 Consensus pattern (42 bp): TTTTTTTTTCTTTCTTTCTTTCCTTTTCTTTCTTTCTTCTCT Found at i:40998429 original size:34 final size:33 Alignment explanation

Indices: 40998400--40998511 Score: 128 Period size: 34 Copynumber: 3.4 Consensus size: 33 40998390 TTTTTTCTTT 40998400 CTTCTCATTTCCTTTTCTTTCTTTCTTTTTCTTT 1 CTTCTC-TTTCCTTTTCTTTCTTTCTTTTTCTTT * 40998434 CTTCTCCTTTCATTTTCTTTCTTTC--TTTC-TT 1 CTTCT-CTTTCCTTTTCTTTCTTTCTTTTTCTTT 40998465 C-TC-CTTTCCTTTTCTTTCTTTTTCTTTTTCTTT 1 CTTCTCTTTCCTTTTCTTTC--TTTCTTTTTCTTT 40998498 CTT-TCTTCTCCTTT 1 CTTCTCTT-TCCTTT 40998512 CCCTCTCATT Statistics Matches: 67, Mismatches: 2, Indels: 17 0.78 0.02 0.20 Matches are distributed among these distances: 28 14 0.21 30 6 0.09 31 3 0.04 32 8 0.12 33 3 0.04 34 26 0.39 35 7 0.10 ACGTcount: A:0.02, C:0.29, G:0.00, T:0.70 Consensus pattern (33 bp): CTTCTCTTTCCTTTTCTTTCTTTCTTTTTCTTT Found at i:40998511 original size:10 final size:10 Alignment explanation

Indices: 40998373--40998512 Score: 84 Period size: 10 Copynumber: 14.2 Consensus size: 10 40998363 CTTCCTTCCC 40998373 TCTTCTTC-T 1 TCTTCTTCTT 40998382 TC-TCTT-TT 1 TCTTCTTCTT * 40998390 T-TTTTTCTT 1 TCTTCTTCTT 40998399 TCTTC-TCATT 1 TCTTCTTC-TT 40998409 TCCTTTTCTTTCTT 1 T-C--TTC-TTCTT * 40998423 TCTTTTTCTT 1 TCTTCTTCTT * 40998433 TCTTCTCCTT 1 TCTTCTTCTT 40998443 TCATT-TTCTT 1 TC-TTCTTCTT 40998453 TC-T-TTCTT 1 TCTTCTTCTT * 40998461 TCTTCTCCTT 1 TCTTCTTCTT 40998471 TCCTT-TTCTT 1 T-CTTCTTCTT * 40998481 TCTTTTTCTT 1 TCTTCTTCTT 40998491 T-TTCTTTCTT 1 TCTTC-TTCTT * 40998501 TCTTCTCCTT 1 TCTTCTTCTT 40998511 TC 1 TC 40998513 CCTCTCATTT Statistics Matches: 104, Mismatches: 10, Indels: 33 0.71 0.07 0.22 Matches are distributed among these distances: 8 17 0.16 9 13 0.12 10 54 0.52 11 11 0.11 13 4 0.04 14 3 0.03 15 2 0.02 ACGTcount: A:0.01, C:0.28, G:0.00, T:0.71 Consensus pattern (10 bp): TCTTCTTCTT Found at i:40998525 original size:62 final size:62 Alignment explanation

Indices: 40998395--40998530 Score: 163 Period size: 62 Copynumber: 2.2 Consensus size: 62 40998385 CTTTTTTTTT * * * * 40998395 TCTTTCTTCTCATTTCCTTTTCTTTCTTTCTTTTTCTTTCTTCTCCTTTCATTTTCTTTCTT 1 TCTTTCTTCTCCTTTCCTTTTCTTTCTTTCTTTTTCTTTCTTCTCCTTTCATTTCCTCTCTA * 40998457 TCTTTCTTCTCCTTTCCTTTTCTTTCTTTTTCTTTTTCTTTCTT-T-CTTCTCCTTTCC-CTCTC 1 TCTTTCTTCTCCTTTCCTTTTCTTTC--TTTCTTTTTCTTTCTTCTCCTT-TCATTTCCTCTCT- 40998519 A 62 A 40998520 T-TTTCTTCTCC 1 TCTTTCTTCTCC 40998531 ACCCACCAGC Statistics Matches: 65, Mismatches: 5, Indels: 8 0.83 0.06 0.10 Matches are distributed among these distances: 62 41 0.63 63 8 0.12 64 16 0.25 ACGTcount: A:0.02, C:0.31, G:0.00, T:0.67 Consensus pattern (62 bp): TCTTTCTTCTCCTTTCCTTTTCTTTCTTTCTTTTTCTTTCTTCTCCTTTCATTTCCTCTCTA Found at i:40999710 original size:10 final size:10 Alignment explanation

Indices: 40999695--40999724 Score: 51 Period size: 10 Copynumber: 3.0 Consensus size: 10 40999685 ATTTAAATTC 40999695 TAAAGATAAA 1 TAAAGATAAA 40999705 TAAAGATAAA 1 TAAAGATAAA * 40999715 TAAAGGTAAA 1 TAAAGATAAA 40999725 AGCTAAAATT Statistics Matches: 19, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 10 19 1.00 ACGTcount: A:0.67, C:0.00, G:0.13, T:0.20 Consensus pattern (10 bp): TAAAGATAAA Found at i:41001480 original size:8 final size:8 Alignment explanation

Indices: 41001467--41001516 Score: 57 Period size: 8 Copynumber: 6.1 Consensus size: 8 41001457 GTGCAAGAAA 41001467 ATAAAAAT 1 ATAAAAAT 41001475 ATAAAAAT 1 ATAAAAAT 41001483 ATAAAAAAT 1 AT-AAAAAT * 41001492 ATATAAAT 1 ATAAAAAT * 41001500 A-AAATAAA 1 ATAAA-AAT 41001508 ATAAAAAT 1 ATAAAAAT 41001516 A 1 A 41001517 AAATTGGGTT Statistics Matches: 35, Mismatches: 4, Indels: 6 0.78 0.09 0.13 Matches are distributed among these distances: 7 2 0.06 8 22 0.63 9 11 0.31 ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24 Consensus pattern (8 bp): ATAAAAAT Found at i:41001491 original size:17 final size:16 Alignment explanation

Indices: 41001469--41001519 Score: 68 Period size: 17 Copynumber: 3.1 Consensus size: 16 41001459 GCAAGAAAAT 41001469 AAAAATATAAAAATATA 1 AAAAATATAAAAATA-A * 41001486 AAAAATATATAAATAA 1 AAAAATATAAAAATAA 41001502 AATAAA-ATAAAAATAA 1 AA-AAATATAAAAATAA 41001518 AA 1 AA 41001520 TTGGGTTGCC Statistics Matches: 31, Mismatches: 2, Indels: 3 0.86 0.06 0.08 Matches are distributed among these distances: 16 14 0.45 17 17 0.55 ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22 Consensus pattern (16 bp): AAAAATATAAAAATAA Found at i:41001520 original size:11 final size:11 Alignment explanation

Indices: 41001464--41001520 Score: 52 Period size: 11 Copynumber: 5.5 Consensus size: 11 41001454 AAAGTGCAAG 41001464 AAAATAAAAAT 1 AAAATAAAAAT 41001475 ---ATAAAAAT 1 AAAATAAAAAT * 41001483 ATAAA-AAATAT 1 A-AAATAAAAAT 41001494 ATAAAT-AAAAT 1 A-AAATAAAAAT 41001505 AAAATAAAAAT 1 AAAATAAAAAT 41001516 AAAAT 1 AAAAT 41001521 TGGGTTGCCT Statistics Matches: 38, Mismatches: 2, Indels: 12 0.73 0.04 0.23 Matches are distributed among these distances: 8 8 0.21 10 4 0.11 11 25 0.66 12 1 0.03 ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23 Consensus pattern (11 bp): AAAATAAAAAT Found at i:41002644 original size:13 final size:13 Alignment explanation

Indices: 41002626--41002652 Score: 54 Period size: 13 Copynumber: 2.1 Consensus size: 13 41002616 TTTTCAAAAA 41002626 TTATGCATTTATT 1 TTATGCATTTATT 41002639 TTATGCATTTATT 1 TTATGCATTTATT 41002652 T 1 T 41002653 AATGTTGACT Statistics Matches: 14, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 14 1.00 ACGTcount: A:0.22, C:0.07, G:0.07, T:0.63 Consensus pattern (13 bp): TTATGCATTTATT Found at i:41002894 original size:50 final size:52 Alignment explanation

Indices: 41002758--41002894 Score: 156 Period size: 50 Copynumber: 2.7 Consensus size: 52 41002748 GTAAAGAGGT * * * * * * 41002758 CCCATTTAAGACCATGTCTAGGATATGGCGTTGGCACCGAGATGAGAGATCT 1 CCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGAGATGAGAGATCA * * 41002810 CCC--GTAAGACCATGTCTGGGACATGGCATCGGCATCGATATGAGA-A-CA 1 CCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGAGATGAGAGATCA * * 41002858 CCCATGTAAGACCATGTTTGGGACATGGCTTTGGCAT 1 CCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT 41002895 GTTATTATCA Statistics Matches: 72, Mismatches: 11, Indels: 6 0.81 0.12 0.07 Matches are distributed among these distances: 48 4 0.06 49 1 0.01 50 64 0.89 52 3 0.04 ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24 Consensus pattern (52 bp): CCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGAGATGAGAGATCA Found at i:41015484 original size:12 final size:12 Alignment explanation

Indices: 41015467--41015491 Score: 50 Period size: 12 Copynumber: 2.1 Consensus size: 12 41015457 TTTATTATTA 41015467 TTATTTCTTTAT 1 TTATTTCTTTAT 41015479 TTATTTCTTTAT 1 TTATTTCTTTAT 41015491 T 1 T 41015492 AATATTATTT Statistics Matches: 13, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 12 13 1.00 ACGTcount: A:0.16, C:0.08, G:0.00, T:0.76 Consensus pattern (12 bp): TTATTTCTTTAT Found at i:41017084 original size:6 final size:6 Alignment explanation

Indices: 41017070--41017108 Score: 60 Period size: 6 Copynumber: 6.5 Consensus size: 6 41017060 TTTTGTTTTG * * 41017070 TTTTGT TTTTAT TTTTAT TTTTAT TTTTAT TGTTAT TTT 1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTT 41017109 CTTCTATTTA Statistics Matches: 30, Mismatches: 3, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 6 30 1.00 ACGTcount: A:0.13, C:0.00, G:0.05, T:0.82 Consensus pattern (6 bp): TTTTAT Found at i:41017096 original size:18 final size:18 Alignment explanation

Indices: 41017070--41017164 Score: 61 Period size: 18 Copynumber: 5.1 Consensus size: 18 41017060 TTTTGTTTTG * * 41017070 TTTTGTTTTTATTTTTAT 1 TTTTATTTTTATTGTTAT 41017088 TTTTATTTTTATTGTTAT 1 TTTTATTTTTATTGTTAT * 41017106 TTTCT-TCTATTTA-TGTCAT 1 TTT-TAT-T-TTTATTGTTAT * * 41017125 TTTTATCTTTTGAACT-ATAT 1 TTTTAT-TTTT--ATTGTTAT * 41017145 TTTTATTTTTATGGTTAT 1 TTTTATTTTTATTGTTAT 41017163 TT 1 TT 41017165 CTAATCGAGT Statistics Matches: 61, Mismatches: 8, Indels: 16 0.72 0.09 0.19 Matches are distributed among these distances: 17 1 0.02 18 29 0.48 19 17 0.28 20 13 0.21 21 1 0.02 ACGTcount: A:0.17, C:0.05, G:0.06, T:0.72 Consensus pattern (18 bp): TTTTATTTTTATTGTTAT Found at i:41018916 original size:17 final size:17 Alignment explanation

Indices: 41018894--41018932 Score: 69 Period size: 17 Copynumber: 2.3 Consensus size: 17 41018884 TATTACATAA 41018894 AAGTCTGCAAGAAAGAT 1 AAGTCTGCAAGAAAGAT * 41018911 AAGTCTGCATGAAAGAT 1 AAGTCTGCAAGAAAGAT 41018928 AAGTC 1 AAGTC 41018933 CGTTGACTTT Statistics Matches: 21, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 17 21 1.00 ACGTcount: A:0.44, C:0.13, G:0.23, T:0.21 Consensus pattern (17 bp): AAGTCTGCAAGAAAGAT Found at i:41036310 original size:21 final size:21 Alignment explanation

Indices: 41036286--41036337 Score: 95 Period size: 21 Copynumber: 2.5 Consensus size: 21 41036276 AGAGGGATTG * 41036286 AAATTGTATAAATTGAAATCA 1 AAATTGTAAAAATTGAAATCA 41036307 AAATTGTAAAAATTGAAATCA 1 AAATTGTAAAAATTGAAATCA 41036328 AAATTGTAAA 1 AAATTGTAAA 41036338 GAGAAACAGA Statistics Matches: 30, Mismatches: 1, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 21 30 1.00 ACGTcount: A:0.56, C:0.04, G:0.10, T:0.31 Consensus pattern (21 bp): AAATTGTAAAAATTGAAATCA Found at i:41040039 original size:22 final size:24 Alignment explanation

Indices: 41039987--41040040 Score: 67 Period size: 25 Copynumber: 2.3 Consensus size: 24 41039977 TTTTTTATGA 41039987 TTAAATTATTGTTATTAAATATGCT 1 TTAAATTATTGTTATTAAATAT-CT * * 41040012 TGAAATTATTG-TATTATATAT-T 1 TTAAATTATTGTTATTAAATATCT 41040034 TTAAATT 1 TTAAATT 41040041 GAATTTATAA Statistics Matches: 26, Mismatches: 3, Indels: 3 0.81 0.09 0.09 Matches are distributed among these distances: 22 7 0.27 24 9 0.35 25 10 0.38 ACGTcount: A:0.37, C:0.02, G:0.07, T:0.54 Consensus pattern (24 bp): TTAAATTATTGTTATTAAATATCT Found at i:41043034 original size:22 final size:22 Alignment explanation

Indices: 41042992--41043034 Score: 52 Period size: 22 Copynumber: 2.0 Consensus size: 22 41042982 AAAAGATATA * * 41042992 AAATTAATTAAATAATGAAAAC 1 AAATTAAATAAATAATCAAAAC 41043014 AAATTAAATAAA-ACATCAAAA 1 AAATTAAATAAATA-ATCAAAA 41043035 GAGAACACTA Statistics Matches: 18, Mismatches: 2, Indels: 2 0.82 0.09 0.09 Matches are distributed among these distances: 21 1 0.06 22 17 0.94 ACGTcount: A:0.67, C:0.07, G:0.02, T:0.23 Consensus pattern (22 bp): AAATTAAATAAATAATCAAAAC Found at i:41044639 original size:20 final size:18 Alignment explanation

Indices: 41044602--41044641 Score: 53 Period size: 20 Copynumber: 2.1 Consensus size: 18 41044592 TTAAGGTTAA * 41044602 AATAGTAAAAAGTAAAAT 1 AATAGTAAAAAATAAAAT 41044620 AATATGTAATAAAATAAAAT 1 AATA-GTAA-AAAATAAAAT 41044640 AA 1 AA 41044642 AACATGTTAA Statistics Matches: 19, Mismatches: 1, Indels: 2 0.86 0.05 0.09 Matches are distributed among these distances: 18 4 0.21 19 4 0.21 20 11 0.58 ACGTcount: A:0.68, C:0.00, G:0.07, T:0.25 Consensus pattern (18 bp): AATAGTAAAAAATAAAAT Found at i:41045593 original size:42 final size:42 Alignment explanation

Indices: 41045493--41045649 Score: 176 Period size: 43 Copynumber: 3.7 Consensus size: 42 41045483 TGTGATATCA * 41045493 TGTAAGACCACGTCTAGGACTTTGGCATCG-ATTTGAGATTTACG 1 TGTAAGACCACGTCTAGGACATTGGCATCGTATTT--GA-TTACG * * * 41045537 TGTAAGACCATGTCTAGGACATTGGCGTCGTATATGATTACG 1 TGTAAGACCACGTCTAGGACATTGGCATCGTATTTGATTACG * * 41045579 TGTAAGACC-CTGTCT-GAGACAGTGGCATCGTTATTTGATTACA 1 TGTAAGACCAC-GTCTAG-GACATTGGCATCG-TATTTGATTACG * 41045622 TGTAAGACCACGTCTAGGACGTTGGCAT 1 TGTAAGACCACGTCTAGGACATTGGCAT 41045650 TGTACGAGCT Statistics Matches: 96, Mismatches: 11, Indels: 13 0.80 0.09 0.11 Matches are distributed among these distances: 41 1 0.01 42 29 0.30 43 34 0.35 44 29 0.30 45 3 0.03 ACGTcount: A:0.25, C:0.18, G:0.25, T:0.31 Consensus pattern (42 bp): TGTAAGACCACGTCTAGGACATTGGCATCGTATTTGATTACG Found at i:41052486 original size:52 final size:52 Alignment explanation

Indices: 41052423--41052526 Score: 190 Period size: 52 Copynumber: 2.0 Consensus size: 52 41052413 CAACAAAGTC * 41052423 ATTCTACTCTTAAAACGCAAAACTAACTTAAAGGTCCATCCGGACCACTGAT 1 ATTCTACTCTTAAAACGCAAAACTAACTTAAAGGCCCATCCGGACCACTGAT * 41052475 ATTCTATTCTTAAAACGCAAAACTAACTTAAAGGCCCATCCGGACCACTGAT 1 ATTCTACTCTTAAAACGCAAAACTAACTTAAAGGCCCATCCGGACCACTGAT 41052527 CCTAACCAAC Statistics Matches: 50, Mismatches: 2, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 52 50 1.00 ACGTcount: A:0.37, C:0.27, G:0.12, T:0.25 Consensus pattern (52 bp): ATTCTACTCTTAAAACGCAAAACTAACTTAAAGGCCCATCCGGACCACTGAT Found at i:41052692 original size:16 final size:16 Alignment explanation

Indices: 41052654--41052695 Score: 50 Period size: 16 Copynumber: 2.6 Consensus size: 16 41052644 ATCAATTGTT * 41052654 TAAATAATTTTATAAA 1 TAAATATTTTTATAAA * 41052670 TATATATTTTTAATAAA 1 TAAATATTTTT-ATAAA 41052687 -AAATATTTT 1 TAAATATTTT 41052696 CATTCACCGG Statistics Matches: 22, Mismatches: 3, Indels: 2 0.81 0.11 0.07 Matches are distributed among these distances: 16 17 0.77 17 5 0.23 ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50 Consensus pattern (16 bp): TAAATATTTTTATAAA Found at i:41060710 original size:3 final size:3 Alignment explanation

Indices: 41060702--41060745 Score: 88 Period size: 3 Copynumber: 14.7 Consensus size: 3 41060692 TTTTTTAAAG 41060702 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA 1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA 41060746 GATATTTTAG Statistics Matches: 41, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 3 41 1.00 ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32 Consensus pattern (3 bp): AAT Found at i:41062046 original size:16 final size:16 Alignment explanation

Indices: 41062025--41062063 Score: 51 Period size: 16 Copynumber: 2.4 Consensus size: 16 41062015 AATAATGGAA 41062025 ATATATAAAAACATGT 1 ATATATAAAAACATGT * ** 41062041 ATATATGAAAGTATGT 1 ATATATAAAAACATGT 41062057 ATATATA 1 ATATATA 41062064 TAAATTAAAG Statistics Matches: 19, Mismatches: 4, Indels: 0 0.83 0.17 0.00 Matches are distributed among these distances: 16 19 1.00 ACGTcount: A:0.51, C:0.03, G:0.10, T:0.36 Consensus pattern (16 bp): ATATATAAAAACATGT Found at i:41062111 original size:31 final size:31 Alignment explanation

Indices: 41062076--41062142 Score: 73 Period size: 31 Copynumber: 2.2 Consensus size: 31 41062066 AATTAAAGAG * 41062076 TATATAAAAAGTATAGAAT-TACATATATATA 1 TATATAAAAAGTA-AGAATATACATATAAATA * * ** 41062107 TATATGAAAATTAAGAATATGTATATAAATA 1 TATATAAAAAGTAAGAATATACATATAAATA 41062138 TATAT 1 TATAT 41062143 GTATATATAA Statistics Matches: 30, Mismatches: 5, Indels: 2 0.81 0.14 0.05 Matches are distributed among these distances: 30 5 0.17 31 25 0.83 ACGTcount: A:0.54, C:0.01, G:0.07, T:0.37 Consensus pattern (31 bp): TATATAAAAAGTAAGAATATACATATAAATA Found at i:41063478 original size:15 final size:15 Alignment explanation

Indices: 41063445--41063493 Score: 59 Period size: 15 Copynumber: 3.4 Consensus size: 15 41063435 CTTTTGAATA 41063445 TTGGGCTATAGGT--T 1 TTGGGCT-TAGGTGAT 41063459 TTGGGCTTAGGTGAT 1 TTGGGCTTAGGTGAT * 41063474 TTGGGTTTAGGTGA- 1 TTGGGCTTAGGTGAT 41063488 TTGGGC 1 TTGGGC 41063494 CTTGGGTCAA Statistics Matches: 31, Mismatches: 2, Indels: 4 0.84 0.05 0.11 Matches are distributed among these distances: 13 5 0.16 14 12 0.39 15 14 0.45 ACGTcount: A:0.12, C:0.06, G:0.41, T:0.41 Consensus pattern (15 bp): TTGGGCTTAGGTGAT Found at i:41063569 original size:19 final size:20 Alignment explanation

Indices: 41063547--41063605 Score: 86 Period size: 20 Copynumber: 3.0 Consensus size: 20 41063537 CAAAATTTAA * 41063547 AATTTTTATAAA-TATTTTG 1 AATTTTTAAAAATTATTTTG * 41063566 AA-TTTTAAAAATTATTTTC 1 AATTTTTAAAAATTATTTTG 41063585 AATTTTTAAAAATTATTTTG 1 AATTTTTAAAAATTATTTTG 41063605 A 1 A 41063606 TTATTTTGTA Statistics Matches: 35, Mismatches: 3, Indels: 3 0.85 0.07 0.07 Matches are distributed among these distances: 18 8 0.23 19 10 0.29 20 17 0.49 ACGTcount: A:0.41, C:0.02, G:0.03, T:0.54 Consensus pattern (20 bp): AATTTTTAAAAATTATTTTG Found at i:41063850 original size:5 final size:5 Alignment explanation

Indices: 41063840--41063865 Score: 52 Period size: 5 Copynumber: 5.2 Consensus size: 5 41063830 TTTAATTTTT 41063840 TCGAA TCGAA TCGAA TCGAA TCGAA T 1 TCGAA TCGAA TCGAA TCGAA TCGAA T 41063866 TTTATTCGCC Statistics Matches: 21, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 5 21 1.00 ACGTcount: A:0.38, C:0.19, G:0.19, T:0.23 Consensus pattern (5 bp): TCGAA Found at i:41073724 original size:37 final size:37 Alignment explanation

Indices: 41073621--41073829 Score: 343 Period size: 37 Copynumber: 5.7 Consensus size: 37 41073611 TACGTATGAT * * 41073621 CACTTATCAC-TTG-TCCCTGATCAGATAAGTGTAGC 1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC * 41073656 CACCTATCACTTTGTTTC-TGATCAGATAAGTGTAGC 1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC 41073692 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC 1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC * 41073729 CACTTATCACTTTATTTCTTGATCAGATAAGTGTAGC 1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC * 41073766 CACTTATCACTTTGTTTCTTGATAAGATAAGTGTAGC 1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC * 41073803 CACTTATCACTTTGTCTCTTGATCAGA 1 CACTTATCACTTTGTTTCTTGATCAGA 41073830 AGTACTCAAA Statistics Matches: 163, Mismatches: 8, Indels: 4 0.93 0.05 0.02 Matches are distributed among these distances: 35 9 0.06 36 38 0.23 37 116 0.71 ACGTcount: A:0.25, C:0.21, G:0.15, T:0.38 Consensus pattern (37 bp): CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC Found at i:41081844 original size:19 final size:19 Alignment explanation

Indices: 41081820--41081868 Score: 53 Period size: 20 Copynumber: 2.5 Consensus size: 19 41081810 CACTTCGTGT * 41081820 GCCAATATGCGCTTTGTGC 1 GCCAATATGCGCTTTGAGC ** 41081839 GCCAATGATGATCTTTGAGC 1 GCCAAT-ATGCGCTTTGAGC * 41081859 ACCAATATGC 1 GCCAATATGC 41081869 ACTATATGTG Statistics Matches: 24, Mismatches: 5, Indels: 2 0.77 0.16 0.06 Matches are distributed among these distances: 19 9 0.38 20 15 0.62 ACGTcount: A:0.24, C:0.24, G:0.22, T:0.29 Consensus pattern (19 bp): GCCAATATGCGCTTTGAGC Found at i:41083220 original size:17 final size:19 Alignment explanation

Indices: 41083198--41083233 Score: 58 Period size: 19 Copynumber: 2.0 Consensus size: 19 41083188 AAAATTTATG 41083198 AAAAATT-TT-AAAATATA 1 AAAAATTATTAAAAATATA 41083215 AAAAATTATTAAAAATATA 1 AAAAATTATTAAAAATATA 41083234 GAAAGTGGAA Statistics Matches: 17, Mismatches: 0, Indels: 2 0.89 0.00 0.11 Matches are distributed among these distances: 17 7 0.41 18 2 0.12 19 8 0.47 ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33 Consensus pattern (19 bp): AAAAATTATTAAAAATATA Found at i:41083261 original size:17 final size:18 Alignment explanation

Indices: 41083225--41083262 Score: 51 Period size: 17 Copynumber: 2.2 Consensus size: 18 41083215 AAAAATTATT * * 41083225 AAAAATATAGAAAGTGGA 1 AAAAATATAGAAAATAGA 41083243 AAAAATATA-AAAATAGA 1 AAAAATATAGAAAATAGA 41083260 AAA 1 AAA 41083263 TTTTAAAAAT Statistics Matches: 18, Mismatches: 2, Indels: 1 0.86 0.10 0.05 Matches are distributed among these distances: 17 9 0.50 18 9 0.50 ACGTcount: A:0.71, C:0.00, G:0.13, T:0.16 Consensus pattern (18 bp): AAAAATATAGAAAATAGA Found at i:41083648 original size:10 final size:10 Alignment explanation

Indices: 41083630--41083691 Score: 53 Period size: 10 Copynumber: 6.4 Consensus size: 10 41083620 TAAGTTTCTA * 41083630 ATAACATTTT 1 ATAATATTTT 41083640 ATAATATTTT 1 ATAATATTTT 41083650 -TAA-ATTTTT 1 ATAATA-TTTT 41083659 ATTAAT-TTTT 1 A-TAATATTTT 41083669 -TAATAATTTT 1 ATAAT-ATTTT 41083679 A-AATATTTT 1 ATAATATTTT 41083688 ATAA 1 ATAA 41083692 AATCATAATT Statistics Matches: 43, Mismatches: 1, Indels: 16 0.72 0.02 0.27 Matches are distributed among these distances: 8 5 0.12 9 13 0.30 10 22 0.51 11 3 0.07 ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58 Consensus pattern (10 bp): ATAATATTTT Found at i:41083678 original size:28 final size:29 Alignment explanation

Indices: 41083635--41083689 Score: 85 Period size: 28 Copynumber: 1.9 Consensus size: 29 41083625 TTCTAATAAC * 41083635 ATTTTATAATATTTTTAAAT-TTTTATTA 1 ATTTTATAATAATTTTAAATATTTTATTA * 41083663 ATTTTTTAATAATTTTAAATATTTTAT 1 ATTTTATAATAATTTTAAATATTTTAT 41083690 AAAATCATAA Statistics Matches: 24, Mismatches: 2, Indels: 1 0.89 0.07 0.04 Matches are distributed among these distances: 28 18 0.75 29 6 0.25 ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64 Consensus pattern (29 bp): ATTTTATAATAATTTTAAATATTTTATTA Found at i:41083731 original size:15 final size:16 Alignment explanation

Indices: 41083711--41083768 Score: 61 Period size: 15 Copynumber: 3.8 Consensus size: 16 41083701 TATTACAATT 41083711 TTTATATATTTT-TAA 1 TTTATATATTTTATAA 41083726 TTTATAT-TTTTATAA 1 TTTATATATTTTATAA * 41083741 TATATAT-TTTATATAA 1 TTTATATATTT-TATAA * 41083757 TTT-TTTATTTTA 1 TTTATATATTTTA 41083769 ATAAAGTTTC Statistics Matches: 37, Mismatches: 3, Indels: 6 0.80 0.07 0.13 Matches are distributed among these distances: 14 4 0.11 15 23 0.62 16 10 0.27 ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67 Consensus pattern (16 bp): TTTATATATTTTATAA Done.