Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.04

Sequence: scaffold1154

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: 1159333
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.30

Warning! 97731 characters in sequence are not A, C, G, or T


File 3 of 3

Found at i:527578 original size:83 final size:84

Alignment explanation

Indices: 527439--527602 Score: 276 Period size: 83 Copynumber: 2.0 Consensus size: 84 527429 TAATGCTCTA * 527439 CTAATAGTTTAAAGAAATAACTCAAACAGGGTAGCAAATGATATTGAATTAG-TTTTTTTTACAA 1 CTAATAGTTTAAAGAAATAACTCAAACAGGGTAGCAAATGATATTCAATTAGTTTTTTTTTACAA 527503 TTATTAATTTAATTTTATT 66 TTATTAATTTAATTTTATT * * 527522 CTAATAGTTTAAAGAAATAACTCAAACAGGGTAGCAAATGATATTCAGTTAGTTTTTTTTTTCCA 1 CTAATAGTTTAAAGAAATAACTCAAACAGGGTAGCAAATGATATTCAATTAG-TTTTTTTTTACA * 527587 ATTTTTAATTTAATTT 65 ATTATTAATTTAATTT 527603 AATTAGGGTA Statistics Matches: 75, Mismatches: 4, Indels: 2 0.93 0.05 0.02 Matches are distributed among these distances: 83 50 0.67 85 25 0.33 ACGTcount: A:0.38, C:0.09, G:0.11, T:0.43 Consensus pattern (84 bp): CTAATAGTTTAAAGAAATAACTCAAACAGGGTAGCAAATGATATTCAATTAGTTTTTTTTTACAA TTATTAATTTAATTTTATT Found at i:531259 original size:4 final size:4 Alignment explanation

Indices: 531250--531293 Score: 88 Period size: 4 Copynumber: 11.0 Consensus size: 4 531240 ACTTTCAAGT 531250 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA 1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA 531294 TATATATATA Statistics Matches: 40, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 4 40 1.00 ACGTcount: A:0.50, C:0.00, G:0.25, T:0.25 Consensus pattern (4 bp): GATA Found at i:531298 original size:2 final size:2 Alignment explanation

Indices: 531291--531322 Score: 64 Period size: 2 Copynumber: 16.0 Consensus size: 2 531281 AGATAGATAG 531291 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT 1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT 531323 NNNNNNNNNN Statistics Matches: 30, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 30 1.00 ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50 Consensus pattern (2 bp): AT Found at i:534475 original size:2 final size:2 Alignment explanation

Indices: 534470--534513 Score: 88 Period size: 2 Copynumber: 22.0 Consensus size: 2 534460 NNNNNNTACC 534470 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA 1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA 534512 TA 1 TA 534514 AGCTAAACTA Statistics Matches: 42, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 42 1.00 ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50 Consensus pattern (2 bp): TA Found at i:549268 original size:21 final size:21 Alignment explanation

Indices: 549205--549270 Score: 55 Period size: 21 Copynumber: 3.2 Consensus size: 21 549195 GGCAAGCCAG 549205 TTATTTATGTCACAT-T-CAAC 1 TTATTTATGTCA-ATATGCAAC * ** * ** 549225 TTAGTTATGTTGACATGTTAC 1 TTATTTATGTCAATATGCAAC 549246 TTATTTATGTCAATATGCAAC 1 TTATTTATGTCAATATGCAAC 549267 TTAT 1 TTAT 549271 GTTGGCATGC Statistics Matches: 32, Mismatches: 12, Indels: 3 0.68 0.26 0.06 Matches are distributed among these distances: 19 1 0.03 20 10 0.31 21 21 0.66 ACGTcount: A:0.29, C:0.14, G:0.11, T:0.47 Consensus pattern (21 bp): TTATTTATGTCAATATGCAAC Found at i:549334 original size:21 final size:21 Alignment explanation

Indices: 549283--549335 Score: 54 Period size: 21 Copynumber: 2.5 Consensus size: 21 549273 TGGCATGCAT ** 549283 CTTATTTATGTTGACATGCAA 1 CTTATTTATGTTGACATAAAA * * 549304 CATGA-ATATGTTGACATAAAA 1 C-TTATTTATGTTGACATAAAA 549325 CTTATTTATGT 1 CTTATTTATGT 549336 CAACATACGA Statistics Matches: 24, Mismatches: 6, Indels: 4 0.71 0.18 0.12 Matches are distributed among these distances: 20 2 0.08 21 20 0.83 22 2 0.08 ACGTcount: A:0.34, C:0.11, G:0.13, T:0.42 Consensus pattern (21 bp): CTTATTTATGTTGACATAAAA Found at i:549341 original size:21 final size:21 Alignment explanation

Indices: 549317--549356 Score: 53 Period size: 21 Copynumber: 1.9 Consensus size: 21 549307 GAATATGTTG * 549317 ACATAAAACTTATTTATGTCA 1 ACATAAAACTTAATTATGTCA ** 549338 ACATACGACTTAATTATGT 1 ACATAAAACTTAATTATGT 549357 TTAAATACAA Statistics Matches: 16, Mismatches: 3, Indels: 0 0.84 0.16 0.00 Matches are distributed among these distances: 21 16 1.00 ACGTcount: A:0.40, C:0.15, G:0.07, T:0.38 Consensus pattern (21 bp): ACATAAAACTTAATTATGTCA Found at i:573711 original size:30 final size:30 Alignment explanation

Indices: 573686--574143 Score: 684 Period size: 30 Copynumber: 15.3 Consensus size: 30 573676 CAGCCCAAAA * * 573686 ATCCAAAACAAGAAACTGAAAAGCCCAGAG 1 ATCCAATACAGGAAACTGAAAAGCCCAGAG * 573716 ATCCAATACAAGAAACTGAAAAGCCCAGAG 1 ATCCAATACAGGAAACTGAAAAGCCCAGAG * * 573746 ATCCAATACAAGAAACTGAAAAGCCCAGAA 1 ATCCAATACAGGAAACTGAAAAGCCCAGAG * 573776 ATCCAATACAAGAAACTGAAAAGCCCAGAG 1 ATCCAATACAGGAAACTGAAAAGCCCAGAG * 573806 ATCCGATACAGGAAACTGAAAAGCCCAGAG 1 ATCCAATACAGGAAACTGAAAAGCCCAGAG * * * 573836 ATCCAATACAAGAAACTGAAGAGCCCAGAA 1 ATCCAATACAGGAAACTGAAAAGCCCAGAG * 573866 ATCCAATACAGAAAACTGAAAAGCCCAGAG 1 ATCCAATACAGGAAACTGAAAAGCCCAGAG * * * * 573896 ATCCAGTAAAGGAAACTGAAAAGTCCAGAA 1 ATCCAATACAGGAAACTGAAAAGCCCAGAG 573926 ATCCAATACAGGAAACTGAAAAGCCCAGAG 1 ATCCAATACAGGAAACTGAAAAGCCCAGAG * * 573956 ATCCAATACAAGAAACTGAAAAGCCCAGAA 1 ATCCAATACAGGAAACTGAAAAGCCCAGAG * 573986 ATTCAATACAGGAAACTGAAAAGCCCAGAG 1 ATCCAATACAGGAAACTGAAAAGCCCAGAG * * * * 574016 ATCCAGTA-ATGGAAACTAAAAAGTCCAGAA 1 ATCCAATACA-GGAAACTGAAAAGCCCAGAG 574046 ATCCAATACAGGAAACTGAAAAGCCCAGAG 1 ATCCAATACAGGAAACTGAAAAGCCCAGAG 574076 ATCCAATACAGGAAACTGAAAAGCCCAGAG 1 ATCCAATACAGGAAACTGAAAAGCCCAGAG * * 574106 ATCCAATACAGGAAACTGAAAAGTCCAGAA 1 ATCCAATACAGGAAACTGAAAAGCCCAGAG 574136 ATCCAATA 1 ATCCAATA 574144 AAGAAGCAGC Statistics Matches: 388, Mismatches: 38, Indels: 4 0.90 0.09 0.01 Matches are distributed among these distances: 29 1 0.00 30 386 0.99 31 1 0.00 ACGTcount: A:0.49, C:0.22, G:0.17, T:0.11 Consensus pattern (30 bp): ATCCAATACAGGAAACTGAAAAGCCCAGAG Found at i:575880 original size:2 final size:2 Alignment explanation

Indices: 575873--575911 Score: 60 Period size: 2 Copynumber: 19.5 Consensus size: 2 575863 AACAGAGAAA * * 575873 CT CT CT CT CT CC CT CT CT CT CT CT CT CT TT 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 C 575912 GTGAATTCAA Statistics Matches: 33, Mismatches: 4, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 2 33 1.00 ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49 Consensus pattern (2 bp): CT Found at i:576138 original size:43 final size:45 Alignment explanation

Indices: 576077--576289 Score: 169 Period size: 47 Copynumber: 4.8 Consensus size: 45 576067 TTTGAGGTAT * * 576077 TTTCTGATATCAGAAAATGA-T-TTTTTGATATCAAGATTTCTAA 1 TTTCTGATATCAGAAAATGATTATTTTTGATATCAAGAATTCGAA * 576120 TTTCTGATATCAGAAAATGATTTAATTTTTGATATCAAGAATTCGGA 1 TTTCTGATATCAGAAAATGA-TT-ATTTTTGATATCAAGAATTCGAA * * * * * 576167 -TTCTTGATATCAGAAAATACGATCCATTTTTCTTATATCAAAAAATCGAT 1 TTTC-TGATATCAGAAAAT--GAT-TA-TTTT-TGATATCAAGAATTCGAA * * 576217 TTTGTGATATC--AAAAT-ATCA-TTTTGATATC-AGAAATTCG-A 1 TTTCTGATATCAGAAAATGATTATTTTTGATATCAAG-AATTCGAA * 576257 TTTTTGATATCAGAAAATGA-T-TTTTTGATATCA 1 TTTCTGATATCAGAAAATGATTATTTTTGATATCA 576290 GAAATTCAAA Statistics Matches: 137, Mismatches: 16, Indels: 34 0.73 0.09 0.18 Matches are distributed among these distances: 40 11 0.08 41 11 0.08 42 18 0.13 43 21 0.15 44 2 0.01 45 3 0.02 46 3 0.02 47 33 0.24 48 7 0.05 49 6 0.04 50 20 0.15 51 2 0.01 ACGTcount: A:0.36, C:0.10, G:0.12, T:0.42 Consensus pattern (45 bp): TTTCTGATATCAGAAAATGATTATTTTTGATATCAAGAATTCGAA Found at i:576239 original size:21 final size:22 Alignment explanation

Indices: 576075--576343 Score: 125 Period size: 22 Copynumber: 11.8 Consensus size: 22 576065 TTTTTGAGGT 576075 ATTTTCTGATATCAGAAA-AT-G 1 ATTTT-TGATATCAGAAATATCG * * * 576096 ATTTTTTGATATCA-AGATTTCTA 1 A-TTTTTGATATCAGAAATATC-G * ** 576119 ATTTCTGATATCAGAAAATGATTTA 1 ATTTTTGATATCAG-AAAT-A-TCG 576144 ATTTTTGATATCA-AGAAT-TCGG 1 ATTTTTGATATCAGA-AATATC-G * * 576166 ATTCTTGATATCAGAAAATACGATCC 1 ATTTTTGATATCAG-AAAT---ATCG * * 576192 ATTTTTCTTATATCA-AAAAATCG 1 A-TTTT-TGATATCAGAAATATCG 576215 ATTTTGTGATATCA-AAATATC- 1 ATTTT-TGATATCAGAAATATCG 576236 A-TTTTGATATCAGAAAT-TCG 1 ATTTTTGATATCAGAAATATCG 576256 ATTTTTGATATCAGAAA-AT-G 1 ATTTTTGATATCAGAAATATCG * 576276 ATTTTTTGATATCAGAAATTCAAACTG 1 A-TTTTTGATATCAGAAA-T--ATC-G * 576303 ATTTTTTGATATCAAGAATTAT-- 1 A-TTTTTGATATC-AGAAATATCG 576325 ATTTTTTGATATCAGAAAT 1 A-TTTTTGATATCAGAAAT 576344 TCAAATAAAA Statistics Matches: 195, Mismatches: 23, Indels: 60 0.70 0.08 0.22 Matches are distributed among these distances: 19 10 0.05 20 12 0.06 21 49 0.25 22 57 0.29 23 9 0.05 24 7 0.04 25 15 0.08 26 5 0.03 27 20 0.10 28 11 0.06 ACGTcount: A:0.37, C:0.10, G:0.12, T:0.42 Consensus pattern (22 bp): ATTTTTGATATCAGAAATATCG Found at i:576259 original size:20 final size:21 Alignment explanation

Indices: 576201--576345 Score: 111 Period size: 21 Copynumber: 6.6 Consensus size: 21 576191 CATTTTTCTT * * 576201 ATATCAAAAAATCGATTTTGTG 1 ATATCAGAAATTCGATTTT-TG 576223 ATATCA-AAATATC-A-TTTTG 1 ATATCAGAAAT-TCGATTTTTG 576242 ATATCAGAAATTCGATTTTTG 1 ATATCAGAAATTCGATTTTTG * 576263 ATATCAGAAAAT-GATTTTTTG 1 ATATCAGAAATTCGA-TTTTTG 576284 ATATCAGAAATTCAAACTGATTTTTTG 1 ATATCAGAAATT----C-GA-TTTTTG ** 576311 ATATCA-AGAATTATATTTTTTG 1 ATATCAGA-AATTCGA-TTTTTG 576333 ATATCAGAAATTC 1 ATATCAGAAATTC 576346 AAATAAAATG Statistics Matches: 104, Mismatches: 6, Indels: 26 0.76 0.04 0.19 Matches are distributed among these distances: 19 10 0.10 20 10 0.10 21 37 0.36 22 26 0.25 23 1 0.01 26 1 0.01 27 19 0.18 ACGTcount: A:0.39, C:0.09, G:0.11, T:0.41 Consensus pattern (21 bp): ATATCAGAAATTCGATTTTTG Found at i:576283 original size:42 final size:41 Alignment explanation

Indices: 576201--576345 Score: 141 Period size: 49 Copynumber: 3.3 Consensus size: 41 576191 CATTTTTCTT * * * 576201 ATATCAAAAAATCGATTTTGTGATATC--AAAATATCATTTTG 1 ATATCAGAAATTCGATTTT-TGATATCAGAAAATAT-TTTTTG 576242 ATATCAGAAATTCGATTTTTGATATCAGAAAATGATTTTTTG 1 ATATCAGAAATTCGATTTTTGATATCAGAAAAT-ATTTTTTG * 576284 ATATCAGAAATTCAAACTGATTTTTTGATATCAAGAATTATATTTTTTG 1 ATATCAGAAATT----C-GA-TTTTTGATATC-AGAA-AATATTTTTTG 576333 ATATCAGAAATTC 1 ATATCAGAAATTC 576346 AAATAAAATG Statistics Matches: 89, Mismatches: 4, Indels: 18 0.80 0.04 0.16 Matches are distributed among these distances: 40 7 0.08 41 17 0.19 42 22 0.25 43 2 0.02 45 1 0.01 46 1 0.01 47 2 0.02 48 11 0.12 49 24 0.27 50 2 0.02 ACGTcount: A:0.39, C:0.09, G:0.11, T:0.41 Consensus pattern (41 bp): ATATCAGAAATTCGATTTTTGATATCAGAAAATATTTTTTG Found at i:576312 original size:27 final size:26 Alignment explanation

Indices: 576271--576349 Score: 105 Period size: 27 Copynumber: 3.2 Consensus size: 26 576261 TGATATCAGA 576271 AAATGATTTTTTGATATCAGAAATTC 1 AAATGATTTTTTGATATCAGAAATTC 576297 AAACTGATTTTTTGATATCA-AGAATT- 1 AAA-TGATTTTTTGATATCAGA-AATTC 576323 --AT-ATTTTTTGATATCAGAAATTC 1 AAATGATTTTTTGATATCAGAAATTC 576346 AAAT 1 AAAT 576350 AAAATGGCGA Statistics Matches: 47, Mismatches: 0, Indels: 13 0.78 0.00 0.22 Matches are distributed among these distances: 22 18 0.38 23 2 0.04 24 1 0.02 25 2 0.04 26 4 0.09 27 20 0.43 ACGTcount: A:0.39, C:0.08, G:0.10, T:0.43 Consensus pattern (26 bp): AAATGATTTTTTGATATCAGAAATTC Found at i:577052 original size:22 final size:22 Alignment explanation

Indices: 577024--577153 Score: 129 Period size: 22 Copynumber: 5.7 Consensus size: 22 577014 TGTAGGTCTT 577024 ATTTTCTGATATCAAAAAATCG 1 ATTTTCTGATATCAAAAAATCG * 577046 ATTTTCTGATATCAGAAAATACAAATG 1 ATTTTCTGATATCAAAAAAT-C----G * * 577073 ATTTTTTGATATGAAAAAAT-G 1 ATTTTCTGATATCAAAAAATCG * * 577094 ATTTTTCTGATATCAAGAATTCG 1 A-TTTTCTGATATCAAAAAATCG * 577117 ATTTTTTTGATATCAAAAAAT-G 1 A-TTTTCTGATATCAAAAAATCG 577139 ATTTTCTGATATCAA 1 ATTTTCTGATATCAA 577154 GAATTCAAAA Statistics Matches: 89, Mismatches: 12, Indels: 15 0.77 0.10 0.13 Matches are distributed among these distances: 21 15 0.17 22 36 0.40 23 20 0.22 27 18 0.20 ACGTcount: A:0.39, C:0.09, G:0.11, T:0.41 Consensus pattern (22 bp): ATTTTCTGATATCAAAAAATCG Found at i:577091 original size:27 final size:28 Alignment explanation

Indices: 577040--577092 Score: 72 Period size: 27 Copynumber: 1.9 Consensus size: 28 577030 TGATATCAAA * 577040 AAATCGATTTTCTGATATCAGAAAATAC 1 AAATCGATTTTCTGATATCAAAAAATAC * * 577068 AAAT-GATTTTTTGATATGAAAAAAT 1 AAATCGATTTTCTGATATCAAAAAAT 577093 GATTTTTCTG Statistics Matches: 22, Mismatches: 3, Indels: 1 0.85 0.12 0.04 Matches are distributed among these distances: 27 18 0.82 28 4 0.18 ACGTcount: A:0.45, C:0.08, G:0.11, T:0.36 Consensus pattern (28 bp): AAATCGATTTTCTGATATCAAAAAATAC Found at i:577135 original size:44 final size:46 Alignment explanation

Indices: 577023--577162 Score: 185 Period size: 49 Copynumber: 3.0 Consensus size: 46 577013 ATGTAGGTCT * * * 577023 TATTTTCTGATATCAAAAAATCGATTTTCTGATATCAGAAAATACAAA 1 TATTTTTTGATATCAAAAAAT-GATTTTCTGATATCA-AGAATTCAAA * * 577071 TGATTTTTTGATATGAAAAAATGATTTTTCTGATATCAAGAATTC-GA 1 T-ATTTTTTGATATCAAAAAATGA-TTTTCTGATATCAAGAATTCAAA 577118 T-TTTTTTGATATCAAAAAATGATTTTCTGATATCAAGAATTCAAA 1 TATTTTTTGATATCAAAAAATGATTTTCTGATATCAAGAATTCAAA 577163 AAAATAAAAT Statistics Matches: 82, Mismatches: 7, Indels: 9 0.84 0.07 0.09 Matches are distributed among these distances: 44 20 0.24 45 21 0.26 47 2 0.02 48 8 0.10 49 31 0.38 ACGTcount: A:0.40, C:0.09, G:0.11, T:0.40 Consensus pattern (46 bp): TATTTTTTGATATCAAAAAATGATTTTCTGATATCAAGAATTCAAA Found at i:577293 original size:22 final size:21 Alignment explanation

Indices: 577257--577325 Score: 77 Period size: 21 Copynumber: 3.3 Consensus size: 21 577247 GAATTTGTGG 577257 TATCAAAAAATGATTTTCTGA 1 TATCAAAAAATGATTTTCTGA * * 577278 TATCACAAAATAGATTTTTTGA 1 TATCAAAAAAT-GATTTTCTGA * * * 577300 TATC-AATAATTATTTTATGA 1 TATCAAAAAATGATTTTCTGA 577320 TATCAA 1 TATCAA 577326 TAATTCGAAT Statistics Matches: 40, Mismatches: 6, Indels: 4 0.80 0.12 0.08 Matches are distributed among these distances: 20 12 0.30 21 15 0.38 22 13 0.32 ACGTcount: A:0.42, C:0.09, G:0.07, T:0.42 Consensus pattern (21 bp): TATCAAAAAATGATTTTCTGA Found at i:577320 original size:20 final size:20 Alignment explanation

Indices: 577291--577330 Score: 71 Period size: 20 Copynumber: 2.0 Consensus size: 20 577281 CACAAAATAG * 577291 ATTTTTTGATATCAATAATT 1 ATTTTATGATATCAATAATT 577311 ATTTTATGATATCAATAATT 1 ATTTTATGATATCAATAATT 577331 CGAATTATTG Statistics Matches: 19, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 20 19 1.00 ACGTcount: A:0.38, C:0.05, G:0.05, T:0.53 Consensus pattern (20 bp): ATTTTATGATATCAATAATT Found at i:577342 original size:42 final size:40 Alignment explanation

Indices: 577226--577368 Score: 124 Period size: 42 Copynumber: 3.4 Consensus size: 40 577216 GAAATTCATC * * * 577226 ATTTTTTGATATCAAGAATTCGAATTTGTGGTATCAAAAAATG 1 ATTTTTTGATATCAA-AATTCGAATTT-TGATATC-AATAATT * * * * 577269 ATTTTCTGATATCACAAAATAGATTTTTTGATATCAATAATT 1 ATTTTTTGATATCA-AAATTCGA-ATTTTGATATCAATAATT * * 577311 ATTTTATGATATCAATAATTCGAATTATTGATATCAGATATTT 1 ATTTTTTGATATCAA-AATTCGAATT-TTGATATCA-ATAATT 577354 ATTTTTTTGATATCA 1 A-TTTTTTGATATCA 577369 GAAAATACCT Statistics Matches: 81, Mismatches: 13, Indels: 11 0.77 0.12 0.10 Matches are distributed among these distances: 41 3 0.04 42 32 0.40 43 30 0.37 44 16 0.20 ACGTcount: A:0.36, C:0.08, G:0.10, T:0.45 Consensus pattern (40 bp): ATTTTTTGATATCAAAATTCGAATTTTGATATCAATAATT Found at i:577345 original size:22 final size:19 Alignment explanation

Indices: 577296--577356 Score: 59 Period size: 20 Copynumber: 2.9 Consensus size: 19 577286 AATAGATTTT * 577296 TTGATATCAATAATTATTT 1 TTGATATCAATAATTATTA 577315 TATGATATCAATAATTCGAATTA 1 T-TGATATCAATAATT---ATTA * 577338 TTGATATCAGATATTTATT 1 TTGATATCA-ATAATTATT 577357 TTTTTGATAT Statistics Matches: 35, Mismatches: 2, Indels: 9 0.76 0.04 0.20 Matches are distributed among these distances: 19 1 0.03 20 17 0.49 22 8 0.23 23 9 0.26 ACGTcount: A:0.38, C:0.07, G:0.08, T:0.48 Consensus pattern (19 bp): TTGATATCAATAATTATTA Found at i:577370 original size:22 final size:20 Alignment explanation

Indices: 577291--577368 Score: 75 Period size: 22 Copynumber: 3.7 Consensus size: 20 577281 CACAAAATAG * 577291 ATTTTTTGATATCAATAATT 1 ATTTTTTGATATCAATATTT * * 577311 ATTTTATGATATCAATAATTCG 1 ATTTTTTGATATCAAT-ATT-T * * 577333 AATTATTGATATCAGATATTT 1 ATTTTTTGATATCA-ATATTT 577354 ATTTTTTTGATATCA 1 A-TTTTTTGATATCA 577369 GAAAATACCT Statistics Matches: 45, Mismatches: 9, Indels: 6 0.75 0.15 0.10 Matches are distributed among these distances: 20 15 0.33 21 3 0.07 22 25 0.56 23 2 0.04 ACGTcount: A:0.35, C:0.06, G:0.08, T:0.51 Consensus pattern (20 bp): ATTTTTTGATATCAATATTT Found at i:577933 original size:21 final size:21 Alignment explanation

Indices: 577909--577977 Score: 68 Period size: 21 Copynumber: 3.3 Consensus size: 21 577899 AAATTACAGT * * 577909 ATATAATTATGTTAGC-ACTGC 1 ATATAATGATGTTA-CAAATGC 577930 ATATAATGATGTTACAAATGC 1 ATATAATGATGTTACAAATGC * * * * 577951 ATATAATGTTATTACTATTGC 1 ATATAATGATGTTACAAATGC 577972 ATATAA 1 ATATAA 577978 AAGATATACC Statistics Matches: 41, Mismatches: 6, Indels: 2 0.84 0.12 0.04 Matches are distributed among these distances: 20 1 0.02 21 40 0.98 ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39 Consensus pattern (21 bp): ATATAATGATGTTACAAATGC Found at i:578775 original size:19 final size:19 Alignment explanation

Indices: 578751--578789 Score: 51 Period size: 19 Copynumber: 2.1 Consensus size: 19 578741 TTCAAAGGGC * 578751 ACCTGCACCAAAAACTTTA 1 ACCTGCACCAAAAACCTTA * * 578770 ACCTGCTCTAAAAACCTTA 1 ACCTGCACCAAAAACCTTA 578789 A 1 A 578790 TCTCCTCCAG Statistics Matches: 17, Mismatches: 3, Indels: 0 0.85 0.15 0.00 Matches are distributed among these distances: 19 17 1.00 ACGTcount: A:0.41, C:0.31, G:0.05, T:0.23 Consensus pattern (19 bp): ACCTGCACCAAAAACCTTA Found at i:579245 original size:18 final size:20 Alignment explanation

Indices: 579222--579262 Score: 68 Period size: 20 Copynumber: 2.1 Consensus size: 20 579212 TTGAGTTTTT 579222 TCAAAT-TT-GAGAAAAAAC 1 TCAAATATTGGAGAAAAAAC 579240 TCAAATATTGGAGAAAAAAC 1 TCAAATATTGGAGAAAAAAC 579260 TCA 1 TCA 579263 GACTTTAAGT Statistics Matches: 21, Mismatches: 0, Indels: 2 0.91 0.00 0.09 Matches are distributed among these distances: 18 6 0.29 19 2 0.10 20 13 0.62 ACGTcount: A:0.54, C:0.12, G:0.12, T:0.22 Consensus pattern (20 bp): TCAAATATTGGAGAAAAAAC Found at i:583268 original size:16 final size:16 Alignment explanation

Indices: 583245--583294 Score: 82 Period size: 16 Copynumber: 3.1 Consensus size: 16 583235 GCCCGAGTTT 583245 CAGGAGAAAACGTACC 1 CAGGAGAAAACGTACC * 583261 CGGGAGAAAACGTACC 1 CAGGAGAAAACGTACC * 583277 CAGGAGAAAACATACC 1 CAGGAGAAAACGTACC 583293 CA 1 CA 583295 ATCTTTACCC Statistics Matches: 31, Mismatches: 3, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 16 31 1.00 ACGTcount: A:0.44, C:0.26, G:0.24, T:0.06 Consensus pattern (16 bp): CAGGAGAAAACGTACC Found at i:587470 original size:47 final size:47 Alignment explanation

Indices: 587416--587580 Score: 224 Period size: 47 Copynumber: 3.5 Consensus size: 47 587406 CCTTACAACA * * 587416 AACTACAGGTAAGTACCCTTCATTCCAAAGACAGTGTAACATTGACC 1 AACTACAGGTAAGTACCGTTCATTCCAAAGACAGTGTAACATTAACC * * 587463 AACTACAGGTAAGTACCGTTCATTCCAATGACAGTGTACCATTAACC 1 AACTACAGGTAAGTACCGTTCATTCCAAAGACAGTGTAACATTAACC * * ** * 587510 ACCTACAGGTAAGTACTGTTCATTCCATGGACAGTGT-ACTGTTAACC 1 AACTACAGGTAAGTACCGTTCATTCCAAAGACAGTGTAAC-ATTAACC * 587557 AACTACAGGTAAGTACCGATCATT 1 AACTACAGGTAAGTACCGTTCATT 587581 TGATGGTCAT Statistics Matches: 104, Mismatches: 13, Indels: 2 0.87 0.11 0.02 Matches are distributed among these distances: 46 1 0.01 47 103 0.99 ACGTcount: A:0.33, C:0.24, G:0.16, T:0.26 Consensus pattern (47 bp): AACTACAGGTAAGTACCGTTCATTCCAAAGACAGTGTAACATTAACC Found at i:587600 original size:47 final size:47 Alignment explanation

Indices: 587416--587651 Score: 192 Period size: 47 Copynumber: 5.0 Consensus size: 47 587406 CCTTACAACA ** ** * * * 587416 AACTACAGGTAAGTACCCTTCATTCCAAAGACAGTGTAAC-ATTGACC 1 AACTACAGGTAAGTACCGATCATTCCATGGACAGTCT-ACTGTTAACC * * ** 587463 AACTACAGGTAAGTACCGTTCATTCCAAT-GACAGTGTACCATTAACC 1 AACTACAGGTAAGTACCGATCATTCC-ATGGACAGTCTACTGTTAACC * * * * 587510 ACCTACAGGTAAGTACTGTTCATTCCATGGACAGTGTACTGTTAACC 1 AACTACAGGTAAGTACCGATCATTCCATGGACAGTCTACTGTTAACC ** * * 587557 AACTACAGGTAAGTACCGATCATTTGATGGTCA-TACTATTGTTAACC 1 AACTACAGGTAAGTACCGATCATTCCATGGACAGT-CTACTGTTAACC * ** * * 587604 AACTACAGGTAAGTAAC-ATTCATTCCACAGTCAGTGTACTGTTAACC 1 AACTACAGGTAAGTACCGA-TCATTCCATGGACAGTCTACTGTTAACC 587651 A 1 A 587652 CTTTTATTGT Statistics Matches: 161, Mismatches: 22, Indels: 12 0.83 0.11 0.06 Matches are distributed among these distances: 46 6 0.04 47 153 0.95 48 2 0.01 ACGTcount: A:0.33, C:0.23, G:0.16, T:0.28 Consensus pattern (47 bp): AACTACAGGTAAGTACCGATCATTCCATGGACAGTCTACTGTTAACC Found at i:590078 original size:53 final size:51 Alignment explanation

Indices: 589952--590381 Score: 169 Period size: 51 Copynumber: 8.5 Consensus size: 51 589942 TTAACAGTAT * * 589952 AGTCTGGCTACCTGATGCA--TGTTAACTT-T-TTATCTATTTTTACAGTTAG 1 AGTCTGGCTACCTGATGCATGTGTTAA-TTGTCTGA-CTATTATTACAGTTAG * * * 590001 AGTCCT-GCCACCTGAAGTATGTGTTAATTGTCTGACTATTATTACAGGTATAG 1 AGT-CTGGCTACCTGATGCATGTGTTAATTGTCTGACTATTATTACA-GT-TAG * * * * * 590054 CGTCTGGCTACCTGATGCATGTGTTAA-TGTCAGACTTTTGTTAGAG-T-G 1 AGTCTGGCTACCTGATGCATGTGTTAATTGTCTGACTATTATTACAGTTAG * ** *** * * 590102 A--CTGGTTACCTCCTGCACACAG-TAACTT-TCTGGCTATTGTTACAGTTAG 1 AGTCTGGCTACCTGATGCA-TGTGTTAA-TTGTCTGACTATTATTACAGTTAG * * * * * * * * * * * 590151 AATCTGGCTACATGAAGCATTTGTTGACTGTGTGTCCATTTTTATAGTTAG 1 AGTCTGGCTACCTGATGCATGTGTTAATTGTCTGACTATTATTACAGTTAG * * * * 590202 ATTCTGGCTACCTG-T--ATGGTGTTAA-TGTCAGACTTTTGTTACAGTTAG 1 AGTCTGGCTACCTGATGCAT-GTGTTAATTGTCTGACTATTATTACAGTTAG * * * * * * * * 590250 AGTCTGGCTACTTGAAGCATGTGTTAACTGCCTGGCTATTGTTTCAGTGAG 1 AGTCTGGCTACCTGATGCATGTGTTAATTGTCTGACTATTATTACAGTTAG * * * * 590301 AGTCTGGTTACTTGAAGCATTTAATTTGTTAACTT-TCT-ATCTAATT-TTACAGTTAG 1 AGTCTGGCTACCTGATGC-----ATGTGTTAA-TTGTCTGA-CT-ATTATTACAGTTAG * 590357 AGTCTGGCTACCTGAAGCATGTGTT 1 AGTCTGGCTACCTGATGCATGTGTT 590382 TTCAGTATTT Statistics Matches: 281, Mismatches: 70, Indels: 58 0.69 0.17 0.14 Matches are distributed among these distances: 46 16 0.06 47 14 0.05 48 33 0.12 49 21 0.07 50 13 0.05 51 101 0.36 52 20 0.07 53 23 0.08 56 36 0.13 57 4 0.01 ACGTcount: A:0.23, C:0.17, G:0.21, T:0.39 Consensus pattern (51 bp): AGTCTGGCTACCTGATGCATGTGTTAATTGTCTGACTATTATTACAGTTAG Found at i:591049 original size:8 final size:8 Alignment explanation

Indices: 591036--591094 Score: 64 Period size: 8 Copynumber: 7.4 Consensus size: 8 591026 GGAATCACCT 591036 TGTCCGTC 1 TGTCCGTC 591044 TGTCCGTC 1 TGTCCGTC 591052 TGTCCGTC 1 TGTCCGTC * * 591060 CGTCTGTC 1 TGTCCGTC * * 591068 CGTCAGTC 1 TGTCCGTC 591076 TGTCCGTC 1 TGTCCGTC * * 591084 CGTCTGTC 1 TGTCCGTC 591092 TGT 1 TGT 591095 GCAATCGTGT Statistics Matches: 43, Mismatches: 8, Indels: 0 0.84 0.16 0.00 Matches are distributed among these distances: 8 43 1.00 ACGTcount: A:0.02, C:0.36, G:0.25, T:0.37 Consensus pattern (8 bp): TGTCCGTC Found at i:591062 original size:12 final size:12 Alignment explanation

Indices: 591045--591091 Score: 85 Period size: 12 Copynumber: 3.9 Consensus size: 12 591035 TTGTCCGTCT 591045 GTCCGTCTGTCC 1 GTCCGTCTGTCC 591057 GTCCGTCTGTCC 1 GTCCGTCTGTCC * 591069 GTCAGTCTGTCC 1 GTCCGTCTGTCC 591081 GTCCGTCTGTC 1 GTCCGTCTGTC 591092 TGTGCAATCG Statistics Matches: 33, Mismatches: 2, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 12 33 1.00 ACGTcount: A:0.02, C:0.38, G:0.26, T:0.34 Consensus pattern (12 bp): GTCCGTCTGTCC Found at i:591094 original size:4 final size:4 Alignment explanation

Indices: 591037--591087 Score: 57 Period size: 4 Copynumber: 12.8 Consensus size: 4 591027 GAATCACCTT * * * * * 591037 GTCC GTCT GTCC GTCT GTCC GTCC GTCT GTCC GTCA GTCT GTCC GTCC 1 GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC 591085 GTC 1 GTC 591088 TGTCTGTGCA Statistics Matches: 38, Mismatches: 9, Indels: 0 0.81 0.19 0.00 Matches are distributed among these distances: 4 38 1.00 ACGTcount: A:0.02, C:0.39, G:0.25, T:0.33 Consensus pattern (4 bp): GTCC Found at i:591902 original size:146 final size:146 Alignment explanation

Indices: 591099--591900 Score: 1149 Period size: 146 Copynumber: 5.5 Consensus size: 146 591089 GTCTGTGCAA 591099 TCGTGTCCGGTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGATTGC 1 TCGTGTCCGGTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGATTGC * * 591164 TTATGACCTAAGGGTGTGTC-TGACCTTGACCCAAGGTCATTCGGGCAATGTCAAGGTAACTGGC 66 TTATGACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATTCGGGCAAGGTCAAGGTCACTGGC * 591228 AGAAATAA-TACAAAAT 131 AGAAA-AAGTGCAAAAT * * 591244 TCGTGTCCGGTCCATATCTTTCTTATTGAGAAACATTGGAAGTTCTTAATTCACACAAAGATTGC 1 TCGTGTCCGGTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGATTGC * * * 591309 TTATGACCTAAGGGTGTGTAATGACCTTGACCCAAGGTTATTCGGGCAAGGTCAAGGTCACTGGT 66 TTATGACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATTCGGGCAAGGTCAAGGTCACTGGC * * 591374 AGAAAAAATACAAAAAT 131 AGAAAAAGTGC-AAAAT * * * * 591391 TCTTGTCCGGTCCACATCTTTCGTATGGAGAAACATTGGAAATTCTTACTTCACACAAAGATTGC 1 TCGTGTCCGGTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGATTGC 591456 TTATGACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATTCGGGCAAGGTCAAGGTCACTGGC 66 TTATGACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATTCGGGCAAGGTCAAGGTCACTGGC 591521 AGAAAAAAG-GCAAAAGT 131 AG-AAAAAGTGCAAAA-T * 591538 T-GTGTCCGGCCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTTA-TTCACACAAAGATTG 1 TCGTGTCCGGTCCATATCTTTCTTATGGAGAAACATTGGAAGTTC-TTACTTCACACAAAGATTG * * * ** 591601 CTTATGACTTAATGGTGTGTCATGACCTTGATCCAAGGTCATTCGGGCAAGGTCAAGGTCGTTGG 65 CTTATGACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATTCGGGCAAGGTCAAGGTCACTGG 591666 --GAAAATAGTGCAAAAT 130 CAGAAAA-AGTGCAAAAT * * * * * 591682 TCGTGTCCGGT-CATTATCTTACTTATGGAGAAGCATT-GAATGTTCTAACTTAACACAAATATT 1 TCGTGTCCGGTCCA-TATCTTTCTTATGGAGAAACATTGGAA-GTTCTTACTTCACACAAAGATT * * * * 591745 GCTTAGGACCAAAGGGTGTGTCATGACCTTGACCCAAGGTCATTTGGGCAAGGTTAAGGTCACTG 64 GCTTATGACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATTCGGGCAAGGTCAAGGTCACTG 591810 GCAGAAAAAGTGCAAAAT 129 GCAGAAAAAGTGCAAAAT * * * 591828 TCGTGTCTGGT-CATTATCTTTCTTATGGAGAAGCATT-GAATGTTCTTACTTCACACAAATATT 1 TCGTGTCCGGTCCA-TATCTTTCTTATGGAGAAACATTGGAA-GTTCTTACTTCACACAAAGATT 591891 GCTTATGACC 64 GCTTATGACC 591901 AACAGTTTTA Statistics Matches: 595, Mismatches: 48, Indels: 27 0.89 0.07 0.04 Matches are distributed among these distances: 143 4 0.01 144 12 0.02 145 192 0.32 146 243 0.41 147 139 0.23 148 5 0.01 ACGTcount: A:0.30, C:0.19, G:0.22, T:0.30 Consensus pattern (146 bp): TCGTGTCCGGTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGATTGC TTATGACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATTCGGGCAAGGTCAAGGTCACTGGC AGAAAAAGTGCAAAAT Found at i:594174 original size:15 final size:15 Alignment explanation

Indices: 594132--594174 Score: 50 Period size: 15 Copynumber: 2.7 Consensus size: 15 594122 CTTTGCACAG 594132 TATTTTTTATTCTATTT 1 TATTTTTT-TT-TATTT * * 594149 TAATTTATTTTATTT 1 TATTTTTTTTTATTT 594164 TATTTTTTTTT 1 TATTTTTTTTT 594175 TTAGAAATTT Statistics Matches: 22, Mismatches: 4, Indels: 2 0.79 0.14 0.07 Matches are distributed among these distances: 15 14 0.64 16 2 0.09 17 6 0.27 ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79 Consensus pattern (15 bp): TATTTTTTTTTATTT Found at i:594176 original size:5 final size:5 Alignment explanation

Indices: 594136--594173 Score: 51 Period size: 5 Copynumber: 7.8 Consensus size: 5 594126 GCACAGTATT * * 594136 TTTTA TTCTA TTTTA ATTTA TTTTA TTTTA TTTT- TTTT 1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT 594174 TTTAGAAATT Statistics Matches: 29, Mismatches: 4, Indels: 1 0.85 0.12 0.03 Matches are distributed among these distances: 4 4 0.14 5 25 0.86 ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79 Consensus pattern (5 bp): TTTTA Found at i:597042 original size:13 final size:13 Alignment explanation

Indices: 597024--597085 Score: 67 Period size: 13 Copynumber: 4.8 Consensus size: 13 597014 TAGATTGTAC 597024 TGTGTAAATGAAA 1 TGTGTAAATGAAA * 597037 TGTGTAAATGTAA 1 TGTGTAAATGAAA * 597050 TGTGTAAGTGTAAA 1 TGTGTAAATG-AAA 597064 --TGTAAAT-ATAA 1 TGTGTAAATGA-AA 597075 TGTGTAAATGA 1 TGTGTAAATGA 597086 CTCTGTGATA Statistics Matches: 40, Mismatches: 4, Indels: 9 0.75 0.08 0.17 Matches are distributed among these distances: 10 1 0.03 11 2 0.05 12 6 0.15 13 28 0.70 14 3 0.08 ACGTcount: A:0.42, C:0.00, G:0.23, T:0.35 Consensus pattern (13 bp): TGTGTAAATGAAA Found at i:597079 original size:19 final size:19 Alignment explanation

Indices: 597026--597084 Score: 68 Period size: 19 Copynumber: 3.1 Consensus size: 19 597016 GATTGTACTG 597026 TGTAAATGA-AATGTGTAAA 1 TGTAAAT-ATAATGTGTAAA * * 597045 TGTAATGTGTAA-GTGTAAA 1 TGTAA-ATATAATGTGTAAA 597064 TGTAAATATAATGTGTAAA 1 TGTAAATATAATGTGTAAA 597083 TG 1 TG 597085 ACTCTGTGAT Statistics Matches: 33, Mismatches: 4, Indels: 6 0.77 0.09 0.14 Matches are distributed among these distances: 18 4 0.12 19 26 0.79 20 3 0.09 ACGTcount: A:0.42, C:0.00, G:0.22, T:0.36 Consensus pattern (19 bp): TGTAAATATAATGTGTAAA Found at i:598821 original size:4 final size:4 Alignment explanation

Indices: 598806--598843 Score: 51 Period size: 4 Copynumber: 9.8 Consensus size: 4 598796 ATCACCCGTT * * 598806 GTCC GT-C GTCC GTCC GTCC GTCT GTCT GTCC GTCC GTC 1 GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTC 598844 TGTAAACTTT Statistics Matches: 31, Mismatches: 2, Indels: 2 0.89 0.06 0.06 Matches are distributed among these distances: 3 3 0.10 4 28 0.90 ACGTcount: A:0.00, C:0.42, G:0.26, T:0.32 Consensus pattern (4 bp): GTCC Found at i:598838 original size:16 final size:16 Alignment explanation

Indices: 598806--598846 Score: 66 Period size: 16 Copynumber: 2.6 Consensus size: 16 598796 ATCACCCGTT 598806 GTCCGTC-GTCCGTCC 1 GTCCGTCTGTCCGTCC * 598821 GTCCGTCTGTCTGTCC 1 GTCCGTCTGTCCGTCC 598837 GTCCGTCTGT 1 GTCCGTCTGT 598847 AAACTTTTCA Statistics Matches: 24, Mismatches: 1, Indels: 1 0.92 0.04 0.04 Matches are distributed among these distances: 15 7 0.29 16 17 0.71 ACGTcount: A:0.00, C:0.39, G:0.27, T:0.34 Consensus pattern (16 bp): GTCCGTCTGTCCGTCC Found at i:599622 original size:333 final size:331 Alignment explanation

Indices: 599013--600183 Score: 1888 Period size: 333 Copynumber: 3.6 Consensus size: 331 599003 GGTGCATGTC 599013 TTTAAAAATCTTCTTCTCAAGAACCACTGCACCAGAAATGCCAATATTTACACAAAAGCTTGTTA 1 TTTAAAAATCTTCTTCTCAAGAACCACTGCACCAGAAATGCCAATATTTACACAAAAGCTTGTTA 599078 ACATAGTGAAGATTCTAAATTGTAAAAATCGTGACCCTCGGACCAAAACTGGGGCCCCAGGCGGG 66 ACATAGTGAAGATTCTAAATTGTAAAAATCGTGACCCTCGGACCAAAACTGGGGCCCCAGGCGGG 599143 GTTCAAAGTTTAACATAGAAATACATAGGAAAATGTTTTAAAAATCTTCTTCTCAAGAACCACTG 131 GTTCAAAGTTTAACATAGAAATACATAGGAAAATG-TTTAAAAATCTTCTTCTCAAGAACCACTG * * * * 599208 CACCAGAAATGCCAATATTTACACAAAAACTTGTATATATAGTGAAGATTCTAAATTGTAAAAAT 195 CACCAGAAATGCCAATATTTACACAAAAGCTTGTATGTATAATGAAGATTCTAAATTGTAGAAAT *** * 599273 CGTGACCCTCGGACCAAAACTGGGGCCCCAGGCGGGGTTCAAAGTTTAACATGGAACTACATATG 260 CGTGACCCTCGGACCAAAACTACAGCCCCAGGCGGGGTTCAAAGTTTAACATAGAACTACATATG 599338 GAAAATG 325 GAAAATG * 599345 TTTAAAAAATCTTCTTCTCAAGAACTACTGCACCAGAAATGCCAATATTTACACAAAAGCTTG-T 1 TTT-AAAAATCTTCTTCTCAAGAACCACTGCACCAGAAATGCCAATATTTACACAAAAGCTTGTT * 599409 ATATATAGTGAAGATTCTAAATTGTAAAAATCGTGACCCTCGGACCAAAACTGGGGCCCCAGGCG 65 A-ACATAGTGAAGATTCTAAATTGTAAAAATCGTGACCCTCGGACCAAAACTGGGGCCCCAGGCG * 599474 GGGTTCAAAGTTTAACATAGAAATACATAGGAAAATGTTTAAAAAATCTTCTTCTCAAGAACTAC 129 GGGTTCAAAGTTTAACATAGAAATACATAGGAAAATGTTT-AAAAATCTTCTTCTCAAGAACCAC 599539 TGCACCAGAAATGCCAATATTTACACAAAAGCTTGTATGTATAATGAAGATTCTAAATTGTAGAA 193 TGCACCAGAAATGCCAATATTTACACAAAAGCTTGTATGTATAATGAAGATTCTAAATTGTAGAA * 599604 ATCGTGACCCTCGGACCAAAACTACAGCCCCAGGCGGGGTTCAAAGTTTAACATAGAAATACATA 258 ATCGTGACCCTCGGACCAAAACTACAGCCCCAGGCGGGGTTCAAAGTTTAACATAGAACTACATA 599669 -GGAAAATG 323 TGGAAAATG * 599677 TTTAAAAATCTTCTTCTCAAGAACCACTGCATCAGAAATGCCAATATTTACACAAAAGCTTGTTA 1 TTTAAAAATCTTCTTCTCAAGAACCACTGCACCAGAAATGCCAATATTTACACAAAAGCTTGTTA 599742 ACATAGTGAAGATTCTAAATTGTAAAAATCGTGACCCTCGGACCAAAACTGGGGCCCCAGGCGGG 66 ACATAGTGAAGATTCTAAATTGTAAAAATCGTGACCCTCGGACCAAAACTGGGGCCCCAGGCGGG 599807 GTTCAAAGTTTAACATAGAAATACATAGGAAAATGTTTAAAAATCTTCTTCTCAAGAACCACTGC 131 GTTCAAAGTTTAACATAGAAATACATAGGAAAATGTTTAAAAATCTTCTTCTCAAGAACCACTGC * 599872 ATCAGAAATGCCAATATTTACACAAAAGCTTGTATGTATAATGAAGATTCTAAATTGTAGAAATC 196 ACCAGAAATGCCAATATTTACACAAAAGCTTGTATGTATAATGAAGATTCTAAATTGTAGAAATC * * 599937 GTGACCCTCAGACCAAAACTACAGCCCCAGGCGGGGTTCAAAGTTTAACATAGAACTACATATGA 261 GTGACCCTCGGACCAAAACTACAGCCCCAGGCGGGGTTCAAAGTTTAACATAGAACTACATATGG 600002 AAAATG 326 AAAATG * * * ** * 600008 TTTAAAAATTTTCTTCTCAAGAACCACTTCACCAAAAATGCCAATACATACACAAAAGGTTG-TA 1 TTTAAAAATCTTCTTCTCAAGAACCACTGCACCAGAAATGCCAATATTTACACAAAAGCTTGTTA * * * * * ** 600072 TATATAGTGAAG-------ATTGTAAAAATCGTGACCCCCGAACAAAAAGTGGGGCCCCAGTAGG 66 -ACATAGTGAAGATTCTAAATTGTAAAAATCGTGACCCTCGGACCAAAACTGGGGCCCCAGGCGG * * * * 600130 GGTTTAGATTTTAACAT----AT--ATAGGAAAATGTTTTAAAATCTTCTTCTCAAGAAC 130 GGTTCAAAGTTTAACATAGAAATACATAGGAAAATGTTTAAAAATCTTCTTCTCAAGAAC 600184 TATAGTGCAA Statistics Matches: 795, Mismatches: 38, Indels: 26 0.93 0.04 0.03 Matches are distributed among these distances: 318 34 0.04 320 2 0.00 324 54 0.07 330 152 0.19 331 231 0.29 332 21 0.03 333 301 0.38 ACGTcount: A:0.38, C:0.19, G:0.17, T:0.26 Consensus pattern (331 bp): TTTAAAAATCTTCTTCTCAAGAACCACTGCACCAGAAATGCCAATATTTACACAAAAGCTTGTTA ACATAGTGAAGATTCTAAATTGTAAAAATCGTGACCCTCGGACCAAAACTGGGGCCCCAGGCGGG GTTCAAAGTTTAACATAGAAATACATAGGAAAATGTTTAAAAATCTTCTTCTCAAGAACCACTGC ACCAGAAATGCCAATATTTACACAAAAGCTTGTATGTATAATGAAGATTCTAAATTGTAGAAATC GTGACCCTCGGACCAAAACTACAGCCCCAGGCGGGGTTCAAAGTTTAACATAGAACTACATATGG AAAATG Found at i:599776 original size:165 final size:165 Alignment explanation

Indices: 599013--600183 Score: 1814 Period size: 166 Copynumber: 7.1 Consensus size: 165 599003 GGTGCATGTC 599013 TTTAAAAATCTTCTTCTCAAGAACCACTGCACCAGAAATGCCAATATTTACACAAAAGCTTGT-T 1 TTTAAAAATCTTCTTCTCAAGAACCACTGCACCAGAAATGCCAATATTTACACAAAAGCTTGTAT * 599077 AACATAGTGAAGATTCTAAATTGTAAAAATCGTGACCCTCGGACCAAAACTGGGGCCCCAGGCGG 66 -ATATAGTGAAGATTCTAAATTGTAAAAATCGTGACCCTCGGACCAAAACTGGGGCCCCAGGCGG 599142 GGTTCAAAGTTTAACATAGAAATACATAGGAAAATG 130 GGTTCAAAGTTTAACATAGAAATACATAGGAAAATG * 599178 TTTTAAAAATCTTCTTCTCAAGAACCACTGCACCAGAAATGCCAATATTTACACAAAAACTTGTA 1 -TTTAAAAATCTTCTTCTCAAGAACCACTGCACCAGAAATGCCAATATTTACACAAAAGCTTGTA 599243 TATATAGTGAAGATTCTAAATTGTAAAAATCGTGACCCTCGGACCAAAACTGGGGCCCCAGGCGG 65 TATATAGTGAAGATTCTAAATTGTAAAAATCGTGACCCTCGGACCAAAACTGGGGCCCCAGGCGG * * 599308 GGTTCAAAGTTTAACATGGAACTACATATGGAAAATG 130 GGTTCAAAGTTTAACATAGAAATACATA-GGAAAATG * 599345 TTTAAAAAATCTTCTTCTCAAGAACTACTGCACCAGAAATGCCAATATTTACACAAAAGCTTGTA 1 TTT-AAAAATCTTCTTCTCAAGAACCACTGCACCAGAAATGCCAATATTTACACAAAAGCTTGTA 599410 TATATAGTGAAGATTCTAAATTGTAAAAATCGTGACCCTCGGACCAAAACTGGGGCCCCAGGCGG 65 TATATAGTGAAGATTCTAAATTGTAAAAATCGTGACCCTCGGACCAAAACTGGGGCCCCAGGCGG 599475 GGTTCAAAGTTTAACATAGAAATACATAGGAAAATG 130 GGTTCAAAGTTTAACATAGAAATACATAGGAAAATG * 599511 TTTAAAAAATCTTCTTCTCAAGAACTACTGCACCAGAAATGCCAATATTTACACAAAAGCTTGTA 1 TTT-AAAAATCTTCTTCTCAAGAACCACTGCACCAGAAATGCCAATATTTACACAAAAGCTTGTA * * * *** 599576 TGTATAATGAAGATTCTAAATTGTAGAAATCGTGACCCTCGGACCAAAACTACAGCCCCAGGCGG 65 TATATAGTGAAGATTCTAAATTGTAAAAATCGTGACCCTCGGACCAAAACTGGGGCCCCAGGCGG 599641 GGTTCAAAGTTTAACATAGAAATACATAGGAAAATG 130 GGTTCAAAGTTTAACATAGAAATACATAGGAAAATG * 599677 TTTAAAAATCTTCTTCTCAAGAACCACTGCATCAGAAATGCCAATATTTACACAAAAGCTTGT-T 1 TTTAAAAATCTTCTTCTCAAGAACCACTGCACCAGAAATGCCAATATTTACACAAAAGCTTGTAT * 599741 AACATAGTGAAGATTCTAAATTGTAAAAATCGTGACCCTCGGACCAAAACTGGGGCCCCAGGCGG 66 -ATATAGTGAAGATTCTAAATTGTAAAAATCGTGACCCTCGGACCAAAACTGGGGCCCCAGGCGG 599806 GGTTCAAAGTTTAACATAGAAATACATAGGAAAATG 130 GGTTCAAAGTTTAACATAGAAATACATAGGAAAATG * 599842 TTTAAAAATCTTCTTCTCAAGAACCACTGCATCAGAAATGCCAATATTTACACAAAAGCTTGTAT 1 TTTAAAAATCTTCTTCTCAAGAACCACTGCACCAGAAATGCCAATATTTACACAAAAGCTTGTAT * * * * *** 599907 GTATAATGAAGATTCTAAATTGTAGAAATCGTGACCCTCAGACCAAAACTACAGCCCCAGGCGGG 66 ATATAGTGAAGATTCTAAATTGTAAAAATCGTGACCCTCGGACCAAAACTGGGGCCCCAGGCGGG * * 599972 GTTCAAAGTTTAACATAGAACTACATATGAAAAATG 131 GTTCAAAGTTTAACATAGAAATACATA-GGAAAATG * * * ** * 600008 TTTAAAAATTTTCTTCTCAAGAACCACTTCACCAAAAATGCCAATACATACACAAAAGGTTGTAT 1 TTTAAAAATCTTCTTCTCAAGAACCACTGCACCAGAAATGCCAATATTTACACAAAAGCTTGTAT * * * * ** 600073 ATATAGTGAAG-------ATTGTAAAAATCGTGACCCCCGAACAAAAAGTGGGGCCCCAGTAGGG 66 ATATAGTGAAGATTCTAAATTGTAAAAATCGTGACCCTCGGACCAAAACTGGGGCCCCAGGCGGG * * * 600131 GTTTAGATTTTAACAT----AT--ATAGGAAAATG 131 GTTCAAAGTTTAACATAGAAATACATAGGAAAATG * 600160 TTTTAAAATCTTCTTCTCAAGAAC 1 TTTAAAAATCTTCTTCTCAAGAAC 600184 TATAGTGCAA Statistics Matches: 939, Mismatches: 60, Indels: 26 0.92 0.06 0.03 Matches are distributed among these distances: 152 29 0.03 153 3 0.00 155 1 0.00 159 49 0.05 164 1 0.00 165 297 0.32 166 400 0.43 167 159 0.17 ACGTcount: A:0.38, C:0.19, G:0.17, T:0.26 Consensus pattern (165 bp): TTTAAAAATCTTCTTCTCAAGAACCACTGCACCAGAAATGCCAATATTTACACAAAAGCTTGTAT ATATAGTGAAGATTCTAAATTGTAAAAATCGTGACCCTCGGACCAAAACTGGGGCCCCAGGCGGG GTTCAAAGTTTAACATAGAAATACATAGGAAAATG Found at i:607358 original size:4 final size:4 Alignment explanation

Indices: 607351--607392 Score: 61 Period size: 4 Copynumber: 11.0 Consensus size: 4 607341 AGAGAGAGAG * 607351 AGAC AGAC AGAC AGAC AG-- AGAC AGAC GGAC AGAC AGAC AGAC 1 AGAC AGAC AGAC AGAC AGAC AGAC AGAC AGAC AGAC AGAC AGAC 607393 TGACTGACCT Statistics Matches: 34, Mismatches: 2, Indels: 4 0.85 0.05 0.10 Matches are distributed among these distances: 2 2 0.06 4 32 0.94 ACGTcount: A:0.48, C:0.24, G:0.29, T:0.00 Consensus pattern (4 bp): AGAC Found at i:607372 original size:18 final size:18 Alignment explanation

Indices: 607349--607387 Score: 69 Period size: 18 Copynumber: 2.2 Consensus size: 18 607339 CTAGAGAGAG 607349 AGAGACAGACAGACAGAC 1 AGAGACAGACAGACAGAC * 607367 AGAGACAGACGGACAGAC 1 AGAGACAGACAGACAGAC 607385 AGA 1 AGA 607388 CAGACTGACT Statistics Matches: 20, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 18 20 1.00 ACGTcount: A:0.49, C:0.21, G:0.31, T:0.00 Consensus pattern (18 bp): AGAGACAGACAGACAGAC Found at i:607376 original size:22 final size:22 Alignment explanation

Indices: 607345--607391 Score: 76 Period size: 22 Copynumber: 2.1 Consensus size: 22 607335 TAGTCTAGAG * 607345 AGAGAGAGACAGACAGACAGAC 1 AGAGACAGACAGACAGACAGAC * 607367 AGAGACAGACGGACAGACAGAC 1 AGAGACAGACAGACAGACAGAC 607389 AGA 1 AGA 607392 CTGACTGACC Statistics Matches: 23, Mismatches: 2, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 22 23 1.00 ACGTcount: A:0.49, C:0.19, G:0.32, T:0.00 Consensus pattern (22 bp): AGAGACAGACAGACAGACAGAC Found at i:625293 original size:8 final size:8 Alignment explanation

Indices: 625272--625329 Score: 82 Period size: 8 Copynumber: 7.4 Consensus size: 8 625262 GATCACATTT 625272 TGTCCGTC 1 TGTCCGTC 625280 -GTCCGTC 1 TGTCCGTC 625287 TGTCCGTC 1 TGTCCGTC * 625295 CGTCCGTC 1 TGTCCGTC * 625303 TGTCTGTC 1 TGTCCGTC * 625311 TGTCTGTC 1 TGTCCGTC 625319 TGTCCGTC 1 TGTCCGTC 625327 TGT 1 TGT 625330 AAACTTTTTA Statistics Matches: 45, Mismatches: 4, Indels: 2 0.88 0.08 0.04 Matches are distributed among these distances: 7 7 0.16 8 38 0.84 ACGTcount: A:0.00, C:0.34, G:0.26, T:0.40 Consensus pattern (8 bp): TGTCCGTC Found at i:625296 original size:12 final size:12 Alignment explanation

Indices: 625273--625329 Score: 62 Period size: 12 Copynumber: 4.8 Consensus size: 12 625263 ATCACATTTT 625273 GTCCGTC-GTCC 1 GTCCGTCTGTCC * * 625284 GTCTGTCCGTCC 1 GTCCGTCTGTCC * 625296 GTCCGTCTGTCT 1 GTCCGTCTGTCC * * 625308 GTCTGTCTGTCT 1 GTCCGTCTGTCC 625320 GTCCGTCTGT 1 GTCCGTCTGT 625330 AAACTTTTTA Statistics Matches: 39, Mismatches: 6, Indels: 1 0.85 0.13 0.02 Matches are distributed among these distances: 11 6 0.15 12 33 0.85 ACGTcount: A:0.00, C:0.35, G:0.26, T:0.39 Consensus pattern (12 bp): GTCCGTCTGTCC Found at i:634047 original size:41 final size:41 Alignment explanation

Indices: 633976--634343 Score: 529 Period size: 41 Copynumber: 9.0 Consensus size: 41 633966 TACACCAAAG * * ** * * * 633976 TCATATCCACTGGTTACACCGCGCTGTGTACCAGTACTTGC 1 TCATTTCCACTGGCTACACCATGCTATGTACCAGGACTTAC * * 634017 TCATTTCCACTAGCTACACCATGCTATGTACCAGCACTTAC 1 TCATTTCCACTGGCTACACCATGCTATGTACCAGGACTTAC * 634058 TCATATCCACTGGCTACACCATGCTATGTACCAGGACTTAC 1 TCATTTCCACTGGCTACACCATGCTATGTACCAGGACTTAC * * 634099 TCATATCCACTGGCTACACCATGCTATGTACCAGAACTTAC 1 TCATTTCCACTGGCTACACCATGCTATGTACCAGGACTTAC * * * * 634140 TCAATTCCACTGGCTACACCATGCTATATGCCAGGACTTGC 1 TCATTTCCACTGGCTACACCATGCTATGTACCAGGACTTAC * * 634181 TCATTTCAACTGGCTACACCATGCTATGTACCAGGACTTGC 1 TCATTTCCACTGGCTACACCATGCTATGTACCAGGACTTAC * 634222 TCATTTCAACTGGCTACACCATGCTATGTACCAGGACTTAC 1 TCATTTCCACTGGCTACACCATGCTATGTACCAGGACTTAC ** * 634263 TCAACTCCACTGGCTACACCATGCTATGTACCAGGACTTGC 1 TCATTTCCACTGGCTACACCATGCTATGTACCAGGACTTAC * 634304 TCATTTCAACTGGCTACACCATGCTATGTACCAGGACTTA 1 TCATTTCCACTGGCTACACCATGCTATGTACCAGGACTTA 634344 ACTCCAAAAA Statistics Matches: 296, Mismatches: 31, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 41 296 1.00 ACGTcount: A:0.26, C:0.31, G:0.15, T:0.28 Consensus pattern (41 bp): TCATTTCCACTGGCTACACCATGCTATGTACCAGGACTTAC Found at i:636162 original size:19 final size:19 Alignment explanation

Indices: 636115--636168 Score: 81 Period size: 19 Copynumber: 2.8 Consensus size: 19 636105 AGACCACTCT 636115 CCCAAATGGGATATAATAG 1 CCCAAATGGGATATAATAG *** 636134 CCCGTTTGGGATATAATAG 1 CCCAAATGGGATATAATAG 636153 CCCAAATGGGATATAA 1 CCCAAATGGGATATAA 636169 ATTTTAAGTG Statistics Matches: 29, Mismatches: 6, Indels: 0 0.83 0.17 0.00 Matches are distributed among these distances: 19 29 1.00 ACGTcount: A:0.37, C:0.17, G:0.22, T:0.24 Consensus pattern (19 bp): CCCAAATGGGATATAATAG Found at i:645872 original size:167 final size:167 Alignment explanation

Indices: 645596--645931 Score: 672 Period size: 167 Copynumber: 2.0 Consensus size: 167 645586 TATCATTGGC 645596 ATGATATGTACACAAAAGTAATGTAATTAGAACCATTTTAACTATAGCTTGGACTTTGGGTAGTT 1 ATGATATGTACACAAAAGTAATGTAATTAGAACCATTTTAACTATAGCTTGGACTTTGGGTAGTT 645661 GTGTCAAACAGCAATGTGACGTAGGCCTGTCTATTTCATTGCTGGCCACTCAGCCAAGGCTCTGT 66 GTGTCAAACAGCAATGTGACGTAGGCCTGTCTATTTCATTGCTGGCCACTCAGCCAAGGCTCTGT 645726 GACATTAACAAGATGTGTCTGGCTTTTGAGCTAAGAT 131 GACATTAACAAGATGTGTCTGGCTTTTGAGCTAAGAT 645763 ATGATATGTACACAAAAGTAATGTAATTAGAACCATTTTAACTATAGCTTGGACTTTGGGTAGTT 1 ATGATATGTACACAAAAGTAATGTAATTAGAACCATTTTAACTATAGCTTGGACTTTGGGTAGTT 645828 GTGTCAAACAGCAATGTGACGTAGGCCTGTCTATTTCATTGCTGGCCACTCAGCCAAGGCTCTGT 66 GTGTCAAACAGCAATGTGACGTAGGCCTGTCTATTTCATTGCTGGCCACTCAGCCAAGGCTCTGT 645893 GACATTAACAAGATGTGTCTGGCTTTTGAGCTAAGAT 131 GACATTAACAAGATGTGTCTGGCTTTTGAGCTAAGAT 645930 AT 1 AT 645932 TTGAGGCAAT Statistics Matches: 169, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 167 169 1.00 ACGTcount: A:0.29, C:0.17, G:0.22, T:0.32 Consensus pattern (167 bp): ATGATATGTACACAAAAGTAATGTAATTAGAACCATTTTAACTATAGCTTGGACTTTGGGTAGTT GTGTCAAACAGCAATGTGACGTAGGCCTGTCTATTTCATTGCTGGCCACTCAGCCAAGGCTCTGT GACATTAACAAGATGTGTCTGGCTTTTGAGCTAAGAT Found at i:651614 original size:165 final size:166 Alignment explanation

Indices: 651342--651968 Score: 852 Period size: 166 Copynumber: 3.8 Consensus size: 166 651332 GTGAATATGC * * * * * 651342 AAAATAAGCAAAGTCGA-CATTTAACAGAAAGCTGGCATCCGATTGGTACAGAAATATATCCCAC 1 AAAATAAACAAAGTC-ATCATTTAACAGGAAGTTGACATCCGATTGGTACAAAAATATATCCCAC * * * * * 651406 AATATGGCATGCCTAAACAAATAGTGTGTTAAAATTTCAAGCATCTGCGATAAACAGTTGCTGAG 65 CATATGGCATGCCTTAACAAACACTGTGTTAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAG ** 651471 AAATCTGAGAGGAAAATTTGTTTGAAAATTTTGGCT- 130 AAATCTTTGAGGAAAATTTGTTTGAAAATTTTGGCTA * ** 651507 AAAATAAACAAAGT-ACTCATTTAACAGGAAGTTGACATCCGATTGGTACAAAAATAAATATCAC 1 AAAATAAACAAAGTCA-TCATTTAACAGGAAGTTGACATCCGATTGGTACAAAAATATATCCCAC * * * * 651571 GATATGGCATGCCTTAACAAACACTGTGTAAAAATTTCAAGCATCTGCGATAAAAAGCTGCTGAG 65 CATATGGCATGCCTTAACAAACACTGTGTTAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAG * 651636 AAATCTTTGA-CATAAATTTGTTTGAAAATTTTGGCTA 130 AAATCTTTGAGGA-AAATTTGTTTGAAAATTTTGGCTA * * * * * 651673 AAAAAAAACAAAGTCATTATTTCACAGGAAGTTGACGTCCGATTGATACAAAAATATATCCCACC 1 AAAATAAACAAAGTCATCATTTAACAGGAAGTTGACATCCGATTGGTACAAAAATATATCCCACC * * 651738 ATATGGCATGCC-TATACAAATAGTGTGTTAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAG 66 ATATGGCATGCCTTA-ACAAACACTGTGTTAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAG * 651802 AAATCTTTGACGG-AAATTTGTTTGAAAATTTTTGCTA 130 AAATCTTTGA-GGAAAATTTGTTTGAAAATTTTGGCTA * * * * 651839 AAAATAAGCAAAGTCGTCATTTAACAGGAAGTTGGCGTCCGATTGGTACAAAAATATATCCCACC 1 AAAATAAACAAAGTCATCATTTAACAGGAAGTTGACATCCGATTGGTACAAAAATATATCCCACC * * * 651904 ATATGGCATACCTTAACAAACACCGTGTTAAAATTTCAAGCATCTGCGACAAATAGTTGCTGAGA 66 ATATGGCATGCCTTAACAAACACTGTGTTAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGA 651969 TAAATGCGAC Statistics Matches: 407, Mismatches: 46, Indels: 17 0.87 0.10 0.04 Matches are distributed among these distances: 163 1 0.00 164 1 0.00 165 144 0.35 166 258 0.63 167 3 0.01 ACGTcount: A:0.39, C:0.16, G:0.17, T:0.28 Consensus pattern (166 bp): AAAATAAACAAAGTCATCATTTAACAGGAAGTTGACATCCGATTGGTACAAAAATATATCCCACC ATATGGCATGCCTTAACAAACACTGTGTTAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGA AATCTTTGAGGAAAATTTGTTTGAAAATTTTGGCTA Found at i:652012 original size:12 final size:12 Alignment explanation

Indices: 651995--652030 Score: 54 Period size: 12 Copynumber: 3.0 Consensus size: 12 651985 TTTTGTTACG 651995 GACGGACAGACA 1 GACGGACAGACA * 652007 GACGGACTGACA 1 GACGGACAGACA * 652019 GACAGACAGACA 1 GACGGACAGACA 652031 CACAAGGGTA Statistics Matches: 21, Mismatches: 3, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 12 21 1.00 ACGTcount: A:0.42, C:0.25, G:0.31, T:0.03 Consensus pattern (12 bp): GACGGACAGACA Found at i:652013 original size:16 final size:16 Alignment explanation

Indices: 651992--652025 Score: 59 Period size: 16 Copynumber: 2.1 Consensus size: 16 651982 AATTTTTGTT 651992 ACGGACGGACAGACAG 1 ACGGACGGACAGACAG * 652008 ACGGACTGACAGACAG 1 ACGGACGGACAGACAG 652024 AC 1 AC 652026 AGACACACAA Statistics Matches: 17, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 16 17 1.00 ACGTcount: A:0.38, C:0.26, G:0.32, T:0.03 Consensus pattern (16 bp): ACGGACGGACAGACAG Found at i:657814 original size:160 final size:158 Alignment explanation

Indices: 657504--657989 Score: 589 Period size: 160 Copynumber: 3.0 Consensus size: 158 657494 AATGAATGTG ** * * * 657504 AACTGCAAATATTTGGAACTTTTCTATGTCCAAGAGCCATAACTCTGTCGAAAATTGCTCTATCA 1 AACTGCAAATAACTGGAATTTTTCTACGTCCAAGAGCCATAACTCTGTCGAAAATTGCTCGAT-A * * * * * 657569 TACCCAAAATCAAACCTGAGCTAGATATTATCATGATAAACCTGTATACAAAATTTCTTATCAGT 65 TACCCAATATC-AACTTGACCTAGATATTATCATGATAAACCTGTATACCAAATTTCTT-TCAAT * * 657634 ATGTGCACCCTCTG-AAAGAAAATGAGCGGA 128 ATGTTCATCCTCTGCAAAGAAAATGAGCGGA * * * * 657664 AACTGCAAATAACTGGAATTTTTCTACGTCTAAGAGCCATAACTCTG-CTGAAAATTACTCGCTG 1 AACTGCAAATAACTGGAATTTTTCTACGTCCAAGAGCCATAACTCTGTC-GAAAATTGCTCGATA * * * 657728 TACCCAATATCATACTTGACCTAGATGTAATCATGATAAACATGTATACCAAATTTCGTTTCAAT 65 TACCCAATATCA-ACTTGACCTAGATATTATCATGATAAACCTGTATACCAAATTTC-TTTCAAT 657793 ATGTTCATCCTCTGCAAAGAAAATGAGCGGA 128 ATGTTCATCCTCTGCAAAGAAAATGAGCGGA * * * * * * * * 657824 AACTGCAAATAACTGAAATTTTTCAACGTCCAAGGGCTATCACTCTGTCGAAAACTGCTTGATCT 1 AACTGCAAATAACTGGAATTTTTCTACGTCCAAGAGCCATAACTCTGTCGAAAATTGCTCGATAT * * 657889 ACCCAATATTGAACTTGACCTAGATATTATCATGATAAACCTGTATACCAAATGTCATTTTCAAT 66 ACCCAATA-TCAACTTGACCTAGATATTATCATGATAAACCTGTATACCAAATTTC--TTTCAAT * ** 657954 ATGTTCATCCTCTGCGAAGAAAATGAAAGGA 128 ATGTTCATCCTCTGCAAAGAAAATGAGCGGA 657985 AACTG 1 AACTG 657990 TAGATGGACC Statistics Matches: 280, Mismatches: 39, Indels: 13 0.84 0.12 0.04 Matches are distributed among these distances: 158 1 0.00 159 65 0.23 160 171 0.61 161 43 0.15 ACGTcount: A:0.36, C:0.21, G:0.14, T:0.29 Consensus pattern (158 bp): AACTGCAAATAACTGGAATTTTTCTACGTCCAAGAGCCATAACTCTGTCGAAAATTGCTCGATAT ACCCAATATCAACTTGACCTAGATATTATCATGATAAACCTGTATACCAAATTTCTTTCAATATG TTCATCCTCTGCAAAGAAAATGAGCGGA Found at i:659857 original size:13 final size:13 Alignment explanation

Indices: 659839--659880 Score: 63 Period size: 13 Copynumber: 3.5 Consensus size: 13 659829 AAAGCATTGT 659839 AAATATTTGTTGA 1 AAATATTTGTTGA 659852 AAATATTTG-T-- 1 AAATATTTGTTGA 659862 AAATATTTGTTGA 1 AAATATTTGTTGA 659875 AAATAT 1 AAATAT 659881 GTAAATATAC Statistics Matches: 26, Mismatches: 0, Indels: 6 0.81 0.00 0.19 Matches are distributed among these distances: 10 9 0.35 11 1 0.04 12 1 0.04 13 15 0.58 ACGTcount: A:0.43, C:0.00, G:0.12, T:0.45 Consensus pattern (13 bp): AAATATTTGTTGA Found at i:659861 original size:23 final size:22 Alignment explanation

Indices: 659834--659888 Score: 94 Period size: 23 Copynumber: 2.5 Consensus size: 22 659824 GTTTTAAAGC 659834 ATTGTAAATATTTGTTGAAAAT 1 ATTGTAAATATTTGTTGAAAAT 659856 ATTTGTAAATATTTGTTGAAAAT 1 A-TTGTAAATATTTGTTGAAAAT 659879 A-TGTAAATAT 1 ATTGTAAATAT 659889 ACTTCCAATG Statistics Matches: 32, Mismatches: 0, Indels: 3 0.91 0.00 0.09 Matches are distributed among these distances: 21 9 0.28 22 1 0.03 23 22 0.69 ACGTcount: A:0.42, C:0.00, G:0.13, T:0.45 Consensus pattern (22 bp): ATTGTAAATATTTGTTGAAAAT Found at i:666015 original size:45 final size:45 Alignment explanation

Indices: 665949--666034 Score: 145 Period size: 45 Copynumber: 1.9 Consensus size: 45 665939 GGAGGGTAAC * 665949 AGTTGAAATTGACACCCCGAGAAAACCACTGTCAACTGACGTGAA 1 AGTTGAAATTGACACCCCGAGAAAACCACTGTCAACCGACGTGAA * * 665994 AGTTGAAATTGACACCTCGAGAAAACCATTGTCAACCGACG 1 AGTTGAAATTGACACCCCGAGAAAACCACTGTCAACCGACG 666035 CGAAGTGGAG Statistics Matches: 38, Mismatches: 3, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 45 38 1.00 ACGTcount: A:0.37, C:0.24, G:0.20, T:0.19 Consensus pattern (45 bp): AGTTGAAATTGACACCCCGAGAAAACCACTGTCAACCGACGTGAA Found at i:667109 original size:44 final size:44 Alignment explanation

Indices: 667011--668010 Score: 1334 Period size: 44 Copynumber: 23.3 Consensus size: 44 667001 AACAATAATT * 667011 CACTGACAAAGCTGTGTACTTTACTTTACTGACACACAGACTCACA 1 CACTGACAAAGCTGTGTACTTTACTTTACTG--ACACAGACTTACA 667057 CACTGACAAAGCTGTGTACTTTACTTTACTGACACAGACTTACA 1 CACTGACAAAGCTGTGTACTTTACTTTACTGACACAGACTTACA * ** * 667101 CACAGACAATTCTGTGTACTTTACTTTACTGACACACAGACTAACA 1 CACTGACAAAGCTGTGTACTTTACTTTACTG--ACACAGACTTACA * * * 667147 CACTAACAAAGCTGGGTAGTTTACTTTACTGACACAGACTTACA 1 CACTGACAAAGCTGTGTACTTTACTTTACTGACACAGACTTACA 667191 CACTGACAAAGCTGTGTACTTTACTTTACTGACACACAGACTTACA 1 CACTGACAAAGCTGTGTACTTTACTTTACTG--ACACAGACTTACA * * ** 667237 CACTGACAAAGCTATGTACTTTACTTTATTGACATACAGACAAACA 1 CACTGACAAAGCTGTGTACTTTACTTTACTGAC--ACAGACTTACA * * * 667283 CACTGACAAAGCTGTATACTTTACTTTACTAACACACAGACTAACA 1 CACTGACAAAGCTGTGTACTTTACTTTACT--GACACAGACTTACA * * * * 667329 CACTGAGAAAGCTGTGTACTTCACTTTACTGACACACAGTCTAACA 1 CACTGACAAAGCTGTGTACTTTACTTTACTG--ACACAGACTTACA * * 667375 CAATGACAAAGCTGTGTACTTTACTTCACTGACACAGACTT--A 1 CACTGACAAAGCTGTGTACTTTACTTTACTGACACAGACTTACA * * 667417 TACTGACAAAGCTGTGTACTTTACTTCACTGACACAGACTTACA 1 CACTGACAAAGCTGTGTACTTTACTTTACTGACACAGACTTACA * * 667461 CACTGACAAAGCTGTGTACTTTACTTCACTGACACAGACTAACA 1 CACTGACAAAGCTGTGTACTTTACTTTACTGACACAGACTTACA * 667505 CACTGACAAAGCTGTGTACTTTAC-TAAC--ACACAGACTTACA 1 CACTGACAAAGCTGTGTACTTTACTTTACTGACACAGACTTACA * * * 667546 CACTGACAAAGTTTTGTACTTTACTTCACTGACACAGACTT--A 1 CACTGACAAAGCTGTGTACTTTACTTTACTGACACAGACTTACA 667588 CACTGACAAAGCTGTG-----TACTTTACTG--ACAGACTTACA 1 CACTGACAAAGCTGTGTACTTTACTTTACTGACACAGACTTACA 667625 CACTGACAAAGCTGTGTACTTTACTTTACTGACACAGACTTACA 1 CACTGACAAAGCTGTGTACTTTACTTTACTGACACAGACTTACA 667669 CACTGACAAAGCTGTGTACTTTACTTTACTGACACAGACTTACA 1 CACTGACAAAGCTGTGTACTTTACTTTACTGACACAGACTTACA 667713 CACTGACAAAGCTGTG-----TACTTTACTGACACAGACTTACA 1 CACTGACAAAGCTGTGTACTTTACTTTACTGACACAGACTTACA * * * 667752 CACTGACAAAGCTGTGTACTTTAC-TGAC--ACACATACTAACA 1 CACTGACAAAGCTGTGTACTTTACTTTACTGACACAGACTTACA * 667793 CACTGACAAAACTGTGTACTTTACTTTACTGACACAGACTT--- 1 CACTGACAAAGCTGTGTACTTTACTTTACTGACACAGACTTACA 667834 -ACTGACAAAGCTGTG-----TACTTTACTGACACAGACTTACA 1 CACTGACAAAGCTGTGTACTTTACTTTACTGACACAGACTTACA 667872 CACTGACAAAGCTGTG-----TACTTTACTGACACAGACTTACA 1 CACTGACAAAGCTGTGTACTTTACTTTACTGACACAGACTTACA 667911 CACTGACAAAGCTGTGTACTTTACTTTACTGACACAGACTTACA 1 CACTGACAAAGCTGTGTACTTTACTTTACTGACACAGACTTACA * 667955 CACTGACAAAGCTGTGTACTTCACTTTACTGACACAGACTTACA 1 CACTGACAAAGCTGTGTACTTTACTTTACTGACACAGACTTACA 667999 CACTGACAAAGC 1 CACTGACAAAGC 668011 GTAATGTGTA Statistics Matches: 857, Mismatches: 56, Indels: 84 0.86 0.06 0.08 Matches are distributed among these distances: 35 28 0.03 37 26 0.03 39 93 0.11 40 14 0.02 41 68 0.08 42 71 0.08 43 6 0.01 44 327 0.38 46 222 0.26 48 2 0.00 ACGTcount: A:0.34, C:0.25, G:0.13, T:0.28 Consensus pattern (44 bp): CACTGACAAAGCTGTGTACTTTACTTTACTGACACAGACTTACA Found at i:667122 original size:90 final size:88 Alignment explanation

Indices: 667011--668010 Score: 1334 Period size: 90 Copynumber: 11.6 Consensus size: 88 667001 AACAATAATT * 667011 CACTGACAAAGCTGTGTACTTTACTTTACTGACACACAGACTCACACACTGACAAAGCTGTGTAC 1 CACTGACAAAGCTGTGTACTTTACTTTACTG--ACACAGACTTACACACTGACAAAGCTGTGTAC 667076 TTTACTTTACTGACACAGACTTACA 64 TTTACTTTACTGACACAGACTTACA * ** * * * * 667101 CACAGACAATTCTGTGTACTTTACTTTACTGACACACAGACTAACACACTAACAAAGCTGGGTAG 1 CACTGACAAAGCTGTGTACTTTACTTTACTG--ACACAGACTTACACACTGACAAAGCTGTGTAC 667166 TTTACTTTACTGACACAGACTTACA 64 TTTACTTTACTGACACAGACTTACA * 667191 CACTGACAAAGCTGTGTACTTTACTTTACTGACACACAGACTTACACACTGACAAAGCTATGTAC 1 CACTGACAAAGCTGTGTACTTTACTTTACTG--ACACAGACTTACACACTGACAAAGCTGTGTAC * ** 667256 TTTACTTTATTGACATACAGACAAACA 64 TTTACTTTACTGAC--ACAGACTTACA * * * * 667283 CACTGACAAAGCTGTATACTTTACTTTACTAACACACAGACTAACACACTGAGAAAGCTGTGTAC 1 CACTGACAAAGCTGTGTACTTTACTTTACT--GACACAGACTTACACACTGACAAAGCTGTGTAC * * * 667348 TTCACTTTACTGACACACAGTCTAACA 64 TTTACTTTACTG--ACACAGACTTACA * * * 667375 CAATGACAAAGCTGTGTACTTTACTTCACTGACACAGACTT--ATACTGACAAAGCTGTGTACTT 1 CACTGACAAAGCTGTGTACTTTACTTTACTGACACAGACTTACACACTGACAAAGCTGTGTACTT * 667438 TACTTCACTGACACAGACTTACA 66 TACTTTACTGACACAGACTTACA * * 667461 CACTGACAAAGCTGTGTACTTTACTTCACTGACACAGACTAACACACTGACAAAGCTGTGTACTT 1 CACTGACAAAGCTGTGTACTTTACTTTACTGACACAGACTTACACACTGACAAAGCTGTGTACTT * 667526 TAC-TAAC--ACACAGACTTACA 66 TACTTTACTGACACAGACTTACA * * * 667546 CACTGACAAAGTTTTGTACTTTACTTCACTGACACAGACTT--ACACTGACAAAGCTGTG----- 1 CACTGACAAAGCTGTGTACTTTACTTTACTGACACAGACTTACACACTGACAAAGCTGTGTACTT 667604 TACTTTACTG--ACAGACTTACA 66 TACTTTACTGACACAGACTTACA 667625 CACTGACAAAGCTGTGTACTTTACTTTACTGACACAGACTTACACACTGACAAAGCTGTGTACTT 1 CACTGACAAAGCTGTGTACTTTACTTTACTGACACAGACTTACACACTGACAAAGCTGTGTACTT 667690 TACTTTACTGACACAGACTTACA 66 TACTTTACTGACACAGACTTACA 667713 CACTGACAAAGCTGTG-----TACTTTACTGACACAGACTTACACACTGACAAAGCTGTGTACTT 1 CACTGACAAAGCTGTGTACTTTACTTTACTGACACAGACTTACACACTGACAAAGCTGTGTACTT * * * 667773 TAC-TGAC--ACACATACTAACA 66 TACTTTACTGACACAGACTTACA * 667793 CACTGACAAAACTGTGTACTTTACTTTACTGACACAGACTT----ACTGACAAAGCTGTG----- 1 CACTGACAAAGCTGTGTACTTTACTTTACTGACACAGACTTACACACTGACAAAGCTGTGTACTT 667849 TACTTTACTGACACAGACTTACA 66 TACTTTACTGACACAGACTTACA 667872 CACTGACAAAGCTGTG-----TACTTTACTGACACAGACTTACACACTGACAAAGCTGTGTACTT 1 CACTGACAAAGCTGTGTACTTTACTTTACTGACACAGACTTACACACTGACAAAGCTGTGTACTT 667932 TACTTTACTGACACAGACTTACA 66 TACTTTACTGACACAGACTTACA * 667955 CACTGACAAAGCTGTGTACTTCACTTTACTGACACAGACTTACACACTGACAAAGC 1 CACTGACAAAGCTGTGTACTTTACTTTACTGACACAGACTTACACACTGACAAAGC 668011 GTAATGTGTA Statistics Matches: 810, Mismatches: 58, Indels: 86 0.85 0.06 0.09 Matches are distributed among these distances: 74 20 0.02 76 3 0.00 77 3 0.00 78 18 0.02 79 78 0.10 80 26 0.03 81 32 0.04 82 3 0.00 83 103 0.13 85 71 0.09 86 60 0.07 87 3 0.00 88 113 0.14 90 162 0.20 92 113 0.14 94 2 0.00 ACGTcount: A:0.34, C:0.25, G:0.13, T:0.28 Consensus pattern (88 bp): CACTGACAAAGCTGTGTACTTTACTTTACTGACACAGACTTACACACTGACAAAGCTGTGTACTT TACTTTACTGACACAGACTTACA Found at i:667449 original size:26 final size:26 Alignment explanation

Indices: 667418--667494 Score: 80 Period size: 26 Copynumber: 3.3 Consensus size: 26 667408 ACAGACTTAT 667418 ACTGACAAAGCTGTGTACTTTACTTC 1 ACTGACAAAGCTGTGTACTTTACTTC * * 667444 ACTGAC--A-C--AG-AC-TTAC-AC 1 ACTGACAAAGCTGTGTACTTTACTTC 667462 ACTGACAAAGCTGTGTACTTTACTTC 1 ACTGACAAAGCTGTGTACTTTACTTC 667488 ACTGACA 1 ACTGACA 667495 CAGACTAACA Statistics Matches: 39, Mismatches: 4, Indels: 16 0.66 0.07 0.27 Matches are distributed among these distances: 18 7 0.18 19 4 0.10 20 3 0.08 21 2 0.05 23 2 0.05 24 3 0.08 25 4 0.10 26 14 0.36 ACGTcount: A:0.31, C:0.26, G:0.14, T:0.29 Consensus pattern (26 bp): ACTGACAAAGCTGTGTACTTTACTTC Found at i:667613 original size:21 final size:21 Alignment explanation

Indices: 667589--667649 Score: 60 Period size: 21 Copynumber: 3.1 Consensus size: 21 667579 ACAGACTTAC 667589 ACTGACAAAGCTGTGTACTTT 1 ACTGACAAAGCTGTGTACTTT * ** 667610 ACTGACAGA-C--T-TAC-AC 1 ACTGACAAAGCTGTGTACTTT 667626 ACTGACAAAGCTGTGTACTTT 1 ACTGACAAAGCTGTGTACTTT 667647 ACT 1 ACT 667650 TTACTGACAC Statistics Matches: 29, Mismatches: 6, Indels: 10 0.64 0.13 0.22 Matches are distributed among these distances: 16 8 0.28 17 4 0.14 18 1 0.03 19 1 0.03 20 4 0.14 21 11 0.38 ACGTcount: A:0.31, C:0.23, G:0.16, T:0.30 Consensus pattern (21 bp): ACTGACAAAGCTGTGTACTTT Found at i:667655 original size:26 final size:26 Alignment explanation

Indices: 667626--667702 Score: 73 Period size: 26 Copynumber: 3.3 Consensus size: 26 667616 AGACTTACAC 667626 ACTGACAAAGCTGTGTACTTTACTTT 1 ACTGACAAAGCTGTGTACTTTACTTT * 667652 ACTGACACAGAC--T-TAC---AC--- 1 ACTGACAAAG-CTGTGTACTTTACTTT 667670 ACTGACAAAGCTGTGTACTTTACTTT 1 ACTGACAAAGCTGTGTACTTTACTTT 667696 ACTGACA 1 ACTGACA 667703 CAGACTTACA Statistics Matches: 39, Mismatches: 2, Indels: 20 0.64 0.03 0.33 Matches are distributed among these distances: 17 1 0.03 18 9 0.23 19 1 0.03 20 3 0.08 21 2 0.05 23 2 0.05 24 3 0.08 25 1 0.03 26 16 0.41 27 1 0.03 ACGTcount: A:0.31, C:0.23, G:0.14, T:0.31 Consensus pattern (26 bp): ACTGACAAAGCTGTGTACTTTACTTT Found at i:667719 original size:18 final size:18 Alignment explanation

Indices: 667696--667759 Score: 58 Period size: 18 Copynumber: 3.4 Consensus size: 18 667686 ACTTTACTTT 667696 ACTGACACAGACTTACAC 1 ACTGACACAGACTTACAC * ** 667714 ACTGACAAAG-CTGTGTACTTT 1 ACTGACACAGAC--T-TAC-AC 667735 ACTGACACAGACTTACAC 1 ACTGACACAGACTTACAC 667753 ACTGACA 1 ACTGACA 667760 AAGCTGTGTA Statistics Matches: 35, Mismatches: 6, Indels: 10 0.69 0.12 0.20 Matches are distributed among these distances: 17 1 0.03 18 16 0.46 19 4 0.11 20 4 0.11 21 9 0.26 22 1 0.03 ACGTcount: A:0.36, C:0.28, G:0.14, T:0.22 Consensus pattern (18 bp): ACTGACACAGACTTACAC Found at i:667740 original size:21 final size:21 Alignment explanation

Indices: 667714--667780 Score: 70 Period size: 21 Copynumber: 3.3 Consensus size: 21 667704 AGACTTACAC 667714 ACTGACAAAGCTGTGTACTTT 1 ACTGACAAAGCTGTGTACTTT * ** 667735 ACTGACACAGAC--T-TAC-AC 1 ACTGACAAAG-CTGTGTACTTT 667753 ACTGACAAAGCTGTGTACTTT 1 ACTGACAAAGCTGTGTACTTT 667774 ACTGACA 1 ACTGACA 667781 CACATACTAA Statistics Matches: 35, Mismatches: 6, Indels: 10 0.69 0.12 0.20 Matches are distributed among these distances: 17 1 0.03 18 9 0.26 19 4 0.11 20 4 0.11 21 16 0.46 22 1 0.03 ACGTcount: A:0.33, C:0.24, G:0.16, T:0.27 Consensus pattern (21 bp): ACTGACAAAGCTGTGTACTTT Found at i:667856 original size:21 final size:21 Alignment explanation

Indices: 667832--667935 Score: 80 Period size: 21 Copynumber: 5.2 Consensus size: 21 667822 TGACACAGAC 667832 TTACTGACAAAGCTGTGTACT 1 TTACTGACAAAGCTGTGTACT * 667853 TTACTGACACAGAC--T-TAC- 1 TTACTGACAAAG-CTGTGTACT ** 667871 ACACTGACAAAGCTGTGTACT 1 TTACTGACAAAGCTGTGTACT * 667892 TTACTGACACAGAC--T-TAC- 1 TTACTGACAAAG-CTGTGTACT ** 667910 ACACTGACAAAGCTGTGTACT 1 TTACTGACAAAGCTGTGTACT 667931 TTACT 1 TTACT 667936 TTACTGACAC Statistics Matches: 61, Mismatches: 12, Indels: 20 0.66 0.13 0.22 Matches are distributed among these distances: 17 2 0.03 18 18 0.30 19 8 0.13 20 8 0.13 21 23 0.38 22 2 0.03 ACGTcount: A:0.32, C:0.24, G:0.15, T:0.29 Consensus pattern (21 bp): TTACTGACAAAGCTGTGTACT Found at i:667878 original size:18 final size:18 Alignment explanation

Indices: 667855--667918 Score: 58 Period size: 18 Copynumber: 3.4 Consensus size: 18 667845 TGTGTACTTT 667855 ACTGACACAGACTTACAC 1 ACTGACACAGACTTACAC * ** 667873 ACTGACAAAG-CTGTGTACTTT 1 ACTGACACAGAC--T-TAC-AC 667894 ACTGACACAGACTTACAC 1 ACTGACACAGACTTACAC 667912 ACTGACA 1 ACTGACA 667919 AAGCTGTGTA Statistics Matches: 35, Mismatches: 6, Indels: 10 0.69 0.12 0.20 Matches are distributed among these distances: 17 1 0.03 18 16 0.46 19 4 0.11 20 4 0.11 21 9 0.26 22 1 0.03 ACGTcount: A:0.36, C:0.28, G:0.14, T:0.22 Consensus pattern (18 bp): ACTGACACAGACTTACAC Found at i:668935 original size:128 final size:128 Alignment explanation

Indices: 668775--669009 Score: 409 Period size: 128 Copynumber: 1.8 Consensus size: 128 668765 CTATATGATT 668775 AGTAAATAGCAAAAAAACTTTCCTATTCTATAAATGACTTTCATATATTCGACTTCAATCAAT-A 1 AGTAAATAGCAAAAAAACTTTCCTATTCTATAAATGACTTTCATATATTCGACTTCAATCAATAA 668839 CTAAAACACTATAAGTATACATGTTTAATAGATACAAATTATATGTTACATTTATCATATAAAC 66 CTAAAACACTA-AAGTATACATGTTTAATAGATACAAATTATATGTTACATTTATCATATAAAC * * * * * 668903 AGTAAATAGCAAAAAGACTTTCCTATTCTATAAATGACTTTCATGTATTTGACTTTATTCAATAA 1 AGTAAATAGCAAAAAAACTTTCCTATTCTATAAATGACTTTCATATATTCGACTTCAATCAATAA 668968 CTAAAACACTAAAGTATACATGTTTAATAGATACAAATTATA 66 CTAAAACACTAAAGTATACATGTTTAATAGATACAAATTATA 669010 CATCCTATTA Statistics Matches: 101, Mismatches: 5, Indels: 2 0.94 0.05 0.02 Matches are distributed among these distances: 128 89 0.88 129 12 0.12 ACGTcount: A:0.43, C:0.14, G:0.07, T:0.35 Consensus pattern (128 bp): AGTAAATAGCAAAAAAACTTTCCTATTCTATAAATGACTTTCATATATTCGACTTCAATCAATAA CTAAAACACTAAAGTATACATGTTTAATAGATACAAATTATATGTTACATTTATCATATAAAC Found at i:669026 original size:128 final size:128 Alignment explanation

Indices: 668775--669043 Score: 398 Period size: 128 Copynumber: 2.1 Consensus size: 128 668765 CTATATGATT 668775 AGTAAATAGCAAAAAAACTTTCCTATTCTATAAATGACTTTCATATATTCGACTTCAATCAATAC 1 AGTAAATAGCAAAAAAACTTTCCTATTCTATAAATGACTTTCATATATTCGACTTCAATCAATAC ** * * 668840 TAAAACACTATAAGTATACATGTTTAATAGATACAAATTATATGTTACATTTATCATATAAAC 66 TAAAACACTATAAGTATACATGTTTAATAGATACAAATTATATCATACATTAACCATATAAAC * * * * * 668903 AGTAAATAGCAAAAAGACTTTCCTATTCTATAAATGACTTTCATGTATTTGACTTTATTCAATAA 1 AGTAAATAGCAAAAAAACTTTCCTATTCTATAAATGACTTTCATATATTCGACTTCAATCAAT-A * 668968 CTAAAACACTA-AAGTATACATGTTTAATAGATACAAATTATA-CATCCTATTAACCATATAAAC 65 CTAAAACACTATAAGTATACATGTTTAATAGATACAAATTATATCATAC-ATTAACCATATAAAC * * 669031 AGTTAATGGCAAA 1 AGTAAATAGCAAA 669044 CATCTTTTCT Statistics Matches: 127, Mismatches: 12, Indels: 4 0.89 0.08 0.03 Matches are distributed among these distances: 127 2 0.02 128 113 0.89 129 12 0.09 ACGTcount: A:0.43, C:0.15, G:0.07, T:0.34 Consensus pattern (128 bp): AGTAAATAGCAAAAAAACTTTCCTATTCTATAAATGACTTTCATATATTCGACTTCAATCAATAC TAAAACACTATAAGTATACATGTTTAATAGATACAAATTATATCATACATTAACCATATAAAC Found at i:670171 original size:180 final size:180 Alignment explanation

Indices: 669869--670303 Score: 845 Period size: 180 Copynumber: 2.4 Consensus size: 180 669859 ACCCTACATG 669869 TATATGCAACATTTTGCCAAAAAATGACTAAGTTCAAAAGCTGGTATTTTTTTC-ATAAATTATC 1 TATATGCAACATTTTGCCAAAAAATGACTAAGTTCAAAAGCTGGTA-TTTTTTCGATAAATTATC 669933 GGAAATCAAAATCCTAGCAATATGCACACCTCTGATATATGTACAATTGATCTGCAAAAGAACAA 65 GGAAATCAAAATCCTAGCAATATGCACACCTCTGATATATGTACAATTGATCTGCAAAAGAACAA 669998 CTTCCTATCTTGAGAACTGTAGGAGGAGTTATCCGTACAATGAGGGTACCC 130 CTTCCTATCTTGAGAACTGTAGGAGGAGTTATCCGTACAATGAGGGTACCC * 670049 TATATGCAATATTTTGCCAAAAAATGACTAAGTTCAAAAGCTGGTATTTTTTCGATAAATTATCG 1 TATATGCAACATTTTGCCAAAAAATGACTAAGTTCAAAAGCTGGTATTTTTTCGATAAATTATCG 670114 GAAATCAAAATCCTAGCAATATGCACACCTCTGATATATGTACAATTGATCTGCAAAAGAACAAC 66 GAAATCAAAATCCTAGCAATATGCACACCTCTGATATATGTACAATTGATCTGCAAAAGAACAAC 670179 TTCCTATCTTGAGAACTGTAGGAGGAGTTATCCGTACAATGAGGGTACCC 131 TTCCTATCTTGAGAACTGTAGGAGGAGTTATCCGTACAATGAGGGTACCC 670229 TATATGCAACATTTTGCCAAAAAATGACTAAGTTCAAAAGCTGGTATTTTTTCGATAAATTATCG 1 TATATGCAACATTTTGCCAAAAAATGACTAAGTTCAAAAGCTGGTATTTTTTCGATAAATTATCG 670294 GAAATCAAAA 66 GAAATCAAAA 670304 NNNNNNNNNN Statistics Matches: 252, Mismatches: 2, Indels: 2 0.98 0.01 0.01 Matches are distributed among these distances: 179 7 0.03 180 245 0.97 ACGTcount: A:0.37, C:0.17, G:0.16, T:0.30 Consensus pattern (180 bp): TATATGCAACATTTTGCCAAAAAATGACTAAGTTCAAAAGCTGGTATTTTTTCGATAAATTATCG GAAATCAAAATCCTAGCAATATGCACACCTCTGATATATGTACAATTGATCTGCAAAAGAACAAC TTCCTATCTTGAGAACTGTAGGAGGAGTTATCCGTACAATGAGGGTACCC Found at i:673379 original size:41 final size:41 Alignment explanation

Indices: 673334--673415 Score: 139 Period size: 41 Copynumber: 2.0 Consensus size: 41 673324 CCCCCTTCTT * 673334 TTGAAACATCTGTGAAA-AAAATGAATGGAAACTGCAAATAA 1 TTGAAACATCTG-CAAAGAAAATGAATGGAAACTGCAAATAA 673375 TTGAAACATCTGCAAAGAAAATGAATGGAAACTGCAAATAA 1 TTGAAACATCTGCAAAGAAAATGAATGGAAACTGCAAATAA 673416 CTGGAATTTT Statistics Matches: 39, Mismatches: 1, Indels: 2 0.93 0.02 0.05 Matches are distributed among these distances: 40 3 0.08 41 36 0.92 ACGTcount: A:0.51, C:0.11, G:0.17, T:0.21 Consensus pattern (41 bp): TTGAAACATCTGCAAAGAAAATGAATGGAAACTGCAAATAA Found at i:673737 original size:161 final size:158 Alignment explanation

Indices: 673383--673891 Score: 574 Period size: 161 Copynumber: 3.2 Consensus size: 158 673373 AATTGAAACA * * ** 673383 TCTGCAAAGAAAATGAATGGAAACTGCAAATAACTGGAATTTTTCTA-AGTCCAAGGGACATAAC 1 TCTGCGAAGAAAATGAACGGAAACTGCAAATAA-TTAAATTTTTCTACA-TCCAAGGG-CATAAC * * * * * * * 673447 TCTGTATTAATTTTGCTTGTTCAAACTCAATATAAAACTTGACCTAGATGTTATCATGATAAACC 63 TCTGTA-TAA-ATTGCTCGATCGAACCCAATATAGAACTTGACCTAGATATTATCATGATAAACC * * 673512 TGTATACCAAATTTCATTTCAATATCTTCATCC 126 TGAATACCAAATTTCATTTCAATATGTTCATCC * * * ** 673545 TCTGCAAAGAAAATGAATGGAAACGGCAAATAATTCAAATTTTTCTACATCCAATGGGCATTGCT 1 TCTGCGAAGAAAATGAACGGAAACTGCAAATAATT-AAATTTTTCTACATCCAA-GGGCATAACT * * * * 673610 CTGTATAAACTTGCTCGATCGAACCCAATATGGAACTTAACCTAGATATTATCATGATTAACATG 64 CTGTATAAA-TTGCTCGATCGAACCCAATATAGAACTTGACCTAGATATTATCATGATAAACCTG * * * 673675 CATTCCAAAGTTC-TATTCAATATGTTCATCC 128 AATACCAAATTTCAT-TTCAATATGTTCATCC * * * * * * 673706 TCTGTGAAGAAAATGAGCAGAAACTGCAAATAATTAGAATTTTTCTGCGTCCAAGAGGCATACCT 1 TCTGCGAAGAAAATGAACGGAAACTGCAAATAATTA-AATTTTTCTACATCCAAG-GGCATAACT ** * * 673771 CTGTCGAAATTGCTCAATCGAACCCAATATCGAACTTGACCTAGATATTATCATGATAAACCTGA 64 CTGTATAAATTGCTCGATCGAACCCAATATAGAACTTGACCTAGATATTATCATGATAAACCTGA 673836 ATACCAAATTTCATTTCAATATGTTCA-CC 129 ATACCAAATTTCATTTCAATATGTTCATCC 673865 TTCTGCGAAGAAAATGAACGGAAACTG 1 -TCTGCGAAGAAAATGAACGGAAACTG 673892 TTGGTGGACT Statistics Matches: 295, Mismatches: 43, Indels: 20 0.82 0.12 0.06 Matches are distributed among these distances: 159 2 0.01 160 99 0.34 161 133 0.45 162 57 0.19 163 4 0.01 ACGTcount: A:0.36, C:0.19, G:0.14, T:0.30 Consensus pattern (158 bp): TCTGCGAAGAAAATGAACGGAAACTGCAAATAATTAAATTTTTCTACATCCAAGGGCATAACTCT GTATAAATTGCTCGATCGAACCCAATATAGAACTTGACCTAGATATTATCATGATAAACCTGAAT ACCAAATTTCATTTCAATATGTTCATCC Found at i:682051 original size:2 final size:2 Alignment explanation

Indices: 682044--682089 Score: 92 Period size: 2 Copynumber: 23.0 Consensus size: 2 682034 TATGAGATAC 682044 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 682086 AG AG 1 AG AG 682090 TTTTAAATTG Statistics Matches: 44, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 44 1.00 ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00 Consensus pattern (2 bp): AG Found at i:685451 original size:1 final size:1 Alignment explanation

Indices: 685409--685442 Score: 68 Period size: 1 Copynumber: 34.0 Consensus size: 1 685399 TACTTCTTTC 685409 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 685443 AGAATTTTTA Statistics Matches: 33, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 1 33 1.00 ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00 Consensus pattern (1 bp): T Found at i:685868 original size:2 final size:2 Alignment explanation

Indices: 685861--685885 Score: 50 Period size: 2 Copynumber: 12.5 Consensus size: 2 685851 TTTTGATAAG 685861 AT AT AT AT AT AT AT AT AT AT AT AT A 1 AT AT AT AT AT AT AT AT AT AT AT AT A 685886 NNNNNNNNNN 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:0.52, C:0.00, G:0.00, T:0.48 Consensus pattern (2 bp): AT Found at i:697604 original size:2 final size:2 Alignment explanation

Indices: 697597--697668 Score: 144 Period size: 2 Copynumber: 36.0 Consensus size: 2 697587 TGACATTATA 697597 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 697639 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 697669 GNNNNNNNNN Statistics Matches: 70, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 70 1.00 ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00 Consensus pattern (2 bp): AG Found at i:701577 original size:1 final size:1 Alignment explanation

Indices: 701573--701616 Score: 88 Period size: 1 Copynumber: 44.0 Consensus size: 1 701563 NNNGGGGGGG 701573 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 701617 ACAAAAAACC Statistics Matches: 43, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 1 43 1.00 ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00 Consensus pattern (1 bp): T Found at i:705749 original size:10 final size:10 Alignment explanation

Indices: 705734--705768 Score: 52 Period size: 10 Copynumber: 3.4 Consensus size: 10 705724 CTAAGAAAAG 705734 TTTTTTATAT 1 TTTTTTATAT 705744 TTTTTTATAT 1 TTTTTTATAT * 705754 ATTTTATATAT 1 -TTTTTTATAT 705765 TTTT 1 TTTT 705769 GTTACCATGA Statistics Matches: 23, Mismatches: 1, Indels: 2 0.88 0.04 0.08 Matches are distributed among these distances: 10 14 0.61 11 9 0.39 ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77 Consensus pattern (10 bp): TTTTTTATAT Found at i:711287 original size:4 final size:4 Alignment explanation

Indices: 711278--711306 Score: 58 Period size: 4 Copynumber: 7.2 Consensus size: 4 711268 CTTTGTGCCC 711278 TTTA TTTA TTTA TTTA TTTA TTTA TTTA T 1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA T 711307 GTGAGACCAT Statistics Matches: 25, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 4 25 1.00 ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76 Consensus pattern (4 bp): TTTA Found at i:720357 original size:53 final size:54 Alignment explanation

Indices: 720276--720389 Score: 185 Period size: 53 Copynumber: 2.1 Consensus size: 54 720266 CTTAATTATT * 720276 TATATTAATCAAATAAGAAAGTGCTATCTAATCGAAG-TATATGTATTTTGATAG 1 TATA-TAATCAAATAAGAAAGTGCTATCTAATCAAAGATATATGTATTTTGATAG * 720330 TATATAATCAAATGAGAAAGTGCTATCTAATCAAAGTATATATGTATTTTGATAG 1 TATATAATCAAATAAGAAAGTGCTATCTAATCAAAG-ATATATGTATTTTGATAG 720385 TATAT 1 TATAT 720390 CTATGAAAAT Statistics Matches: 56, Mismatches: 2, Indels: 3 0.92 0.03 0.05 Matches are distributed among these distances: 53 30 0.54 54 4 0.07 55 22 0.39 ACGTcount: A:0.41, C:0.07, G:0.14, T:0.38 Consensus pattern (54 bp): TATATAATCAAATAAGAAAGTGCTATCTAATCAAAGATATATGTATTTTGATAG Found at i:722341 original size:22 final size:22 Alignment explanation

Indices: 722315--722362 Score: 96 Period size: 22 Copynumber: 2.2 Consensus size: 22 722305 AAATATCACA 722315 AACATATTGACACATGTAATAC 1 AACATATTGACACATGTAATAC 722337 AACATATTGACACATGTAATAC 1 AACATATTGACACATGTAATAC 722359 AACA 1 AACA 722363 ATGTAAAATA Statistics Matches: 26, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 22 26 1.00 ACGTcount: A:0.48, C:0.19, G:0.08, T:0.25 Consensus pattern (22 bp): AACATATTGACACATGTAATAC Found at i:726647 original size:22 final size:22 Alignment explanation

Indices: 726619--726681 Score: 126 Period size: 22 Copynumber: 2.9 Consensus size: 22 726609 TCTGGCTGGG 726619 TTACCTGATGTCATTAATGTCA 1 TTACCTGATGTCATTAATGTCA 726641 TTACCTGATGTCATTAATGTCA 1 TTACCTGATGTCATTAATGTCA 726663 TTACCTGATGTCATTAATG 1 TTACCTGATGTCATTAATG 726682 GCCCCCGATC Statistics Matches: 41, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 22 41 1.00 ACGTcount: A:0.27, C:0.17, G:0.14, T:0.41 Consensus pattern (22 bp): TTACCTGATGTCATTAATGTCA Found at i:726653 original size:13 final size:13 Alignment explanation

Indices: 726619--726678 Score: 64 Period size: 13 Copynumber: 5.2 Consensus size: 13 726609 TCTGGCTGGG 726619 TTACCTGATGTCA 1 TTACCTGATGTCA 726632 TTA----ATGTCA 1 TTACCTGATGTCA 726641 TTACCTGATGTCA 1 TTACCTGATGTCA 726654 TTA----ATGTCA 1 TTACCTGATGTCA 726663 TTACCTGATGTCA 1 TTACCTGATGTCA 726676 TTA 1 TTA 726679 ATGGCCCCCG Statistics Matches: 39, Mismatches: 0, Indels: 16 0.71 0.00 0.29 Matches are distributed among these distances: 9 18 0.46 13 21 0.54 ACGTcount: A:0.27, C:0.18, G:0.13, T:0.42 Consensus pattern (13 bp): TTACCTGATGTCA Found at i:726867 original size:21 final size:21 Alignment explanation

Indices: 726841--727021 Score: 118 Period size: 21 Copynumber: 8.6 Consensus size: 21 726831 CAATGACTAT * 726841 AAAGGTCAAATCATAGCATCA 1 AAAGGTCATATCATAGCATCA * * 726862 AAAGGTGATATCTTAGCATCA 1 AAAGGTCATATCATAGCATCA * * 726883 AAAGGTGATATCTTAGCATCA 1 AAAGGTCATATCATAGCATCA * * 726904 AAGGGTCACATCATAGCA-CTA 1 AAAGGTCATATCATAGCATC-A ** * * 726925 AAAGGTCGCATCAAAGCATTTA 1 AAAGGTCATATCATAGCA-TCA ** 726947 AAA-AACATGAT-ATAGCATCA 1 AAAGGTCAT-ATCATAGCATCA * * ** 726967 AAAGGTCACATCAAATTATCA 1 AAAGGTCATATCATAGCATCA * 726988 AAATGTCATATCATA-CTATCA 1 AAAGGTCATATCATAGC-ATCA * * 727009 AAAGATCACATCA 1 AAAGGTCATATCA 727022 AAAGACATAT Statistics Matches: 123, Mismatches: 30, Indels: 14 0.74 0.18 0.08 Matches are distributed among these distances: 20 8 0.07 21 109 0.89 22 6 0.05 ACGTcount: A:0.44, C:0.18, G:0.14, T:0.24 Consensus pattern (21 bp): AAAGGTCATATCATAGCATCA Found at i:727111 original size:20 final size:21 Alignment explanation

Indices: 727058--727129 Score: 92 Period size: 21 Copynumber: 3.5 Consensus size: 21 727048 ATCAAATCAC * 727058 CAAAAGGACATATCTTAGCAT 1 CAAAAGGTCATATCTTAGCAT 727079 CAAAAGGTCATATCTTAGCAT 1 CAAAAGGTCATATCTTAGCAT * * * 727100 CAAAA-TTCATATCATAACAT 1 CAAAAGGTCATATCTTAGCAT * 727120 CTAAAGGTCA 1 CAAAAGGTCA 727130 ATCATATCAT Statistics Matches: 44, Mismatches: 6, Indels: 2 0.85 0.12 0.04 Matches are distributed among these distances: 20 16 0.36 21 28 0.64 ACGTcount: A:0.43, C:0.19, G:0.11, T:0.26 Consensus pattern (21 bp): CAAAAGGTCATATCTTAGCAT Found at i:727152 original size:16 final size:16 Alignment explanation

Indices: 727131--727161 Score: 53 Period size: 16 Copynumber: 1.9 Consensus size: 16 727121 TAAAGGTCAA 727131 TCATATCATCAGTTCG 1 TCATATCATCAGTTCG * 727147 TCATATCGTCAGTTC 1 TCATATCATCAGTTC 727162 AAATTATCAA 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:0.23, C:0.26, G:0.13, T:0.39 Consensus pattern (16 bp): TCATATCATCAGTTCG Found at i:735174 original size:2 final size:2 Alignment explanation

Indices: 735167--735214 Score: 96 Period size: 2 Copynumber: 24.0 Consensus size: 2 735157 TCTTCATAAC 735167 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 735209 AG AG AG 1 AG AG AG 735215 CTACCCACCT 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:739564 original size:16 final size:16 Alignment explanation

Indices: 739543--739573 Score: 53 Period size: 16 Copynumber: 1.9 Consensus size: 16 739533 TAAATTTATT * 739543 GTCTAAATGGAAAAAA 1 GTCTAAATAGAAAAAA 739559 GTCTAAATAGAAAAA 1 GTCTAAATAGAAAAA 739574 TATTTGTTCA 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:0.58, C:0.06, G:0.16, T:0.19 Consensus pattern (16 bp): GTCTAAATAGAAAAAA Found at i:746581 original size:4 final size:4 Alignment explanation

Indices: 746566--746623 Score: 73 Period size: 4 Copynumber: 14.8 Consensus size: 4 746556 ATCACTTTTT * * * 746566 GTCC GT-C GTCC GTCC GTCC GTCC GTCT GTCC GTCC GTCT GTCC GTCT 1 GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC * 746613 GTCT GTCC GTC 1 GTCC GTCC GTC 746624 TGTAAACTTT Statistics Matches: 47, Mismatches: 6, Indels: 2 0.85 0.11 0.04 Matches are distributed among these distances: 3 3 0.06 4 44 0.94 ACGTcount: A:0.00, C:0.41, G:0.26, T:0.33 Consensus pattern (4 bp): GTCC Found at i:746626 original size:12 final size:12 Alignment explanation

Indices: 746572--746623 Score: 86 Period size: 12 Copynumber: 4.3 Consensus size: 12 746562 TTTTGTCCGT * 746572 CGTCCGTCCGTC 1 CGTCCGTCTGTC 746584 CGTCCGTCTGTC 1 CGTCCGTCTGTC 746596 CGTCCGTCTGTC 1 CGTCCGTCTGTC * 746608 CGTCTGTCTGTC 1 CGTCCGTCTGTC 746620 CGTC 1 CGTC 746624 TGTAAACTTT Statistics Matches: 38, Mismatches: 2, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 12 38 1.00 ACGTcount: A:0.00, C:0.42, G:0.25, T:0.33 Consensus pattern (12 bp): CGTCCGTCTGTC Found at i:751028 original size:31 final size:31 Alignment explanation

Indices: 750993--751086 Score: 88 Period size: 31 Copynumber: 3.2 Consensus size: 31 750983 CAGCCCTAGT * * 750993 GAACACAGCCAGGGATAGTCCATCCCTCATA 1 GAACACATCCAGGGATAGTCCATCCATCATA * * 751024 GAACACATCC----ATAGTCTATCCTTCATA 1 GAACACATCCAGGGATAGTCCATCCATCATA * * * 751051 TAACAAATTCAGGGATAGTCCATCCATCATA 1 GAACACATCCAGGGATAGTCCATCCATCATA * 751082 AAACA 1 GAACA 751087 TGTCTAGGGA Statistics Matches: 50, Mismatches: 9, Indels: 8 0.75 0.13 0.12 Matches are distributed among these distances: 27 22 0.44 31 28 0.56 ACGTcount: A:0.37, C:0.28, G:0.13, T:0.22 Consensus pattern (31 bp): GAACACATCCAGGGATAGTCCATCCATCATA Found at i:753686 original size:25 final size:25 Alignment explanation

Indices: 753652--753706 Score: 101 Period size: 25 Copynumber: 2.2 Consensus size: 25 753642 GAAATGCAAA 753652 AACAATTAAAATATGATTTCCCAAT 1 AACAATTAAAATATGATTTCCCAAT * 753677 AACAATTAAAATATTATTTCCCAAT 1 AACAATTAAAATATGATTTCCCAAT 753702 AACAA 1 AACAA 753707 AAACTATTTT Statistics Matches: 29, Mismatches: 1, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 25 29 1.00 ACGTcount: A:0.51, C:0.16, G:0.02, T:0.31 Consensus pattern (25 bp): AACAATTAAAATATGATTTCCCAAT Found at i:756357 original size:13 final size:13 Alignment explanation

Indices: 756339--756365 Score: 54 Period size: 13 Copynumber: 2.1 Consensus size: 13 756329 GTAAAATGTC 756339 AATAATTGTTTGT 1 AATAATTGTTTGT 756352 AATAATTGTTTGT 1 AATAATTGTTTGT 756365 A 1 A 756366 CTTAAGCTAT Statistics Matches: 14, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 14 1.00 ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52 Consensus pattern (13 bp): AATAATTGTTTGT Found at i:763385 original size:17 final size:17 Alignment explanation

Indices: 763363--763477 Score: 126 Period size: 22 Copynumber: 6.3 Consensus size: 17 763353 ACAGCACTAT 763363 GCCACTGTAACACTACA 1 GCCACTGTAACACTACA 763380 GCCACTGTAACACTACA 1 GCCACTGTAACACTACA 763397 GCCACTGTAACGTAACACTACA 1 GCCAC--T---GTAACACTACA 763419 GCCACTGTAACGTAACACTACA 1 GCCAC--T---GTAACACTACA 763441 GCCACTGTAACACTA-A 1 GCCACTGTAACACTACA 763457 GCCACTGTAACACTA-A 1 GCCACTGTAACACTACA 763473 GCCAC 1 GCCAC 763478 CTGATGCTCA Statistics Matches: 93, Mismatches: 0, Indels: 11 0.89 0.00 0.11 Matches are distributed among these distances: 16 22 0.24 17 31 0.33 19 1 0.01 20 1 0.01 22 38 0.41 ACGTcount: A:0.36, C:0.34, G:0.13, T:0.17 Consensus pattern (17 bp): GCCACTGTAACACTACA Found at i:763411 original size:22 final size:22 Alignment explanation

Indices: 763386--763451 Score: 132 Period size: 22 Copynumber: 3.0 Consensus size: 22 763376 TACAGCCACT 763386 GTAACACTACAGCCACTGTAAC 1 GTAACACTACAGCCACTGTAAC 763408 GTAACACTACAGCCACTGTAAC 1 GTAACACTACAGCCACTGTAAC 763430 GTAACACTACAGCCACTGTAAC 1 GTAACACTACAGCCACTGTAAC 763452 ACTAAGCCAC Statistics Matches: 44, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 22 44 1.00 ACGTcount: A:0.36, C:0.32, G:0.14, T:0.18 Consensus pattern (22 bp): GTAACACTACAGCCACTGTAAC Found at i:763412 original size:39 final size:40 Alignment explanation

Indices: 763366--763477 Score: 135 Period size: 39 Copynumber: 2.9 Consensus size: 40 763356 GCACTATGCC * * 763366 ACTGTAACACTACAGCCACTGTAACACTACAGCCACTGTA 1 ACTGTAACACTACAGCCACTGTAACACTACAGCCACAGCA * * * 763406 AC-GTAACACTACAGCCACTGTAAC-GTAACA-CTACAGCC 1 ACTGTAACACTACAGCCACTGTAACACT-ACAGCCACAGCA 763444 ACTGTAACACTA-AGCCACTGTAACACTA-AGCCAC 1 ACTGTAACACTACAGCCACTGTAACACTACAGCCAC 763478 CTGATGCTCA Statistics Matches: 61, Mismatches: 7, Indels: 10 0.78 0.09 0.13 Matches are distributed among these distances: 37 1 0.02 38 23 0.38 39 35 0.57 40 2 0.03 ACGTcount: A:0.37, C:0.33, G:0.12, T:0.18 Consensus pattern (40 bp): ACTGTAACACTACAGCCACTGTAACACTACAGCCACAGCA Found at i:768814 original size:15 final size:15 Alignment explanation

Indices: 768790--768819 Score: 51 Period size: 15 Copynumber: 2.0 Consensus size: 15 768780 TCAAAGTTTG 768790 CAATAATTTTGTTGT 1 CAATAATTTTGTTGT * 768805 CAATATTTTTGTTGT 1 CAATAATTTTGTTGT 768820 TGTAAACCTA Statistics Matches: 14, Mismatches: 1, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 15 14 1.00 ACGTcount: A:0.23, C:0.07, G:0.13, T:0.57 Consensus pattern (15 bp): CAATAATTTTGTTGT Found at i:774824 original size:15 final size:16 Alignment explanation

Indices: 774795--774824 Score: 53 Period size: 16 Copynumber: 1.9 Consensus size: 16 774785 CAACCAAAAA 774795 AACCAAAAGGTGTACC 1 AACCAAAAGGTGTACC 774811 AACCAAAA-GTGTAC 1 AACCAAAAGGTGTAC 774825 AAAAAACCCA Statistics Matches: 14, Mismatches: 0, Indels: 1 0.93 0.00 0.07 Matches are distributed among these distances: 15 6 0.43 16 8 0.57 ACGTcount: A:0.47, C:0.23, G:0.17, T:0.13 Consensus pattern (16 bp): AACCAAAAGGTGTACC Found at i:777666 original size:2 final size:2 Alignment explanation

Indices: 777659--777707 Score: 98 Period size: 2 Copynumber: 24.5 Consensus size: 2 777649 AAAATACAGA 777659 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 777701 AG AG AG A 1 AG AG AG A 777708 TATGACTGTG Statistics Matches: 47, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 47 1.00 ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00 Consensus pattern (2 bp): AG Found at i:791262 original size:17 final size:18 Alignment explanation

Indices: 791240--791274 Score: 63 Period size: 18 Copynumber: 2.0 Consensus size: 18 791230 GCTACAACAT 791240 TTTAAAAA-TTTGAATAA 1 TTTAAAAATTTTGAATAA 791257 TTTAAAAATTTTGAATAA 1 TTTAAAAATTTTGAATAA 791275 ACTGATATCT Statistics Matches: 17, Mismatches: 0, Indels: 1 0.94 0.00 0.06 Matches are distributed among these distances: 17 8 0.47 18 9 0.53 ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43 Consensus pattern (18 bp): TTTAAAAATTTTGAATAA Found at i:800972 original size:2 final size:2 Alignment explanation

Indices: 800965--800994 Score: 60 Period size: 2 Copynumber: 15.0 Consensus size: 2 800955 TCTCAATTTT 800965 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 800995 TTTAATTATA Statistics Matches: 28, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 28 1.00 ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00 Consensus pattern (2 bp): GA Found at i:803147 original size:3 final size:3 Alignment explanation

Indices: 803141--803191 Score: 102 Period size: 3 Copynumber: 17.0 Consensus size: 3 803131 AAATTTAAAT 803141 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA 1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA 803189 GAA 1 GAA 803192 ATTTATACAA Statistics Matches: 48, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 3 48 1.00 ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00 Consensus pattern (3 bp): GAA Found at i:803769 original size:2 final size:2 Alignment explanation

Indices: 803762--803821 Score: 113 Period size: 2 Copynumber: 30.5 Consensus size: 2 803752 GTTATTGCAA 803762 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T- TC TC 1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 803803 TC TC TC TC TC TC TC TC TC T 1 TC TC TC TC TC TC TC TC TC T 803822 GAGAATTATT Statistics Matches: 57, Mismatches: 0, Indels: 2 0.97 0.00 0.03 Matches are distributed among these distances: 1 1 0.02 2 56 0.98 ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52 Consensus pattern (2 bp): TC Found at i:806969 original size:7 final size:7 Alignment explanation

Indices: 806938--806969 Score: 50 Period size: 7 Copynumber: 4.9 Consensus size: 7 806928 CCCCCCCCCC 806938 AAAAA-A 1 AAAAACA 806944 AAAAA-A 1 AAAAACA 806950 AAAAACA 1 AAAAACA 806957 AAAAACA 1 AAAAACA 806964 AAAAAC 1 AAAAAC 806970 CAGACAAGAC Statistics Matches: 25, Mismatches: 0, Indels: 1 0.96 0.00 0.04 Matches are distributed among these distances: 6 11 0.44 7 14 0.56 ACGTcount: A:0.91, C:0.09, G:0.00, T:0.00 Consensus pattern (7 bp): AAAAACA Found at i:817020 original size:2 final size:2 Alignment explanation

Indices: 817013--817065 Score: 106 Period size: 2 Copynumber: 26.5 Consensus size: 2 817003 CAAATCTCAC 817013 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 817055 GA GA GA GA GA G 1 GA GA GA GA GA G 817066 GGGTTTTTTT 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:0.49, C:0.00, G:0.51, T:0.00 Consensus pattern (2 bp): GA Found at i:817482 original size:18 final size:18 Alignment explanation

Indices: 817459--817493 Score: 70 Period size: 18 Copynumber: 1.9 Consensus size: 18 817449 TCTAACAAGA 817459 GCTGCTGATTATATAATC 1 GCTGCTGATTATATAATC 817477 GCTGCTGATTATATAAT 1 GCTGCTGATTATATAAT 817494 TTAGATTAAT Statistics Matches: 17, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 18 17 1.00 ACGTcount: A:0.29, C:0.14, G:0.17, T:0.40 Consensus pattern (18 bp): GCTGCTGATTATATAATC Found at i:826506 original size:2 final size:2 Alignment explanation

Indices: 826499--826532 Score: 68 Period size: 2 Copynumber: 17.0 Consensus size: 2 826489 ATTTAATGTA 826499 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 826533 AGAGAGAGAG Statistics Matches: 32, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 32 1.00 ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50 Consensus pattern (2 bp): TG Found at i:826537 original size:2 final size:2 Alignment explanation

Indices: 826532--826588 Score: 114 Period size: 2 Copynumber: 28.5 Consensus size: 2 826522 GTGTGTGTGT 826532 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 826574 GA GA GA GA GA GA GA G 1 GA GA GA GA GA GA GA G 826589 GTGTACACAC Statistics Matches: 55, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 55 1.00 ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00 Consensus pattern (2 bp): GA Found at i:828187 original size:22 final size:22 Alignment explanation

Indices: 828132--828187 Score: 53 Period size: 22 Copynumber: 2.5 Consensus size: 22 828122 AAAACATGAA 828132 ATAAATTAAACT-GAAATATATT 1 ATAAATTAAA-TGGAAATATATT * ** 828154 ATAAGTGGAATGGATAATA-ATT 1 ATAAATTAAATGGA-AATATATT 828176 ATAAATTAAATG 1 ATAAATTAAATG 828188 TGATTGAAGT Statistics Matches: 26, Mismatches: 6, Indels: 4 0.72 0.17 0.11 Matches are distributed among these distances: 21 1 0.04 22 21 0.81 23 4 0.15 ACGTcount: A:0.52, C:0.02, G:0.12, T:0.34 Consensus pattern (22 bp): ATAAATTAAATGGAAATATATT Found at i:828254 original size:2 final size:2 Alignment explanation

Indices: 828247--828273 Score: 54 Period size: 2 Copynumber: 13.5 Consensus size: 2 828237 GCAATACGCC 828247 TA 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 TA T 828274 TCTTTACTAT Statistics Matches: 25, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 25 1.00 ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52 Consensus pattern (2 bp): TA Found at i:835418 original size:151 final size:153 Alignment explanation

Indices: 835174--835475 Score: 454 Period size: 151 Copynumber: 2.0 Consensus size: 153 835164 ACCTTATTGT * * * 835174 AAACTATTTTGAATTTTTTTTTATATACACATGTATGACATTTTATTTGCATGTGAAAAAGTATA 1 AAACTATTTTGAATTTTTATTTAAATACACATGTATGACATTTTATTTGCATGTGAAAAAGTACA * 835239 TCAATTATTGTAAAGGGAGAGGGCTACATAAGTTTTA-GAA-CT-TGTGCCCAATCGCATCGTAA 66 TCAATTATTGTAAAGGGAGAGGGCTACATAAG-TTTAGGAACCTGTGTGCCCAATCCCATCGTAA 835301 -TATATTAAAATAAAATAAGATAA 130 TTATATTAAAATAAAATAAGATAA 835324 AAAC-ATTTTGAATCTTTATATTTAAATACACATGTATGACATTTTATTTGCATGTGAAAAATGT 1 AAACTATTTTGAAT-TTT-TATTTAAATACACATGTATGACATTTTATTTGCATGTGAAAAA-GT * * 835388 ACATCAATTATTGTAAAGGGAG-GGGTTACATAAGTTTAGGAACCTGTGTGCCCAATCCCATTGT 63 ACATCAATTATTGTAAAGGGAGAGGGCTACATAAGTTTAGGAACCTGTGTGCCCAATCCCATCGT * * 835452 AATTGTATTACAATAAAATAAGAT 128 AATTATATTAAAATAAAATAAGAT 835476 CAAACCAAAC Statistics Matches: 137, Mismatches: 8, Indels: 10 0.88 0.05 0.06 Matches are distributed among these distances: 149 9 0.07 150 11 0.08 151 55 0.40 152 25 0.18 153 18 0.13 154 19 0.14 ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36 Consensus pattern (153 bp): AAACTATTTTGAATTTTTATTTAAATACACATGTATGACATTTTATTTGCATGTGAAAAAGTACA TCAATTATTGTAAAGGGAGAGGGCTACATAAGTTTAGGAACCTGTGTGCCCAATCCCATCGTAAT TATATTAAAATAAAATAAGATAA Found at i:837896 original size:2 final size:2 Alignment explanation

Indices: 837889--837938 Score: 100 Period size: 2 Copynumber: 25.0 Consensus size: 2 837879 CACCTGCATA 837889 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 837931 TC TC TC TC 1 TC TC TC TC 837939 AAAATCAGCT Statistics Matches: 48, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 48 1.00 ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50 Consensus pattern (2 bp): TC Found at i:838094 original size:18 final size:19 Alignment explanation

Indices: 838071--838112 Score: 52 Period size: 18 Copynumber: 2.3 Consensus size: 19 838061 TTGTGAAATG * * 838071 AAAAACCCAATAAAA-AAA 1 AAAAACCAAAAAAAACAAA 838089 AAAAA-CAAAAAAAACAAA 1 AAAAACCAAAAAAAACAAA 838107 AAAAAC 1 AAAAAC 838113 AACAACAACG Statistics Matches: 20, Mismatches: 2, Indels: 3 0.80 0.08 0.12 Matches are distributed among these distances: 17 7 0.35 18 13 0.65 ACGTcount: A:0.83, C:0.14, G:0.00, T:0.02 Consensus pattern (19 bp): AAAAACCAAAAAAAACAAA Found at i:838100 original size:9 final size:9 Alignment explanation

Indices: 838082--838114 Score: 59 Period size: 9 Copynumber: 3.8 Consensus size: 9 838072 AAAACCCAAT 838082 AAAA-AAAA 1 AAAACAAAA 838090 AAAACAAAA 1 AAAACAAAA 838099 AAAACAAAA 1 AAAACAAAA 838108 AAAACAA 1 AAAACAA 838115 CAACAACGTC Statistics Matches: 24, Mismatches: 0, Indels: 1 0.96 0.00 0.04 Matches are distributed among these distances: 8 4 0.17 9 20 0.83 ACGTcount: A:0.91, C:0.09, G:0.00, T:0.00 Consensus pattern (9 bp): AAAACAAAA Found at i:848078 original size:2 final size:2 Alignment explanation

Indices: 848071--848097 Score: 54 Period size: 2 Copynumber: 13.5 Consensus size: 2 848061 CACCTTACAT 848071 TA 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 TA T 848098 GTGTGTGTGT Statistics Matches: 25, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 25 1.00 ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52 Consensus pattern (2 bp): TA Found at i:848124 original size:2 final size:2 Alignment explanation

Indices: 848119--848150 Score: 64 Period size: 2 Copynumber: 16.0 Consensus size: 2 848109 NNNNNNNNNN 848119 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA 1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA 848151 AGACAGGGCT Statistics Matches: 30, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 30 1.00 ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50 Consensus pattern (2 bp): TA Found at i:850983 original size:2 final size:2 Alignment explanation

Indices: 850976--851034 Score: 75 Period size: 2 Copynumber: 29.5 Consensus size: 2 850966 AAGATAATTG * * * 850976 CT CT CT CT CT CT CT CT CT CT CAT -T CT CT CT CT CA CA CA CT CT 1 CT CT CT CT CT CT CT CT CT CT C-T CT CT CT CT CT CT CT CT CT CT 851018 CT CT CT CT CT CT CT CT C 1 CT CT CT CT CT CT CT CT C 851035 CGTCTGAATA Statistics Matches: 53, Mismatches: 2, Indels: 4 0.90 0.03 0.07 Matches are distributed among these distances: 1 1 0.02 2 51 0.96 3 1 0.02 ACGTcount: A:0.07, C:0.49, G:0.00, T:0.44 Consensus pattern (2 bp): CT Found at i:851217 original size:5 final size:5 Alignment explanation

Indices: 851207--851307 Score: 118 Period size: 5 Copynumber: 20.4 Consensus size: 5 851197 GTATAAATTC * * * 851207 CGTTT CGTTT CGTTT CGATT --TTT GGTTT CGTTT CGTTT TGTTT CGTTT 1 CGTTT CGTTT CGTTT CGTTT CGTTT CGTTT CGTTT CGTTT CGTTT CGTTT * * 851255 CGTTT CGATT GGTTT CGTTT CGTTT CG-TT CGATTT CGTTT CGATTT CGTTT 1 CGTTT CGTTT CGTTT CGTTT CGTTT CGTTT CG-TTT CGTTT CG-TTT CGTTT 851306 CG 1 CG 851308 CACTTTACAG Statistics Matches: 82, Mismatches: 9, Indels: 10 0.81 0.09 0.10 Matches are distributed among these distances: 3 2 0.02 4 4 0.05 5 67 0.82 6 9 0.11 ACGTcount: A:0.04, C:0.17, G:0.22, T:0.57 Consensus pattern (5 bp): CGTTT Found at i:853940 original size:2 final size:2 Alignment explanation

Indices: 853933--853959 Score: 54 Period size: 2 Copynumber: 13.5 Consensus size: 2 853923 AATTAGGCCA 853933 TC TC TC TC TC TC TC TC TC TC TC TC TC T 1 TC TC TC TC TC TC TC TC TC TC TC TC TC T 853960 TAAGATGTCC Statistics Matches: 25, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 25 1.00 ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52 Consensus pattern (2 bp): TC Found at i:862776 original size:15 final size:14 Alignment explanation

Indices: 862744--862788 Score: 54 Period size: 15 Copynumber: 3.1 Consensus size: 14 862734 GTGGTACTTT * * 862744 TTTGTTTTTGTTTG 1 TTTGTTTTTTTTTA 862758 TTTGGTTTTTTTTTA 1 TTT-GTTTTTTTTTA 862773 TTTGTTTCTTTTTTA 1 TTTGTTT-TTTTTTA 862788 T 1 T 862789 ATTCTCTAAA Statistics Matches: 27, Mismatches: 2, Indels: 3 0.84 0.06 0.09 Matches are distributed among these distances: 14 7 0.26 15 20 0.74 ACGTcount: A:0.04, C:0.02, G:0.13, T:0.80 Consensus pattern (14 bp): TTTGTTTTTTTTTA Found at i:862785 original size:19 final size:19 Alignment explanation

Indices: 862742--862786 Score: 54 Period size: 19 Copynumber: 2.3 Consensus size: 19 862732 AAGTGGTACT * * 862742 TTTTTGTTTTTGTTTGTTTG 1 TTTTT-TTTTTATTTGTTTC * 862762 GTTTTTTTTTATTTGTTTC 1 TTTTTTTTTTATTTGTTTC 862781 TTTTTT 1 TTTTTT 862787 ATATTCTCTA Statistics Matches: 21, Mismatches: 4, Indels: 1 0.81 0.15 0.04 Matches are distributed among these distances: 19 17 0.81 20 4 0.19 ACGTcount: A:0.02, C:0.02, G:0.13, T:0.82 Consensus pattern (19 bp): TTTTTTTTTTATTTGTTTC Found at i:867394 original size:106 final size:106 Alignment explanation

Indices: 867226--867424 Score: 380 Period size: 106 Copynumber: 1.9 Consensus size: 106 867216 TTCTTTATAT * 867226 GCGTTAATGGAAACGTAGATCAGCAAGGGGTTCTTTGTCGTGCAAGCACCCACTTAATAGATTGT 1 GCGTTAATGGAAACGTAGATCAGCAAGGGGTTCTTTGTCATGCAAGCACCCACTTAATAGATTGT 867291 TACACGGATCTAAAACGATGACAAATATTTTTTCCGTTATG 66 TACACGGATCTAAAACGATGACAAATATTTTTTCCGTTATG * 867332 GCGTTAATGGAAACGTAGATCAGCAAGGGGTTCTTTGTCATGCAAGCACCTACTTAATAGATTGT 1 GCGTTAATGGAAACGTAGATCAGCAAGGGGTTCTTTGTCATGCAAGCACCCACTTAATAGATTGT 867397 TACACGGATCTAAAACGATGACAAATAT 66 TACACGGATCTAAAACGATGACAAATAT 867425 CGAAAAGGCA Statistics Matches: 91, Mismatches: 2, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 106 91 1.00 ACGTcount: A:0.32, C:0.18, G:0.22, T:0.29 Consensus pattern (106 bp): GCGTTAATGGAAACGTAGATCAGCAAGGGGTTCTTTGTCATGCAAGCACCCACTTAATAGATTGT TACACGGATCTAAAACGATGACAAATATTTTTTCCGTTATG Done.