Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.04

Sequence: scaffold601

Parameters: 2 7 7 80 10 50 500

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

Length: 1259944
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.29

Warning! 136746 characters in sequence are not A, C, G, or T


File 5 of 5

Found at i:953326 original size:22 final size:22

Alignment explanation

Indices: 953279--953327 Score: 64 Period size: 22 Copynumber: 2.2 Consensus size: 22 953269 ATGTGTGACT * * 953279 GAAAGATGACTGAAAGATGATT 1 GAAAAATGACTGAAAGATGATA 953301 GAAAAATGACTGAAAGATG-TCA 1 GAAAAATGACTGAAAGATGAT-A 953323 GAAAA 1 GAAAA 953328 GTAATAGAAA Statistics Matches: 24, Mismatches: 2, Indels: 2 0.86 0.07 0.07 Matches are distributed among these distances: 21 1 0.04 22 23 0.96 ACGTcount: A:0.51, C:0.06, G:0.24, T:0.18 Consensus pattern (22 bp): GAAAAATGACTGAAAGATGATA Found at i:961362 original size:12 final size:12 Alignment explanation

Indices: 961345--961374 Score: 51 Period size: 12 Copynumber: 2.5 Consensus size: 12 961335 TGTTATGCCA 961345 TTGTTTTTTTTT 1 TTGTTTTTTTTT 961357 TTGTTTTTTTTT 1 TTGTTTTTTTTT * 961369 TGGTTT 1 TTGTTT 961375 ATTGAATTAA Statistics Matches: 17, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 12 17 1.00 ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87 Consensus pattern (12 bp): TTGTTTTTTTTT Found at i:963161 original size:21 final size:21 Alignment explanation

Indices: 963135--963449 Score: 391 Period size: 21 Copynumber: 15.0 Consensus size: 21 963125 TCTTCATAAT * 963135 ATGATGATACTTCAACATTAC 1 ATGATGATACTTTAACATTAC * * 963156 ATGATGGTACTTCAACATTAC 1 ATGATGATACTTTAACATTAC 963177 AT-ACTGATA-TTTCAACATTAC 1 ATGA-TGATACTTT-AACATTAC * 963198 ATGATGGTACTTTAACATTAC 1 ATGATGATACTTTAACATTAC * * 963219 ATGCTGATACTTCAACATTAC 1 ATGATGATACTTTAACATTAC * * 963240 ATGATGGTGCTTTAACATTAC 1 ATGATGATACTTTAACATTAC * * 963261 ATGCTGATACTTCAACATTAC 1 ATGATGATACTTTAACATTAC * * 963282 GTGATGGTACTTTAACATTAC 1 ATGATGATACTTTAACATTAC * 963303 ATGATGGTACTTTAACATTAC 1 ATGATGATACTTTAACATTAC * * 963324 GTGCTGATACTTTAACATTAC 1 ATGATGATACTTTAACATTAC * 963345 ATGCTGATACTTTAACATTAC 1 ATGATGATACTTTAACATTAC * 963366 ATGCTGATACTTTAACATTAC 1 ATGATGATACTTTAACATTAC * * 963387 ATGCTGATACTTCAACATTAC 1 ATGATGATACTTTAACATTAC * 963408 ATGCTGATACTTTAACATTAC 1 ATGATGATACTTTAACATTAC * * 963429 ATGATGGTACTATGAACATTA 1 ATGATGATACT-TTAACATTA 963450 TCTACATAAG Statistics Matches: 260, Mismatches: 29, Indels: 9 0.87 0.10 0.03 Matches are distributed among these distances: 20 3 0.01 21 245 0.94 22 12 0.05 ACGTcount: A:0.33, C:0.18, G:0.12, T:0.36 Consensus pattern (21 bp): ATGATGATACTTTAACATTAC Found at i:963185 original size:42 final size:42 Alignment explanation

Indices: 963139--963449 Score: 442 Period size: 42 Copynumber: 7.4 Consensus size: 42 963129 CATAATATGA * * 963139 TGATACTTCAACATTACATGATGGTACTTCAACATTACATAC 1 TGATACTTCAACATTACATGATGGTACTTTAACATTACATGC * 963181 TGATATTTCAACATTACATGATGGTACTTTAACATTACATGC 1 TGATACTTCAACATTACATGATGGTACTTTAACATTACATGC * 963223 TGATACTTCAACATTACATGATGGTGCTTTAACATTACATGC 1 TGATACTTCAACATTACATGATGGTACTTTAACATTACATGC * * 963265 TGATACTTCAACATTACGTGATGGTACTTTAACATTACATGA 1 TGATACTTCAACATTACATGATGGTACTTTAACATTACATGC * * * * * 963307 TGGTACTTTAACATTACGTGCTGATACTTTAACATTACATGC 1 TGATACTTCAACATTACATGATGGTACTTTAACATTACATGC * * * 963349 TGATACTTTAACATTACATGCTGATACTTTAACATTACATGC 1 TGATACTTCAACATTACATGATGGTACTTTAACATTACATGC * * * 963391 TGATACTTCAACATTACATGCTGATACTTTAACATTACATGA 1 TGATACTTCAACATTACATGATGGTACTTTAACATTACATGC * * 963433 TGGTACTATGAACATTA 1 TGATACT-TCAACATTA 963450 TCTACATAAG Statistics Matches: 249, Mismatches: 19, Indels: 1 0.93 0.07 0.00 Matches are distributed among these distances: 42 241 0.97 43 8 0.03 ACGTcount: A:0.33, C:0.18, G:0.12, T:0.36 Consensus pattern (42 bp): TGATACTTCAACATTACATGATGGTACTTTAACATTACATGC Found at i:964243 original size:2 final size:2 Alignment explanation

Indices: 964236--964296 Score: 77 Period size: 2 Copynumber: 30.5 Consensus size: 2 964226 CCGTATGTGT * * * 964236 TC TC TC TC TC TC TC TC TC TC TT TC TC TC TT TC TT TC TC TC TC 1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC * * 964278 TC TC TC TT TT TC TC TC TC T 1 TC TC TC TC TC TC TC TC TC T 964297 GAGTGTCTGC Statistics Matches: 51, Mismatches: 8, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 2 51 1.00 ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59 Consensus pattern (2 bp): TC Found at i:964556 original size:2 final size:2 Alignment explanation

Indices: 964551--964603 Score: 106 Period size: 2 Copynumber: 26.5 Consensus size: 2 964541 GGGGGGGTTG 964551 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT 1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT 964593 CT CT CT CT CT C 1 CT CT CT CT CT C 964604 CATGTTTTGC Statistics Matches: 51, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 51 1.00 ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49 Consensus pattern (2 bp): CT Found at i:964940 original size:2 final size:2 Alignment explanation

Indices: 964933--964980 Score: 96 Period size: 2 Copynumber: 24.0 Consensus size: 2 964923 CTGTGCAAAA 964933 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT 1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT 964975 CT CT CT 1 CT CT CT 964981 GTGTGTAAAC Statistics Matches: 46, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 46 1.00 ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50 Consensus pattern (2 bp): CT Found at i:996176 original size:2 final size:2 Alignment explanation

Indices: 996169--996209 Score: 82 Period size: 2 Copynumber: 20.5 Consensus size: 2 996159 NNNNNNNNNN 996169 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C 1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C 996210 ACACACAAAT Statistics Matches: 39, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 39 1.00 ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49 Consensus pattern (2 bp): CT Found at i:999770 original size:2 final size:2 Alignment explanation

Indices: 999763--999810 Score: 96 Period size: 2 Copynumber: 24.0 Consensus size: 2 999753 AACATAAACA 999763 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG 1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG 999805 AG AG AG 1 AG AG AG 999811 TGTGTGTGGG Statistics Matches: 46, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 46 1.00 ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00 Consensus pattern (2 bp): AG Found at i:999815 original size:2 final size:2 Alignment explanation

Indices: 999810--999858 Score: 80 Period size: 2 Copynumber: 24.5 Consensus size: 2 999800 GAGAGAGAGA * * 999810 GT GT GT GT GG GT GT GG GT GT GT GT GT GT GT GT GT GT GT GT GT 1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT 999852 GT GT GT G 1 GT GT GT G 999859 ACACCCATTG Statistics Matches: 43, Mismatches: 4, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 2 43 1.00 ACGTcount: A:0.00, C:0.00, G:0.55, T:0.45 Consensus pattern (2 bp): GT Found at i:1001262 original size:50 final size:50 Alignment explanation

Indices: 1001204--1001317 Score: 156 Period size: 50 Copynumber: 2.3 Consensus size: 50 1001194 TTGGAAAAAG * 1001204 TTTTCAAAGTGCGTCAAATTTGGGACCAAATCAACGCACTTTGAAATTTT 1 TTTTCAAAGTGCGTCAAATTTGGGACCAAATCAACCCACTTTGAAATTTT * * ** * * 1001254 TTTTCAAAGTTCGTTAAATTTTTGACCAAGTTAACCCACTTTGAAATTTT 1 TTTTCAAAGTGCGTCAAATTTGGGACCAAATCAACCCACTTTGAAATTTT * 1001304 GTTTCAAAGTGCGT 1 TTTTCAAAGTGCGT 1001318 TTAGATGGTA Statistics Matches: 55, Mismatches: 9, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 50 55 1.00 ACGTcount: A:0.30, C:0.17, G:0.15, T:0.39 Consensus pattern (50 bp): TTTTCAAAGTGCGTCAAATTTGGGACCAAATCAACCCACTTTGAAATTTT Found at i:1011338 original size:2 final size:2 Alignment explanation

Indices: 1011331--1011355 Score: 50 Period size: 2 Copynumber: 12.5 Consensus size: 2 1011321 NNNNNNNNNN 1011331 TA TA TA TA TA TA TA TA TA TA TA TA T 1 TA TA TA TA TA TA TA TA TA TA TA TA T 1011356 TACGTTATAT Statistics Matches: 23, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 23 1.00 ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52 Consensus pattern (2 bp): TA Found at i:1012405 original size:2 final size:2 Alignment explanation

Indices: 1012398--1012482 Score: 143 Period size: 2 Copynumber: 42.5 Consensus size: 2 1012388 TGATAATAAT 1012398 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG 1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG * * * 1012440 AG GG GG AG AG AG AG AG AG AG GG AG AG AG AG AG AG AG AG AG AG 1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG 1012482 A 1 A 1012483 TCCAACTAAT Statistics Matches: 79, Mismatches: 4, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 2 79 1.00 ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00 Consensus pattern (2 bp): AG Found at i:1017693 original size:17 final size:17 Alignment explanation

Indices: 1017671--1017705 Score: 70 Period size: 17 Copynumber: 2.1 Consensus size: 17 1017661 ATCACTTTGC 1017671 AACCACTATTGAAATAA 1 AACCACTATTGAAATAA 1017688 AACCACTATTGAAATAA 1 AACCACTATTGAAATAA 1017705 A 1 A 1017706 TTATTTAATT Statistics Matches: 18, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 17 18 1.00 ACGTcount: A:0.54, C:0.17, G:0.06, T:0.23 Consensus pattern (17 bp): AACCACTATTGAAATAA Found at i:1018158 original size:53 final size:53 Alignment explanation

Indices: 1018073--1018210 Score: 204 Period size: 53 Copynumber: 2.6 Consensus size: 53 1018063 GGGGTTACTT * * * * 1018073 CACTGTTGAAATATAGTATTTCAATAGTGGTTAAGGATGCGATTCATTTCAAC 1 CACTATTGAAATAAAGTATTTCAATAGTGGTTAAGGATACCATTCATTTCAAC ** * * 1018126 CACTATTGAAATAATTTATTTCAATAGTGGTTAGGGATACCTTTCATTTCAAC 1 CACTATTGAAATAAAGTATTTCAATAGTGGTTAAGGATACCATTCATTTCAAC 1018179 CACTATTGAAATAAAGTATTTCAATAGTGGTT 1 CACTATTGAAATAAAGTATTTCAATAGTGGTT 1018211 GATTATGCAT Statistics Matches: 75, Mismatches: 10, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 53 75 1.00 ACGTcount: A:0.33, C:0.13, G:0.16, T:0.38 Consensus pattern (53 bp): CACTATTGAAATAAAGTATTTCAATAGTGGTTAAGGATACCATTCATTTCAAC Found at i:1018506 original size:53 final size:53 Alignment explanation

Indices: 1018439--1018622 Score: 190 Period size: 53 Copynumber: 3.5 Consensus size: 53 1018429 ATAACATCCT * * * * 1018439 ACCACTATTAAAATATTTTATTTCAATAATGGTTGTAATGAACCACAT-TCTGA 1 ACCACTATTGAAATAATTTATTTCAATAATGGTTGTAATGAAACACATACCT-A * * * ** 1018492 ACCACAATTGAAATAAATTATTTCAATAGTGGTTGTAATGAAATGCATACCTA 1 ACCACTATTGAAATAATTTATTTCAATAATGGTTGTAATGAAACACATACCTA * * ** * * * * 1018545 ACCACTATTGAAATAATTTATTTCAATAGTGGATAAAATAAAACGCAGACCCA 1 ACCACTATTGAAATAATTTATTTCAATAATGGTTGTAATGAAACACATACCTA * 1018598 ACCACTATTGAAATAATCTATTTCA 1 ACCACTATTGAAATAATTTATTTCA 1018623 TTCAATATTG Statistics Matches: 111, Mismatches: 19, Indels: 2 0.84 0.14 0.02 Matches are distributed among these distances: 53 109 0.98 54 2 0.02 ACGTcount: A:0.41, C:0.16, G:0.10, T:0.33 Consensus pattern (53 bp): ACCACTATTGAAATAATTTATTTCAATAATGGTTGTAATGAAACACATACCTA Found at i:1019430 original size:17 final size:17 Alignment explanation

Indices: 1019405--1019439 Score: 52 Period size: 17 Copynumber: 2.1 Consensus size: 17 1019395 ATTAAAATTA * 1019405 TTTACTTCAATAGTGGT 1 TTTACTTCAAAAGTGGT * 1019422 TTTATTTCAAAAGTGGT 1 TTTACTTCAAAAGTGGT 1019439 T 1 T 1019440 GCAGGGTGAT Statistics Matches: 16, Mismatches: 2, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 17 16 1.00 ACGTcount: A:0.26, C:0.09, G:0.17, T:0.49 Consensus pattern (17 bp): TTTACTTCAAAAGTGGT Found at i:1019438 original size:84 final size:83 Alignment explanation

Indices: 1019291--1019509 Score: 296 Period size: 84 Copynumber: 2.6 Consensus size: 83 1019281 AGTTCTTATC * * * * 1019291 ATGAAATACATCCCCAACCTCTATTAAATCA-TTACTTCAATAGTGGTTGTATTTCAATAGTGGT 1 ATGAAATACATCCCCAACCACTATTAAATAATTTACTTCAATAGTGGTTTTATTTCAAAAGTGGT 1019355 TGCAAAGTCATTTTTCTA 66 TGCAAAGTCATTTTTCTA * * 1019373 ATGAAATACGTCCCCAACCACTATTAAAATTATTTACTTCAATAGTGGTTTTATTTCAAAAGTGG 1 ATGAAATACATCCCCAACCACTATT-AAATAATTTACTTCAATAGTGGTTTTATTTCAAAAGTGG ** * 1019438 TTGCAGGGTGATTTTTCTA 65 TTGCAAAGTCATTTTTCTA * * * * 1019457 ATGAAATGCATTCTCAACCACTATTGAAATAATTTATTTCAATAGTGGTTTTA 1 ATGAAATACATCCCCAACCACTATT-AAATAATTTACTTCAATAGTGGTTTTA 1019510 AGGTAAAGTC Statistics Matches: 120, Mismatches: 15, Indels: 2 0.88 0.11 0.01 Matches are distributed among these distances: 82 23 0.19 83 5 0.04 84 92 0.77 ACGTcount: A:0.32, C:0.16, G:0.13, T:0.38 Consensus pattern (83 bp): ATGAAATACATCCCCAACCACTATTAAATAATTTACTTCAATAGTGGTTTTATTTCAAAAGTGGT TGCAAAGTCATTTTTCTA Found at i:1029468 original size:25 final size:25 Alignment explanation

Indices: 1029435--1029483 Score: 98 Period size: 25 Copynumber: 2.0 Consensus size: 25 1029425 ATACTTTTAC 1029435 ACAATACTGACCAAAGGAAAAAAAT 1 ACAATACTGACCAAAGGAAAAAAAT 1029460 ACAATACTGACCAAAGGAAAAAAA 1 ACAATACTGACCAAAGGAAAAAAA 1029484 AAATATAGGG Statistics Matches: 24, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 25 24 1.00 ACGTcount: A:0.61, C:0.16, G:0.12, T:0.10 Consensus pattern (25 bp): ACAATACTGACCAAAGGAAAAAAAT Found at i:1030242 original size:18 final size:16 Alignment explanation

Indices: 1030219--1030258 Score: 62 Period size: 16 Copynumber: 2.4 Consensus size: 16 1030209 ACAAAATCGG 1030219 GAGAGAGAGAAAGAACAA 1 GAGAGAGAG-AA-AACAA 1030237 GAGAGAGAGAAAACAA 1 GAGAGAGAGAAAACAA 1030253 GAGAGA 1 GAGAGA 1030259 AAACAAGCGA Statistics Matches: 22, Mismatches: 0, Indels: 2 0.92 0.00 0.08 Matches are distributed among these distances: 16 11 0.50 17 2 0.09 18 9 0.41 ACGTcount: A:0.60, C:0.05, G:0.35, T:0.00 Consensus pattern (16 bp): GAGAGAGAGAAAACAA Found at i:1030270 original size:14 final size:12 Alignment explanation

Indices: 1030240--1030271 Score: 55 Period size: 12 Copynumber: 2.7 Consensus size: 12 1030230 AGAACAAGAG 1030240 AGAGAGAAAACA 1 AGAGAGAAAACA 1030252 AGAGAGAAAACA 1 AGAGAGAAAACA * 1030264 AGCGAGAA 1 AGAGAGAA 1030272 GAATGTTAGC Statistics Matches: 19, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 12 19 1.00 ACGTcount: A:0.62, C:0.09, G:0.28, T:0.00 Consensus pattern (12 bp): AGAGAGAAAACA Found at i:1040379 original size:3 final size:3 Alignment explanation

Indices: 1040371--1040431 Score: 122 Period size: 3 Copynumber: 20.3 Consensus size: 3 1040361 AAATTAATTT 1040371 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG 1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG 1040419 ATG ATG ATG ATG A 1 ATG ATG ATG ATG A 1040432 AGTAAGCATT Statistics Matches: 58, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 3 58 1.00 ACGTcount: A:0.34, C:0.00, G:0.33, T:0.33 Consensus pattern (3 bp): ATG Found at i:1046777 original size:20 final size:20 Alignment explanation

Indices: 1046740--1046779 Score: 53 Period size: 20 Copynumber: 2.0 Consensus size: 20 1046730 TTTCATATTA * ** 1046740 AATAAGAGGTCTTTTGACCT 1 AATAACAGGTCTAATGACCT 1046760 AATAACAGGTCTAATGACCT 1 AATAACAGGTCTAATGACCT 1046780 GTAATAAAAA Statistics Matches: 17, Mismatches: 3, Indels: 0 0.85 0.15 0.00 Matches are distributed among these distances: 20 17 1.00 ACGTcount: A:0.35, C:0.17, G:0.17, T:0.30 Consensus pattern (20 bp): AATAACAGGTCTAATGACCT Found at i:1048943 original size:2 final size:2 Alignment explanation

Indices: 1048936--1048982 Score: 94 Period size: 2 Copynumber: 23.5 Consensus size: 2 1048926 TTTGTACTTT 1048936 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG 1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG 1048978 AG AG A 1 AG AG A 1048983 TAACATAGTG Statistics Matches: 45, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 45 1.00 ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00 Consensus pattern (2 bp): AG Found at i:1050375 original size:173 final size:173 Alignment explanation

Indices: 1050111--1050591 Score: 479 Period size: 173 Copynumber: 2.8 Consensus size: 173 1050101 GGGCAACAAT * 1050111 GGGGGTCGAAGTTTTACATAGGAATATATAGAGTAAATCTTTAAATATCTTCTTCTCAGAAACTA 1 GGGGGTCGAAGTTTTACATAGGAATATATAGAGTAAATCTTTAAATATCTTCTTCTCAGAAACAA * * * * 1050176 ATTAGCCAGGAAAGCTGAAACTTGTGTGGTAA-CAT-TCTCAGGTAGTGTAGATTCAAAGATG-G 66 ATTAGCCAGGAAAACTGAAACTTGTGT-GAAAGCATCT-TCAGATAATGTAGATTCAAAGATGTG * 1050238 AAAAATCATGATCCCCGGTTGTAGGGTGGGGCCACAATGGGGGGGG 129 -AAAATCATGACCCCCGGTTGTAGGGTGGGGCCACAATGGGGGGGG ** 1050284 GGGGGTCGATA-TTTTACATAGGAATATATAGAGTACTTCTTTAGAA-ATCTTCTTCTCAGAAAC 1 GGGGGTCGA-AGTTTTACATAGGAATATATAGAGTAAATCTTTA-AATATCTTCTTCTCAGAAAC * * * 1050347 AAATCT-GCCAGTAAAACTGAACCTTGTGTGAAAGCATCTTCAGATAATGTAGATTCAAAGTTGT 64 AAAT-TAGCCAGGAAAACTGAAACTTGTGTGAAAGCATCTTCAGATAATGTAGATTCAAAGATGT * ** * ** * 1050411 GAAAATCATGACCCCCAGAGGTAGGTTAAGGCCACAAT-------A 128 GAAAATCATGACCCCCGGTTGTAGGGTGGGGCCACAATGGGGGGGG ** * * * * * * ** 1050450 GTTGATCGAAATTTTACATAGAAATA-AAAGAGTAAATCTTTAAAAATCTTCTTTTCAGAAAGTA 1 GGGGGTCGAAGTTTTACATAGGAATATATAGAGTAAATCTTTAAATATCTTCTTCTCAGAAACAA * * * * * * * 1050514 ATGAGCCAGGAAAGCTGAAACTTGTGTGAAAGCATCCTGA-AGTAGTGTAGATTCAAAGTTATGA 66 ATTAGCCAGGAAAACTGAAACTTGTGTGAAAGCATCTTCAGA-TAATGTAGATTCAAAGATGTGA 1050578 AAATCATGACCCCC 130 AAATCATGACCCCC 1050592 TGGGGTAGAG Statistics Matches: 262, Mismatches: 36, Indels: 28 0.80 0.11 0.09 Matches are distributed among these distances: 164 3 0.01 165 97 0.37 166 20 0.08 172 3 0.01 173 133 0.51 174 6 0.02 ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28 Consensus pattern (173 bp): GGGGGTCGAAGTTTTACATAGGAATATATAGAGTAAATCTTTAAATATCTTCTTCTCAGAAACAA ATTAGCCAGGAAAACTGAAACTTGTGTGAAAGCATCTTCAGATAATGTAGATTCAAAGATGTGAA AATCATGACCCCCGGTTGTAGGGTGGGGCCACAATGGGGGGGG Found at i:1050549 original size:165 final size:163 Alignment explanation

Indices: 1050018--1050652 Score: 631 Period size: 165 Copynumber: 3.8 Consensus size: 163 1050008 ACCTTAAAAA * * * 1050018 AGGAAAGCTGAAACTTGTGAT-ATAGCATTCTCAGGTAGTGAAGATTCAAAGTTGTGAAAATCAT 1 AGGAAAGCTGAAACTTGTG-TGAAAGCATTCTCAGATAGTGTAGATTCAAAGTTGTGAAAATCAT * * 1050082 GACCCCCTAGGGTAAGGTGGGGCAACAATGGGGGTCGAAGTTTTACATAGGAATATATAGAGTAA 65 GACCCCC-AGGGT-AGGTGGGGCCACAATGGGGGTCGAAATTTTACATAGGAATATATAGAGTAA * * 1050147 ATCTTTAAATATCTTCTTCTCAGAAACTAATTAGCC 128 ATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGCC * * * 1050183 AGGAAAGCTGAAACTTGTGTGGTAA-CATTCTCAGGTAGTGTAGATTCAAAGATG-GAAAAATCA 1 AGGAAAGCTGAAACTTGTGT-GAAAGCATTCTCAGATAGTGTAGATTCAAAGTTGTG-AAAATCA * * 1050246 TGATCCCC-GGTTGTAGGGTGGGGCCACAATGGGGGGGGGGGGGTCGATATTTTACATAGGAATA 64 TGACCCCCAGG--GTA-GGTGGGGCCACAAT--------GGGGGTCGAAATTTTACATAGGAATA ** * * * 1050310 TATAGAGTACTTCTTTAGAAATCTTCTTCTCAGAAACAAATCTGCC 118 TATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGCC * * * * 1050356 AGTAAAACTGAACCTTGTGTGAAAGCA-TCTTCAGATAATGTAGATTCAAAGTTGTGAAAATCAT 1 AGGAAAGCTGAAACTTGTGTGAAAGCATTC-TCAGATAGTGTAGATTCAAAGTTGTGAAAATCAT ** ** * * * 1050420 GACCCCCAGAGGTAGGTTAAGGCCACAATAGTTGATCGAAATTTTACATAGAAATA-AAAGAGTA 65 GACCCCCAG-GGTAGG-TGGGGCCACAAT-GGGGGTCGAAATTTTACATAGGAATATATAGAGTA * * * 1050484 AATCTTTAAAAATCTTCTTTTCAGAAAGTAATGAGCC 127 AATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGCC * * * 1050521 AGGAAAGCTGAAACTTGTGTGAAAGCATCCTGA-AGTAGTGTAGATTCAAAGTTATGAAAATCAT 1 AGGAAAGCTGAAACTTGTGTGAAAGCATTCTCAGA-TAGTGTAGATTCAAAGTTGTGAAAATCAT * * * ** * 1050585 GACCCCCTGGGGTAGAGT--AGCCACAATTGGGGGTCGAAGTTTTTTATAGGAATATATTGAGTA 65 GACCCCC-AGGGTAG-GTGGGGCCACAA-TGGGGGTCGAAATTTTACATAGGAATATATAGAGTA 1050648 AATCT 127 AATCT 1050653 ACCTCTGGTA Statistics Matches: 386, Mismatches: 58, Indels: 53 0.78 0.12 0.11 Matches are distributed among these distances: 163 28 0.07 164 16 0.04 165 177 0.46 166 25 0.06 172 7 0.02 173 130 0.34 174 2 0.01 175 1 0.00 ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28 Consensus pattern (163 bp): AGGAAAGCTGAAACTTGTGTGAAAGCATTCTCAGATAGTGTAGATTCAAAGTTGTGAAAATCATG ACCCCCAGGGTAGGTGGGGCCACAATGGGGGTCGAAATTTTACATAGGAATATATAGAGTAAATC TTTAAAAATCTTCTTCTCAGAAACTAATCAGCC Found at i:1051247 original size:16 final size:16 Alignment explanation

Indices: 1051223--1051266 Score: 79 Period size: 16 Copynumber: 2.8 Consensus size: 16 1051213 ATGGTAGACG * 1051223 GACATCTCGGCCCAAC 1 GACACCTCGGCCCAAC 1051239 GACACCTCGGCCCAAC 1 GACACCTCGGCCCAAC 1051255 GACACCTCGGCC 1 GACACCTCGGCC 1051267 AAGGGCTTTT Statistics Matches: 27, Mismatches: 1, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 16 27 1.00 ACGTcount: A:0.23, C:0.48, G:0.20, T:0.09 Consensus pattern (16 bp): GACACCTCGGCCCAAC Found at i:1052512 original size:16 final size:16 Alignment explanation

Indices: 1052491--1052544 Score: 81 Period size: 16 Copynumber: 3.4 Consensus size: 16 1052481 GACCCGTCTT * * 1052491 GGCCGAGGTGTCCTGG 1 GGCCGAGGTGTCGTTG * 1052507 GGCCGAAGTGTCGTTG 1 GGCCGAGGTGTCGTTG 1052523 GGCCGAGGTGTCGTTG 1 GGCCGAGGTGTCGTTG 1052539 GGCCGA 1 GGCCGA 1052545 CATAGAGTTA Statistics Matches: 34, Mismatches: 4, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 16 34 1.00 ACGTcount: A:0.09, C:0.22, G:0.48, T:0.20 Consensus pattern (16 bp): GGCCGAGGTGTCGTTG Found at i:1055641 original size:2 final size:2 Alignment explanation

Indices: 1055636--1055704 Score: 113 Period size: 2 Copynumber: 35.0 Consensus size: 2 1055626 TATATATATA * 1055636 TG TG TG TG TG CG TG TG TG TG TG TG TG TG TG TG T- TG TG TG TG 1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG * 1055677 TG TG TA TG TG TG TG TG TG TG TG TG TG TG 1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG 1055705 CATTTGATAT Statistics Matches: 62, Mismatches: 4, Indels: 2 0.91 0.06 0.03 Matches are distributed among these distances: 1 1 0.02 2 61 0.98 ACGTcount: A:0.01, C:0.01, G:0.48, T:0.49 Consensus pattern (2 bp): TG Found at i:1059395 original size:20 final size:19 Alignment explanation

Indices: 1059372--1059419 Score: 53 Period size: 22 Copynumber: 2.4 Consensus size: 19 1059362 CAAATAAACA 1059372 ATGTTAAGACTTTATTTTAG 1 ATGTTAAGA-TTTATTTTAG 1059392 ATGTTTAGAAGATTTATTTTAG 1 ATG-TT--AAGATTTATTTTAG 1059414 AT-TTAA 1 ATGTTAA 1059420 ACCTAAATAT Statistics Matches: 25, Mismatches: 0, Indels: 8 0.76 0.00 0.24 Matches are distributed among these distances: 18 2 0.08 20 5 0.20 21 2 0.08 22 12 0.48 23 4 0.16 ACGTcount: A:0.33, C:0.02, G:0.15, T:0.50 Consensus pattern (19 bp): ATGTTAAGATTTATTTTAG Found at i:1065481 original size:19 final size:19 Alignment explanation

Indices: 1065457--1065509 Score: 81 Period size: 19 Copynumber: 2.8 Consensus size: 19 1065447 ATGCAAGACT 1065457 CCAAAGTTCGATGGTTACG 1 CCAAAGTTCGATGGTTACG 1065476 CCAAAG-TCTGATGGTTACG 1 CCAAAGTTC-GATGGTTACG * 1065495 CCAAAGTCCGATGGT 1 CCAAAGTTCGATGGT 1065510 ATGTTGCCGA Statistics Matches: 31, Mismatches: 1, Indels: 4 0.86 0.03 0.11 Matches are distributed among these distances: 18 2 0.06 19 28 0.90 20 1 0.03 ACGTcount: A:0.26, C:0.23, G:0.26, T:0.25 Consensus pattern (19 bp): CCAAAGTTCGATGGTTACG Found at i:1066061 original size:5 final size:5 Alignment explanation

Indices: 1066053--1066085 Score: 66 Period size: 5 Copynumber: 6.6 Consensus size: 5 1066043 CAATGTCATG 1066053 TGTAA TGTAA TGTAA TGTAA TGTAA TGTAA TGT 1 TGTAA TGTAA TGTAA TGTAA TGTAA TGTAA TGT 1066086 CATGCCATTA Statistics Matches: 28, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 5 28 1.00 ACGTcount: A:0.36, C:0.00, G:0.21, T:0.42 Consensus pattern (5 bp): TGTAA Found at i:1077093 original size:2 final size:2 Alignment explanation

Indices: 1077088--1077126 Score: 78 Period size: 2 Copynumber: 19.5 Consensus size: 2 1077078 ATATTTCAAC 1077088 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A 1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A 1077127 ATATTTAAGT Statistics Matches: 37, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 37 1.00 ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00 Consensus pattern (2 bp): AG Found at i:1081590 original size:20 final size:20 Alignment explanation

Indices: 1081565--1081647 Score: 166 Period size: 20 Copynumber: 4.2 Consensus size: 20 1081555 AACAAAACTG 1081565 CAACTGGTTACAATCCATAT 1 CAACTGGTTACAATCCATAT 1081585 CAACTGGTTACAATCCATAT 1 CAACTGGTTACAATCCATAT 1081605 CAACTGGTTACAATCCATAT 1 CAACTGGTTACAATCCATAT 1081625 CAACTGGTTACAATCCATAT 1 CAACTGGTTACAATCCATAT 1081645 CAA 1 CAA 1081648 TTTGTTTTTA Statistics Matches: 63, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 20 63 1.00 ACGTcount: A:0.36, C:0.25, G:0.10, T:0.29 Consensus pattern (20 bp): CAACTGGTTACAATCCATAT Found at i:1082986 original size:1 final size:1 Alignment explanation

Indices: 1082930--1082967 Score: 76 Period size: 1 Copynumber: 38.0 Consensus size: 1 1082920 ACTTTACTGA 1082930 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 1082968 ATATATATAT Statistics Matches: 37, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 1 37 1.00 ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00 Consensus pattern (1 bp): T Found at i:1091191 original size:44 final size:44 Alignment explanation

Indices: 1091126--1091211 Score: 145 Period size: 44 Copynumber: 2.0 Consensus size: 44 1091116 TCAGCAAAAG * 1091126 TAGAATTAAGATGTTTTGTTTATCGGAATATTCCATTTTATTCA 1 TAGAATTAAGATGTTTCGTTTATCGGAATATTCCATTTTATTCA * * 1091170 TAGAATTAAGATGTTTCGTTTATCGGAGTATTTCATTTTATT 1 TAGAATTAAGATGTTTCGTTTATCGGAATATTCCATTTTATT 1091212 TAACCAATTA Statistics Matches: 39, Mismatches: 3, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 44 39 1.00 ACGTcount: A:0.28, C:0.08, G:0.15, T:0.49 Consensus pattern (44 bp): TAGAATTAAGATGTTTCGTTTATCGGAATATTCCATTTTATTCA Found at i:1100072 original size:21 final size:21 Alignment explanation

Indices: 1100045--1100165 Score: 111 Period size: 21 Copynumber: 5.8 Consensus size: 21 1100035 GTCGACAGAC * 1100045 CTGACAAGTTATCATAAAGAT 1 CTGACAAGTTGTCATAAAGAT * * 1100066 TTGACAAGTTGTCATGAAGAT 1 CTGACAAGTTGTCATAAAGAT * 1100087 CTGTCAAGTTGTCA-AAATGAT 1 CTGACAAGTTGTCATAAA-GAT * * * 1100108 TTCACAAGTTGTCATAAAGGT 1 CTGACAAGTTGTCATAAAGAT * * 1100129 CTGACAAGTTGATGAGAAA-AT 1 CTGACAAGTTG-TCATAAAGAT * * 1100150 CTAACAAGTTGACATA 1 CTGACAAGTTGTCATA 1100166 GTTATCGATC Statistics Matches: 78, Mismatches: 19, Indels: 7 0.75 0.18 0.07 Matches are distributed among these distances: 20 4 0.05 21 66 0.85 22 8 0.10 ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30 Consensus pattern (21 bp): CTGACAAGTTGTCATAAAGAT Found at i:1100109 original size:42 final size:42 Alignment explanation

Indices: 1100045--1100139 Score: 129 Period size: 42 Copynumber: 2.3 Consensus size: 42 1100035 GTCGACAGAC * * * 1100045 CTGACAAGTTATCATAAAGATTTGACAAGTTGTCATGAAGAT 1 CTGACAAGTTGTCATAAAGATTTCACAAGTTGTCATAAAGAT * * 1100087 CTGTCAAGTTGTCA-AAATGATTTCACAAGTTGTCATAAAGGT 1 CTGACAAGTTGTCATAAA-GATTTCACAAGTTGTCATAAAGAT 1100129 CTGACAAGTTG 1 CTGACAAGTTG 1100140 ATGAGAAAAT Statistics Matches: 46, Mismatches: 6, Indels: 2 0.85 0.11 0.04 Matches are distributed among these distances: 41 3 0.07 42 43 0.93 ACGTcount: A:0.35, C:0.14, G:0.20, T:0.32 Consensus pattern (42 bp): CTGACAAGTTGTCATAAAGATTTCACAAGTTGTCATAAAGAT Found at i:1101030 original size:11 final size:11 Alignment explanation

Indices: 1101008--1101113 Score: 131 Period size: 11 Copynumber: 9.6 Consensus size: 11 1100998 AAGCTTGATT * 1101008 TAAACACAGAG 1 TAAACCCAGAG * 1101019 TGAACCCAGAG 1 TAAACCCAGAG * 1101030 TAAACCCAAAG 1 TAAACCCAGAG * 1101041 TGAACCCAGAG 1 TAAACCCAGAG * 1101052 TAAACCCAAAG 1 TAAACCCAGAG * 1101063 TGAACCCAGAG 1 TAAACCCAGAG * 1101074 TAAACCCAAAG 1 TAAACCCAGAG 1101085 TAAACCCAGAG 1 TAAACCCAGAG * 1101096 TAAACCCAAAG 1 TAAACCCAGAG * 1101107 TGAACCC 1 TAAACCC 1101114 CAACTGGACA Statistics Matches: 80, Mismatches: 15, Indels: 0 0.84 0.16 0.00 Matches are distributed among these distances: 11 80 1.00 ACGTcount: A:0.46, C:0.27, G:0.17, T:0.09 Consensus pattern (11 bp): TAAACCCAGAG Found at i:1101042 original size:22 final size:22 Alignment explanation

Indices: 1101017--1101113 Score: 185 Period size: 22 Copynumber: 4.4 Consensus size: 22 1101007 TTAAACACAG 1101017 AGTGAACCCAGAGTAAACCCAA 1 AGTGAACCCAGAGTAAACCCAA 1101039 AGTGAACCCAGAGTAAACCCAA 1 AGTGAACCCAGAGTAAACCCAA 1101061 AGTGAACCCAGAGTAAACCCAA 1 AGTGAACCCAGAGTAAACCCAA * 1101083 AGTAAACCCAGAGTAAACCCAA 1 AGTGAACCCAGAGTAAACCCAA 1101105 AGTGAACCC 1 AGTGAACCC 1101114 CAACTGGACA Statistics Matches: 73, Mismatches: 2, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 22 73 1.00 ACGTcount: A:0.45, C:0.28, G:0.18, T:0.09 Consensus pattern (22 bp): AGTGAACCCAGAGTAAACCCAA Found at i:1102333 original size:173 final size:173 Alignment explanation

Indices: 1102136--1102512 Score: 453 Period size: 173 Copynumber: 2.2 Consensus size: 173 1102126 TGGGTCCTAA 1102136 ATTTCAGATGCTGGAGGAGGTTAAGGTTTTTAGAGCTGGTTAAAGTGTTT-GTTGCAGGTGCCCT 1 ATTTCAGATGCTGGAGGAGGTTAAGGTTTTTAGAGCTGGTTAAAGT-TTTCGTTGCAGGTGCCCT * * * 1102200 TTGATAGAAATT-TC-TAAGTAACTGCTGGTCCTACCAACTTCACCAAACTTGCATGGATTAG-T 65 CTGAT-GAAATTATCTTAA-TAACTACTGGT-CT--CAACTTCACCAAACTTGCATGG-TGAGTT * * * 1102262 CT-T-ATACTGATGAACCAGA-CAGCTTGAATGCTAAATCTGAGCTATAG 124 CTATGATAATGATGAACCAGAGAAGCTTGAATGCTAAATCTGAGCCATAG * * 1102309 GTTTCAGATGCTGGAGGAGGTTAAGGTTTTTAGAGCTGGTTAAAGTTTTCGTTGCAGGTGTCCTC 1 ATTTCAGATGCTGGAGGAGGTTAAGGTTTTTAGAGCTGGTTAAAGTTTTCGTTGCAGGTGCCCTC ** * * * * 1102374 TGATGATTTTATCTTAATTACTACTGGTCTTAACTTCACCAAACTTGCATGGTGCGTTTTATGAT 66 TGATGAAATTATCTTAATAACTACTGGTCTCAACTTCACCAAACTTGCATGGTGAGTTCTATGAT ** 1102439 AATGATGCTCCAGAGAAGCTTGAATGCTAAATCTGAGCCATAG 131 AATGATGAACCAGAGAAGCTTGAATGCTAAATCTGAGCCATAG ** * * * 1102482 ATTTTGGATGCTGGATGAGGTTTAGTTTTTT 1 ATTTCAGATGCTGGAGGAGGTTAAGGTTTTT 1102513 TGGAACAGGT Statistics Matches: 175, Mismatches: 22, Indels: 14 0.83 0.10 0.07 Matches are distributed among these distances: 169 2 0.01 170 23 0.13 171 1 0.01 172 22 0.13 173 124 0.71 174 3 0.02 ACGTcount: A:0.25, C:0.15, G:0.24, T:0.36 Consensus pattern (173 bp): ATTTCAGATGCTGGAGGAGGTTAAGGTTTTTAGAGCTGGTTAAAGTTTTCGTTGCAGGTGCCCTC TGATGAAATTATCTTAATAACTACTGGTCTCAACTTCACCAAACTTGCATGGTGAGTTCTATGAT AATGATGAACCAGAGAAGCTTGAATGCTAAATCTGAGCCATAG Found at i:1104834 original size:23 final size:23 Alignment explanation

Indices: 1104807--1104851 Score: 74 Period size: 23 Copynumber: 2.0 Consensus size: 23 1104797 AAACAATTAC 1104807 AAAACAAATAAAT-AGAATAAATT 1 AAAACAAATAAATAAG-ATAAATT 1104830 AAAACAAATAAATAAGATAAAT 1 AAAACAAATAAATAAGATAAAT 1104852 ACTGATGGTA Statistics Matches: 21, Mismatches: 0, Indels: 2 0.91 0.00 0.09 Matches are distributed among these distances: 23 19 0.90 24 2 0.10 ACGTcount: A:0.71, C:0.04, G:0.04, T:0.20 Consensus pattern (23 bp): AAAACAAATAAATAAGATAAATT Found at i:1107897 original size:63 final size:63 Alignment explanation

Indices: 1107819--1108386 Score: 1100 Period size: 63 Copynumber: 9.0 Consensus size: 63 1107809 TTGTCTCAAT * 1107819 AATAATGGTGCCCTTAGGATGCAACATGAACCTCATGTACATCAGAATACTACGGAAGATGAC 1 AATAATGGTGCCCTTAGGATGCAACATGAACCTCAGGTACATCAGAATACTACGGAAGATGAC * 1107882 AATAATGGTGCCCTTAGGATGCAACATGAACCTCGGGTACATCAGAATACTACGGAAGATGAC 1 AATAATGGTGCCCTTAGGATGCAACATGAACCTCAGGTACATCAGAATACTACGGAAGATGAC 1107945 AATAATGGTGCCCTTAGGATGCAACATGAACCTCAGGTACATCAGAATACTACGGAAGATGAC 1 AATAATGGTGCCCTTAGGATGCAACATGAACCTCAGGTACATCAGAATACTACGGAAGATGAC 1108008 AATAATGGTGCCCTTAGGATGCAACATGAACCTCAGGTACATCAGAATACTACGGAAGATGAC 1 AATAATGGTGCCCTTAGGATGCAACATGAACCTCAGGTACATCAGAATACTACGGAAGATGAC 1108071 AATAATGGTGCCCTTAGGATGCAACATGAACCTCAGGTACATCAGAATACTACGGAAGATGAC 1 AATAATGGTGCCCTTAGGATGCAACATGAACCTCAGGTACATCAGAATACTACGGAAGATGAC 1108134 AATAATGGTGCCCTTAGGATGCAACATGAACCTCAGGTACATCAGAATACTACGGAAGATGAC 1 AATAATGGTGCCCTTAGGATGCAACATGAACCTCAGGTACATCAGAATACTACGGAAGATGAC 1108197 AATAATGGTGCCCTTAGGATGCAACATGAACCTCAGGTACATCAGAATACTACGGAAGATGAC 1 AATAATGGTGCCCTTAGGATGCAACATGAACCTCAGGTACATCAGAATACTACGGAAGATGAC 1108260 AATAATGGTGCCCTTAGGATGCAACATGAACCTCAGGTACATCAGAATACTACGGAAGATGAC 1 AATAATGGTGCCCTTAGGATGCAACATGAACCTCAGGTACATCAGAATACTACGGAAGATGAC * * 1108323 AATAATGGTGCCCTTAGGATGCAACATGAACCTCGGGTACATCAGAATACTACGGTAGATGAC 1 AATAATGGTGCCCTTAGGATGCAACATGAACCTCAGGTACATCAGAATACTACGGAAGATGAC 1108386 A 1 A 1108387 TTCCATTCCA Statistics Matches: 500, Mismatches: 5, Indels: 0 0.99 0.01 0.00 Matches are distributed among these distances: 63 500 1.00 ACGTcount: A:0.36, C:0.21, G:0.22, T:0.21 Consensus pattern (63 bp): AATAATGGTGCCCTTAGGATGCAACATGAACCTCAGGTACATCAGAATACTACGGAAGATGAC Found at i:1108753 original size:38 final size:38 Alignment explanation

Indices: 1108702--1109516 Score: 1477 Period size: 38 Copynumber: 21.4 Consensus size: 38 1108692 GGGGAAGACC * 1108702 CAGACCAATACCACAGTCCTAACTGTAGGTAAGTGTAG 1 CAGACCAATACCACAGCCCTAACTGTAGGTAAGTGTAG * 1108740 CAGACCAATACCACAGCCCTAACTGTCGGTAAGTGTAG 1 CAGACCAATACCACAGCCCTAACTGTAGGTAAGTGTAG 1108778 CAGACCAATACCACAGCCCTAACTGTAGGTAAGTGTAG 1 CAGACCAATACCACAGCCCTAACTGTAGGTAAGTGTAG * 1108816 CAGACCAATACCACAGCCCTAACTGTCGGTAAGTGTAG 1 CAGACCAATACCACAGCCCTAACTGTAGGTAAGTGTAG 1108854 CAGACCAATACCACAGCCCTAACTGTAGGTAAGTGTAG 1 CAGACCAATACCACAGCCCTAACTGTAGGTAAGTGTAG * 1108892 CAGACCAATACCACAGCCCTAACTGTCGGTAAGTGTAG 1 CAGACCAATACCACAGCCCTAACTGTAGGTAAGTGTAG 1108930 CAGACCAATACCACAGCCCTAACTGTAGGTAAGTGTAG 1 CAGACCAATACCACAGCCCTAACTGTAGGTAAGTGTAG 1108968 CAGACCAATACCACAGCCCTAACTGTAGGTAAGTGTAG 1 CAGACCAATACCACAGCCCTAACTGTAGGTAAGTGTAG * 1109006 CAGACCAATACCACAGCCCTAACTGTCGGTAAGTGTAG 1 CAGACCAATACCACAGCCCTAACTGTAGGTAAGTGTAG * 1109044 CAGACCAATACCACAGCCCTAACTGTCGGTAAGTGTAG 1 CAGACCAATACCACAGCCCTAACTGTAGGTAAGTGTAG 1109082 CAGACCAATACCACAGCCCTAACTGTAGGTAAGTGTAG 1 CAGACCAATACCACAGCCCTAACTGTAGGTAAGTGTAG 1109120 CAGACCAATACCACAGCCCTAACTGTAGGTAAGTGTAG 1 CAGACCAATACCACAGCCCTAACTGTAGGTAAGTGTAG * * 1109158 CAGACCAATACCACAGCCCTAACTGTCGGTAAGTGTAT 1 CAGACCAATACCACAGCCCTAACTGTAGGTAAGTGTAG * * 1109196 CAGACCTATACCACAGCCCTAACTGTCGGTAAGTGTAG 1 CAGACCAATACCACAGCCCTAACTGTAGGTAAGTGTAG 1109234 CAGACCAATACCACAGCCCTAACTGTAGGTAAGTGTAG 1 CAGACCAATACCACAGCCCTAACTGTAGGTAAGTGTAG 1109272 CAGACCAATACCACAGCCCTAACTGTAGGTAAGTGTAG 1 CAGACCAATACCACAGCCCTAACTGTAGGTAAGTGTAG 1109310 CAGACCAATACCACAGCCCTAACTGTAGGTAAGTGTAG 1 CAGACCAATACCACAGCCCTAACTGTAGGTAAGTGTAG 1109348 CAGACCAATACCACAGCCCTAACTGTAGGTAAGTGTAG 1 CAGACCAATACCACAGCCCTAACTGTAGGTAAGTGTAG 1109386 CAGACCAATACCACAGCCCTAACTGTAGGTAAGTGTAG 1 CAGACCAATACCACAGCCCTAACTGTAGGTAAGTGTAG ** * * 1109424 CAGACCAATACCACAGCCCTAACTGTCTGTAAGGGTAT 1 CAGACCAATACCACAGCCCTAACTGTAGGTAAGTGTAG * * 1109462 CAAACCAATACCACAGCCCTAACTGTAGGTAAGTGTAT 1 CAGACCAATACCACAGCCCTAACTGTAGGTAAGTGTAG * 1109500 CAGACCGATACCACAGC 1 CAGACCAATACCACAGC 1109517 GTTAAGGTAG Statistics Matches: 752, Mismatches: 25, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 38 752 1.00 ACGTcount: A:0.33, C:0.27, G:0.20, T:0.19 Consensus pattern (38 bp): CAGACCAATACCACAGCCCTAACTGTAGGTAAGTGTAG Found at i:1109934 original size:24 final size:24 Alignment explanation

Indices: 1109886--1109934 Score: 57 Period size: 24 Copynumber: 2.0 Consensus size: 24 1109876 AAGATGGGAT * 1109886 AAATTTGTTAAAATTTAGAATTGA 1 AAATTTGTTAAAATTTAGAAATGA 1109910 AAATTT-TTAAAAATTTA-AAGATGA 1 AAATTTGTT-AAAATTTAGAA-ATGA 1109934 A 1 A 1109935 TCTTTATTAT Statistics Matches: 22, Mismatches: 1, Indels: 4 0.81 0.04 0.15 Matches are distributed among these distances: 23 4 0.18 24 18 0.82 ACGTcount: A:0.51, C:0.00, G:0.10, T:0.39 Consensus pattern (24 bp): AAATTTGTTAAAATTTAGAAATGA Found at i:1111584 original size:15 final size:16 Alignment explanation

Indices: 1111564--1111596 Score: 50 Period size: 17 Copynumber: 2.1 Consensus size: 16 1111554 TCACAGGGAA 1111564 TGAAA-GTCAATTCAT 1 TGAAACGTCAATTCAT 1111579 TGAAAGCGTCAATTCAT 1 TGAAA-CGTCAATTCAT 1111596 T 1 T 1111597 ATAAGCTTGT Statistics Matches: 16, Mismatches: 0, Indels: 2 0.89 0.00 0.11 Matches are distributed among these distances: 15 5 0.31 17 11 0.69 ACGTcount: A:0.36, C:0.15, G:0.15, T:0.33 Consensus pattern (16 bp): TGAAACGTCAATTCAT Found at i:1112317 original size:35 final size:35 Alignment explanation

Indices: 1112278--1112411 Score: 162 Period size: 35 Copynumber: 3.8 Consensus size: 35 1112268 GGCTGGGGAC 1112278 AACCCCTGGGTAAGTGACTGGTTTGTGTGATAGGG 1 AACCCCTGGGTAAGTGACTGGTTTGTGTGATAGGG ** 1112313 AACCCCTGGGTTTGTGACTGGTTTGTGTGATAGGG 1 AACCCCTGGGTAAGTGACTGGTTTGTGTGATAGGG * * ** 1112348 AACCCCTGGGTATGGGACTGGTTTGTGTGGGA-GG 1 AACCCCTGGGTAAGTGACTGGTTTGTGTGATAGGG * * * * 1112382 AGACCTCTTGGTAAGTGACCGATTTGTGTG 1 A-ACCCCTGGGTAAGTGACTGGTTTGTGTG 1112412 TGTGTGTGGG Statistics Matches: 86, Mismatches: 12, Indels: 2 0.86 0.12 0.02 Matches are distributed among these distances: 34 3 0.03 35 83 0.97 ACGTcount: A:0.17, C:0.15, G:0.37, T:0.31 Consensus pattern (35 bp): AACCCCTGGGTAAGTGACTGGTTTGTGTGATAGGG Found at i:1112946 original size:35 final size:36 Alignment explanation

Indices: 1112902--1112969 Score: 86 Period size: 35 Copynumber: 1.9 Consensus size: 36 1112892 AAGTTGGCCT 1112902 CTGGATAAGTGACC-GATTTGTGTG-GTAGGGGACCC 1 CTGGATAAGTGACCTG-TTTGTGTGTGTAGGGGACCC * * * 1112937 CTGGGTAAGTGGCCTGTTTGTGTGTGTGGGGGA 1 CTGGATAAGTGACCTGTTTGTGTGTGTAGGGGA 1112970 GGGGGGCACT Statistics Matches: 28, Mismatches: 3, Indels: 3 0.82 0.09 0.09 Matches are distributed among these distances: 35 20 0.71 36 8 0.29 ACGTcount: A:0.15, C:0.13, G:0.43, T:0.29 Consensus pattern (36 bp): CTGGATAAGTGACCTGTTTGTGTGTGTAGGGGACCC Found at i:1113096 original size:94 final size:93 Alignment explanation

Indices: 1112935--1113104 Score: 220 Period size: 93 Copynumber: 1.8 Consensus size: 93 1112925 GGTAGGGGAC * * * * * 1112935 CCCTGGGTAAGTGGCCTGTTTGTGTGTGTGGGGGAGGGGGGCACTCTGGGTAAAGGACTGGTTTG 1 CCCTGCGTAAGTGACCTGTTTGTGTATGTGGGGGAGGGGGGAACTCTGGATAAAGGACTGGTTTG * 1113000 TGTGTGTGTGTTTTTGTCTAGGGGGGTG 66 TGTGTATGTGTTTTTGTCTAGGGGGGTG * 1113028 CCCTGCGTAAGTGACC-GTTATGTGTATG-GGGGGGGGGGGAGAACTCCTGGAT-AAGTGACTGG 1 CCCTGCGTAAGTGACCTGTT-TGTGTATGTGGGGGAGGGGG-GAACT-CTGGATAAAG-GACTGG 1113090 TTTGTGTGTATGTGT 62 TTTGTGTGTATGTGT 1113105 GTTGGGGGGG Statistics Matches: 66, Mismatches: 7, Indels: 7 0.82 0.09 0.09 Matches are distributed among these distances: 92 13 0.20 93 28 0.42 94 25 0.38 ACGTcount: A:0.13, C:0.12, G:0.44, T:0.32 Consensus pattern (93 bp): CCCTGCGTAAGTGACCTGTTTGTGTATGTGGGGGAGGGGGGAACTCTGGATAAAGGACTGGTTTG TGTGTATGTGTTTTTGTCTAGGGGGGTG Found at i:1116666 original size:22 final size:22 Alignment explanation

Indices: 1116626--1116672 Score: 58 Period size: 22 Copynumber: 2.1 Consensus size: 22 1116616 GAGTAAACCT * * 1116626 AAAGTAAACAGCGAGTGGACCC 1 AAAGTAAACACCGAATGGACCC * * 1116648 AAAGTAAACCCCGAATGGACGC 1 AAAGTAAACACCGAATGGACCC 1116670 AAA 1 AAA 1116673 TTTTCAAAAA Statistics Matches: 21, Mismatches: 4, Indels: 0 0.84 0.16 0.00 Matches are distributed among these distances: 22 21 1.00 ACGTcount: A:0.45, C:0.23, G:0.23, T:0.09 Consensus pattern (22 bp): AAAGTAAACACCGAATGGACCC Found at i:1117238 original size:18 final size:18 Alignment explanation

Indices: 1117215--1117252 Score: 67 Period size: 18 Copynumber: 2.1 Consensus size: 18 1117205 TATGCACACT * 1117215 TGTACATGTATCTTCTCA 1 TGTACATGTAACTTCTCA 1117233 TGTACATGTAACTTCTCA 1 TGTACATGTAACTTCTCA 1117251 TG 1 TG 1117253 GCATAGCAAA Statistics Matches: 19, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 18 19 1.00 ACGTcount: A:0.24, C:0.21, G:0.13, T:0.42 Consensus pattern (18 bp): TGTACATGTAACTTCTCA Found at i:1120078 original size:79 final size:80 Alignment explanation

Indices: 1119940--1120091 Score: 243 Period size: 79 Copynumber: 1.9 Consensus size: 80 1119930 TTGTTATGTG * * * 1119940 TGTTGTTATATTGTAGCTGTGGATAATTGTCAAACTTGTTTGGTCAATTTGTATTGTTATTTATT 1 TGTTGTTATATTGTAGCTATGGATAATTGTCAAACTTGTTTGGTCAATTTGCATAGTTATTTATT 1120005 TCTGATATTAGTCGA 66 TCTGATATTAGTCGA * * * 1120020 TGTTGTTATATT-TAGCTATGGTTAATTGTCAAATTTGTTTGGTCAGTTTGCATAGTTATTTATT 1 TGTTGTTATATTGTAGCTATGGATAATTGTCAAACTTGTTTGGTCAATTTGCATAGTTATTTATT 1120084 TCTGATAT 66 TCTGATAT 1120092 CTGCCTATTT Statistics Matches: 66, Mismatches: 6, Indels: 1 0.90 0.08 0.01 Matches are distributed among these distances: 79 54 0.82 80 12 0.18 ACGTcount: A:0.22, C:0.07, G:0.19, T:0.51 Consensus pattern (80 bp): TGTTGTTATATTGTAGCTATGGATAATTGTCAAACTTGTTTGGTCAATTTGCATAGTTATTTATT TCTGATATTAGTCGA Found at i:1123490 original size:2 final size:2 Alignment explanation

Indices: 1123483--1123521 Score: 69 Period size: 2 Copynumber: 19.5 Consensus size: 2 1123473 CATTCGACAA * 1123483 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT TT CT C 1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C 1123522 GTTTTGAAGG Statistics Matches: 35, Mismatches: 2, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 2 35 1.00 ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51 Consensus pattern (2 bp): CT Found at i:1123842 original size:2 final size:2 Alignment explanation

Indices: 1123835--1123876 Score: 84 Period size: 2 Copynumber: 21.0 Consensus size: 2 1123825 TGCGTAAAAC 1123835 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA 1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA 1123877 TATATATATA Statistics Matches: 40, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 40 1.00 ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00 Consensus pattern (2 bp): CA Found at i:1127224 original size:20 final size:20 Alignment explanation

Indices: 1127174--1127224 Score: 50 Period size: 20 Copynumber: 2.5 Consensus size: 20 1127164 ACAAATAAAA * 1127174 CCTTACAAATCGAAACAAAT 1 CCTTACAAATCGAAACAAAC * * 1127194 CCTAACAAAAT-GAAACGAAC 1 CCTTAC-AAATCGAAACAAAC 1127214 CCTTACGAAAT 1 CCTTAC-AAAT 1127225 AAAATGATAT Statistics Matches: 25, Mismatches: 5, Indels: 2 0.78 0.16 0.06 Matches are distributed among these distances: 20 21 0.84 21 4 0.16 ACGTcount: A:0.49, C:0.25, G:0.08, T:0.18 Consensus pattern (20 bp): CCTTACAAATCGAAACAAAC Found at i:1129750 original size:30 final size:30 Alignment explanation

Indices: 1129714--1129770 Score: 105 Period size: 30 Copynumber: 1.9 Consensus size: 30 1129704 ACAGCCGACN * 1129714 CCGGTCAATAGACTTCGATCTATTGGATCG 1 CCGGTCAATAGACTGCGATCTATTGGATCG 1129744 CCGGTCAATAGACTGCGATCTATTGGA 1 CCGGTCAATAGACTGCGATCTATTGGA 1129771 CCGGCAACGT Statistics Matches: 26, Mismatches: 1, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 30 26 1.00 ACGTcount: A:0.25, C:0.23, G:0.25, T:0.28 Consensus pattern (30 bp): CCGGTCAATAGACTGCGATCTATTGGATCG Found at i:1138432 original size:15 final size:16 Alignment explanation

Indices: 1138395--1138434 Score: 55 Period size: 17 Copynumber: 2.5 Consensus size: 16 1138385 CCGTGAGTTC 1138395 ACTTCGAGAGATCAAGA 1 ACTTCGAGAGATC-AGA 1138412 ACTTCGAGAGATC-GA 1 ACTTCGAGAGATCAGA * 1138427 AGTTCGAG 1 ACTTCGAG 1138435 CCATCAAGTG Statistics Matches: 22, Mismatches: 1, Indels: 2 0.88 0.04 0.08 Matches are distributed among these distances: 15 9 0.41 17 13 0.59 ACGTcount: A:0.35, C:0.17, G:0.28, T:0.20 Consensus pattern (16 bp): ACTTCGAGAGATCAGA Found at i:1150553 original size:21 final size:21 Alignment explanation

Indices: 1150519--1150595 Score: 75 Period size: 21 Copynumber: 3.7 Consensus size: 21 1150509 AATTTAATGC * * 1150519 TATGCTATGGTATGCGATTT- 1 TATGATATGCTATGCGATTTG 1150539 TAATGATATGCTATGCGATTTG 1 T-ATGATATGCTATGCGATTTG * * * 1150561 TATGCTATGCTATGAGATCTG 1 TATGATATGCTATGCGATTTG * * 1150582 TATGCTATGATATG 1 TATGATATGCTATG 1150596 AGAAATTGAA Statistics Matches: 49, Mismatches: 6, Indels: 3 0.84 0.10 0.05 Matches are distributed among these distances: 20 1 0.02 21 47 0.96 22 1 0.02 ACGTcount: A:0.25, C:0.10, G:0.23, T:0.42 Consensus pattern (21 bp): TATGATATGCTATGCGATTTG Found at i:1150596 original size:21 final size:21 Alignment explanation

Indices: 1150545--1150598 Score: 81 Period size: 21 Copynumber: 2.6 Consensus size: 21 1150535 ATTTTAATGA * * 1150545 TATGCTATGCGATTTGTATGC 1 TATGCTATGAGATCTGTATGC 1150566 TATGCTATGAGATCTGTATGC 1 TATGCTATGAGATCTGTATGC * 1150587 TATGATATGAGA 1 TATGCTATGAGA 1150599 AATTGAAATG Statistics Matches: 30, Mismatches: 3, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 21 30 1.00 ACGTcount: A:0.26, C:0.11, G:0.24, T:0.39 Consensus pattern (21 bp): TATGCTATGAGATCTGTATGC Found at i:1150642 original size:15 final size:15 Alignment explanation

Indices: 1150622--1150650 Score: 58 Period size: 15 Copynumber: 1.9 Consensus size: 15 1150612 TGCTTAATGA 1150622 TATGGTATGCTATGC 1 TATGGTATGCTATGC 1150637 TATGGTATGCTATG 1 TATGGTATGCTATG 1150651 AGATTTGAAC Statistics Matches: 14, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 15 14 1.00 ACGTcount: A:0.21, C:0.10, G:0.28, T:0.41 Consensus pattern (15 bp): TATGGTATGCTATGC Found at i:1150840 original size:21 final size:21 Alignment explanation

Indices: 1150814--1150890 Score: 127 Period size: 21 Copynumber: 3.7 Consensus size: 21 1150804 ATGCTATGGT * * 1150814 ATGCTATGGTATGAGATTCCA 1 ATGCTATGCTATGAGATTTCA 1150835 ATGCTATGCTATGAGATTTCA 1 ATGCTATGCTATGAGATTTCA * 1150856 ATGCTATGCTATGAGATTTTA 1 ATGCTATGCTATGAGATTTCA 1150877 ATGCTATGCTATGA 1 ATGCTATGCTATGA 1150891 TATGGCGTAC Statistics Matches: 53, Mismatches: 3, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 21 53 1.00 ACGTcount: A:0.29, C:0.13, G:0.21, T:0.38 Consensus pattern (21 bp): ATGCTATGCTATGAGATTTCA Found at i:1158346 original size:2 final size:2 Alignment explanation

Indices: 1158339--1158388 Score: 91 Period size: 2 Copynumber: 25.0 Consensus size: 2 1158329 TTGACCACAT * 1158339 GA GA GA GA GA GA GA GA AA GA GA GA GA GA GA GA GA GA GA GA GA 1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 1158381 GA GA GA GA 1 GA GA GA GA 1158389 AGTTGAATGA Statistics Matches: 46, Mismatches: 2, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 2 46 1.00 ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00 Consensus pattern (2 bp): GA Found at i:1158921 original size:11 final size:11 Alignment explanation

Indices: 1158905--1158944 Score: 55 Period size: 11 Copynumber: 3.7 Consensus size: 11 1158895 TAAGCAAGTC 1158905 CTTAAAGGTGG 1 CTTAAAGGTGG * 1158916 CTTAAAGGTGA 1 CTTAAAGGTGG * 1158927 CTTAAAGG-AG 1 CTTAAAGGTGG 1158937 CTTAAAGG 1 CTTAAAGG 1158945 CTATACAACC Statistics Matches: 26, Mismatches: 3, Indels: 1 0.87 0.10 0.03 Matches are distributed among these distances: 10 8 0.31 11 18 0.69 ACGTcount: A:0.35, C:0.10, G:0.30, T:0.25 Consensus pattern (11 bp): CTTAAAGGTGG Found at i:1159031 original size:11 final size:11 Alignment explanation

Indices: 1159015--1159064 Score: 66 Period size: 11 Copynumber: 4.6 Consensus size: 11 1159005 GTCCAAACTT 1159015 CTTTAAGCCAC 1 CTTTAAGCCAC 1159026 CTTTAAGCCAC 1 CTTTAAGCCAC * * 1159037 ATTTTAGCCAC 1 CTTTAAGCCAC * 1159048 CTTTAAG-CAT 1 CTTTAAGCCAC 1159058 CTTTAAG 1 CTTTAAG 1159065 TGGCATTTAC Statistics Matches: 34, Mismatches: 5, Indels: 1 0.85 0.12 0.03 Matches are distributed among these distances: 10 9 0.26 11 25 0.74 ACGTcount: A:0.28, C:0.28, G:0.10, T:0.34 Consensus pattern (11 bp): CTTTAAGCCAC Found at i:1159082 original size:22 final size:22 Alignment explanation

Indices: 1159057--1159117 Score: 70 Period size: 22 Copynumber: 2.8 Consensus size: 22 1159047 CCTTTAAGCA * * 1159057 TCTTTAAGTGGCATTTACGCTC 1 TCTTTAAGTGGCCTTTACACTC * * 1159079 TCTTTACACT-GCCTTTACACTG 1 TCTTTA-AGTGGCCTTTACACTC 1159101 TCTTTAAGTGGCCTTTA 1 TCTTTAAGTGGCCTTTA 1159118 AGTCAATATT Statistics Matches: 32, Mismatches: 5, Indels: 4 0.78 0.12 0.10 Matches are distributed among these distances: 21 2 0.06 22 28 0.88 23 2 0.06 ACGTcount: A:0.18, C:0.25, G:0.15, T:0.43 Consensus pattern (22 bp): TCTTTAAGTGGCCTTTACACTC Found at i:1159453 original size:2 final size:2 Alignment explanation

Indices: 1159448--1159501 Score: 108 Period size: 2 Copynumber: 27.0 Consensus size: 2 1159438 GTGAAAAAAA 1159448 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 1159490 TC TC TC TC TC TC 1 TC TC TC TC TC TC 1159502 AGTTCATCCG Statistics Matches: 52, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 52 1.00 ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50 Consensus pattern (2 bp): TC Found at i:1159912 original size:112 final size:112 Alignment explanation

Indices: 1159715--1159937 Score: 428 Period size: 112 Copynumber: 2.0 Consensus size: 112 1159705 AGTTTTGTTC * 1159715 GTTTGTGTATATCTAATTAGAGTCTATTGTTTGTCCAACTTAAGAAAACCCCTGGAACTAACACA 1 GTTTGTGTATATCTAATTAAAGTCTATTGTTTGTCCAACTTAAGAAAACCCCTGGAACTAACACA * 1159780 GAATATACAAGATATACACAACAGTTGTGTCGTGTGCCCAGGTGCAT 66 GAATATACAAGATATACACAACAGGTGTGTCGTGTGCCCAGGTGCAT 1159827 GTTTGTGTATATCTAATTAAAGTCTATTGTTTGTCCAACTTAAGAAAACCCCTGGAACTAACACA 1 GTTTGTGTATATCTAATTAAAGTCTATTGTTTGTCCAACTTAAGAAAACCCCTGGAACTAACACA 1159892 GAATATACAAGATATACACAACAGGTGTGTCGTGTGCCCAGGTGCA 66 GAATATACAAGATATACACAACAGGTGTGTCGTGTGCCCAGGTGCA 1159938 CGTCAGGGTT Statistics Matches: 109, Mismatches: 2, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 112 109 1.00 ACGTcount: A:0.33, C:0.19, G:0.19, T:0.30 Consensus pattern (112 bp): GTTTGTGTATATCTAATTAAAGTCTATTGTTTGTCCAACTTAAGAAAACCCCTGGAACTAACACA GAATATACAAGATATACACAACAGGTGTGTCGTGTGCCCAGGTGCAT Found at i:1160968 original size:11 final size:11 Alignment explanation

Indices: 1160952--1161005 Score: 90 Period size: 11 Copynumber: 4.9 Consensus size: 11 1160942 AACTTTTTTA 1160952 TGGCTTAAAGG 1 TGGCTTAAAGG 1160963 TGGCTTAAAGG 1 TGGCTTAAAGG * * 1160974 TAGCTAAAAGG 1 TGGCTTAAAGG 1160985 TGGCTTAAAGG 1 TGGCTTAAAGG 1160996 TGGCTTAAAG 1 TGGCTTAAAG 1161006 AAGTTTGGAC Statistics Matches: 39, Mismatches: 4, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 11 39 1.00 ACGTcount: A:0.31, C:0.09, G:0.33, T:0.26 Consensus pattern (11 bp): TGGCTTAAAGG Found at i:1161053 original size:11 final size:11 Alignment explanation

Indices: 1161037--1161065 Score: 58 Period size: 11 Copynumber: 2.6 Consensus size: 11 1161027 ATAAGTTGTC 1161037 CTTAAAGGTGG 1 CTTAAAGGTGG 1161048 CTTAAAGGTGG 1 CTTAAAGGTGG 1161059 CTTAAAG 1 CTTAAAG 1161066 ATAGTCTTTA Statistics Matches: 18, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 11 18 1.00 ACGTcount: A:0.31, C:0.10, G:0.31, T:0.28 Consensus pattern (11 bp): CTTAAAGGTGG Found at i:1161147 original size:11 final size:11 Alignment explanation

Indices: 1161131--1161162 Score: 55 Period size: 11 Copynumber: 2.9 Consensus size: 11 1161121 GCAATACATA 1161131 TAGCTTAAAGG 1 TAGCTTAAAGG 1161142 TAGCTTAAAGG 1 TAGCTTAAAGG * 1161153 TGGCTTAAAG 1 TAGCTTAAAG 1161163 ATCGTCTTTA Statistics Matches: 20, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 11 20 1.00 ACGTcount: A:0.34, C:0.09, G:0.28, T:0.28 Consensus pattern (11 bp): TAGCTTAAAGG Found at i:1161184 original size:11 final size:11 Alignment explanation

Indices: 1161168--1161206 Score: 53 Period size: 11 Copynumber: 3.6 Consensus size: 11 1161158 TAAAGATCGT 1161168 CTTTAAGCTAC 1 CTTTAAGCTAC * 1161179 CTTTAAAC-AC 1 CTTTAAGCTAC * 1161189 CTTTAAGCTAT 1 CTTTAAGCTAC 1161200 CTTTAAG 1 CTTTAAG 1161207 GAGGACTTAA Statistics Matches: 24, Mismatches: 3, Indels: 2 0.83 0.10 0.07 Matches are distributed among these distances: 10 9 0.38 11 15 0.62 ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38 Consensus pattern (11 bp): CTTTAAGCTAC Found at i:1161311 original size:20 final size:21 Alignment explanation

Indices: 1161272--1161312 Score: 57 Period size: 22 Copynumber: 2.0 Consensus size: 21 1161262 AGTAATTTAG * 1161272 AAATACATTTTTAAAAAGAGGA 1 AAATACAGTTTT-AAAAGAGGA 1161294 AAATACAGTTTT-AAAGAGG 1 AAATACAGTTTTAAAAGAGG 1161313 CACACTGATT Statistics Matches: 18, Mismatches: 1, Indels: 2 0.86 0.05 0.10 Matches are distributed among these distances: 20 7 0.39 22 11 0.61 ACGTcount: A:0.51, C:0.05, G:0.17, T:0.27 Consensus pattern (21 bp): AAATACAGTTTTAAAAGAGGA Found at i:1165801 original size:25 final size:25 Alignment explanation

Indices: 1165763--1165814 Score: 86 Period size: 25 Copynumber: 2.1 Consensus size: 25 1165753 CACAATTCAG * * 1165763 GAAAACACTTCTTGCCTACAGGGAT 1 GAAAACACTACTTGCCTACAGCGAT 1165788 GAAAACACTACTTGCCTACAGCGAT 1 GAAAACACTACTTGCCTACAGCGAT 1165813 GA 1 GA 1165815 TATCCCGAGC Statistics Matches: 25, Mismatches: 2, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 25 25 1.00 ACGTcount: A:0.35, C:0.25, G:0.19, T:0.21 Consensus pattern (25 bp): GAAAACACTACTTGCCTACAGCGAT Found at i:1182292 original size:162 final size:157 Alignment explanation

Indices: 1181965--1182340 Score: 366 Period size: 157 Copynumber: 2.3 Consensus size: 157 1181955 ACCAGGTTCA * * * * * * * 1181965 AATTTAATTTTTTCTAAACCTTATTGTACATCGATAGGACAGTCCCTATCATATCCCAAGAGATG 1 AATTTAAATTTTT-AAAACCTTATTGTACATC-TTAAGACAGCCCCTATCATATCCCAAAAGATA * * * * * 1182030 ATGTGTCTATTCATTAAATCATAAGAGTTCTGGGATCTAGGTTTTTTAAGGAGGGGTAAAGTCAA 64 ATGTATATATTCATTAAATCATAAGAGTTCTGGGATCTAAGTTTTTTAAGGAAGGATAAAGTCAA * * * * 1182095 TTTTCTCTACTATTTTTCTTCCTGGATGT 129 TTTCCTCTACTATTTTTCTGCATGGATGC * * * 1182124 AATTTAAA-TTTTAAAACCTTATTGCACATCTTTAAGACAGCCCCTATCATATTCCAAAATATAA 1 AATTTAAATTTTTAAAACCTTATTGTACATC-TTAAGACAGCCCCTATCATATCCCAAAAGATAA * * * * 1182188 TGTATATATATTCATTATATCATAAGAGGAATTCTGGGATC-AAGTTTTTTTATGAATGATAAAC 65 TG--TATATATTCATTAAATCATAAGA-G--TTCTGGGATCTAAGTTTTTTAAGGAAGGATAAA- 1182252 GTCAATTTCCGT-TACT-TTTTTACTGCATGGATGC 124 GTCAATTTCC-TCTACTATTTTT-CTGCATGGATGC ** * 1182286 AATTTAAATTTTTTAAAA-CTTACCGTACATCTAAAGGACAGCCCCTATCATATCC 1 AATTTAAA-TTTTTAAAACCTTATTGTACATCTTAA-GACAGCCCCTATCATATCC 1182341 TAAGCGATGG Statistics Matches: 177, Mismatches: 29, Indels: 18 0.79 0.13 0.08 Matches are distributed among these distances: 157 44 0.25 158 4 0.02 159 27 0.15 160 1 0.01 161 21 0.12 162 43 0.24 163 29 0.16 164 8 0.05 ACGTcount: A:0.32, C:0.17, G:0.13, T:0.38 Consensus pattern (157 bp): AATTTAAATTTTTAAAACCTTATTGTACATCTTAAGACAGCCCCTATCATATCCCAAAAGATAAT GTATATATTCATTAAATCATAAGAGTTCTGGGATCTAAGTTTTTTAAGGAAGGATAAAGTCAATT TCCTCTACTATTTTTCTGCATGGATGC Found at i:1184817 original size:38 final size:38 Alignment explanation

Indices: 1184764--1185144 Score: 593 Period size: 38 Copynumber: 10.1 Consensus size: 38 1184754 GGGGACGACC * 1184764 CAGACCAATACCACAGCCCTAACTGTAGGTAAGTGTAG 1 CAGACCAATACCACAGCCCTAACTGTAGGTAAGTGTAT * * * 1184802 CCGACCAATACCACAGCCCTAACTGTCGGTAAGTGTAG 1 CAGACCAATACCACAGCCCTAACTGTAGGTAAGTGTAT ** * 1184840 CAGACCAATACCACAGCCCTATTTGTAGGTAAGTGTAG 1 CAGACCAATACCACAGCCCTAACTGTAGGTAAGTGTAT * 1184878 CAGACCAATACCACAGCCCTAACTGTAGTTAAGTGTAT 1 CAGACCAATACCACAGCCCTAACTGTAGGTAAGTGTAT * 1184916 CAGACCAATACCACAGCCCTAACTGTAGGTAAGTGTTT 1 CAGACCAATACCACAGCCCTAACTGTAGGTAAGTGTAT 1184954 CAGACCAATACCACAGCCCTAACTGTAGGTAAGTGTAT 1 CAGACCAATACCACAGCCCTAACTGTAGGTAAGTGTAT * * 1184992 CACACCAATACCACAGCCCTAACTGTAGGTAAGTGGAT 1 CAGACCAATACCACAGCCCTAACTGTAGGTAAGTGTAT * * 1185030 CACACCAATACCACAGCCCTAACTGTCGGTAAGTGTAT 1 CAGACCAATACCACAGCCCTAACTGTAGGTAAGTGTAT * * 1185068 CAGACCAATACCACAGCCCTAACTGTCGGT-AGTGTAA 1 CAGACCAATACCACAGCCCTAACTGTAGGTAAGTGTAT * * * 1185105 CAAACCCATACCATAGCCCTAACTGTAGGTAAGTGTAT 1 CAGACCAATACCACAGCCCTAACTGTAGGTAAGTGTAT 1185143 CA 1 CA 1185145 AACAAAAGGT Statistics Matches: 318, Mismatches: 24, Indels: 2 0.92 0.07 0.01 Matches are distributed among these distances: 37 32 0.10 38 286 0.90 ACGTcount: A:0.33, C:0.28, G:0.18, T:0.21 Consensus pattern (38 bp): CAGACCAATACCACAGCCCTAACTGTAGGTAAGTGTAT Found at i:1185749 original size:166 final size:167 Alignment explanation

Indices: 1185468--1185801 Score: 445 Period size: 166 Copynumber: 2.0 Consensus size: 167 1185458 GGTGCGTGTC * * * * ** * * 1185468 TTTAAAAATCTTCTTTTCAAGGACCACTGCACTAGAAATGCAAATTTTTACACAAAAGCTTGTAT 1 TTTAAAAATCTTCCTCTCAAGAACCACTGCACCAGAAATGCAAATAATAACACAAAAGCATGTAT * * * * ** * * 1185533 ATATTGTGAAAATTCTAAATTGTAAAAATCTTGACCCTCGGATTAAAATTGGGGCCCCAGGTGGG 66 ATATAGTGAAAATTCTAAATTGTAAAAATCGTAACCCTCAGACCAAAATTGAGGCCCCAGGCGGG * * * 1185598 GTTCAAAGTTCAACATAGAAATATATAGG-AAAATGT 131 GTTCAAAATTAAACATAGAAATACATAGGAAAAATGT * * * 1185634 TTTAAAAATCTTCCTCTCAAGAATCACTGCACCAGAAATGCCAATAATAACACAAAGGCATGTAT 1 TTTAAAAATCTTCCTCTCAAGAACCACTGCACCAGAAATGCAAATAATAACACAAAAGCATGTAT * 1185699 ATATAGTGAAGATTCTAAATTGTAAAAATCGTAACCCTCAGACCAAAATTGAGGCCCCAGGCGGG 66 ATATAGTGAAAATTCTAAATTGTAAAAATCGTAACCCTCAGACCAAAATTGAGGCCCCAGGCGGG * 1185764 GTTCAAAATTAAATATAGAAATACATAGGAAAAATGT 131 GTTCAAAATTAAACATAGAAATACATAGGAAAAATGT 1185801 T 1 T 1185802 AACATGAGTT Statistics Matches: 143, Mismatches: 24, Indels: 1 0.85 0.14 0.01 Matches are distributed among these distances: 166 135 0.94 167 8 0.06 ACGTcount: A:0.40, C:0.16, G:0.16, T:0.28 Consensus pattern (167 bp): TTTAAAAATCTTCCTCTCAAGAACCACTGCACCAGAAATGCAAATAATAACACAAAAGCATGTAT ATATAGTGAAAATTCTAAATTGTAAAAATCGTAACCCTCAGACCAAAATTGAGGCCCCAGGCGGG GTTCAAAATTAAACATAGAAATACATAGGAAAAATGT Found at i:1187690 original size:11 final size:11 Alignment explanation

Indices: 1187648--1187690 Score: 50 Period size: 11 Copynumber: 3.7 Consensus size: 11 1187638 CTAAACCCTA 1187648 GGTTTACTTTCTG 1 GGTTTAC-TT-TG ** 1187661 GGTTTACGCTG 1 GGTTTACTTTG 1187672 GGTTTACTTTG 1 GGTTTACTTTG 1187683 GGTTTACT 1 GGTTTACT 1187691 GAGTGGACCC Statistics Matches: 26, Mismatches: 4, Indels: 2 0.81 0.12 0.06 Matches are distributed among these distances: 11 19 0.73 13 7 0.27 ACGTcount: A:0.09, C:0.14, G:0.28, T:0.49 Consensus pattern (11 bp): GGTTTACTTTG Found at i:1187933 original size:11 final size:11 Alignment explanation

Indices: 1187891--1187934 Score: 61 Period size: 11 Copynumber: 4.0 Consensus size: 11 1187881 CTGCAATTTA 1187891 AAAGTAAACCC 1 AAAGTAAACCC * * 1187902 AAACTAAACAC 1 AAAGTAAACCC * 1187913 AGAGTAAACCC 1 AAAGTAAACCC 1187924 AAAGTAAACCC 1 AAAGTAAACCC 1187935 CGAGTGGACC Statistics Matches: 27, Mismatches: 6, Indels: 0 0.82 0.18 0.00 Matches are distributed among these distances: 11 27 1.00 ACGTcount: A:0.55, C:0.27, G:0.09, T:0.09 Consensus pattern (11 bp): AAAGTAAACCC Found at i:1188548 original size:42 final size:42 Alignment explanation

Indices: 1188489--1188571 Score: 148 Period size: 42 Copynumber: 2.0 Consensus size: 42 1188479 TAATGTAGTG * 1188489 GAACCAAGACTTATCTTTCTTGATGTTGTTCTGTACAGTCTA 1 GAACCAAAACTTATCTTTCTTGATGTTGTTCTGTACAGTCTA * 1188531 GAACCAAAAGTTATCTTTCTTGATGTTGTTCTGTACAGTCT 1 GAACCAAAACTTATCTTTCTTGATGTTGTTCTGTACAGTCT 1188572 GAGAGTTCTT Statistics Matches: 39, Mismatches: 2, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 42 39 1.00 ACGTcount: A:0.24, C:0.18, G:0.17, T:0.41 Consensus pattern (42 bp): GAACCAAAACTTATCTTTCTTGATGTTGTTCTGTACAGTCTA Found at i:1189179 original size:42 final size:42 Alignment explanation

Indices: 1189133--1189246 Score: 156 Period size: 42 Copynumber: 2.7 Consensus size: 42 1189123 CATGAAACAA * 1189133 ACCTTCTACCCCAGGGGAACTTAACTCTACCCCAGGAGTACG 1 ACCTTCTACCCCAGGGGAACTTAACTCGACCCCAGGAGTACG * ** * 1189175 ACCTTCCACCCCAGGGGAACTTTTCTCGACCCCAGGAGTACT 1 ACCTTCTACCCCAGGGGAACTTAACTCGACCCCAGGAGTACG * * * 1189217 ACCTTCTACCACAGGGGGACTTATCTCGAC 1 ACCTTCTACCCCAGGGGAACTTAACTCGAC 1189247 TCCATCAGAT Statistics Matches: 63, Mismatches: 9, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 42 63 1.00 ACGTcount: A:0.24, C:0.36, G:0.19, T:0.21 Consensus pattern (42 bp): ACCTTCTACCCCAGGGGAACTTAACTCGACCCCAGGAGTACG Found at i:1194356 original size:8 final size:8 Alignment explanation

Indices: 1194335--1194400 Score: 80 Period size: 8 Copynumber: 8.4 Consensus size: 8 1194325 GATCACTTTT 1194335 TGTCCGTC 1 TGTCCGTC 1194343 -GTCCGTC 1 TGTCCGTC 1194350 TGTCCGTC 1 TGTCCGTC * 1194358 CGTCCGTC 1 TGTCCGTC 1194366 TGTCCGTC 1 TGTCCGTC * * 1194374 CGTCTGTC 1 TGTCCGTC * * 1194382 CGTCTGTC 1 TGTCCGTC 1194390 TGTCCGTC 1 TGTCCGTC 1194398 TGT 1 TGT 1194401 AAACTTTTTA Statistics Matches: 51, Mismatches: 6, Indels: 2 0.86 0.10 0.03 Matches are distributed among these distances: 7 7 0.14 8 44 0.86 ACGTcount: A:0.00, C:0.38, G:0.26, T:0.36 Consensus pattern (8 bp): TGTCCGTC Found at i:1194358 original size:4 final size:4 Alignment explanation

Indices: 1194336--1194397 Score: 72 Period size: 4 Copynumber: 15.8 Consensus size: 4 1194326 ATCACTTTTT * * * 1194336 GTCC GT-C GTCC GTCT GTCC GTCC GTCC GTCT GTCC GTCC GTCT GTCC 1 GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC * * 1194383 GTCT GTCT GTCC GTC 1 GTCC GTCC GTCC GTC 1194398 TGTAAACTTT Statistics Matches: 49, Mismatches: 8, Indels: 2 0.83 0.14 0.03 Matches are distributed among these distances: 3 3 0.06 4 46 0.94 ACGTcount: A:0.00, C:0.40, G:0.26, T:0.34 Consensus pattern (4 bp): GTCC Found at i:1194359 original size:12 final size:12 Alignment explanation

Indices: 1194336--1194397 Score: 90 Period size: 12 Copynumber: 5.2 Consensus size: 12 1194326 ATCACTTTTT 1194336 GTCCGTC-GTCC 1 GTCCGTCTGTCC * * 1194347 GTCTGTCCGTCC 1 GTCCGTCTGTCC 1194359 GTCCGTCTGTCC 1 GTCCGTCTGTCC 1194371 GTCCGTCTGTCC 1 GTCCGTCTGTCC * 1194383 GTCTGTCTGTCC 1 GTCCGTCTGTCC 1194395 GTC 1 GTC 1194398 TGTAAACTTT Statistics Matches: 46, Mismatches: 4, Indels: 1 0.90 0.08 0.02 Matches are distributed among these distances: 11 6 0.13 12 40 0.87 ACGTcount: A:0.00, C:0.40, G:0.26, T:0.34 Consensus pattern (12 bp): GTCCGTCTGTCC Found at i:1195991 original size:186 final size:186 Alignment explanation

Indices: 1195734--1196106 Score: 746 Period size: 186 Copynumber: 2.0 Consensus size: 186 1195724 AAGTAAAAAA 1195734 AATTGTCAAAATTTATTAAGAAAATTTTCAAAGTCTGTTCTTCCAGAAACAAACTTTAACAACTT 1 AATTGTCAAAATTTATTAAGAAAATTTTCAAAGTCTGTTCTTCCAGAAACAAACTTTAACAACTT 1195799 ATTGTATTGTAAACTTAACCTTTTTTAGCTCACCTGAGCCAAAGGCTCAAGTGAGCTTTTCTGAT 66 ATTGTATTGTAAACTTAACCTTTTTTAGCTCACCTGAGCCAAAGGCTCAAGTGAGCTTTTCTGAT 1195864 CACAATTTCTCCGTTGTCTGTCGTCGTCGTTGTTGTCGTTGTTGTAAACTTTTCAC 131 CACAATTTCTCCGTTGTCTGTCGTCGTCGTTGTTGTCGTTGTTGTAAACTTTTCAC 1195920 AATTGTCAAAATTTATTAAGAAAATTTTCAAAGTCTGTTCTTCCAGAAACAAACTTTAACAACTT 1 AATTGTCAAAATTTATTAAGAAAATTTTCAAAGTCTGTTCTTCCAGAAACAAACTTTAACAACTT 1195985 ATTGTATTGTAAACTTAACCTTTTTTAGCTCACCTGAGCCAAAGGCTCAAGTGAGCTTTTCTGAT 66 ATTGTATTGTAAACTTAACCTTTTTTAGCTCACCTGAGCCAAAGGCTCAAGTGAGCTTTTCTGAT 1196050 CACAATTTCTCCGTTGTCTGTCGTCGTCGTTGTTGTCGTTGTTGTAAACTTTTCAC 131 CACAATTTCTCCGTTGTCTGTCGTCGTCGTTGTTGTCGTTGTTGTAAACTTTTCAC 1196106 A 1 A 1196107 TTTTCATCTT Statistics Matches: 187, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 186 187 1.00 ACGTcount: A:0.28, C:0.19, G:0.14, T:0.39 Consensus pattern (186 bp): AATTGTCAAAATTTATTAAGAAAATTTTCAAAGTCTGTTCTTCCAGAAACAAACTTTAACAACTT ATTGTATTGTAAACTTAACCTTTTTTAGCTCACCTGAGCCAAAGGCTCAAGTGAGCTTTTCTGAT CACAATTTCTCCGTTGTCTGTCGTCGTCGTTGTTGTCGTTGTTGTAAACTTTTCAC Found at i:1196532 original size:165 final size:165 Alignment explanation

Indices: 1196261--1197082 Score: 786 Period size: 166 Copynumber: 5.0 Consensus size: 165 1196251 GTTGGTATTT * * * * * * * * 1196261 TTTAAAAATCTTCTTCTCAAAAACTATTCGGCC-TGAAAGCTTAAACTTGTGTGGAGGCATCATT 1 TTTAAAAATCTTCTTCTCAAAAACTATTAGGCCAGGAAAGCTCAAATTTGAGTGGAAGCATCCTC * * 1196325 AGGTAGTGTAGATTCAAGTTTGATCAAATCATAGTCCCCGGGGGTAGGGTGGGGCCACAATAGGG 66 AGATAGTGTAGATTCAAGTTTGTTCAAATCATAGTCCCCGGGGGTAGGGTGGGGCCACAAT-GGG * 1196390 GG-T-CATGTTTTACATAGGAATATATAGAGAAAATC 130 GGATAAAT-TTTTACATAGGAATATATAGAGAAAATC 1196425 TTTAAAAATCTTCTTCTCAAAAACTATTAGGCCAGGAAAGCTCAAATTTGAGTGGAAGCATCCTC 1 TTTAAAAATCTTCTTCTCAAAAACTATTAGGCCAGGAAAGCTCAAATTTGAGTGGAAGCATCCTC * 1196490 AGATAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATTGGG 66 AGATAGTGTAGATTCAAGTTTGTTCAAATCATAGTCCCCGGGGGTAGGGTGGGGCCACAA-TGGG * ** * * * 1196555 GGATCAGGTTTTATATCGGAATATATAGAGGAAATC 130 GGATAAATTTTTACATAGGAATATATAGAGAAAATC * * * * * * 1196591 TTTTAAAAATCTTCTTCTC-AAAATTATTTGGCCAAGAAAGCTCAAATTGGCA-TGTAACCATCC 1 -TTTAAAAATCTTCTTCTCAAAAACTATTAGGCCAGGAAAGCTCAAATTTG-AGTGGAAGCATCC * * * * * 1196654 TTAGGA-AGTGTAGATTCAAGTTTGTTCAAATCATTGTCCCTGGGGGTAGGGCGGGGTCACAATG 64 TCA-GATAGTGTAGATTCAAGTTTGTTCAAATCATAGTCCCCGGGGGTAGGGTGGGGCCACAATG 1196718 GGGGATAAATTTTT--ATA-G-----ATAGAGAAAATC 128 GGGGATAAATTTTTACATAGGAATATATAGAGAAAATC * * * 1196748 TTTAAAAGTCTTCTTCTCAAAAA-TATTAGGCCAGGAAAGCCCAAATTTGAGTGGAAGCATCCCC 1 TTTAAAAATCTTCTTCTCAAAAACTATTAGGCCAGGAAAGCTCAAATTTGAGTGGAAGCATCCTC * * * * * * * * 1196812 AGATCA-TATAGATTCAAATTTGTTTAAATAATAGT--CCAGTGGTATGGTGAGGCCACAATGGG 66 AGAT-AGTGTAGATTCAAGTTTGTTCAAATCATAGTCCCCGGGGGTAGGGTGGGGCCACAATGGG * * 1196874 GGATGAATTTTTACTTAGGAATATATAGAGAAAATC 130 GGATAAATTTTTACATAGGAATATATAGAGAAAATC * * * * * * * * * * 1196910 TTTAAAAATCTTCTTTTTAAAGACTATTTGGCCAGAAAAGGTTTAAAATTGTA-TAGAGGCATCC 1 TTTAAAAATCTTCTTCTCAAAAACTATTAGGCCAGGAAA-GCTCAAATTTG-AGTGGAAGCATCC * * * * ** * * * *** 1196974 TCCGGTAGTGTAAATTCAAGTTTG--CAAAATCACAGTCCCTAGTGGTAGGGCGGGACCGTGATG 64 TCAGATAGTGTAGATTCAAGTTTGTTC-AAATCATAGTCCCCGGGGGTAGGGTGGGGCCACAATG ** * * 1197037 GCGGTTTGAATTTTTACATAGGAATATAAAGAGAAAATC 128 G-GGGATAAATTTTTACATAGGAATATATAGAGAAAATC 1197076 TTTAAAA 1 TTTAAAA 1197083 GTATTCTTGG Statistics Matches: 542, Mismatches: 89, Indels: 52 0.79 0.13 0.08 Matches are distributed among these distances: 154 31 0.06 155 3 0.01 156 75 0.14 157 17 0.03 162 32 0.06 163 24 0.04 164 64 0.12 165 118 0.22 166 157 0.29 167 21 0.04 ACGTcount: A:0.33, C:0.15, G:0.23, T:0.30 Consensus pattern (165 bp): TTTAAAAATCTTCTTCTCAAAAACTATTAGGCCAGGAAAGCTCAAATTTGAGTGGAAGCATCCTC AGATAGTGTAGATTCAAGTTTGTTCAAATCATAGTCCCCGGGGGTAGGGTGGGGCCACAATGGGG GATAAATTTTTACATAGGAATATATAGAGAAAATC Found at i:1196703 original size:331 final size:318 Alignment explanation

Indices: 1196260--1196947 Score: 832 Period size: 331 Copynumber: 2.1 Consensus size: 318 1196250 TGTTGGTATT * * * ** 1196260 TTTTAAAAATCTTCTTCTCAAAAACTATTCGGCCTGAAAGCTTAAACTTGTGTGGAGGCATCATT 1 TTTTAAAAATCTTCTTCTC-AAAACTATTTGGCCAGAAAGCTCAAACTTGTGTGGAACCATCATT * * 1196325 AGGTAGTGTAGATTCAAGTTTGATCAAATCATAGTCCCCGGGGGTAGGGTGGGGCCACAATAGGG 65 AGGAAGTGTAGATTCAAGTTTGATCAAATCATAGTCCCCGGGGGTAGGGCGGGGCCACAAT-GGG * 1196390 GG-T-CATGTTTTACATAGGAATATATAGAGAAAATCTTTAAAAATCTTCTTCTCAAAAACTATT 129 GGATAAAT-TTTT--ATA-G-----ATAGAGAAAATCTTTAAAAATCTTCTTCTCAAAAA-TATT * * * * 1196453 AGGCCAGGAAAGCTCAAATTTGAGTGGAAGCATCCTCAGAT-AGTGTAGATTCAAGTTTGTTCAA 184 AGGCCAGGAAAGCCCAAATTTGAGTGGAAGCATCCCCAGATCA-TATAGATTCAAATTTGTTCAA * * * * * * 1196517 ATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATTGGGGGATCAGGTTTTA-TATCGGAATATAT 248 ATAATAGT--CCAGGGGTAGGGTGAGGCCACAA-TGGGGGATCAAGTTTTACT-TAGGAATATAT * 1196581 AGAGGAAATC 309 AGAGAAAATC * * * 1196591 TTTTAAAAATCTTCTTCTCAAAATTATTTGGCCAAGAAAGCTCAAA-TTG-GCATGTAACCATCC 1 TTTTAAAAATCTTCTTCTCAAAACTATTTGGCC-AGAAAGCTCAAACTTGTG--TGGAACCATCA * * * * 1196654 TTAGGAAGTGTAGATTCAAGTTTGTTCAAATCATTGTCCCTGGGGGTAGGGCGGGGTCACAATGG 63 TTAGGAAGTGTAGATTCAAGTTTGATCAAATCATAGTCCCCGGGGGTAGGGCGGGGCCACAATGG * 1196719 GGGATAAATTTTTATAGATAGAGAAAATCTTTAAAAGTCTTCTTCTCAAAAATATTAGGCCAGGA 128 GGGATAAATTTTTATAGATAGAGAAAATCTTTAAAAATCTTCTTCTCAAAAATATTAGGCCAGGA * 1196784 AAGCCCAAATTTGAGTGGAAGCATCCCCAGATCATATAGATTCAAATTTGTTTAAATAATAGTCC 193 AAGCCCAAATTTGAGTGGAAGCATCCCCAGATCATATAGATTCAAATTTGTTCAAATAATAGTCC * * * * 1196849 AGTGGTATGGTGAGGCCACAATGGGGGATGAATTTTTACTTAGGAATATATAGAGAAAATC 258 AGGGGTAGGGTGAGGCCACAATGGGGGATCAAGTTTTACTTAGGAATATATAGAGAAAATC * * 1196910 -TTTAAAAATCTTCTTTTTAAAGACTATTTGGCCAGAAA 1 TTTTAAAAATCTTCTTCTCAAA-ACTATTTGGCCAGAAA 1196948 AGGTTTAAAA Statistics Matches: 314, Mismatches: 35, Indels: 29 0.83 0.09 0.08 Matches are distributed among these distances: 318 24 0.08 319 43 0.14 320 20 0.06 322 67 0.21 323 35 0.11 328 1 0.00 329 4 0.01 330 20 0.06 331 98 0.31 332 2 0.01 ACGTcount: A:0.33, C:0.15, G:0.22, T:0.30 Consensus pattern (318 bp): TTTTAAAAATCTTCTTCTCAAAACTATTTGGCCAGAAAGCTCAAACTTGTGTGGAACCATCATTA GGAAGTGTAGATTCAAGTTTGATCAAATCATAGTCCCCGGGGGTAGGGCGGGGCCACAATGGGGG ATAAATTTTTATAGATAGAGAAAATCTTTAAAAATCTTCTTCTCAAAAATATTAGGCCAGGAAAG CCCAAATTTGAGTGGAAGCATCCCCAGATCATATAGATTCAAATTTGTTCAAATAATAGTCCAGG GGTAGGGTGAGGCCACAATGGGGGATCAAGTTTTACTTAGGAATATATAGAGAAAATC Found at i:1197862 original size:2 final size:2 Alignment explanation

Indices: 1197855--1197897 Score: 86 Period size: 2 Copynumber: 21.5 Consensus size: 2 1197845 TCCATAACAC 1197855 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG 1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG 1197897 T 1 T 1197898 AAATTGCACA Statistics Matches: 41, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 41 1.00 ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51 Consensus pattern (2 bp): TG Found at i:1198004 original size:163 final size:165 Alignment explanation

Indices: 1197710--1198014 Score: 515 Period size: 163 Copynumber: 1.8 Consensus size: 165 1197700 GGGTGGGTGG 1197710 GTGTGTGTGTGTGTGTGACAAAATTGCACAATCTCTGTCTGGAAGGAAAAATTAGAACAGAGTAC 1 GTGTGTGTGTGTGTGTGACAAAATTGCACAATCTCTGTCTGGAAGGAAAAATTAGAACAGAG-A- * * 1197775 TAGTTTGGTATTTTAAAATCTGAATCGGTTAACTAAATTTATAACTGTCGCATTAGCATTCTGAT 64 TA-TCTGGTATTTTAAAATCTAAATCGGTTAACTAAATTTATAACTGTCGCATTAGCATTCTGAT 1197840 TGGCTTCCATAACACTGTGTGTGTGTGTGTGTGTGTGT 128 TGGCTTCCATAACACTGTGTGTGTGTGTGTGTGTGTGT *** 1197878 GTGTGTGTGTGTGTGTGTGTAAATTGCACAATCTCTGTCTGGAAGGAAAAATTAGAACAGAG-T- 1 GTGTGTGTGTGTGTGTGACAAAATTGCACAATCTCTGTCTGGAAGGAAAAATTAGAACAGAGATA * 1197941 TCTGGTATTTTAAAATCTAAATCGGTTAACTAAATTTATAACTTTCGCATTAGCATTCTGATTGG 66 TCTGGTATTTTAAAATCTAAATCGGTTAACTAAATTTATAACTGTCGCATTAGCATTCTGATTGG 1198006 CTTCCATAA 131 CTTCCATAA 1198015 TACATTTATA Statistics Matches: 131, Mismatches: 6, Indels: 5 0.92 0.04 0.04 Matches are distributed among these distances: 163 71 0.54 165 1 0.01 168 59 0.45 ACGTcount: A:0.28, C:0.13, G:0.23, T:0.36 Consensus pattern (165 bp): GTGTGTGTGTGTGTGTGACAAAATTGCACAATCTCTGTCTGGAAGGAAAAATTAGAACAGAGATA TCTGGTATTTTAAAATCTAAATCGGTTAACTAAATTTATAACTGTCGCATTAGCATTCTGATTGG CTTCCATAACACTGTGTGTGTGTGTGTGTGTGTGT Found at i:1198399 original size:16 final size:16 Alignment explanation

Indices: 1198371--1199007 Score: 506 Period size: 16 Copynumber: 37.6 Consensus size: 16 1198361 AAGAATTTTT * 1198371 ATGCTACATTACAATG 1 ATGCTGCATTACAATG * * 1198387 ATGTTGTATTACAATG 1 ATGCTGCATTACAATG * 1198403 ATGCTGCATTGCAATG 1 ATGCTGCATTACAATG * * 1198419 ATGCTACATTTCAATG 1 ATGCTGCATTACAATG 1198435 ATGCTGCATTA-ATATG 1 ATGCTGCATTACA-ATG * 1198451 ATGCTGTATTACAATG 1 ATGCTGCATTACAATG * * * 1198467 ATGCTGTAGTAGAATG 1 ATGCTGCATTACAATG ** * 1198483 ATTATACATTACAATG 1 ATGCTGCATTACAATG 1198499 ATGCTGCATTACAATG 1 ATGCTGCATTACAATG * * 1198515 AAGCTACATTACAATG 1 ATGCTGCATTACAATG * * 1198531 ATGCTGTATTACAATA 1 ATGCTGCATTACAATG * * * 1198547 ATACTGCATGACAATT 1 ATGCTGCATTACAATG 1198563 ATGCTGCATTACATAACAATG 1 ATGCTGCA-T---T-ACAATG * 1198584 ATGCTACATTACAATG 1 ATGCTGCATTACAATG * * * * 1198600 ACGCTACATTGCAAAG 1 ATGCTGCATTACAATG 1198616 ATGCTGCATTACAATG 1 ATGCTGCATTACAATG * * 1198632 ATTCGGCATTACAATG 1 ATGCTGCATTACAATG * 1198648 ATGCCGCATTACAATG 1 ATGCTGCATTACAATG 1198664 ATGCTGCATTACATTACAATG 1 ATGCTG-----CATTACAATG 1198685 ATGCTAG-ATTGA-AATG 1 ATGCT-GCATT-ACAATG * * 1198701 TTGCTGCATTACAATT 1 ATGCTGCATTACAATG * * 1198717 ATTCTGCAGTACAATG 1 ATGCTGCATTACAATG * * 1198733 ATGCTACATTACAGTG 1 ATGCTGCATTACAATG * 1198749 ATGCTGTATTACAATG 1 ATGCTGCATTACAATG 1198765 ATGCTGCATTACAATG 1 ATGCTGCATTACAATG * 1198781 GTGCTGCATTACAATG 1 ATGCTGCATTACAATG * 1198797 ATGCTGCATTACATTACAACG 1 ATGCTG-----CATTACAATG * 1198818 ATGCTGCATTACATTACAACG 1 ATGCTG-----CATTACAATG 1198839 ATGCTGTATTACATTACAATG 1 ATGCTG-----CATTACAATG 1198860 ATGCTGCATTGCATTACAATG 1 A---TGC--TGCATTACAATG * 1198881 ATGCTACATTACAATG 1 ATGCTGCATTACAATG 1198897 ATGCTGCATTACAATG 1 ATGCTGCATTACAATG 1198913 ATGCTGCATTACAATG 1 ATGCTGCATTACAATG 1198929 ATGCTGTATTACATTACAATG 1 ATGCTG-----CATTACAATG * * 1198950 ATGCTACCTTACAATG 1 ATGCTGCATTACAATG * * * 1198966 TTGCTACATTGCAATG 1 ATGCTGCATTACAATG * 1198982 ATGCTGCATTACAATC 1 ATGCTGCATTACAATG 1198998 ATGCTGCATT 1 ATGCTGCATT 1199008 GCAAGCTCTC Statistics Matches: 512, Mismatches: 78, Indels: 62 0.79 0.12 0.10 Matches are distributed among these distances: 15 3 0.01 16 392 0.77 17 4 0.01 18 3 0.01 20 1 0.00 21 103 0.20 22 1 0.00 24 3 0.01 26 2 0.00 ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33 Consensus pattern (16 bp): ATGCTGCATTACAATG Found at i:1198581 original size:21 final size:21 Alignment explanation

Indices: 1198557--1198596 Score: 62 Period size: 21 Copynumber: 1.9 Consensus size: 21 1198547 ATACTGCATG * * 1198557 ACAATTATGCTGCATTACATA 1 ACAATGATGCTACATTACATA 1198578 ACAATGATGCTACATTACA 1 ACAATGATGCTACATTACA 1198597 ATGACGCTAC Statistics Matches: 17, Mismatches: 2, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 21 17 1.00 ACGTcount: A:0.40, C:0.20, G:0.10, T:0.30 Consensus pattern (21 bp): ACAATGATGCTACATTACATA Found at i:1198623 original size:69 final size:69 Alignment explanation

Indices: 1198509--1198644 Score: 166 Period size: 69 Copynumber: 2.0 Consensus size: 69 1198499 ATGCTGCATT * ** * * 1198509 ACAATGAAGCTACATTACAATGATGCTGTATTACAATAATACTGCATGACAATTATGCTGCATTA 1 ACAATGAAGCTACATTACAATGACGCTACATTACAATAATACTGCATGACAATGATGCGGCATTA 1198574 CATA 66 CATA * * * * * 1198578 ACAATGATGCTACATTACAATGACGCTACATTGCAA-AGATGCTGCATTACAATGATTCGGCATT 1 ACAATGAAGCTACATTACAATGACGCTACATTACAATA-ATACTGCATGACAATGATGCGGCATT 1198642 ACA 65 ACA 1198645 ATGATGCCGC Statistics Matches: 56, Mismatches: 10, Indels: 2 0.82 0.15 0.03 Matches are distributed among these distances: 68 1 0.02 69 55 0.98 ACGTcount: A:0.38, C:0.19, G:0.15, T:0.29 Consensus pattern (69 bp): ACAATGAAGCTACATTACAATGACGCTACATTACAATAATACTGCATGACAATGATGCGGCATTA CATA Found at i:1198962 original size:21 final size:21 Alignment explanation

Indices: 1198787--1198954 Score: 186 Period size: 21 Copynumber: 8.7 Consensus size: 21 1198777 AATGGTGCTG 1198787 CATTACAATGATGCTGCATTA 1 CATTACAATGATGCTGCATTA * 1198808 CATTACAACGATGCTGCATTA 1 CATTACAATGATGCTGCATTA * * 1198829 CATTACAACGATGCTGTATTA 1 CATTACAATGATGCTGCATTA * 1198850 CATTACAATGATGCTGCATTG 1 CATTACAATGATGCTGCATTA 1198871 CATTACAATGA---TGC--TA 1 CATTACAATGATGCTGCATTA 1198887 CATTACAATGATGCTG----- 1 CATTACAATGATGCTGCATTA 1198903 CATTACAATGATGCTGCA--- 1 CATTACAATGATGCTGCATTA * 1198921 --TTACAATGATGCTGTATTA 1 CATTACAATGATGCTGCATTA 1198940 CATTACAATGATGCT 1 CATTACAATGATGCT 1198955 ACCTTACAAT Statistics Matches: 130, Mismatches: 7, Indels: 20 0.83 0.04 0.13 Matches are distributed among these distances: 16 43 0.33 18 3 0.02 19 2 0.02 21 82 0.63 ACGTcount: A:0.33, C:0.19, G:0.15, T:0.33 Consensus pattern (21 bp): CATTACAATGATGCTGCATTA Found at i:1203368 original size:20 final size:20 Alignment explanation

Indices: 1203343--1203447 Score: 101 Period size: 20 Copynumber: 5.3 Consensus size: 20 1203333 GTACTGTAAA 1203343 ATATACCATGTACATCATAG 1 ATATACCATGTACATCATAG * * 1203363 ATATACCATTTACA-CAGTGAA 1 ATATACCATGTACATCA-T-AG 1203384 ATATACCATGTACATCATAG 1 ATATACCATGTACATCATAG * * * * 1203404 ATATACCATTTACACCGTAAA 1 ATATACCATGTACATCAT-AG 1203425 ATATACCATGT--AT-ATAG 1 ATATACCATGTACATCATAG 1203442 ATATAC 1 ATATAC 1203448 TATTTACACT Statistics Matches: 69, Mismatches: 12, Indels: 11 0.75 0.13 0.12 Matches are distributed among these distances: 17 7 0.10 18 1 0.01 19 3 0.04 20 30 0.43 21 26 0.38 22 2 0.03 ACGTcount: A:0.42, C:0.19, G:0.09, T:0.30 Consensus pattern (20 bp): ATATACCATGTACATCATAG Found at i:1203398 original size:41 final size:41 Alignment explanation

Indices: 1203335--1203685 Score: 366 Period size: 41 Copynumber: 8.5 Consensus size: 41 1203325 GTGGGAGTGT 1203335 ACTGTAAAATATACCATGTACATCATAGATATACCATTTAC 1 ACTGTAAAATATACCATGTACATCATAGATATACCATTTAC * * 1203376 ACAGTGAAATATACCATGTACATCATAGATATACCATTTAC 1 ACTGTAAAATATACCATGTACATCATAGATATACCATTTAC * * 1203417 ACCGTAAAATATACCATGT--AT-ATAGATATACTATTTAC 1 ACTGTAAAATATACCATGTACATCATAGATATACCATTTAC * 1203455 ACTGTAAAATATACCATGT--AT-ATAGATATACTATTTAC 1 ACTGTAAAATATACCATGTACATCATAGATATACCATTTAC * 1203493 ACTGTAAAATATACCATGTACA-C---CATATACCATTTAC 1 ACTGTAAAATATACCATGTACATCATAGATATACCATTTAC * * * 1203530 ACTGTGAAAA-ATACTATGTACACCATAGATATACAATTTAC 1 ACTGT-AAAATATACCATGTACATCATAGATATACCATTTAC * * * 1203571 ACTGTGAAATATACCATGTACACTGTAAAATATACCATGATATACCGTTTAC 1 ACTGTAAAATATACCATGTACA---T----CAT---A-GATATACCATTTAC * * 1203623 ACTGTAAAATATACCATGTACACCATAGATATTA-TATTTAC 1 ACTGTAAAATATACCATGTACATCATAGATA-TACCATTTAC * 1203664 ACTGTAAAATATACCACGTACA 1 ACTGTAAAATATACCATGTACA 1203686 CTGTAAAATA Statistics Matches: 266, Mismatches: 23, Indels: 42 0.80 0.07 0.13 Matches are distributed among these distances: 37 28 0.11 38 77 0.29 39 2 0.01 40 4 0.02 41 114 0.43 42 3 0.01 45 2 0.01 48 2 0.01 51 1 0.00 52 33 0.12 ACGTcount: A:0.42, C:0.19, G:0.09, T:0.31 Consensus pattern (41 bp): ACTGTAAAATATACCATGTACATCATAGATATACCATTTAC Found at i:1203447 original size:17 final size:17 Alignment explanation

Indices: 1203425--1203485 Score: 50 Period size: 17 Copynumber: 3.4 Consensus size: 17 1203415 ACACCGTAAA 1203425 ATATACCATGTATATAG 1 ATATACCATGTATATAG * * * * 1203442 ATATACTATTTACACTGTAAA 1 ATATACCATGT--A-TAT-AG 1203463 ATATACCATGTATATAG 1 ATATACCATGTATATAG 1203480 ATATAC 1 ATATAC 1203486 TATTTACACT Statistics Matches: 32, Mismatches: 8, Indels: 8 0.67 0.17 0.17 Matches are distributed among these distances: 17 16 0.50 18 2 0.06 19 2 0.06 20 2 0.06 21 10 0.31 ACGTcount: A:0.43, C:0.13, G:0.08, T:0.36 Consensus pattern (17 bp): ATATACCATGTATATAG Found at i:1203522 original size:16 final size:16 Alignment explanation

Indices: 1203501--1203531 Score: 53 Period size: 16 Copynumber: 1.9 Consensus size: 16 1203491 ACACTGTAAA 1203501 ATATACCATGTACACC 1 ATATACCATGTACACC * 1203517 ATATACCATTTACAC 1 ATATACCATGTACAC 1203532 TGTGAAAAAT Statistics Matches: 14, Mismatches: 1, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 16 14 1.00 ACGTcount: A:0.39, C:0.29, G:0.03, T:0.29 Consensus pattern (16 bp): ATATACCATGTACACC Found at i:1203609 original size:21 final size:21 Alignment explanation

Indices: 1203480--1203609 Score: 103 Period size: 21 Copynumber: 6.5 Consensus size: 21 1203470 ATGTATATAG * * 1203480 ATATACTATTTACACTGTAAA 1 ATATACCATGTACACTGTAAA * 1203501 ATATACCATGTACAC-----C 1 ATATACCATGTACACTGTAAA * 1203517 ATATACCATTTACACTGTGAAA 1 ATATACCATGTACACTGT-AAA * ** * 1203539 A-ATACTATGTACACCAT-AG 1 ATATACCATGTACACTGTAAA * * * 1203558 ATATACAATTTACACTGTGAA 1 ATATACCATGTACACTGTAAA 1203579 ATATACCATGTACACTGTAAA 1 ATATACCATGTACACTGTAAA 1203600 ATATACCATG 1 ATATACCATG 1203610 ATATACCGTT Statistics Matches: 83, Mismatches: 18, Indels: 16 0.71 0.15 0.14 Matches are distributed among these distances: 16 14 0.17 19 2 0.02 20 12 0.14 21 54 0.65 22 1 0.01 ACGTcount: A:0.42, C:0.19, G:0.08, T:0.31 Consensus pattern (21 bp): ATATACCATGTACACTGTAAA Found at i:1203614 original size:31 final size:31 Alignment explanation

Indices: 1203579--1203648 Score: 106 Period size: 31 Copynumber: 2.3 Consensus size: 31 1203569 ACACTGTGAA 1203579 ATATACCATGTACACTGTAAAATATACCATG 1 ATATACCATGTACACTGTAAAATATACCATG * * 1203610 ATATACCGTTTACACTGTAAAATATACCATG 1 ATATACCATGTACACTGTAAAATATACCATG * 1203641 -TACACCAT 1 ATATACCAT 1203649 AGATATTATA Statistics Matches: 35, Mismatches: 4, Indels: 1 0.88 0.10 0.03 Matches are distributed among these distances: 30 6 0.17 31 29 0.83 ACGTcount: A:0.40, C:0.21, G:0.09, T:0.30 Consensus pattern (31 bp): ATATACCATGTACACTGTAAAATATACCATG Found at i:1203636 original size:21 final size:21 Alignment explanation

Indices: 1203610--1203758 Score: 95 Period size: 21 Copynumber: 6.8 Consensus size: 21 1203600 ATATACCATG * * 1203610 ATATACCGTTTACACTGTAAA 1 ATATACCATGTACACTGTAAA ** * 1203631 ATATACCATGTACACCAT-AG 1 ATATACCATGTACACTGTAAA * * 1203651 ATATTA-TATTTACACTGTAAA 1 ATA-TACCATGTACACTGTAAA * 1203672 ATATACCACGTACACTGTAAAATATAAA 1 ATATACCATGTACACTG-------TAAA * 1203700 ATATACCATGTACACTGTAGA 1 ATATACCATGTACACTGTAAA * * 1203721 ATATACAATGTACACTGCAAAA 1 ATATACCATGTACACTG-TAAA * 1203743 ATATACCATATACACT 1 ATATACCATGTACACT 1203759 CTATTGGACT Statistics Matches: 97, Mismatches: 20, Indels: 21 0.70 0.14 0.15 Matches are distributed among these distances: 20 14 0.14 21 47 0.48 22 16 0.16 28 20 0.21 ACGTcount: A:0.44, C:0.19, G:0.08, T:0.30 Consensus pattern (21 bp): ATATACCATGTACACTGTAAA Found at i:1203647 original size:93 final size:93 Alignment explanation

Indices: 1203480--1203735 Score: 306 Period size: 93 Copynumber: 2.7 Consensus size: 93 1203470 ATGTATATAG * * 1203480 ATATACTATTTACACTGTAAAATATACCATGTACACCATATACCATTTACACTGTGAAAA-ATAC 1 ATATACCATGTACACTGTAAAATATACCATG------ATATACCATTTACACTGT-AAAATATAC * * 1203544 TATGTACACCATAGATA-TACAATTTACACTGTGAA 59 AATGTACACCATAGATATTA-AATTTACACTGTAAA * * 1203579 ATATACCATGTACACTGTAAAATATACCATGATATACCGTTTACACTGTAAAATATACCATGTAC 1 ATATACCATGTACACTGTAAAATATACCATGATATACCATTTACACTGTAAAATATACAATGTAC * 1203644 ACCATAGATATTATATTTACACTGTAAA 66 ACCATAGATATTAAATTTACACTGTAAA * * * * 1203672 ATATACCACGTACACTGTAAAATATA--A-AATATACCATGTACACTGTAGAATATACAATGTAC 1 ATATACCATGTACACTGTAAAATATACCATGATATACCATTTACACTGTAAAATATACAATGTAC 1203734 AC 66 AC 1203736 TGCAAAAATA Statistics Matches: 143, Mismatches: 12, Indels: 13 0.85 0.07 0.08 Matches are distributed among these distances: 90 32 0.22 91 1 0.01 92 4 0.03 93 75 0.52 94 2 0.01 99 29 0.20 ACGTcount: A:0.42, C:0.19, G:0.09, T:0.30 Consensus pattern (93 bp): ATATACCATGTACACTGTAAAATATACCATGATATACCATTTACACTGTAAAATATACAATGTAC ACCATAGATATTAAATTTACACTGTAAA Found at i:1203712 original size:28 final size:28 Alignment explanation

Indices: 1203668--1203725 Score: 98 Period size: 28 Copynumber: 2.1 Consensus size: 28 1203658 ATTTACACTG 1203668 TAAAATATACCACGTACACTGTAAAATA 1 TAAAATATACCACGTACACTGTAAAATA * * 1203696 TAAAATATACCATGTACACTGTAGAATA 1 TAAAATATACCACGTACACTGTAAAATA 1203724 TA 1 TA 1203726 CAATGTACAC Statistics Matches: 28, Mismatches: 2, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 28 28 1.00 ACGTcount: A:0.48, C:0.16, G:0.09, T:0.28 Consensus pattern (28 bp): TAAAATATACCACGTACACTGTAAAATA Found at i:1204880 original size:4 final size:4 Alignment explanation

Indices: 1204873--1204953 Score: 63 Period size: 4 Copynumber: 20.2 Consensus size: 4 1204863 ATTTCTTCAT * * * * * 1204873 TCAA TCAA TCAC TCAC TCAA TCAA TCAA TCAA TCGA TCGA CCAA TCAA 1 TCAA TCAA TCAA TCAA TCAA TCAA TCAA TCAA TCAA TCAA TCAA TCAA * ** * * * 1204921 TCGA TTGA TCAA TCAA TCGA TCGA CCAA TCAA T 1 TCAA TCAA TCAA TCAA TCAA TCAA TCAA TCAA T 1204954 TGATCAATTA Statistics Matches: 63, Mismatches: 14, Indels: 0 0.82 0.18 0.00 Matches are distributed among these distances: 4 63 1.00 ACGTcount: A:0.40, C:0.28, G:0.07, T:0.25 Consensus pattern (4 bp): TCAA Found at i:1204917 original size:16 final size:16 Alignment explanation

Indices: 1204898--1204958 Score: 95 Period size: 16 Copynumber: 3.8 Consensus size: 16 1204888 CTCAATCAAT 1204898 CAATCAATCGATCGAC 1 CAATCAATCGATCGAC * * 1204914 CAATCAATCGATTGAT 1 CAATCAATCGATCGAC 1204930 CAATCAATCGATCGAC 1 CAATCAATCGATCGAC * 1204946 CAATCAATTGATC 1 CAATCAATCGATC 1204959 AATTAACCAA Statistics Matches: 40, Mismatches: 5, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 16 40 1.00 ACGTcount: A:0.38, C:0.26, G:0.11, T:0.25 Consensus pattern (16 bp): CAATCAATCGATCGAC Found at i:1209517 original size:21 final size:21 Alignment explanation

Indices: 1209493--1209579 Score: 111 Period size: 21 Copynumber: 4.1 Consensus size: 21 1209483 GACCGTGGTG 1209493 GTTGTTGCTGGAATAGTTGTT 1 GTTGTTGCTGGAATAGTTGTT * 1209514 GTTGTTGCTGGGATAGTTGTT 1 GTTGTTGCTGGAATAGTTGTT * * * * * 1209535 GTTGTTGTTTGAATTGTGGTG 1 GTTGTTGCTGGAATAGTTGTT * 1209556 GTTGTTGTTGGAATAGTTGTT 1 GTTGTTGCTGGAATAGTTGTT 1209577 GTT 1 GTT 1209580 AGTTCAGCAG Statistics Matches: 55, Mismatches: 11, Indels: 0 0.83 0.17 0.00 Matches are distributed among these distances: 21 55 1.00 ACGTcount: A:0.11, C:0.02, G:0.36, T:0.51 Consensus pattern (21 bp): GTTGTTGCTGGAATAGTTGTT Found at i:1209610 original size:18 final size:18 Alignment explanation

Indices: 1209571--1210274 Score: 261 Period size: 18 Copynumber: 37.8 Consensus size: 18 1209561 TGTTGGAATA * ** 1209571 GTTGTTGTTAGTTCAGCA 1 GTTGTTGTTTGTTCAGTG * 1209589 GTTGTTGTTTGTTGAGTGG 1 GTTGTTGTTTGTTCAGT-G * 1209608 TTGTTGTTGTTATTGGCTCAGTG 1 --GTTGTTG-T-TT-GTTCAGTG * 1209631 GTTGTTGTTTGTTCTGTTG 1 GTTGTTGTTTGTTCAG-TG * * 1209650 TTGTTGTTGTAATTGGCTCAGTT 1 --GTTGTTGT--TT-GTTCAGTG * 1209673 GTTGTTGTTTGTTCAGTA 1 GTTGTTGTTTGTTCAGTG 1209691 GTTGTTGTAATTGGTTCAGTG 1 GTTGTTGT--TT-GTTCAGTG * * 1209712 GATGTTGTTTGTTCTGTAGTT 1 GTTGTTGTTTGTTC---AGTG * 1209733 GTTGTTATTTGTTCAGTG 1 GTTGTTGTTTGTTCAGTG **** * 1209751 GTTGTTGTCAACTCAATG 1 GTTGTTGTTTGTTCAGTG * 1209769 GTGGTTGTTTGTTCAGTG 1 GTTGTTGTTTGTTCAGTG * * 1209787 GTTGTTGTTTGTTCTGTT 1 GTTGTTGTTTGTTCAGTG 1209805 GTTGTTGTTATTGGTTCAGTG 1 GTTGTTG-T-TT-GTTCAGTG * * 1209826 GATGTTGTTTGTTCTA-TT 1 GTTGTTGTTTGTTC-AGTG 1209844 GTTGTTGTGATTGGTTCAGTG 1 GTTGTTGT--TT-GTTCAGTG ** 1209865 GTTG-TAATTGATTCAGTG 1 GTTGTTGTTTG-TTCAGTG * * 1209883 GTTGTTGTTTGTTCTGTT 1 GTTGTTGTTTGTTCAGTG * * 1209901 GTTGTTGATTGTTCAGTA 1 GTTGTTGTTTGTTCAGTG * * * 1209919 GTCGATGTTTGTTCA-TCA 1 GTTGTTGTTTGTTCAGT-G * 1209937 GTTGTTGTTGGTT--GCTG 1 GTTGTTGTTTGTTCAG-TG * 1209954 AGTTGTTGTTTGTTC-CTCG 1 -GTTGTTGTTTGTTCAGT-G * * ** 1209973 GTGGTTGTTTGTTCTGCA 1 GTTGTTGTTTGTTCAGTG * * * 1209991 GTTGTTGTTTGCTC-CTCA 1 GTTGTTGTTTGTTCAGT-G * ** 1210009 GTTGTTGTTTGTTCTGCA 1 GTTGTTGTTTGTTCAGTG * 1210027 GTTGTTGTTTG--CATTTCG 1 GTTGTTGTTTGTTCA-GT-G ** 1210045 GTTGTTGTTTGTTCAGCA 1 GTTGTTGTTTGTTCAGTG * * 1210063 GTTGTTGTTTGTTC-CTCA 1 GTTGTTGTTTGTTCAGT-G * * * * 1210081 GTAGTTGTTTGCTC-CTCA 1 GTTGTTGTTTGTTCAGT-G * ** 1210099 GTTGTTGTTTGTTCTGCA 1 GTTGTTGTTTGTTCAGTG * * 1210117 GTTGTTGTTTGCTC-TTCG 1 GTTGTTGTTTGTTCAGT-G * ** 1210135 GTTGTTGTTTGTTGAGCA 1 GTTGTTGTTTGTTCAGTG * * 1210153 GTTGTTGTTTGTTC-CTCA 1 GTTGTTGTTTGTTCAGT-G * * 1210171 GTTGTTGTTTGTTC-TTCA 1 GTTGTTGTTTGTTCAGT-G * * * 1210189 GTTGTTGTTTGCTC-CTCA 1 GTTGTTGTTTGTTCAGT-G * ** 1210207 GTTGTTGTTTGTTCTGCA 1 GTTGTTGTTTGTTCAGTG * * 1210225 GTTGTTGTTTGCTC-TTCG 1 GTTGTTGTTTGTTCAGT-G * ** 1210243 GTTGTTGTTTGTTCTGCA 1 GTTGTTGTTTGTTCAGTG 1210261 GTTGTTGTTTGTTC 1 GTTGTTGTTTGTTC 1210275 CTCAGTTGTT Statistics Matches: 527, Mismatches: 110, Indels: 98 0.72 0.15 0.13 Matches are distributed among these distances: 16 1 0.00 17 2 0.00 18 399 0.76 19 17 0.03 20 12 0.02 21 80 0.15 22 1 0.00 23 6 0.01 24 9 0.02 ACGTcount: A:0.08, C:0.10, G:0.29, T:0.53 Consensus pattern (18 bp): GTTGTTGTTTGTTCAGTG Found at i:1209630 original size:24 final size:24 Alignment explanation

Indices: 1209603--1209681 Score: 80 Period size: 24 Copynumber: 3.5 Consensus size: 24 1209593 TTGTTTGTTG 1209603 AGTGGTTGTTGTTGTTATTGGCTC 1 AGTGGTTGTTGTTGTTATTGGCTC * 1209627 AGTGGTTGTTG-T-TTGTT--CT- 1 AGTGGTTGTTGTTGTTATTGGCTC * * 1209646 -GTTGTTGTTGTTGTAATTGGCTC 1 AGTGGTTGTTGTTGTTATTGGCTC * 1209669 AGTTGTTGTTGTT 1 AGTGGTTGTTGTT 1209682 TGTTCAGTAG Statistics Matches: 45, Mismatches: 4, Indels: 12 0.74 0.07 0.20 Matches are distributed among these distances: 18 9 0.20 19 1 0.02 20 5 0.11 22 6 0.13 23 1 0.02 24 23 0.51 ACGTcount: A:0.08, C:0.06, G:0.32, T:0.54 Consensus pattern (24 bp): AGTGGTTGTTGTTGTTATTGGCTC Found at i:1209699 original size:39 final size:39 Alignment explanation

Indices: 1209610--1209920 Score: 278 Period size: 39 Copynumber: 8.1 Consensus size: 39 1209600 TTGAGTGGTT * * * 1209610 GTTGTTGTTATTGGCTCAGTGGTTGTTGTTTGTTCTGTT 1 GTTGTTGTTATTGGTTCAGTGGTTGTTGTTTGTTCAGTA * * 1209649 GTTGTTGTTGTAATTGGCTCAGTTGTTGTTGTTTGTTCAGTA 1 GTTGTTG-T-T-ATTGGTTCAGTGGTTGTTGTTTGTTCAGTA * * * 1209691 GTTGTTGTAATTGGTTCAGTGGATGTTGTTTGTTCTGTA 1 GTTGTTGTTATTGGTTCAGTGGTTGTTGTTTGTTCAGTA * **** * * 1209730 GTTGTTGTTATTTGTTCAGTGGTTGTTGTCAACTCAATG 1 GTTGTTGTTATTGGTTCAGTGGTTGTTGTTTGTTCAGTA * * * 1209769 GTGGTTG-T-TT-GTTCAGTGGTTGTTGTTTGTTCTGTT 1 GTTGTTGTTATTGGTTCAGTGGTTGTTGTTTGTTCAGTA * * 1209805 GTTGTTGTTATTGGTTCAGTGGATGTTGTTTGTTCTA-TT 1 GTTGTTGTTATTGGTTCAGTGGTTGTTGTTTGTTC-AGTA * ** * 1209844 GTTGTTGTGATTGGTTCAGTGGTTG-TAATTGATTCAGTG 1 GTTGTTGTTATTGGTTCAGTGGTTGTTGTTTG-TTCAGTA * * * 1209883 GTTGTTG-T-TT-GTTCTGTTGTTGTTGATTGTTCAGTA 1 GTTGTTGTTATTGGTTCAGTGGTTGTTGTTTGTTCAGTA 1209919 GT 1 GT 1209921 CGATGTTTGT Statistics Matches: 223, Mismatches: 39, Indels: 23 0.78 0.14 0.08 Matches are distributed among these distances: 36 43 0.19 37 10 0.04 38 8 0.04 39 125 0.56 40 1 0.00 41 2 0.01 42 34 0.15 ACGTcount: A:0.10, C:0.06, G:0.30, T:0.53 Consensus pattern (39 bp): GTTGTTGTTATTGGTTCAGTGGTTGTTGTTTGTTCAGTA Found at i:1209805 original size:15 final size:17 Alignment explanation

Indices: 1209673--1211601 Score: 408 Period size: 18 Copynumber: 105.5 Consensus size: 17 1209663 TGGCTCAGTT * 1209673 GTTGTTGTTTGTTCAGTA 1 GTTGTTGTTTGTTCA-TG 1209691 GTTGTTGTAATTGGTTCAGTG 1 GTTGTTGT--TT-GTTCA-TG * 1209712 GATGTTGTTTGTTC-TG 1 GTTGTTGTTTGTTCATG 1209728 TAGTTGTTGTTATTTGTTCAGTG 1 --GTTGTTG---TTTGTTCA-TG **** 1209751 GTTGTTGTCAACTCAATG 1 GTTGTTGTTTGTTC-ATG * 1209769 GTGGTTGTTTGTTCAGTG 1 GTTGTTGTTTGTTCA-TG 1209787 GTTGTTGTTTGTTC-TG 1 GTTGTTGTTTGTTCATG 1209803 TTGTTGTTGTTATTGGTTCAGTG 1 --GTTGTTG-T-TT-GTTCA-TG * * 1209826 GATGTTGTTTGTTCTATT 1 GTTGTTGTTTGTTC-ATG 1209844 GTTGTTGTGATTGGTTCAGTG 1 GTTGTTGT--TT-GTTCA-TG ** 1209865 GTTG-TAATTGATTCAGTG 1 GTTGTTGTTTG-TTCA-TG 1209883 GTTGTTGTTTGTTC-TG 1 GTTGTTGTTTGTTCATG * * 1209899 TTGTTGTTGATTGTTCAGTA 1 --GTTGTTGTTTGTTCA-TG * * * 1209919 GTCGATGTTTGTTCATCA 1 GTTGTTGTTTGTTCAT-G * 1209937 GTTGTTGTTGGTTGC-TG 1 GTTGTTGTTTGTT-CATG * 1209954 AGTTGTTGTTTGTTCCTCG 1 -GTTGTTGTTTGTTCAT-G * 1209973 GTGGTTGTTTGTTC-TG 1 GTTGTTGTTTGTTCATG * * * 1209989 CAGTTGTTGTTTGCTCCTCA 1 --GTTGTTGTTTGTTCAT-G 1210009 GTTGTTGTTTGTTC-TG 1 GTTGTTGTTTGTTCATG 1210025 CAGTTGTTGTTTG--CATTTCG 1 --GTTGTTGTTTGTTCA--T-G 1210045 GTTGTTGTTTGTTCA-G 1 GTTGTTGTTTGTTCATG * * 1210061 CAGTTGTTGTTTGTTCCTCA 1 --GTTGTTGTTTGTTCAT-G * * * * 1210081 GTAGTTGTTTGCTCCTCA 1 GTTGTTGTTTGTTCAT-G 1210099 GTTGTTGTTTGTTC-TG 1 GTTGTTGTTTGTTCATG * * 1210115 CAGTTGTTGTTTGCTCTTCG 1 --GTTGTTGTTTGTTCAT-G * 1210135 GTTGTTGTTTGTTGA-G 1 GTTGTTGTTTGTTCATG * * 1210151 CAGTTGTTGTTTGTTCCTCA 1 --GTTGTTGTTTGTTCAT-G * * 1210171 GTTGTTGTTTGTTCTTCA 1 GTTGTTGTTTGTTCAT-G * * * 1210189 GTTGTTGTTTGCTCCTCA 1 GTTGTTGTTTGTTCAT-G 1210207 GTTGTTGTTTGTTC-TG 1 GTTGTTGTTTGTTCATG * * 1210223 CAGTTGTTGTTTGCTCTTCG 1 --GTTGTTGTTTGTTCAT-G 1210243 GTTGTTGTTTGTTC-TG 1 GTTGTTGTTTGTTCATG * 1210259 CAGTTGTTGTTTGTTCCTCAGTT 1 --GTTGTTGTTTG-T--TCA-TG * 1210282 GTTGTTGTTTCTTC-T- 1 GTTGTTGTTTGTTCATG * * 1210297 GTCG-TGCTTTGTTCTTG 1 GTTGTTG-TTTGTTCATG ** * 1210314 AGTTGTTGTTACCTCCTCGGTTG 1 -GTTGTTGTT---TGTTC--ATG * * * * 1210337 TTGTTGTTATTTGCTCCTCA 1 --GTTGTTGTTTGTTCAT-G * * * * 1210357 GTAGTTGTTTGCTCCTCA 1 GTTGTTGTTTGTTCAT-G * * 1210375 GTTGTTGTTTGTTCTTCT 1 GTTGTTGTTTGTTCAT-G * * * 1210393 GTCGTGGTTTGTTCTTGG 1 GTTGTTGTTTGTTCAT-G * * 1210411 GTTGTTGTTTGTTCTTCT 1 GTTGTTGTTTGTTCAT-G * * * 1210429 GTCGTGGTTTGTTCTTGG 1 GTTGTTGTTTGTTCAT-G * 1210447 GTTGTTGTTTGCTC-TG 1 GTTGTTGTTTGTTCATG * * * 1210463 CAGTTGTTGTTTGCTCCTCA 1 --GTTGTTGTTTGTTCAT-G * 1210483 GTTGTTGTTTGCTT-TTCG 1 GTTGTTGTTTG-TTCAT-G * * * 1210501 GTTGTTGTTTGCTCCTCA 1 GTTGTTGTTTGTTCAT-G * 1210519 GTTGTTGTTTGTTCTTCG 1 GTTGTTGTTTGTTCAT-G * * * * 1210537 GTCGTGGTTTGTTCCTCA 1 GTTGTTGTTTGTTCAT-G * * 1210555 GTTGTTGTTTGTTCTTCT 1 GTTGTTGTTTGTTCAT-G * * 1210573 GTCGTTGTTTGCTCATCG 1 GTTGTTGTTTGTTCAT-G * 1210591 GTTGTTGTTTGTTCTTG 1 GTTGTTGTTTGTTCATG * * * 1210608 CGTTGTTGTTTGCTCTTCC 1 -GTTGTTGTTTGTTCAT-G * * * 1210627 GTTGTTGTTTGCTCCTCA 1 GTTGTTGTTTGTTCAT-G * * 1210645 GCTGTTGTTTGTTCTTCG 1 GTTGTTGTTTGTTCAT-G * * * * 1210663 GTCGTGGTTTGTTCCTCA 1 GTTGTTGTTTGTTCAT-G * * 1210681 GTTGTTGTTTGTTCTTCT 1 GTTGTTGTTTGTTCAT-G * * * 1210699 GTCGTTGTTTGCTCCTCG 1 GTTGTTGTTTGTTCAT-G * 1210717 GTTGTTGTTTGTTCTTG 1 GTTGTTGTTTGTTCATG * * * 1210734 CGTTGTTGTTTGCTCTTCC 1 -GTTGTTGTTTGTTCAT-G * * * 1210753 GTTGTTGTTTGCTCCTCA 1 GTTGTTGTTTGTTCAT-G * * * 1210771 GCTGTTGTTTGTTCTTCT 1 GTTGTTGTTTGTTCAT-G * * * * 1210789 GTCGTGGTTTGTTCCTCA 1 GTTGTTGTTTGTTCAT-G * * 1210807 GTTGTTGTTTGTTCTTCC 1 GTTGTTGTTTGTTCAT-G * * * 1210825 GTTGTTGTTTGCTCCTCA 1 GTTGTTGTTTGTTCAT-G * * * 1210843 GCTGTTGTTTGTTCTTCT 1 GTTGTTGTTTGTTCAT-G * * * 1210861 GTTGTGGTTTGTTCTTCT 1 GTTGTTGTTTGTTCAT-G * * 1210879 GTTGTGGTTTGTTCCTCG 1 GTTGTTGTTTGTTCAT-G * * * * 1210897 GTTGTGGTTTGTCCTTCT 1 GTTGTTGTTTGTTCAT-G * * * 1210915 GTTGTTGTTTGCTCCTCA 1 GTTGTTGTTTGTTCAT-G * 1210933 GTTGTTGTTTGTTCTTCG 1 GTTGTTGTTTGTTCAT-G * * * 1210951 GTCGTTGTTTGTTCCTCA 1 GTTGTTGTTTGTTCAT-G * 1210969 GTTGTTGTTTGTTCTTCG 1 GTTGTTGTTTGTTCAT-G 1210987 GTTGTTGTTTGCTCCTCGGATG 1 GTTGTTGTTTG-T--TC--ATG * 1211009 CTGTTGTTGTTTGTTCCTCG 1 --GTTGTTGTTTGTTCAT-G * * * * 1211029 ATTGTTGTTTGCTCCTCA 1 GTTGTTGTTTGTTCAT-G * 1211047 GTTGTTGTTTGTTCTTG 1 GTTGTTGTTTGTTCATG * * * 1211064 CGTTGTTGTTTGCTCTTCT 1 -GTTGTTGTTTGTTCAT-G * * * 1211083 GTTGTTGTTTGCTCCTCA 1 GTTGTTGTTTGTTCAT-G * 1211101 GTTGTTGTTTGTTCTTCG 1 GTTGTTGTTTGTTCAT-G * * * * 1211119 GTCGTGGTTTGTTCCTCA 1 GTTGTTGTTTGTTCAT-G * 1211137 GTTGTTGTTTGTTCTTCG 1 GTTGTTGTTTGTTCAT-G 1211155 GTTGTTGTTTGCTCCTCGGATG 1 GTTGTTGTTTG-T--TC--ATG * * 1211177 CTGTTGTTATTTGTTCCTCG 1 --GTTGTTGTTTGTTCAT-G 1211197 GTTGTTGTTTGCTCCTCAT- 1 GTTGTTGTTTG-T--TCATG * 1211216 -TTGTTGTTTGTTCTTG 1 GTTGTTGTTTGTTCATG * * * 1211232 CGTTGTTGTTTGCTCTTCT 1 -GTTGTTGTTTGTTCAT-G * * * 1211251 GTTGTTGTTTGCTCCTCA 1 GTTGTTGTTTGTTCAT-G * 1211269 GTTGTTGTTTGTTCTTCG 1 GTTGTTGTTTGTTCAT-G * * * * 1211287 GTCGTGGTTTGTTCCTCA 1 GTTGTTGTTTGTTCAT-G * * 1211305 GTTGTTGTTTGTTCTTCT 1 GTTGTTGTTTGTTCAT-G * * 1211323 GTTGTGGTTTGTTCTTGG 1 GTTGTTGTTTGTTCAT-G ** * 1211341 GTTGTTGTTTGCCCCTCG 1 GTTGTTGTTTGTTCAT-G * * * 1211359 GTTGTTGTTTGCTCCTCA 1 GTTGTTGTTTGTTCAT-G * 1211377 GTTGTTGTTTGTTCCTCG 1 GTTGTTGTTTGTTCAT-G * * * 1211395 GTTGTTGTTTGCTCCTCA 1 GTTGTTGTTTGTTCAT-G * * 1211413 GTTGTTGTTTGTTCTTCT 1 GTTGTTGTTTGTTCAT-G * * * 1211431 GTCGTGGTTTGTTCTTGG 1 GTTGTTGTTTGTTCAT-G ** * 1211449 GTTGTTGTTTGCCCCTCG 1 GTTGTTGTTTGTTCAT-G * * * 1211467 GTTGTTGTTTGCTCTTCT 1 GTTGTTGTTTGTTCAT-G * * * 1211485 GTTGTGGTTTGTTCTTCT 1 GTTGTTGTTTGTTCAT-G * * 1211503 GTTGTGGTTTGTTCCTCG 1 GTTGTTGTTTGTTCAT-G * * * 1211521 GTTGTGGTTTGTCCTTCG 1 GTTGTTGTTTGTTCAT-G * * 1211539 GTTGTTGTTTGCTCTTCG 1 GTTGTTGTTTGTTCAT-G * * * 1211557 GTTGTTGATTGCTCCTCG 1 GTTGTTGTTTGTTCAT-G * * 1211575 GTTGTTGTTTGCTCCTCG 1 GTTGTTGTTTGTTCAT-G 1211593 GTTGTTGTT 1 GTTGTTGTT 1211602 GTTGTTGTTT Statistics Matches: 1522, Mismatches: 272, Indels: 234 0.75 0.13 0.12 Matches are distributed among these distances: 14 2 0.00 15 12 0.01 16 14 0.01 17 14 0.01 18 1314 0.86 19 28 0.02 20 18 0.01 21 77 0.05 22 2 0.00 23 12 0.01 24 29 0.02 ACGTcount: A:0.04, C:0.15, G:0.27, T:0.54 Consensus pattern (17 bp): GTTGTTGTTTGTTCATG Found at i:1209824 original size:114 final size:114 Alignment explanation

Indices: 1209667--1209920 Score: 355 Period size: 114 Copynumber: 2.2 Consensus size: 114 1209657 TGTAATTGGC * 1209667 TCAGTTGTTGTTGTTTGTTCAGTAGTTGTTGTAATTGGTTCAGTGGATGTTGTTTGTTCTGTAGT 1 TCAGTTGTTGTTGTTTGTTCAGTAGTTGTTGTAATTGGTTCAGTGGATGTTGTTTGTTCTATAGT * * ** 1209732 TGTTGTTATTTGTTCAGTGGTTGTTGTCAACTCAATGGTGGTTGTTTGT 66 TGTTGTGATTGGTTCAGTGGTTGTAATCAACTCAATGGTGGTTGTTTGT * * * * * 1209781 TCAGTGGTTGTTGTTTGTTCTGTTGTTGTTGTTATTGGTTCAGTGGATGTTGTTTGTTCTATTGT 1 TCAGTTGTTGTTGTTTGTTCAGTAGTTGTTGTAATTGGTTCAGTGGATGTTGTTTGTTCTATAGT ** * * * 1209846 TGTTGTGATTGGTTCAGTGGTTGTAATTGATTCAGTGGTTGTTGTTTGT 66 TGTTGTGATTGGTTCAGTGGTTGTAATCAACTCAATGGTGGTTGTTTGT * * 1209895 TCTGTTGTTGTTGATTGTTCAGTAGT 1 TCAGTTGTTGTTGTTTGTTCAGTAGT 1209921 CGATGTTTGT Statistics Matches: 120, Mismatches: 20, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 114 120 1.00 ACGTcount: A:0.11, C:0.06, G:0.30, T:0.53 Consensus pattern (114 bp): TCAGTTGTTGTTGTTTGTTCAGTAGTTGTTGTAATTGGTTCAGTGGATGTTGTTTGTTCTATAGT TGTTGTGATTGGTTCAGTGGTTGTAATCAACTCAATGGTGGTTGTTTGT Found at i:1210280 original size:18 final size:18 Alignment explanation

Indices: 1209924--1211702 Score: 1359 Period size: 18 Copynumber: 98.3 Consensus size: 18 1209914 CAGTAGTCGA * 1209924 TGTTTGTTCATCAGTTGT 1 TGTTTGTTCCTCAGTTGT * * * 1209942 TGTTGGTTGCTGAGTTGT 1 TGTTTGTTCCTCAGTTGT * * 1209960 TGTTTGTTCCTCGGTGGT 1 TGTTTGTTCCTCAGTTGT 1209978 TGTTTGTT-CTGCAGTTGT 1 TGTTTGTTCCT-CAGTTGT * 1209996 TGTTTGCTCCTCAGTTGT 1 TGTTTGTTCCTCAGTTGT 1210014 TGTTTGTT-CTGCAGTTGT 1 TGTTTGTTCCT-CAGTTGT * 1210032 TGTTTGCATT--TCGGTTGT 1 TGTTTG--TTCCTCAGTTGT ** 1210050 TGTTTGTTCAGCAGTTGT 1 TGTTTGTTCCTCAGTTGT * 1210068 TGTTTGTTCCTCAGTAGT 1 TGTTTGTTCCTCAGTTGT * 1210086 TGTTTGCTCCTCAGTTGT 1 TGTTTGTTCCTCAGTTGT 1210104 TGTTTGTT-CTGCAGTTGT 1 TGTTTGTTCCT-CAGTTGT * * * 1210122 TGTTTGCTCTTCGGTTGT 1 TGTTTGTTCCTCAGTTGT *** 1210140 TGTTTGTTGAGCAGTTGT 1 TGTTTGTTCCTCAGTTGT 1210158 TGTTTGTTCCTCAGTTGT 1 TGTTTGTTCCTCAGTTGT * 1210176 TGTTTGTTCTTCAGTTGT 1 TGTTTGTTCCTCAGTTGT * 1210194 TGTTTGCTCCTCAGTTGT 1 TGTTTGTTCCTCAGTTGT 1210212 TGTTTGTT-CTGCAGTTGT 1 TGTTTGTTCCT-CAGTTGT * * * 1210230 TGTTTGCTCTTCGGTTGT 1 TGTTTGTTCCTCAGTTGT 1210248 TGTTTGTT-CTGCAGTTGT 1 TGTTTGTTCCT-CAGTTGT 1210266 TGTTTGTTCCTCAGTTGT 1 TGTTTGTTCCTCAGTTGT * * * 1210284 TG-TTGTTTCTTCTGTCG- 1 TGTTTG-TTCCTCAGTTGT * * 1210301 TGCTTTGTTCTTGAGTTGT 1 TG-TTTGTTCCTCAGTTGT *** * 1210320 TGTTACCTCCTCGGTTGTTGT 1 TGTTTGTTCCTC---AGTTGT * * 1210341 TGTTATTTGCTCCTCAGTAGT 1 TG---TTTGTTCCTCAGTTGT * 1210362 TGTTTGCTCCTCAGTTGT 1 TGTTTGTTCCTCAGTTGT * * * 1210380 TGTTTGTTCTTCTGTCGT 1 TGTTTGTTCCTCAGTTGT * * ** 1210398 GGTTTGTTCTTGGGTTGT 1 TGTTTGTTCCTCAGTTGT * * * 1210416 TGTTTGTTCTTCTGTCGT 1 TGTTTGTTCCTCAGTTGT * * ** 1210434 GGTTTGTTCTTGGGTTGT 1 TGTTTGTTCCTCAGTTGT * 1210452 TGTTTGCT-CTGCAGTTGT 1 TGTTTGTTCCT-CAGTTGT * 1210470 TGTTTGCTCCTCAGTTGT 1 TGTTTGTTCCTCAGTTGT * * 1210488 TGTTTGCTT-TTCGGTTGT 1 TGTTTG-TTCCTCAGTTGT * 1210506 TGTTTGCTCCTCAGTTGT 1 TGTTTGTTCCTCAGTTGT * * * 1210524 TGTTTGTTCTTCGGTCGT 1 TGTTTGTTCCTCAGTTGT * 1210542 GGTTTGTTCCTCAGTTGT 1 TGTTTGTTCCTCAGTTGT * * * 1210560 TGTTTGTTCTTCTGTCGT 1 TGTTTGTTCCTCAGTTGT * * * 1210578 TGTTTGCTCATCGGTTGT 1 TGTTTGTTCCTCAGTTGT * 1210596 TGTTTGTTCTTGC-GTTGT 1 TGTTTGTTCCT-CAGTTGT * * * 1210614 TGTTTGCTCTTCCGTTGT 1 TGTTTGTTCCTCAGTTGT * * 1210632 TGTTTGCTCCTCAGCTGT 1 TGTTTGTTCCTCAGTTGT * * * 1210650 TGTTTGTTCTTCGGTCGT 1 TGTTTGTTCCTCAGTTGT * 1210668 GGTTTGTTCCTCAGTTGT 1 TGTTTGTTCCTCAGTTGT * * * 1210686 TGTTTGTTCTTCTGTCGT 1 TGTTTGTTCCTCAGTTGT * * 1210704 TGTTTGCTCCTCGGTTGT 1 TGTTTGTTCCTCAGTTGT * 1210722 TGTTTGTTCTTGC-GTTGT 1 TGTTTGTTCCT-CAGTTGT * * * 1210740 TGTTTGCTCTTCCGTTGT 1 TGTTTGTTCCTCAGTTGT * * 1210758 TGTTTGCTCCTCAGCTGT 1 TGTTTGTTCCTCAGTTGT * * * 1210776 TGTTTGTTCTTCTGTCGT 1 TGTTTGTTCCTCAGTTGT * 1210794 GGTTTGTTCCTCAGTTGT 1 TGTTTGTTCCTCAGTTGT * * 1210812 TGTTTGTTCTTCCGTTGT 1 TGTTTGTTCCTCAGTTGT * * 1210830 TGTTTGCTCCTCAGCTGT 1 TGTTTGTTCCTCAGTTGT * * 1210848 TGTTTGTTCTTCTGTTGT 1 TGTTTGTTCCTCAGTTGT * * * 1210866 GGTTTGTTCTTCTGTTGT 1 TGTTTGTTCCTCAGTTGT * * 1210884 GGTTTGTTCCTCGGTTGT 1 TGTTTGTTCCTCAGTTGT * * 1210902 GGTTTG-TCCTTCTGTTGT 1 TGTTTGTTCC-TCAGTTGT * 1210920 TGTTTGCTCCTCAGTTGT 1 TGTTTGTTCCTCAGTTGT * * * 1210938 TGTTTGTTCTTCGGTCGT 1 TGTTTGTTCCTCAGTTGT 1210956 TGTTTGTTCCTCAGTTGT 1 TGTTTGTTCCTCAGTTGT * * 1210974 TGTTTGTTCTTCGGTTGT 1 TGTTTGTTCCTCAGTTGT * 1210992 TGTTTGCTCCTCGGATGCTGTTGT 1 TGTTTGTTCCTC--A----GTTGT 1211016 TGTTTGTTCCTC-GATTGT 1 TGTTTGTTCCTCAG-TTGT * 1211034 TGTTTGCTCCTCAGTTGT 1 TGTTTGTTCCTCAGTTGT * 1211052 TGTTTGTTCTTGC-GTTGT 1 TGTTTGTTCCT-CAGTTGT * * * 1211070 TGTTTGCTCTTCTGTTGT 1 TGTTTGTTCCTCAGTTGT * 1211088 TGTTTGCTCCTCAGTTGT 1 TGTTTGTTCCTCAGTTGT * * * 1211106 TGTTTGTTCTTCGGTCGT 1 TGTTTGTTCCTCAGTTGT * 1211124 GGTTTGTTCCTCAGTTGT 1 TGTTTGTTCCTCAGTTGT * * 1211142 TGTTTGTTCTTCGGTTGT 1 TGTTTGTTCCTCAGTTGT * 1211160 TGTTTGCTCCTCGGATGCTGTTGT 1 TGTTTGTTCCTC--A----GTTGT * * 1211184 TATTTGTTCCTCGGTTGT 1 TGTTTGTTCCTCAGTTGT * * 1211202 TGTTTGCTCCTCATTTGT 1 TGTTTGTTCCTCAGTTGT * 1211220 TGTTTGTTCTTGC-GTTGT 1 TGTTTGTTCCT-CAGTTGT * * * 1211238 TGTTTGCTCTTCTGTTGT 1 TGTTTGTTCCTCAGTTGT * 1211256 TGTTTGCTCCTCAGTTGT 1 TGTTTGTTCCTCAGTTGT * * * 1211274 TGTTTGTTCTTCGGTCGT 1 TGTTTGTTCCTCAGTTGT * 1211292 GGTTTGTTCCTCAGTTGT 1 TGTTTGTTCCTCAGTTGT * * 1211310 TGTTTGTTCTTCTGTTGT 1 TGTTTGTTCCTCAGTTGT * * ** 1211328 GGTTTGTTCTTGGGTTGT 1 TGTTTGTTCCTCAGTTGT ** * 1211346 TGTTTGCCCCTCGGTTGT 1 TGTTTGTTCCTCAGTTGT * 1211364 TGTTTGCTCCTCAGTTGT 1 TGTTTGTTCCTCAGTTGT * 1211382 TGTTTGTTCCTCGGTTGT 1 TGTTTGTTCCTCAGTTGT * 1211400 TGTTTGCTCCTCAGTTGT 1 TGTTTGTTCCTCAGTTGT * * * 1211418 TGTTTGTTCTTCTGTCGT 1 TGTTTGTTCCTCAGTTGT * * ** 1211436 GGTTTGTTCTTGGGTTGT 1 TGTTTGTTCCTCAGTTGT ** * 1211454 TGTTTGCCCCTCGGTTGT 1 TGTTTGTTCCTCAGTTGT * * * 1211472 TGTTTGCTCTTCTGTTGT 1 TGTTTGTTCCTCAGTTGT * * * 1211490 GGTTTGTTCTTCTGTTGT 1 TGTTTGTTCCTCAGTTGT * * 1211508 GGTTTGTTCCTCGGTTGT 1 TGTTTGTTCCTCAGTTGT * * 1211526 GGTTTG-TCCTTCGGTTGT 1 TGTTTGTTCC-TCAGTTGT * * * 1211544 TGTTTGCTCTTCGGTTGT 1 TGTTTGTTCCTCAGTTGT * * * 1211562 TGATTGCTCCTCGGTTGT 1 TGTTTGTTCCTCAGTTGT * 1211580 TGTTTGCTCCTC-G--GT 1 TGTTTGTTCCTCAGTTGT 1211595 TG-TTG-T--T--GTTGT 1 TGTTTGTTCCTCAGTTGT * * 1211607 TGTTTG-CCCTTCGGTTGT 1 TGTTTGTTCC-TCAGTTGT * 1211625 TGTTTGCTCCTCAGTTGT 1 TGTTTGTTCCTCAGTTGT * * * 1211643 TGTTTGTTCTTCTGTCG- 1 TGTTTGTTCCTCAGTTGT * * 1211660 TGCCTTGTTCCTCGGTTGT 1 TG-TTTGTTCCTCAGTTGT 1211679 TGTTTGTT-CTGCAGTTGT 1 TGTTTGTTCCT-CAGTTGT 1211697 TGTTTG 1 TGTTTG 1211703 CTCTTCTGTC Statistics Matches: 1429, Mismatches: 267, Indels: 130 0.78 0.15 0.07 Matches are distributed among these distances: 10 1 0.00 11 1 0.00 12 4 0.00 13 4 0.00 14 3 0.00 15 4 0.00 16 3 0.00 17 32 0.02 18 1294 0.91 19 29 0.02 20 2 0.00 21 13 0.01 24 39 0.03 ACGTcount: A:0.03, C:0.17, G:0.26, T:0.54 Consensus pattern (18 bp): TGTTTGTTCCTCAGTTGT Found at i:1211608 original size:45 final size:45 Alignment explanation

Indices: 1211557--1211646 Score: 146 Period size: 45 Copynumber: 2.0 Consensus size: 45 1211547 TTGCTCTTCG * 1211557 GTTGTTGATTGCTCC-TCGGTTGTTGTTTGCTCCTCGGTTGTTGTT 1 GTTGTTGATTGC-CCTTCGGTTGTTGTTTGCTCCTCAGTTGTTGTT * 1211602 GTTGTTGTTTGCCCTTCGGTTGTTGTTTGCTCCTCAGTTGTTGTT 1 GTTGTTGATTGCCCTTCGGTTGTTGTTTGCTCCTCAGTTGTTGTT 1211647 TGTTCTTCTG Statistics Matches: 42, Mismatches: 2, Indels: 2 0.91 0.04 0.04 Matches are distributed among these distances: 44 2 0.05 45 40 0.95 ACGTcount: A:0.02, C:0.18, G:0.28, T:0.52 Consensus pattern (45 bp): GTTGTTGATTGCCCTTCGGTTGTTGTTTGCTCCTCAGTTGTTGTT Found at i:1211610 original size:27 final size:27 Alignment explanation

Indices: 1211575--1211628 Score: 92 Period size: 27 Copynumber: 2.0 Consensus size: 27 1211565 TTGCTCCTCG 1211575 GTTGTTGTTTGCTCC-TCGGTTGTTGTT 1 GTTGTTGTTTGC-CCTTCGGTTGTTGTT 1211602 GTTGTTGTTTGCCCTTCGGTTGTTGTT 1 GTTGTTGTTTGCCCTTCGGTTGTTGTT 1211629 TGCTCCTCAG Statistics Matches: 26, Mismatches: 0, Indels: 2 0.93 0.00 0.07 Matches are distributed among these distances: 26 2 0.08 27 24 0.92 ACGTcount: A:0.00, C:0.15, G:0.30, T:0.56 Consensus pattern (27 bp): GTTGTTGTTTGCCCTTCGGTTGTTGTT Found at i:1211672 original size:81 final size:81 Alignment explanation

Indices: 1211521--1211682 Score: 209 Period size: 81 Copynumber: 2.0 Consensus size: 81 1211511 TTGTTCCTCG * * * * * 1211521 GTTGTGGTTTGTCCTTCGGTTGTTGTTTGCTCTTCGGTTGTTGATTGCTCCTCGGTTGTTGTTTG 1 GTTGTGGTTTGCCCTTCGGTTGTTGTTTGCTCCTCAGTTGTTGATTGCTCCTCGGTCGTTGCTTG 1211586 CTCCTCGGTTGTTGTT 66 CTCCTCGGTTGTTGTT * * * * * 1211602 GTTGTTGTTTGCCCTTCGGTTGTTGTTTGCTCCTCAGTTGTTGTTTGTTCTTCTGTCG-TGCCTT 1 GTTGTGGTTTGCCCTTCGGTTGTTGTTTGCTCCTCAGTTGTTGATTGCTCCTCGGTCGTTG-CTT * 1211666 GTTCCTCGGTTGTTGTT 65 GCTCCTCGGTTGTTGTT 1211683 TGTTCTGCAG Statistics Matches: 69, Mismatches: 11, Indels: 2 0.84 0.13 0.02 Matches are distributed among these distances: 80 2 0.03 81 67 0.97 ACGTcount: A:0.01, C:0.19, G:0.28, T:0.52 Consensus pattern (81 bp): GTTGTGGTTTGCCCTTCGGTTGTTGTTTGCTCCTCAGTTGTTGATTGCTCCTCGGTCGTTGCTTG CTCCTCGGTTGTTGTT Found at i:1211696 original size:99 final size:99 Alignment explanation

Indices: 1211518--1211700 Score: 237 Period size: 99 Copynumber: 1.8 Consensus size: 99 1211508 GGTTTGTTCC * * 1211518 TCGGTTGTGGTTTGTCCTTCGGTTGTTGTTTGCTCTTCGGTTGTTGATTGCTCCTCGGTTGTTGT 1 TCGGTTGTGGTTTGTCCTTCAGTTGTTGTTTGCTCTTCGGTCGTTGATTGCTCCTCGGTTGTTGT * 1211583 TTGCTCCTCGGTTGTTGTTGTTGTTGTTTGCCCT 66 TTGCTCCTCAGTTGTTGTTGTTGTTGTTTGCCCT * * * * * 1211617 TCGGTTGTTGTTTGCTCC-TCAGTTGTTGTTTGTTCTTCTGTCG-TGCCTTGTTCCTCGGTTGTT 1 TCGGTTGTGGTTTG-TCCTTCAGTTGTTGTTTGCTCTTCGGTCGTTG-ATTGCTCCTCGGTTGTT * 1211680 GTTTG-TTCTGCAGTTGTTGTT 64 GTTTGCTCCT-CAGTTGTTGTT 1211701 TGCTCTTCTG Statistics Matches: 72, Mismatches: 9, Indels: 6 0.83 0.10 0.07 Matches are distributed among these distances: 98 5 0.07 99 64 0.89 100 3 0.04 ACGTcount: A:0.02, C:0.18, G:0.28, T:0.52 Consensus pattern (99 bp): TCGGTTGTGGTTTGTCCTTCAGTTGTTGTTTGCTCTTCGGTCGTTGATTGCTCCTCGGTTGTTGT TTGCTCCTCAGTTGTTGTTGTTGTTGTTTGCCCT Found at i:1211743 original size:18 final size:18 Alignment explanation

Indices: 1211720--1211754 Score: 61 Period size: 18 Copynumber: 1.9 Consensus size: 18 1211710 GTCGTCGTTA 1211720 CTTCGTCCGTTGTTGTTT 1 CTTCGTCCGTTGTTGTTT * 1211738 CTTCGTCGGTTGTTGTT 1 CTTCGTCCGTTGTTGTT 1211755 GGTTCAGTAG Statistics Matches: 16, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 18 16 1.00 ACGTcount: A:0.00, C:0.20, G:0.26, T:0.54 Consensus pattern (18 bp): CTTCGTCCGTTGTTGTTT Found at i:1212007 original size:18 final size:18 Alignment explanation

Indices: 1211986--1212572 Score: 274 Period size: 18 Copynumber: 32.8 Consensus size: 18 1211976 TGGTTCGGTG * * 1211986 GTTGTTATTTGTTCATCA 1 GTTGTTGTTTGTTCTTCA * 1212004 GTTGTTGTTTGTTCCTGC- 1 GTTGTTGTTTGTT-CTTCA ** 1212022 GTTGTTGTTTGTTCTTTT 1 GTTGTTGTTTGTTCTTCA * 1212040 GTTGTTGTCTGTTCTTCA 1 GTTGTTGTTTGTTCTTCA * 1212058 GTTGTTGTTAG---TTCA 1 GTTGTTGTTTGTTCTTCA * * 1212073 GTTGTTGCTTGTTCTTCG 1 GTTGTTGTTTGTTCTTCA * * 1212091 GTTGTTGTTTGTACATT-T 1 GTTGTTGTTTGTTC-TTCA * 1212109 GTTGTTGTCTGTTCTTCA 1 GTTGTTGTTTGTTCTTCA * * * * 1212127 GTAGTAGTCTGTTCTTCG 1 GTTGTTGTTTGTTCTTCA * * 1212145 GTTGTTGTTTGTTCAGT-G 1 GTTGTTGTTTGTTC-TTCA * * 1212163 GTTGTTGTTTGCTCCTCA 1 GTTGTTGTTTGTTCTTCA * * * * 1212181 GTTGTAGTTGGTTCAAT-G 1 GTTGTTGTTTGTTC-TTCA * 1212199 GTTGTTGTCTGTTCTTCA 1 GTTGTTGTTTGTTCTTCA * * 1212217 GTTGTTGTTGGTTCAAT-A 1 GTTGTTGTTTGTTC-TTCA * * * 1212235 ATTGTAGTCTGTTCTTCA 1 GTTGTTGTTTGTTCTTCA ** * 1212253 GTTGTTGTTAATTCAAT-A 1 GTTGTTGTTTGTTC-TTCA * * 1212271 CTTGTTGTCTGTTCTTC- 1 GTTGTTGTTTGTTCTTCA * 1212288 GATTGTTG-TTGATTCAAT-A 1 G-TTGTTGTTTG-TTC-TTCA * * 1212307 GTTGTAGTCTGTTCTTCA 1 GTTGTTGTTTGTTCTTCA * *** 1212325 GTTGTTGTTGGTTCCGAA 1 GTTGTTGTTTGTTCTTCA * * 1212343 GTTGTTGTCTGTTCTTCG 1 GTTGTTGTTTGTTCTTCA * * 1212361 GTTGTTG-TCGATTCAAT-A 1 GTTGTTGTTTG-TTC-TTCA * * 1212379 GTTGTAGTCTGTTCTTCA 1 GTTGTTGTTTGTTCTTCA ** * 1212397 GTTGTTGTTAATTCAAT-A 1 GTTGTTGTTTGTTC-TTCA * * 1212415 GTTGTAGTCTGTTCTTCA 1 GTTGTTGTTTGTTCTTCA * 1212433 GTTGTTG-TTGATTCAAT-A 1 GTTGTTGTTTG-TTC-TTCA * * 1212451 GTTGTAGTCTGTTCTTCA 1 GTTGTTGTTTGTTCTTCA * *** 1212469 GTTGTTGTTGGTTCCGAA 1 GTTGTTGTTTGTTCTTCA * * 1212487 GTTGTTGTCTGTTCTTCG 1 GTTGTTGTTTGTTCTTCA * *** 1212505 GTTGTTGTTGGTTCCGAA 1 GTTGTTGTTTGTTCTTCA * * 1212523 GTTGTTGTCTGTTCTTCG 1 GTTGTTGTTTGTTCTTCA * * * 1212541 GTTGTTGTTTTTTCGGT-G 1 GTTGTTGTTTGTTC-TTCA 1212559 GTTGTTGTTTGTTC 1 GTTGTTGTTTGTTC 1212573 CCCAGTGGTT Statistics Matches: 409, Mismatches: 128, Indels: 64 0.68 0.21 0.11 Matches are distributed among these distances: 15 13 0.03 17 17 0.04 18 360 0.88 19 19 0.05 ACGTcount: A:0.10, C:0.12, G:0.25, T:0.53 Consensus pattern (18 bp): GTTGTTGTTTGTTCTTCA Found at i:1212062 original size:21 final size:19 Alignment explanation

Indices: 1211944--1212066 Score: 60 Period size: 21 Copynumber: 6.3 Consensus size: 19 1211934 TTGGGCCCCG * 1211944 GTTGTTGTCTCTTCTTCGGTT 1 GTTGTTGT-TGTTCTTC-GTT * * * 1211965 GTTGTTGTTATTGGTTCGGTG 1 GTTGTTGTTGTT-CTTC-GTT * * 1211986 GTTGTTATTTGTTCATCAGTT 1 GTTGTT-GTTGTTCTTC-GTT * 1212007 GTTG-T-TTGTTCCTGCGTT 1 GTTGTTGTTGTT-CTTCGTT 1212025 GTTG-T-TTGTTCTT--TT 1 GTTGTTGTTGTTCTTCGTT 1212040 GTTGTTGTCTGTTCTTCAGTT 1 GTTGTTGT-TGTTCTTC-GTT 1212061 GTTGTT 1 GTTGTT 1212067 AGTTCAGTTG Statistics Matches: 81, Mismatches: 12, Indels: 18 0.73 0.11 0.16 Matches are distributed among these distances: 15 6 0.07 16 1 0.01 17 3 0.04 18 25 0.31 19 2 0.02 20 4 0.05 21 36 0.44 22 4 0.05 ACGTcount: A:0.04, C:0.11, G:0.26, T:0.59 Consensus pattern (19 bp): GTTGTTGTTGTTCTTCGTT Found at i:1212062 original size:33 final size:33 Alignment explanation

Indices: 1212025--1212128 Score: 95 Period size: 33 Copynumber: 3.1 Consensus size: 33 1212015 TTCCTGCGTT 1212025 GTTGTTTGTTCTTTTGTTGTTGTCTGTTCTTCA 1 GTTGTTTGTTCTTTTGTTGTTGTCTGTTCTTCA * ** * 1212058 GTTG-TTGTTAGTTCAGTTGTTG-CTTGTTCTTCGGTT 1 GTTGTTTGTT-CTTTTGTTGTTGTC-TGTTCTTC---A * * 1212094 GTTGTTTGTACATTTGTTGTTGTCTGTTCTTCA 1 GTTGTTTGTTCTTTTGTTGTTGTCTGTTCTTCA 1212127 GT 1 GT 1212129 AGTAGTCTGT Statistics Matches: 54, Mismatches: 10, Indels: 14 0.69 0.13 0.18 Matches are distributed among these distances: 32 6 0.11 33 23 0.43 36 20 0.37 37 5 0.09 ACGTcount: A:0.06, C:0.12, G:0.24, T:0.59 Consensus pattern (33 bp): GTTGTTTGTTCTTTTGTTGTTGTCTGTTCTTCA Found at i:1212167 original size:69 final size:68 Alignment explanation

Indices: 1212025--1212168 Score: 159 Period size: 69 Copynumber: 2.1 Consensus size: 68 1212015 TTCCTGCGTT * * * 1212025 GTTGTTTGTTCTTTTGTTGTTGTCTGTTCTTCAGTTGTTGTTAGTTCAGTTGTTGCTTGTTCTTC 1 GTTGTTTGTACATTTGTTGTTGTCTGTTCTTCAGTTGTTGTTACTTCAGTTGTTGC-TGTTCTTC * * 1212090 GGTT 65 AGTG * * 1212094 GTTGTTTGTACATTTGTTGTTGTCTGTTCTTCAGTAGTAGTCTGTT-CTTCGGTTGTTG-T-TTG 1 GTTGTTTGTACATTTGTTGTTGTCTGTTCTTCAGT--T-GT-TGTTACTTCAGTTGTTGCTGTTC 1212156 TTCAGTG 62 TTCAGTG 1212163 GTTGTT 1 GTTGTT 1212169 GTTTGCTCCT Statistics Matches: 64, Mismatches: 7, Indels: 8 0.81 0.09 0.10 Matches are distributed among these distances: 69 46 0.72 70 1 0.02 71 1 0.02 72 12 0.19 73 4 0.06 ACGTcount: A:0.06, C:0.11, G:0.26, T:0.57 Consensus pattern (68 bp): GTTGTTTGTACATTTGTTGTTGTCTGTTCTTCAGTTGTTGTTACTTCAGTTGTTGCTGTTCTTCA GTG Found at i:1212572 original size:72 final size:72 Alignment explanation

Indices: 1212133--1212549 Score: 536 Period size: 72 Copynumber: 5.8 Consensus size: 72 1212123 TTCAGTAGTA * * * * * * * 1212133 GTCTGTTCTTCGGTTGTTGTTTG-TTCAGTGGTTGTTGTTTGCTCCTCAGTTGTAGTTGGTTCAA 1 GTCTGTTCTTCGGTTGTTG-TTGATTCAATAGTTGTAGTCTGTTCTTCAGTTGTTGTTGGTTCAA * 1212197 TGGTTGTT 65 TAGTTGTT * * * ** 1212205 GTCTGTTCTTCAGTTGTTGTTGGTTCAATAATTGTAGTCTGTTCTTCAGTTGTTGTTAATTCAAT 1 GTCTGTTCTTCGGTTGTTGTTGATTCAATAGTTGTAGTCTGTTCTTCAGTTGTTGTTGGTTCAAT * 1212270 ACTTGTT 66 AGTTGTT * * 1212277 GTCTGTTCTTCGATTGTTGTTGATTCAATAGTTGTAGTCTGTTCTTCAGTTGTTGTTGGTTCCGA 1 GTCTGTTCTTCGGTTGTTGTTGATTCAATAGTTGTAGTCTGTTCTTCAGTTGTTGTTGGTT-CAA 1212342 -AGTTGTT 65 TAGTTGTT * ** 1212349 GTCTGTTCTTCGGTTGTTGTCGATTCAATAGTTGTAGTCTGTTCTTCAGTTGTTGTTAATTCAAT 1 GTCTGTTCTTCGGTTGTTGTTGATTCAATAGTTGTAGTCTGTTCTTCAGTTGTTGTTGGTTCAAT * 1212414 AGTTGTA 66 AGTTGTT * * 1212421 GTCTGTTCTTCAGTTGTTGTTGATTCAATAGTTGTAGTCTGTTCTTCAGTTGTTGTTGGTTCCGA 1 GTCTGTTCTTCGGTTGTTGTTGATTCAATAGTTGTAGTCTGTTCTTCAGTTGTTGTTGGTT-CAA 1212486 -AGTTGTT 65 TAGTTGTT * * * * 1212493 GTCTGTTCTTCGGTTGTTGTTGGTTCCGA-AGTTGTTGTCTGTTCTTCGGTTGTTGTT 1 GTCTGTTCTTCGGTTGTTGTTGATT-CAATAGTTGTAGTCTGTTCTTCAGTTGTTGTT 1212550 TTTTCGGTGG Statistics Matches: 302, Mismatches: 38, Indels: 10 0.86 0.11 0.03 Matches are distributed among these distances: 71 5 0.02 72 291 0.96 73 6 0.02 ACGTcount: A:0.12, C:0.13, G:0.25, T:0.51 Consensus pattern (72 bp): GTCTGTTCTTCGGTTGTTGTTGATTCAATAGTTGTAGTCTGTTCTTCAGTTGTTGTTGGTTCAAT AGTTGTT Done.