Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Chr12 ID=Chr12-JGI_221_v2.0

Parameters: 2 7 7 80 10 50 1000

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

Length: 35429946
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33

Warning! 509281 characters in sequence are not A, C, G, or T


File 91 of 120

Found at i:27072738 original size:15 final size:15

Alignment explanation

Indices: 27072718--27072749 Score: 64 Period size: 15 Copynumber: 2.1 Consensus size: 15 27072708 CAAAATAAGC 27072718 TAGTTTAAATATAAT 1 TAGTTTAAATATAAT 27072733 TAGTTTAAATATAAT 1 TAGTTTAAATATAAT 27072748 TA 1 TA 27072750 CATACAATTT Statistics Matches: 17, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 15 17 1.00 ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47 Consensus pattern (15 bp): TAGTTTAAATATAAT Found at i:27076792 original size:30 final size:30 Alignment explanation

Indices: 27076733--27076812 Score: 99 Period size: 30 Copynumber: 2.7 Consensus size: 30 27076723 ACACAAAGTG * 27076733 CTTGGAAACTATAA-CACTAGTACATAGTA 1 CTTGGAAACTATAATCACCAGTACATAGTA * * * 27076762 CTTGGAAACTGTAATCACCGGTATATAGTA 1 CTTGGAAACTATAATCACCAGTACATAGTA * * 27076792 CCTGGAAACTAAAATCACCAG 1 CTTGGAAACTATAATCACCAG 27076813 CACCTAGTGC Statistics Matches: 42, Mismatches: 8, Indels: 1 0.82 0.16 0.02 Matches are distributed among these distances: 29 13 0.31 30 29 0.69 ACGTcount: A:0.39, C:0.20, G:0.16, T:0.25 Consensus pattern (30 bp): CTTGGAAACTATAATCACCAGTACATAGTA Found at i:27080378 original size:26 final size:26 Alignment explanation

Indices: 27080334--27080432 Score: 135 Period size: 26 Copynumber: 3.8 Consensus size: 26 27080324 TATCATCCTT * ** * 27080334 ATTTTACCTTTAGCGAAATTTTGACG 1 ATTTTACCCTTAGTAAAATTTTGATG * 27080360 ATTTTACCCTTGGTAAAATTTTGATG 1 ATTTTACCCTTAGTAAAATTTTGATG 27080386 ATTTTACCCTTAGTAAAATTTTGATG 1 ATTTTACCCTTAGTAAAATTTTGATG * * 27080412 ATTTTGCCCCTAGTAAAATTT 1 ATTTTACCCTTAGTAAAATTT 27080433 CGAGAAAATA Statistics Matches: 65, Mismatches: 8, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 26 65 1.00 ACGTcount: A:0.28, C:0.14, G:0.13, T:0.44 Consensus pattern (26 bp): ATTTTACCCTTAGTAAAATTTTGATG Found at i:27080592 original size:6 final size:6 Alignment explanation

Indices: 27080581--27080619 Score: 69 Period size: 6 Copynumber: 6.5 Consensus size: 6 27080571 GCAAATGAAT * 27080581 CATTTC CATTTC CATTTC CATTTC CATTTT CATTTC CAT 1 CATTTC CATTTC CATTTC CATTTC CATTTC CATTTC CAT 27080620 ATCTAGTTTT Statistics Matches: 31, Mismatches: 2, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 6 31 1.00 ACGTcount: A:0.18, C:0.31, G:0.00, T:0.51 Consensus pattern (6 bp): CATTTC Found at i:27090638 original size:20 final size:20 Alignment explanation

Indices: 27090604--27090657 Score: 72 Period size: 20 Copynumber: 2.6 Consensus size: 20 27090594 TATCTAAATA * 27090604 TTTAATATTATAATTTTATATT 1 TTTAAT-TTA-AATTTAATATT 27090626 TTTAATTTAAATTTAATATT 1 TTTAATTTAAATTTAATATT * 27090646 TTTATTTTAAAT 1 TTTAATTTAAAT 27090658 AAATCTAATT Statistics Matches: 30, Mismatches: 2, Indels: 2 0.88 0.06 0.06 Matches are distributed among these distances: 20 21 0.70 21 3 0.10 22 6 0.20 ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63 Consensus pattern (20 bp): TTTAATTTAAATTTAATATT Found at i:27093878 original size:28 final size:26 Alignment explanation

Indices: 27093841--27093928 Score: 81 Period size: 28 Copynumber: 3.2 Consensus size: 26 27093831 AATATGAAAA * 27093841 ATCAAGATTCATCCTTTCATTTCTCATC 1 ATCAAAATTCAT-CTTTCATTT-TCATC * * 27093869 ATCAAAATTCAT-TTGGTAATTGTTCTTC 1 ATCAAAATTCATCTT--TCATT-TTCATC 27093897 ATC-AAATTCATCTCTTCATTTTCATC 1 ATCAAAATTCATCT-TTCATTTTCATC 27093923 ATCAAA 1 ATCAAA 27093929 GTCTTTTTCT Statistics Matches: 49, Mismatches: 5, Indels: 13 0.73 0.07 0.19 Matches are distributed among these distances: 26 10 0.20 27 14 0.29 28 23 0.47 29 2 0.04 ACGTcount: A:0.30, C:0.23, G:0.05, T:0.43 Consensus pattern (26 bp): ATCAAAATTCATCTTTCATTTTCATC Found at i:27094709 original size:16 final size:16 Alignment explanation

Indices: 27094685--27094715 Score: 53 Period size: 16 Copynumber: 1.9 Consensus size: 16 27094675 GTTTATTTGC 27094685 ATTTAAAATTTTTTTA 1 ATTTAAAATTTTTTTA * 27094701 ATTTCAAATTTTTTT 1 ATTTAAAATTTTTTT 27094716 CAATATGTAT 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:0.32, C:0.03, G:0.00, T:0.65 Consensus pattern (16 bp): ATTTAAAATTTTTTTA Found at i:27095663 original size:3 final size:3 Alignment explanation

Indices: 27095657--27095681 Score: 50 Period size: 3 Copynumber: 8.3 Consensus size: 3 27095647 GACCACCACA 27095657 AAG AAG AAG AAG AAG AAG AAG AAG A 1 AAG AAG AAG AAG AAG AAG AAG AAG A 27095682 CGACAATCAT Statistics Matches: 22, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 3 22 1.00 ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00 Consensus pattern (3 bp): AAG Found at i:27102010 original size:41 final size:39 Alignment explanation

Indices: 27101942--27102055 Score: 140 Period size: 41 Copynumber: 2.8 Consensus size: 39 27101932 GAGTTTTTGG * 27101942 GGTCTTTAGCGGCATTTTCTGAAAAGCGCCGCTAATGCTC 1 GGTCTTTAGCGGCGTTTT-TGAAAAGCGCCGCTAATGCTC * 27101982 AGGTCTTTAGCGGCGTTTTTGAATAAGCGCTGCTAATGCTC 1 -GGTCTTTAGCGGCGTTTTTGAA-AAGCGCCGCTAATGCTC * 27102023 -GTACCTTTAGCGGCGTTTTTGAGGAAGCGCCGC 1 GGT--CTTTAGCGGCGTTTTTGA-AAAGCGCCGC 27102056 AAAAACATTT Statistics Matches: 65, Mismatches: 4, Indels: 8 0.84 0.05 0.10 Matches are distributed among these distances: 39 2 0.03 40 4 0.06 41 59 0.91 ACGTcount: A:0.18, C:0.23, G:0.28, T:0.31 Consensus pattern (39 bp): GGTCTTTAGCGGCGTTTTTGAAAAGCGCCGCTAATGCTC Found at i:27102200 original size:26 final size:26 Alignment explanation

Indices: 27102152--27102202 Score: 66 Period size: 26 Copynumber: 2.0 Consensus size: 26 27102142 AAAATGGATA ** * * 27102152 AATTTGAAATAATGACACGTAGAAAT 1 AATTTGAAATAAAAAAACATAGAAAT 27102178 AATTTGAAATAAAAAAACATAGAAA 1 AATTTGAAATAAAAAAACATAGAAA 27102203 AATATTTGTT Statistics Matches: 21, Mismatches: 4, Indels: 0 0.84 0.16 0.00 Matches are distributed among these distances: 26 21 1.00 ACGTcount: A:0.59, C:0.06, G:0.12, T:0.24 Consensus pattern (26 bp): AATTTGAAATAAAAAAACATAGAAAT Found at i:27102837 original size:89 final size:89 Alignment explanation

Indices: 27102687--27102890 Score: 365 Period size: 89 Copynumber: 2.3 Consensus size: 89 27102677 NNNNNNNNNN * * * 27102687 ATTAAATAATGTTTAAGGGTTA-GGGTTAGTGATTTAGGGTCGAGTTAGGGTTTAGGATTTAGAT 1 ATTAAATAATGTTTAGGGGTTAGGGGTTAGTGATTCAGGGTCGACTTAGGGTTTAGGATTTAGAT 27102751 TAATTAGTGTTTTTTAATTTATAT 66 TAATTAGTGTTTTTTAATTTATAT 27102775 ATTAAATAATGTTTAGGGGTTAGGGGTTAGTGATTCAGGGTCGACTTAGGGTTTAGGATTTAGAT 1 ATTAAATAATGTTTAGGGGTTAGGGGTTAGTGATTCAGGGTCGACTTAGGGTTTAGGATTTAGAT 27102840 TAATTAGTGTTTTTTAATTTATAT 66 TAATTAGTGTTTTTTAATTTATAT * 27102864 ATTAAATAATGTTTAGGGTTTAGGGGT 1 ATTAAATAATGTTTAGGGGTTAGGGGT 27102891 AGGGGTTTGG Statistics Matches: 111, Mismatches: 4, Indels: 1 0.96 0.03 0.01 Matches are distributed among these distances: 88 21 0.19 89 90 0.81 ACGTcount: A:0.28, C:0.02, G:0.26, T:0.44 Consensus pattern (89 bp): ATTAAATAATGTTTAGGGGTTAGGGGTTAGTGATTCAGGGTCGACTTAGGGTTTAGGATTTAGAT TAATTAGTGTTTTTTAATTTATAT Found at i:27103361 original size:2 final size:2 Alignment explanation

Indices: 27103349--27103392 Score: 81 Period size: 2 Copynumber: 22.5 Consensus size: 2 27103339 TATTTAAGAG 27103349 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT 1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT 27103390 AT A 1 AT A 27103393 GATCACTTTA Statistics Matches: 41, Mismatches: 0, Indels: 2 0.95 0.00 0.05 Matches are distributed among these distances: 1 1 0.02 2 40 0.98 ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48 Consensus pattern (2 bp): AT Found at i:27103686 original size:23 final size:22 Alignment explanation

Indices: 27103639--27103693 Score: 60 Period size: 23 Copynumber: 2.5 Consensus size: 22 27103629 TAATTTTATC 27103639 AAAAACTTT--TAAATATTACT 1 AAAAACTTTAATAAATATTACT * * 27103659 TAAAACTTTAATAATTATTTACT 1 AAAAACTTTAATAAATA-TTACT * 27103682 AAAAATTTTAAT 1 AAAAACTTTAAT 27103694 GAAAATACAA Statistics Matches: 28, Mismatches: 4, Indels: 3 0.80 0.11 0.09 Matches are distributed among these distances: 20 8 0.29 22 5 0.18 23 15 0.54 ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44 Consensus pattern (22 bp): AAAAACTTTAATAAATATTACT Found at i:27105904 original size:33 final size:33 Alignment explanation

Indices: 27105867--27105929 Score: 108 Period size: 33 Copynumber: 1.9 Consensus size: 33 27105857 GATCTTTAAG ** 27105867 TTGGTTATATTTTTTTTGTATAGTTTAATTTTT 1 TTGGTTATATTTTAGTTGTATAGTTTAATTTTT 27105900 TTGGTTATATTTTAGTTGTATAGTTTAATT 1 TTGGTTATATTTTAGTTGTATAGTTTAATT 27105930 ATTATTTTTC Statistics Matches: 28, Mismatches: 2, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 33 28 1.00 ACGTcount: A:0.21, C:0.00, G:0.14, T:0.65 Consensus pattern (33 bp): TTGGTTATATTTTAGTTGTATAGTTTAATTTTT Found at i:27106988 original size:9 final size:9 Alignment explanation

Indices: 27106976--27107806 Score: 190 Period size: 9 Copynumber: 92.1 Consensus size: 9 27106966 TTAAAATAGT 27106976 TAACTTACA 1 TAACTTACA 27106985 TAACTTA-A 1 TAACTTACA 27106993 TGAA-TTA-A 1 T-AACTTACA * * 27107001 T-ATTATATA 1 TAACT-TACA 27107010 TAACTTACA 1 TAACTTACA 27107019 TAACTTAC- 1 TAACTTACA 27107027 -AACTTACA 1 TAACTTACA 27107035 TAACTTACA 1 TAACTTACA * 27107044 TTAATATTAAACA 1 -TAA-CTT--ACA * 27107057 TAAATTACA 1 TAACTTACA 27107066 TAACTTACA 1 TAACTTACA * 27107075 TTAATATTATACA 1 -T-A-ACT-TACA * 27107088 TAAATTACA 1 TAACTTACA 27107097 TAACTTA-A 1 TAACTTACA 27107105 TTAA-TTA-A 1 -TAACTTACA * 27107113 T-ATTATACA 1 TAACT-TACA * 27107122 TAAATTACA 1 TAACTTACA 27107131 TAACTTA-A 1 TAACTTACA 27107139 TTAA-TTA-A 1 -TAACTTACA * 27107147 T-ATTATACA 1 TAACT-TACA * 27107156 TAAATTACA 1 TAACTTACA 27107165 TAACTTACA 1 TAACTTACA * 27107174 TTAATATTATACA 1 -T-A-ACT-TACA * 27107187 TAAATTACA 1 TAACTTACA 27107196 TAACTTA-A 1 TAACTTACA 27107204 TTAA-TTA-A 1 -TAACTTACA * 27107212 T-ATTATACA 1 TAACT-TACA * 27107221 TAAATTACA 1 TAACTTACA * 27107230 TAACTTGCA 1 TAACTTACA * 27107239 TTAATATTATACA 1 -T-A-ACT-TACA * 27107252 TAAATTACA 1 TAACTTACA * 27107261 TGACTTA-A 1 TAACTTACA 27107269 TTAA-TTA-A 1 -TAACTTACA * * 27107277 T-ATTATACC 1 TAACT-TACA * 27107286 TAAGTTACA 1 TAACTTACA 27107295 TAACTTACA 1 TAACTTACA * 27107304 TTAATGCAATACA 1 -TAA--C-TTACA * 27107317 TAAATTACA 1 TAACTTACA 27107326 TAACTTA-A 1 TAACTTACA 27107334 TTAA-TTA-A 1 -TAACTTACA * 27107342 T-ATTATACA 1 TAACT-TACA 27107351 TAACTTACA 1 TAACTTACA * 27107360 TAAGTTAC- 1 TAACTTACA 27107368 -AACTTACA 1 TAACTTACA * * 27107376 CAACTTACTT 1 TAACTTAC-A *** 27107386 TTTTTTA-A 1 TAACTTACA * 27107394 TTA-TT-CA 1 TAACTTACA * 27107401 TAAATTACA 1 TAACTTACA 27107410 TAACTTACA 1 TAACTTACA * 27107419 TTAATGCAATACA 1 -TAA--C-TTACA * 27107432 TAAATTACA 1 TAACTTACA 27107441 TAACTTA-A 1 TAACTTACA * 27107449 TTAA-ATA-A 1 -TAACTTACA * 27107457 T-ATTATACA 1 TAACT-TACA 27107466 TAACTTACA 1 TAACTTACA 27107475 TAACTTAC- 1 TAACTTACA 27107483 -AACTTACA 1 TAACTTACA * 27107491 TAACTTACTT 1 TAACTTAC-A *** 27107501 TTTTTTA-A 1 TAACTTACA * 27107509 TTA-TT-CA 1 TAACTTACA * 27107516 TAAATTACA 1 TAACTTACA 27107525 TAACTTACA 1 TAACTTACA * 27107534 TTAATGCAATACA 1 -TAA--C-TTACA * 27107547 TAAATTACA 1 TAACTTACA 27107556 TAACTTA-A 1 TAACTTACA 27107564 TTAA-TTA-A 1 -TAACTTACA * 27107572 T-ATTATACA 1 TAACT-TACA 27107581 TAACTTACA 1 TAACTTACA 27107590 TAACTTACA 1 TAACTTACA *** 27107599 TTTGTTTA-A 1 -TAACTTACA * 27107608 TTA-TT-CA 1 TAACTTACA * 27107615 TAAATTACA 1 TAACTTACA * 27107624 TAACTTACT 1 TAACTTACA * * 27107633 TAATTTTCA 1 TAACTTACA * 27107642 TAA--TAAA 1 TAACTTACA 27107649 TAACTTACA 1 TAACTTACA 27107658 TAACTTACA 1 TAACTTACA * 27107667 TTAATATTATACA 1 -T-A-ACT-TACA * 27107680 TAAATTACA 1 TAACTTACA 27107689 TAACTTA-A 1 TAACTTACA 27107697 TTAA-TATACA 1 -TAACT-TACA * 27107707 TAAATTACA 1 TAACTTACA 27107716 TAACTTACA 1 TAACTTACA * 27107725 TTAATATTATACA 1 -T-A-ACT-TACA * 27107738 TAAATTACA 1 TAACTTACA ** 27107747 TAACTTAGT 1 TAACTTACA 27107756 TAA-TT-CA 1 TAACTTACA * 27107763 T-ATTATACA 1 TAACT-TACA 27107772 TAACTTACA 1 TAACTTACA 27107781 TAACTTAC- 1 TAACTTACA 27107789 -AACTTACA 1 TAACTTACA 27107797 TAACTTACA 1 TAACTTACA 27107806 T 1 T 27107807 TTTTAATTAT Statistics Matches: 628, Mismatches: 88, Indels: 212 0.68 0.09 0.23 Matches are distributed among these distances: 6 9 0.01 7 63 0.10 8 74 0.12 9 345 0.55 10 58 0.09 11 15 0.02 12 30 0.05 13 34 0.05 ACGTcount: A:0.46, C:0.13, G:0.01, T:0.39 Consensus pattern (9 bp): TAACTTACA Found at i:27107032 original size:16 final size:16 Alignment explanation

Indices: 27107011--27107043 Score: 66 Period size: 16 Copynumber: 2.1 Consensus size: 16 27107001 TATTATATAT 27107011 AACTTACATAACTTAC 1 AACTTACATAACTTAC 27107027 AACTTACATAACTTAC 1 AACTTACATAACTTAC 27107043 A 1 A 27107044 TTAATATTAA Statistics Matches: 17, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 16 17 1.00 ACGTcount: A:0.45, C:0.24, G:0.00, T:0.30 Consensus pattern (16 bp): AACTTACATAACTTAC Found at i:27107065 original size:47 final size:49 Alignment explanation

Indices: 27106977--27107074 Score: 137 Period size: 47 Copynumber: 2.0 Consensus size: 49 27106967 TAAAATAGTT * * * 27106977 AACTTACATAACTTAATGAATTAATATTATATATAACTTACATAACTTAC 1 AACTTACATAACTTAA-GAATTAATATTAAACATAAATTACATAACTTAC * 27107027 AACTTACATAACTT-A-CATTAATATTAAACATAAATTACATAACTTAC 1 AACTTACATAACTTAAGAATTAATATTAAACATAAATTACATAACTTAC 27107074 A 1 A 27107075 TTAATATTAT Statistics Matches: 44, Mismatches: 4, Indels: 3 0.86 0.08 0.06 Matches are distributed among these distances: 47 29 0.66 49 1 0.02 50 14 0.32 ACGTcount: A:0.48, C:0.15, G:0.01, T:0.36 Consensus pattern (49 bp): AACTTACATAACTTAAGAATTAATATTAAACATAAATTACATAACTTAC Found at i:27107123 original size:65 final size:65 Alignment explanation

Indices: 27107043--27107789 Score: 486 Period size: 65 Copynumber: 11.5 Consensus size: 65 27107033 CATAACTTAC * 27107043 ATTAATATTAAACATAAATTACATAACTTACATTAATATTATACATAAATTACATAACTTAATTA 1 ATTAATATTATACATAAATTACATAACTTACATTAATATTATACATAAATTACATAACTTAATTA * 27107108 ATTAATATTATACATAAATTACATAACTTAATTAATTAATATTATACATAAATTACATAACTT-A 1 ATTAATATTATACATAAATTACATAACTT-A--CATTAATATTATACATAAATTACATAACTTAA * 27107172 --C 63 TTA * 27107173 ATTAATATTATACATAAATTACATAACTTAATTAATTAATATTATACATAAATTACATAAC-T-- 1 ATTAATATTATACATAAATTACATAACTT-A--CATTAATATTATACATAAATTACATAACTTAA ** 27107235 TGC 63 TTA * * * * 27107238 ATTAATATTATACATAAATTACATGACTTAATTAATTAATATTATACCTAAGTTACATAACTTAC 1 ATTAATATTATACATAAATTACATAACTT-A--CATTAATATTATACATAAATTACATAACTTA- 27107303 ATTA 62 ATTA ** * * * 27107307 A-T-GCA--ATACATAAATTACATAACTTAATTAATTAATATTATACATAACTTACATAAGTTAC 1 ATTAATATTATACATAAATTACATAACTT-A--CATTAATATTATACATAAATTACATAACTT-- 27107368 AACTTACACA 61 AA-TT----A * * * * * *** 27107378 ACTTACTTTTTTTTA-ATTATTCATAAATTACATAACTTACATTAATGCAATACATAAATTACAT 1 A-TTA--ATATTATACA-TA--AATT----ACATAACTTACATTAATATTATACATAAATTACAT 27107442 AACTTAATTA 56 AACTTAATTA * * * * * *** 27107452 AATAATATTATACATAACTTACATAACTTAC----A-ACT-TACATAACTTACTTTTTTTTAATT 1 ATTAATATTATACATAAATTACATAACTTACATTAATATTATACATAAATTAC-ATAACTTAATT 27107511 - 65 A * * * ** 27107511 ATTCATA-AATTACATAACTTAC---A-TTA-A-T-GCA--ATACATAAATTACATAACTTAATT 1 ATTAATATTA-TACATAAATTACATAACTTACATTAATATTATACATAAATTACATAACTTAATT 27107566 A 65 A * ** * * 27107567 ATTAATATTATACATAACTTACATAACTTACATTTGTTTAATTATTCATAAATTACATAACTTAC 1 ATTAATATTATACATAAATTACATAACTTACA-TT-AAT-ATTATACATAAATTACATAACTTAA 27107632 TTA 63 TTA * * * * 27107635 ATT-TTCATAATAAATAACTTACATAACTTACATTAATATTATACATAAATTACATAAC----TT 1 ATTAAT-ATTATACATAAATTACATAACTTACATTAATATTATACATAAATTACATAACTTAATT 27107695 A 65 A * 27107696 ATT-A-A-TATACATAAATTACATAACTTACATTAATATTATACATAAATTACATAACTTAGTTA 1 ATTAATATTATACATAAATTACATAACTTACATTAATATTATACATAAATTACATAACTTAATTA * * 27107758 ATTCATATTATACATAACTTACATAACTTACA 1 ATTAATATTATACATAAATTACATAACTTACA 27107790 ACTTACATAA Statistics Matches: 557, Mismatches: 66, Indels: 118 0.75 0.09 0.16 Matches are distributed among these distances: 55 10 0.02 56 30 0.05 57 2 0.00 58 48 0.09 59 30 0.05 60 11 0.02 61 8 0.01 62 6 0.01 63 2 0.00 64 2 0.00 65 252 0.45 66 5 0.01 67 8 0.01 68 80 0.14 69 3 0.01 71 9 0.02 72 1 0.00 73 3 0.01 74 2 0.00 77 1 0.00 78 6 0.01 79 2 0.00 80 2 0.00 81 24 0.04 83 1 0.00 84 9 0.02 ACGTcount: A:0.46, C:0.13, G:0.01, T:0.40 Consensus pattern (65 bp): ATTAATATTATACATAAATTACATAACTTACATTAATATTATACATAAATTACATAACTTAATTA Found at i:27107132 original size:43 final size:34 Alignment explanation

Indices: 27107043--27107787 Score: 559 Period size: 34 Copynumber: 21.9 Consensus size: 34 27107033 CATAACTTAC * * 27107043 ATTAATATTAAACATAAATTACATAACTT-A--C 1 ATTAATATTATACATAAATTACATAACTTAATTA 27107074 ATTAATATTATACATAAATTACATAACTTAATTA 1 ATTAATATTATACATAAATTACATAACTTAATTA 27107108 ATTAATATTATACATAAATTACATAACTTAATTA 1 ATTAATATTATACATAAATTACATAACTTAATTA * 27107142 ATTAATATTATACATAAATTACATAACTT-A--C 1 ATTAATATTATACATAAATTACATAACTTAATTA 27107173 ATTAATATTATACATAAATTACATAACTTAATTA 1 ATTAATATTATACATAAATTACATAACTTAATTA ** 27107207 ATTAATATTATACATAAATTACATAAC-T--TGC 1 ATTAATATTATACATAAATTACATAACTTAATTA * 27107238 ATTAATATTATACATAAATTACATGACTTAATTA 1 ATTAATATTATACATAAATTACATAACTTAATTA * * 27107272 ATTAATATTATACCTAAGTTACATAACTTACATTA 1 ATTAATATTATACATAAATTACATAACTTA-ATTA ** 27107307 A-T-GCA--ATACATAAATTACATAACTTAATTA 1 ATTAATATTATACATAAATTACATAACTTAATTA * * 27107337 ATTAATATTATACATAACTTACATAAGTTACAACTTA 1 ATTAATATTATACATAAATTACATAACTT--AA-TTA * *** * * 27107374 CA-CAACTTACTT-TTTTTTAATTATTCATAAATTACA-TA 1 -ATTAA--TA-TTATACATAAATTA--CATAACTTA-ATTA * 27107412 ACTTACATTAATGCAATACATAAATTACATAACTTAATTA 1 A-TTA-A-T-AT--TATACATAAATTACATAACTTAATTA * * 27107452 AATAATATTATACATAACTTACATAACTTACAACTTA 1 ATTAATATTATACATAAATTACATAACTT--AA-TTA *** * * 27107489 CA-TAACTTACTT-TTTTTTAATTATTCATAAATTACA-TA 1 -ATTAA--TA-TTATACATAAATTA--CATAACTTA-ATTA * 27107527 ACTTACATTAATGCAATACATAAATTACATAACTTAATTA 1 A-TTA-A-T-AT--TATACATAAATTACATAACTTAATTA * * 27107567 ATTAATATTATACATAACTTACATAACTTACATTT 1 ATTAATATTATACATAAATTACATAACTTA-ATTA * * * * 27107602 GTTTA-ATTATTCATAAATTACATAACTTACTTA 1 ATTAATATTATACATAAATTACATAACTTAATTA * * * * * 27107635 ATT-TTCATAATAAATAACTTACATAACTT-A--C 1 ATTAAT-ATTATACATAAATTACATAACTTAATTA 27107666 ATTAATATTATACATAAATTACATAAC----TTA 1 ATTAATATTATACATAAATTACATAACTTAATTA * 27107696 ATT-A-A-TATACATAAATTACATAACTT-A-C- 1 ATTAATATTATACATAAATTACATAACTTAATTA * 27107724 ATTAATATTATACATAAATTACATAACTTAGTTA 1 ATTAATATTATACATAAATTACATAACTTAATTA * * 27107758 ATTCATATTATACATAACTTACATAACTTA 1 ATTAATATTATACATAAATTACATAACTTA 27107788 CAACTTACAT Statistics Matches: 573, Mismatches: 76, Indels: 127 0.74 0.10 0.16 Matches are distributed among these distances: 27 19 0.03 28 4 0.01 29 2 0.00 30 9 0.02 31 146 0.25 32 5 0.01 33 7 0.01 34 245 0.43 35 11 0.02 36 8 0.01 37 15 0.03 38 8 0.01 39 34 0.06 40 32 0.06 41 14 0.02 42 14 0.02 ACGTcount: A:0.46, C:0.13, G:0.01, T:0.40 Consensus pattern (34 bp): ATTAATATTATACATAAATTACATAACTTAATTA Found at i:27107397 original size:50 final size:50 Alignment explanation

Indices: 27107343--27107533 Score: 157 Period size: 50 Copynumber: 3.5 Consensus size: 50 27107333 ATTAATTAAT * * * 27107343 ATTATACATAACTTACATAAGTTACAACTTACACAACTTACTTTTTTTTA 1 ATTATACATAAATTACATAACTTACAACTTACATAACTTACTTTTTTTTA * * * * * 27107393 ATTATTCATAAATTACATAACTTACATTAATGCAATACATAAATTACATAACTTAATTAAATAA 1 ATTATACATAAATTACATAACTTAC---AA--C-TTACATAACTTAC-T---TT--TT--TTTA * 27107457 TATTATACATAACTTACATAACTTACAACTTACATAACTTACTTTTTTTTA 1 -ATTATACATAAATTACATAACTTACAACTTACATAACTTACTTTTTTTTA * 27107508 ATTATTCATAAATTACATAACTTACA 1 ATTATACATAAATTACATAACTTACA 27107534 TTAATGCAAT Statistics Matches: 110, Mismatches: 16, Indels: 30 0.71 0.10 0.19 Matches are distributed among these distances: 50 46 0.42 51 2 0.02 53 4 0.04 55 3 0.03 56 10 0.09 57 1 0.01 58 1 0.01 59 11 0.10 60 3 0.03 62 4 0.04 64 2 0.02 65 23 0.21 ACGTcount: A:0.43, C:0.16, G:0.01, T:0.40 Consensus pattern (50 bp): ATTATACATAAATTACATAACTTACAACTTACATAACTTACTTTTTTTTA Found at i:27107416 original size:115 final size:115 Alignment explanation

Indices: 27107290--27107598 Score: 591 Period size: 115 Copynumber: 2.7 Consensus size: 115 27107280 TATACCTAAG 27107290 TTACATAACTTACATTAATGCAATACATAAATTACATAACTTAATTAATTAATATTATACATAAC 1 TTACATAACTTACATTAATGCAATACATAAATTACATAACTTAATTAATTAATATTATACATAAC * 27107355 TTACATAAGTTACAACTTACACAACTTACTTTTTTTTAATTATTCATAAA 66 TTACATAACTTACAACTTACACAACTTACTTTTTTTTAATTATTCATAAA * 27107405 TTACATAACTTACATTAATGCAATACATAAATTACATAACTTAATTAAATAATATTATACATAAC 1 TTACATAACTTACATTAATGCAATACATAAATTACATAACTTAATTAATTAATATTATACATAAC * 27107470 TTACATAACTTACAACTTACATAACTTACTTTTTTTTAATTATTCATAAA 66 TTACATAACTTACAACTTACACAACTTACTTTTTTTTAATTATTCATAAA 27107520 TTACATAACTTACATTAATGCAATACATAAATTACATAACTTAATTAATTAATATTATACATAAC 1 TTACATAACTTACATTAATGCAATACATAAATTACATAACTTAATTAATTAATATTATACATAAC 27107585 TTACATAACTTACA 66 TTACATAACTTACA 27107599 TTTGTTTAAT Statistics Matches: 190, Mismatches: 4, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 115 190 1.00 ACGTcount: A:0.45, C:0.15, G:0.01, T:0.39 Consensus pattern (115 bp): TTACATAACTTACATTAATGCAATACATAAATTACATAACTTAATTAATTAATATTATACATAAC TTACATAACTTACAACTTACACAACTTACTTTTTTTTAATTATTCATAAA Found at i:27107421 original size:25 final size:25 Alignment explanation

Indices: 27107393--27107498 Score: 58 Period size: 25 Copynumber: 4.0 Consensus size: 25 27107383 CTTTTTTTTA 27107393 ATTATTCATAAATTACATAACTTAC 1 ATTATTCATAAATTACATAACTTAC 27107418 ATTAATGCAATACATAAATTACATAACTTA- 1 ATT-AT----T-CATAAATTACATAACTTAC * 27107448 ATTA--AATAATATTATACATAACTTAC 1 ATTATTCATAA-A-T-TACATAACTTAC * * * 27107474 ATAACTT-ACAACTTACATAACTTAC 1 ATTA-TTCATAAATTACATAACTTAC 27107499 TTTTTTTTAA Statistics Matches: 64, Mismatches: 4, Indels: 26 0.68 0.04 0.28 Matches are distributed among these distances: 22 4 0.06 23 1 0.02 24 1 0.02 25 26 0.41 26 6 0.09 28 3 0.05 29 1 0.02 30 4 0.06 31 18 0.28 ACGTcount: A:0.47, C:0.16, G:0.01, T:0.36 Consensus pattern (25 bp): ATTATTCATAAATTACATAACTTAC Found at i:27107488 original size:16 final size:16 Alignment explanation

Indices: 27107467--27107498 Score: 64 Period size: 16 Copynumber: 2.0 Consensus size: 16 27107457 TATTATACAT 27107467 AACTTACATAACTTAC 1 AACTTACATAACTTAC 27107483 AACTTACATAACTTAC 1 AACTTACATAACTTAC 27107499 TTTTTTTTAA Statistics Matches: 16, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 16 16 1.00 ACGTcount: A:0.44, C:0.25, G:0.00, T:0.31 Consensus pattern (16 bp): AACTTACATAACTTAC Found at i:27107656 original size:25 final size:28 Alignment explanation

Indices: 27107505--27107570 Score: 60 Period size: 31 Copynumber: 2.2 Consensus size: 28 27107495 TTACTTTTTT * 27107505 TTAATTATTCATAAATTACATAACTTAC 1 TTAATTATTCATAAATTAAATAACTTAC * * * * 27107533 ATTAATGCAATACATAAATTACATAACTTAA 1 -TTAAT--TATTCATAAATTAAATAACTTAC 27107564 TTAATTA 1 TTAATTA 27107571 ATATTATACA Statistics Matches: 31, Mismatches: 4, Indels: 5 0.77 0.10 0.12 Matches are distributed among these distances: 28 1 0.03 29 5 0.16 30 5 0.16 31 20 0.65 ACGTcount: A:0.47, C:0.12, G:0.02, T:0.39 Consensus pattern (28 bp): TTAATTATTCATAAATTAAATAACTTAC Found at i:27107794 original size:16 final size:16 Alignment explanation

Indices: 27107773--27107805 Score: 66 Period size: 16 Copynumber: 2.1 Consensus size: 16 27107763 TATTATACAT 27107773 AACTTACATAACTTAC 1 AACTTACATAACTTAC 27107789 AACTTACATAACTTAC 1 AACTTACATAACTTAC 27107805 A 1 A 27107806 TTTTTAATTA Statistics Matches: 17, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 16 17 1.00 ACGTcount: A:0.45, C:0.24, G:0.00, T:0.30 Consensus pattern (16 bp): AACTTACATAACTTAC Found at i:27111242 original size:66 final size:65 Alignment explanation

Indices: 27111135--27111300 Score: 226 Period size: 66 Copynumber: 2.5 Consensus size: 65 27111125 GAGCAAATTA * * * * 27111135 CACAACTTAAAGCGGAGGCAACATCGAGAGAAGCTGAGGTTCAA-AAAAGATATGAAGAACTCCA 1 CACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAG-TATGAAGAACTCCA 27111199 G 65 G * 27111200 CTACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACGAAAGTATGAAGAACTCCA 1 C-ACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAGTATGAAGAACTCCA 27111265 G 65 G * * * 27111266 CAGCAGCTTAAAGCAGATGCGGCAGCAAGAGAAGC 1 CA-CAACTTAAAGCAGATGCAGCAGCGAGAGAAGC 27111301 AAAGGCGGCA Statistics Matches: 90, Mismatches: 8, Indels: 5 0.87 0.08 0.05 Matches are distributed among these distances: 65 2 0.02 66 84 0.93 67 4 0.04 ACGTcount: A:0.40, C:0.20, G:0.27, T:0.13 Consensus pattern (65 bp): CACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAGTATGAAGAACTCCAG Found at i:27111332 original size:21 final size:21 Alignment explanation

Indices: 27111303--27111388 Score: 100 Period size: 21 Copynumber: 4.1 Consensus size: 21 27111293 AGAGAAGCAA * * * 27111303 AGGCGGCAGCGAGAGAAGTAC 1 AGGCTGCAGCGAGGGAAGTAG * * 27111324 AAGCTGCAGCGAGGGAAGCAG 1 AGGCTGCAGCGAGGGAAGTAG ** 27111345 AGGCTATAGCGAGGGAAGTAG 1 AGGCTGCAGCGAGGGAAGTAG * 27111366 AGGCTGCAGCGAGGGAAGCAG 1 AGGCTGCAGCGAGGGAAGTAG 27111387 AG 1 AG 27111389 CAGCGTCAAA Statistics Matches: 53, Mismatches: 12, Indels: 0 0.82 0.18 0.00 Matches are distributed among these distances: 21 53 1.00 ACGTcount: A:0.33, C:0.16, G:0.44, T:0.07 Consensus pattern (21 bp): AGGCTGCAGCGAGGGAAGTAG Found at i:27111333 original size:42 final size:42 Alignment explanation

Indices: 27111287--27111385 Score: 117 Period size: 42 Copynumber: 2.4 Consensus size: 42 27111277 AGCAGATGCG * * * 27111287 GCAGCAAGAGAAGCAAAGGCGGCAGCGAGAGAAGTACAAGCT 1 GCAGCGAGGGAAGCAAAGGCGACAGCGAGAGAAGTACAAGCT * * * * * * 27111329 GCAGCGAGGGAAGCAGAGGCTATAGCGAGGGAAGTAGAGGCT 1 GCAGCGAGGGAAGCAAAGGCGACAGCGAGAGAAGTACAAGCT 27111371 GCAGCGAGGGAAGCA 1 GCAGCGAGGGAAGCA 27111386 GAGCAGCGTC Statistics Matches: 48, Mismatches: 9, Indels: 0 0.84 0.16 0.00 Matches are distributed among these distances: 42 48 1.00 ACGTcount: A:0.35, C:0.17, G:0.41, T:0.06 Consensus pattern (42 bp): GCAGCGAGGGAAGCAAAGGCGACAGCGAGAGAAGTACAAGCT Found at i:27111851 original size:44 final size:43 Alignment explanation

Indices: 27111720--27111855 Score: 164 Period size: 43 Copynumber: 3.1 Consensus size: 43 27111710 AGGTGTTGGC * * * * * * 27111720 CTTTAGTGGCATTTTTGGTAAAAGCGCCGCTAAATATAAGGGT 1 CTTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGATCAGGGT * * * 27111763 CTTTAGCGGCGTTTGTGGAAAAAGTGCCACTAAAGATCATGGT 1 CTTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGATCAGGGT * * 27111806 CTTTAGCGGCGTTTGTGGGGAAAAGCGCCGCTAGAGATCAGGGT 1 CTTTAGCGGCGTTTGT-GGAAAAAGCGCCGCTAAAGATCAGGGT 27111850 CTTTAG 1 CTTTAG 27111856 AGGTGCTTCC Statistics Matches: 78, Mismatches: 14, Indels: 1 0.84 0.15 0.01 Matches are distributed among these distances: 43 50 0.64 44 28 0.36 ACGTcount: A:0.25, C:0.16, G:0.30, T:0.29 Consensus pattern (43 bp): CTTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGATCAGGGT Found at i:27112052 original size:31 final size:31 Alignment explanation

Indices: 27112017--27112088 Score: 126 Period size: 31 Copynumber: 2.3 Consensus size: 31 27112007 CTTTTCAAAG * 27112017 CGCCGCTAAAAGTATTTGCGGCGCTAAAAAA 1 CGCCGCTAAAAGTATTTGCGGCACTAAAAAA * 27112048 CGCCGCTAAAAGTATTTGCGGCACTAAAAAG 1 CGCCGCTAAAAGTATTTGCGGCACTAAAAAA 27112079 CGCCGCTAAA 1 CGCCGCTAAA 27112089 GGCCTAAAAA Statistics Matches: 39, Mismatches: 2, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 31 39 1.00 ACGTcount: A:0.35, C:0.25, G:0.22, T:0.18 Consensus pattern (31 bp): CGCCGCTAAAAGTATTTGCGGCACTAAAAAA Found at i:27112101 original size:22 final size:22 Alignment explanation

Indices: 27112073--27112116 Score: 72 Period size: 22 Copynumber: 2.0 Consensus size: 22 27112063 TTGCGGCACT 27112073 AAAAAGCGCCGC-TAAAGGCCTA 1 AAAAAGCGCCGCTTAAA-GCCTA 27112095 AAAAAGCGCCGCTTAAAGCCTA 1 AAAAAGCGCCGCTTAAAGCCTA 27112117 TTTTGGTGTA Statistics Matches: 21, Mismatches: 0, Indels: 2 0.91 0.00 0.09 Matches are distributed among these distances: 22 17 0.81 23 4 0.19 ACGTcount: A:0.41, C:0.27, G:0.20, T:0.11 Consensus pattern (22 bp): AAAAAGCGCCGCTTAAAGCCTA Found at i:27115376 original size:9 final size:9 Alignment explanation

Indices: 27115362--27115392 Score: 53 Period size: 9 Copynumber: 3.4 Consensus size: 9 27115352 GTTAAACGAA 27115362 TCGAGTTAT 1 TCGAGTTAT * 27115371 TCGAGTTAA 1 TCGAGTTAT 27115380 TCGAGTTAT 1 TCGAGTTAT 27115389 TCGA 1 TCGA 27115393 ATCAACTCGA Statistics Matches: 20, Mismatches: 2, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 9 20 1.00 ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39 Consensus pattern (9 bp): TCGAGTTAT Found at i:27115462 original size:9 final size:9 Alignment explanation

Indices: 27115445--27115481 Score: 65 Period size: 9 Copynumber: 4.1 Consensus size: 9 27115435 TGAGTTTTCG 27115445 AATTCGAAT 1 AATTCGAAT * 27115454 AACTCGAAT 1 AATTCGAAT 27115463 AATTCGAAT 1 AATTCGAAT 27115472 AATTCGAAT 1 AATTCGAAT 27115481 A 1 A 27115482 TCAAACTATA Statistics Matches: 26, Mismatches: 2, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 9 26 1.00 ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30 Consensus pattern (9 bp): AATTCGAAT Found at i:27121606 original size:5 final size:5 Alignment explanation

Indices: 27121596--27121627 Score: 64 Period size: 5 Copynumber: 6.4 Consensus size: 5 27121586 TCTTGTAAAT 27121596 ATTTG ATTTG ATTTG ATTTG ATTTG ATTTG AT 1 ATTTG ATTTG ATTTG ATTTG ATTTG ATTTG AT 27121628 GTAATCTTGT Statistics Matches: 27, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 5 27 1.00 ACGTcount: A:0.22, C:0.00, G:0.19, T:0.59 Consensus pattern (5 bp): ATTTG Found at i:27124479 original size:51 final size:52 Alignment explanation

Indices: 27124407--27124593 Score: 207 Period size: 53 Copynumber: 3.5 Consensus size: 52 27124397 AAATTTTTTT * * * 27124407 TTGGGTGTTGGCACACTAATGGCCGGCACCCTTGTACCAGATTTTAAAAAAA 1 TTGGGTGCTGGGACACTAATGGCCGGCACCCTTGTACCAGATTTAAAAAAAA * * 27124459 TT-GGTGCTGGGACACTAATGGCCGACATCCTTGTACCAGAATTTAAAAAAAA 1 TTGGGTGCTGGGACACTAATGGCCGGCACCCTTGTACCAG-ATTTAAAAAAAA * * * * * * 27124511 TTAGATGCTGGGACACTGATAGCCGGCACTCTTGTATCAGATTTAAAAAAAAA 1 TTGGGTGCTGGGACACTAATGGCCGGCACCCTTGTACCAGATTT-AAAAAAAA * 27124564 TTTGGGGTG-TCGAGACACTAATGGCCGGCA 1 -TT-GGGTGCT-GGGACACTAATGGCCGGCA 27124594 ACCACTTAGT Statistics Matches: 112, Mismatches: 17, Indels: 9 0.81 0.12 0.07 Matches are distributed among these distances: 51 33 0.29 52 19 0.17 53 38 0.34 54 3 0.03 55 19 0.17 ACGTcount: A:0.31, C:0.19, G:0.24, T:0.26 Consensus pattern (52 bp): TTGGGTGCTGGGACACTAATGGCCGGCACCCTTGTACCAGATTTAAAAAAAA Found at i:27127349 original size:22 final size:22 Alignment explanation

Indices: 27127324--27127374 Score: 59 Period size: 22 Copynumber: 2.3 Consensus size: 22 27127314 TAGTGGTCAA 27127324 CGGTGGTCGGCGA-TGGAACTTG 1 CGGTGGTCGG-GAGTGGAACTTG * * * 27127346 CGGTGGTTGGTAGTGGAATTTG 1 CGGTGGTCGGGAGTGGAACTTG 27127368 CGGTGGT 1 CGGTGGT 27127375 GAGACAACTG Statistics Matches: 25, Mismatches: 3, Indels: 2 0.83 0.10 0.07 Matches are distributed among these distances: 21 1 0.04 22 24 0.96 ACGTcount: A:0.12, C:0.12, G:0.47, T:0.29 Consensus pattern (22 bp): CGGTGGTCGGGAGTGGAACTTG Found at i:27127832 original size:28 final size:29 Alignment explanation

Indices: 27127808--27127868 Score: 81 Period size: 28 Copynumber: 2.1 Consensus size: 29 27127798 CATTTTTATT 27127808 TTTTATTAC-TTTATTT-ATTTATTTTAAC 1 TTTTA-TACTTTTATTTAATTTATTTTAAC * 27127836 TTTTATACTTTTATTTAATTTAATTTACAC 1 TTTTATACTTTTATTTAATTTATTTTA-AC 27127866 TTT 1 TTT 27127869 ATTTATTTAT Statistics Matches: 29, Mismatches: 1, Indels: 4 0.85 0.03 0.12 Matches are distributed among these distances: 27 3 0.10 28 12 0.41 29 9 0.31 30 5 0.17 ACGTcount: A:0.26, C:0.08, G:0.00, T:0.66 Consensus pattern (29 bp): TTTTATACTTTTATTTAATTTATTTTAAC Found at i:27127869 original size:29 final size:27 Alignment explanation

Indices: 27127808--27127882 Score: 79 Period size: 24 Copynumber: 2.9 Consensus size: 27 27127798 CATTTTTATT * 27127808 TTTTATTACTTTATTTATTTATTTTAAC 1 TTTTA-TACTTTATTTATTTAATTTAAC 27127836 TTTTATAC--T-TTTATTTAATTTAA- 1 TTTTATACTTTATTTATTTAATTTAAC * * 27127859 -TTTACACTTTATTTATTTATTTTA 1 TTTTATACTTTATTTATTTAATTTA 27127883 CTCTATTTCA Statistics Matches: 41, Mismatches: 3, Indels: 9 0.77 0.06 0.17 Matches are distributed among these distances: 22 6 0.15 24 14 0.34 25 13 0.32 27 3 0.07 28 5 0.12 ACGTcount: A:0.27, C:0.07, G:0.00, T:0.67 Consensus pattern (27 bp): TTTTATACTTTATTTATTTAATTTAAC Found at i:27131026 original size:54 final size:54 Alignment explanation

Indices: 27130860--27131029 Score: 135 Period size: 56 Copynumber: 3.1 Consensus size: 54 27130850 CCCTAACCAA * * * * 27130860 AAAATTTTTT-TTGTATCTGATAAAGTGGGTGTCGGCCATCTATGTGCTAGCACCC 1 AAAATTTTTTATT-T-TCTGGTAAAGTGGGTGTTGGCCATCTATGTGCCAGAACCC * * * * * * * * * * ** 27130915 AAAAATATTATATTTTTTTGTAATAATATGGTGTTGGCAATCAAAGTCCCCCAACCC 1 -AAAATTTTTTATTTTCTGGTAA-AGT-GGGTGTTGGCCATCTATGTGCCAGAACCC * 27130972 AAAATTTTTTATTTTCTGGTAAAGTGGGTGTTGGCCATCTATGTGCCAGTACCC 1 AAAATTTTTTATTTTCTGGTAAAGTGGGTGTTGGCCATCTATGTGCCAGAACCC 27131026 AAAA 1 AAAA 27131030 AAAAAATTTT Statistics Matches: 82, Mismatches: 29, Indels: 8 0.69 0.24 0.07 Matches are distributed among these distances: 54 25 0.30 55 7 0.09 56 29 0.35 57 21 0.26 ACGTcount: A:0.29, C:0.17, G:0.18, T:0.36 Consensus pattern (54 bp): AAAATTTTTTATTTTCTGGTAAAGTGGGTGTTGGCCATCTATGTGCCAGAACCC Found at i:27132907 original size:9 final size:9 Alignment explanation

Indices: 27132893--27132923 Score: 53 Period size: 9 Copynumber: 3.4 Consensus size: 9 27132883 GTTAAACGAA 27132893 TCGAGTTAT 1 TCGAGTTAT * 27132902 TCGAGTTAA 1 TCGAGTTAT 27132911 TCGAGTTAT 1 TCGAGTTAT 27132920 TCGA 1 TCGA 27132924 ATCAACTTGA Statistics Matches: 20, Mismatches: 2, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 9 20 1.00 ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39 Consensus pattern (9 bp): TCGAGTTAT Found at i:27133003 original size:9 final size:9 Alignment explanation

Indices: 27132976--27133021 Score: 67 Period size: 9 Copynumber: 5.1 Consensus size: 9 27132966 TGAGTTTTCG * 27132976 AATTTGAAT 1 AATTCGAAT 27132985 AACTTC-AAT 1 AA-TTCGAAT 27132994 AATTCGAAT 1 AATTCGAAT 27133003 AATTCGAAT 1 AATTCGAAT 27133012 AATTCGAAT 1 AATTCGAAT 27133021 A 1 A 27133022 TCAAACTATA Statistics Matches: 34, Mismatches: 1, Indels: 4 0.87 0.03 0.10 Matches are distributed among these distances: 8 3 0.09 9 29 0.85 10 2 0.06 ACGTcount: A:0.46, C:0.11, G:0.09, T:0.35 Consensus pattern (9 bp): AATTCGAAT Found at i:27136374 original size:19 final size:19 Alignment explanation

Indices: 27136346--27136385 Score: 62 Period size: 19 Copynumber: 2.1 Consensus size: 19 27136336 TTATTCATAA 27136346 AATTAGATAATAAAAATAT 1 AATTAGATAATAAAAATAT * * 27136365 AATTATATAATATAAATAT 1 AATTAGATAATAAAAATAT 27136384 AA 1 AA 27136386 ATTTTACATA Statistics Matches: 19, Mismatches: 2, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 19 19 1.00 ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35 Consensus pattern (19 bp): AATTAGATAATAAAAATAT Found at i:27137647 original size:8 final size:9 Alignment explanation

Indices: 27137624--27137666 Score: 52 Period size: 10 Copynumber: 4.6 Consensus size: 9 27137614 TACGTTTTTT 27137624 TATTTTTAA 1 TATTTTTAA 27137633 TAATTTTTAA 1 T-ATTTTTAA 27137643 T-TTTTTAA 1 TATTTTTAA 27137651 TAGTTTTATAA 1 TA-TTTT-TAA 27137662 TATTT 1 TATTT 27137667 GAAACCACAC Statistics Matches: 30, Mismatches: 0, Indels: 7 0.81 0.00 0.19 Matches are distributed among these distances: 8 8 0.27 9 1 0.03 10 16 0.53 11 5 0.17 ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65 Consensus pattern (9 bp): TATTTTTAA Found at i:27137647 original size:18 final size:19 Alignment explanation

Indices: 27137626--27137662 Score: 58 Period size: 18 Copynumber: 2.0 Consensus size: 19 27137616 CGTTTTTTTA 27137626 TTTTTAATAATTTT-TAAT 1 TTTTTAATAATTTTATAAT * 27137644 TTTTTAATAGTTTTATAAT 1 TTTTTAATAATTTTATAAT 27137663 ATTTGAAACC Statistics Matches: 17, Mismatches: 1, Indels: 1 0.89 0.05 0.05 Matches are distributed among these distances: 18 13 0.76 19 4 0.24 ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65 Consensus pattern (19 bp): TTTTTAATAATTTTATAAT Found at i:27141858 original size:34 final size:34 Alignment explanation

Indices: 27141814--27141879 Score: 107 Period size: 34 Copynumber: 1.9 Consensus size: 34 27141804 CAGTAAAATA 27141814 TTTTCCGTAAAATGATTT-CTGGAAAATATTTTAC 1 TTTTCCGTAAAATGATTTACT-GAAAATATTTTAC * 27141848 TTTTCTGTAAAATGATTTACTGAAAATATTTT 1 TTTTCCGTAAAATGATTTACTGAAAATATTTT 27141880 CTGGTGTTTG Statistics Matches: 30, Mismatches: 1, Indels: 2 0.91 0.03 0.06 Matches are distributed among these distances: 34 28 0.93 35 2 0.07 ACGTcount: A:0.33, C:0.09, G:0.11, T:0.47 Consensus pattern (34 bp): TTTTCCGTAAAATGATTTACTGAAAATATTTTAC Found at i:27148078 original size:2 final size:2 Alignment explanation

Indices: 27148066--27148100 Score: 61 Period size: 2 Copynumber: 17.5 Consensus size: 2 27148056 TACCAACATG * 27148066 TA TA CA TA 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 TA TA TA TA T 27148101 TCAATTTCAA Statistics Matches: 31, Mismatches: 2, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 2 31 1.00 ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49 Consensus pattern (2 bp): TA Found at i:27154989 original size:2 final size:2 Alignment explanation

Indices: 27154982--27155015 Score: 50 Period size: 2 Copynumber: 17.0 Consensus size: 2 27154972 CTGTTTCTTT * * 27154982 TC TC TC TC CC TC TC AC 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 27155016 GGGATTGGGA Statistics Matches: 28, Mismatches: 4, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 2 28 1.00 ACGTcount: A:0.03, C:0.53, G:0.00, T:0.44 Consensus pattern (2 bp): TC Found at i:27156593 original size:2 final size:2 Alignment explanation

Indices: 27156588--27156642 Score: 110 Period size: 2 Copynumber: 27.5 Consensus size: 2 27156578 ATATACATAT 27156588 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC 1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC 27156630 AC AC AC AC AC AC A 1 AC AC AC AC AC AC A 27156643 TATATATATA Statistics Matches: 53, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 53 1.00 ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00 Consensus pattern (2 bp): AC Found at i:27156647 original size:2 final size:2 Alignment explanation

Indices: 27156642--27156666 Score: 50 Period size: 2 Copynumber: 12.5 Consensus size: 2 27156632 ACACACACAC 27156642 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 27156667 CACACACACA 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:27156701 original size:2 final size:2 Alignment explanation

Indices: 27156696--27156753 Score: 116 Period size: 2 Copynumber: 29.0 Consensus size: 2 27156686 TCACTCACAC 27156696 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 27156738 TA TA TA TA TA TA TA TA 1 TA TA TA TA TA TA TA TA 27156754 ATTGATGGAG Statistics Matches: 56, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 56 1.00 ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50 Consensus pattern (2 bp): TA Found at i:27167618 original size:19 final size:20 Alignment explanation

Indices: 27167594--27167637 Score: 63 Period size: 20 Copynumber: 2.2 Consensus size: 20 27167584 TTTCTACTTC * 27167594 TTCTTCTC-GTATGTTTCTT 1 TTCTTCTCTGTACGTTTCTT * 27167613 TTCTTCTCTTTACGTTTCTT 1 TTCTTCTCTGTACGTTTCTT 27167633 TTCTT 1 TTCTT 27167638 TTCTTCATTT Statistics Matches: 22, Mismatches: 2, Indels: 1 0.88 0.08 0.04 Matches are distributed among these distances: 19 8 0.36 20 14 0.64 ACGTcount: A:0.05, C:0.23, G:0.07, T:0.66 Consensus pattern (20 bp): TTCTTCTCTGTACGTTTCTT Found at i:27168160 original size:25 final size:25 Alignment explanation

Indices: 27168132--27168192 Score: 95 Period size: 25 Copynumber: 2.4 Consensus size: 25 27168122 GTGTTATAAT * * 27168132 GTTCATGTTTTGGTTTCTGTATTAG 1 GTTCATGTTTTGGTTTCAGTATTAA 27168157 GTTCATGTTTTGGTTTCAGTATTAA 1 GTTCATGTTTTGGTTTCAGTATTAA * 27168182 GTTGATGTTTT 1 GTTCATGTTTT 27168193 CCATTTGTGT Statistics Matches: 33, Mismatches: 3, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 25 33 1.00 ACGTcount: A:0.15, C:0.07, G:0.23, T:0.56 Consensus pattern (25 bp): GTTCATGTTTTGGTTTCAGTATTAA Found at i:27168174 original size:13 final size:13 Alignment explanation

Indices: 27168133--27168174 Score: 52 Period size: 13 Copynumber: 3.3 Consensus size: 13 27168123 TGTTATAATG 27168133 TTCATGTTTTGGT 1 TTCATGTTTTGGT * 27168146 TTC-TGTATTAGG- 1 TTCATGT-TTTGGT 27168158 TTCATGTTTTGGT 1 TTCATGTTTTGGT 27168171 TTCA 1 TTCA 27168175 GTATTAAGTT Statistics Matches: 24, Mismatches: 2, Indels: 6 0.75 0.06 0.19 Matches are distributed among these distances: 12 10 0.42 13 14 0.58 ACGTcount: A:0.12, C:0.10, G:0.21, T:0.57 Consensus pattern (13 bp): TTCATGTTTTGGT Found at i:27169797 original size:29 final size:32 Alignment explanation

Indices: 27169757--27169816 Score: 74 Period size: 29 Copynumber: 2.0 Consensus size: 32 27169747 TCTTTGCTTC * 27169757 TTTCTTTAATTT-GGCCC-AATTAT-TTCCTT 1 TTTCTTTAATTTAGCCCCAAATTATATTCCTT 27169786 TTTCTTCT-ATTTAGCCCCAAATTATATTCCT 1 TTTCTT-TAATTTAGCCCCAAATTATATTCCT 27169817 GCACAAAATT Statistics Matches: 26, Mismatches: 1, Indels: 5 0.81 0.03 0.16 Matches are distributed among these distances: 29 10 0.38 30 5 0.19 31 6 0.23 32 5 0.19 ACGTcount: A:0.20, C:0.23, G:0.05, T:0.52 Consensus pattern (32 bp): TTTCTTTAATTTAGCCCCAAATTATATTCCTT Found at i:27177945 original size:31 final size:32 Alignment explanation

Indices: 27177886--27177950 Score: 123 Period size: 32 Copynumber: 2.1 Consensus size: 32 27177876 GGCAAATTAC 27177886 AAGAGTAATTGAATCCTAATAAAAACTCTTTA 1 AAGAGTAATTGAATCCTAATAAAAACTCTTTA 27177918 AAGAGTAATTGAATCCTAAT-AAAACTCTTTA 1 AAGAGTAATTGAATCCTAATAAAAACTCTTTA 27177949 AA 1 AA 27177951 ATTATCTAAG Statistics Matches: 33, Mismatches: 0, Indels: 1 0.97 0.00 0.03 Matches are distributed among these distances: 31 13 0.39 32 20 0.61 ACGTcount: A:0.48, C:0.12, G:0.09, T:0.31 Consensus pattern (32 bp): AAGAGTAATTGAATCCTAATAAAAACTCTTTA Found at i:27181262 original size:18 final size:18 Alignment explanation

Indices: 27181220--27181262 Score: 50 Period size: 19 Copynumber: 2.3 Consensus size: 18 27181210 TTTCGAAAAA 27181220 TATTTTTTTTGTTCAAAT 1 TATTTTTTTTGTTCAAAT * * * 27181238 AATTTTTTTTTGTTTAAGT 1 TA-TTTTTTTTGTTCAAAT 27181257 TATTTT 1 TATTTT 27181263 ATTCCACTGT Statistics Matches: 20, Mismatches: 4, Indels: 2 0.77 0.15 0.08 Matches are distributed among these distances: 18 5 0.25 19 15 0.75 ACGTcount: A:0.21, C:0.02, G:0.07, T:0.70 Consensus pattern (18 bp): TATTTTTTTTGTTCAAAT Found at i:27186875 original size:41 final size:41 Alignment explanation

Indices: 27186818--27186926 Score: 164 Period size: 41 Copynumber: 2.6 Consensus size: 41 27186808 GACTATACGT * 27186818 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC 1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAAC * 27186859 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAGC 1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAAC * * * 27186900 CTAGCTGGCCAAGTGCTGGTGAATCTG 1 CTAGCAGGCTAAGTGCCGGTG-ATCTG 27186927 TTAAATTAAG Statistics Matches: 62, Mismatches: 5, Indels: 1 0.91 0.07 0.01 Matches are distributed among these distances: 41 57 0.92 42 5 0.08 ACGTcount: A:0.26, C:0.21, G:0.29, T:0.24 Consensus pattern (41 bp): CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAAC Found at i:27188031 original size:16 final size:15 Alignment explanation

Indices: 27187998--27188030 Score: 50 Period size: 15 Copynumber: 2.2 Consensus size: 15 27187988 TAACTCATCA 27187998 TTTAATTTTAATATT 1 TTTAATTTTAATATT 27188013 TTTAACTTTTAAT-TT 1 TTTAA-TTTTAATATT 27188028 TTT 1 TTT 27188031 TTTCAAATAT Statistics Matches: 17, Mismatches: 0, Indels: 2 0.89 0.00 0.11 Matches are distributed among these distances: 15 10 0.59 16 7 0.41 ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70 Consensus pattern (15 bp): TTTAATTTTAATATT Found at i:27193942 original size:91 final size:91 Alignment explanation

Indices: 27193817--27194024 Score: 326 Period size: 91 Copynumber: 2.3 Consensus size: 91 27193807 TTGATTTTAG * 27193817 TAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATTAT 1 TAAATTCATATAAGAA-AATTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATTAT * * 27193882 ATTTAATATTAATTATTTTAAATTGTA 65 ATGTAATATTAATTATTTTAAATTATA * 27193909 TAAATTCATATAAGAAAATTTATTATTAAGAATTTTATGAAATTATATATTATTATTAAATTATA 1 TAAATTCATATAAGAAAATTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATTATA * 27193974 TGTAATATTTATTATTTTAAATTATA 66 TGTAATATTAATTATTTTAAATTATA * * * * 27194000 CAAATTCATAAAATATAATTTATTA 1 TAAATTCATATAAGAAAATTTATTA 27194025 GTTATAATTA Statistics Matches: 107, Mismatches: 9, Indels: 1 0.91 0.08 0.01 Matches are distributed among these distances: 91 91 0.85 92 16 0.15 ACGTcount: A:0.45, C:0.03, G:0.04, T:0.48 Consensus pattern (91 bp): TAAATTCATATAAGAAAATTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATTATA TGTAATATTAATTATTTTAAATTATA Found at i:27193944 original size:44 final size:44 Alignment explanation

Indices: 27193817--27193955 Score: 122 Period size: 47 Copynumber: 3.0 Consensus size: 44 27193807 TTGATTTTAG * 27193817 TAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTA 1 TAAATTCATATAAGAA-AATTTATTATTAAGAATTTTA-GAAATTA * * * ** * 27193863 TATA-TCATTATTAA-ATTATATTTAATATTAATTATTTTA-AATTGTA 1 TAAATTCA-TA-TAAGA--AAATTTATTATTAAGAATTTTAGAAAT-TA 27193909 TAAATTCATATAAGAAAATTTATTATTAAGAATTTTATGAAATTA 1 TAAATTCATATAAGAAAATTTATTATTAAGAATTTTA-GAAATTA 27193954 TA 1 TA 27193956 TATTATTATT Statistics Matches: 71, Mismatches: 13, Indels: 19 0.69 0.13 0.18 Matches are distributed among these distances: 44 18 0.25 45 13 0.18 46 17 0.24 47 22 0.31 48 1 0.01 ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47 Consensus pattern (44 bp): TAAATTCATATAAGAAAATTTATTATTAAGAATTTTAGAAATTA Found at i:27193986 original size:27 final size:28 Alignment explanation

Indices: 27193928--27193999 Score: 85 Period size: 26 Copynumber: 2.6 Consensus size: 28 27193918 ATAAGAAAAT * 27193928 TTATTATTAAGAATTTTATGAAATTATATA 1 TTATTATT-A-AATTATATGAAATTATATA * * 27193958 TTATTATTAAATTATATGTAA-TATTTA 1 TTATTATTAAATTATATGAAATTATATA 27193985 TTATT-TTAAATTATA 1 TTATTATTAAATTATA 27194000 CAAATTCATA Statistics Matches: 39, Mismatches: 3, Indels: 4 0.85 0.07 0.09 Matches are distributed among these distances: 26 10 0.26 27 10 0.26 28 10 0.26 29 1 0.03 30 8 0.21 ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54 Consensus pattern (28 bp): TTATTATTAAATTATATGAAATTATATA Found at i:27193991 original size:47 final size:47 Alignment explanation

Indices: 27193849--27193992 Score: 138 Period size: 47 Copynumber: 3.1 Consensus size: 47 27193839 ATTATTAAGA * 27193849 ATTTTATGAAATTATATATCATTATTAAATTATATTTAATATTAATT 1 ATTTTATGAAATTATATATAATTATTAAATTATATTTAATATTAATT * * * ** 27193896 A-TTT-T-AAATTGTATA-AATTCATATAAGA--AAATTTATTATTAAGA 1 ATTTTATGAAATTATATATAATT-AT-TAA-ATTATATTTAATATTAATT * * * 27193940 ATTTTATGAAATTATATATTATTATTAAATTATATGTAATATTTATT 1 ATTTTATGAAATTATATATAATTATTAAATTATATTTAATATTAATT 27193987 ATTTTA 1 ATTTTA 27193993 AATTATACAA Statistics Matches: 74, Mismatches: 14, Indels: 18 0.70 0.13 0.17 Matches are distributed among these distances: 43 3 0.04 44 24 0.32 45 8 0.11 46 8 0.11 47 28 0.38 48 3 0.04 ACGTcount: A:0.43, C:0.01, G:0.04, T:0.51 Consensus pattern (47 bp): ATTTTATGAAATTATATATAATTATTAAATTATATTTAATATTAATT Found at i:27193999 original size:44 final size:43 Alignment explanation

Indices: 27193857--27193999 Score: 119 Period size: 44 Copynumber: 3.2 Consensus size: 43 27193847 GAATTTTATG * 27193857 AAATTATATATCATTATTAAATTATATTTAATATTAATTATTTT 1 AAATTATATATTATTATTAAATTATA-TTAATATTAATTATTTT * ** * ** * 27193901 AAATTGTATAAATTCATATAAGAAAATT-TATTATTAAGAATT-TTATG 1 AAA-T-TATATATT-AT-T-ATTAAATTATATTAATATTAATTATT-TT * 27193948 AAATTATATATTATTATTAAATTATATGTAATATTTATTATTTT 1 AAATTATATATTATTATTAAATTATAT-TAATATTAATTATTTT 27193992 AAATTATA 1 AAATTATA 27194000 CAAATTCATA Statistics Matches: 74, Mismatches: 16, Indels: 18 0.69 0.15 0.17 Matches are distributed among these distances: 42 6 0.08 43 4 0.05 44 21 0.28 45 10 0.14 46 9 0.12 47 15 0.20 48 3 0.04 49 6 0.08 ACGTcount: A:0.45, C:0.01, G:0.03, T:0.50 Consensus pattern (43 bp): AAATTATATATTATTATTAAATTATATTAATATTAATTATTTT Found at i:27194721 original size:45 final size:44 Alignment explanation

Indices: 27194632--27194726 Score: 136 Period size: 45 Copynumber: 2.1 Consensus size: 44 27194622 TTACACCTCT * 27194632 ATTACATTCAACCAAACACAGGATTACTATTACGCCTCTATTCC 1 ATTACATTCAACCAAACACAGGATTACTATTACACCTCTATTCC *** * 27194676 ATTACATTCAACCAAACAGTTGATTTGCTATTACACCTCTATTCC 1 ATTACATTCAACCAAACACAGGA-TTACTATTACACCTCTATTCC 27194721 ATTACA 1 ATTACA 27194727 CCTCTATTCC Statistics Matches: 45, Mismatches: 5, Indels: 1 0.88 0.10 0.02 Matches are distributed among these distances: 44 20 0.44 45 25 0.56 ACGTcount: A:0.34, C:0.27, G:0.06, T:0.33 Consensus pattern (44 bp): ATTACATTCAACCAAACACAGGATTACTATTACACCTCTATTCC Found at i:27194726 original size:16 final size:16 Alignment explanation

Indices: 27194705--27194774 Score: 95 Period size: 16 Copynumber: 4.4 Consensus size: 16 27194695 TTGATTTGCT * 27194705 ATTACACCTCTATTCC 1 ATTACACCTCTAATCC * 27194721 ATTACACCTCTATTCC 1 ATTACACCTCTAATCC * 27194737 ATTACACATCTAATCC 1 ATTACACCTCTAATCC * 27194753 AATACACCTCTAATCC 1 ATTACACCTCTAATCC * 27194769 AATACA 1 ATTACA 27194775 GCGAACCAAA Statistics Matches: 50, Mismatches: 4, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 16 50 1.00 ACGTcount: A:0.34, C:0.34, G:0.00, T:0.31 Consensus pattern (16 bp): ATTACACCTCTAATCC Found at i:27195596 original size:60 final size:61 Alignment explanation

Indices: 27195479--27195608 Score: 244 Period size: 60 Copynumber: 2.1 Consensus size: 61 27195469 ATCTAGTAGA 27195479 CAAGTTCAGATACCAAAGTGAACGAAAAAAAAAGTACAGGTACCAAAGTGGACTTAGTTGC 1 CAAGTTCAGATACCAAAGTGAACGAAAAAAAAAGTACAGGTACCAAAGTGGACTTAGTTGC * 27195540 CAAGTTCAGATACCAAAGTGAACG-AAAAAAAAGTATAGGTACCAAAGTGGACTTAGTTGC 1 CAAGTTCAGATACCAAAGTGAACGAAAAAAAAAGTACAGGTACCAAAGTGGACTTAGTTGC 27195600 CAAGTTCAG 1 CAAGTTCAG 27195609 GGGCTAAAAT Statistics Matches: 68, Mismatches: 1, Indels: 1 0.97 0.01 0.01 Matches are distributed among these distances: 60 44 0.65 61 24 0.35 ACGTcount: A:0.43, C:0.16, G:0.22, T:0.19 Consensus pattern (61 bp): CAAGTTCAGATACCAAAGTGAACGAAAAAAAAAGTACAGGTACCAAAGTGGACTTAGTTGC Found at i:27197336 original size:95 final size:96 Alignment explanation

Indices: 27197173--27197365 Score: 327 Period size: 95 Copynumber: 2.0 Consensus size: 96 27197163 AATATAATGC * 27197173 TTAGACCCAACCCACACCCTACCCGGTCCATCAACATCTCATAATAATACAGTCACTGAAAGGTG 1 TTAGACCCAACCCACACCCGACCCGGTCCATCAACATCTCATAATAATACAGTCACTGAAAGGTG * 27197238 AAATGTTGTGATAGTGCTTGGAC-TTTTCTT 66 AAATGTTGTGATAATGCTTGGACTTTTTCTT * * 27197268 TTAGACCCAGCCCACACCCGACCCGGTCCATCAACATCTCATAATAATATAGTCACTGATAA-GT 1 TTAGACCCAACCCACACCCGACCCGGTCCATCAACATCTCATAATAATACAGTCACTGA-AAGGT 27197332 GAAATGTTGTGATAATGCTTGGACTTTTTCTT 65 GAAATGTTGTGATAATGCTTGGACTTTTTCTT 27197364 TT 1 TT 27197366 TCTTTTATAG Statistics Matches: 92, Mismatches: 4, Indels: 3 0.93 0.04 0.03 Matches are distributed among these distances: 95 81 0.88 96 11 0.12 ACGTcount: A:0.29, C:0.25, G:0.16, T:0.30 Consensus pattern (96 bp): TTAGACCCAACCCACACCCGACCCGGTCCATCAACATCTCATAATAATACAGTCACTGAAAGGTG AAATGTTGTGATAATGCTTGGACTTTTTCTT Found at i:27199285 original size:18 final size:18 Alignment explanation

Indices: 27199258--27199293 Score: 54 Period size: 18 Copynumber: 2.0 Consensus size: 18 27199248 TTGCTATACT * * 27199258 TTTATTTTTTTTGAGCAA 1 TTTATATTTTTCGAGCAA 27199276 TTTATATTTTTCGAGCAA 1 TTTATATTTTTCGAGCAA 27199294 GGCGAGCTTA Statistics Matches: 16, Mismatches: 2, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 18 16 1.00 ACGTcount: A:0.25, C:0.08, G:0.11, T:0.56 Consensus pattern (18 bp): TTTATATTTTTCGAGCAA Found at i:27200874 original size:14 final size:15 Alignment explanation

Indices: 27200847--27200888 Score: 50 Period size: 14 Copynumber: 2.9 Consensus size: 15 27200837 CATGCAAGCC * 27200847 TATTAATTATAATT- 1 TATTAATTAAAATTA * 27200861 TATTAAATAAAATTA 1 TATTAATTAAAATTA * 27200876 TCTTAATTAAAAT 1 TATTAATTAAAAT 27200889 ATTTAAATTT Statistics Matches: 23, Mismatches: 4, Indels: 1 0.82 0.14 0.04 Matches are distributed among these distances: 14 12 0.52 15 11 0.48 ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48 Consensus pattern (15 bp): TATTAATTAAAATTA Found at i:27214802 original size:17 final size:15 Alignment explanation

Indices: 27214780--27214815 Score: 54 Period size: 17 Copynumber: 2.3 Consensus size: 15 27214770 ATAATAATTT 27214780 AAAATTCAAAAATTCAA 1 AAAATTC-AAAATT-AA 27214797 AAAATTCAAAATTAA 1 AAAATTCAAAATTAA 27214812 AAAA 1 AAAA 27214816 AATATAAAAT Statistics Matches: 19, Mismatches: 0, Indels: 2 0.90 0.00 0.10 Matches are distributed among these distances: 15 6 0.32 16 6 0.32 17 7 0.37 ACGTcount: A:0.69, C:0.08, G:0.00, T:0.22 Consensus pattern (15 bp): AAAATTCAAAATTAA Found at i:27214818 original size:17 final size:17 Alignment explanation

Indices: 27214780--27214816 Score: 58 Period size: 16 Copynumber: 2.2 Consensus size: 17 27214770 ATAATAATTT * 27214780 AAAATTCAAAAATTCAA 1 AAAATTCAAAAATTAAA 27214797 AAAATTC-AAAATTAAA 1 AAAATTCAAAAATTAAA 27214813 AAAA 1 AAAA 27214817 ATATAAAATT Statistics Matches: 19, Mismatches: 1, Indels: 1 0.90 0.05 0.05 Matches are distributed among these distances: 16 12 0.63 17 7 0.37 ACGTcount: A:0.70, C:0.08, G:0.00, T:0.22 Consensus pattern (17 bp): AAAATTCAAAAATTAAA Found at i:27221198 original size:10 final size:10 Alignment explanation

Indices: 27221173--27221218 Score: 56 Period size: 10 Copynumber: 4.5 Consensus size: 10 27221163 ACTGGAAAAA 27221173 TTTAAAAATT 1 TTTAAAAATT 27221183 CTTTAAAAATT 1 -TTTAAAAATT * 27221194 GTTAAAAATT 1 TTTAAAAATT * * 27221204 ATTAAGAATT 1 TTTAAAAATT 27221214 TTTAA 1 TTTAA 27221219 TTTCTTTAAA Statistics Matches: 31, Mismatches: 4, Indels: 1 0.86 0.11 0.03 Matches are distributed among these distances: 10 21 0.68 11 10 0.32 ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46 Consensus pattern (10 bp): TTTAAAAATT Found at i:27221740 original size:21 final size:19 Alignment explanation

Indices: 27221705--27221748 Score: 52 Period size: 20 Copynumber: 2.2 Consensus size: 19 27221695 CAAAACAAAA * 27221705 TTTTAAATTTTTTTACTAAT 1 TTTTAAATTTATTTA-TAAT * 27221725 TTTTATAATTTATTTATAGT 1 TTTTA-AATTTATTTATAAT 27221745 TTTT 1 TTTT 27221749 GCAGGTTTTT Statistics Matches: 21, Mismatches: 2, Indels: 2 0.84 0.08 0.08 Matches are distributed among these distances: 20 12 0.57 21 9 0.43 ACGTcount: A:0.27, C:0.02, G:0.02, T:0.68 Consensus pattern (19 bp): TTTTAAATTTATTTATAAT Found at i:27233158 original size:13 final size:13 Alignment explanation

Indices: 27233140--27233164 Score: 50 Period size: 13 Copynumber: 1.9 Consensus size: 13 27233130 TGTCCTACTG 27233140 AGTTTTTTTGATA 1 AGTTTTTTTGATA 27233153 AGTTTTTTTGAT 1 AGTTTTTTTGAT 27233165 GAGGTAGCAT Statistics Matches: 12, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 12 1.00 ACGTcount: A:0.20, C:0.00, G:0.16, T:0.64 Consensus pattern (13 bp): AGTTTTTTTGATA Found at i:27237102 original size:15 final size:15 Alignment explanation

Indices: 27237084--27237132 Score: 53 Period size: 15 Copynumber: 3.0 Consensus size: 15 27237074 CTATAAAACC 27237084 TTTATTATTAAAATA 1 TTTATTATTAAAATA * 27237099 TTTATAATTGTAATAAATA 1 TTTATTA-T-T-A-AAATA 27237118 TTTATTATTAAAATA 1 TTTATTATTAAAATA 27237133 ATATTAAATA Statistics Matches: 28, Mismatches: 2, Indels: 8 0.74 0.05 0.21 Matches are distributed among these distances: 15 11 0.39 16 2 0.07 17 2 0.07 18 2 0.07 19 11 0.39 ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51 Consensus pattern (15 bp): TTTATTATTAAAATA Found at i:27237132 original size:19 final size:19 Alignment explanation

Indices: 27237094--27237137 Score: 54 Period size: 19 Copynumber: 2.4 Consensus size: 19 27237084 TTTATTATTA ** 27237094 AAATATTTATAATTGTAAT 1 AAATATTTATAATTAAAAT * 27237113 AAATATTTATTATTAAAAT 1 AAATATTTATAATTAAAAT 27237132 -AATATT 1 AAATATT 27237138 AAATATTTTT Statistics Matches: 22, Mismatches: 3, Indels: 1 0.85 0.12 0.04 Matches are distributed among these distances: 18 6 0.27 19 16 0.73 ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48 Consensus pattern (19 bp): AAATATTTATAATTAAAAT Found at i:27241821 original size:18 final size:17 Alignment explanation

Indices: 27241772--27241822 Score: 50 Period size: 18 Copynumber: 2.9 Consensus size: 17 27241762 ATTTAAAATG * 27241772 AAAAATTATAAAATATTT 1 AAAAAATATAAAA-ATTT * 27241790 AAAAAAT-TATAAATTT 1 AAAAAATATAAAAATTT * 27241806 ATAAAACTATAAAAATT 1 A-AAAAATATAAAAATT 27241823 CAAGAAATAA Statistics Matches: 27, Mismatches: 4, Indels: 4 0.77 0.11 0.11 Matches are distributed among these distances: 16 5 0.19 17 9 0.33 18 13 0.48 ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35 Consensus pattern (17 bp): AAAAAATATAAAAATTT Found at i:27242132 original size:4 final size:4 Alignment explanation

Indices: 27242125--27242154 Score: 60 Period size: 4 Copynumber: 7.5 Consensus size: 4 27242115 AAAAAGTACA 27242125 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA 1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA 27242155 TAACCTTATC Statistics Matches: 26, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 4 26 1.00 ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23 Consensus pattern (4 bp): AAAT Found at i:27244134 original size:125 final size:123 Alignment explanation

Indices: 27243949--27244299 Score: 540 Period size: 125 Copynumber: 2.8 Consensus size: 123 27243939 TAATTTCGAG * * 27243949 TTGACATTTCTGATCAAATAGTATAAAATCGCTTCTAACAGGATGCTATTTGAGAAGAATTTGTG 1 TTGACATTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTG * * * 27244014 AAATCGCGCCCTCGTGGATGCACTTTAGCTACAGTAGGTCATGGAAGAAATAATTTTTTT 66 AAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAGGTCATGGAAGAAATAA--TTTTT * * * 27244074 TTGACATTTCTGAGAAAATAGTATAAAATCGCTTCTAGTAGGATGCTATTTGAGAAGAATTTGTA 1 TTGACATTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTG * * 27244139 AAATTGCGCCCTCGTGGACGCGCTTTTGCTACAGTCGGTCATGGAAGAAATAATTTTT 66 AAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAGGTCATGGAAGAAATAATTTTT * * * 27244197 TTGACGTTTTTGAGCAAATAGTATAAAATCGTTTCTAGCAGGATGCTATTTGAGAAGAATTTGTG 1 TTGACATTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTG * * 27244262 AAAATCACGCCCTTGTGGACGCGCTTTTGCTACAGTAG 66 -AAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAG 27244300 CATGTTTGGG Statistics Matches: 205, Mismatches: 20, Indels: 3 0.90 0.09 0.01 Matches are distributed among these distances: 123 64 0.31 124 33 0.16 125 108 0.53 ACGTcount: A:0.30, C:0.15, G:0.22, T:0.33 Consensus pattern (123 bp): TTGACATTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTG AAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAGGTCATGGAAGAAATAATTTTT Found at i:27247373 original size:54 final size:54 Alignment explanation

Indices: 27247312--27247493 Score: 152 Period size: 54 Copynumber: 3.2 Consensus size: 54 27247302 TAAGTTCGTG * 27247312 AAATTATTAATTGATAAATTGTATTAATGGTTAGTAAAATTATCAAATTATATA 1 AAATTATTAATTGATAAATTGTATTAATGATTAGTAAAATTATCAAATTATATA * *** ** ** * * * * 27247366 AAATTATTAATTGTTAGTACCAGTCA--AAACATTTTTCTAAATCTAACATTATGTGAATGTA 1 AAATTATTAATTGATA--AATTGT-ATTAATGATTAGT-AAAAT-TATCA-AAT-T--ATATA 27247427 AAATTATTAATTGATAAATTGTATTAATGATTAGTAAAATTATCAAATTATATA 1 AAATTATTAATTGATAAATTGTATTAATGATTAGTAAAATTATCAAATTATATA 27247481 AAATTATTAATTG 1 AAATTATTAATTG 27247494 TTAGTACCAG Statistics Matches: 92, Mismatches: 25, Indels: 22 0.66 0.18 0.16 Matches are distributed among these distances: 54 32 0.35 55 5 0.05 56 8 0.09 57 7 0.08 58 7 0.08 59 8 0.09 60 6 0.07 61 19 0.21 ACGTcount: A:0.45, C:0.05, G:0.09, T:0.42 Consensus pattern (54 bp): AAATTATTAATTGATAAATTGTATTAATGATTAGTAAAATTATCAAATTATATA Found at i:27247492 original size:17 final size:17 Alignment explanation

Indices: 27247425--27247492 Score: 57 Period size: 17 Copynumber: 3.8 Consensus size: 17 27247415 TATGTGAATG * 27247425 TAAAATTATTAATT-GA 1 TAAAATTATTAATTATA * * 27247441 TAAATTGTATTAATGATTA 1 TAAAAT-TATTAATTA-TA * 27247460 GTAAAATTATCAAATTATA 1 -TAAAATTAT-TAATTATA 27247479 TAAAATTATTAATT 1 TAAAATTATTAATT 27247493 GTTAGTACCA Statistics Matches: 40, Mismatches: 7, Indels: 9 0.71 0.12 0.16 Matches are distributed among these distances: 16 5 0.12 17 11 0.28 18 9 0.22 19 6 0.15 20 9 0.22 ACGTcount: A:0.49, C:0.01, G:0.06, T:0.44 Consensus pattern (17 bp): TAAAATTATTAATTATA Found at i:27247612 original size:46 final size:46 Alignment explanation

Indices: 27247549--27248133 Score: 440 Period size: 45 Copynumber: 13.1 Consensus size: 46 27247539 AGTAAAATTA * 27247549 TTAATTTAGTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAT 1 TTAA-TTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAT * *** 27247596 TTAATTAGGTTAGGGTTTTTAATTTAAGGGGGTTAGGG---TT--T 1 TTAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAT * * * * 27247637 TT-A--AGTTTAGGGTTTTTAATTTAATTAGGTTAGGATTTTTAAG 1 TTAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAT *** * *** * 27247680 TTAAGGGGGTTAGGGTTTTTAAGTT-TAGGGGGTTAGGATTTTTAAGT 1 TTAATTAGGTTAGGGTTTTTAA-TTAAATTAGGTTAGGGTTTTTAA-T * * ** * 27247727 TT-A-GAGTTTAAAGATTTTAATTAAATTAGGTTAGGGTTTTTAAGT 1 TTAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAA-T * * 27247772 TT-A--GGGTTTAGGGTTTTTAAGTT-AATTAGGTTAGGGTTTTTAAG 1 TTAATTAGG-TTAGGGTTTTTAA-TTAAATTAGGTTAGGGTTTTTAAT *** * 27247816 TTAAAGGGGTTAGGGTTTTTAAGTT---TAAGGTTTAGGGTTTTTTAAT 1 TTAATTAGGTTAGGGTTTTTAA-TTAAATTAGG-TTAGGG-TTTTTAAT * * 27247862 TTAATTAGGTTAGGG-TTTTAATTTAATTAGGTTAGGGTTTTTAAG 1 TTAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAT * * 27247907 TT-A--GGGTTTAGGG-TTTTAATTAAATTAGGTTAGAGTTTTTAA- 1 TTAATTAGG-TTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAT * * 27247949 GT--TTAGGTTTAGGGTTTTTAATTAAATTAGGTTGGGGTTTTTAAT 1 TTAATTAGG-TTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAT * * * 27247994 TAAATTAGGTTAGGGTTTTTAATTTAATTAGGTTA-GGTTTTTAAG 1 TTAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAT * *** 27248039 TTAATTAGGTTAGGGTTTTAAAGTT-AAGGGGGTTAGGGTTTTTAAGT 1 TTAATTAGGTTAGGGTTTTTAA-TTAAATTAGGTTAGGGTTTTTAA-T * * 27248086 TT-A--GGGTTTAAGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAT 1 TTAATTAGG-TTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAT 27248130 TTAA 1 TTAA 27248134 GGGTATTAAT Statistics Matches: 439, Mismatches: 65, Indels: 70 0.76 0.11 0.12 Matches are distributed among these distances: 38 27 0.06 40 1 0.00 41 5 0.01 42 3 0.01 43 46 0.10 44 47 0.11 45 149 0.34 46 139 0.32 47 22 0.05 ACGTcount: A:0.26, C:0.00, G:0.26, T:0.48 Consensus pattern (46 bp): TTAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAT Found at i:27247621 original size:28 final size:23 Alignment explanation

Indices: 27247548--27248130 Score: 344 Period size: 23 Copynumber: 26.1 Consensus size: 23 27247538 AAGTAAAATT * * 27247548 ATTAATTTAGTTTAGGGTTTTTA 1 ATTAAATTAGGTTAGGGTTTTTA 27247571 ATTAAATTAGGTTAGGGTTTTTA 1 ATTAAATTAGGTTAGGGTTTTTA * 27247594 ATTTAATTAGGTTAGGGTTTTTA 1 ATTAAATTAGGTTAGGGTTTTTA * *** 27247617 ATTTAAGGGGGTTAGGGTTTTTA 1 ATTAAATTAGGTTAGGGTTTTTA * * 27247640 AGT---TTAGGGTT---TTTAATTTA 1 ATTAAATTA-GGTTAGGGTT--TTTA ** 27247660 ATTAGGTTAGG--A---TTTTTA 1 ATTAAATTAGGTTAGGGTTTTTA *** 27247678 AGTT-AAGGGGGTTAGGGTTTTTA 1 A-TTAAATTAGGTTAGGGTTTTTA * *** * 27247701 AGTT-TAGGGGGTTAGGATTTTTA 1 A-TTAAATTAGGTTAGGGTTTTTA * ** * 27247724 AGT---TTAGAGTTTAAAGATTTTA 1 ATTAAATTAG-G-TTAGGGTTTTTA 27247746 ATTAAATTAGGTTAGGGTTTTTA 1 ATTAAATTAGGTTAGGGTTTTTA * 27247769 AGT---TTAGGGTTTAGGGTTTTTA 1 ATTAAATTA-GG-TTAGGGTTTTTA 27247791 AGTT-AATTAGGTTAGGGTTTTTA 1 A-TTAAATTAGGTTAGGGTTTTTA ** 27247814 AGTTAAA-GGGGTTAGGGTTTTTA 1 A-TTAAATTAGGTTAGGGTTTTTA * 27247837 AGTT---TAAGGTTTAGGGTTTTTTA 1 A-TTAAATTAGG-TTAGGG-TTTTTA * 27247860 ATTTAATTAGGTTAGGG-TTTTA 1 ATTAAATTAGGTTAGGGTTTTTA * 27247882 ATTTAATTAGGTTAGGGTTTTTA 1 ATTAAATTAGGTTAGGGTTTTTA * 27247905 AGTT--A--GGGTTTAGGG-TTTTA 1 A-TTAAATTAGG-TTAGGGTTTTTA * 27247925 ATTAAATTAGGTTAGAGTTTTTA 1 ATTAAATTAGGTTAGGGTTTTTA * 27247948 AGT---TTAGGTTTAGGGTTTTTA 1 ATTAAATTAGG-TTAGGGTTTTTA * 27247969 ATTAAATTAGGTTGGGGTTTTTA 1 ATTAAATTAGGTTAGGGTTTTTA 27247992 ATTAAATTAGGTTAGGGTTTTTA 1 ATTAAATTAGGTTAGGGTTTTTA * 27248015 ATTTAATTAGGTTA-GGTTTTTA 1 ATTAAATTAGGTTAGGGTTTTTA * 27248037 AGTT-AATTAGGTTAGGGTTTTAA 1 A-TTAAATTAGGTTAGGGTTTTTA *** 27248060 AGTT-AAGGGGGTTAGGGTTTTTA 1 A-TTAAATTAGGTTAGGGTTTTTA * * 27248083 AGT---TTAGGGTTTAAGGTTTTTA 1 ATTAAATTA-GG-TTAGGGTTTTTA 27248105 ATTAAATTAGGTTAGGGTTTTTA 1 ATTAAATTAGGTTAGGGTTTTTA 27248128 ATT 1 ATT 27248131 TAAGGGTATT Statistics Matches: 452, Mismatches: 59, Indels: 98 0.74 0.10 0.16 Matches are distributed among these distances: 18 9 0.02 19 4 0.01 20 26 0.06 21 31 0.07 22 95 0.21 23 253 0.56 24 20 0.04 25 14 0.03 ACGTcount: A:0.26, C:0.00, G:0.26, T:0.48 Consensus pattern (23 bp): ATTAAATTAGGTTAGGGTTTTTA Found at i:27247647 original size:38 final size:38 Alignment explanation

Indices: 27247605--27247735 Score: 129 Period size: 38 Copynumber: 3.2 Consensus size: 38 27247595 TTTAATTAGG * 27247605 TTAGGGTTTTTAATTTAAGGGGGTTAGGGTTTTTAAGT 1 TTAGGGTTTTTAATTTAAGGGGGTTAGGATTTTTAAGT *** 27247643 TTAGGGTTTTTAATTTAATTAGGTTAGGATTTTTAAGTT 1 TTAGGGTTTTTAATTTAAGGGGGTTAGGATTTTTAAG-T 27247682 AAGGGGGTTAGGGTTTTTAAGTTT-AGGGGGTTAGGATTTTTAAGT 1 -------TTAGGGTTTTTAA-TTTAAGGGGGTTAGGATTTTTAAGT * 27247727 TTAGAGTTT 1 TTAGGGTTT 27247736 AAAGATTTTA Statistics Matches: 76, Mismatches: 8, Indels: 18 0.75 0.08 0.18 Matches are distributed among these distances: 38 41 0.54 39 1 0.01 45 1 0.01 46 30 0.39 47 3 0.04 ACGTcount: A:0.23, C:0.00, G:0.30, T:0.47 Consensus pattern (38 bp): TTAGGGTTTTTAATTTAAGGGGGTTAGGATTTTTAAGT Found at i:27247659 original size:14 final size:15 Alignment explanation

Indices: 27247628--27247659 Score: 57 Period size: 15 Copynumber: 2.2 Consensus size: 15 27247618 TTTAAGGGGG 27247628 TTAGGGTTTTTAAGT 1 TTAGGGTTTTTAAGT 27247643 TTAGGGTTTTTAA-T 1 TTAGGGTTTTTAAGT 27247657 TTA 1 TTA 27247660 ATTAGGTTAG Statistics Matches: 17, Mismatches: 0, Indels: 1 0.94 0.00 0.06 Matches are distributed among these distances: 14 4 0.24 15 13 0.76 ACGTcount: A:0.22, C:0.00, G:0.22, T:0.56 Consensus pattern (15 bp): TTAGGGTTTTTAAGT Found at i:27247812 original size:136 final size:133 Alignment explanation

Indices: 27247580--27248133 Score: 478 Period size: 136 Copynumber: 4.2 Consensus size: 133 27247570 AATTAAATTA * * * * *** 27247580 GGTTAGGG-TTTTTAATTTAATTAGGTTAGGGTTTTTAATTTAAGGGGGTTAGGGTTTTT-A--- 1 GGTTAGGGATTTTTAATTTAATGAGGTTA-AGATTTTAATTAAATTAGGTTAGGGTTTTTAAGTT * 27247640 A--GTTTAGGGTTTTTAATTTAATTAGGTTAGGATTTTTAAGTTAAGGGGGTTAGGGTTTTTAAG 65 AGGGTTTAGGGTTTTTAA-TTAATTAGGTTAGGGTTTTTAAGTTAA-GGGGTTAGGGTTTTTAAG * 27247703 TTTAGGG 128 TTTA-AG * 27247710 GGTTA-GGATTTTTAAGTTT-A-GAGTTTAAAGATTTTAATTAAATTAGGTTAGGGTTTTTAAGT 1 GGTTAGGGATTTTTAA-TTTAATGAGGTT-AAGATTTTAATTAAATTAGGTTAGGGTTTTTAAG- 27247772 TTAGGGTTTAGGGTTTTTAAGTTAATTAGGTTAGGGTTTTTAAGTTAAAGGGGTTAGGGTTTTTA 63 TTAGGGTTTAGGGTTTTTAA-TTAATTAGGTTAGGGTTTTTAAGTT-AAGGGGTTAGGGTTTTTA 27247837 AGTTTAAG 126 AGTTTAAG * * * * * * 27247845 GTTTAGGGTTTTTTAATTTAATTAGGTTAGGGTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTA 1 GGTTAGGGATTTTTAATTTAATGAGGTTAAGATTTTAATTAAATTAGGTTAGGGTTTTTAAGTTA * * * 27247910 GGGTTTAGGG-TTTTAATTAAATTAGGTTAGAGTTTTTAAGTTTA-GGTTTAGGGTTTTTAA-TT 66 GGGTTTAGGGTTTTTAATT-AATTAGGTTAGGGTTTTTAAGTTAAGGGGTTAGGGTTTTTAAGTT * * 27247972 AAATTA 130 TAA--G * * * * * * 27247978 GGTT-GGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTTAATTAGGTTA-GGTTTTTAAGTT 1 GGTTAGGGATTTTTAATTTAATGAGGTTA-AGATTTTAATTAAATTAGGTTAGGGTTTTTAAGTT * * *** * * * 27248041 AATTAGG-TTAGGGTTTTAAAGTTAAGGGGGTTAGGGTTTTTAAGTTTAGGGTTTAAGGTTTTTA 65 -A--GGGTTTAGGGTTTTTAA-TTAATTAGGTTAGGGTTTTTAAGTTAAGGGGTTAGGGTTTTTA * * 27248105 A-TTAAATTA 126 AGTTTAA--G 27248114 GGTTAGGG-TTTTTAATTTAA 1 GGTTAGGGATTTTTAATTTAA 27248134 GGGTATTAAT Statistics Matches: 364, Mismatches: 35, Indels: 44 0.82 0.08 0.10 Matches are distributed among these distances: 129 30 0.08 130 15 0.04 131 7 0.02 132 49 0.13 133 28 0.08 134 35 0.10 135 49 0.13 136 142 0.39 137 9 0.02 ACGTcount: A:0.26, C:0.00, G:0.27, T:0.48 Consensus pattern (133 bp): GGTTAGGGATTTTTAATTTAATGAGGTTAAGATTTTAATTAAATTAGGTTAGGGTTTTTAAGTTA GGGTTTAGGGTTTTTAATTAATTAGGTTAGGGTTTTTAAGTTAAGGGGTTAGGGTTTTTAAGTTT AAG Found at i:27248013 original size:155 final size:158 Alignment explanation

Indices: 27247779--27248080 Score: 413 Period size: 155 Copynumber: 1.9 Consensus size: 158 27247769 AGTTTAGGGT * * 27247779 TTAGGGTTTTTAAGTTAATTAGGTTAGGGTTTTTAAGTTAAAGGGGTTAGGGTTTTTAAGTTTAA 1 TTAGAGTTTTTAAGTT-ATTAGGTTAGGGTTTTTAAGTTAAAGAGGTTAGGGTTTTTAAGTTTAA * * 27247844 GGTTTAGGGTTTTTTAATTTAATTAGGTTAGGGTTTTAATTTAATTAGGTTAGGGTTTTTAAGTT 65 GGTTTAGGGTTTTTTAATTTAATTAGGTTAGGGTTTTAAGTTAATTAGGTTAGGGTTTTAAAGTT * 27247909 -A-GGGTTTAGGGTTTTAATTAAATTAGG 130 AAGGGGGTTAGGGTTTTAATTAAATTAGG * * 27247936 TTAGAGTTTTTAAG-T-TTAGGTTTAGGGTTTTTAA-TTAAATTAGGTTGGGGTTTTTAA-TTAA 1 TTAGAGTTTTTAAGTTATTAGG-TTAGGGTTTTTAAGTTAAA-GAGGTTAGGGTTTTTAAGTT-- * * 27247997 ATTAGG-TTAGGG-TTTTTAATTTAATTAGGTTAGGTTTTTAAGTTAATTAGGTTAGGGTTTTAA 62 -TAAGGTTTAGGGTTTTTTAATTTAATTAGGTTAGGGTTTTAAGTTAATTAGGTTAGGGTTTTAA 27248060 AGTTAAGGGGGTTAGGGTTTT 126 AGTTAAGGGGGTTAGGGTTTT 27248081 TAAGTTTAGG Statistics Matches: 129, Mismatches: 9, Indels: 14 0.85 0.06 0.09 Matches are distributed among these distances: 154 12 0.09 155 79 0.61 156 8 0.06 157 30 0.23 ACGTcount: A:0.25, C:0.00, G:0.26, T:0.48 Consensus pattern (158 bp): TTAGAGTTTTTAAGTTATTAGGTTAGGGTTTTTAAGTTAAAGAGGTTAGGGTTTTTAAGTTTAAG GTTTAGGGTTTTTTAATTTAATTAGGTTAGGGTTTTAAGTTAATTAGGTTAGGGTTTTAAAGTTA AGGGGGTTAGGGTTTTAATTAAATTAGG Found at i:27248073 original size:68 final size:68 Alignment explanation

Indices: 27247641--27248130 Score: 396 Period size: 68 Copynumber: 7.2 Consensus size: 68 27247631 GGGTTTTTAA * * *** 27247641 GTTTAGGGTTTTTAATTTAATTAGGTTAGGATTTTTAAGTTAAGGGGGTTAGGGTTTTTAAG-T- 1 GTTTAGGGTTTTTAA-TTAATTAGGTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTA 27247704 TTAGGG 65 TTA--G * * * ** * * 27247710 GGTTAGGATTTTTAAGT--TTAGAGTTTAAAGATTTTAATTAAATTAGGTTAGGGTTTTTAAG-T 1 GTTTAGGGTTTTTAATTAATTAG-G-TTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTT 27247772 -TTAGG 64 ATTA-G * *** 27247777 GTTTAGGGTTTTTAAGTTAATTAGGTTAGGGTTTTTAAGTTAAAGGGGTTAGGGTTTTTAAGTT- 1 GTTTAGGGTTTTTAA-TTAATTAGGTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTA * 27247841 TAAG 65 TTAG 27247845 GTTTAGGGTTTTTTAATTTAATTAGGTTAGGG-TTTTAATTTAATTAGGTTAGGGTTTTTAAGTT 1 GTTTAGGG-TTTTTAA-TTAATTAGGTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTT * 27247909 A--GG 64 ATTAG * * 27247912 GTTTAGGG-TTTTAATTAAATTAGGTTAGAGTTTTTAA-GT--TTAGGTTTAGGGTTTTTAA-TT 1 GTTTAGGGTTTTTAATT-AATTAGGTTAGGGTTTTTAATTTAATTAGG-TTAGGGTTTTTAAGTT 27247972 AAATTAG 64 --ATTAG * 27247979 G-TTGGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTTAATTAGGTTA-GGTTTTTAAGTTA 1 GTTTAGGGTTTTTAATT-AATTAGGTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTT- 27248042 ATTAG 64 ATTAG * *** * * 27248047 G-TTAGGGTTTTAAAGTTAAGGGGGTTAGGGTTTTTAAGTTT-A--GGGTTTAAGGTTTTTAA-T 1 GTTTAGGGTTTTTAA-TTAATTAGGTTAGGGTTTTTAA-TTTAATTAGG-TTAGGGTTTTTAAGT 27248107 TAAATTAG 63 T--ATTAG 27248115 G-TTAGGGTTTTTAATT 1 GTTTAGGGTTTTTAATT 27248131 TAAGGGTATT Statistics Matches: 353, Mismatches: 43, Indels: 52 0.79 0.10 0.12 Matches are distributed among these distances: 63 7 0.02 64 15 0.04 65 20 0.06 66 17 0.05 67 62 0.18 68 174 0.49 69 49 0.14 70 9 0.03 ACGTcount: A:0.26, C:0.00, G:0.26, T:0.48 Consensus pattern (68 bp): GTTTAGGGTTTTTAATTAATTAGGTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAT TAG Found at i:27248679 original size:18 final size:18 Alignment explanation

Indices: 27248656--27248691 Score: 63 Period size: 18 Copynumber: 2.0 Consensus size: 18 27248646 CGGAAAAGGG * 27248656 TACATATAAGGGTTAGGA 1 TACATATAAGGGCTAGGA 27248674 TACATATAAGGGCTAGGA 1 TACATATAAGGGCTAGGA 27248692 AACGCACCTG Statistics Matches: 17, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 18 17 1.00 ACGTcount: A:0.39, C:0.08, G:0.28, T:0.25 Consensus pattern (18 bp): TACATATAAGGGCTAGGA Found at i:27249555 original size:20 final size:20 Alignment explanation

Indices: 27249530--27249567 Score: 60 Period size: 20 Copynumber: 1.9 Consensus size: 20 27249520 TTTATTTTTA 27249530 AAAATCT-ATATAATAATTGT 1 AAAATCTAATATAA-AATTGT 27249550 AAAATCTAATATAAAATT 1 AAAATCTAATATAAAATT 27249568 TACCTCGTTA Statistics Matches: 17, Mismatches: 0, Indels: 2 0.89 0.00 0.11 Matches are distributed among these distances: 20 11 0.65 21 6 0.35 ACGTcount: A:0.55, C:0.05, G:0.03, T:0.37 Consensus pattern (20 bp): AAAATCTAATATAAAATTGT Found at i:27250521 original size:11 final size:11 Alignment explanation

Indices: 27250505--27250546 Score: 66 Period size: 11 Copynumber: 3.8 Consensus size: 11 27250495 AAAAAAGGAG 27250505 TTAAGAGAAAC 1 TTAAGAGAAAC * 27250516 TTAAGAGGAAC 1 TTAAGAGAAAC * 27250527 TTAAGAGGAAC 1 TTAAGAGAAAC 27250538 TTAAGAGAA 1 TTAAGAGAA 27250547 TTTTTGAAGA Statistics Matches: 29, Mismatches: 2, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 11 29 1.00 ACGTcount: A:0.50, C:0.07, G:0.24, T:0.19 Consensus pattern (11 bp): TTAAGAGAAAC Found at i:27255589 original size:19 final size:19 Alignment explanation

Indices: 27255545--27255607 Score: 83 Period size: 20 Copynumber: 3.3 Consensus size: 19 27255535 TTTCTTAACA * 27255545 AAAATTAAAAATAATTTTCA 1 AAAATTAAAAATAATTTT-T * 27255565 AAAATTCAAAATAATTTTT 1 AAAATTAAAAATAATTTTT * 27255584 AAAATTAAAAAT-ATTTAT 1 AAAATTAAAAATAATTTTT 27255602 AAAATT 1 AAAATT 27255608 TACAAAATTC Statistics Matches: 39, Mismatches: 4, Indels: 2 0.87 0.09 0.04 Matches are distributed among these distances: 18 11 0.28 19 11 0.28 20 17 0.44 ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38 Consensus pattern (19 bp): AAAATTAAAAATAATTTTT Found at i:27255614 original size:39 final size:42 Alignment explanation

Indices: 27255545--27255629 Score: 108 Period size: 39 Copynumber: 2.1 Consensus size: 42 27255535 TTTCTTAACA 27255545 AAAATTAAAAATAATTTTCAAAAATTCAAAA-T-A-ATTTTT 1 AAAATTAAAAATAATTTTCAAAAATTCAAAATTCATATTTTT * 27255584 AAAATTAAAAAT-ATTTAT-AAAATTTACAAAATTCATATTTTT 1 AAAATTAAAAATAATTT-TCAAAAATT-CAAAATTCATATTTTT 27255626 AAAA 1 AAAA 27255630 AAATTTAAAA Statistics Matches: 40, Mismatches: 1, Indels: 7 0.83 0.02 0.15 Matches are distributed among these distances: 38 10 0.25 39 18 0.45 40 1 0.03 41 1 0.03 42 10 0.25 ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39 Consensus pattern (42 bp): AAAATTAAAAATAATTTTCAAAAATTCAAAATTCATATTTTT Found at i:27270954 original size:24 final size:23 Alignment explanation

Indices: 27270906--27270954 Score: 55 Period size: 24 Copynumber: 2.0 Consensus size: 23 27270896 TTTTGTAAAA * 27270906 AAAAAAAAATTAAACTCTATAAGT 1 AAAAAAAAATTAAAC-ATATAAGT 27270930 AAAAAAAAATATAAA-ATATAGAGT 1 AAAAAAAAAT-TAAACATATA-AGT 27270954 A 1 A 27270955 GCCTTTATCT Statistics Matches: 22, Mismatches: 1, Indels: 4 0.81 0.04 0.15 Matches are distributed among these distances: 23 4 0.18 24 14 0.64 25 4 0.18 ACGTcount: A:0.67, C:0.04, G:0.06, T:0.22 Consensus pattern (23 bp): AAAAAAAAATTAAACATATAAGT Found at i:27275619 original size:10 final size:10 Alignment explanation

Indices: 27275606--27275630 Score: 50 Period size: 10 Copynumber: 2.5 Consensus size: 10 27275596 TTTTTTAATT 27275606 TAAAACTATA 1 TAAAACTATA 27275616 TAAAACTATA 1 TAAAACTATA 27275626 TAAAA 1 TAAAA 27275631 TTATTAATTA Statistics Matches: 15, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 10 15 1.00 ACGTcount: A:0.64, C:0.08, G:0.00, T:0.28 Consensus pattern (10 bp): TAAAACTATA Found at i:27275649 original size:30 final size:28 Alignment explanation

Indices: 27275615--27275673 Score: 75 Period size: 30 Copynumber: 2.0 Consensus size: 28 27275605 TTAAAACTAT * 27275615 ATAAAACTA-TATAAAATTATTAATTATTAA 1 ATAAAAATAGTAT-AAATTATT-ATT-TTAA 27275645 ATAAAAATAGTATAAATTATTATTTTAA 1 ATAAAAATAGTATAAATTATTATTTTAA 27275673 A 1 A 27275674 AATATAAACA Statistics Matches: 27, Mismatches: 1, Indels: 4 0.84 0.03 0.12 Matches are distributed among these distances: 28 5 0.19 29 3 0.11 30 16 0.59 31 3 0.11 ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41 Consensus pattern (28 bp): ATAAAAATAGTATAAATTATTATTTTAA Found at i:27275877 original size:20 final size:20 Alignment explanation

Indices: 27275852--27275901 Score: 82 Period size: 20 Copynumber: 2.5 Consensus size: 20 27275842 ACAAATTATC * 27275852 TTGGTAAATTGTTAGATATT 1 TTGGTAAATCGTTAGATATT * 27275872 TTGGTAGATCGTTAGATATT 1 TTGGTAAATCGTTAGATATT 27275892 TTGGTAAATC 1 TTGGTAAATC 27275902 TTTAAAAATA Statistics Matches: 27, Mismatches: 3, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 20 27 1.00 ACGTcount: A:0.28, C:0.04, G:0.22, T:0.46 Consensus pattern (20 bp): TTGGTAAATCGTTAGATATT Found at i:27277425 original size:30 final size:29 Alignment explanation

Indices: 27277361--27277416 Score: 78 Period size: 29 Copynumber: 1.9 Consensus size: 29 27277351 CCCAAATCGA * * 27277361 TTAAAAATAATTTTTCTAATAAAAATTAC 1 TTAAAAATAAATTTTCTAACAAAAATTAC 27277390 TTAAAAATAAATTTTC-AACAAACAATT 1 TTAAAAATAAATTTTCTAACAAA-AATT 27277417 GATATAAAAG Statistics Matches: 24, Mismatches: 2, Indels: 2 0.86 0.07 0.07 Matches are distributed among these distances: 28 5 0.21 29 19 0.79 ACGTcount: A:0.54, C:0.09, G:0.00, T:0.38 Consensus pattern (29 bp): TTAAAAATAAATTTTCTAACAAAAATTAC Found at i:27279162 original size:18 final size:19 Alignment explanation

Indices: 27279139--27279177 Score: 55 Period size: 18 Copynumber: 2.1 Consensus size: 19 27279129 GAAACTCTAT 27279139 ATCCTTC-AGGGATTTT-AA 1 ATCCTTCTA-GGATTTTCAA 27279157 ATCCTTCTAGGATTTTCAA 1 ATCCTTCTAGGATTTTCAA 27279176 AT 1 AT 27279178 AAAATTCACT Statistics Matches: 19, Mismatches: 0, Indels: 3 0.86 0.00 0.14 Matches are distributed among these distances: 18 14 0.74 19 5 0.26 ACGTcount: A:0.28, C:0.18, G:0.13, T:0.41 Consensus pattern (19 bp): ATCCTTCTAGGATTTTCAA Found at i:27286709 original size:2 final size:2 Alignment explanation

Indices: 27286702--27286728 Score: 54 Period size: 2 Copynumber: 13.5 Consensus size: 2 27286692 TCTTATAATT 27286702 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 27286729 AAATATATAT 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:27288577 original size:12 final size:12 Alignment explanation

Indices: 27288556--27288584 Score: 51 Period size: 12 Copynumber: 2.5 Consensus size: 12 27288546 ATTTTTTTAT 27288556 AATT-AGGAAAA 1 AATTAAGGAAAA 27288567 AATTAAGGAAAA 1 AATTAAGGAAAA 27288579 AATTAA 1 AATTAA 27288585 TCTTATGACT Statistics Matches: 17, Mismatches: 0, Indels: 1 0.94 0.00 0.06 Matches are distributed among these distances: 11 4 0.24 12 13 0.76 ACGTcount: A:0.66, C:0.00, G:0.14, T:0.21 Consensus pattern (12 bp): AATTAAGGAAAA Found at i:27290571 original size:17 final size:18 Alignment explanation

Indices: 27290551--27290597 Score: 64 Period size: 18 Copynumber: 2.8 Consensus size: 18 27290541 ATTTTTCGAA 27290551 AAATAA-ATTTTTTGTTC 1 AAATAATATTTTTTGTTC * 27290568 AAATAATTTTTTTTGTTC 1 AAATAATATTTTTTGTTC 27290586 AAAT--TATTTTTT 1 AAATAATATTTTTT 27290598 TCCTGTTGGA Statistics Matches: 27, Mismatches: 2, Indels: 3 0.84 0.06 0.09 Matches are distributed among these distances: 16 7 0.26 17 6 0.22 18 14 0.52 ACGTcount: A:0.32, C:0.04, G:0.04, T:0.60 Consensus pattern (18 bp): AAATAATATTTTTTGTTC Found at i:27290614 original size:20 final size:18 Alignment explanation

Indices: 27290558--27290617 Score: 75 Period size: 18 Copynumber: 3.2 Consensus size: 18 27290548 GAAAAATAAA 27290558 TTTTTTGTTCAAATAATT 1 TTTTTTGTTCAAATAATT * 27290576 TTTTTTGTTCAAATTATT 1 TTTTTTGTTCAAATAATT ** 27290594 TTTTTCCTGTTGGAATAATT 1 TTTTT--TGTTCAAATAATT 27290614 TTTT 1 TTTT 27290618 GAAAAATAAT Statistics Matches: 36, Mismatches: 4, Indels: 2 0.86 0.10 0.05 Matches are distributed among these distances: 18 22 0.61 20 14 0.39 ACGTcount: A:0.22, C:0.07, G:0.08, T:0.63 Consensus pattern (18 bp): TTTTTTGTTCAAATAATT Found at i:27294806 original size:66 final size:66 Alignment explanation

Indices: 27294708--27294833 Score: 166 Period size: 66 Copynumber: 1.9 Consensus size: 66 27294698 GCTGTAGATG * * * 27294708 GAGTTCGTCATATTTTCTTGTTGCCTCTGCTTC-CTTCGCTACTACCTCCGCTTTAAGTTGTAGC 1 GAGTTCATCATATTTTCTTGTAGCCTCTGCTTCTC-TCGATACTACCTCCGCTTTAAGTTGTAGC 27294772 TA 65 TA * * * 27294774 GAGTTCATTATATTTTCTT-TGAGCCTCTGCTTCTCTCGATGCTACCTCCGTTTTAAGTTG 1 GAGTTCATCATATTTTCTTGT-AGCCTCTGCTTCTCTCGATACTACCTCCGCTTTAAGTTG 27294834 AGCAATTTGC Statistics Matches: 52, Mismatches: 6, Indels: 4 0.84 0.10 0.06 Matches are distributed among these distances: 65 1 0.02 66 50 0.96 67 1 0.02 ACGTcount: A:0.14, C:0.25, G:0.17, T:0.44 Consensus pattern (66 bp): GAGTTCATCATATTTTCTTGTAGCCTCTGCTTCTCTCGATACTACCTCCGCTTTAAGTTGTAGCT A Found at i:27299993 original size:45 final size:45 Alignment explanation

Indices: 27299942--27301391 Score: 484 Period size: 45 Copynumber: 31.6 Consensus size: 45 27299932 CTTCGATCCA * * * 27299942 CTCCACTACAACTTCAGGGAGATAAGACTTGCTATCTTCAGTTTG 1 CTCCACTGCAACTTCAGGGAGATAAGACTTGCTATCTTCAATCTG * * * * * * 27299987 CTCCACTACAAATTCAGGAAGATAAGACTTGCTATGGTAAATTTAATCCG 1 CTCCACTGCAACTTCAGGGAGATAAGACTTGCTA---T--CTTCAATCTG * * * * * * 27300037 AC-CTACTGCAACCTCAGAGG-TATAGGA-TT-C-ATCATTTTAATCCG 1 -CTCCACTGCAACTTCAG-GGAGATAAGACTTGCTATC--TTCAATCTG * * * * * 27300081 CTCCACTACAACTTCAGGAAGAGAGGA-TTAG-TAGCTTCAATCTG 1 CTCCACTGCAACTTCAGGGAGATAAGACTT-GCTATCTTCAATCTG * * * * 27300125 CTCCATTGTAACTTCAGGGAGATAAG-GTT--TATGGCTTTAATCTG 1 CTCCACTGCAACTTCAGGGAGATAAGACTTGCTAT--CTTCAATCTG * * 27300169 CTCCACTGCAACTTCAGGGAGATAAGATTTATAGCCTATCTTCAATTTG 1 CTCCACTGCAACTTCAGGGAGATAAGA-CT-T-G-CTATCTTCAATCTG * * * * * * 27300218 CTCTACTGCAACTTGAGGGAGATAAGA-TTGATTATTTTTAACCTG 1 CTCCACTGCAACTTCAGGGAGATAAGACTTG-CTATCTTCAATCTG * * ** * * * 27300263 CTCTACTACAACTTCAGGGAGATAAGGTTTG--AT-AT-GATCTA 1 CTCCACTGCAACTTCAGGGAGATAAGACTTGCTATCTTCAATCTG * * ** * 27300304 CTCTACTGCAACTTCAGAGAGATAAGATCTGTAATTTACAACTTCAATCTG 1 CTCCACTGCAACTTCAGGGAGATAAGA-CT-T--GCT--ATCTTCAATCTG * * * 27300355 TTCCACTGCAACTTCAGGGAAATAAGA-TTCGCTATCTTCAGTCTG 1 CTCCACTGCAACTTCAGGGAGATAAGACTT-GCTATCTTCAATCTG * * * * * * 27300400 CTCTACTGCAACTTTAGGGAGATAAGACTTGTTATGGTAGATTTAATCCG 1 CTCCACTGCAACTTCAGGGAGATAAGACTTGCTA---T--CTTCAATCTG * * * * 27300450 AC-CTACTGCAACTTCAGAGGTG-TAGGA-TT-C-ATCTTTTTAATCTG 1 -CTCCACTGCAACTTCAG-GGAGATAAGACTTGCTATC--TTCAATCTG * ** * 27300494 CTCCACTGCAACTTTAGGGAGATAAGGTTTGTAGCTTGTCTTCAATCTG 1 CTCCACTGCAACTTCAGGGAGATAA-GACT-T-GC-TATCTTCAATCTG * * * 27300543 CTTCACTGCAACTTCAGGGAGATAAGA-TTAGTTATCTTCAGTCTG 1 CTCCACTGCAACTTCAGGGAGATAAGACTT-GCTATCTTCAATCTG * * * * 27300588 TTCCACTACAACTTTAGGGAGATAAGACTTGCTATCTTCAGTCTG 1 CTCCACTGCAACTTCAGGGAGATAAGACTTGCTATCTTCAATCTG * * * * * * 27300633 CTCCACTACAATTTCAAGGAGATATGACTTGCTATTTTCAGTCTG 1 CTCCACTGCAACTTCAGGGAGATAAGACTTGCTATCTTCAATCTG * * * * * * 27300678 TTCCACTGCAAATTCAGGGAGATAAGAC-TGATTTATTTTTAACCTG 1 CTCCACTGCAACTTCAGGGAGATAAGACTTG--CTATCTTCAATCTG * * ** * * 27300724 CTCCACTACAACTTCAGGAAGATAAGGTTTGGTA---T-GATCTG 1 CTCCACTGCAACTTCAGGGAGATAAGACTTGCTATCTTCAATCTG * * ** * 27300765 CTCTACTGCAACTAT-AGAGAGATAAGATCTATAATTTATAGCTTCAATTTG 1 CTCCACTGCAACT-TCAGGGAGATAAGA-CT-T--GCTAT--CTTCAATCTG * ** * * * 27300816 TTCCACTAAAACTTCAGGGAAATAAGA-TTCACTATCTTCAGTCTG 1 CTCCACTGCAACTTCAGGGAGATAAGACTT-GCTATCTTCAATCTG ** * * 27300861 CTCCACCACAATTTCAAGGAGATAAGACTTGCTATCTTCAATCTG 1 CTCCACTGCAACTTCAGGGAGATAAGACTTGCTATCTTCAATCTG * * * * 27300906 -TCCCACTGCAACTTCAAGGG-GATAAGA-TTAG-TAGCCTCAATTTA 1 CT-CCACTGCAACTTC-AGGGAGATAAGACTT-GCTATCTTCAATCTG * * ** * * 27300950 CTCCACTGCAACTTCAAGGAGATAAGA-TTCGACTTTGGTAAATTTG 1 CTCCACTGCAACTTCAGGGAGATAAGACTT-G-CTATCTTCAATCTG * * * * 27300996 ATCCGACCTATTGCAACTTCAGAGG-TATAGGATTTGTCGT-T-TT-AAT-TCG 1 CTCC-A-C---TGCAACTTCAG-GGAGATAAGACTTG-C-TATCTTCAATCT-G * * * ** 27301045 CTCCACTCCAACTTCAGGGAGATAGGATATATAATTTATAGCTTCAATCTG 1 CTCCACTGCAACTTCAGGGAGATAAGA-CT-T--GCTAT--CTTCAATCTG * * * * * * * 27301096 TTCCTCTGCAACTTCAGGGAAATGAG-TTTGCTATCTTTAGTCTG 1 CTCCACTGCAACTTCAGGGAGATAAGACTTGCTATCTTCAATCTG * * * * 27301140 CTCCATTGCAACTTCAGGGAGATAAGA-TT-CGTAACTTTAATCTA 1 CTCCACTGCAACTTCAGGGAGATAAGACTTGC-TATCTTCAATCTG * * * 27301184 CCCCACTGCAACTTCAGTGG-GATAAGA-TTAGCTA---T-GATCTT 1 CTCCACTGCAACTTCAG-GGAGATAAGACTT-GCTATCTTCAATCTG * * * ** 27301225 CTCTACTGTAACTTCAGAGAGATAAGATCTGTAATTTATAGCTTCAATCTG 1 CTCCACTGCAACTTCAGGGAGATAAGA-CT-T--GCTAT--CTTCAATCTG * * * * * 27301276 TTCCACTGCAACTTCAAGGAAATAAGA-TTCGCTATCCTCAGTCTG 1 CTCCACTGCAACTTCAGGGAGATAAGACTT-GCTATCTTCAATCTG * * 27301321 CTCCACTGCAACTTCAAGGAGATAAAACTTG-T-TGCTTCAATCTG 1 CTCCACTGCAACTTCAGGGAGATAAGACTTGCTAT-CTTCAATCTG * * 27301365 -TCCCATTGCAACTTCAGGGGGATAAGA 1 CT-CCACTGCAACTTCAGGGAGATAAGA 27301392 TTTGTGGTTT Statistics Matches: 1053, Mismatches: 235, Indels: 235 0.69 0.15 0.15 Matches are distributed among these distances: 40 1 0.00 41 76 0.07 42 8 0.01 43 19 0.02 44 264 0.25 45 319 0.30 46 70 0.07 47 18 0.02 48 11 0.01 49 81 0.08 50 52 0.05 51 128 0.12 52 6 0.01 ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32 Consensus pattern (45 bp): CTCCACTGCAACTTCAGGGAGATAAGACTTGCTATCTTCAATCTG Found at i:27300380 original size:137 final size:138 Alignment explanation

Indices: 27300134--27300425 Score: 315 Period size: 137 Copynumber: 2.1 Consensus size: 138 27300124 GCTCCATTGT * * * * 27300134 AACTTCAGGGAGATAAGGTTTATGGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTT 1 AACTTCAGGGAGATAAGGTTTATGGATATAATCTACTCCACTGCAACTTCAGAGAGATAAGATTT * * * * * * * * * 27300199 ATAGCCTATCTTCAATTTGCTCTACTGCAACTTGAGGGAGATAAGATT-GATTATTTTTAACCTG 66 ATAGACTAACTTCAATCTGCTCCACTGCAACTTCAGGGAAATAAGATTCG-CTATCTTCAACCTG 27300263 CTCTACTAC 130 CTCTACTAC * * 27300272 AACTTCAGGGAGATAAGG-TT-T-GATATGATCTACTCTACTGCAACTTCAGAGAGATAAGATCT 1 AACTTCAGGGAGATAAGGTTTATGGATATAATCTACTCCACTGCAACTTCAGAGAGATAAGAT-T ** * ** 27300334 GTAATTTAC-AACTTCAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTCGCTATCTTCAGTC 65 -T-ATAGACTAACTTCAATCTGCTCCACTGCAACTTCAGGGAAATAAGATTCGCTATCTTCAACC * 27300398 TGCTCTACTGC 128 TGCTCTACTAC * 27300409 AACTTTAGGGAGATAAG 1 AACTTCAGGGAGATAAG 27300426 ACTTGTTATG Statistics Matches: 128, Mismatches: 22, Indels: 9 0.81 0.14 0.06 Matches are distributed among these distances: 135 33 0.26 136 2 0.02 137 71 0.55 138 22 0.17 ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32 Consensus pattern (138 bp): AACTTCAGGGAGATAAGGTTTATGGATATAATCTACTCCACTGCAACTTCAGAGAGATAAGATTT ATAGACTAACTTCAATCTGCTCCACTGCAACTTCAGGGAAATAAGATTCGCTATCTTCAACCTGC TCTACTAC Found at i:27300858 original size:228 final size:225 Alignment explanation

Indices: 27300222--27301393 Score: 840 Period size: 228 Copynumber: 5.1 Consensus size: 225 27300212 AATTTGCTCT * * 27300222 ACTGCAACTTGAGGGAGATAAGATTGATTATTTTTAACCTGCTCTACTACAACTTCAGGGAGATA 1 ACTGCAACTTCAGGGAGATAAGATTGATTATTTTTAACCTGCTCCACTACAACTTCAGGGAGATA * * * 27300287 AGGTTTGATATGATCTACTCTACTGCAACTTCAGAGAGATAAGATCTGTAATTTACAACTTCAAT 66 AGGTTTGGTATGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCT-TAATTTA-TACTTCAAT * * * 27300352 CTGTTCCACTGCAACTTCAGGGAAATAAGATTCGCTATCTTCAGTCTGCTCTACTGCAACTTT-A 129 CTGTTCCACTACAACTTCAGGGAAATAAGATTCGCTATCTTCAGTCTGCTCCACTACAA-TTTCA * * * * 27300416 GGGAGATAAGACTTGTTATGGTAGATTTAATCCG-ACC 193 AGGAGATAAGACTTGCTAT--T---TTCAATCTGTACC * * * * * * * 27300453 TACTGCAACTTCAGAGGTG-TAGGATTCA-TCTTTTTAATCTGCTCCACTGCAACTTTAGGGAGA 1 -ACTGCAACTTCAG-GGAGATAAGATTGATTATTTTTAACCTGCTCCACTACAACTTCAGGGAGA * * 27300516 TAAGGTTT-GTAGCTTGTCTTCAATCTGCT-TCACTGCAACTTCAGGGAGATAAGA--TT-AGTT 64 TAAGGTTTGGTA---TG------ATCTGCTCT-ACTGCAACTTCAGAGAGATAAGATCTTAATTT * * * 27300576 AT-CTTCAGTCTGTTCCACTACAACTTTAGGGAGATAAGACTT-GCTATCTTCAGTCTGCTCCAC 119 ATACTTCAATCTGTTCCACTACAACTTCAGGGAAATAAGA-TTCGCTATCTTCAGTCTGCTCCAC * * * 27300639 TACAATTTCAAGGAGATATGACTTGCTATTTTCAGTCTGTTCC 183 TACAATTTCAAGGAGATAAGACTTGCTATTTTCAATCTGTACC * * * 27300682 ACTGCAAATTCAGGGAGATAAGACTGATTTATTTTTAACCTGCTCCACTACAACTTCAGGAAGAT 1 ACTGCAACTTCAGGGAGATAAGATTGA-TTATTTTTAACCTGCTCCACTACAACTTCAGGGAGAT 27300747 AAGGTTTGGTATGATCTGCTCTACTGCAACTAT-AGAGAGATAAGATCTATAATTTATAGCTTCA 65 AAGGTTTGGTATGATCTGCTCTACTGCAACT-TCAGAGAGATAAGATCT-TAATTTATA-CTTCA * * * * 27300811 ATTTGTTCCACTAAAACTTCAGGGAAATAAGATTCACTATCTTCAGTCTGCTCCACCACAATTTC 127 ATCTGTTCCACTACAACTTCAGGGAAATAAGATTCGCTATCTTCAGTCTGCTCCACTACAATTTC * * 27300876 AAGGAGATAAGACTTGCTATCTTCAATCTGTCCC 192 AAGGAGATAAGACTTGCTATTTTCAATCTGTACC * *** * ** * * * 27300910 ACTGCAACTTCAAGGG-GATAAGATT-AGTAGCCTCAATTTACTCCACTGCAACTTCAAGGAGAT 1 ACTGCAACTTC-AGGGAGATAAGATTGATTATTTTTAACCTGCTCCACTACAACTTCAGGGAGAT * * * * 27300973 AAGATTCGACTTTGGTAAATTTGATCCGAC-CTATTGCAACTTCAGAG-GTATAGGAT-TT-GTC 65 AAG----G--TTTGGT--A--TGATCTG-CTCTACTGCAACTTCAGAGAG-ATAAGATCTTAAT- * * * * * *** * 27301034 GT-T--TT-AAT-TCGCTCCACTCCAACTTCAGGGAGATAGGATATATAATTTATAGCTTCAATC 117 TTATACTTCAATCT-GTTCCACTACAACTTCAGGGAAATA--AGAT-T-CGCTAT--CTTCAGTC * * * * * * * * * 27301094 TGTTCCTCTGCAACTTCAGGGAAATGAG-TTTGCTATCTTT-AGTCTGCT-CC 175 TGCTCCACTACAATTTCAAGGAGATAAGACTTGCTAT-TTTCAATCTG-TACC * ** * * * * 27301144 ATTGCAACTTCAGGGAGATAAGATTCG--TAACTTTAATCTACCCCACTGCAACTTCAGTGG-GA 1 ACTGCAACTTCAGGGAGATAAGATT-GATTATTTTTAACCTGCTCCACTACAACTTCAG-GGAGA * * * * * 27301206 TAAGATTAGCTATGATCTTCTCTACTGTAACTTCAGAGAGATAAGATCTGTAATTTATAGCTTCA 64 TAAGGTTTGGTATGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCT-TAATTTATA-CTTCA * * * * * 27301271 ATCTGTTCCACTGCAACTTCAAGGAAATAAGATTCGCTATCCTCAGTCTGCTCCACTGCAACTTC 127 ATCTGTTCCACTACAACTTCAGGGAAATAAGATTCGCTATCTTCAGTCTGCTCCACTACAATTTC * * * 27301336 AAGGAGATAAAACTTG-T-TGCTTCAATCTGTCCC 192 AAGGAGATAAGACTTGCTAT-TTTCAATCTGTACC * * 27301369 ATTGCAACTTCAGGGGGATAAGATT 1 ACTGCAACTTCAGGGAGATAAGATT 27301394 TGTGGTTTCA Statistics Matches: 745, Mismatches: 126, Indels: 145 0.73 0.12 0.14 Matches are distributed among these distances: 222 27 0.04 223 3 0.00 224 31 0.04 225 63 0.08 226 40 0.05 227 11 0.01 228 140 0.19 229 33 0.04 230 45 0.06 231 69 0.09 232 30 0.04 233 88 0.12 234 68 0.09 235 39 0.05 236 27 0.04 237 2 0.00 238 1 0.00 239 28 0.04 ACGTcount: A:0.29, C:0.21, G:0.18, T:0.33 Consensus pattern (225 bp): ACTGCAACTTCAGGGAGATAAGATTGATTATTTTTAACCTGCTCCACTACAACTTCAGGGAGATA AGGTTTGGTATGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTTAATTTATACTTCAATCT GTTCCACTACAACTTCAGGGAAATAAGATTCGCTATCTTCAGTCTGCTCCACTACAATTTCAAGG AGATAAGACTTGCTATTTTCAATCTGTACC Found at i:27301178 original size:44 final size:45 Alignment explanation

Indices: 27301101--27301217 Score: 123 Period size: 44 Copynumber: 2.6 Consensus size: 45 27301091 ATCTGTTCCT * * * * * * * 27301101 CTGCAACTTCAGGGAAATGAG-TTTGCTATCTTTAGTCTGCTCCA 1 CTGCAACTTCAGGGAGATAAGATTCGCTAACTTTAATCTACCCCA * 27301145 TTGCAACTTCAGGGAGATAAGATTCG-TAACTTTAATCTACCCCA 1 CTGCAACTTCAGGGAGATAAGATTCGCTAACTTTAATCTACCCCA * 27301189 CTGCAACTTCAGTGG-GATAAGATTAGCTA 1 CTGCAACTTCAG-GGAGATAAGATTCGCTA 27301218 TGATCTTCTC Statistics Matches: 60, Mismatches: 10, Indels: 5 0.80 0.13 0.07 Matches are distributed among these distances: 44 53 0.88 45 7 0.12 ACGTcount: A:0.28, C:0.21, G:0.20, T:0.31 Consensus pattern (45 bp): CTGCAACTTCAGGGAGATAAGATTCGCTAACTTTAATCTACCCCA Found at i:27301389 original size:181 final size:180 Alignment explanation

Indices: 27301054--27301393 Score: 475 Period size: 181 Copynumber: 1.9 Consensus size: 180 27301044 GCTCCACTCC * * * * 27301054 AACTTCAGGGAGATAGGATATATAATTTATAGCTTCAATCTGTTCCTCTGCAACTTCAGGGAAAT 1 AACTTCAGAGAGATAAGATATATAATTTATAGCTTCAATCTGTTCCACTGCAACTTCAAGGAAAT * * * * * * * * 27301119 GAGTTTGCTATCTTTAGTCTGCTCCATTGCAACTTCAGGGAGATAAGATTCGTAACTTTAATCTA 66 AAGTTCGCTATCCTCAGTCTGCTCCACTGCAACTTCAAGGAGATAAAATTCGTAACTTCAATCTA * 27301184 CCCCACTGCAACTTCAGTGGGATAAGATTAGCTATGATCTTCTCTACTGT 131 CCCCACTGCAACTTCAGGGGGATAAGATTAGCTATGATCTTCTCTACTGT * * 27301234 AACTTCAGAGAGATAAGATCTGTAATTTATAGCTTCAATCTGTTCCACTGCAACTTCAAGGAAAT 1 AACTTCAGAGAGATAAGATATATAATTTATAGCTTCAATCTGTTCCACTGCAACTTCAAGGAAAT ** 27301299 AAGATTCGCTATCCTCAGTCTGCTCCACTGCAACTTCAAGGAGATAAAACTT-GTTGCTTCAATC 66 AAG-TTCGCTATCCTCAGTCTGCTCCACTGCAACTTCAAGGAGATAAAA-TTCGTAACTTCAATC ** * 27301363 TGTCCCATTGCAACTTCAGGGGGATAAGATT 129 TACCCCACTGCAACTTCAGGGGGATAAGATT 27301394 TGTGGTTTCA Statistics Matches: 138, Mismatches: 20, Indels: 3 0.86 0.12 0.02 Matches are distributed among these distances: 180 61 0.44 181 75 0.54 182 2 0.01 ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32 Consensus pattern (180 bp): AACTTCAGAGAGATAAGATATATAATTTATAGCTTCAATCTGTTCCACTGCAACTTCAAGGAAAT AAGTTCGCTATCCTCAGTCTGCTCCACTGCAACTTCAAGGAGATAAAATTCGTAACTTCAATCTA CCCCACTGCAACTTCAGGGGGATAAGATTAGCTATGATCTTCTCTACTGT Found at i:27302265 original size:20 final size:21 Alignment explanation

Indices: 27302229--27302296 Score: 86 Period size: 20 Copynumber: 3.2 Consensus size: 21 27302219 GGCCTCTCCT 27302229 TTTTCTTTTTCTTTTTCTTTTC 1 TTTTC-TTTTCTTTTTCTTTTC 27302251 TTTTCTTTT-TTTTTCTTTTC 1 TTTTCTTTTCTTTTTCTTTTC * 27302271 TATTCTTTTCATTTTTCATTTT- 1 TTTTCTTTTC-TTTTTC-TTTTC 27302293 TTTT 1 TTTT 27302297 AAAGTGAAGT Statistics Matches: 41, Mismatches: 2, Indels: 6 0.84 0.04 0.12 Matches are distributed among these distances: 20 19 0.46 21 4 0.10 22 14 0.34 23 4 0.10 ACGTcount: A:0.04, C:0.15, G:0.00, T:0.81 Consensus pattern (21 bp): TTTTCTTTTCTTTTTCTTTTC Found at i:27302269 original size:25 final size:26 Alignment explanation

Indices: 27302229--27302286 Score: 82 Period size: 25 Copynumber: 2.2 Consensus size: 26 27302219 GGCCTCTCCT * 27302229 TTTTCTTTTTCTTTTTCTTTTCTTTTC 1 TTTT-TTTTTCTTTTTCTATTCTTTTC 27302256 TTTTTTTTTC-TTTTCTATTCTTTTC 1 TTTTTTTTTCTTTTTCTATTCTTTTC * 27302281 ATTTTT 1 TTTTTT 27302287 CATTTTTTTT Statistics Matches: 29, Mismatches: 2, Indels: 2 0.88 0.06 0.06 Matches are distributed among these distances: 25 19 0.66 26 6 0.21 27 4 0.14 ACGTcount: A:0.03, C:0.16, G:0.00, T:0.81 Consensus pattern (26 bp): TTTTTTTTTCTTTTTCTATTCTTTTC Found at i:27302292 original size:6 final size:5 Alignment explanation

Indices: 27302229--27302285 Score: 69 Period size: 5 Copynumber: 10.8 Consensus size: 5 27302219 GGCCTCTCCT * * 27302229 TTTTC TTTTTC TTTTTC TTTTC TTTTC TTTTT TTTTC TTTTC TATTC TTTTC 1 TTTTC -TTTTC -TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC 27302281 ATTTT 1 -TTTT 27302286 TCATTTTTTT Statistics Matches: 46, Mismatches: 4, Indels: 2 0.88 0.08 0.04 Matches are distributed among these distances: 5 31 0.67 6 15 0.33 ACGTcount: A:0.04, C:0.16, G:0.00, T:0.81 Consensus pattern (5 bp): TTTTC Found at i:27302294 original size:25 final size:23 Alignment explanation

Indices: 27302229--27302294 Score: 71 Period size: 25 Copynumber: 2.7 Consensus size: 23 27302219 GGCCTCTCCT * 27302229 TTTTCTTTTTC-TTTTTCTTTTC 1 TTTTCTTTTTCTTTTTTCTATTC * 27302251 TTTTCTTTTTTTTTCTTTTCTATTC 1 TTTTC-TTTTTCTT-TTTTCTATTC 27302276 TTTTCATTTTTCATTTTTT 1 TTTTC-TTTTTC-TTTTTT 27302295 TTAAAGTGAA Statistics Matches: 36, Mismatches: 4, Indels: 5 0.80 0.09 0.11 Matches are distributed among these distances: 22 5 0.14 23 5 0.14 24 1 0.03 25 23 0.64 26 2 0.06 ACGTcount: A:0.05, C:0.15, G:0.00, T:0.80 Consensus pattern (23 bp): TTTTCTTTTTCTTTTTTCTATTC Found at i:27315571 original size:5 final size:5 Alignment explanation

Indices: 27315563--27315594 Score: 57 Period size: 5 Copynumber: 6.6 Consensus size: 5 27315553 TTAATTTATT 27315563 TAATA TAATA TAATA TAATA TAATA T-ATA TAA 1 TAATA TAATA TAATA TAATA TAATA TAATA TAA 27315595 ATCATAAAAA Statistics Matches: 26, Mismatches: 0, Indels: 2 0.93 0.00 0.07 Matches are distributed among these distances: 4 4 0.15 5 22 0.85 ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41 Consensus pattern (5 bp): TAATA Found at i:27321688 original size:23 final size:23 Alignment explanation

Indices: 27321618--27321701 Score: 106 Period size: 21 Copynumber: 3.9 Consensus size: 23 27321608 CCTGATCAGT 27321618 ATACGACACAT-AAGTGCCTGA- 1 ATACGACACATAAAGTGCCTGAG ** 27321639 A-ACGACACACGAAGTGCCT--G 1 ATACGACACATAAAGTGCCTGAG * 27321659 ATACGACACATAAAGTGCTTGAG 1 ATACGACACATAAAGTGCCTGAG 27321682 ATACGACACATAAAGTGCCT 1 ATACGACACATAAAGTGCCT 27321702 AATCGGCAAA Statistics Matches: 53, Mismatches: 5, Indels: 8 0.80 0.08 0.12 Matches are distributed among these distances: 20 9 0.17 21 24 0.45 23 20 0.38 ACGTcount: A:0.38, C:0.24, G:0.20, T:0.18 Consensus pattern (23 bp): ATACGACACATAAAGTGCCTGAG Found at i:27321698 original size:44 final size:41 Alignment explanation

Indices: 27321618--27321701 Score: 114 Period size: 44 Copynumber: 2.0 Consensus size: 41 27321608 CCTGATCAGT * 27321618 ATACGACACATAAGTGCCTGAAACGACACACGAAGTGCCTG 1 ATACGACACATAAGTGCCTGAAACGACACACAAAGTGCCTG * * 27321659 ATACGACACATAAAGTGCTTGAGATACGACACATAAAGTGCCT 1 ATACGACACAT-AAGTGCCTGA-A-ACGACACACAAAGTGCCT 27321702 AATCGGCAAA Statistics Matches: 37, Mismatches: 3, Indels: 3 0.86 0.07 0.07 Matches are distributed among these distances: 41 11 0.30 42 9 0.24 43 1 0.03 44 16 0.43 ACGTcount: A:0.38, C:0.24, G:0.20, T:0.18 Consensus pattern (41 bp): ATACGACACATAAGTGCCTGAAACGACACACAAAGTGCCTG Found at i:27322629 original size:17 final size:18 Alignment explanation

Indices: 27322595--27322630 Score: 56 Period size: 17 Copynumber: 2.1 Consensus size: 18 27322585 TTAGCTATTC * 27322595 TGTTTCTATTTCTTCTTT 1 TGTTTCTATTTATTCTTT 27322613 TGTTTCT-TTTATTCTTT 1 TGTTTCTATTTATTCTTT 27322630 T 1 T 27322631 ATTTTTTTTT Statistics Matches: 17, Mismatches: 1, Indels: 1 0.89 0.05 0.05 Matches are distributed among these distances: 17 10 0.59 18 7 0.41 ACGTcount: A:0.06, C:0.14, G:0.06, T:0.75 Consensus pattern (18 bp): TGTTTCTATTTATTCTTT Found at i:27322639 original size:17 final size:17 Alignment explanation

Indices: 27322597--27322638 Score: 50 Period size: 17 Copynumber: 2.5 Consensus size: 17 27322587 AGCTATTCTG * * 27322597 TTTCTATTTCTTCTTTTG 1 TTTCT-TTTATTCTTTTA 27322615 TTTCTTTTATTCTTTTA 1 TTTCTTTTATTCTTTTA 27322632 TTT-TTTT 1 TTTCTTTT 27322639 TTCCCTTTTA Statistics Matches: 22, Mismatches: 2, Indels: 2 0.85 0.08 0.08 Matches are distributed among these distances: 16 4 0.18 17 13 0.59 18 5 0.23 ACGTcount: A:0.07, C:0.12, G:0.02, T:0.79 Consensus pattern (17 bp): TTTCTTTTATTCTTTTA Found at i:27322832 original size:5 final size:5 Alignment explanation

Indices: 27322824--27322855 Score: 57 Period size: 5 Copynumber: 6.6 Consensus size: 5 27322814 TTAATTTATT 27322824 TAATA TAATA TAATA TAATA TAATA T-ATA TAA 1 TAATA TAATA TAATA TAATA TAATA TAATA TAA 27322856 ATCATAAAAA Statistics Matches: 26, Mismatches: 0, Indels: 2 0.93 0.00 0.07 Matches are distributed among these distances: 4 4 0.15 5 22 0.85 ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41 Consensus pattern (5 bp): TAATA Found at i:27327156 original size:22 final size:22 Alignment explanation

Indices: 27327108--27327168 Score: 54 Period size: 22 Copynumber: 2.8 Consensus size: 22 27327098 AGCATTAACA * * 27327108 CAAAATAGTAGCAACATAATAG 1 CAAAATAGTAGCAAAACAATAG * * * 27327130 TAAAATTGTAGCAAAACAATGG 1 CAAAATAGTAGCAAAACAATAG 27327152 CAAAA-AGTGAG-AAAACA 1 CAAAATAGT-AGCAAAACA 27327169 GTGGCGAAAC Statistics Matches: 31, Mismatches: 7, Indels: 3 0.76 0.17 0.07 Matches are distributed among these distances: 21 8 0.26 22 23 0.74 ACGTcount: A:0.56, C:0.11, G:0.16, T:0.16 Consensus pattern (22 bp): CAAAATAGTAGCAAAACAATAG Done.