Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Chr10 129486693 

Parameters: 2 7 7 80 10 50 1000

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

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

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


File 332 of 444

Found at i:95859894 original size:79 final size:80

Alignment explanation

Indices: 95859698--95859900 Score: 257 Period size: 79 Copynumber: 2.5 Consensus size: 80 95859688 TGAATGAAAC * * * * * 95859698 CCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTATATTCGGGCTAAGACCCGAAGGCATTCG 1 CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGGTTATATCCGGGCTAAGACCCGAAGGCATTCG * *** 95859763 TGCGAGTTGTTAAAT 66 TGCAAGTTACCAAAT * * * 95859778 CCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTTGTTATA-CCGGGCTAAGACCCGAAGGCATTT 1 CCGGGCTAAGACCCGAAGGCAATT-GTGCTAGTGGTTATATCCGGGCTAAGACCCGAAGGCATTC 95859841 GTGCAAGTTACCAAAT 65 GTGCAAGTTACCAAAT * * 95859857 CCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTATATCCGG 1 CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGGTTATATCCGG 95859901 TTAGATTCCG Statistics Matches: 104, Mismatches: 16, Indels: 6 0.83 0.13 0.05 Matches are distributed among these distances: 79 67 0.64 80 37 0.36 ACGTcount: A:0.25, C:0.22, G:0.29, T:0.25 Consensus pattern (80 bp): CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGGTTATATCCGGGCTAAGACCCGAAGGCATTCG TGCAAGTTACCAAAT Found at i:95867846 original size:39 final size:38 Alignment explanation

Indices: 95867756--95867903 Score: 120 Period size: 39 Copynumber: 3.8 Consensus size: 38 95867746 ATCACGATTT * 95867756 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATGACTC 1 GCAC-AATGCCTTC-GGTCTTAGCCCGGATAGAATGACTA * 95867796 GCACGAATGCCTTCGGTCTTAGCCCGGAT-GTA-GCCACTA 1 GCAC-AATGCCTTCGGTCTTAGCCCGGATAGAATG--ACTA * * * ** * 95867835 GCACAATTGCCTTCGGTCTTAACCCGGTTATAATTTCCA 1 GCACAA-TGCCTTCGGTCTTAGCCCGGATAGAATGACTA * * * 95867874 GCATAATTGTCTTCGGGCTTAGCCCGGATA 1 GCACAA-TGCCTTCGGTCTTAGCCCGGATA 95867904 TCATTCAATT Statistics Matches: 88, Mismatches: 15, Indels: 11 0.77 0.13 0.10 Matches are distributed among these distances: 37 1 0.01 38 4 0.05 39 69 0.78 40 14 0.16 ACGTcount: A:0.22, C:0.28, G:0.23, T:0.27 Consensus pattern (38 bp): GCACAATGCCTTCGGTCTTAGCCCGGATAGAATGACTA Found at i:95868091 original size:28 final size:28 Alignment explanation

Indices: 95868030--95868127 Score: 108 Period size: 28 Copynumber: 3.5 Consensus size: 28 95868020 GGGTATNTTG ** * * 95868030 GCACTAAGTGTGCGGGTTCAAATTATACA 1 GCACTAAGTGTGCAAGTTC-GATTATATA * 95868059 GCACTAAGTGTGCAAGTTTGATTATATA 1 GCACTAAGTGTGCAAGTTCGATTATATA * * 95868087 GCACTAAGTGTGCGAGTTCGACTAT-TAA 1 GCACTAAGTGTGCAAGTTCGATTATAT-A 95868115 GCACTAAGTGTGC 1 GCACTAAGTGTGC 95868128 GGGCTTATTG Statistics Matches: 60, Mismatches: 8, Indels: 3 0.85 0.11 0.04 Matches are distributed among these distances: 27 1 0.02 28 43 0.72 29 16 0.27 ACGTcount: A:0.30, C:0.16, G:0.24, T:0.30 Consensus pattern (28 bp): GCACTAAGTGTGCAAGTTCGATTATATA Found at i:95879997 original size:40 final size:39 Alignment explanation

Indices: 95879952--95880159 Score: 236 Period size: 40 Copynumber: 5.2 Consensus size: 39 95879942 CGGATTACAA * 95879952 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGC 1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC * * 95879992 CCGGATATAACGACTTGCACAAATGCCTTCGGGTATTAGC 1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC * * * 95880032 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGC 1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC * ** * * 95880072 CCGGATGTAGTCACTAGCACAATTGCCTTCGGGTCTTAAC 1 CCGGATATAACCACT-GCACAAATGCCTTCGGGTCTTAGC ** * * 95880112 CCGGATATAATTACTAGCACAAATGTCTTCGGGACTTAGC 1 CCGGATATAACCACT-GCACAAATGCCTTCGGGTCTTAGC 95880152 CCGGATAT 1 CCGGATAT 95880160 CATTCAATTG Statistics Matches: 145, Mismatches: 22, Indels: 2 0.86 0.13 0.01 Matches are distributed among these distances: 39 1 0.01 40 144 0.99 ACGTcount: A:0.25, C:0.26, G:0.22, T:0.26 Consensus pattern (39 bp): CCGGATATAACCACTGCACAAATGCCTTCGGGTCTTAGC Found at i:95880092 original size:80 final size:80 Alignment explanation

Indices: 95879952--95880159 Score: 265 Period size: 80 Copynumber: 2.6 Consensus size: 80 95879942 CGGATTACAA * * * 95879952 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGCCCGGATATAACGACTTGCACAAATG 1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATATAACGACTAGCACAAATG * 95880017 CCTTCGGGTATTAGC 66 CCTTCGGGTATTAAC * * * * 95880032 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGTC-ACTAGCACAATT 1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATATA-ACGACTAGCACAAAT * 95880096 GCCTTCGGGTCTTAAC 65 GCCTTCGGGTATTAAC ** * * * * 95880112 CCGGATATAATTACTAGCACAAATGTCTTCGGGACTTAGCCCGGATAT 1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATAT 95880160 CATTCAATTG Statistics Matches: 110, Mismatches: 17, Indels: 2 0.85 0.13 0.02 Matches are distributed among these distances: 80 109 0.99 81 1 0.01 ACGTcount: A:0.25, C:0.26, G:0.22, T:0.26 Consensus pattern (80 bp): CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATATAACGACTAGCACAAATG CCTTCGGGTATTAAC Found at i:95888132 original size:40 final size:39 Alignment explanation

Indices: 95888087--95888294 Score: 236 Period size: 40 Copynumber: 5.2 Consensus size: 39 95888077 CGGATTACAA * 95888087 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGC 1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC * * 95888127 CCGGATATAACGACTTGCACAAATGCCTTCGGGTATTAGC 1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC * * * 95888167 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGC 1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC * ** * * 95888207 CCGGATGTAGTCACTAGCACAATTGCCTTCGGGTCTTAAC 1 CCGGATATAACCACT-GCACAAATGCCTTCGGGTCTTAGC ** * * 95888247 CCGGATATAATTACTAGCACAAATGTCTTCGGGACTTAGC 1 CCGGATATAACCACT-GCACAAATGCCTTCGGGTCTTAGC 95888287 CCGGATAT 1 CCGGATAT 95888295 CATTCAATTG Statistics Matches: 145, Mismatches: 22, Indels: 2 0.86 0.13 0.01 Matches are distributed among these distances: 39 1 0.01 40 144 0.99 ACGTcount: A:0.25, C:0.26, G:0.22, T:0.26 Consensus pattern (39 bp): CCGGATATAACCACTGCACAAATGCCTTCGGGTCTTAGC Found at i:95888227 original size:80 final size:80 Alignment explanation

Indices: 95888087--95888294 Score: 265 Period size: 80 Copynumber: 2.6 Consensus size: 80 95888077 CGGATTACAA * * * 95888087 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGCCCGGATATAACGACTTGCACAAATG 1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATATAACGACTAGCACAAATG * 95888152 CCTTCGGGTATTAGC 66 CCTTCGGGTATTAAC * * * * 95888167 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGTC-ACTAGCACAATT 1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATATA-ACGACTAGCACAAAT * 95888231 GCCTTCGGGTCTTAAC 65 GCCTTCGGGTATTAAC ** * * * * 95888247 CCGGATATAATTACTAGCACAAATGTCTTCGGGACTTAGCCCGGATAT 1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATAT 95888295 CATTCAATTG Statistics Matches: 110, Mismatches: 17, Indels: 2 0.85 0.13 0.02 Matches are distributed among these distances: 80 109 0.99 81 1 0.01 ACGTcount: A:0.25, C:0.26, G:0.22, T:0.26 Consensus pattern (80 bp): CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATATAACGACTAGCACAAATG CCTTCGGGTATTAAC Found at i:95890430 original size:38 final size:40 Alignment explanation

Indices: 95890378--95890571 Score: 162 Period size: 38 Copynumber: 4.6 Consensus size: 40 95890368 ATGTACAACT * * 95890378 GTGGCATATTCACTTAGCACCACGTTACATGT-T-TAACC 1 GTGGTATATCCACTTAGCACCACGTTACATGTATGTAACC * * 95890416 GTGATATATCCACTTAGCACCACGTTAATGAATCAATATATGTAACC 1 GTGGTATATCCACTTAGCACCACG-T--T--A-C-ATGTATGTAACC * * 95890463 GTGGCATATCCACTTAGCACCACGTTACATGTATCAATATGTGTAATC 1 GTGGTATATCCACTTAGCACCACGTTACATG------TA--TGTAACC * 95890511 GTGGTATATCCACTTAGCACCACGTTACACGTA--TAACC 1 GTGGTATATCCACTTAGCACCACGTTACATGTATGTAACC 95890549 GTGGTATATCCACTTAGCACCAC 1 GTGGTATATCCACTTAGCACCAC 95890572 ATTTTTTTCA Statistics Matches: 128, Mismatches: 11, Indels: 34 0.74 0.06 0.20 Matches are distributed among these distances: 38 48 0.38 39 1 0.01 40 2 0.02 41 2 0.02 42 3 0.02 43 1 0.01 44 2 0.02 45 3 0.02 46 4 0.03 47 27 0.21 48 35 0.27 ACGTcount: A:0.30, C:0.25, G:0.15, T:0.29 Consensus pattern (40 bp): GTGGTATATCCACTTAGCACCACGTTACATGTATGTAACC Found at i:95890520 original size:48 final size:48 Alignment explanation

Indices: 95890406--95890544 Score: 208 Period size: 48 Copynumber: 2.9 Consensus size: 48 95890396 ACCACGTTAC * * * 95890406 ATGTTTAACCGTGATATATCCACTTAGCACCACGTTA-ATGAATCAAT 1 ATGTGTAACCGTGGTATATCCACTTAGCACCACGTTACATGTATCAAT * * 95890453 ATATGTAACCGTGGCATATCCACTTAGCACCACGTTACATGTATCAAT 1 ATGTGTAACCGTGGTATATCCACTTAGCACCACGTTACATGTATCAAT * * 95890501 ATGTGTAATCGTGGTATATCCACTTAGCACCACGTTACACGTAT 1 ATGTGTAACCGTGGTATATCCACTTAGCACCACGTTACATGTAT 95890545 AACCGTGGTA Statistics Matches: 82, Mismatches: 9, Indels: 1 0.89 0.10 0.01 Matches are distributed among these distances: 47 33 0.40 48 49 0.60 ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31 Consensus pattern (48 bp): ATGTGTAACCGTGGTATATCCACTTAGCACCACGTTACATGTATCAAT Found at i:95892468 original size:13 final size:13 Alignment explanation

Indices: 95892450--95892474 Score: 50 Period size: 13 Copynumber: 1.9 Consensus size: 13 95892440 CTAAATCATA 95892450 ATTTTAGTAAAAT 1 ATTTTAGTAAAAT 95892463 ATTTTAGTAAAA 1 ATTTTAGTAAAA 95892475 CCTTTTTTTT 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:0.48, C:0.00, G:0.08, T:0.44 Consensus pattern (13 bp): ATTTTAGTAAAAT Found at i:95893354 original size:18 final size:19 Alignment explanation

Indices: 95893332--95893374 Score: 54 Period size: 18 Copynumber: 2.4 Consensus size: 19 95893322 TTTATACATT 95893332 AATTTAT-ATTTTTATAAA 1 AATTTATAATTTTTATAAA * * 95893350 CATTT-TAATTTTTTTAAA 1 AATTTATAATTTTTATAAA 95893368 AATTTAT 1 AATTTAT 95893375 CCCACAATTC Statistics Matches: 20, Mismatches: 3, Indels: 3 0.77 0.12 0.12 Matches are distributed among these distances: 17 1 0.05 18 18 0.90 19 1 0.05 ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58 Consensus pattern (19 bp): AATTTATAATTTTTATAAA Found at i:95894195 original size:54 final size:54 Alignment explanation

Indices: 95894132--95894249 Score: 218 Period size: 54 Copynumber: 2.2 Consensus size: 54 95894122 TAAATATCAA * 95894132 GGTCTCAATGAGCTGGACAGTGAATCTGTGATGGAAATTTTGTTGCCTAAAGCT 1 GGTCTCAATGAGCTGGACAGTGAATCTGTGATAGAAATTTTGTTGCCTAAAGCT * 95894186 GGTCTCAATGAGCTGGACTGTGAATCTGTGATAGAAATTTTGTTGCCTAAAGCT 1 GGTCTCAATGAGCTGGACAGTGAATCTGTGATAGAAATTTTGTTGCCTAAAGCT 95894240 GGTCTCAATG 1 GGTCTCAATG 95894250 GCCCAGAACT Statistics Matches: 62, Mismatches: 2, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 54 62 1.00 ACGTcount: A:0.25, C:0.15, G:0.27, T:0.32 Consensus pattern (54 bp): GGTCTCAATGAGCTGGACAGTGAATCTGTGATAGAAATTTTGTTGCCTAAAGCT Found at i:95894416 original size:22 final size:22 Alignment explanation

Indices: 95894388--95894434 Score: 85 Period size: 22 Copynumber: 2.1 Consensus size: 22 95894378 GAATAGGATT * 95894388 TGTTTTGTACAGTATTCGTCGG 1 TGTTTTGTACAGTATTAGTCGG 95894410 TGTTTTGTACAGTATTAGTCGG 1 TGTTTTGTACAGTATTAGTCGG 95894432 TGT 1 TGT 95894435 CATTCGATAA Statistics Matches: 24, Mismatches: 1, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 22 24 1.00 ACGTcount: A:0.15, C:0.11, G:0.28, T:0.47 Consensus pattern (22 bp): TGTTTTGTACAGTATTAGTCGG Found at i:95895060 original size:25 final size:26 Alignment explanation

Indices: 95895032--95895082 Score: 77 Period size: 26 Copynumber: 2.0 Consensus size: 26 95895022 AGTTTTTAAT 95895032 TGAG-AAGAAAAAAAGAAAATATGAA 1 TGAGAAAGAAAAAAAGAAAATATGAA * * 95895057 TGAGAAAGAAAAATAGAATATATGAA 1 TGAGAAAGAAAAAAAGAAAATATGAA 95895083 AAATAGAATA Statistics Matches: 23, Mismatches: 2, Indels: 1 0.88 0.08 0.04 Matches are distributed among these distances: 25 4 0.17 26 19 0.83 ACGTcount: A:0.65, C:0.00, G:0.20, T:0.16 Consensus pattern (26 bp): TGAGAAAGAAAAAAAGAAAATATGAA Found at i:95895097 original size:18 final size:16 Alignment explanation

Indices: 95895064--95895095 Score: 64 Period size: 16 Copynumber: 2.0 Consensus size: 16 95895054 GAATGAGAAA 95895064 GAAAAATAGAATATAT 1 GAAAAATAGAATATAT 95895080 GAAAAATAGAATATAT 1 GAAAAATAGAATATAT 95895096 ATCTCTATTT 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:0.62, C:0.00, G:0.12, T:0.25 Consensus pattern (16 bp): GAAAAATAGAATATAT Found at i:95898677 original size:2 final size:2 Alignment explanation

Indices: 95898670--95898700 Score: 62 Period size: 2 Copynumber: 15.5 Consensus size: 2 95898660 CATATGTAGG 95898670 TA 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 T 95898701 GAAGATATAC Statistics Matches: 29, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 29 1.00 ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52 Consensus pattern (2 bp): TA Found at i:95900256 original size:49 final size:49 Alignment explanation

Indices: 95900193--95900325 Score: 203 Period size: 49 Copynumber: 2.7 Consensus size: 49 95900183 TATTTGCTAT * * ** 95900193 CTTCAGTCTGTTCCACTGCAACTTCAGAGAGATAGGATCTGTAATTTAG 1 CTTCAATCTGTTCCACTGCAACTTCAGAGAAATAAAATCTGTAATTTAG * 95900242 CTTCAATCTGTTCCACTGCAACTTCAGGGAAATAAAATCTGTAATTTAG 1 CTTCAATCTGTTCCACTGCAACTTCAGAGAAATAAAATCTGTAATTTAG * * 95900291 CTTCAATCTATTCCACTGCAACTTCAGGGAAATAA 1 CTTCAATCTGTTCCACTGCAACTTCAGAGAAATAA 95900326 GATTCGCTAT Statistics Matches: 78, Mismatches: 6, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 49 78 1.00 ACGTcount: A:0.31, C:0.22, G:0.16, T:0.32 Consensus pattern (49 bp): CTTCAATCTGTTCCACTGCAACTTCAGAGAAATAAAATCTGTAATTTAG Found at i:95900574 original size:45 final size:42 Alignment explanation

Indices: 95900520--95901107 Score: 172 Period size: 45 Copynumber: 13.5 Consensus size: 42 95900510 ACTTCTGCTA * * 95900520 TGTTTCCCTACTGCTTAGAGGGTTAAGATTCGTCAATCTTCAGCC 1 TGTTACCCTACTGCTTAG-GGGTTAAGATTCGTCAAT-TTCA-TC ** * * 95900565 TGTTACCCTACTATTTAGGGGTTTAAGGCTT-GTCACATTTGATC 1 TGTTACCCTACTGCTTAGGGG-TTAA-GATTCGTCA-ATTTCATC * * * * 95900609 TATTTCCCTACTGCTTAGGGGGTTAAGA-TCTGTGAA-TTCAACC 1 TGTTACCCTACTGCTTA-GGGGTTAAGATTC-GTCAATTTC-ATC * * * * * 95900652 TGTTAACCTACTGTTTAGGGGGTTTAGGTTTGTCAATCTTCGATC 1 TGTTACCCTACTGCTTA-GGGGTTAAGATTCGTCAAT-TTC-ATC * * * * 95900697 TGTT-CCACTACTGTTTAGGGAGATAAGATTTGT-AATTTGATC 1 TGTTACC-CTACTGCTTAGGG-GTTAAGATTCGTCAATTTCATC 95900739 TGTTACCCTACTGCTTAGGGGTTTAAGACCATTCGTC---TTCGATC 1 TGTTACCCTACTGCTTAGGGG-TTAAG---ATTCGTCAATTTC-ATC * * *** * * * 95900783 TGCT-CCACTACTGCGTAAAAAGAT-A-ATTTGT-AATTTTCAGC 1 TGTTACC-CTACTGC-TTAGGGGTTAAGATTCGTCAA-TTTCATC * *** * * * 95900824 TTGTTACCCTACTGCATAGGGGTTTAAGGCCCATCACTTTTGC-TA 1 -TGTTACCCTACTGCTTAGGGG-TTAAGATTCGTCA-ATTT-CATC * * * 95900869 TGTTTCCCTACTGTTTAGGGGGTTAAGATTCGTCAATCTTCAGCC 1 TGTTACCCTACTGCTTA-GGGGTTAAGATTCGTCAAT-TTCA-TC * * * * 95900914 TGTTACCCTACTGTTTAGGGGTTTAAGGCTT-GTCACCTTTGATC 1 TGTTACCCTACTGCTTAGGGG-TTAA-GATTCGTCA-ATTTCATC * * * * 95900958 TGTTTCCTTACTGCTTAGGGGGTTAAGA-TCTGTGAA-TTCAACC 1 TGTTACCCTACTGCTTA-GGGGTTAAGATTC-GTCAATTTC-ATC ** * 95901001 TGTTACCCTACTATTTAGGGGGTTAAGATTTC-TCAATCTTTGATC 1 TGTTACCCTACTGCTTA-GGGGTTAAGA-TTCGTCAA--TTTCATC * * * * ** 95901046 TGCT-CCACCACTACTTAGGGAGATAAGA-TCTGT-AATTTGGTC 1 TGTTACC-CTACTGCTTAGGG-GTTAAGATTC-GTCAATTTCATC 95901088 TGTTACCCTACTGCTTAGGG 1 TGTTACCCTACTGCTTAGGG 95901108 AGATAAGGCT Statistics Matches: 395, Mismatches: 94, Indels: 111 0.66 0.16 0.19 Matches are distributed among these distances: 39 5 0.01 41 5 0.01 42 63 0.16 43 78 0.20 44 105 0.27 45 127 0.32 46 12 0.03 ACGTcount: A:0.21, C:0.20, G:0.21, T:0.38 Consensus pattern (42 bp): TGTTACCCTACTGCTTAGGGGTTAAGATTCGTCAATTTCATC Found at i:95900620 original size:89 final size:86 Alignment explanation

Indices: 95900463--95901107 Score: 447 Period size: 89 Copynumber: 7.4 Consensus size: 86 95900453 GAAAAAATTT * ** *** * * 95900463 GTAATTTTCAGCCTGTTACCCTATTGCATAGGGGTTTAAGGCCCATCACTTCTGCTATGTTTCCC 1 GTAA-TTTCAGCCTGTTACCCTACTGTTTAGGGGTTTAAGGCTTGTCACTT-TGATCTGTTTCCC * 95900528 TACTGCTTAGAGGGTTAAGATTC 64 TACTGCTTAGGGGGTTAAGATTC * * 95900551 GTCAATCTTCAGCCTGTTACCCTACTATTTAGGGGTTTAAGGCTTGTCACATTTGATCTATTTCC 1 GT-AAT-TTCAGCCTGTTACCCTACTGTTTAGGGGTTTAAGGCTTGTCAC-TTTGATCTGTTTCC 95900616 CTACTGCTTAGGGGGTTAAGA-TC 63 CTACTGCTTAGGGGGTTAAGATTC * * * * 95900639 TGTGAA-TTCAACCTGTTAACCTACTGTTTAGGGGGTTT-AGGTTTGTCAATCTTCGATCTG-TT 1 -GT-AATTTCAGCCTGTTACCCTACTGTTTA-GGGGTTTAAGGCTTGTC-A-CTTTGATCTGTTT * * * * 95900701 CCACTACTGTTTAGGGAGATAAGATTT 61 CC-CTACTGCTTAGGGGGTTAAGATTC * * * * * * 95900728 GTAATTTGA-TCTGTTACCCTACTGCTTAGGGGTTTAAGACCATTCGT--CTTCGATCTG-CTCC 1 GTAATTTCAGCCTGTTACCCTACTGTTTAGGGGTTTAAG-GC-TT-GTCACTTTGATCTGTTTCC * **** * * 95900789 ACTACTGCGTAAAAAGAT-A-ATTT 63 -CTACTGCTTAGGGGGTTAAGATTC * ** *** * * 95900812 GTAATTTTCAGCTTGTTACCCTACTGCATAGGGGTTTAAGGCCCATCACTTTTGCTATGTTTCCC 1 GTAA-TTTCAGCCTGTTACCCTACTGTTTAGGGGTTTAAGGCTTGTCAC-TTTGATCTGTTTCCC * 95900877 TACTGTTTAGGGGGTTAAGATTC 64 TACTGCTTAGGGGGTTAAGATTC 95900900 GTCAATCTTCAGCCTGTTACCCTACTGTTTAGGGGTTTAAGGCTTGTCACCTTTGATCTGTTTCC 1 GT-AAT-TTCAGCCTGTTACCCTACTGTTTAGGGGTTTAAGGCTTGTCA-CTTTGATCTGTTTCC * 95900965 TTACTGCTTAGGGGGTTAAGA-TC 63 CTACTGCTTAGGGGGTTAAGATTC * * * ** * * 95900988 TGTGAA-TTCAACCTGTTACCCTACTATTTAGGGGGTTAAGATTTCTCAATCTTTGATCTG-CTC 1 -GT-AATTTCAGCCTGTTACCCTACTGTTTAGGGGTTTAAGGCTTGTC-A-CTTTGATCTGTTTC * * * * 95901051 CACCACTACTTAGGGAGATAAGA-TC 62 C-CTACTGCTTAGGGGGTTAAGATTC * * * 95901076 TGTAATTT-GGTCTGTTACCCTACTGCTTAGGG 1 -GTAATTTCAGCCTGTTACCCTACTGTTTAGGG 95901108 AGATAAGGCT Statistics Matches: 445, Mismatches: 83, Indels: 59 0.76 0.14 0.10 Matches are distributed among these distances: 83 1 0.00 84 8 0.02 85 7 0.02 86 75 0.17 87 116 0.26 88 85 0.19 89 148 0.33 90 5 0.01 ACGTcount: A:0.21, C:0.21, G:0.21, T:0.37 Consensus pattern (86 bp): GTAATTTCAGCCTGTTACCCTACTGTTTAGGGGTTTAAGGCTTGTCACTTTGATCTGTTTCCCTA CTGCTTAGGGGGTTAAGATTC Found at i:95900895 original size:44 final size:44 Alignment explanation

Indices: 95900825--95900984 Score: 133 Period size: 44 Copynumber: 3.6 Consensus size: 44 95900815 ATTTTCAGCT * * * * * 95900825 TGTTACCCTACTGCATAGGGGTTTAAGGCCCATCACTTTTGCTA 1 TGTTACCCTACTGCTTAGGGGGTTAAGGCTCGTCACTTTTGCTC * * ** ** 95900869 TGTTTCCCTACTGTTTAGGGGGTTAAGATTCGTCAATCTTCAGC-C 1 TGTTACCCTACTGCTTAGGGGGTTAAGGCTCGTC-A-CTTTTGCTC * * * * * 95900914 TGTTACCCTACTGTTTAGGGGTTTAAGGCTTGTCACCTTTGATC 1 TGTTACCCTACTGCTTAGGGGGTTAAGGCTCGTCACTTTTGCTC * * 95900958 TGTTTCCTTACTGCTTAGGGGGTTAAG 1 TGTTACCCTACTGCTTAGGGGGTTAAG 95900985 ATCTGTGAAT Statistics Matches: 89, Mismatches: 24, Indels: 6 0.75 0.20 0.05 Matches are distributed among these distances: 43 3 0.03 44 51 0.57 45 30 0.34 46 5 0.06 ACGTcount: A:0.17, C:0.21, G:0.23, T:0.38 Consensus pattern (44 bp): TGTTACCCTACTGCTTAGGGGGTTAAGGCTCGTCACTTTTGCTC Found at i:95901097 original size:349 final size:349 Alignment explanation

Indices: 95900458--95901107 Score: 1111 Period size: 349 Copynumber: 1.9 Consensus size: 349 95900448 AGGGAGAAAA * 95900458 AATTTGTAATTTTCAGCCTGTTACCCTATTGCATAGGGGTTTAAGGCCCATCACTTCTGCTATGT 1 AATTTGTAATTTTCAGCCTGTTACCCTACTGCATAGGGGTTTAAGGCCCATCACTTCTGCTATGT 95900523 TTCCCTACTGCTTAGAGGGTTAAGATTCGTCAATCTTCAGCCTGTTACCCTACTATTTAGGGGTT 66 TTCCCTACTGCTTAGAGGGTTAAGATTCGTCAATCTTCAGCCTGTTACCCTACTATTTAGGGGTT 95900588 TAAGGCTTGTCACATTTGATCTATTTCCCTACTGCTTAGGGGGTTAAGATCTGTGAATTCAACCT 131 TAAGGCTTGTCACATTTGATCTATTTCCCTACTGCTTAGGGGGTTAAGATCTGTGAATTCAACCT * * * * * * ** 95900653 GTTAACCTACTGTTTAGGGGGTTTAGGTTTGTCAATCTTCGATCTGTTCCACTACTGTTTAGGGA 196 GTTAACCTACTATTTAGGGGGTTAAGATTTCTCAATCTTCGATCTGCTCCACCACTACTTAGGGA * 95900718 GATAAGATTTGTAATTTGATCTGTTACCCTACTGCTTAGGGGTTTAAGACCATTCGTCTTCGATC 261 GATAAGATCTGTAATTTGATCTGTTACCCTACTGCTTAGGGGTTTAAGACCATTCGTCTTCGATC 95900783 TGCTCCACTACTGCGTAAAAAGAT 326 TGCTCCACTACTGCGTAAAAAGAT * * 95900807 AATTTGTAATTTTCAGCTTGTTACCCTACTGCATAGGGGTTTAAGGCCCATCACTTTTGCTATGT 1 AATTTGTAATTTTCAGCCTGTTACCCTACTGCATAGGGGTTTAAGGCCCATCACTTCTGCTATGT * * * 95900872 TTCCCTACTGTTTAGGGGGTTAAGATTCGTCAATCTTCAGCCTGTTACCCTACTGTTTAGGGGTT 66 TTCCCTACTGCTTAGAGGGTTAAGATTCGTCAATCTTCAGCCTGTTACCCTACTATTTAGGGGTT * * * 95900937 TAAGGCTTGTCACCTTTGATCTGTTTCCTTACTGCTTAGGGGGTTAAGATCTGTGAATTCAACCT 131 TAAGGCTTGTCACATTTGATCTATTTCCCTACTGCTTAGGGGGTTAAGATCTGTGAATTCAACCT * * 95901002 GTTACCCTACTATTTAGGGGGTTAAGATTTCTCAATCTTTGATCTGCTCCACCACTACTTAGGGA 196 GTTAACCTACTATTTAGGGGGTTAAGATTTCTCAATCTTCGATCTGCTCCACCACTACTTAGGGA * 95901067 GATAAGATCTGTAATTTGGTCTGTTACCCTACTGCTTAGGG 261 GATAAGATCTGTAATTTGATCTGTTACCCTACTGCTTAGGG 95901108 AGATAAGGCT Statistics Matches: 280, Mismatches: 21, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 349 280 1.00 ACGTcount: A:0.21, C:0.20, G:0.21, T:0.38 Consensus pattern (349 bp): AATTTGTAATTTTCAGCCTGTTACCCTACTGCATAGGGGTTTAAGGCCCATCACTTCTGCTATGT TTCCCTACTGCTTAGAGGGTTAAGATTCGTCAATCTTCAGCCTGTTACCCTACTATTTAGGGGTT TAAGGCTTGTCACATTTGATCTATTTCCCTACTGCTTAGGGGGTTAAGATCTGTGAATTCAACCT GTTAACCTACTATTTAGGGGGTTAAGATTTCTCAATCTTCGATCTGCTCCACCACTACTTAGGGA GATAAGATCTGTAATTTGATCTGTTACCCTACTGCTTAGGGGTTTAAGACCATTCGTCTTCGATC TGCTCCACTACTGCGTAAAAAGAT Found at i:95905995 original size:27 final size:26 Alignment explanation

Indices: 95905948--95905998 Score: 75 Period size: 27 Copynumber: 1.9 Consensus size: 26 95905938 CGTGCTCTCC * 95905948 TTCTTTCTTGCTTCTTTTCTAGCTCT 1 TTCTTTCTTGCTTCTTGTCTAGCTCT * 95905974 TTCTTTCTTTGTTTCTTGTCTAGCT 1 TTCTTTC-TTGCTTCTTGTCTAGCT 95905999 TAAATCCTAA Statistics Matches: 22, Mismatches: 2, Indels: 1 0.88 0.08 0.04 Matches are distributed among these distances: 26 7 0.32 27 15 0.68 ACGTcount: A:0.04, C:0.24, G:0.10, T:0.63 Consensus pattern (26 bp): TTCTTTCTTGCTTCTTGTCTAGCTCT Found at i:95907431 original size:24 final size:24 Alignment explanation

Indices: 95907404--95907453 Score: 73 Period size: 24 Copynumber: 2.1 Consensus size: 24 95907394 AAATCTCGTG 95907404 ATCCAATTGATCATGGAACTCGCA 1 ATCCAATTGATCATGGAACTCGCA ** * 95907428 ATCCTCTTGATCATGGAACTTGCA 1 ATCCAATTGATCATGGAACTCGCA 95907452 AT 1 AT 95907454 AATTCTTTAC Statistics Matches: 23, Mismatches: 3, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 24 23 1.00 ACGTcount: A:0.30, C:0.24, G:0.16, T:0.30 Consensus pattern (24 bp): ATCCAATTGATCATGGAACTCGCA Found at i:95913257 original size:2 final size:2 Alignment explanation

Indices: 95913214--95913240 Score: 54 Period size: 2 Copynumber: 13.5 Consensus size: 2 95913204 AACAGTAATA 95913214 AT 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 AT A 95913241 AATGATGACG 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:0.52, C:0.00, G:0.00, T:0.48 Consensus pattern (2 bp): AT Found at i:95913768 original size:3 final size:3 Alignment explanation

Indices: 95913762--95913824 Score: 126 Period size: 3 Copynumber: 21.0 Consensus size: 3 95913752 ACACTACTAT 95913762 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA 1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA 95913810 ATA ATA ATA ATA ATA 1 ATA ATA ATA ATA ATA 95913825 TAGAAATGCA Statistics Matches: 60, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 3 60 1.00 ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33 Consensus pattern (3 bp): ATA Found at i:95917050 original size:22 final size:22 Alignment explanation

Indices: 95917025--95917076 Score: 61 Period size: 22 Copynumber: 2.4 Consensus size: 22 95917015 TAAATTTGGA 95917025 ACATATATACA-ATATCATTTAT 1 ACATATATACATATAT-ATTTAT ** 95917047 ACATATATTTATATATATTTAT 1 ACATATATACATATATATTTAT * 95917069 ATATATAT 1 ACATATAT 95917077 TATTTTTTAC Statistics Matches: 26, Mismatches: 3, Indels: 2 0.84 0.10 0.06 Matches are distributed among these distances: 22 22 0.85 23 4 0.15 ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48 Consensus pattern (22 bp): ACATATATACATATATATTTAT Found at i:95917058 original size:12 final size:12 Alignment explanation

Indices: 95917030--95917077 Score: 55 Period size: 12 Copynumber: 4.0 Consensus size: 12 95917020 TTGGAACATA 95917030 TATACAATATCATT 1 TATAC-ATAT-ATT 95917044 TATACATATATT 1 TATACATATATT 95917056 TAT--ATATATT 1 TATACATATATT * 95917066 TATATATATATT 1 TATACATATATT 95917078 ATTTTTTACA Statistics Matches: 32, Mismatches: 0, Indels: 6 0.84 0.00 0.16 Matches are distributed among these distances: 10 10 0.31 12 13 0.41 13 4 0.12 14 5 0.16 ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52 Consensus pattern (12 bp): TATACATATATT Found at i:95917064 original size:10 final size:10 Alignment explanation

Indices: 95917049--95917079 Score: 53 Period size: 10 Copynumber: 3.0 Consensus size: 10 95917039 TCATTTATAC 95917049 ATATATTTAT 1 ATATATTTAT 95917059 ATATATTTAT 1 ATATATTTAT 95917069 ATATATATTAT 1 ATATAT-TTAT 95917080 TTTTTACATT Statistics Matches: 20, Mismatches: 0, Indels: 1 0.95 0.00 0.05 Matches are distributed among these distances: 10 16 0.80 11 4 0.20 ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58 Consensus pattern (10 bp): ATATATTTAT Found at i:95925656 original size:17 final size:17 Alignment explanation

Indices: 95925617--95925662 Score: 51 Period size: 18 Copynumber: 2.6 Consensus size: 17 95925607 TTTACCCCCA 95925617 TTTACTTTCCCTC-AAACT 1 TTTA-TTTCCC-CAAAACT 95925635 TTTA-TTCCCCAAAACTT 1 TTTATTTCCCCAAAAC-T 95925652 TTTATTTCCCC 1 TTTATTTCCCC 95925663 CCTAAACTTC Statistics Matches: 25, Mismatches: 0, Indels: 6 0.81 0.00 0.19 Matches are distributed among these distances: 15 1 0.04 16 9 0.36 17 5 0.20 18 10 0.40 ACGTcount: A:0.22, C:0.33, G:0.00, T:0.46 Consensus pattern (17 bp): TTTATTTCCCCAAAACT Found at i:95928162 original size:17 final size:17 Alignment explanation

Indices: 95928126--95928226 Score: 67 Period size: 17 Copynumber: 5.9 Consensus size: 17 95928116 AAATTATGAA * * * 95928126 TTCACACCAAACAACTG 1 TTCATACCAAATAACAG ** 95928143 TTCATATGAAATAACAG 1 TTCATACCAAATAACAG * * * 95928160 TTCTTACCAAATGACAA 1 TTCATACCAAATAACAG * * * * 95928177 CTCATGCAAAATAATAG 1 TTCATACCAAATAACAG ** * 95928194 TTCATATGAAATATCAG 1 TTCATACCAAATAACAG 95928211 TTCATACCAAATAACA 1 TTCATACCAAATAACA 95928227 ATTTATGCAA Statistics Matches: 58, Mismatches: 26, Indels: 0 0.69 0.31 0.00 Matches are distributed among these distances: 17 58 1.00 ACGTcount: A:0.45, C:0.21, G:0.08, T:0.27 Consensus pattern (17 bp): TTCATACCAAATAACAG Found at i:95928202 original size:51 final size:51 Alignment explanation

Indices: 95928142--95928249 Score: 162 Period size: 51 Copynumber: 2.1 Consensus size: 51 95928132 CCAAACAACT * * 95928142 GTTCATATGAAATAACAGTTCTTACCAAATGACAACTCATGCAAAATAATA 1 GTTCATATGAAATAACAGTTCATACCAAATAACAACTCATGCAAAATAATA * * * * 95928193 GTTCATATGAAATATCAGTTCATACCAAATAACAATTTATGCAAAATAATT 1 GTTCATATGAAATAACAGTTCATACCAAATAACAACTCATGCAAAATAATA 95928244 GTTCAT 1 GTTCAT 95928250 GCTTAATCAT Statistics Matches: 51, Mismatches: 6, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 51 51 1.00 ACGTcount: A:0.44, C:0.16, G:0.09, T:0.31 Consensus pattern (51 bp): GTTCATATGAAATAACAGTTCATACCAAATAACAACTCATGCAAAATAATA Found at i:95928939 original size:18 final size:18 Alignment explanation

Indices: 95928894--95928928 Score: 61 Period size: 18 Copynumber: 1.9 Consensus size: 18 95928884 AGTTTGACAA * 95928894 ATTAATACAGCTCACCAT 1 ATTAATACAGATCACCAT 95928912 ATTAATACAGATCACCA 1 ATTAATACAGATCACCA 95928929 ATTTAACACA Statistics Matches: 16, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 18 16 1.00 ACGTcount: A:0.43, C:0.26, G:0.06, T:0.26 Consensus pattern (18 bp): ATTAATACAGATCACCAT Found at i:95932755 original size:45 final size:45 Alignment explanation

Indices: 95932671--95932891 Score: 270 Period size: 45 Copynumber: 5.0 Consensus size: 45 95932661 AATATCGCAC * * * * ** 95932671 AATAATATTCAGGCCTTTGAGCCAAGCAAGCTATGATGCCGGTGA 1 AATACTATTCGGGCCTTTGAGCCTAGCAGGCTACAATGCCGGTGA * * 95932716 GATACTATTCGGGCCTTTGAGCCTAGTAGGCTACAATGCCGGTGA 1 AATACTATTCGGGCCTTTGAGCCTAGCAGGCTACAATGCCGGTGA * * 95932761 GATACTATTCGAGCCTTTGAGCCTAGCAGGCTACAATGCCGGTGA 1 AATACTATTCGGGCCTTTGAGCCTAGCAGGCTACAATGCCGGTGA ** * 95932806 AATACTATTCGGGCCTTCAAGCCTAGCAGGCTATAATGCCGGTGA 1 AATACTATTCGGGCCTTTGAGCCTAGCAGGCTACAATGCCGGTGA * * 95932851 AATGA-TA-TCGGG-CTTCGAGCCTAGCAGGCGA-AATGCCGGTG 1 AAT-ACTATTCGGGCCTTTGAGCCTAGCAGGCTACAATGCCGGTG 95932892 GATGAATTCG Statistics Matches: 158, Mismatches: 17, Indels: 5 0.88 0.09 0.03 Matches are distributed among these distances: 42 10 0.06 43 17 0.11 44 5 0.03 45 125 0.79 46 1 0.01 ACGTcount: A:0.26, C:0.23, G:0.28, T:0.24 Consensus pattern (45 bp): AATACTATTCGGGCCTTTGAGCCTAGCAGGCTACAATGCCGGTGA Found at i:95935726 original size:21 final size:21 Alignment explanation

Indices: 95935687--95935726 Score: 55 Period size: 20 Copynumber: 1.9 Consensus size: 21 95935677 AAAACATTCA * 95935687 ATTTGCTTAAATTCATTAAGT 1 ATTTGCTTAAATTAATTAAGT 95935708 ATTT-CTTAAATTAAGTTAA 1 ATTTGCTTAAATTAA-TTAA 95935727 AATAACTTTT Statistics Matches: 17, Mismatches: 1, Indels: 2 0.85 0.05 0.10 Matches are distributed among these distances: 20 9 0.53 21 8 0.47 ACGTcount: A:0.38, C:0.07, G:0.07, T:0.47 Consensus pattern (21 bp): ATTTGCTTAAATTAATTAAGT Found at i:95936421 original size:32 final size:31 Alignment explanation

Indices: 95936356--95936422 Score: 82 Period size: 32 Copynumber: 2.1 Consensus size: 31 95936346 ACCTAAAATT * * * 95936356 ATTAATTCTAATTATTCTAATATTTTATTTA 1 ATTAATTCTAATTATTCTAATATATAATCTA 95936387 ATTAATTCATAATTATTC-AATTATATAATCTA 1 ATTAATTC-TAATTATTCTAA-TATATAATCTA 95936419 ATTA 1 ATTA 95936423 TGGTTTTCGG Statistics Matches: 31, Mismatches: 3, Indels: 3 0.84 0.08 0.08 Matches are distributed among these distances: 31 10 0.32 32 21 0.68 ACGTcount: A:0.40, C:0.07, G:0.00, T:0.52 Consensus pattern (31 bp): ATTAATTCTAATTATTCTAATATATAATCTA Found at i:95936713 original size:73 final size:73 Alignment explanation

Indices: 95936594--95936743 Score: 300 Period size: 73 Copynumber: 2.1 Consensus size: 73 95936584 GGACTACATG 95936594 TTTAAAAACCTCACATTTAGAAAATTCAATTAGCTTGAATTGTGTCTTTCCATTTTGACCAATCT 1 TTTAAAAACCTCACATTTAGAAAATTCAATTAGCTTGAATTGTGTCTTTCCATTTTGACCAATCT 95936659 TTTCTATT 66 TTTCTATT 95936667 TTTAAAAACCTCACATTTAGAAAATTCAATTAGCTTGAATTGTGTCTTTCCATTTTGACCAATCT 1 TTTAAAAACCTCACATTTAGAAAATTCAATTAGCTTGAATTGTGTCTTTCCATTTTGACCAATCT 95936732 TTTCTATT 66 TTTCTATT 95936740 TTTA 1 TTTA 95936744 TATTCCTTAT Statistics Matches: 77, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 73 77 1.00 ACGTcount: A:0.30, C:0.17, G:0.08, T:0.45 Consensus pattern (73 bp): TTTAAAAACCTCACATTTAGAAAATTCAATTAGCTTGAATTGTGTCTTTCCATTTTGACCAATCT TTTCTATT Found at i:95938467 original size:2 final size:2 Alignment explanation

Indices: 95938460--95938497 Score: 67 Period size: 2 Copynumber: 19.0 Consensus size: 2 95938450 AACTATCTTA * 95938460 AT AT AT AT AT AT AT AT AT AT AT AC 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 95938498 GTGTGTGTAT Statistics Matches: 34, Mismatches: 2, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 2 34 1.00 ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47 Consensus pattern (2 bp): AT Found at i:95941996 original size:39 final size:39 Alignment explanation

Indices: 95941915--95942077 Score: 263 Period size: 39 Copynumber: 4.2 Consensus size: 39 95941905 TATGGTAACC * * 95941915 CGCACAAATGCCTTCGGGACTTAACCCGGATATCACAACT 1 CGCACAATTGCCTTCGGG-CTTAGCCCGGATATCACAACT * * 95941955 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAGCT 1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT * 95941994 CGCACCATTGCCTTCGGGCTTAGCCCGGATATCACAACT 1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT * 95942033 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAATT 1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT 95942072 CGCACA 1 CGCACA 95942078 TTCATACACA Statistics Matches: 114, Mismatches: 9, Indels: 1 0.92 0.07 0.01 Matches are distributed among these distances: 39 97 0.85 40 17 0.15 ACGTcount: A:0.24, C:0.33, G:0.20, T:0.23 Consensus pattern (39 bp): CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT Found at i:95949989 original size:38 final size:39 Alignment explanation

Indices: 95949892--95950053 Score: 263 Period size: 39 Copynumber: 4.2 Consensus size: 39 95949882 TATGGTAACC * * 95949892 CGCACAAATGCCTTCGGGACTTAACCCGGATATCACAACT 1 CGCACAATTGCCTTCGGG-CTTAGCCCGGATATCACAACT * * 95949932 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAGCT 1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT 95949971 CGCAC-ATTGCCTTCGGGCTTAGCCCGGATATCACAACT 1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT * 95950009 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAATT 1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT 95950048 CGCACA 1 CGCACA 95950054 TTCATACACA Statistics Matches: 114, Mismatches: 7, Indels: 3 0.92 0.06 0.02 Matches are distributed among these distances: 38 36 0.32 39 61 0.54 40 17 0.15 ACGTcount: A:0.24, C:0.33, G:0.20, T:0.23 Consensus pattern (39 bp): CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT Found at i:95950051 original size:77 final size:78 Alignment explanation

Indices: 95949900--95950055 Score: 269 Period size: 77 Copynumber: 2.0 Consensus size: 78 95949890 CCCGCACAAA 95949900 TGCCTTCGGGACTTAACCCGGATATCACAACTCGCACAATTGCCTTCGGGCTTAGCCCGGATATC 1 TGCCTTCGGGACTTAACCCGGATATCACAACTCGCACAATTGCCTTCGGGCTTAGCCCGGATATC * * 95949965 ATAGCTCGCACAT 66 ACAACTCGCACAT * 95949978 TGCCTTCGGG-CTTAGCCCGGATATCACAACTCGCACAATTGCCTTCGGGCTTAGCCCGGATATC 1 TGCCTTCGGGACTTAACCCGGATATCACAACTCGCACAATTGCCTTCGGGCTTAGCCCGGATATC * 95950042 ACAATTCGCACAT 66 ACAACTCGCACAT 95950055 T 1 T 95950056 CATACACATC Statistics Matches: 74, Mismatches: 4, Indels: 1 0.94 0.05 0.01 Matches are distributed among these distances: 77 64 0.86 78 10 0.14 ACGTcount: A:0.22, C:0.32, G:0.21, T:0.25 Consensus pattern (78 bp): TGCCTTCGGGACTTAACCCGGATATCACAACTCGCACAATTGCCTTCGGGCTTAGCCCGGATATC ACAACTCGCACAT Found at i:95953958 original size:38 final size:38 Alignment explanation

Indices: 95953916--95953990 Score: 107 Period size: 38 Copynumber: 2.0 Consensus size: 38 95953906 CTTAAAGACC 95953916 CGCAGGCTAT-ATGCTAGAATTATATCCGGGTTAAATCA 1 CGCAGGCT-TCATGCTAGAATTATATCCGGGTTAAATCA * * * 95953954 CGCAGGCTTCGTGCTGGTATTATATCCGGGTTAAATC 1 CGCAGGCTTCATGCTAGAATTATATCCGGGTTAAATC 95953991 CCGAAGGCCT Statistics Matches: 33, Mismatches: 3, Indels: 2 0.87 0.08 0.05 Matches are distributed among these distances: 37 1 0.03 38 32 0.97 ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31 Consensus pattern (38 bp): CGCAGGCTTCATGCTAGAATTATATCCGGGTTAAATCA Found at i:95954006 original size:38 final size:38 Alignment explanation

Indices: 95953934--95954017 Score: 132 Period size: 38 Copynumber: 2.2 Consensus size: 38 95953924 ATATGCTAGA * * * 95953934 ATTATATCCGGGTTAAATCACGCAGGCTTCGTGCTGGT 1 ATTATATCCGGGTTAAATCACGAAGGCCTAGTGCTGGT * 95953972 ATTATATCCGGGTTAAATCCCGAAGGCCTAGTGCTGGT 1 ATTATATCCGGGTTAAATCACGAAGGCCTAGTGCTGGT 95954010 ATTATATC 1 ATTATATC 95954018 TGAGTTTAAA Statistics Matches: 42, Mismatches: 4, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 38 42 1.00 ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32 Consensus pattern (38 bp): ATTATATCCGGGTTAAATCACGAAGGCCTAGTGCTGGT Found at i:95954408 original size:26 final size:26 Alignment explanation

Indices: 95954371--95954480 Score: 186 Period size: 26 Copynumber: 4.2 Consensus size: 26 95954361 TGATACAAAT * 95954371 TGATAATAGGTTAGGTAAATG-TTCAA 1 TGATAATGGGTTAGGTAAATGTTTC-A * 95954397 TGATAATGGGTTAGGTAAATGTTCCA 1 TGATAATGGGTTAGGTAAATGTTTCA 95954423 TGATAATGGGTTAGGTAAATGTTTCA 1 TGATAATGGGTTAGGTAAATGTTTCA 95954449 TGATAATGGGTTAGGTAAATGTTTCA 1 TGATAATGGGTTAGGTAAATGTTTCA 95954475 TGATAA 1 TGATAA 95954481 GAATTTCATG Statistics Matches: 80, Mismatches: 3, Indels: 2 0.94 0.04 0.02 Matches are distributed among these distances: 26 78 0.98 27 2 0.03 ACGTcount: A:0.34, C:0.05, G:0.25, T:0.36 Consensus pattern (26 bp): TGATAATGGGTTAGGTAAATGTTTCA Found at i:95956571 original size:46 final size:46 Alignment explanation

Indices: 95956504--95956598 Score: 190 Period size: 46 Copynumber: 2.1 Consensus size: 46 95956494 GACAAGAAAA 95956504 CACCGAGTGAGTTTACAACTCAGTAAGTCATAAGCATTCATCAATC 1 CACCGAGTGAGTTTACAACTCAGTAAGTCATAAGCATTCATCAATC 95956550 CACCGAGTGAGTTTACAACTCAGTAAGTCATAAGCATTCATCAATC 1 CACCGAGTGAGTTTACAACTCAGTAAGTCATAAGCATTCATCAATC 95956596 CAC 1 CAC 95956599 TGATAAAGTT Statistics Matches: 49, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 46 49 1.00 ACGTcount: A:0.35, C:0.25, G:0.15, T:0.25 Consensus pattern (46 bp): CACCGAGTGAGTTTACAACTCAGTAAGTCATAAGCATTCATCAATC Found at i:95957045 original size:29 final size:29 Alignment explanation

Indices: 95957017--95957118 Score: 150 Period size: 29 Copynumber: 3.5 Consensus size: 29 95957007 CCTCCGAGCT ** * * * 95957017 CGCACACCCAGTGCCGTATTTTTCCAGCT 1 CGCACACTTAGTGCCATATATTTCCAGCA * 95957046 TGCACACTTAGTGCCATATATTTCCAGCA 1 CGCACACTTAGTGCCATATATTTCCAGCA 95957075 CGCACACTTAGTGCCATATATTTCCAGCA 1 CGCACACTTAGTGCCATATATTTCCAGCA 95957104 CGCACACTTAGTGCC 1 CGCACACTTAGTGCC 95957119 GATCTCGTCA Statistics Matches: 66, Mismatches: 7, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 29 66 1.00 ACGTcount: A:0.24, C:0.33, G:0.16, T:0.27 Consensus pattern (29 bp): CGCACACTTAGTGCCATATATTTCCAGCA Found at i:95959052 original size:28 final size:26 Alignment explanation

Indices: 95959010--95959084 Score: 87 Period size: 26 Copynumber: 2.8 Consensus size: 26 95959000 AAAAGTAGCT * 95959010 AAATTACTATAATACCCCTATGTATGGA 1 AAATTACTATTATACCCCTA-G-ATGGA * * 95959038 AAATTACTATTATACCCCTAGGTGTA 1 AAATTACTATTATACCCCTAGATGGA ** 95959064 AAATTACCGTTATACCCCTAG 1 AAATTACTATTATACCCCTAG 95959085 GGTTAATTTT Statistics Matches: 42, Mismatches: 5, Indels: 2 0.86 0.10 0.04 Matches are distributed among these distances: 26 22 0.52 27 1 0.02 28 19 0.45 ACGTcount: A:0.36, C:0.21, G:0.11, T:0.32 Consensus pattern (26 bp): AAATTACTATTATACCCCTAGATGGA Found at i:95959229 original size:27 final size:27 Alignment explanation

Indices: 95959188--95959326 Score: 174 Period size: 27 Copynumber: 5.2 Consensus size: 27 95959178 GAGGAAGCGT * 95959188 TCTGGTGGCTATGCCACAAATATCTGA 1 TCTGGTGGCTCTGCCACAAATATCTGA 95959215 TCTGGTGGCTCTGCCACAAATATCTGA 1 TCTGGTGGCTCTGCCACAAATATCTGA * * 95959242 TCTGGTGGCTCTGCCACATATATCTGT 1 TCTGGTGGCTCTGCCACAAATATCTGA * * 95959269 TCTGGTGGC-CTGCCACGATTATCTGTA 1 TCTGGTGGCTCTGCCACAAATATCTG-A * * * * 95959296 TCTGGTGACTCTGTCAC-ATTATCTGT 1 TCTGGTGGCTCTGCCACAAATATCTGA 95959322 TCTGG 1 TCTGG 95959327 CAGCCATGCT Statistics Matches: 100, Mismatches: 10, Indels: 5 0.87 0.09 0.04 Matches are distributed among these distances: 26 18 0.18 27 76 0.76 28 6 0.06 ACGTcount: A:0.18, C:0.24, G:0.23, T:0.35 Consensus pattern (27 bp): TCTGGTGGCTCTGCCACAAATATCTGA Found at i:95959273 original size:54 final size:54 Alignment explanation

Indices: 95959188--95959326 Score: 192 Period size: 54 Copynumber: 2.6 Consensus size: 54 95959178 GAGGAAGCGT * * * 95959188 TCTGGTGGCTATGCCACAAATATCTGATCTGGTGGCTCTGCCACAAATATCTG-A 1 TCTGGTGGCTCTGCCACATATATCTGTTCTGGTGGC-CTGCCACAAATATCTGTA * * 95959242 TCTGGTGGCTCTGCCACATATATCTGTTCTGGTGGCCTGCCACGATTATCTGTA 1 TCTGGTGGCTCTGCCACATATATCTGTTCTGGTGGCCTGCCACAAATATCTGTA * * 95959296 TCTGGTGACTCTGTCACAT-TATCTGTTCTGG 1 TCTGGTGGCTCTGCCACATATATCTGTTCTGG 95959327 CAGCCATGCT Statistics Matches: 77, Mismatches: 7, Indels: 3 0.89 0.08 0.03 Matches are distributed among these distances: 53 26 0.34 54 51 0.66 ACGTcount: A:0.18, C:0.24, G:0.23, T:0.35 Consensus pattern (54 bp): TCTGGTGGCTCTGCCACATATATCTGTTCTGGTGGCCTGCCACAAATATCTGTA Found at i:95963704 original size:40 final size:39 Alignment explanation

Indices: 95963539--95963722 Score: 138 Period size: 40 Copynumber: 4.6 Consensus size: 39 95963529 AAATTGAATG * * * 95963539 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAAT--T 1 ATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCAAATCGT * * * * * * 95963579 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT 1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-T * * * * * 95963619 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCATT 1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATC-GT * 95963659 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT 1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT * * * 95963698 GATATCCGGGTTAAGTCCCGTAGGC 1 -ATATCCGGGCTAAGACCCGAAGGC 95963723 CTTGGTGCGG Statistics Matches: 113, Mismatches: 26, Indels: 10 0.76 0.17 0.07 Matches are distributed among these distances: 37 4 0.04 38 2 0.02 39 3 0.03 40 104 0.92 ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22 Consensus pattern (39 bp): ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT Found at i:95963747 original size:80 final size:81 Alignment explanation

Indices: 95963579--95963767 Score: 186 Period size: 80 Copynumber: 2.4 Consensus size: 81 95963569 GCTGGAAATT * * * * 95963579 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCTACATCCGGGCTAAGACCCGAAGGCA 1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA * 95963644 TTCGTGCGAGTCATTC 66 TTCGTGCGAGTCATCC * * * * * * 95963660 -TATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-TGATATCCGGGTTAAGTCCCGTAGGC 1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCT-ACATCCGGGCTAAGACCCGAAGGC * * * * 95963723 CTTGGTGCGGGTTA-CC 65 ATTCGTGCGAGTCATCC * * * 95963739 ATAACCGGGCTATGTCCCGAAGGCGATTG 1 ATAACCGGGCTAAGACCCGAAGGCAATTG 95963768 ATCGAGTAGC Statistics Matches: 86, Mismatches: 20, Indels: 5 0.77 0.18 0.05 Matches are distributed among these distances: 79 2 0.02 80 84 0.98 ACGTcount: A:0.23, C:0.24, G:0.30, T:0.23 Consensus pattern (81 bp): ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA TTCGTGCGAGTCATCC Found at i:95971819 original size:40 final size:39 Alignment explanation

Indices: 95971654--95971837 Score: 138 Period size: 40 Copynumber: 4.6 Consensus size: 39 95971644 AAATTGAATG * * * 95971654 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAAT--T 1 ATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCAAATCGT * * * * * * 95971694 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT 1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-T * * * * * 95971734 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCATT 1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATC-GT * 95971774 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT 1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT * * * 95971813 GATATCCGGGTTAAGTCCCGTAGGC 1 -ATATCCGGGCTAAGACCCGAAGGC 95971838 CTTGGTGCGG Statistics Matches: 113, Mismatches: 26, Indels: 10 0.76 0.17 0.07 Matches are distributed among these distances: 37 4 0.04 38 2 0.02 39 3 0.03 40 104 0.92 ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22 Consensus pattern (39 bp): ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT Found at i:95971862 original size:80 final size:81 Alignment explanation

Indices: 95971694--95971882 Score: 186 Period size: 80 Copynumber: 2.4 Consensus size: 81 95971684 GCTGGAAATT * * * * 95971694 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCTACATCCGGGCTAAGACCCGAAGGCA 1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA * 95971759 TTCGTGCGAGTCATTC 66 TTCGTGCGAGTCATCC * * * * * * 95971775 -TATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-TGATATCCGGGTTAAGTCCCGTAGGC 1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCT-ACATCCGGGCTAAGACCCGAAGGC * * * * 95971838 CTTGGTGCGGGTTA-CC 65 ATTCGTGCGAGTCATCC * * * 95971854 ATAACCGGGCTATGTCCCGAAGGCGATTG 1 ATAACCGGGCTAAGACCCGAAGGCAATTG 95971883 ATCGAGTAGC Statistics Matches: 86, Mismatches: 20, Indels: 5 0.77 0.18 0.05 Matches are distributed among these distances: 79 2 0.02 80 84 0.98 ACGTcount: A:0.23, C:0.24, G:0.30, T:0.23 Consensus pattern (81 bp): ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA TTCGTGCGAGTCATCC Found at i:95974767 original size:26 final size:25 Alignment explanation

Indices: 95974731--95974840 Score: 148 Period size: 26 Copynumber: 4.2 Consensus size: 25 95974721 TGATACAAAT 95974731 TGATAATAGGTTAGGTAAATGTTCAA 1 TGATAATAGGTTAGGTAAATGTTC-A * 95974757 TGATAATAGGTTAGGTAAATATTCCA 1 TGATAATAGGTTAGGTAAATGTT-CA * 95974783 TGATAATGGGTTAGGTAAATGTTTCA 1 TGATAATAGGTTAGGTAAATG-TTCA * 95974809 TGATAATGGGTTAGGTAAATGTTTCA 1 TGATAATAGGTTAGGTAAATG-TTCA * 95974835 CGATAA 1 TGATAA 95974841 GAATTTCATG Statistics Matches: 78, Mismatches: 4, Indels: 4 0.91 0.05 0.05 Matches are distributed among these distances: 26 75 0.96 27 3 0.04 ACGTcount: A:0.35, C:0.05, G:0.24, T:0.35 Consensus pattern (25 bp): TGATAATAGGTTAGGTAAATGTTCA Found at i:95976322 original size:28 final size:26 Alignment explanation

Indices: 95976289--95976353 Score: 85 Period size: 26 Copynumber: 2.4 Consensus size: 26 95976279 AAGTACTATA * * 95976289 ATACCCCTATGTACGGAAAATTACTGTT 1 ATACCCCTAGGT--GGAAAATTACCGTT * 95976317 ATACCCCTAGGTGTAAAATTACCGTT 1 ATACCCCTAGGTGGAAAATTACCGTT 95976343 ATACCCCTAGG 1 ATACCCCTAGG 95976354 GTTAATTTTG Statistics Matches: 34, Mismatches: 3, Indels: 2 0.87 0.08 0.05 Matches are distributed among these distances: 26 23 0.68 28 11 0.32 ACGTcount: A:0.31, C:0.25, G:0.15, T:0.29 Consensus pattern (26 bp): ATACCCCTAGGTGGAAAATTACCGTT Found at i:95976497 original size:27 final size:27 Alignment explanation

Indices: 95976456--95976595 Score: 165 Period size: 27 Copynumber: 5.2 Consensus size: 27 95976446 GAGGAAGCGT * 95976456 TCTGGTGGCTATGCCACAAATATCTGA 1 TCTGGTGGCTCTGCCACAAATATCTGA 95976483 TCTGGTGGCTCTGCCACAAATATCTGA 1 TCTGGTGGCTCTGCCACAAATATCTGA * * 95976510 TCTGGTGGCTCTGCCACATATATCTGT 1 TCTGGTGGCTCTGCCACAAATATCTGA * * * 95976537 TCTGGTGGCCCTGCCACGATTATCTGTA 1 TCTGGTGGCTCTGCCACAAATATCTG-A * * * * * 95976565 TCTAGTGACTCTGTCAC-ATTATCTGT 1 TCTGGTGGCTCTGCCACAAATATCTGA 95976591 TCTGG 1 TCTGG 95976596 CAGCCATGCT Statistics Matches: 98, Mismatches: 14, Indels: 3 0.85 0.12 0.03 Matches are distributed among these distances: 26 4 0.04 27 81 0.83 28 13 0.13 ACGTcount: A:0.19, C:0.25, G:0.22, T:0.34 Consensus pattern (27 bp): TCTGGTGGCTCTGCCACAAATATCTGA Found at i:95976541 original size:54 final size:55 Alignment explanation

Indices: 95976456--95976595 Score: 185 Period size: 54 Copynumber: 2.6 Consensus size: 55 95976446 GAGGAAGCGT * * * * 95976456 TCTGGTGGCTATGCCACAAATATCTGATCTGGTGGCTCTGCCACAAATATCTG-A 1 TCTGGTGGCTCTGCCACATATATCTGTTCTGGTGGCCCTGCCACAAATATCTGTA * * 95976510 TCTGGTGGCTCTGCCACATATATCTGTTCTGGTGGCCCTGCCACGATTATCTGTA 1 TCTGGTGGCTCTGCCACATATATCTGTTCTGGTGGCCCTGCCACAAATATCTGTA * * * 95976565 TCTAGTGACTCTGTCACAT-TATCTGTTCTGG 1 TCTGGTGGCTCTGCCACATATATCTGTTCTGG 95976596 CAGCCATGCT Statistics Matches: 76, Mismatches: 9, Indels: 2 0.87 0.10 0.02 Matches are distributed among these distances: 54 59 0.78 55 17 0.22 ACGTcount: A:0.19, C:0.25, G:0.22, T:0.34 Consensus pattern (55 bp): TCTGGTGGCTCTGCCACATATATCTGTTCTGGTGGCCCTGCCACAAATATCTGTA Found at i:95983392 original size:31 final size:31 Alignment explanation

Indices: 95983354--95983417 Score: 110 Period size: 31 Copynumber: 2.1 Consensus size: 31 95983344 CCTTTTCATA * 95983354 TTTCATATTTCATAATACTGGGCCGAAGCCT 1 TTTCATATTTCATAATACTGGGCCAAAGCCT * 95983385 TTTCATATTTCATATTACTGGGCCAAAGCCT 1 TTTCATATTTCATAATACTGGGCCAAAGCCT 95983416 TT 1 TT 95983418 ACTGTAAACG Statistics Matches: 31, Mismatches: 2, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 31 31 1.00 ACGTcount: A:0.25, C:0.22, G:0.14, T:0.39 Consensus pattern (31 bp): TTTCATATTTCATAATACTGGGCCAAAGCCT Found at i:95983661 original size:24 final size:24 Alignment explanation

Indices: 95983609--95983824 Score: 355 Period size: 24 Copynumber: 9.0 Consensus size: 24 95983599 GCTTTATCAT * * 95983609 ATAACTGGAGGCCT-AGCCTCTTTTA 1 ATAACTGG-GGCATAAGCC-CTTTTG * 95983634 ATAACTGGGGCAAAAGCCCTTTTG 1 ATAACTGGGGCATAAGCCCTTTTG 95983658 ATAACTGGGGCATAAGCCCTTTTG 1 ATAACTGGGGCATAAGCCCTTTTG 95983682 ATAACTGGGGCATAAGCCCTTTTG 1 ATAACTGGGGCATAAGCCCTTTTG * 95983706 ATAACTGGGGCATAAGCCCTTTTA 1 ATAACTGGGGCATAAGCCCTTTTG 95983730 ATAACTGGGGCATAAGCCCTTTTG 1 ATAACTGGGGCATAAGCCCTTTTG 95983754 ATAACTGGGGCATAAGCCCTTTTG 1 ATAACTGGGGCATAAGCCCTTTTG * 95983778 ATAACTGGGGCATAAGCCC-TTTA 1 ATAACTGGGGCATAAGCCCTTTTG 95983801 ATAACTGGGGCATAAGCCCTTTTG 1 ATAACTGGGGCATAAGCCCTTTTG 95983825 CACTTCCTCC Statistics Matches: 181, Mismatches: 8, Indels: 5 0.93 0.04 0.03 Matches are distributed among these distances: 23 22 0.12 24 147 0.81 25 12 0.07 ACGTcount: A:0.26, C:0.21, G:0.24, T:0.29 Consensus pattern (24 bp): ATAACTGGGGCATAAGCCCTTTTG Found at i:95983895 original size:9 final size:9 Alignment explanation

Indices: 95983881--95983937 Score: 51 Period size: 9 Copynumber: 5.9 Consensus size: 9 95983871 ATCTCATGTG 95983881 CATATCATA 1 CATATCATA * 95983890 CATATCATGTG 1 CATATCA--TA 95983901 CATATCATA 1 CATATCATA * * 95983910 CATGTCATGTG 1 CATATCA--TA 95983921 CATATCATA 1 CATATCATA 95983930 CATATCAT 1 CATATCAT 95983938 GTTTATCAAA Statistics Matches: 38, Mismatches: 6, Indels: 8 0.73 0.12 0.15 Matches are distributed among these distances: 9 23 0.61 11 15 0.39 ACGTcount: A:0.35, C:0.21, G:0.09, T:0.35 Consensus pattern (9 bp): CATATCATA Found at i:95983897 original size:20 final size:20 Alignment explanation

Indices: 95983869--95983939 Score: 124 Period size: 20 Copynumber: 3.5 Consensus size: 20 95983859 GCATTTATGA * 95983869 ACATCTCATGTGCATATCAT 1 ACATATCATGTGCATATCAT 95983889 ACATATCATGTGCATATCAT 1 ACATATCATGTGCATATCAT * 95983909 ACATGTCATGTGCATATCAT 1 ACATATCATGTGCATATCAT 95983929 ACATATCATGT 1 ACATATCATGT 95983940 TTATCAAAAT Statistics Matches: 48, Mismatches: 3, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 20 48 1.00 ACGTcount: A:0.32, C:0.21, G:0.11, T:0.35 Consensus pattern (20 bp): ACATATCATGTGCATATCAT Found at i:95983904 original size:11 final size:11 Alignment explanation

Indices: 95983874--95983928 Score: 55 Period size: 11 Copynumber: 5.4 Consensus size: 11 95983864 TATGAACATC 95983874 TCATGTGCATA 1 TCATGTGCATA * 95983885 TCA--TACATA 1 TCATGTGCATA 95983894 TCATGTGCATA 1 TCATGTGCATA * * 95983905 TCA--TACATG 1 TCATGTGCATA 95983914 TCATGTGCATA 1 TCATGTGCATA 95983925 TCAT 1 TCAT 95983929 ACATATCATG Statistics Matches: 34, Mismatches: 6, Indels: 8 0.71 0.12 0.17 Matches are distributed among these distances: 9 15 0.44 11 19 0.56 ACGTcount: A:0.31, C:0.20, G:0.13, T:0.36 Consensus pattern (11 bp): TCATGTGCATA Found at i:95985252 original size:26 final size:26 Alignment explanation

Indices: 95985154--95985236 Score: 121 Period size: 27 Copynumber: 3.1 Consensus size: 26 95985144 GGGCATATTC * * * 95985154 GTCATTTTACCATACAGGGGTATTACG 1 GTCACTTTACCCTACAGGGCT-TTACG 95985181 GTCACTTTACCCTACAAGGGCTTTACG 1 GTCACTTTACCCTAC-AGGGCTTTACG 95985208 GTCACTTTACCCTACAGGGCTTTACG 1 GTCACTTTACCCTACAGGGCTTTACG 95985234 GTC 1 GTC 95985237 TTTTTACCTA Statistics Matches: 52, Mismatches: 3, Indels: 3 0.90 0.05 0.05 Matches are distributed among these distances: 26 14 0.27 27 33 0.63 28 5 0.10 ACGTcount: A:0.22, C:0.27, G:0.20, T:0.31 Consensus pattern (26 bp): GTCACTTTACCCTACAGGGCTTTACG Found at i:95985328 original size:27 final size:27 Alignment explanation

Indices: 95985275--95985510 Score: 199 Period size: 27 Copynumber: 8.8 Consensus size: 27 95985265 TTTCATCCTA * * ** 95985275 CAAGGGTGTTTTGGTAAATCAACAAAC 1 CAAGGGTATTTTGGTAATTTTACAAAC * * ** 95985302 CAAAGGTATTTTAGTAATTTTGTAAAC 1 CAAGGGTATTTTGGTAATTTTACAAAC * * * ** 95985329 CAATGGTATTTCT-ATAATTTTTAGAAGT 1 CAAGGGTATTT-TGGTAA-TTTTACAAAC * ** * 95985357 CAAGGGTATTTT-GTAACTTTGTAAAT 1 CAAGGGTATTTTGGTAATTTTACAAAC * * 95985383 CAGGGGTATTTTGGTAATTTTACAAAT 1 CAAGGGTATTTTGGTAATTTTACAAAC ** * * 95985410 TGAGGGTATTTCGGTAATTTCACAAA- 1 CAAGGGTATTTTGGTAATTTTACAAAC 95985436 CAAGGGTATTTTGGTAATTTTACAAAC 1 CAAGGGTATTTTGGTAATTTTACAAAC * * 95985463 TAGGGGTATTTTGGTAATTTTACAAAC 1 CAAGGGTATTTTGGTAATTTTACAAAC * 95985490 CAAGGGTATTTTAGTAATTTT 1 CAAGGGTATTTTGGTAATTTT 95985511 GTAAATCGAG Statistics Matches: 167, Mismatches: 38, Indels: 8 0.78 0.18 0.04 Matches are distributed among these distances: 26 39 0.23 27 111 0.66 28 17 0.10 ACGTcount: A:0.32, C:0.09, G:0.19, T:0.39 Consensus pattern (27 bp): CAAGGGTATTTTGGTAATTTTACAAAC Found at i:95985522 original size:27 final size:27 Alignment explanation

Indices: 95985306--95985578 Score: 169 Period size: 27 Copynumber: 10.1 Consensus size: 27 95985296 ACAAACCAAA * * * 95985306 GGTATTTTAGTAATTTTGTAAACCAAT 1 GGTATTTTAGTAATTTTATAAATCAAG 95985333 GGTATTTCTA-TAATTTT-TAGAAGTCAAG 1 GGTATTT-TAGTAATTTTATA-AA-TCAAG * * * 95985361 GGTATTTT-GTAACTTTGTAAATCAGG 1 GGTATTTTAGTAATTTTATAAATCAAG * * ** 95985387 GGTATTTTGGTAATTTTACAAATTGAG 1 GGTATTTTAGTAATTTTATAAATCAAG ** * * 95985414 GGTATTTCGGTAATTTCACAAA-CAAG 1 GGTATTTTAGTAATTTTATAAATCAAG * * * 95985440 GGTATTTTGGTAATTTTACAAA-CTAGG 1 GGTATTTTAGTAATTTTATAAATC-AAG * * * 95985467 GGTATTTTGGTAATTTTACAAACCAAG 1 GGTATTTTAGTAATTTTATAAATCAAG * * 95985494 GGTATTTTAGTAATTTTGTAAATCGAG 1 GGTATTTTAGTAATTTTATAAATCAAG **** * * 95985521 GGTAAAACAGTAATTCTGTAAATCAAG 1 GGTATTTTAGTAATTTTATAAATCAAG **** * * 95985548 GGTAAAACAGTAATTCTATAAATCGAG 1 GGTATTTTAGTAATTTTATAAATCAAG 95985575 GGTA 1 GGTA 95985579 AAATGGTAAT Statistics Matches: 207, Mismatches: 31, Indels: 16 0.81 0.12 0.06 Matches are distributed among these distances: 26 37 0.18 27 155 0.75 28 15 0.07 ACGTcount: A:0.34, C:0.08, G:0.20, T:0.38 Consensus pattern (27 bp): GGTATTTTAGTAATTTTATAAATCAAG Found at i:95985524 original size:54 final size:54 Alignment explanation

Indices: 95985306--95985524 Score: 203 Period size: 53 Copynumber: 4.1 Consensus size: 54 95985296 ACAAACCAAA * ** * * * * 95985306 GGTATTTTAGTAATTTTGTAAACCAATGGTATTTCTA-TAATTTTTAGAAGTCAAG 1 GGTATTTTGGTAATTTTACAAACCAAGGGTATTT-TAGTAA-TTTTACAAATCGAG * ** * * * * 95985361 GGTATTTT-GTAACTTTGTAAATCAGGGGTATTTTGGTAATTTTACAAATTGAG 1 GGTATTTTGGTAATTTTACAAACCAAGGGTATTTTAGTAATTTTACAAATCGAG * * * * 95985414 GGTATTTCGGTAATTTCACAAA-CAAGGGTATTTTGGTAATTTTACAAA-CTAGG 1 GGTATTTTGGTAATTTTACAAACCAAGGGTATTTTAGTAATTTTACAAATCGA-G ** 95985467 GGTATTTTGGTAATTTTACAAACCAAGGGTATTTTAGTAATTTTGTAAATCGAG 1 GGTATTTTGGTAATTTTACAAACCAAGGGTATTTTAGTAATTTTACAAATCGAG 95985521 GGTA 1 GGTA 95985525 AAACAGTAAT Statistics Matches: 136, Mismatches: 23, Indels: 11 0.80 0.14 0.06 Matches are distributed among these distances: 52 1 0.01 53 64 0.47 54 61 0.45 55 10 0.07 ACGTcount: A:0.31, C:0.08, G:0.21, T:0.41 Consensus pattern (54 bp): GGTATTTTGGTAATTTTACAAACCAAGGGTATTTTAGTAATTTTACAAATCGAG Found at i:95985534 original size:54 final size:54 Alignment explanation

Indices: 95985476--95985636 Score: 151 Period size: 54 Copynumber: 3.0 Consensus size: 54 95985466 GGGTATTTTG * **** * * 95985476 GTAATTTTACAAACCAAGGGTATTTTAGTAATTTTGTAAATCGAGGGTAAAACA 1 GTAATTCTACAAACCAAGGGTAAAACAGTAATTCTATAAATCGAGGGTAAAACA ** * ** 95985530 GTAATTCTGTAAATCAAGGGTAAAACAGTAATTCTATAAATCGAGGGTAAAATG 1 GTAATTCTACAAACCAAGGGTAAAACAGTAATTCTATAAATCGAGGGTAAAACA ** * * * * * 95985584 GTAATTCTGTAAATCGAGGGTAAAACGGTAATTCTGTAAGTCGAGGGTAAAAC 1 GTAATTCTACAAACCAAGGGTAAAACAGTAATTCTATAAATCGAGGGTAAAAC 95985637 GATAATATGT Statistics Matches: 90, Mismatches: 17, Indels: 0 0.84 0.16 0.00 Matches are distributed among these distances: 54 90 1.00 ACGTcount: A:0.39, C:0.10, G:0.22, T:0.29 Consensus pattern (54 bp): GTAATTCTACAAACCAAGGGTAAAACAGTAATTCTATAAATCGAGGGTAAAACA Found at i:95985579 original size:27 final size:27 Alignment explanation

Indices: 95985502--95985711 Score: 250 Period size: 27 Copynumber: 7.9 Consensus size: 27 95985492 AGGGTATTTT * 95985502 AGTAATTTTGTAAATCGAGGGTAAAAC 1 AGTAATTCTGTAAATCGAGGGTAAAAC * 95985529 AGTAATTCTGTAAATCAAGGGTAAAAC 1 AGTAATTCTGTAAATCGAGGGTAAAAC * * 95985556 AGTAATTCTATAAATCGAGGGTAAAAT 1 AGTAATTCTGTAAATCGAGGGTAAAAC * 95985583 GGTAATTCTGTAAATCGAGGGTAAAAC 1 AGTAATTCTGTAAATCGAGGGTAAAAC * * 95985610 GGTAATTCTGTAAGTCGAGGGTAAAAC 1 AGTAATTCTGTAAATCGAGGGTAAAAC * 95985637 -GATAA-TATGTAAATC-AGGGGTAAAAC 1 AG-TAATTCTGTAAATCGA-GGGTAAAAC * * 95985663 -GTAATTATGTAAAT-TAGGGGTAAAAC 1 AGTAATTCTGTAAATCGA-GGGTAAAAC * * 95985689 GGTAATTCTGTAAATCGGGGGTA 1 AGTAATTCTGTAAATCGAGGGTA 95985712 CTTTGGTAAT Statistics Matches: 163, Mismatches: 14, Indels: 12 0.86 0.07 0.06 Matches are distributed among these distances: 25 4 0.02 26 39 0.24 27 120 0.74 ACGTcount: A:0.40, C:0.09, G:0.24, T:0.28 Consensus pattern (27 bp): AGTAATTCTGTAAATCGAGGGTAAAAC Found at i:95985731 original size:106 final size:108 Alignment explanation

Indices: 95985492--95985738 Score: 286 Period size: 106 Copynumber: 2.3 Consensus size: 108 95985482 TTACAAACCA * * * * 95985492 AGGGTATTTTAGTAATTTTGTAAATCGAGGGTAAAACAGTAATTCTGTAAATCAAGGGTAAAACA 1 AGGGTAATTTGGTAATTTTGTAAGTCGAGGGTAAAACAGTAATTATGTAAATCAAGGGTAAAACA * * * 95985557 GTAATTCTATAAATCGAGGGTAAAATGGTAATTCTGTAAATCG 66 GTAATTATATAAATAGAGGGTAAAACGGTAATTCTGTAAATCG *** * * 95985600 AGGGTAAAACGGTAATTCTGTAAGTCGAGGGTAAAAC-GATAA-TATGTAAATCAGGGGTAAAAC 1 AGGGTAATTTGGTAATTTTGTAAGTCGAGGGTAAAACAG-TAATTATGTAAATCAAGGGTAAAAC * 95985663 -GTAATTATGTAAATTAG-GGGTAAAACGGTAATTCTGTAAATCG 65 AGTAATTATATAAA-TAGAGGGTAAAACGGTAATTCTGTAAATCG * * ** * 95985706 GGGGTACTTTGGTAATTTTACAAGTCGAAGGTA 1 AGGGTAATTTGGTAATTTTGTAAGTCGAGGGTA 95985739 TTTCGGTAAA Statistics Matches: 115, Mismatches: 22, Indels: 6 0.80 0.15 0.04 Matches are distributed among these distances: 106 60 0.52 107 22 0.19 108 33 0.29 ACGTcount: A:0.38, C:0.09, G:0.24, T:0.30 Consensus pattern (108 bp): AGGGTAATTTGGTAATTTTGTAAGTCGAGGGTAAAACAGTAATTATGTAAATCAAGGGTAAAACA GTAATTATATAAATAGAGGGTAAAACGGTAATTCTGTAAATCG Found at i:95985758 original size:54 final size:53 Alignment explanation

Indices: 95985700--95985805 Score: 133 Period size: 53 Copynumber: 2.0 Consensus size: 53 95985690 GTAATTCTGT * * * 95985700 AAATCGGGGGTACTTT-GGTAATTTTACAAGTCGAAGGTATTTCGGTAAATTTAC 1 AAATCGAGGGTA-TTTCAGTAATTTTACAA-ACGAAGGTATTTCGGTAAATTTAC * * * 95985754 AAATCGAGGGTATTTCAGTATTTTTACAAACTAAGGTATTTCGGTAATTTTA 1 AAATCGAGGGTATTTCAGTAATTTTACAAACGAAGGTATTTCGGTAAATTTA 95985806 GTAAACTAAA Statistics Matches: 45, Mismatches: 6, Indels: 3 0.83 0.11 0.06 Matches are distributed among these distances: 53 23 0.51 54 22 0.49 ACGTcount: A:0.31, C:0.10, G:0.21, T:0.38 Consensus pattern (53 bp): AAATCGAGGGTATTTCAGTAATTTTACAAACGAAGGTATTTCGGTAAATTTAC Found at i:95985804 original size:26 final size:26 Alignment explanation

Indices: 95985708--95985805 Score: 108 Period size: 27 Copynumber: 3.7 Consensus size: 26 95985698 GTAAATCGGG * 95985708 GGTACTTT-GGTAATTTTACAAGTCGAA 1 GGTA-TTTCGGTAATTTTACAA-ACGAA * * 95985735 GGTATTTCGGTAAATTTACAAATCGAG 1 GGTATTTCGGTAATTTTACAAA-CGAA * * * 95985762 GGTATTTCAGTATTTTTACAAACTAA 1 GGTATTTCGGTAATTTTACAAACGAA 95985788 GGTATTTCGGTAATTTTA 1 GGTATTTCGGTAATTTTA 95985806 GTAAACTAAA Statistics Matches: 59, Mismatches: 10, Indels: 5 0.80 0.14 0.07 Matches are distributed among these distances: 26 21 0.36 27 38 0.64 ACGTcount: A:0.31, C:0.10, G:0.19, T:0.40 Consensus pattern (26 bp): GGTATTTCGGTAATTTTACAAACGAA Found at i:95985811 original size:27 final size:26 Alignment explanation

Indices: 95985708--95985820 Score: 102 Period size: 27 Copynumber: 4.2 Consensus size: 26 95985698 GTAAATCGGG * * 95985708 GGTACTTT-GGTAATTTTACAAGTCGAA 1 GGTA-TTTCGGTAATTTTACAA-ACTAA * * * 95985735 GGTATTTCGGTAAATTTACAAATCGAG 1 GGTATTTCGGTAATTTTACAAA-CTAA * * 95985762 GGTATTTCAGTATTTTTACAAACTAA 1 GGTATTTCGGTAATTTTACAAACTAA * 95985788 GGTATTTCGGTAATTTTAGTAAACTAA 1 GGTATTTCGGTAATTTTA-CAAACTAA * 95985815 AGTATT 1 GGTATT 95985821 CTAAACAGGG Statistics Matches: 71, Mismatches: 12, Indels: 6 0.80 0.13 0.07 Matches are distributed among these distances: 26 21 0.30 27 50 0.70 ACGTcount: A:0.33, C:0.10, G:0.19, T:0.39 Consensus pattern (26 bp): GGTATTTCGGTAATTTTACAAACTAA Found at i:95988582 original size:31 final size:31 Alignment explanation

Indices: 95988544--95988607 Score: 119 Period size: 31 Copynumber: 2.1 Consensus size: 31 95988534 CCTTTTCATA 95988544 TTTCATATTTCATAATACTGGGCCGAAGCCT 1 TTTCATATTTCATAATACTGGGCCGAAGCCT * 95988575 TTTCATATTTCATATTACTGGGCCGAAGCCT 1 TTTCATATTTCATAATACTGGGCCGAAGCCT 95988606 TT 1 TT 95988608 ACTGTAAACG Statistics Matches: 32, Mismatches: 1, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 31 32 1.00 ACGTcount: A:0.23, C:0.22, G:0.16, T:0.39 Consensus pattern (31 bp): TTTCATATTTCATAATACTGGGCCGAAGCCT Found at i:95988825 original size:24 final size:24 Alignment explanation

Indices: 95988798--95989010 Score: 335 Period size: 24 Copynumber: 9.0 Consensus size: 24 95988788 GCTTTATCAT * * * 95988798 ATAACTGGAGGCCT-AGCCTTTTTA 1 ATAACTGG-GGCATAAGCCCTTTTG * 95988822 ATAACTGGGGCAAAAGCCCTTTTG 1 ATAACTGGGGCATAAGCCCTTTTG 95988846 ATAACTGGGGCATAAGCCCTTTTG 1 ATAACTGGGGCATAAGCCCTTTTG 95988870 ATAACT-GGGCATAAGCCCTTTTG 1 ATAACTGGGGCATAAGCCCTTTTG * 95988893 ATAACTGGGGCATAAGCCCTTTTA 1 ATAACTGGGGCATAAGCCCTTTTG 95988917 ATAACTGGGGCATAAGCCCTTTTG 1 ATAACTGGGGCATAAGCCCTTTTG 95988941 ATAACTGGGGCATAAGCCCTTTTG 1 ATAACTGGGGCATAAGCCCTTTTG * 95988965 ATAACT-GGGCATAAGCCC-TTTA 1 ATAACTGGGGCATAAGCCCTTTTG 95988987 ATAACTGGGGCATAAGCCCTTTTG 1 ATAACTGGGGCATAAGCCCTTTTG 95989011 CACTTCCTCC Statistics Matches: 176, Mismatches: 9, Indels: 8 0.91 0.05 0.04 Matches are distributed among these distances: 22 9 0.05 23 50 0.28 24 117 0.66 ACGTcount: A:0.27, C:0.21, G:0.23, T:0.29 Consensus pattern (24 bp): ATAACTGGGGCATAAGCCCTTTTG Found at i:95988910 original size:71 final size:72 Alignment explanation

Indices: 95988798--95989010 Score: 344 Period size: 71 Copynumber: 3.0 Consensus size: 72 95988788 GCTTTATCAT * * * * * 95988798 ATAACTGGAGGCCT-AGCCTTTTTAATAACTGGGGCAAAAGCCCTTTTGATAACTGGGGCATAAG 1 ATAACTGG-GGCATAAGCCCTTTTGATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAG 95988862 CCCTTTTG 65 CCCTTTTG 95988870 ATAACT-GGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGC 1 ATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGC 95988934 CCTTTTG 66 CCTTTTG 95988941 ATAACTGGGGCATAAGCCCTTTTGATAACT-GGGCATAAGCCC-TTTAATAACTGGGGCATAAGC 1 ATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGC 95989004 CCTTTTG 66 CCTTTTG 95989011 CACTTCCTCC Statistics Matches: 134, Mismatches: 5, Indels: 6 0.92 0.03 0.04 Matches are distributed among these distances: 70 32 0.24 71 73 0.54 72 29 0.22 ACGTcount: A:0.27, C:0.21, G:0.23, T:0.29 Consensus pattern (72 bp): ATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGC CCTTTTG Found at i:95988918 original size:95 final size:94 Alignment explanation

Indices: 95988798--95989009 Score: 363 Period size: 95 Copynumber: 2.2 Consensus size: 94 95988788 GCTTTATCAT * * 95988798 ATAACTGGAGGCCT-AGCCTTTTTAATAACTGGGGCAAAAGCCCTTTTGATAACTGGGGCATAAG 1 ATAACTGG-GGCATAAGCCCTTTTAATAACTGGGGCAAAAGCCCTTTTGATAACTGGGGCATAAG * 95988862 CCCTTTTGATAACTGGGCATAAGCCCTTTTG 65 CCCTTTTGATAACTGGGCATAAGCCC-TTTA * 95988893 ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGC 1 ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCAAAAGCCCTTTTGATAACTGGGGCATAAGC 95988958 CCTTTTGATAACTGGGCATAAGCCCTTTA 66 CCTTTTGATAACTGGGCATAAGCCCTTTA 95988987 ATAACTGGGGCATAAGCCCTTTT 1 ATAACTGGGGCATAAGCCCTTTT 95989010 GCACTTCCTC Statistics Matches: 112, Mismatches: 4, Indels: 3 0.94 0.03 0.03 Matches are distributed among these distances: 94 30 0.27 95 82 0.73 ACGTcount: A:0.27, C:0.21, G:0.23, T:0.29 Consensus pattern (94 bp): ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCAAAAGCCCTTTTGATAACTGGGGCATAAGC CCTTTTGATAACTGGGCATAAGCCCTTTA Found at i:95989079 original size:9 final size:9 Alignment explanation

Indices: 95989065--95989121 Score: 51 Period size: 9 Copynumber: 5.9 Consensus size: 9 95989055 ATCTCATGTG 95989065 CATATCATA 1 CATATCATA * 95989074 CATATCATGTG 1 CATATCA--TA 95989085 CATATCATA 1 CATATCATA * * 95989094 CATGTCATGTG 1 CATATCA--TA 95989105 CATATCATA 1 CATATCATA 95989114 CATATCAT 1 CATATCAT 95989122 GTTTATCAAA Statistics Matches: 38, Mismatches: 6, Indels: 8 0.73 0.12 0.15 Matches are distributed among these distances: 9 23 0.61 11 15 0.39 ACGTcount: A:0.35, C:0.21, G:0.09, T:0.35 Consensus pattern (9 bp): CATATCATA Found at i:95989081 original size:20 final size:20 Alignment explanation

Indices: 95989053--95989123 Score: 124 Period size: 20 Copynumber: 3.5 Consensus size: 20 95989043 GCATTTATGA * 95989053 ACATCTCATGTGCATATCAT 1 ACATATCATGTGCATATCAT 95989073 ACATATCATGTGCATATCAT 1 ACATATCATGTGCATATCAT * 95989093 ACATGTCATGTGCATATCAT 1 ACATATCATGTGCATATCAT 95989113 ACATATCATGT 1 ACATATCATGT 95989124 TTATCAAAAT Statistics Matches: 48, Mismatches: 3, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 20 48 1.00 ACGTcount: A:0.32, C:0.21, G:0.11, T:0.35 Consensus pattern (20 bp): ACATATCATGTGCATATCAT Found at i:95989088 original size:11 final size:11 Alignment explanation

Indices: 95989058--95989112 Score: 55 Period size: 11 Copynumber: 5.4 Consensus size: 11 95989048 TATGAACATC 95989058 TCATGTGCATA 1 TCATGTGCATA * 95989069 TCA--TACATA 1 TCATGTGCATA 95989078 TCATGTGCATA 1 TCATGTGCATA * * 95989089 TCA--TACATG 1 TCATGTGCATA 95989098 TCATGTGCATA 1 TCATGTGCATA 95989109 TCAT 1 TCAT 95989113 ACATATCATG Statistics Matches: 34, Mismatches: 6, Indels: 8 0.71 0.12 0.17 Matches are distributed among these distances: 9 15 0.44 11 19 0.56 ACGTcount: A:0.31, C:0.20, G:0.13, T:0.36 Consensus pattern (11 bp): TCATGTGCATA Found at i:95990441 original size:27 final size:27 Alignment explanation

Indices: 95990341--95990424 Score: 125 Period size: 27 Copynumber: 3.1 Consensus size: 27 95990331 GGGCATATTC * * 95990341 GTCATTTTACCATACAGGGG-TATTACG 1 GTCACTTTACCCTACAGGGGCT-TTACG * 95990368 GTCACTTTACCCTACAAGGGCTTTACG 1 GTCACTTTACCCTACAGGGGCTTTACG 95990395 GTCACTTTACCCTACAGGGGCTTTACG 1 GTCACTTTACCCTACAGGGGCTTTACG 95990422 GTC 1 GTC 95990425 TTTTTACCTA Statistics Matches: 52, Mismatches: 4, Indels: 2 0.90 0.07 0.03 Matches are distributed among these distances: 27 51 0.98 28 1 0.02 ACGTcount: A:0.21, C:0.26, G:0.21, T:0.31 Consensus pattern (27 bp): GTCACTTTACCCTACAGGGGCTTTACG Found at i:95990516 original size:27 final size:27 Alignment explanation

Indices: 95990463--95990701 Score: 192 Period size: 27 Copynumber: 8.8 Consensus size: 27 95990453 TTTCATCCTA * * ** 95990463 CAAGGGTGTTTTGGTAAATCAACAAAC 1 CAAGGGTATTTTGGTAATTTTACAAAC * * ** 95990490 CAAAGGTATTTTAGTAATTTTGTAAAC 1 CAAGGGTATTTTGGTAATTTTACAAAC * * * ** 95990517 CAATGGTATTTCT-ATAATTTTTAGAAGGT 1 CAAGGGTATTT-TGGTAA-TTTTACAA-AC * * ** * 95990546 CAAGGGTATTTTTGTAACTTTGTAAAT 1 CAAGGGTATTTTGGTAATTTTACAAAC * * 95990573 CAGGGGTATTTTGGTAATTTTACAAAT 1 CAAGGGTATTTTGGTAATTTTACAAAC ** * * 95990600 TGAGGGTATTTCGGTAATTTCACAAAC 1 CAAGGGTATTTTGGTAATTTTACAAAC * 95990627 TAAGGGTATTTTGGTAATTTTACAAAC 1 CAAGGGTATTTTGGTAATTTTACAAAC * * 95990654 TAGGGGTATTTTGGTAATTTTACAAAC 1 CAAGGGTATTTTGGTAATTTTACAAAC * 95990681 CAAGGGTATTTTAGTAATTTT 1 CAAGGGTATTTTGGTAATTTT 95990702 GTAAATCGAG Statistics Matches: 170, Mismatches: 38, Indels: 8 0.79 0.18 0.04 Matches are distributed among these distances: 27 144 0.85 28 13 0.08 29 13 0.08 ACGTcount: A:0.32, C:0.09, G:0.20, T:0.40 Consensus pattern (27 bp): CAAGGGTATTTTGGTAATTTTACAAAC Found at i:95990687 original size:81 final size:81 Alignment explanation

Indices: 95990494--95990700 Score: 213 Period size: 81 Copynumber: 2.5 Consensus size: 81 95990484 ACAAACCAAA * ** * * * ** 95990494 GGTATTTTAGTAATTTTGTAAACCAATGGTATTTCTA-TAATTTTTAGAAGGTCAAGGGTATTTT 1 GGTATTTTGGTAATTTTACAAACCAAGGGTATTTC-AGTAA-TTTCACAAACT-AAGGGTATTTT * * 95990558 TGTAACTTTGTAAATCAGG 63 GGTAACTTTGTAAAACAGG *** * 95990577 GGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGTAATTTCACAAACTAAGGGTATTTTGGT 1 GGTATTTTGGTAATTTTACAAACCAAGGGTATTTCAGTAATTTCACAAACTAAGGGTATTTTGGT 95990642 AA-TTT-TACAAACTAGG 66 AACTTTGTA-AAAC-AGG * 95990658 GGTATTTTGGTAATTTTACAAACCAAGGGTATTTTAGTAATTT 1 GGTATTTTGGTAATTTTACAAACCAAGGGTATTTCAGTAATTT 95990701 TGTAAATCGA Statistics Matches: 102, Mismatches: 19, Indels: 8 0.79 0.15 0.06 Matches are distributed among these distances: 79 2 0.02 80 6 0.06 81 56 0.55 82 7 0.07 83 31 0.30 ACGTcount: A:0.30, C:0.08, G:0.20, T:0.42 Consensus pattern (81 bp): GGTATTTTGGTAATTTTACAAACCAAGGGTATTTCAGTAATTTCACAAACTAAGGGTATTTTGGT AACTTTGTAAAACAGG Found at i:95990713 original size:27 final size:27 Alignment explanation

Indices: 95990494--95990769 Score: 155 Period size: 27 Copynumber: 10.1 Consensus size: 27 95990484 ACAAACCAAA * * * 95990494 GGTATTTTAGTAATTTTGTAAACCAAT 1 GGTATTTTAGTAATTTTATAAATCAAG 95990521 GGTATTTCTA-TAATTTT-TAGAAGGTCAAG 1 GGTATTT-TAGTAATTTTATA-AA--TCAAG * * * * 95990550 GGTATTTTTGTAACTTTGTAAATCAGG 1 GGTATTTTAGTAATTTTATAAATCAAG * * ** 95990577 GGTATTTTGGTAATTTTACAAATTGAG 1 GGTATTTTAGTAATTTTATAAATCAAG ** * * 95990604 GGTATTTCGGTAATTTCACAAA-CTAAG 1 GGTATTTTAGTAATTTTATAAATC-AAG * * * 95990631 GGTATTTTGGTAATTTTACAAA-CTAGG 1 GGTATTTTAGTAATTTTATAAATC-AAG * * * 95990658 GGTATTTTGGTAATTTTACAAACCAAG 1 GGTATTTTAGTAATTTTATAAATCAAG * * 95990685 GGTATTTTAGTAATTTTGTAAATCGAG 1 GGTATTTTAGTAATTTTATAAATCAAG **** * * 95990712 GGTAAAACAGTAATTCTGTAAATCAAG 1 GGTATTTTAGTAATTTTATAAATCAAG **** * * 95990739 GGTAAAACAGTAATTCTATAAATCGAG 1 GGTATTTTAGTAATTTTATAAATCAAG 95990766 GGTA 1 GGTA 95990770 AAATGGTAAT Statistics Matches: 208, Mismatches: 33, Indels: 16 0.81 0.13 0.06 Matches are distributed among these distances: 26 2 0.01 27 182 0.88 28 4 0.02 29 18 0.09 30 2 0.01 ACGTcount: A:0.33, C:0.08, G:0.20, T:0.38 Consensus pattern (27 bp): GGTATTTTAGTAATTTTATAAATCAAG Found at i:95990725 original size:54 final size:54 Alignment explanation

Indices: 95990667--95990827 Score: 142 Period size: 54 Copynumber: 3.0 Consensus size: 54 95990657 GGGTATTTTG * **** * * 95990667 GTAATTTTACAAACCAAGGGTATTTTAGTAATTTTGTAAATCGAGGGTAAAACA 1 GTAATTCTACAAACCAAGGGTAAAACAGTAATTCTATAAATCGAGGGTAAAACA ** * ** 95990721 GTAATTCTGTAAATCAAGGGTAAAACAGTAATTCTATAAATCGAGGGTAAAATG 1 GTAATTCTACAAACCAAGGGTAAAACAGTAATTCTATAAATCGAGGGTAAAACA ** * * * * * * 95990775 GTAATTCTGTAAATCGAGGGTAAAACGGTAATTCTGTAAGTTGAGGGTAAAAC 1 GTAATTCTACAAACCAAGGGTAAAACAGTAATTCTATAAATCGAGGGTAAAAC 95990828 GATAATCATG Statistics Matches: 89, Mismatches: 18, Indels: 0 0.83 0.17 0.00 Matches are distributed among these distances: 54 89 1.00 ACGTcount: A:0.39, C:0.09, G:0.22, T:0.30 Consensus pattern (54 bp): GTAATTCTACAAACCAAGGGTAAAACAGTAATTCTATAAATCGAGGGTAAAACA Found at i:95990742 original size:81 final size:81 Alignment explanation

Indices: 95990667--95990897 Score: 216 Period size: 81 Copynumber: 2.9 Consensus size: 81 95990657 GGGTATTTTG * *** * 95990667 GTAATTTTACAAACCAAGGGTATTTTAGTAATTTTGTAAATCGAGGGTAAAACAGTAATTCTGTA 1 GTAATTCTACAAACCAAGGGTAAAATAGTAATTCTGTAAATCGAGGGTAAAACAGTAATTCTGTA 95990732 AATCAAGGGTAAAACA 66 AATCAAGGGTAAAACA * * * * * 95990748 GTAATTCTATAAATCGAGGGTAAAATGGTAATTCTGTAAATCGAGGGTAAAACGGTAATTCTGTA 1 GTAATTCTACAAACCAAGGGTAAAATAGTAATTCTGTAAATCGAGGGTAAAACAGTAATTCTGTA * ** 95990813 AGTTGAGGGTAAAAC- 66 AATCAAGGGTAAAACA ** * * ** * * * 95990828 GATAA-TCATGTAAATCAGGGGTAAAACGGTAATTATGTAAAT-TAGGGGTAAAACGGTAATTCT 1 G-TAATTC-TACAAACCAAGGGTAAAATAGTAATTCTGTAAATCGA-GGGTAAAACAGTAATTCT 95990891 GTAAATC 63 GTAAATC 95990898 GGGGGTACTT Statistics Matches: 126, Mismatches: 21, Indels: 6 0.82 0.14 0.04 Matches are distributed among these distances: 80 4 0.03 81 122 0.97 ACGTcount: A:0.39, C:0.09, G:0.22, T:0.29 Consensus pattern (81 bp): GTAATTCTACAAACCAAGGGTAAAATAGTAATTCTGTAAATCGAGGGTAAAACAGTAATTCTGTA AATCAAGGGTAAAACA Found at i:95990770 original size:27 final size:27 Alignment explanation

Indices: 95990694--95990904 Score: 266 Period size: 27 Copynumber: 7.8 Consensus size: 27 95990684 GGGTATTTTA * * 95990694 GTAATTTTGTAAATCGAGGGTAAAACA 1 GTAATTCTGTAAATCGAGGGTAAAACG * * 95990721 GTAATTCTGTAAATCAAGGGTAAAACA 1 GTAATTCTGTAAATCGAGGGTAAAACG * * 95990748 GTAATTCTATAAATCGAGGGTAAAATG 1 GTAATTCTGTAAATCGAGGGTAAAACG 95990775 GTAATTCTGTAAATCGAGGGTAAAACG 1 GTAATTCTGTAAATCGAGGGTAAAACG * * 95990802 GTAATTCTGTAAGTTGAGGGTAAAACG 1 GTAATTCTGTAAATCGAGGGTAAAACG * 95990829 ATAA-TCATGTAAATC-AGGGGTAAAACG 1 GTAATTC-TGTAAATCGA-GGGTAAAACG * * 95990856 GTAATTATGTAAAT-TAGGGGTAAAACG 1 GTAATTCTGTAAATCGA-GGGTAAAACG * 95990883 GTAATTCTGTAAATCGGGGGTA 1 GTAATTCTGTAAATCGAGGGTA 95990905 CTTTGGTAAT Statistics Matches: 161, Mismatches: 18, Indels: 10 0.85 0.10 0.05 Matches are distributed among these distances: 26 3 0.02 27 157 0.98 28 1 0.01 ACGTcount: A:0.39, C:0.09, G:0.25, T:0.28 Consensus pattern (27 bp): GTAATTCTGTAAATCGAGGGTAAAACG Found at i:95990931 original size:27 final size:27 Alignment explanation

Indices: 95990901--95990962 Score: 81 Period size: 27 Copynumber: 2.3 Consensus size: 27 95990891 GTAAATCGGG * * 95990901 GGTACTTT-GGTAATTTTACAAGTCGAA 1 GGTA-TTTCGGTAAATTTACAAATCGAA * 95990928 GGTATTTCGGTAAATTTACAAATCGAG 1 GGTATTTCGGTAAATTTACAAATCGAA 95990955 GGTATTTC 1 GGTATTTC 95990963 AGTATTTTTT Statistics Matches: 31, Mismatches: 3, Indels: 2 0.86 0.08 0.06 Matches are distributed among these distances: 26 3 0.10 27 28 0.90 ACGTcount: A:0.29, C:0.11, G:0.23, T:0.37 Consensus pattern (27 bp): GGTATTTCGGTAAATTTACAAATCGAA Found at i:95994873 original size:2 final size:2 Alignment explanation

Indices: 95994868--95994917 Score: 66 Period size: 2 Copynumber: 24.5 Consensus size: 2 95994858 GTGAAAGTCG * 95994868 TA TA TA TA TA TA TA TA TA TA TA TA GTCG TA TA TA TA TA TA TA TA 1 TA TA TA TA TA TA TA TA TA TA TA TA -T-A TA TA TA TA TA TA TA TA 95994912 T- TA TA T 1 TA TA TA T 95994918 TCTGAAAGTA Statistics Matches: 43, Mismatches: 2, Indels: 6 0.84 0.04 0.12 Matches are distributed among these distances: 1 1 0.02 2 40 0.93 3 2 0.05 ACGTcount: A:0.44, C:0.02, G:0.04, T:0.50 Consensus pattern (2 bp): TA Found at i:95994895 original size:28 final size:27 Alignment explanation

Indices: 95994863--95994917 Score: 101 Period size: 28 Copynumber: 2.0 Consensus size: 27 95994853 TATGTGTGAA 95994863 AGTCGTATATATATATATATATATATAT 1 AGTCGTATATATATATATATAT-TATAT 95994891 AGTCGTATATATATATATATATTATAT 1 AGTCGTATATATATATATATATTATAT 95994918 TCTGAAAGTA Statistics Matches: 27, Mismatches: 0, Indels: 1 0.96 0.00 0.04 Matches are distributed among these distances: 27 5 0.19 28 22 0.81 ACGTcount: A:0.42, C:0.04, G:0.07, T:0.47 Consensus pattern (27 bp): AGTCGTATATATATATATATATTATAT Found at i:95995415 original size:39 final size:40 Alignment explanation

Indices: 95995357--95995513 Score: 137 Period size: 39 Copynumber: 4.0 Consensus size: 40 95995347 TTCAGTGATG * ** 95995357 TATATCAGGACTTAGGGT-CCGCAGGCTCTGTGCTGGAAT 1 TATATCCGGACTTAAAGTCCCGCAGGCTCTGTGCTGGAAT * * 95995396 TATATCCGGACTTAAGGT-CCGCAGGCTAC-GTGCTGGAAA 1 TATATCCGGACTTAAAGTCCCGCAGGCT-CTGTGCTGGAAT * * * * * 95995435 TATGTCCGGGC-TAAAGTCCCGCAGGCTTTGAGCTGGTAT 1 TATATCCGGACTTAAAGTCCCGCAGGCTCTGTGCTGGAAT ** * 95995474 TATA-CCGGGTTTAAATTCCCGCAGGCT-TGTGCTGGTAAT 1 TATATCCGGACTTAAAGTCCCGCAGGCTCTGTGCTGG-AAT 95995513 T 1 T 95995514 GGTTTCAAGT Statistics Matches: 98, Mismatches: 15, Indels: 10 0.80 0.12 0.08 Matches are distributed among these distances: 38 17 0.17 39 80 0.82 40 1 0.01 ACGTcount: A:0.21, C:0.22, G:0.29, T:0.29 Consensus pattern (40 bp): TATATCCGGACTTAAAGTCCCGCAGGCTCTGTGCTGGAAT Found at i:96007218 original size:34 final size:34 Alignment explanation

Indices: 96007175--96007241 Score: 125 Period size: 34 Copynumber: 2.0 Consensus size: 34 96007165 ATATTCAGAG 96007175 TAGACATCCACAAAACAAGGTTTAGAAATAATGT 1 TAGACATCCACAAAACAAGGTTTAGAAATAATGT * 96007209 TAGATATCCACAAAACAAGGTTTAGAAATAATG 1 TAGACATCCACAAAACAAGGTTTAGAAATAATG 96007242 GTTCTGCATG Statistics Matches: 32, Mismatches: 1, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 34 32 1.00 ACGTcount: A:0.48, C:0.13, G:0.15, T:0.24 Consensus pattern (34 bp): TAGACATCCACAAAACAAGGTTTAGAAATAATGT Found at i:96009930 original size:64 final size:63 Alignment explanation

Indices: 96009761--96009933 Score: 168 Period size: 68 Copynumber: 2.6 Consensus size: 63 96009751 GATTGGATGA * * * * * ** 96009761 TACAGATAGTATGTAGCTATGTCACATGTATAGTGCTAAGTGCACATCATGTGTACAAGAGAGC 1 TACAGATA-TATGTAGCTAGGTCGCATGTGTAGTACTAAGTGCACACCATGTAAACAAGAGAGC * * * 96009825 TACAAGACATTATGATGTAGCTAGGTCGCATGGGT-GATACTATGTGTACACCATGTAAACAAGA 1 TAC-AG--A-TAT-ATGTAGCTAGGTCGCATGTGTAG-TACTAAGTGCACACCATGTAAACAAGA * 96009889 GAGT 60 GAGC 96009893 TACATGATATATGTAGCTAGGTCGCATGTGTAGTACTAAGT 1 TACA-GATATATGTAGCTAGGTCGCATGTGTAGTACTAAGT 96009934 ACAGGCTACT Statistics Matches: 88, Mismatches: 13, Indels: 16 0.75 0.11 0.14 Matches are distributed among these distances: 64 30 0.34 65 6 0.07 66 1 0.01 67 4 0.05 68 47 0.53 ACGTcount: A:0.32, C:0.14, G:0.24, T:0.29 Consensus pattern (63 bp): TACAGATATATGTAGCTAGGTCGCATGTGTAGTACTAAGTGCACACCATGTAAACAAGAGAGC Found at i:96010039 original size:49 final size:50 Alignment explanation

Indices: 96009912--96010057 Score: 186 Period size: 49 Copynumber: 2.9 Consensus size: 50 96009902 TATGTAGCTA * * 96009912 GGTCGCATGTGTAGTACTAAGTACAGGCTACTATGCGTACCCGATAACTTT 1 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCCGATAAC-TT * * * * * 96009963 GATCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAA-TT 1 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCCGATAACTT * * * 96010012 GGTCGCATGTGTAATACTAAGTGCAGGCTACTATGCGTACCAGATA 1 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCCGATA 96010058 GTTTGGCTAC Statistics Matches: 81, Mismatches: 14, Indels: 2 0.84 0.14 0.02 Matches are distributed among these distances: 49 41 0.51 51 40 0.49 ACGTcount: A:0.27, C:0.20, G:0.25, T:0.28 Consensus pattern (50 bp): GGTCGCATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCCGATAACTT Found at i:96017588 original size:23 final size:23 Alignment explanation

Indices: 96017562--96017606 Score: 56 Period size: 23 Copynumber: 2.0 Consensus size: 23 96017552 TAGGTATGTG * 96017562 ATGACGTTATCTT-ATAAATATGC 1 ATGAAGTTATCTTGA-AAATATGC * 96017585 ATGAATTTATCTTGAAAATATG 1 ATGAAGTTATCTTGAAAATATG 96017607 TTGAATTGGT Statistics Matches: 19, Mismatches: 2, Indels: 2 0.83 0.09 0.09 Matches are distributed among these distances: 23 18 0.95 24 1 0.05 ACGTcount: A:0.38, C:0.09, G:0.13, T:0.40 Consensus pattern (23 bp): ATGAAGTTATCTTGAAAATATGC Found at i:96018267 original size:19 final size:19 Alignment explanation

Indices: 96018245--96018282 Score: 51 Period size: 19 Copynumber: 2.0 Consensus size: 19 96018235 AATAAGAAAA * 96018245 GAAATAAAAGTAAAT-AAAT 1 GAAAAAAAAG-AAATCAAAT 96018264 GAAAAAAAAGAAATCAAAT 1 GAAAAAAAAGAAATCAAAT 96018283 AAGCAAATCT Statistics Matches: 17, Mismatches: 1, Indels: 2 0.85 0.05 0.10 Matches are distributed among these distances: 18 4 0.24 19 13 0.76 ACGTcount: A:0.71, C:0.03, G:0.11, T:0.16 Consensus pattern (19 bp): GAAAAAAAAGAAATCAAAT Found at i:96025380 original size:16 final size:17 Alignment explanation

Indices: 96025351--96025384 Score: 52 Period size: 16 Copynumber: 2.1 Consensus size: 17 96025341 ATAAATGCAT 96025351 AAAAAGGGACTAAATTG 1 AAAAAGGGACTAAATTG * 96025368 AAAAA-GGAGTAAATTG 1 AAAAAGGGACTAAATTG 96025384 A 1 A 96025385 GTGATAAAAA Statistics Matches: 16, Mismatches: 1, Indels: 1 0.89 0.06 0.06 Matches are distributed among these distances: 16 11 0.69 17 5 0.31 ACGTcount: A:0.56, C:0.03, G:0.24, T:0.18 Consensus pattern (17 bp): AAAAAGGGACTAAATTG Found at i:96026026 original size:48 final size:47 Alignment explanation

Indices: 96025908--96026027 Score: 107 Period size: 48 Copynumber: 2.5 Consensus size: 47 96025898 AGATCCTGTG * * * 96025908 TAAGACCATGTCTGGGACATGGCACCGGCATTGATATGAGATTTCATG 1 TAAGACCATGTCT-GGACATGGCACCGGCATTCATAAGAGATTTCATA * * * ** * * 96025956 TAAGACCATATCAGGTATATGGCTTCGGCA-TCATCAAGTGATTTCGTA 1 TAAGACCATGTCTGG-ACATGGCACCGGCATTCAT-AAGAGATTTCATA 96026004 TAAGACCATGTCTGAGACATGGCA 1 TAAGACCATGTCTG-GACATGGCA 96026028 TCGATATGGG Statistics Matches: 55, Mismatches: 14, Indels: 6 0.73 0.19 0.08 Matches are distributed among these distances: 47 5 0.09 48 49 0.89 49 1 0.02 ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28 Consensus pattern (47 bp): TAAGACCATGTCTGGACATGGCACCGGCATTCATAAGAGATTTCATA Found at i:96026121 original size:90 final size:90 Alignment explanation

Indices: 96026002--96026167 Score: 197 Period size: 90 Copynumber: 1.8 Consensus size: 90 96025992 AGTGATTTCG * ** * * * 96026002 TATAAGACCATGTCTGAGACATGGCATCGATATGGGGTCCCGTATAAGACCATGTTTGGGATATG 1 TATAAGACCATATCTGAGACATGAAATCGATATGGGGTCCCATATAAGACCATGTCTGGGACATG ** 96026067 GTGTTGGCACCGATTCGAGACTTCA 66 GCATTGGCACCGATTCGAGACTTCA * * * * * * * 96026092 TATAAGACCATATCTGGGATATGAAATCGATGTGTGGTTCCATGTAATACCATGTCTGGGACATG 1 TATAAGACCATATCTGAGACATGAAATCGATATGGGGTCCCATATAAGACCATGTCTGGGACATG 96026157 GCATTGGCACC 66 GCATTGGCACC 96026168 CTATTTGGTG Statistics Matches: 61, Mismatches: 15, Indels: 0 0.80 0.20 0.00 Matches are distributed among these distances: 90 61 1.00 ACGTcount: A:0.27, C:0.19, G:0.27, T:0.28 Consensus pattern (90 bp): TATAAGACCATATCTGAGACATGAAATCGATATGGGGTCCCATATAAGACCATGTCTGGGACATG GCATTGGCACCGATTCGAGACTTCA Found at i:96027994 original size:34 final size:35 Alignment explanation

Indices: 96027948--96028030 Score: 132 Period size: 34 Copynumber: 2.4 Consensus size: 35 96027938 GAATACATTT 96027948 TGGGCCTAAGCCCATATTAGTAACAGT-AACAGTC 1 TGGGCCTAAGCCCATATTAGTAACAGTAAACAGTC * * * 96027982 TGGGCCTTAGCCCATTTTAGTATCAGTAAACAGTC 1 TGGGCCTAAGCCCATATTAGTAACAGTAAACAGTC 96028017 TGGGCCTAAGCCCA 1 TGGGCCTAAGCCCA 96028031 CCGCAATATA Statistics Matches: 44, Mismatches: 4, Indels: 1 0.90 0.08 0.02 Matches are distributed among these distances: 34 24 0.55 35 20 0.45 ACGTcount: A:0.28, C:0.25, G:0.22, T:0.25 Consensus pattern (35 bp): TGGGCCTAAGCCCATATTAGTAACAGTAAACAGTC Found at i:96028635 original size:27 final size:27 Alignment explanation

Indices: 96028478--96028650 Score: 161 Period size: 27 Copynumber: 6.4 Consensus size: 27 96028468 GGGCAAAATA * * *** 96028478 GTCATTTTACCCTATAAGGGAATTACA 1 GTCATTTTACCCTATAGGGGTATTTTG * ** * * * 96028505 GTCATTATACATTATAGAGATATTTTA 1 GTCATTTTACCCTATAGGGGTATTTTG * * 96028532 GTCATTTTACCATATAGGGGTATTTCG 1 GTCATTTTACCCTATAGGGGTATTTTG * 96028559 ATCATTTTACCCTAT-GAGGGTATTTTG 1 GTCATTTTACCCTATAG-GGGTATTTTG * * 96028586 GTCATTTTGCCCTATCGGGGTATTTTG 1 GTCATTTTACCCTATAGGGGTATTTTG * 96028613 GTCATTTTATCCTAT-GGGAGTATTTTG 1 GTCATTTTACCCTATAGGG-GTATTTTG 96028640 GTCATTTTACC 1 GTCATTTTACC 96028651 TGATTAAGGG Statistics Matches: 119, Mismatches: 24, Indels: 6 0.80 0.16 0.04 Matches are distributed among these distances: 26 4 0.03 27 114 0.96 28 1 0.01 ACGTcount: A:0.24, C:0.15, G:0.18, T:0.43 Consensus pattern (27 bp): GTCATTTTACCCTATAGGGGTATTTTG Found at i:96029200 original size:21 final size:23 Alignment explanation

Indices: 96029155--96029210 Score: 57 Period size: 21 Copynumber: 2.6 Consensus size: 23 96029145 AAAGTAGGTT * 96029155 ATATATTAT--TTTTATAATATT 1 ATATATTATGATTTTATAATATC 96029176 ATATATTATGATTTT-TAAT-TC 1 ATATATTATGATTTTATAATATC * 96029197 ATATAATAATGATT 1 ATAT-ATTATGATT 96029211 ATATTAAGAA Statistics Matches: 30, Mismatches: 2, Indels: 5 0.81 0.05 0.14 Matches are distributed among these distances: 21 14 0.47 22 12 0.40 23 4 0.13 ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55 Consensus pattern (23 bp): ATATATTATGATTTTATAATATC Found at i:96029237 original size:57 final size:56 Alignment explanation

Indices: 96029164--96029306 Score: 139 Period size: 57 Copynumber: 2.5 Consensus size: 56 96029154 TATATATTAT * 96029164 TTTTA-TAATATTATATATTATGATTTTTAATT-CATATAATAATGATTATATTAAGAA 1 TTTTATTAA-ATTATATATTAT-ATTTTTAATTGCATATAATAATAATTATATTAA-AA * * * 96029221 TTTTATTAAATTATATAATAT-TTTATTAAATTGTATTTAATAATAATTATATTAAAA 1 TTTTATTAAATTATATATTATATTT-TT-AATTGCATATAATAATAATTATATTAAAA * * * * 96029278 TATAATTAAATTATTTATTTTTATTTTTA 1 TTTTATTAAATTATATA-TTATATTTTTA 96029307 TTAAAATATA Statistics Matches: 71, Mismatches: 9, Indels: 12 0.77 0.10 0.13 Matches are distributed among these distances: 55 3 0.04 56 2 0.03 57 37 0.52 58 26 0.37 59 3 0.04 ACGTcount: A:0.42, C:0.01, G:0.03, T:0.55 Consensus pattern (56 bp): TTTTATTAAATTATATATTATATTTTTAATTGCATATAATAATAATTATATTAAAA Found at i:96029286 original size:26 final size:25 Alignment explanation

Indices: 96029229--96029286 Score: 62 Period size: 26 Copynumber: 2.2 Consensus size: 25 96029219 AATTTTATTA * * * 96029229 AATTATATAATATTTTATTAAATTGT 1 AATTA-ATAATATTATATTAAAATAT * 96029255 ATTTAATAATAATTATATTAAAATAT 1 AATTAATAAT-ATTATATTAAAATAT 96029281 AATTAA 1 AATTAA 96029287 ATTATTTATT Statistics Matches: 26, Mismatches: 5, Indels: 2 0.79 0.15 0.06 Matches are distributed among these distances: 25 5 0.19 26 21 0.81 ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48 Consensus pattern (25 bp): AATTAATAATATTATATTAAAATAT Found at i:96029310 original size:61 final size:57 Alignment explanation

Indices: 96029200--96029344 Score: 164 Period size: 61 Copynumber: 2.5 Consensus size: 57 96029190 TTAATTCATA * * * * 96029200 TAATAATGATTATATTAAGAATTTTATTAAATTATATAATATTTTATTAAATTGTATT 1 TAATAATAATTATATTAA-AATTTAATTAAATTATATAATATTTTATTAAAATATATT * ** 96029258 TAATAATAATTATATTAAAATATAATTAAATTATTTATTTTTATTTTTATTAAAATATATT 1 TAATAATAATTATATTAAAATTTAATTAAATTA--TA-TAATA-TTTTATTAAAATATATT * * 96029319 TAACAATAATTTTATTAAAATTTAAT 1 TAATAATAATTATATTAAAATTTAAT 96029345 AACAATAACA Statistics Matches: 73, Mismatches: 10, Indels: 5 0.83 0.11 0.06 Matches are distributed among these distances: 57 13 0.18 58 17 0.23 59 2 0.03 60 3 0.04 61 38 0.52 ACGTcount: A:0.46, C:0.01, G:0.02, T:0.52 Consensus pattern (57 bp): TAATAATAATTATATTAAAATTTAATTAAATTATATAATATTTTATTAAAATATATT Found at i:96029331 original size:26 final size:25 Alignment explanation

Indices: 96029302--96029352 Score: 75 Period size: 26 Copynumber: 2.0 Consensus size: 25 96029292 TTATTTTTAT * 96029302 TTTTATTAAAATATATTTAACAATAA 1 TTTTATTAAAATATA-ATAACAATAA * 96029328 TTTTATTAAAATTTAATAACAATAA 1 TTTTATTAAAATATAATAACAATAA 96029353 CAATAATTAT Statistics Matches: 23, Mismatches: 2, Indels: 1 0.88 0.08 0.04 Matches are distributed among these distances: 25 9 0.39 26 14 0.61 ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45 Consensus pattern (25 bp): TTTTATTAAAATATAATAACAATAA Found at i:96029525 original size:46 final size:44 Alignment explanation

Indices: 96029433--96029525 Score: 123 Period size: 44 Copynumber: 2.1 Consensus size: 44 96029423 TACAACATCT * 96029433 ATTCCATTCAACCAAACACAAGAATCCTATTACAGCTCTATTCC 1 ATTCCATTCAACCAAACACAAGAATACTATTACAGCTCTATTCC *** * 96029477 ATTCCATTCAACCAAACAGTTGAATTACTGATTACAGTTCTATTCC 1 ATTCCATTCAACCAAACACAAGAA-TACT-ATTACAGCTCTATTCC 96029523 ATT 1 ATT 96029526 ACAACTCTAT Statistics Matches: 42, Mismatches: 5, Indels: 2 0.86 0.10 0.04 Matches are distributed among these distances: 44 21 0.50 45 3 0.07 46 18 0.43 ACGTcount: A:0.34, C:0.27, G:0.06, T:0.32 Consensus pattern (44 bp): ATTCCATTCAACCAAACACAAGAATACTATTACAGCTCTATTCC Found at i:96029528 original size:16 final size:16 Alignment explanation

Indices: 96029507--96029561 Score: 74 Period size: 16 Copynumber: 3.4 Consensus size: 16 96029497 TGAATTACTG * 96029507 ATTACAGTTCTATTCC 1 ATTACAGCTCTATTCC * * 96029523 ATTACAACTCTATTCA 1 ATTACAGCTCTATTCC * 96029539 ATTACAGCCCTATTCC 1 ATTACAGCTCTATTCC 96029555 ATTACAG 1 ATTACAG 96029562 TGAACCAAAC Statistics Matches: 33, Mismatches: 6, Indels: 0 0.85 0.15 0.00 Matches are distributed among these distances: 16 33 1.00 ACGTcount: A:0.31, C:0.27, G:0.05, T:0.36 Consensus pattern (16 bp): ATTACAGCTCTATTCC Found at i:96034209 original size:13 final size:13 Alignment explanation

Indices: 96034193--96034219 Score: 54 Period size: 13 Copynumber: 2.1 Consensus size: 13 96034183 TAAAATAAAT 96034193 AAATAAAAATTAA 1 AAATAAAAATTAA 96034206 AAATAAAAATTAA 1 AAATAAAAATTAA 96034219 A 1 A 96034220 GAAATAATAA Statistics Matches: 14, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 14 1.00 ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22 Consensus pattern (13 bp): AAATAAAAATTAA Found at i:96035500 original size:17 final size:17 Alignment explanation

Indices: 96035480--96035567 Score: 60 Period size: 17 Copynumber: 5.5 Consensus size: 17 96035470 AAAAATAGTA 96035480 TATATATTATTTTTTAT 1 TATATATTATTTTTTAT ** 96035497 TATATATTATTCATTA- 1 TATATATTATTTTTTAT * 96035513 TAT-TATT-TATTTTAT 1 TATATATTATTTTTTAT * * 96035528 TATACATT-TTGTTTA- 1 TATATATTATTTTTTAT * * * * 96035543 TAAATTTTATTATATAT 1 TATATATTATTTTTTAT 96035560 TATATATT 1 TATATATT 96035568 TTACTACATA Statistics Matches: 52, Mismatches: 15, Indels: 8 0.69 0.20 0.11 Matches are distributed among these distances: 14 4 0.08 15 12 0.23 16 16 0.31 17 20 0.38 ACGTcount: A:0.33, C:0.02, G:0.01, T:0.64 Consensus pattern (17 bp): TATATATTATTTTTTAT Found at i:96035513 original size:24 final size:22 Alignment explanation

Indices: 96035480--96035562 Score: 60 Period size: 24 Copynumber: 3.5 Consensus size: 22 96035470 AAAAATAGTA * 96035480 TATATATTATTTTTTATTATATAT 1 TATACATTATTTTTTATT-T-TAT * 96035504 TATTCATTATATTATTTATTTTAT 1 TATACATTAT-TT-TTTATTTTAT 96035528 TATACATT-TTGTTTATAAATTTTAT 1 TATACATTATT-TTT-T--ATTTTAT * 96035553 TATATATTAT 1 TATACATTAT 96035563 ATATTTTACT Statistics Matches: 48, Mismatches: 4, Indels: 12 0.75 0.06 0.19 Matches are distributed among these distances: 22 3 0.06 23 3 0.06 24 18 0.38 25 17 0.35 26 7 0.15 ACGTcount: A:0.33, C:0.02, G:0.01, T:0.64 Consensus pattern (22 bp): TATACATTATTTTTTATTTTAT Found at i:96035578 original size:19 final size:19 Alignment explanation

Indices: 96035540--96035578 Score: 51 Period size: 19 Copynumber: 2.1 Consensus size: 19 96035530 TACATTTTGT * * 96035540 TTATAAATTTTATTATATA 1 TTATAAATTTTACTACATA * 96035559 TTATATATTTTACTACATA 1 TTATAAATTTTACTACATA 96035578 T 1 T 96035579 ATTATTCCTT Statistics Matches: 17, Mismatches: 3, Indels: 0 0.85 0.15 0.00 Matches are distributed among these distances: 19 17 1.00 ACGTcount: A:0.38, C:0.05, G:0.00, T:0.56 Consensus pattern (19 bp): TTATAAATTTTACTACATA Found at i:96036200 original size:23 final size:23 Alignment explanation

Indices: 96036134--96036201 Score: 57 Period size: 23 Copynumber: 3.0 Consensus size: 23 96036124 TTTGTATTTT * * 96036134 TGCATGAAATGATAATGTGTATA 1 TGCATGAAATGTTAATGTATATA * ** * * 96036157 TTCATGTTATTTGTGAT-TATATA 1 TGCATGAAATGT-TAATGTATATA 96036180 TGCATGAAATGTTAATGTATAT 1 TGCATGAAATGTTAATGTATAT 96036202 TGTGTGATTT Statistics Matches: 31, Mismatches: 12, Indels: 4 0.66 0.26 0.09 Matches are distributed among these distances: 22 3 0.10 23 25 0.81 24 3 0.10 ACGTcount: A:0.34, C:0.04, G:0.18, T:0.44 Consensus pattern (23 bp): TGCATGAAATGTTAATGTATATA Found at i:96047722 original size:44 final size:44 Alignment explanation

Indices: 96047667--96048204 Score: 754 Period size: 44 Copynumber: 12.2 Consensus size: 44 96047657 GTAGATCACC * 96047667 GATAACAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAA 1 GATAACAGATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCGAA * * * * * 96047711 GATGACAGATTTGGTGTATCTGTATTGTCAGAGAGTAGATCAAA 1 GATAACAGATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCGAA * * 96047755 GATAACAGATTTGGCGTTTTTGTATTGTCAGAGAGCAGATCGAA 1 GATAACAGATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCGAA * * 96047799 GATGACAGATTTGGCGTCTCTATATTGTCAGAGAGCAGATCGAA 1 GATAACAGATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCGAA * 96047843 GATGACAGATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCGAA 1 GATAACAGATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCGAA * * 96047887 GATAACAGATTTGGCGTCTCTGTATTGTCAGAGAGTAGATCAAA 1 GATAACAGATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCGAA * 96047931 GATAACAGATTTGGCGTCTCTGTATTGTCAAAGAGCAGATCGAA 1 GATAACAGATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCGAA * * * * * 96047975 GATGACAGATTCGGTGTCTCTATATTCTCAGAGAGCAGATCGAA 1 GATAACAGATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCGAA * * * * 96048019 TATGACAAATTTGGTGTCTCTGTATTGTCAGAGAGCAGATCGAA 1 GATAACAGATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCGAA * 96048063 GATAACAGATTTGGCGTCTCTGTATTGTCAGAAAGCAGATCGAA 1 GATAACAGATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCGAA * * * * 96048107 GATAGCAGATTTGGCGTGTCTATATTGAT-AGAGAGCAGATCAAA 1 GATAACAGATTTGGCGTCTCTGTATTG-TCAGAGAGCAGATCGAA * * * * * 96048151 GATAACAGATTTGGCATTTCTGTATTGACAAAGAGCATATCGAA 1 GATAACAGATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCGAA * 96048195 GATAGCAGAT 1 GATAACAGAT 96048205 CTGACATTTG Statistics Matches: 439, Mismatches: 53, Indels: 4 0.89 0.11 0.01 Matches are distributed among these distances: 44 438 1.00 45 1 0.00 ACGTcount: A:0.31, C:0.14, G:0.26, T:0.28 Consensus pattern (44 bp): GATAACAGATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCGAA Found at i:96049860 original size:17 final size:17 Alignment explanation

Indices: 96049827--96049860 Score: 50 Period size: 17 Copynumber: 2.0 Consensus size: 17 96049817 AAAAATAGTA ** 96049827 TATATATTATTTTTTAT 1 TATATATTATTCATTAT 96049844 TATATATTATTCATTAT 1 TATATATTATTCATTAT 96049861 ATTATTTATA Statistics Matches: 15, Mismatches: 2, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 17 15 1.00 ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65 Consensus pattern (17 bp): TATATATTATTCATTAT Found at i:96049875 original size:12 final size:13 Alignment explanation

Indices: 96049827--96049877 Score: 52 Period size: 12 Copynumber: 3.9 Consensus size: 13 96049817 AAAAATAGTA * 96049827 TATATATTATTTTT 1 TATATA-TATTATT 96049841 TATTATATATTATT 1 TA-TATATATTATT * 96049855 CAT-TATATTATT 1 TATATATATTATT 96049867 TATAT-TATTAT 1 TATATATATTAT 96049878 ACATTTTATT Statistics Matches: 32, Mismatches: 3, Indels: 6 0.78 0.07 0.15 Matches are distributed among these distances: 12 17 0.53 13 2 0.06 14 9 0.28 15 4 0.12 ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65 Consensus pattern (13 bp): TATATATATTATT Found at i:96049876 original size:17 final size:16 Alignment explanation

Indices: 96049829--96049878 Score: 61 Period size: 14 Copynumber: 3.2 Consensus size: 16 96049819 AAATAGTATA 96049829 TATATTATTT-TTTAT 1 TATATTATTTATTTAT * 96049844 TATA-TA-TTATTCAT 1 TATATTATTTATTTAT 96049858 TATATTATTTATATTAT 1 TATATTATTTAT-TTAT 96049875 TATA 1 TATA 96049879 CATTTTATTT Statistics Matches: 29, Mismatches: 2, Indels: 6 0.78 0.05 0.16 Matches are distributed among these distances: 13 2 0.07 14 10 0.34 15 6 0.21 16 4 0.14 17 7 0.24 ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64 Consensus pattern (16 bp): TATATTATTTATTTAT Found at i:96049886 original size:21 final size:21 Alignment explanation

Indices: 96049838--96049891 Score: 65 Period size: 21 Copynumber: 2.5 Consensus size: 21 96049828 ATATATTATT * 96049838 TTTTATTATATATTATTCATTA 1 TTTTATT-TATATTATTCATCA * 96049860 TATTATTTATATTATT-ATACA 1 TTTTATTTATATTATTCAT-CA 96049881 TTTTATTTATA 1 TTTTATTTATA 96049892 AATTTTATCA Statistics Matches: 28, Mismatches: 3, Indels: 3 0.82 0.09 0.09 Matches are distributed among these distances: 20 2 0.07 21 20 0.71 22 6 0.21 ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63 Consensus pattern (21 bp): TTTTATTTATATTATTCATCA Found at i:96049911 original size:19 final size:21 Alignment explanation

Indices: 96049887--96049930 Score: 74 Period size: 19 Copynumber: 2.2 Consensus size: 21 96049877 TACATTTTAT 96049887 TTATAAATTTTA-T-CATATA 1 TTATAAATTTTACTACATATA 96049906 TTATAAATTTTACTACATATA 1 TTATAAATTTTACTACATATA 96049927 TTAT 1 TTAT 96049931 TCCTTACATT Statistics Matches: 23, Mismatches: 0, Indels: 2 0.92 0.00 0.08 Matches are distributed among these distances: 19 12 0.52 20 1 0.04 21 10 0.43 ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52 Consensus pattern (21 bp): TTATAAATTTTACTACATATA Found at i:96061188 original size:92 final size:92 Alignment explanation

Indices: 96061031--96061213 Score: 357 Period size: 92 Copynumber: 2.0 Consensus size: 92 96061021 AGCAAAGAGA * 96061031 AAGTGAGTTTTATACCTGATACTTCATATATTTTATTATATCATAATCATGTTTCAAGTTATTTT 1 AAGTGAGTTTTATACCTGATAATTCATATATTTTATTATATCATAATCATGTTTCAAGTTATTTT 96061096 CTATTTTTTCCCATATCATATACCGTG 66 CTATTTTTTCCCATATCATATACCGTG 96061123 AAGTGAGTTTTATACCTGATAATTCATATATTTTATTATATCATAATCATGTTTCAAGTTATTTT 1 AAGTGAGTTTTATACCTGATAATTCATATATTTTATTATATCATAATCATGTTTCAAGTTATTTT 96061188 CTATTTTTTCCCATATCATATACCGT 66 CTATTTTTTCCCATATCATATACCGT 96061214 TGCATGTCTT Statistics Matches: 90, Mismatches: 1, Indels: 0 0.99 0.01 0.00 Matches are distributed among these distances: 92 90 1.00 ACGTcount: A:0.29, C:0.15, G:0.08, T:0.48 Consensus pattern (92 bp): AAGTGAGTTTTATACCTGATAATTCATATATTTTATTATATCATAATCATGTTTCAAGTTATTTT CTATTTTTTCCCATATCATATACCGTG Found at i:96063272 original size:32 final size:32 Alignment explanation

Indices: 96063231--96063294 Score: 128 Period size: 32 Copynumber: 2.0 Consensus size: 32 96063221 GTGGATAACA 96063231 TTATCCTATGTTGTTCAGACTCTTTCGTTTTC 1 TTATCCTATGTTGTTCAGACTCTTTCGTTTTC 96063263 TTATCCTATGTTGTTCAGACTCTTTCGTTTTC 1 TTATCCTATGTTGTTCAGACTCTTTCGTTTTC 96063295 CCTAATATGT Statistics Matches: 32, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 32 32 1.00 ACGTcount: A:0.12, C:0.22, G:0.12, T:0.53 Consensus pattern (32 bp): TTATCCTATGTTGTTCAGACTCTTTCGTTTTC Found at i:96070687 original size:27 final size:26 Alignment explanation

Indices: 96070625--96070698 Score: 87 Period size: 26 Copynumber: 2.8 Consensus size: 26 96070615 GCTTTGAAGA * 96070625 CCATTATCACTGAATTGCACCGAGGT 1 CCATTATCATTGAATTGCACCGAGGT * 96070651 CCATTATCATTGAGTTGCACCGATGTGT 1 CCATTATCATTGAATTGCACCGA-G-GT * * 96070679 -CATTATCATTTATTTGCACC 1 CCATTATCATTGAATTGCACC 96070699 AAAGTCTCAC Statistics Matches: 42, Mismatches: 4, Indels: 3 0.86 0.08 0.06 Matches are distributed among these distances: 26 21 0.50 27 19 0.45 28 2 0.05 ACGTcount: A:0.24, C:0.24, G:0.16, T:0.35 Consensus pattern (26 bp): CCATTATCATTGAATTGCACCGAGGT Done.