Tandem Repeats Finder Program written by: Gary Benson Program in Bioinformatics Boston University Version 4.09 Sequence: Gbar_D06 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: 62964862 ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33 Warning! 132689 characters in sequence are not A, C, G, or T File 138 of 207 Found at i:42374781 original size:30 final size:31 Alignment explanation
Indices: 42374723--42374785 Score: 92 Period size: 31 Copynumber: 2.1 Consensus size: 31 42374713 TAAGATAGTT * 42374723 ATTAAATTATTTAAAAATTTTAATTTAAGTC 1 ATTAAATTAATTAAAAATTTTAATTTAAGTC * * 42374754 ATTAAATTAATTGAAAGTTTT-ATTTAAGTC 1 ATTAAATTAATTAAAAATTTTAATTTAAGTC 42374784 AT 1 AT 42374786 CGTATTGTTA Statistics Matches: 29, Mismatches: 3, Indels: 1 0.88 0.09 0.03 Matches are distributed among these distances: 30 11 0.38 31 18 0.62 ACGTcount: A:0.43, C:0.03, G:0.06, T:0.48 Consensus pattern (31 bp): ATTAAATTAATTAAAAATTTTAATTTAAGTC Found at i:42380907 original size:43 final size:43 Alignment explanation
Indices: 42380838--42380923 Score: 145 Period size: 43 Copynumber: 2.0 Consensus size: 43 42380828 ATGGTGATTT 42380838 TTCAAAGCTAACCTACTGCTGCTGTCCAAAACTGTTTTAGTGC 1 TTCAAAGCTAACCTACTGCTGCTGTCCAAAACTGTTTTAGTGC * * * 42380881 TTCAAAGTTAACCTACTGTTGTTGTCCAAAACTGTTTTAGTGC 1 TTCAAAGCTAACCTACTGCTGCTGTCCAAAACTGTTTTAGTGC 42380924 AAGATGTTGA Statistics Matches: 40, Mismatches: 3, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 43 40 1.00 ACGTcount: A:0.26, C:0.22, G:0.16, T:0.36 Consensus pattern (43 bp): TTCAAAGCTAACCTACTGCTGCTGTCCAAAACTGTTTTAGTGC Found at i:42385657 original size:48 final size:50 Alignment explanation
Indices: 42385596--42385750 Score: 127 Period size: 48 Copynumber: 3.3 Consensus size: 50 42385586 TGTATGAACT 42385596 TGATTGTATATTTGTTAAACATGAATTAATAATATTGTACATGAAACACA 1 TGATTGTATATTTGTTAAACATGAATTAATAATATTGTACATGAAACACA * * * * * 42385646 TGATT-TA-ATTTGCTTACTAACTTG---TAA-CATATT-TGCA--AGA-ACT 1 TGATTGTATATTTG-TTA--AACATGAATTAATAATATTGTACATGAAACACA * * * 42385689 TGATTGTATATTTGTTGAACATTAATTAATAATATTGCACATGAAACACA 1 TGATTGTATATTTGTTAAACATGAATTAATAATATTGTACATGAAACACA 42385739 TGATT-TA-ATTTG 1 TGATTGTATATTTG 42385751 CTTACTAACT Statistics Matches: 79, Mismatches: 13, Indels: 28 0.66 0.11 0.23 Matches are distributed among these distances: 42 4 0.05 43 7 0.09 44 6 0.08 45 8 0.10 46 8 0.10 47 7 0.09 48 13 0.16 49 9 0.11 50 12 0.15 51 5 0.06 ACGTcount: A:0.37, C:0.10, G:0.12, T:0.41 Consensus pattern (50 bp): TGATTGTATATTTGTTAAACATGAATTAATAATATTGTACATGAAACACA Found at i:42385691 original size:93 final size:93 Alignment explanation
Indices: 42385569--42385788 Score: 370 Period size: 93 Copynumber: 2.4 Consensus size: 93 42385559 TTATTAACTG * * * 42385569 CTAAATTGTAACATATTTGTATGAACTTGATTGTATATTTGTTAAACATGAATTAATAATATTGT 1 CTAACTTGTAACATATTTGTAAGAACTTGATTGTATATTTGTTAAACATGAATTAATAATATTGC 42385634 ACATGAAACACATGATTTAATTTGCTTA 66 ACATGAAACACATGATTTAATTTGCTTA * * * 42385662 CTAACTTGTAACATATTTGCAAGAACTTGATTGTATATTTGTTGAACATTAATTAATAATATTGC 1 CTAACTTGTAACATATTTGTAAGAACTTGATTGTATATTTGTTAAACATGAATTAATAATATTGC 42385727 ACATGAAACACATGATTTAATTTGCTTA 66 ACATGAAACACATGATTTAATTTGCTTA 42385755 CTAACTTGTAACATATTTGTATA-AACTTGATTGT 1 CTAACTTGTAACATATTTGTA-AGAACTTGATTGT 42385789 CACATATATT Statistics Matches: 119, Mismatches: 7, Indels: 2 0.93 0.05 0.02 Matches are distributed among these distances: 93 118 0.99 94 1 0.01 ACGTcount: A:0.36, C:0.10, G:0.12, T:0.41 Consensus pattern (93 bp): CTAACTTGTAACATATTTGTAAGAACTTGATTGTATATTTGTTAAACATGAATTAATAATATTGC ACATGAAACACATGATTTAATTTGCTTA Found at i:42388243 original size:95 final size:92 Alignment explanation
Indices: 42388080--42388249 Score: 238 Period size: 95 Copynumber: 1.8 Consensus size: 92 42388070 ATTTTAACAC * * 42388080 AAATCTAATTATTCAAACAAACATATAATGTTCAATGTTATATCTTAAAATATACAAATTATTCT 1 AAATCTAATTATTCAAACAAACATATAATGATCAATGTTACATCTTAAAATATACAAATTATTCT * 42388145 TACAATATAATGATCAATTTTAAATCT 66 TACAAAATAATGATCAATTTTAAATCT 42388172 AAATCTAATTATTCAACACAAATCTAATATAATGATCAATG-TACA-CTTAAAACTATACAAATT 1 AAATCTAATTATTCAA-ACAAA-C--ATATAATGATCAATGTTACATCTTAAAA-TATACAAATT 42388235 A-TCATTACAAAATAA 61 ATTC-TTACAAAATAA 42388250 AATAAACTTA Statistics Matches: 69, Mismatches: 3, Indels: 9 0.85 0.04 0.11 Matches are distributed among these distances: 92 16 0.23 93 5 0.07 94 10 0.14 95 24 0.35 96 14 0.20 ACGTcount: A:0.48, C:0.14, G:0.03, T:0.35 Consensus pattern (92 bp): AAATCTAATTATTCAAACAAACATATAATGATCAATGTTACATCTTAAAATATACAAATTATTCT TACAAAATAATGATCAATTTTAAATCT Found at i:42398296 original size:23 final size:23 Alignment explanation
Indices: 42398266--42398310 Score: 81 Period size: 23 Copynumber: 2.0 Consensus size: 23 42398256 ATATGAATTA * 42398266 TGTAATATTCCAAAAATTACTAT 1 TGTAATATCCCAAAAATTACTAT 42398289 TGTAATATCCCAAAAATTACTA 1 TGTAATATCCCAAAAATTACTA 42398311 CAGTAAGAAA Statistics Matches: 21, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 23 21 1.00 ACGTcount: A:0.44, C:0.16, G:0.04, T:0.36 Consensus pattern (23 bp): TGTAATATCCCAAAAATTACTAT Found at i:42398316 original size:23 final size:23 Alignment explanation
Indices: 42398267--42398316 Score: 73 Period size: 23 Copynumber: 2.2 Consensus size: 23 42398257 TATGAATTAT * ** 42398267 GTAATATTCCAAAAATTACTATT 1 GTAATATCCCAAAAATTACTACA 42398290 GTAATATCCCAAAAATTACTACA 1 GTAATATCCCAAAAATTACTACA 42398313 GTAA 1 GTAA 42398317 GAAAGTAGGT Statistics Matches: 24, Mismatches: 3, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 23 24 1.00 ACGTcount: A:0.46, C:0.16, G:0.06, T:0.32 Consensus pattern (23 bp): GTAATATCCCAAAAATTACTACA Found at i:42401206 original size:14 final size:14 Alignment explanation
Indices: 42401177--42401224 Score: 51 Period size: 14 Copynumber: 3.3 Consensus size: 14 42401167 TTTACATACT 42401177 TATACATATATGTATA 1 TATACATATA--TATA * * 42401193 TTTTCATATATATA 1 TATACATATATATA * 42401207 TATACATATACATA 1 TATACATATATATA 42401221 TATA 1 TATA 42401225 TATTTACTTA Statistics Matches: 27, Mismatches: 5, Indels: 2 0.79 0.15 0.06 Matches are distributed among these distances: 14 19 0.70 16 8 0.30 ACGTcount: A:0.44, C:0.08, G:0.02, T:0.46 Consensus pattern (14 bp): TATACATATATATA Found at i:42407484 original size:17 final size:17 Alignment explanation
Indices: 42407462--42407510 Score: 89 Period size: 17 Copynumber: 2.9 Consensus size: 17 42407452 TCTAGCCCGG * 42407462 CGCCGCCACCATTCTGT 1 CGCCGCCACCGTTCTGT 42407479 CGCCGCCACCGTTCTGT 1 CGCCGCCACCGTTCTGT 42407496 CGCCGCCACCGTTCT 1 CGCCGCCACCGTTCT 42407511 AACACCGCGC Statistics Matches: 31, Mismatches: 1, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 17 31 1.00 ACGTcount: A:0.08, C:0.49, G:0.20, T:0.22 Consensus pattern (17 bp): CGCCGCCACCGTTCTGT Found at i:42409221 original size:111 final size:110 Alignment explanation
Indices: 42409028--42409349 Score: 547 Period size: 111 Copynumber: 2.9 Consensus size: 110 42409018 AAGGAAAATT * 42409028 TTTCAAAATAAGGTAATGTTTTGCCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTG 1 TTTCAAAATAAGGCAATGTTTTGCCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTG 42409093 TCGATTTTTCTCATTCAACCAAATGGCTAAATATCCTTTTAAAAA 66 TCGATTTTTCTCATTCAACCAAATGGCTAAATATCCTTTTAAAAA 42409138 TTTCAAAATAAGGCAATGTTTTGCCGTTTGGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGT 1 TTTCAAAATAAGGCAATGTTTTGCCGTTT-GGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGT * * 42409203 GTCGATTTTTCTCGTTCAACCAAATGGCTTAATATCCTTTTAAAAA 65 GTCGATTTTTCTCATTCAACCAAATGGCTAAATATCCTTTTAAAAA * * * 42409249 TTTTAAAATAAGGCAATGTTTTG-CTTTTGGAAATTCGAGAAAACATGCCCTAATGTGCTGGGTG 1 TTTCAAAATAAGGCAATGTTTTGCCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTG * * * 42409313 TCGATTTTTCTCATTTAACCAAATAGCCAAATATCCT 66 TCGATTTTTCTCATTCAACCAAATGGCTAAATATCCT 42409350 CTTGAATTTC Statistics Matches: 200, Mismatches: 11, Indels: 3 0.93 0.05 0.01 Matches are distributed among these distances: 109 67 0.34 110 32 0.16 111 101 0.50 ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34 Consensus pattern (110 bp): TTTCAAAATAAGGCAATGTTTTGCCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTG TCGATTTTTCTCATTCAACCAAATGGCTAAATATCCTTTTAAAAA Found at i:42410609 original size:107 final size:107 Alignment explanation
Indices: 42410420--42410629 Score: 287 Period size: 107 Copynumber: 2.0 Consensus size: 107 42410410 AAATGGGTTT * * * 42410420 TTCACTGTACAAAAAATTAGGTTGTAACTCTATTTCATCAATACAAATCACGTGAGAGGGATTAG 1 TTCACTGTACAAAAAATCAGGTTGCAACTCTATTTCATCAATACAAATCACGTGAGAGGGATCAG * * * 42410485 AAAGATAATGACGTAACATCAATACATGGAACACATTAGCTC 66 AAAAATAACGACATAACATCAATACATGGAACACATTAGCTC * * * ** * 42410527 TTCACTGTACGAAAAATCGGGTTGCAACTCTATTTCTTCTGTACAAATCACGTGAGAGGGA-CCG 1 TTCACTGTACAAAAAATCAGGTTGCAACTCTATTTCATCAATACAAATCACGTGAGAGGGATCAG * 42410591 AAACAATAACGACATAACATCGATACATGGAACACATTA 66 AAA-AATAACGACATAACATCAATACATGGAACACATTA 42410630 TGAATCTTTT Statistics Matches: 89, Mismatches: 13, Indels: 2 0.86 0.12 0.02 Matches are distributed among these distances: 106 4 0.04 107 85 0.96 ACGTcount: A:0.39, C:0.19, G:0.17, T:0.26 Consensus pattern (107 bp): TTCACTGTACAAAAAATCAGGTTGCAACTCTATTTCATCAATACAAATCACGTGAGAGGGATCAG AAAAATAACGACATAACATCAATACATGGAACACATTAGCTC Found at i:42411898 original size:42 final size:42 Alignment explanation
Indices: 42411824--42411997 Score: 165 Period size: 42 Copynumber: 4.1 Consensus size: 42 42411814 ACGCCTCTAA * * * ** * 42411824 ATTTAGCGGCGTTTATGTGAAAAACGCCGCTAAAGGTCATGAC 1 ATTTAGCGGCGCTT-TGTCACAAACGCCGCTAAAGAACATAAC * 42411867 ATTTAGCGGCGCTTTGTCACAAACGTCGCTAAAGAACATAAC 1 ATTTAGCGGCGCTTTGTCACAAACGCCGCTAAAGAACATAAC * * * * 42411909 CTTTAGCAGCGCTTTTATCACAAACGCCACTAAAGAACA-AAC 1 ATTTAGCGGCGC-TTTGTCACAAACGCCGCTAAAGAACATAAC * * 42411951 ATTTAGCGGAGCTTT-TAGCAAAAACGCCGCTAAA-AACATAAC 1 ATTTAGCGGCGCTTTGT--CACAAACGCCGCTAAAGAACATAAC * 42411993 CTTTA 1 ATTTA 42411998 AAAAAAATTA Statistics Matches: 109, Mismatches: 18, Indels: 9 0.80 0.13 0.07 Matches are distributed among these distances: 40 1 0.01 41 7 0.06 42 65 0.60 43 36 0.33 ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24 Consensus pattern (42 bp): ATTTAGCGGCGCTTTGTCACAAACGCCGCTAAAGAACATAAC Found at i:42412403 original size:43 final size:43 Alignment explanation
Indices: 42412337--42412427 Score: 130 Period size: 43 Copynumber: 2.1 Consensus size: 43 42412327 CACATTGCAA * * * 42412337 GGTAATAAAAAATACAATGCATTTTCTTAATCAAGTAAATCTT 1 GGTAATAAAAAATACAATACATTTACTTAATCAAGGAAATCTT * * 42412380 GGTAATAAAAGATATAATACATTTACTTAATCAAGGAAATCTT 1 GGTAATAAAAAATACAATACATTTACTTAATCAAGGAAATCTT 42412423 -GTAAT 1 GGTAAT 42412428 GAACTCAAAG Statistics Matches: 43, Mismatches: 5, Indels: 1 0.88 0.10 0.02 Matches are distributed among these distances: 42 5 0.12 43 38 0.88 ACGTcount: A:0.45, C:0.10, G:0.11, T:0.34 Consensus pattern (43 bp): GGTAATAAAAAATACAATACATTTACTTAATCAAGGAAATCTT Found at i:42414880 original size:29 final size:29 Alignment explanation
Indices: 42414778--42414880 Score: 77 Period size: 29 Copynumber: 3.5 Consensus size: 29 42414768 AAAAAAAATT * 42414778 AAAACCAAAATAAAGAGGAAAAATACTGG 1 AAAAACAAAATAAAGAGGAAAAATACTGG ** * 42414807 AAAAACAAAATAAA-ATCTCAAAGAA-AAT-G 1 AAAAACAAAATAAAGA--GGAAA-AATACTGG * * 42414836 AAGCGAAGAAAATAAAGAGGAAAAATACTGG 1 AA--AAACAAAATAAAGAGGAAAAATACTGG * 42414867 AAAAATAAAATAAA 1 AAAAACAAAATAAA 42414881 ATCAAGGGCC Statistics Matches: 55, Mismatches: 11, Indels: 16 0.67 0.13 0.20 Matches are distributed among these distances: 28 1 0.02 29 28 0.51 30 10 0.18 31 15 0.27 32 1 0.02 ACGTcount: A:0.66, C:0.08, G:0.15, T:0.12 Consensus pattern (29 bp): AAAAACAAAATAAAGAGGAAAAATACTGG Found at i:42415206 original size:23 final size:23 Alignment explanation
Indices: 42415175--42415218 Score: 63 Period size: 22 Copynumber: 1.9 Consensus size: 23 42415165 AAAGATGTCG * 42415175 TTTTAATCTGTTAAAAATTATTTA 1 TTTTAATCTGCT-AAAATTATTTA 42415199 TTTT-ATCTGCTAAAATTATT 1 TTTTAATCTGCTAAAATTATT 42415219 AGTTAAGTGG Statistics Matches: 19, Mismatches: 1, Indels: 2 0.86 0.05 0.09 Matches are distributed among these distances: 22 9 0.47 23 6 0.32 24 4 0.21 ACGTcount: A:0.34, C:0.07, G:0.05, T:0.55 Consensus pattern (23 bp): TTTTAATCTGCTAAAATTATTTA Found at i:42416188 original size:22 final size:21 Alignment explanation
Indices: 42416139--42416188 Score: 64 Period size: 22 Copynumber: 2.3 Consensus size: 21 42416129 AAACCCCAAC * 42416139 CCTTAAACCATAATCCATAAT 1 CCTTAAACCATAATCCATAAA * * 42416160 CCATAAACACATAATCCCTAAA 1 CCTTAAAC-CATAATCCATAAA 42416182 CCTTAAA 1 CCTTAAA 42416189 ATAGTAACTC Statistics Matches: 24, Mismatches: 4, Indels: 1 0.83 0.14 0.03 Matches are distributed among these distances: 21 7 0.29 22 17 0.71 ACGTcount: A:0.46, C:0.30, G:0.00, T:0.24 Consensus pattern (21 bp): CCTTAAACCATAATCCATAAA Found at i:42416398 original size:41 final size:39 Alignment explanation
Indices: 42416301--42416411 Score: 150 Period size: 40 Copynumber: 2.7 Consensus size: 39 42416291 GCTAAAAATA * * * 42416301 GAGCATTAGCGGCGCTTCTTTAAAAACACCGCTAAAGCCT 1 GAGCATTAGCGGCGCTT-TTCAAAAACGCCGCTAAAGCCC * 42416341 GAGCATTAGCGACGCTTTTCCAAAAACGCCGCTAAAGCCCC 1 GAGCATTAGCGGCGCTTTT-CAAAAACGCCGCTAAAG-CCC 42416382 GAGCATTAGCGGCGCTTTTTCAAAAACGCC 1 GAGCATTAGCGGCGC-TTTTCAAAAACGCC 42416412 AAAAACGTCG Statistics Matches: 63, Mismatches: 5, Indels: 5 0.86 0.07 0.07 Matches are distributed among these distances: 39 2 0.03 40 31 0.49 41 26 0.41 42 4 0.06 ACGTcount: A:0.29, C:0.30, G:0.21, T:0.21 Consensus pattern (39 bp): GAGCATTAGCGGCGCTTTTCAAAAACGCCGCTAAAGCCC Found at i:42416569 original size:40 final size:40 Alignment explanation
Indices: 42416472--42416642 Score: 157 Period size: 40 Copynumber: 4.3 Consensus size: 40 42416462 TAGGTTTTTC * *** * * 42416472 GCGGCGCTTTTTGGAAAATGCCGCTAATGCT-AATTTTTA 1 GCGGCGTTTTTTGGAAAGCACCGCTAATGCTCGATCTTTA * **** 42416511 ACGGCGTTTTCCAAAAAGCACCGCTAATGCTCGATCTTTA 1 GCGGCGTTTTTTGGAAAGCACCGCTAATGCTCGATCTTTA * 42416551 GCGGCGTTTTTTGGAAAGCGCCGCTAATGCTCGATCTTTA 1 GCGGCGTTTTTTGGAAAGCACCGCTAATGCTCGATCTTTA * * * * * 42416591 GAGGCATTTTTTGGAAAG-AGCCGCTAATTCTTGATTTTTA 1 GCGGCGTTTTTTGGAAAGCA-CCGCTAATGCTCGATCTTTA * 42416631 GCGGCATTTTTT 1 GCGGCGTTTTTT 42416643 TATCCAAACG Statistics Matches: 106, Mismatches: 24, Indels: 3 0.80 0.18 0.02 Matches are distributed among these distances: 39 22 0.21 40 84 0.79 ACGTcount: A:0.22, C:0.20, G:0.23, T:0.35 Consensus pattern (40 bp): GCGGCGTTTTTTGGAAAGCACCGCTAATGCTCGATCTTTA Found at i:42419427 original size:29 final size:28 Alignment explanation
Indices: 42419387--42419483 Score: 108 Period size: 29 Copynumber: 3.5 Consensus size: 28 42419377 ATAATATATG * * 42419387 TAAATTAAAATATTTAAATAAGTTTAAA 1 TAAATTAAAATATTAAAATAAGTTGAAA 42419415 TAAATTAACAATATTAAAATAAGTTGAAA 1 TAAATTAA-AATATTAAAATAAGTTGAAA * * * 42419444 TGAATTAAAGATGTTAAAAT-ATTTGAAA 1 TAAATTAAA-ATATTAAAATAAGTTGAAA * 42419472 GAAA-TAAAATAT 1 TAAATTAAAATAT 42419484 CTATATAATA Statistics Matches: 59, Mismatches: 8, Indels: 6 0.81 0.11 0.08 Matches are distributed among these distances: 26 3 0.05 27 4 0.07 28 18 0.31 29 34 0.58 ACGTcount: A:0.57, C:0.01, G:0.08, T:0.34 Consensus pattern (28 bp): TAAATTAAAATATTAAAATAAGTTGAAA Found at i:42421033 original size:16 final size:16 Alignment explanation
Indices: 42421012--42421051 Score: 71 Period size: 16 Copynumber: 2.5 Consensus size: 16 42421002 TTTATTTGCA 42421012 TATGGGCTGGGCAAAT 1 TATGGGCTGGGCAAAT 42421028 TATGGGCTGGGCAAAT 1 TATGGGCTGGGCAAAT * 42421044 TTTGGGCT 1 TATGGGCT 42421052 TGTACAACTG Statistics Matches: 23, Mismatches: 1, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 16 23 1.00 ACGTcount: A:0.20, C:0.12, G:0.38, T:0.30 Consensus pattern (16 bp): TATGGGCTGGGCAAAT Found at i:42421488 original size:44 final size:44 Alignment explanation
Indices: 42421421--42421591 Score: 127 Period size: 44 Copynumber: 3.9 Consensus size: 44 42421411 GATGCGATCT * * * 42421421 GCTCTACTATAACTTC-AGAGAGATAAGATCT-CTGGTTTTAATCC 1 GCTCCACTACAACTTCAAG-GAGATAAGAT-TACTGGCTTTAATCC * * * * 42421465 G-TACCACTGCAACTTCAAGGAGATAGGATTATTGGCTTTAATCT 1 GCT-CCACTACAACTTCAAGGAGATAAGATTACTGGCTTTAATCC * * * 42421509 GCTCCGCTACAACTTCAGGGAGATAAGATT-C-GCCATCTTCAATCC 1 GCTCCACTACAACTTCAAGGAGATAAGATTACTGGC-T-TT-AATCC * * * * 42421554 GCTCCACTGCAACTTCAGGGAGATATGATTATTGGCTT 1 GCTCCACTACAACTTCAAGGAGATAAGATTACTGGCTT 42421592 CAATATGCTT Statistics Matches: 99, Mismatches: 19, Indels: 17 0.73 0.14 0.13 Matches are distributed among these distances: 42 2 0.02 43 3 0.03 44 56 0.57 45 35 0.35 46 1 0.01 47 2 0.02 ACGTcount: A:0.27, C:0.23, G:0.19, T:0.30 Consensus pattern (44 bp): GCTCCACTACAACTTCAAGGAGATAAGATTACTGGCTTTAATCC Found at i:42421577 original size:89 final size:89 Alignment explanation
Indices: 42421460--42421633 Score: 242 Period size: 89 Copynumber: 2.0 Consensus size: 89 42421450 CTCTGGTTTT * * 42421460 AATCCGTACCACTGCAACTTCAAGGAGATAGGATTATTGGCTTTAATCTGCTCCGCTACAACTTC 1 AATCCGTACCACTGCAACTTCAAGGAGATAGGATTATTGGCTTCAATATGCTCCGCTACAACTTC * 42421525 AGGGAGATAAGATTCGCCATCTTC 66 AGGGAGATAAGATCCGCCATCTTC * * * ** 42421549 AATCCGCT-CCACTGCAACTTCAGGGAGATATGATTATTGGCTTCAATATGCTTCGCTGTAACTT 1 AATCCG-TACCACTGCAACTTCAAGGAGATAGGATTATTGGCTTCAATATGCTCCGCTACAACTT * * 42421613 TAGGGAGATGAGATCCGCCAT 65 CAGGGAGATAAGATCCGCCAT 42421634 AATTTTTAGC Statistics Matches: 74, Mismatches: 10, Indels: 2 0.86 0.12 0.02 Matches are distributed among these distances: 89 73 0.99 90 1 0.01 ACGTcount: A:0.27, C:0.24, G:0.21, T:0.29 Consensus pattern (89 bp): AATCCGTACCACTGCAACTTCAAGGAGATAGGATTATTGGCTTCAATATGCTCCGCTACAACTTC AGGGAGATAAGATCCGCCATCTTC Found at i:42421612 original size:44 final size:44 Alignment explanation
Indices: 42421471--42421626 Score: 150 Period size: 44 Copynumber: 3.5 Consensus size: 44 42421461 ATCCGTACCA * * * 42421471 CTGCAACTTCAAGGAGATAGGATTATTGGCTTTAATCTGCTCCG 1 CTGCAACTTCAGGGAGATAAGATTATTGGCTTCAATCTGCTCCG * ***** * * 42421515 CTACAACTTCAGGGAGATAAGATTCGCCATCTTCAATCCGCTCCA 1 CTGCAACTTCAGGGAGATAAGATT-ATTGGCTTCAATCTGCTCCG * * * 42421560 CTGCAACTTCAGGGAGATATGATTATTGGCTTCAATATGCTTCG 1 CTGCAACTTCAGGGAGATAAGATTATTGGCTTCAATCTGCTCCG * * * 42421604 CTGTAACTTTAGGGAGATGAGAT 1 CTGCAACTTCAGGGAGATAAGAT 42421627 CCGCCATAAT Statistics Matches: 85, Mismatches: 26, Indels: 2 0.75 0.23 0.02 Matches are distributed among these distances: 44 51 0.60 45 34 0.40 ACGTcount: A:0.27, C:0.21, G:0.22, T:0.30 Consensus pattern (44 bp): CTGCAACTTCAGGGAGATAAGATTATTGGCTTCAATCTGCTCCG Found at i:42434056 original size:29 final size:29 Alignment explanation
Indices: 42434024--42434089 Score: 89 Period size: 29 Copynumber: 2.3 Consensus size: 29 42434014 AATTAAAATT * 42434024 TTAAAATAAGTTTAAATAAATGAACA-ATA 1 TTAAAATAAGTTGAAATAAATGAA-AGATA * * 42434053 TTAAAATAAGTTGAAATGAATTAAAGATA 1 TTAAAATAAGTTGAAATAAATGAAAGATA 42434082 TTAAAATA 1 TTAAAATA 42434090 TTTGAAAGAA Statistics Matches: 33, Mismatches: 3, Indels: 2 0.87 0.08 0.05 Matches are distributed among these distances: 28 1 0.03 29 32 0.97 ACGTcount: A:0.58, C:0.02, G:0.09, T:0.32 Consensus pattern (29 bp): TTAAAATAAGTTGAAATAAATGAAAGATA Found at i:42434431 original size:3 final size:3 Alignment explanation
Indices: 42434419--42434485 Score: 55 Period size: 3 Copynumber: 22.3 Consensus size: 3 42434409 ATAATAGCAG * * * * 42434419 TAA TAG TAA TAA TAT TAA TAA TAA TGAA -AG TAG TAA TAA TAA TAA 1 TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA * * * 42434464 TTA TAA TAA CAA CAA TAA TAA T 1 TAA TAA TAA TAA TAA TAA TAA T 42434486 CCTAATATTA Statistics Matches: 52, Mismatches: 10, Indels: 4 0.79 0.15 0.06 Matches are distributed among these distances: 2 1 0.02 3 49 0.94 4 2 0.04 ACGTcount: A:0.58, C:0.03, G:0.06, T:0.33 Consensus pattern (3 bp): TAA Found at i:42440119 original size:18 final size:18 Alignment explanation
Indices: 42440082--42440119 Score: 51 Period size: 20 Copynumber: 2.1 Consensus size: 18 42440072 TAAATGATGA 42440082 ATTTGAAGTATTAGTTGTT 1 ATTTGAAGTATTA-TTGTT 42440101 ATTTGTAAGTATT-TTGTT 1 ATTTG-AAGTATTATTGTT 42440119 A 1 A 42440120 AGTGATTTTG Statistics Matches: 18, Mismatches: 0, Indels: 3 0.86 0.00 0.14 Matches are distributed among these distances: 18 6 0.33 19 5 0.28 20 7 0.39 ACGTcount: A:0.26, C:0.00, G:0.18, T:0.55 Consensus pattern (18 bp): ATTTGAAGTATTATTGTT Found at i:42441553 original size:20 final size:20 Alignment explanation
Indices: 42441528--42441582 Score: 94 Period size: 20 Copynumber: 2.8 Consensus size: 20 42441518 AAGCTTATGC 42441528 TAAGTAAATGGAATGGAAAG 1 TAAGTAAATGGAATGGAAAG 42441548 TAAGTAAAT-GAAGTGGAAAG 1 TAAGTAAATGGAA-TGGAAAG 42441568 TAAGTAAATGGAATG 1 TAAGTAAATGGAATG 42441583 ATTCATCGTC Statistics Matches: 33, Mismatches: 0, Indels: 4 0.89 0.00 0.11 Matches are distributed among these distances: 19 3 0.09 20 27 0.82 21 3 0.09 ACGTcount: A:0.49, C:0.00, G:0.29, T:0.22 Consensus pattern (20 bp): TAAGTAAATGGAATGGAAAG Found at i:42444576 original size:20 final size:20 Alignment explanation
Indices: 42444551--42444622 Score: 126 Period size: 20 Copynumber: 3.6 Consensus size: 20 42444541 TATAAGCCAC * 42444551 TCCATTTACTTACTTACCAT 1 TCCATTTACTTACTTTCCAT 42444571 TCCATTTACTTACTTTCCAT 1 TCCATTTACTTACTTTCCAT * 42444591 TTCATTTACTTACTTTCCAT 1 TCCATTTACTTACTTTCCAT 42444611 TCCATTTACTTA 1 TCCATTTACTTA 42444623 GCATAAGCTT Statistics Matches: 49, Mismatches: 3, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 20 49 1.00 ACGTcount: A:0.22, C:0.28, G:0.00, T:0.50 Consensus pattern (20 bp): TCCATTTACTTACTTTCCAT Found at i:42444611 original size:15 final size:16 Alignment explanation
Indices: 42444560--42444592 Score: 50 Period size: 15 Copynumber: 2.1 Consensus size: 16 42444550 CTCCATTTAC 42444560 TTACTTACCATTCCAT 1 TTACTTACCATTCCAT * 42444576 TTACTTA-CTTTCCAT 1 TTACTTACCATTCCAT 42444591 TT 1 TT 42444593 CATTTACTTA Statistics Matches: 16, Mismatches: 1, Indels: 1 0.89 0.06 0.06 Matches are distributed among these distances: 15 9 0.56 16 7 0.44 ACGTcount: A:0.21, C:0.27, G:0.00, T:0.52 Consensus pattern (16 bp): TTACTTACCATTCCAT Found at i:42448918 original size:24 final size:25 Alignment explanation
Indices: 42448898--42448957 Score: 74 Period size: 24 Copynumber: 2.6 Consensus size: 25 42448888 AAATTTATCG 42448898 ATATTT-T-TAAAAAAT-ATTTTAT 1 ATATTTATATAAAAAATAATTTTAT * 42448920 ATATTTATATAAAAAATAATTTTAA 1 ATATTTATATAAAAAATAATTTTAT * 42448945 ATA-TTAAATAAAA 1 ATATTTATATAAAA 42448958 TTTAAATTTA Statistics Matches: 33, Mismatches: 2, Indels: 4 0.85 0.05 0.10 Matches are distributed among these distances: 22 6 0.18 23 1 0.03 24 17 0.52 25 9 0.27 ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45 Consensus pattern (25 bp): ATATTTATATAAAAAATAATTTTAT Found at i:42448975 original size:18 final size:18 Alignment explanation
Indices: 42448929--42448977 Score: 53 Period size: 19 Copynumber: 2.6 Consensus size: 18 42448919 TATATTTATA 42448929 TAAAAAATAATTTTAAATAT 1 TAAAAAA-AA-TTTAAATAT * * 42448949 TAAATAAAATTTAAATTT 1 TAAAAAAAATTTAAATAT 42448967 ATAAAAAAAAT 1 -TAAAAAAAAT 42448978 GCACAATGCA Statistics Matches: 25, Mismatches: 3, Indels: 3 0.81 0.10 0.10 Matches are distributed among these distances: 18 8 0.32 19 11 0.44 20 6 0.24 ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37 Consensus pattern (18 bp): TAAAAAAAATTTAAATAT Found at i:42459280 original size:16 final size:16 Alignment explanation
Indices: 42459259--42459289 Score: 53 Period size: 16 Copynumber: 1.9 Consensus size: 16 42459249 TTCACTATTA * 42459259 TGTCTTTTTTATTTTC 1 TGTCTTTTATATTTTC 42459275 TGTCTTTTATATTTT 1 TGTCTTTTATATTTT 42459290 GCATGCATAG Statistics Matches: 14, Mismatches: 1, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 16 14 1.00 ACGTcount: A:0.10, C:0.10, G:0.06, T:0.74 Consensus pattern (16 bp): TGTCTTTTATATTTTC Found at i:42459793 original size:28 final size:30 Alignment explanation
Indices: 42459754--42459810 Score: 100 Period size: 28 Copynumber: 2.0 Consensus size: 30 42459744 CCTCTTTACT 42459754 TTCCCTCCAAAACTTTTACT-CCCTCCCAC 1 TTCCCTCCAAAACTTTTACTCCCCTCCCAC 42459783 TTCCC-CCAAAACTTTTACTCCCCTCCCA 1 TTCCCTCCAAAACTTTTACTCCCCTCCCA 42459811 TCCCCCTTCT Statistics Matches: 27, Mismatches: 0, Indels: 2 0.93 0.00 0.07 Matches are distributed among these distances: 28 14 0.52 29 13 0.48 ACGTcount: A:0.21, C:0.49, G:0.00, T:0.30 Consensus pattern (30 bp): TTCCCTCCAAAACTTTTACTCCCCTCCCAC Found at i:42461526 original size:39 final size:39 Alignment explanation
Indices: 42461434--42461531 Score: 144 Period size: 39 Copynumber: 2.5 Consensus size: 39 42461424 CCCAGCCCAA * ** 42461434 ACCCAATTACCCAACCCAGTAAAACTAAAACTAAAATTT 1 ACCCAATTACCCAACCCAATAAAACTAAAACTAAAAACT * 42461473 ATCCAATTACCCAACCCAATAAAACTAAAACTAAAAGACT 1 ACCCAATTACCCAACCCAATAAAACTAAAACTAAAA-ACT 42461513 ACCCAATTA-CCAACCCAAT 1 ACCCAATTACCCAACCCAAT 42461532 TTACTAAAGC Statistics Matches: 53, Mismatches: 5, Indels: 2 0.88 0.08 0.03 Matches are distributed among these distances: 39 44 0.83 40 9 0.17 ACGTcount: A:0.49, C:0.31, G:0.02, T:0.18 Consensus pattern (39 bp): ACCCAATTACCCAACCCAATAAAACTAAAACTAAAAACT Found at i:42461607 original size:11 final size:11 Alignment explanation
Indices: 42461593--42461631 Score: 53 Period size: 11 Copynumber: 3.6 Consensus size: 11 42461583 GCTGCCATTT * 42461593 TTTTTCCCTAA 1 TTTTTCTCTAA * 42461604 TTTTTCTCT-T 1 TTTTTCTCTAA 42461614 TTTTTCTCTAA 1 TTTTTCTCTAA 42461625 TTTTTCT 1 TTTTTCT 42461632 TGTTCTTCTT Statistics Matches: 24, Mismatches: 3, Indels: 2 0.83 0.10 0.07 Matches are distributed among these distances: 10 9 0.38 11 15 0.62 ACGTcount: A:0.10, C:0.21, G:0.00, T:0.69 Consensus pattern (11 bp): TTTTTCTCTAA Found at i:42461617 original size:21 final size:21 Alignment explanation
Indices: 42461591--42461631 Score: 73 Period size: 21 Copynumber: 2.0 Consensus size: 21 42461581 CGGCTGCCAT 42461591 TTTTTTTCCCTAATTTTTCTC 1 TTTTTTTCCCTAATTTTTCTC * 42461612 TTTTTTTCTCTAATTTTTCT 1 TTTTTTTCCCTAATTTTTCT 42461632 TGTTCTTCTT Statistics Matches: 19, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 21 19 1.00 ACGTcount: A:0.10, C:0.20, G:0.00, T:0.71 Consensus pattern (21 bp): TTTTTTTCCCTAATTTTTCTC Found at i:42462236 original size:31 final size:31 Alignment explanation
Indices: 42462201--42462260 Score: 111 Period size: 31 Copynumber: 1.9 Consensus size: 31 42462191 TGTTTGCAAT * 42462201 TTCTTATCCACTTTCATATGCAATTTCTTAA 1 TTCTTATCCACTTTCATAAGCAATTTCTTAA 42462232 TTCTTATCCACTTTCATAAGCAATTTCTT 1 TTCTTATCCACTTTCATAAGCAATTTCTT 42462261 CCTGCTTTTA Statistics Matches: 28, Mismatches: 1, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 31 28 1.00 ACGTcount: A:0.25, C:0.23, G:0.03, T:0.48 Consensus pattern (31 bp): TTCTTATCCACTTTCATAAGCAATTTCTTAA Found at i:42462677 original size:18 final size:18 Alignment explanation
Indices: 42462645--42462696 Score: 54 Period size: 18 Copynumber: 2.9 Consensus size: 18 42462635 GGTATTTTTC 42462645 GGTAATTCG-GTTAATTCA- 1 GGTAATTCGAG-TAATT-AG * 42462663 GGTAATTTGAGTAATTAG 1 GGTAATTCGAGTAATTAG * 42462681 GGTACTTCGAGTAATT 1 GGTAATTCGAGTAATT 42462697 TTTAACAAAA Statistics Matches: 29, Mismatches: 3, Indels: 4 0.81 0.08 0.11 Matches are distributed among these distances: 17 1 0.03 18 27 0.93 19 1 0.03 ACGTcount: A:0.29, C:0.08, G:0.25, T:0.38 Consensus pattern (18 bp): GGTAATTCGAGTAATTAG Found at i:42469574 original size:22 final size:21 Alignment explanation
Indices: 42469546--42469608 Score: 83 Period size: 20 Copynumber: 3.0 Consensus size: 21 42469536 TCGAAATACT * * 42469546 AACAGAGGCATCGTAGTGCAA 1 AACAGAGGCACCGAAGTGCAA * 42469567 ATACAGAGGCACCAAAGTGC-A 1 A-ACAGAGGCACCGAAGTGCAA 42469588 AACAGAGGCACCGAAGTGCAA 1 AACAGAGGCACCGAAGTGCAA 42469609 TATCATTCAA Statistics Matches: 36, Mismatches: 4, Indels: 4 0.82 0.09 0.09 Matches are distributed among these distances: 20 17 0.47 21 4 0.11 22 15 0.42 ACGTcount: A:0.41, C:0.22, G:0.27, T:0.10 Consensus pattern (21 bp): AACAGAGGCACCGAAGTGCAA Found at i:42471198 original size:7 final size:7 Alignment explanation
Indices: 42471176--42471230 Score: 56 Period size: 7 Copynumber: 7.9 Consensus size: 7 42471166 TTCTTTTCAG * 42471176 CTCAATA 1 CTCAATC * 42471183 CTTAATC 1 CTCAATC 42471190 CTCAATC 1 CTCAATC 42471197 CTCAATC 1 CTCAATC * 42471204 ATCAATC 1 CTCAATC * 42471211 ATCAATC 1 CTCAATC * * 42471218 ATCAATT 1 CTCAATC 42471225 CTCAAT 1 CTCAAT 42471231 TCATAATTAT Statistics Matches: 42, Mismatches: 6, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 7 42 1.00 ACGTcount: A:0.36, C:0.31, G:0.00, T:0.33 Consensus pattern (7 bp): CTCAATC Found at i:42478191 original size:2 final size:2 Alignment explanation
Indices: 42478180--42478216 Score: 67 Period size: 2 Copynumber: 19.0 Consensus size: 2 42478170 CTAGGGTTTA 42478180 CT CT -T CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT 1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT 42478217 TAATCTTTTA Statistics Matches: 34, Mismatches: 0, Indels: 2 0.94 0.00 0.06 Matches are distributed among these distances: 1 1 0.03 2 33 0.97 ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51 Consensus pattern (2 bp): CT Found at i:42480676 original size:19 final size:18 Alignment explanation
Indices: 42480652--42480699 Score: 51 Period size: 19 Copynumber: 2.5 Consensus size: 18 42480642 TTGTATTTTT * * 42480652 AAAAATATTAATTACTATA 1 AAAAATATCAA-TACGATA 42480671 AAAAATTATCAATACGATA 1 AAAAA-TATCAATACGATA 42480690 AAATAATATC 1 AAA-AATATC 42480700 TAAACGAGTA Statistics Matches: 25, Mismatches: 2, Indels: 4 0.81 0.06 0.13 Matches are distributed among these distances: 19 18 0.72 20 7 0.28 ACGTcount: A:0.58, C:0.08, G:0.02, T:0.31 Consensus pattern (18 bp): AAAAATATCAATACGATA Found at i:42481705 original size:30 final size:31 Alignment explanation
Indices: 42481660--42481732 Score: 96 Period size: 30 Copynumber: 2.4 Consensus size: 31 42481650 ATTTTTAAAA * 42481660 AAAAATTGAAGGGGTTAAATTATAAATATTC 1 AAAAATTGAAGGGGTTAAATTAAAAATATTC * * 42481691 AAAAGTTG-AGGGGTTAAATTAAAAATA-TA 1 AAAAATTGAAGGGGTTAAATTAAAAATATTC 42481720 AAAAATTTGAAGG 1 AAAAA-TTGAAGG 42481733 ACTAAAGTTA Statistics Matches: 36, Mismatches: 4, Indels: 4 0.82 0.09 0.09 Matches are distributed among these distances: 29 5 0.14 30 21 0.58 31 10 0.28 ACGTcount: A:0.51, C:0.01, G:0.19, T:0.29 Consensus pattern (31 bp): AAAAATTGAAGGGGTTAAATTAAAAATATTC Found at i:42489223 original size:16 final size:15 Alignment explanation
Indices: 42489202--42489236 Score: 52 Period size: 16 Copynumber: 2.3 Consensus size: 15 42489192 TGAATATAAA * 42489202 TATATAATTATTATTT 1 TATATAATTAAT-TTT 42489218 TATATAATTAATTTT 1 TATATAATTAATTTT 42489233 TATA 1 TATA 42489237 ATATAATATA Statistics Matches: 18, Mismatches: 1, Indels: 1 0.90 0.05 0.05 Matches are distributed among these distances: 15 7 0.39 16 11 0.61 ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60 Consensus pattern (15 bp): TATATAATTAATTTT Found at i:42489236 original size:13 final size:14 Alignment explanation
Indices: 42489202--42489243 Score: 50 Period size: 16 Copynumber: 2.9 Consensus size: 14 42489192 TGAATATAAA 42489202 TATATAATTATTATTT 1 TATATAATTA--ATTT 42489218 TATATAATTAATTT 1 TATATAATTAATTT 42489232 T-TATAATATAAT 1 TATATAAT-TAAT 42489244 ATACTTGTGT Statistics Matches: 25, Mismatches: 0, Indels: 4 0.86 0.00 0.14 Matches are distributed among these distances: 13 6 0.24 14 9 0.36 16 10 0.40 ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57 Consensus pattern (14 bp): TATATAATTAATTT Found at i:42491030 original size:109 final size:109 Alignment explanation
Indices: 42490855--42491072 Score: 373 Period size: 109 Copynumber: 2.0 Consensus size: 109 42490845 TCCTAACAGC * 42490855 ATTTGCCCGCAACTGCCGCACATCCTAACAACAGCCCCGCACATGTCGCGCACGTTCGCCTCCAC 1 ATTTGCCCGCAACCGCCGCACATCCTAACAACAGCCCCGCACATGTCGCGCACGTTCGCCTCCAC * 42490920 GTTGACTGGTCGTACCTGCAGCAAAAAGCAGAAACAAACAGCAA 66 GTTGACTGGTCGTACCTGCAGCAAAAAGCAAAAACAAACAGCAA * * * 42490964 ATTTGCCCGTAGCCGCCGCACATCCTAACAGCAGCCCCGCACATGTCGCGCACGTTCGCCTCCAC 1 ATTTGCCCGCAACCGCCGCACATCCTAACAACAGCCCCGCACATGTCGCGCACGTTCGCCTCCAC * * 42491029 GTTGACTGGTCGTACCTGCAGCAACAAGCAAAAAGAAACAGCAA 66 GTTGACTGGTCGTACCTGCAGCAAAAAGCAAAAACAAACAGCAA 42491073 CGAAATAATA Statistics Matches: 102, Mismatches: 7, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 109 102 1.00 ACGTcount: A:0.28, C:0.36, G:0.20, T:0.16 Consensus pattern (109 bp): ATTTGCCCGCAACCGCCGCACATCCTAACAACAGCCCCGCACATGTCGCGCACGTTCGCCTCCAC GTTGACTGGTCGTACCTGCAGCAAAAAGCAAAAACAAACAGCAA Found at i:42491807 original size:16 final size:15 Alignment explanation
Indices: 42491757--42491821 Score: 58 Period size: 15 Copynumber: 4.1 Consensus size: 15 42491747 CCCTGTTCTA * 42491757 TTTTAATTTCATTTTT 1 TTTTAATTT-GTTTTT * * 42491773 TGGTTATTTTGTTTTT 1 T-TTTAATTTGTTTTT * 42491789 TTTCAATTTGTTTTT 1 TTTTAATTTGTTTTT * 42491804 TTTTAAATTGTTATTT 1 TTTTAATTTGTT-TTT 42491820 TT 1 TT 42491822 AAAATTATTA Statistics Matches: 39, Mismatches: 8, Indels: 4 0.76 0.16 0.08 Matches are distributed among these distances: 15 21 0.54 16 12 0.31 17 6 0.15 ACGTcount: A:0.15, C:0.03, G:0.08, T:0.74 Consensus pattern (15 bp): TTTTAATTTGTTTTT Found at i:42491826 original size:15 final size:15 Alignment explanation
Indices: 42491781--42491827 Score: 58 Period size: 15 Copynumber: 3.1 Consensus size: 15 42491771 TTTGGTTATT * * 42491781 TTGTTTTTTTTCAAT 1 TTGTTTTTTTTAAAA * 42491796 TTGTTTTTTTTTAAA 1 TTGTTTTTTTTAAAA * 42491811 TTGTTATTTTTAAAA 1 TTGTTTTTTTTAAAA 42491826 TT 1 TT 42491828 ATTACTATAT Statistics Matches: 28, Mismatches: 4, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 15 28 1.00 ACGTcount: A:0.21, C:0.02, G:0.06, T:0.70 Consensus pattern (15 bp): TTGTTTTTTTTAAAA Found at i:42492006 original size:11 final size:10 Alignment explanation
Indices: 42491990--42492023 Score: 50 Period size: 11 Copynumber: 3.2 Consensus size: 10 42491980 TTTTAACCTT 42491990 TATATACTTTA 1 TATATA-TTTA 42492001 TATATATTATA 1 TATATATT-TA 42492012 TATATATTTA 1 TATATATTTA 42492022 TA 1 TA 42492024 CATTTCTTTT Statistics Matches: 22, Mismatches: 0, Indels: 3 0.88 0.00 0.12 Matches are distributed among these distances: 10 6 0.27 11 16 0.73 ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56 Consensus pattern (10 bp): TATATATTTA Found at i:42492101 original size:21 final size:21 Alignment explanation
Indices: 42492063--42492102 Score: 53 Period size: 21 Copynumber: 1.9 Consensus size: 21 42492053 ATATACATAC * ** 42492063 TTTTATTTTTATTTTTCTTTA 1 TTTTATTTTCATAATTCTTTA 42492084 TTTTATTTTCATAATTCTT 1 TTTTATTTTCATAATTCTT 42492103 ACATATACAT Statistics Matches: 16, Mismatches: 3, Indels: 0 0.84 0.16 0.00 Matches are distributed among these distances: 21 16 1.00 ACGTcount: A:0.17, C:0.07, G:0.00, T:0.75 Consensus pattern (21 bp): TTTTATTTTCATAATTCTTTA Found at i:42496937 original size:13 final size:13 Alignment explanation
Indices: 42496915--42496966 Score: 56 Period size: 13 Copynumber: 4.1 Consensus size: 13 42496905 TCGTAAAAAT 42496915 AATG-AAATGAAA 1 AATGAAAATGAAA * 42496927 AGTGAAAATGAAA 1 AATGAAAATGAAA 42496940 AATGAAAAATGGAAA 1 AATG-AAAAT-GAAA 42496955 AA-GAAAA-GAAA 1 AATGAAAATGAAA 42496966 A 1 A 42496967 GGAGAGGCCA Statistics Matches: 35, Mismatches: 2, Indels: 7 0.80 0.05 0.16 Matches are distributed among these distances: 11 5 0.14 12 3 0.09 13 15 0.43 14 6 0.17 15 6 0.17 ACGTcount: A:0.69, C:0.00, G:0.19, T:0.12 Consensus pattern (13 bp): AATGAAAATGAAA Found at i:42496954 original size:8 final size:7 Alignment explanation
Indices: 42496919--42496961 Score: 54 Period size: 7 Copynumber: 6.3 Consensus size: 7 42496909 AAAAATAATG 42496919 AAATGAA 1 AAATGAA * 42496926 AAGTG-A 1 AAATGAA 42496932 AAATGAA 1 AAATGAA 42496939 AAATGAA 1 AAATGAA 42496946 AAATGGAA 1 AAAT-GAA 42496954 AAA-GAA 1 AAATGAA 42496960 AA 1 AA 42496962 GAAAAGGAGA Statistics Matches: 32, Mismatches: 2, Indels: 5 0.82 0.05 0.13 Matches are distributed among these distances: 6 10 0.31 7 16 0.50 8 6 0.19 ACGTcount: A:0.70, C:0.00, G:0.19, T:0.12 Consensus pattern (7 bp): AAATGAA Found at i:42498383 original size:44 final size:44 Alignment explanation
Indices: 42498254--42499149 Score: 693 Period size: 44 Copynumber: 20.3 Consensus size: 44 42498244 AAAAGCAGCA * * * *** 42498254 GATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAAGATAGCA 1 GATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGATAATG *** * *** 42498298 GATCTTGTCTTCCCATACTGGTGGTGAAGTAGATC-GAAGATAATG 1 GATCTTGTCTTCATGTA-TTGACATGAAGTAGATCAG-AGATAATG * * * * * 42498343 GATCTTGGCTTCATATATTAACATGAAGTAGATCAGAGATAGTA 1 GATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGATAATG * * * 42498387 GATCTTGTCTTCATGTATTGACATGGAGTAGATCAGAGATAGTA 1 GATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGATAATG * * 42498431 GATCTTATCTTCATGTATTGACATGAAGTAGATC-GAAGATGATG 1 GATCTTGTCTTCATGTATTGACATGAAGTAGATCAG-AGATAATG * * 42498475 GATATTGTCTTCATGTATTGACATGGAGTAGATCAGAGATAGCA-G 1 GATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGATA--ATG * * ** 42498520 G-TATTGCCTTCATGTATTGACATGAAGTAGATCAGAGATAACA 1 GATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGATAATG * * * * 42498563 TATCTTATTTTCATGTATTGACATGAAGTAGATC-GAAGGTAATG 1 GATCTTGTCTTCATGTATTGACATGAAGTAGATCAG-AGATAATG *** 42498607 GATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGATAGCA 1 GATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGATAATG *** * ** * 42498651 GATCTTGTCTTCCCATACTGGTAGTGAAGTAGATC-GAAGGTAATG 1 GATCTTGTCTTCATGTATTGACA-TGAAGTAGATCAG-AGATAATG *** 42498696 GATCTTGTCTTCATGTATTGACAT-AGAGTAGATCAGAGATAGCA 1 GATCTTGTCTTCATGTATTGACATGA-AGTAGATCAGAGATAATG 42498740 GATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGAT-A-G 1 GATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGATAATG * 42498782 GATATCTTATCTTCATGTATTGACATGAAGTAGATC-GAAGATAATG 1 G--ATCTTGTCTTCATGTATTGACATGAAGTAGATCAG-AGATAATG *** 42498828 GATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGATAGCA 1 GATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGATAATG * * 42498872 GATCTTGTCTTCATGTACT-AGCGTGAAGTAGATC-GAAGA-AA-G 1 GATCTTGTCTTCATGTATTGA-CATGAAGTAGATCAG-AGATAATG * * * * ** 42498914 CAGATCTTGTCTTCATGTACTGGCATGAAGTAGATCAAAGAAAACA 1 --GATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGATAATG * * * 42498960 GATATTGTCTTCATGTACTGACGTGAAGTAGATC-GAAGA-AA-G 1 GATCTTGTCTTCATGTATTGACATGAAGTAGATCAG-AGATAATG * * * * * ** 42499002 CAAATCTTGTCTTCCTGTACT-AGCAGTGAAGTATATCAAAGATAACA 1 --GATCTTGTCTTCATGTATTGA-CA-TGAAGTAGATCAGAGATAATG *** * ** * 42499049 GATCTTGTCTTCCCATACTGGTAGCGAAGTAGATC-GAAGA-AA-G 1 GATCTTGTCTTCATGTATTGACA-TGAAGTAGATCAG-AGATAATG * * * * 42499092 CAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATC-GAAGATAGTA 1 --GATCTTGTCTTCATGTATTGACATGAAGTAGATCAG-AGATAATG 42499138 GATCTTGTCTTC 1 GATCTTGTCTTC 42499150 CCATACTGGT Statistics Matches: 692, Mismatches: 116, Indels: 88 0.77 0.13 0.10 Matches are distributed among these distances: 42 2 0.00 43 10 0.01 44 538 0.78 45 137 0.20 46 5 0.01 ACGTcount: A:0.31, C:0.14, G:0.23, T:0.32 Consensus pattern (44 bp): GATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGATAATG Found at i:42498456 original size:88 final size:88 Alignment explanation
Indices: 42498253--42499149 Score: 857 Period size: 88 Copynumber: 10.1 Consensus size: 88 42498243 AAAAAGCAGC * * * *** * 42498253 AGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAAGATAGCAGATCTTGTCTTCCCATACTG 1 AGATCTTGTCTTCATGTATTGACATGAAGTAGATCGAAGATAGCAGATCTTGTCTTCATGTA-TT *** 42498318 GTGGTGAAGTAGATC-GAAGATAAT 65 GACATGAAGTAGATCAG-AGATAAT * * * * * 42498342 GGATCTTGGCTTCATATATTAACATGAAGTAGATC-AGAGATAGTAGATCTTGTCTTCATGTATT 1 AGATCTTGTCTTCATGTATTGACATGAAGTAGATCGA-AGATAGCAGATCTTGTCTTCATGTATT * * 42498406 GACATGGAGTAGATCAGAGATAGT 65 GACATGAAGTAGATCAGAGATAAT * * 42498430 AGATCTTATCTTCATGTATTGACATGAAGTAGATCGAAGAT-G-ATGGATATTGTCTTCATGTAT 1 AGATCTTGTCTTCATGTATTGACATGAAGTAGATCGAAGATAGCA--GATCTTGTCTTCATGTAT * ** 42498493 TGACATGGAGTAGATCAGAGATAGC 64 TGACATGAAGTAGATCAGAGATAAT * * * * * * * 42498518 AGGTATTGCCTTCATGTATTGACATGAAGTAGATC-AGAGATAACATATCTTATTTTCATGTATT 1 AGATCTTGTCTTCATGTATTGACATGAAGTAGATCGA-AGATAGCAGATCTTGTCTTCATGTATT * 42498582 GACATGAAGTAGATC-GAAGGTAAT 65 GACATGAAGTAGATCAG-AGATAAT * *** * 42498606 GGATCTTGTCTTCATGTATTGACATGAAGTAGATC-AGAGATAGCAGATCTTGTCTTCCCATACT 1 AGATCTTGTCTTCATGTATTGACATGAAGTAGATCGA-AGATAGCAGATCTTGTCTTCATGTATT ** * 42498670 GGTAGTGAAGTAGATC-GAAGGTAAT 65 GACA-TGAAGTAGATCAG-AGATAAT * 42498695 GGATCTTGTCTTCATGTATTGACAT-AGAGTAGATC-AGAGATAGCAGATCTTGTCTTCATGTAT 1 AGATCTTGTCTTCATGTATTGACATGA-AGTAGATCGA-AGATAGCAGATCTTGTCTTCATGTAT ** 42498758 TGACATGAAGTAGATCAGAGATAGG 64 TGACATGAAGTAGATCAGAGATAAT * * *** 42498783 ATATCTTATCTTCATGTATTGACATGAAGTAGATCGAAGATAATGGATCTTGTCTTCATGTATTG 1 AGATCTTGTCTTCATGTATTGACATGAAGTAGATCGAAGATAGCAGATCTTGTCTTCATGTATTG ** 42498848 ACATGAAGTAGATCAGAGATAGC 66 ACATGAAGTAGATCAGAGATAAT * * * * 42498871 AGATCTTGTCTTCATGTACT-AGCGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTACT 1 AGATCTTGTCTTCATGTATTGA-CATGAAGTAGATCGAAGATAGCAGATCTTGTCTTCATGTATT * * * * 42498935 GGCATGAAGTAGATCAAAGAAAAC 65 GACATGAAGTAGATCAGAGATAAT * * * * * * * 42498959 AGATATTGTCTTCATGTACTGACGTGAAGTAGATCGAAGAAAGCAAATCTTGTCTTCCTGTACT- 1 AGATCTTGTCTTCATGTATTGACATGAAGTAGATCGAAGATAGCAGATCTTGTCTTCATGTATTG * * * 42499023 AGCAGTGAAGTATATCAAAGATAAC 66 A-CA-TGAAGTAGATCAGAGATAAT *** * ** * * 42499048 AGATCTTGTCTTCCCATACTGGTAGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATT 1 AGATCTTGTCTTCATGTATTGACA-TGAAGTAGATCGAAGATAGCAGATCTTGTCTTCATGTATT * * * 42499113 GGCGTGAAGTAGATC-GAAGATAGT 65 GACATGAAGTAGATCAG-AGATAAT 42499137 AGATCTTGTCTTC 1 AGATCTTGTCTTC 42499150 CCATACTGGT Statistics Matches: 685, Mismatches: 102, Indels: 42 0.83 0.12 0.05 Matches are distributed among these distances: 86 1 0.00 87 4 0.01 88 443 0.65 89 199 0.29 90 38 0.06 ACGTcount: A:0.32, C:0.14, G:0.23, T:0.32 Consensus pattern (88 bp): AGATCTTGTCTTCATGTATTGACATGAAGTAGATCGAAGATAGCAGATCTTGTCTTCATGTATTG ACATGAAGTAGATCAGAGATAAT Found at i:42498901 original size:353 final size:353 Alignment explanation
Indices: 42498252--42499149 Score: 1207 Period size: 353 Copynumber: 2.5 Consensus size: 353 42498242 TAAAAAGCAG * * 42498252 CAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAAGATAGCAGATCTTGTCTTCCCATACT 1 CAGATCTTGTCTTCATGTATTGACGTGAAGTAGATCAGAGATAGCAGATCTTGTCTTCCCATACT * * * 42498317 GGTGGTGAAGTAGATCGAAGATAATGGATCTTGGCTTCATATATTAACATGAAGTAGATCAGAGA 66 GGTAGTGAAGTAGATCGAAGATAATGGATCTTGTCTTCATATATTGACATGAAGTAGATCAGAGA * * 42498382 TAGTAGATCTTGTCTTCATGTATTGACATGGAGTAGATCAGAGATAGTAGATCTTATCTTCATGT 131 TAGCAGATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGATAGTAGATCTTATCTTCATGT * * 42498447 ATTGACATGAAGTAGATCGAAGATGATGGATATTGTCTTCATGTATTGACATGGAGTAGATCAGA 196 ATTGACATGAAGTAGATCGAAGATAATGGATATTGTCTTCATGTATTGACATGAAGTAGATCAGA * * * * 42498512 GATAGCAGGTATTGCCTTCATGTATTGACATGAAGTAGATC-AGAGATAA-CATATCTTATTTTC 261 GATAGCAGATATTGCCTTCATGTATAGACATGAAGTAGATCGA-AGA-AAGCAGATCTTATCTTC * * ** 42498575 ATGTATTGACATGAAGTAGATCGAAGGTAA 324 ATGTACTGACATGAAGTAGATCAAAGAAAA ** * 42498605 TGGATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGATAGCAGATCTTGTCTTCCCATACT 1 CAGATCTTGTCTTCATGTATTGACGTGAAGTAGATCAGAGATAGCAGATCTTGTCTTCCCATACT * * 42498670 GGTAGTGAAGTAGATCGAAGGTAATGGATCTTGTCTTCATGTATTGACAT-AGAGTAGATCAGAG 66 GGTAGTGAAGTAGATCGAAGATAATGGATCTTGTCTTCATATATTGACATGA-AGTAGATCAGAG * * 42498734 ATAGCAGATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGATAGGATATCTTATCTTCATG 130 ATAGCAGATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGATAGTAGATCTTATCTTCATG * 42498799 TATTGACATGAAGTAGATCGAAGATAATGGATCTTGTCTTCATGTATTGACATGAAGTAGATCAG 195 TATTGACATGAAGTAGATCGAAGATAATGGATATTGTCTTCATGTATTGACATGAAGTAGATCAG * * * * 42498864 AGATAGCAGATCTTGTCTTCATGTACTAG-CGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTC 260 AGATAGCAGATATTGCCTTCATGTA-TAGACATGAAGTAGATCGAAGAAAGCAGATCTTATCTTC * 42498928 ATGTACTGGCATGAAGTAGATCAAAGAAAA 324 ATGTACTGACATGAAGTAGATCAAAGAAAA * * * * ** 42498958 CAGATATTGTCTTCATGTACTGACGTGAAGTAGATC-GAAGAAAGCAAATCTTGTCTTCCTGTAC 1 CAGATCTTGTCTTCATGTATTGACGTGAAGTAGATCAG-AGATAGCAGATCTTGTCTTCCCATAC * * * * ** ** * ** * 42499022 TAGCAGTGAAGTATATCAAAGATAACAGATCTTGTCTTCCCATACTGGTAGCGAAGTAGATC-GA 65 TGGTAGTGAAGTAGATCGAAGATAATGGATCTTGTCTTCATATATTGACA-TGAAGTAGATCAG- * * * * 42499086 AGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATC-GAAGATAGTAGATCTTGTCTTC 128 AGATAGCAGATCTTGTCTTCATGTATTGACATGAAGTAGATCAG-AGATAGTAGATCTTATCTTC 42499150 CCATACTGGT Statistics Matches: 477, Mismatches: 59, Indels: 17 0.86 0.11 0.03 Matches are distributed among these distances: 352 4 0.01 353 405 0.85 354 67 0.14 355 1 0.00 ACGTcount: A:0.32, C:0.14, G:0.23, T:0.32 Consensus pattern (353 bp): CAGATCTTGTCTTCATGTATTGACGTGAAGTAGATCAGAGATAGCAGATCTTGTCTTCCCATACT GGTAGTGAAGTAGATCGAAGATAATGGATCTTGTCTTCATATATTGACATGAAGTAGATCAGAGA TAGCAGATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGATAGTAGATCTTATCTTCATGT ATTGACATGAAGTAGATCGAAGATAATGGATATTGTCTTCATGTATTGACATGAAGTAGATCAGA GATAGCAGATATTGCCTTCATGTATAGACATGAAGTAGATCGAAGAAAGCAGATCTTATCTTCAT GTACTGACATGAAGTAGATCAAAGAAAA Found at i:42499221 original size:89 final size:89 Alignment explanation
Indices: 42498808--42499221 Score: 227 Period size: 88 Copynumber: 4.7 Consensus size: 89 42498798 GTATTGACAT ** * * * * * * * 42498808 GAAGTAGATCGAAGATAA-TGGATCTTGTCTTCATGTATTGACATGAAGTAGATCAG-AGATAGC 1 GAAGTAGATCGAAGA-AACCAGATCTTATCTCCATGAATTGGCGTGAAGCAGAT-AGAAGATAGT *** * * * 42498871 AGATCTTGTCTTCATGTACTAG-CGT 64 AGATCTTGTCTTCCCATACTGGTAGC * * * * * * * * ** 42498896 GAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTACTGGCATGAAGTAGATCA-AAGAAAACA 1 GAAGTAGATCGAAGAAACCAGATCTTATCTCCATGAATTGGCGTGAAGCAGAT-AGAAGATAGTA * *** * 42498960 GATATTGTCTTCATGTACT-G-ACGT 65 GATCTTGTCTTCCCATACTGGTA-GC * * * * * * * * * 42498984 GAAGTAGATCGAAGAAAGCAAATCTTGTCTTCC-TGTACTAGCAGTGAAGTATATCA-AAGATAA 1 GAAGTAGATCGAAGAAACCAGATCTTATC-TCCATGAATTGGC-GTGAAGCAGAT-AGAAGATAG * 42499047 CAGATCTTGTCTTCCCATACTGGTAGC 63 TAGATCTTGTCTTCCCATACTGGTAGC * * * * * * 42499074 GAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGTAG 1 GAAGTAGATCGAAGAAACCAGATCTTATCTCCATGAATTGGCGTGAAGCAGATAGAAGATAGTAG * 42499139 ATCTTGTCTTCCCATACTGGTGGC 66 ATCTTGTCTTCCCATACTGGTAGC * * * 42499163 GAAGTAGATCGAAGATACCAG-TCTTATCTCCCTGAAGTT-GCAGTGGAGCAGATAGAAGA 1 GAAGTAGATCGAAGAAACCAGATCTTATCTCCATGAA-TTGGC-GTGAAGCAGATAGAAGA 42499222 AACCAATCCT Statistics Matches: 278, Mismatches: 37, Indels: 21 0.83 0.11 0.06 Matches are distributed among these distances: 87 3 0.01 88 123 0.44 89 114 0.41 90 37 0.13 91 1 0.00 ACGTcount: A:0.32, C:0.16, G:0.24, T:0.28 Consensus pattern (89 bp): GAAGTAGATCGAAGAAACCAGATCTTATCTCCATGAATTGGCGTGAAGCAGATAGAAGATAGTAG ATCTTGTCTTCCCATACTGGTAGC Found at i:42499237 original size:44 final size:44 Alignment explanation
Indices: 42499168--42499259 Score: 121 Period size: 44 Copynumber: 2.1 Consensus size: 44 42499158 GTGGCGAAGT * * * * * 42499168 AGATCGAAGATACCAGTCTTATCTCCCTGAAGTTGCAGTGGAGC 1 AGATAGAAGAAACCAATCCTATCTCCCTGAAGTTGCAATGGAGC * * 42499212 AGATAGAAGAAACCAATCCTATCTCCTTGAAGTTGCAATGGAGT 1 AGATAGAAGAAACCAATCCTATCTCCCTGAAGTTGCAATGGAGC 42499256 AGAT 1 AGAT 42499260 TAAAACCACA Statistics Matches: 41, Mismatches: 7, Indels: 0 0.85 0.15 0.00 Matches are distributed among these distances: 44 41 1.00 ACGTcount: A:0.33, C:0.20, G:0.23, T:0.25 Consensus pattern (44 bp): AGATAGAAGAAACCAATCCTATCTCCCTGAAGTTGCAATGGAGC Found at i:42499681 original size:20 final size:20 Alignment explanation
Indices: 42499652--42499692 Score: 57 Period size: 22 Copynumber: 2.0 Consensus size: 20 42499642 CAATAAACAG 42499652 ACCCAATTAA-TAGCCCAAA 1 ACCCAATTAACTAGCCCAAA 42499671 ACCCAAATTAACCTAGCCCAAA 1 ACCC-AATTAA-CTAGCCCAAA 42499693 CATTAAAATT Statistics Matches: 19, Mismatches: 0, Indels: 3 0.86 0.00 0.14 Matches are distributed among these distances: 19 4 0.21 20 6 0.32 22 9 0.47 ACGTcount: A:0.46, C:0.34, G:0.05, T:0.15 Consensus pattern (20 bp): ACCCAATTAACTAGCCCAAA Found at i:42501339 original size:29 final size:29 Alignment explanation
Indices: 42501284--42501340 Score: 73 Period size: 29 Copynumber: 2.0 Consensus size: 29 42501274 TCTATATTGG * 42501284 ATAAATATAATTATATGTATATGCAATAT 1 ATAAATATAATAATATGTATATGCAATAT 42501313 ATAAATATAA-AATGATGCTATAT-CAATA 1 ATAAATATAATAAT-ATG-TATATGCAATA 42501341 ATTGTGTTAA Statistics Matches: 25, Mismatches: 1, Indels: 4 0.83 0.03 0.13 Matches are distributed among these distances: 28 2 0.08 29 18 0.72 30 5 0.20 ACGTcount: A:0.51, C:0.05, G:0.07, T:0.37 Consensus pattern (29 bp): ATAAATATAATAATATGTATATGCAATAT Found at i:42504158 original size:9 final size:9 Alignment explanation
Indices: 42504144--42504180 Score: 65 Period size: 9 Copynumber: 4.1 Consensus size: 9 42504134 TATAGTTTGA 42504144 TATTCGAAT 1 TATTCGAAT 42504153 TATTCGAAT 1 TATTCGAAT * 42504162 TATTCGAGT 1 TATTCGAAT 42504171 TATTCGAAT 1 TATTCGAAT 42504180 T 1 T 42504181 CGAAAACTCA Statistics Matches: 26, Mismatches: 2, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 9 26 1.00 ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46 Consensus pattern (9 bp): TATTCGAAT Found at i:42504726 original size:20 final size:20 Alignment explanation
Indices: 42504703--42504746 Score: 56 Period size: 20 Copynumber: 2.2 Consensus size: 20 42504693 AGTTTTATAC 42504703 TTTTTAATAATTT-AAATAA 1 TTTTTAATAATTTAAAATAA * 42504722 TTTTTAA-ATTTTAAAAATAA 1 TTTTTAATAATTT-AAAATAA 42504742 TTTTT 1 TTTTT 42504747 TTATAATTTT Statistics Matches: 22, Mismatches: 1, Indels: 3 0.85 0.04 0.12 Matches are distributed among these distances: 18 4 0.18 19 7 0.32 20 11 0.50 ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57 Consensus pattern (20 bp): TTTTTAATAATTTAAAATAA Found at i:42506957 original size:25 final size:25 Alignment explanation
Indices: 42506925--42507058 Score: 178 Period size: 25 Copynumber: 5.4 Consensus size: 25 42506915 ATACAATACA * * 42506925 CCACAAAGACTTTTTAGATAATTCG 1 CCACAAAGGCTTTTCAGATAATTCG * * * * 42506950 CCATAAAGGCTTTACAGATAACTCA 1 CCACAAAGGCTTTTCAGATAATTCG 42506975 CCACAAAGGCTTTTCAGATAATTCG 1 CCACAAAGGCTTTTCAGATAATTCG * * * * 42507000 CCATAAAGGCTTTACAGATAACTCA 1 CCACAAAGGCTTTTCAGATAATTCG 42507025 CCACAAAGGCTTTTCAGATAATTCG 1 CCACAAAGGCTTTTCAGATAATTCG 42507050 CCACAAAGG 1 CCACAAAGG 42507059 TTTGCCACCA Statistics Matches: 91, Mismatches: 18, Indels: 0 0.83 0.17 0.00 Matches are distributed among these distances: 25 91 1.00 ACGTcount: A:0.37, C:0.24, G:0.14, T:0.25 Consensus pattern (25 bp): CCACAAAGGCTTTTCAGATAATTCG Found at i:42506977 original size:50 final size:50 Alignment explanation
Indices: 42506923--42507058 Score: 245 Period size: 50 Copynumber: 2.7 Consensus size: 50 42506913 TCATACAATA * * 42506923 CACCACAAAGACTTTTTAGATAATTCGCCATAAAGGCTTTACAGATAACT 1 CACCACAAAGGCTTTTCAGATAATTCGCCATAAAGGCTTTACAGATAACT 42506973 CACCACAAAGGCTTTTCAGATAATTCGCCATAAAGGCTTTACAGATAACT 1 CACCACAAAGGCTTTTCAGATAATTCGCCATAAAGGCTTTACAGATAACT * 42507023 CACCACAAAGGCTTTTCAGATAATTCGCCACAAAGG 1 CACCACAAAGGCTTTTCAGATAATTCGCCATAAAGG 42507059 TTTGCCACCA Statistics Matches: 83, Mismatches: 3, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 50 83 1.00 ACGTcount: A:0.37, C:0.24, G:0.14, T:0.25 Consensus pattern (50 bp): CACCACAAAGGCTTTTCAGATAATTCGCCATAAAGGCTTTACAGATAACT Found at i:42510138 original size:20 final size:21 Alignment explanation
Indices: 42510101--42510156 Score: 62 Period size: 20 Copynumber: 2.7 Consensus size: 21 42510091 TTCTCTTATA 42510101 TATAT-ATTATATTAAACTTG- 1 TATATGATTAT-TTAAACTTGC * 42510121 TATATGATTATTTTAACTTGC 1 TATATGATTATTTAAACTTGC * 42510142 TTTATAGATTATTTA 1 TATAT-GATTATTTA 42510157 CATTAAGTTG Statistics Matches: 30, Mismatches: 3, Indels: 4 0.81 0.08 0.11 Matches are distributed among these distances: 20 13 0.43 21 9 0.30 22 8 0.27 ACGTcount: A:0.34, C:0.05, G:0.07, T:0.54 Consensus pattern (21 bp): TATATGATTATTTAAACTTGC Found at i:42510153 original size:22 final size:22 Alignment explanation
Indices: 42510121--42510183 Score: 63 Period size: 26 Copynumber: 2.6 Consensus size: 22 42510111 ATTAAACTTG 42510121 TATATGATTATTTTAACTTGCTT 1 TATA-GATTATTTTAACTTGCTT * 42510144 TATAGATTATTTACATTAAGTTGCTT 1 TATAGATTA-TT---TTAACTTGCTT * 42510170 TATATATTATTTTA 1 TATAGATTATTTTA 42510184 TTTTAAGTTA Statistics Matches: 34, Mismatches: 2, Indels: 9 0.76 0.04 0.20 Matches are distributed among these distances: 22 8 0.24 23 6 0.18 25 2 0.06 26 18 0.53 ACGTcount: A:0.30, C:0.06, G:0.08, T:0.56 Consensus pattern (22 bp): TATAGATTATTTTAACTTGCTT Found at i:42510191 original size:27 final size:26 Alignment explanation
Indices: 42510128--42510215 Score: 104 Period size: 26 Copynumber: 3.3 Consensus size: 26 42510118 TTGTATATGA * * 42510128 TTATTTTAACTTGCTTTATAGATTAT 1 TTATTTTAAGTTGCTTTATATATTAT ** 42510154 TTACATTAAGTTGCTTTATATATTATT 1 TTATTTTAAGTTGCTTTATATATTA-T ** * 42510181 TTATTTTAAGTTATTTTATATATTAC 1 TTATTTTAAGTTGCTTTATATATTAT 42510207 TTATTTTAA 1 TTATTTTAA 42510216 AATTAACTTA Statistics Matches: 52, Mismatches: 9, Indels: 2 0.83 0.14 0.03 Matches are distributed among these distances: 26 30 0.58 27 22 0.42 ACGTcount: A:0.30, C:0.06, G:0.06, T:0.59 Consensus pattern (26 bp): TTATTTTAAGTTGCTTTATATATTAT Found at i:42510224 original size:16 final size:17 Alignment explanation
Indices: 42510186--42510226 Score: 50 Period size: 16 Copynumber: 2.5 Consensus size: 17 42510176 TTATTTTATT * * 42510186 TTAAGTTATTTTATATA 1 TTAACTTATTTTATAAA 42510203 TT-ACTTATTTTA-AAA 1 TTAACTTATTTTATAAA 42510218 TTAACTTAT 1 TTAACTTAT 42510227 ACTATTTGCT Statistics Matches: 21, Mismatches: 2, Indels: 3 0.81 0.08 0.12 Matches are distributed among these distances: 15 4 0.19 16 15 0.71 17 2 0.10 ACGTcount: A:0.37, C:0.05, G:0.02, T:0.56 Consensus pattern (17 bp): TTAACTTATTTTATAAA Found at i:42510226 original size:27 final size:27 Alignment explanation
Indices: 42510169--42510232 Score: 67 Period size: 27 Copynumber: 2.3 Consensus size: 27 42510159 TTAAGTTGCT * * ** 42510169 TTATATATTATTTTATTTTAAGTTATT 1 TTATATATTATCTTATTTTAAATTAAC 42510196 TTATATATTA-CTTATTTTAAAATTAAC 1 TTATATATTATCTTATTTT-AAATTAAC 42510223 TTATACTATT 1 TTATA-TATT 42510233 TGCTTTAAAT Statistics Matches: 31, Mismatches: 4, Indels: 3 0.82 0.11 0.08 Matches are distributed among these distances: 26 7 0.23 27 20 0.65 28 4 0.13 ACGTcount: A:0.34, C:0.05, G:0.02, T:0.59 Consensus pattern (27 bp): TTATATATTATCTTATTTTAAATTAAC Found at i:42510388 original size:28 final size:30 Alignment explanation
Indices: 42510324--42510391 Score: 79 Period size: 30 Copynumber: 2.3 Consensus size: 30 42510314 TCTGCGTGTC * 42510324 TATT-TTTAAACTTTATTTTATTATATACT 1 TATTATTTAAACTTTATTTTATTATATAAT * 42510353 TAGTTTATTTCAACTTT-TTTTA-TATATAAT 1 TA--TTATTTAAACTTTATTTTATTATATAAT 42510383 TATTATTTA 1 TATTATTTA 42510392 TATTAAGTTT Statistics Matches: 33, Mismatches: 3, Indels: 7 0.77 0.07 0.16 Matches are distributed among these distances: 28 6 0.18 29 2 0.06 30 9 0.27 31 7 0.21 32 9 0.27 ACGTcount: A:0.31, C:0.06, G:0.01, T:0.62 Consensus pattern (30 bp): TATTATTTAAACTTTATTTTATTATATAAT Found at i:42516079 original size:10 final size:10 Alignment explanation
Indices: 42516066--42516135 Score: 52 Period size: 10 Copynumber: 7.0 Consensus size: 10 42516056 AAATTCAAAG 42516066 AAATATATAA 1 AAATATATAA * 42516076 AAATATGTAA 1 AAATATATAA ** * * 42516086 CTATTTTTAA 1 AAATATATAA * 42516096 AAATAAATAA 1 AAATATATAA * 42516106 TAAA-ATTTAA 1 -AAATATATAA 42516116 AAATATATAA 1 AAATATATAA * 42516126 AAATAAATAA 1 AAATATATAA 42516136 TTTCAAAAAA Statistics Matches: 44, Mismatches: 14, Indels: 4 0.71 0.23 0.06 Matches are distributed among these distances: 9 3 0.07 10 38 0.86 11 3 0.07 ACGTcount: A:0.64, C:0.01, G:0.01, T:0.33 Consensus pattern (10 bp): AAATATATAA Found at i:42516130 original size:26 final size:26 Alignment explanation
Indices: 42516100--42516150 Score: 68 Period size: 26 Copynumber: 2.0 Consensus size: 26 42516090 TTTTAAAAAT * 42516100 AAATAATAAAATTT-AAAAATATATAA 1 AAATAA-AAAATTTCAAAAAAATATAA * 42516126 AAATAAATAATTTCAAAAAAATATA 1 AAATAAAAAATTTCAAAAAAATATA 42516151 GTAAAACTAA Statistics Matches: 22, Mismatches: 2, Indels: 2 0.85 0.08 0.08 Matches are distributed among these distances: 25 6 0.27 26 16 0.73 ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29 Consensus pattern (26 bp): AAATAAAAAATTTCAAAAAAATATAA Found at i:42516552 original size:31 final size:29 Alignment explanation
Indices: 42516482--42516555 Score: 85 Period size: 29 Copynumber: 2.5 Consensus size: 29 42516472 GGCTCAAGTT * * 42516482 ACATTTTAGTCACTTATGTTTGAAATGTT 1 ACATTTTAGTCACTTATGTTTCAAATGTA * ** 42516511 ACGTTTTAGTCACTTATGTTATCATGTTGTA 1 ACATTTTAGTCACTTATGTT-TCA-AATGTA 42516542 ACATTTTAGTCACT 1 ACATTTTAGTCACT 42516556 GAGCCGTTAG Statistics Matches: 37, Mismatches: 6, Indels: 2 0.82 0.13 0.04 Matches are distributed among these distances: 29 19 0.51 30 2 0.05 31 16 0.43 ACGTcount: A:0.26, C:0.14, G:0.14, T:0.47 Consensus pattern (29 bp): ACATTTTAGTCACTTATGTTTCAAATGTA Found at i:42517399 original size:6 final size:6 Alignment explanation
Indices: 42517390--42517438 Score: 57 Period size: 6 Copynumber: 8.3 Consensus size: 6 42517380 TCTTTTAAAT * * 42517390 TTAATA TTAATA TTAATA TTAATA TATAA-A TTAAAA TTATTA TT-ATA 1 TTAATA TTAATA TTAATA TTAATA T-TAATA TTAATA TTAATA TTAATA 42517437 TT 1 TT 42517439 TTTAAAAATA Statistics Matches: 38, Mismatches: 3, Indels: 5 0.83 0.07 0.11 Matches are distributed among these distances: 5 7 0.18 6 28 0.74 7 3 0.08 ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51 Consensus pattern (6 bp): TTAATA Found at i:42517411 original size:18 final size:18 Alignment explanation
Indices: 42517384--42517438 Score: 60 Period size: 18 Copynumber: 3.1 Consensus size: 18 42517374 GAGGGTTCTT * 42517384 TTAAATTTAATATTAATA 1 TTAAAATTAATATTAATA * 42517402 TTAATATTAATATATAA-A 1 TTAAAATTAATAT-TAATA * 42517420 TTAAAATTATTATT-ATA 1 TTAAAATTAATATTAATA 42517437 TT 1 TT 42517439 TTTAAAAATA Statistics Matches: 31, Mismatches: 4, Indels: 5 0.77 0.10 0.12 Matches are distributed among these distances: 16 1 0.03 17 4 0.13 18 23 0.74 19 3 0.10 ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51 Consensus pattern (18 bp): TTAAAATTAATATTAATA Found at i:42517446 original size:21 final size:22 Alignment explanation
Indices: 42517420--42517468 Score: 66 Period size: 22 Copynumber: 2.3 Consensus size: 22 42517410 AATATATAAA * 42517420 TTAAAATTA-TTAT-TATATTT 1 TTAAAAATATTTATGTATATTT * 42517440 TTAAAAATATTTATGTATTTTT 1 TTAAAAATATTTATGTATATTT 42517462 TTAAAAA 1 TTAAAAA 42517469 AAATTTAGAA Statistics Matches: 25, Mismatches: 2, Indels: 2 0.86 0.07 0.07 Matches are distributed among these distances: 20 8 0.32 21 4 0.16 22 13 0.52 ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55 Consensus pattern (22 bp): TTAAAAATATTTATGTATATTT Found at i:42519951 original size:39 final size:39 Alignment explanation
Indices: 42519908--42520040 Score: 214 Period size: 39 Copynumber: 3.4 Consensus size: 39 42519898 AGTTTATCCA 42519908 CCACCCAAGTCACCAAGCAAGCCGCCAACTTACGCTCCT 1 CCACCCAAGTCACCAAGCAAGCCGCCAACTTACGCTCCT * * 42519947 CCACCCAAGTCACCCAGCAAGCCGCCAAGTTACGCTCCT 1 CCACCCAAGTCACCAAGCAAGCCGCCAACTTACGCTCCT * 42519986 CCACCCAAGTCACCCAGCAAGCCGCCAACTTACGCTCCT 1 CCACCCAAGTCACCAAGCAAGCCGCCAACTTACGCTCCT * 42520025 CCGA-CCAAGCCACCAA 1 CC-ACCCAAGTCACCAA 42520041 CTTACGCCCC Statistics Matches: 88, Mismatches: 5, Indels: 2 0.93 0.05 0.02 Matches are distributed among these distances: 39 87 0.99 40 1 0.01 ACGTcount: A:0.28, C:0.47, G:0.14, T:0.11 Consensus pattern (39 bp): CCACCCAAGTCACCAAGCAAGCCGCCAACTTACGCTCCT Found at i:42520041 original size:27 final size:27 Alignment explanation
Indices: 42520003--42520066 Score: 94 Period size: 27 Copynumber: 2.4 Consensus size: 27 42519993 AGTCACCCAG * * 42520003 CAAGCCGCCAACTTACGCTCCTCCGA-C 1 CAAGCCACCAACTTACGCCCCTCC-ACC 42520030 CAAGCCACCAACTTACGCCCCTCCACC 1 CAAGCCACCAACTTACGCCCCTCCACC 42520057 CAAGCCACCA 1 CAAGCCACCA 42520067 GTTTATCCTC Statistics Matches: 34, Mismatches: 2, Indels: 2 0.89 0.05 0.05 Matches are distributed among these distances: 26 1 0.03 27 33 0.97 ACGTcount: A:0.27, C:0.52, G:0.11, T:0.11 Consensus pattern (27 bp): CAAGCCACCAACTTACGCCCCTCCACC Found at i:42520503 original size:2 final size:2 Alignment explanation
Indices: 42520496--42520524 Score: 58 Period size: 2 Copynumber: 14.5 Consensus size: 2 42520486 ATTTGAGTTC 42520496 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A 1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A 42520525 AATGGTTTCT Statistics Matches: 27, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 27 1.00 ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00 Consensus pattern (2 bp): AG Found at i:42522310 original size:24 final size:24 Alignment explanation
Indices: 42522276--42522323 Score: 69 Period size: 24 Copynumber: 2.0 Consensus size: 24 42522266 TTCATTAAAT * 42522276 ATTAATGGAAGATAGAAGTTTATA 1 ATTAATGGAAGATAGAAATTTATA * * 42522300 ATTAATTGAAGATGGAAATTTATA 1 ATTAATGGAAGATAGAAATTTATA 42522324 GATTTCACTA Statistics Matches: 21, Mismatches: 3, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 24 21 1.00 ACGTcount: A:0.46, C:0.00, G:0.19, T:0.35 Consensus pattern (24 bp): ATTAATGGAAGATAGAAATTTATA Found at i:42525107 original size:29 final size:29 Alignment explanation
Indices: 42525036--42525210 Score: 160 Period size: 29 Copynumber: 6.0 Consensus size: 29 42525026 TTTGATTTAT * * 42525036 GTTTAGGGTTTTTGAGTTTGGGGATTTAGG 1 GTTTAGGGTTTTTGAATTTGGGGATTT-TG * * 42525066 GTTTTA-AGTTGTTGAATTTGGGGATTTTG 1 G-TTTAGGGTTTTTGAATTTGGGGATTTTG * * 42525095 GTTTATGGTTGTTGAATTTGGGGATTTT- 1 GTTTAGGGTTTTTGAATTTGGGGATTTTG * * 42525123 TTGTTAGCGG-TTTT-AATTTTGGGGATTTTT 1 GT-TTAG-GGTTTTTGAA-TTTGGGGATTTTG * * 42525153 GTTTAGGGTTTTTTAATATTGGGGATTTTT 1 GTTTAGGGTTTTTGAAT-TTGGGGATTTTG * * 42525183 GTTTAGGGTTTTTAAATTTTGGGATTTT 1 GTTTAGGGTTTTTGAATTTGGGGATTTT 42525211 TTTGTTTTCG Statistics Matches: 125, Mismatches: 11, Indels: 19 0.81 0.07 0.12 Matches are distributed among these distances: 28 9 0.07 29 60 0.48 30 52 0.42 31 4 0.03 ACGTcount: A:0.15, C:0.01, G:0.30, T:0.54 Consensus pattern (29 bp): GTTTAGGGTTTTTGAATTTGGGGATTTTG Found at i:42525182 original size:58 final size:60 Alignment explanation
Indices: 42525029--42525211 Score: 173 Period size: 59 Copynumber: 3.1 Consensus size: 60 42525019 TTGTTATTTT * * * *** * * * 42525029 GATTTATGTTTAGGGTTTTTGAGTTTGGGGATTTAGGGTTTTA-AGTTGTTGAA-TTTGGG 1 GATTTTTGTTTAGGGTTGTTGAATTTGGGGATTTTTTG-TTTAGGGTTTTTAAATTTTGGG * * 42525088 GATTTTGGTTTATGGTTGTTGAATTTGGGGATTTTTTG-TTAGCGG-TTTT-AATTTTGGG 1 GATTTTTGTTTAGGGTTGTTGAATTTGGGGATTTTTTGTTTAG-GGTTTTTAAATTTTGGG * * 42525146 GATTTTTGTTTAGGGTTTTTTAATATTGGGGA-TTTTTGTTTAGGGTTTTTAAATTTT-GG 1 GATTTTTGTTTAGGGTTGTTGAAT-TTGGGGATTTTTTGTTTAGGGTTTTTAAATTTTGGG 42525205 GATTTTT 1 GATTTTT 42525212 TTGTTTTCGA Statistics Matches: 103, Mismatches: 14, Indels: 14 0.79 0.11 0.11 Matches are distributed among these distances: 57 5 0.05 58 37 0.36 59 55 0.53 60 6 0.06 ACGTcount: A:0.16, C:0.01, G:0.30, T:0.54 Consensus pattern (60 bp): GATTTTTGTTTAGGGTTGTTGAATTTGGGGATTTTTTGTTTAGGGTTTTTAAATTTTGGG Found at i:42525682 original size:14 final size:15 Alignment explanation
Indices: 42525646--42525686 Score: 57 Period size: 14 Copynumber: 2.8 Consensus size: 15 42525636 ATATTAATAT * 42525646 TTTGTTTGTCTATAC 1 TTTGTTTGTCTACAC * 42525661 TTTTTTTG-CTACAC 1 TTTGTTTGTCTACAC 42525675 TTTGTTTGTCTA 1 TTTGTTTGTCTA 42525687 TTATTATGGA Statistics Matches: 22, Mismatches: 3, Indels: 2 0.81 0.11 0.07 Matches are distributed among these distances: 14 12 0.55 15 10 0.45 ACGTcount: A:0.12, C:0.15, G:0.12, T:0.61 Consensus pattern (15 bp): TTTGTTTGTCTACAC Found at i:42526197 original size:48 final size:48 Alignment explanation
Indices: 42526130--42526245 Score: 151 Period size: 48 Copynumber: 2.4 Consensus size: 48 42526120 GTTTTTGTGG * * ** 42526130 TGGTAATAAATGTGTTGAGGGTTTAAATGGGGAGGGTGTTAAGGTTGT 1 TGGTAATAAAGGTGATGAGGGTTTAAATAAGGAGGGTGTTAAGGTTGT * * 42526178 TGGTAGTAAAGGTGATGAGGGTTTAAATAAGGAGGGTGTTGAGGTTGT 1 TGGTAATAAAGGTGATGAGGGTTTAAATAAGGAGGGTGTTAAGGTTGT * * * 42526226 TGGCAATAAAAGTGGTGAGG 1 TGGTAATAAAGGTGATGAGG 42526246 TTGAGGGTGG Statistics Matches: 58, Mismatches: 10, Indels: 0 0.85 0.15 0.00 Matches are distributed among these distances: 48 58 1.00 ACGTcount: A:0.28, C:0.01, G:0.41, T:0.31 Consensus pattern (48 bp): TGGTAATAAAGGTGATGAGGGTTTAAATAAGGAGGGTGTTAAGGTTGT Found at i:42526297 original size:81 final size:81 Alignment explanation
Indices: 42526197--42526346 Score: 232 Period size: 81 Copynumber: 1.9 Consensus size: 81 42526187 AGGTGATGAG * 42526197 GGTTTAAATAAGGAGGGTGTTGAGGTTGTTGGCAATAAA-AGTGGTGAGGTTGAGGGTGGTGAAG 1 GGTTTAAATAAGGAGGGTGTGGAGGTTGTTGGCAATAAAGA-TGGTGAGGTTGAGGGTGGTGAAG 42526261 ATGGTGAGAGTGTTGAA 65 ATGGTGAGAGTGTTGAA * * 42526278 GGTTTAAAT-AGGTAGGGTGTGGAGGTTGTTGGCAGTTAAGATGGTGAGGTTGAGGGTGGTGAAG 1 GGTTTAAATAAGG-AGGGTGTGGAGGTTGTTGGCAATAAAGATGGTGAGGTTGAGGGTGGTGAAG * 42526342 GTGGT 65 ATGGT 42526347 AAGGGTATTG Statistics Matches: 63, Mismatches: 4, Indels: 4 0.89 0.06 0.06 Matches are distributed among these distances: 80 3 0.05 81 59 0.94 82 1 0.02 ACGTcount: A:0.24, C:0.01, G:0.45, T:0.29 Consensus pattern (81 bp): GGTTTAAATAAGGAGGGTGTGGAGGTTGTTGGCAATAAAGATGGTGAGGTTGAGGGTGGTGAAGA TGGTGAGAGTGTTGAA Found at i:42528992 original size:158 final size:157 Alignment explanation
Indices: 42528736--42529047 Score: 435 Period size: 158 Copynumber: 2.0 Consensus size: 157 42528726 GGTGAGGGTC * * * * 42528736 ACAACAGAAGATCATGCATTCAACCTAACACAACTGGATCACAAGTATATCGTAAACACTTTTTC 1 ACAACAAAAGATCATGCAATCAACCTAACACAACTAGATCACAAGTATATCATAAACACTTTTTC * * * ** 42528801 ATTGTCAAGTTCCAACATATTTAAATATAATTTGGGGTTTTGTATTTTATTCTCAATCTGATATG 66 ATTCTCAAGTTCCAAAATATTTAAATATAATTTGGGGTTGTG-ATTTTATTCTCAATCTGATACA * 42528866 AGTATAAGAACTAGAAGCCAAAAAAAGA 130 AGTACAAGAACTAGAAGCCAAAAAAAGA * * * 42528894 ACAACAAAATATCATGCAATCAACCTAACACAACTAGATCACAGGTATATCATAAACACTTTTTT 1 ACAACAAAAGATCATGCAATCAACCTAACACAACTAGATCACAAGTATATCATAAACACTTTTTC * * * ** * * 42528959 ATTCTCAAGTTCCAAAATATTTAAATTTAATTTGGGGTTGTGATTTTTTTGTCTGTTTGGTACAA 66 ATTCTCAAGTTCCAAAATATTTAAATATAATTTGGGGTTGTGATTTTATTCTCAATCTGATACAA 42529024 GTACAAGAACTAGAAGCCAAAAAA 131 GTACAAGAACTAGAAGCCAAAAAA 42529048 GGAGGGTATA Statistics Matches: 134, Mismatches: 20, Indels: 1 0.86 0.13 0.01 Matches are distributed among these distances: 157 38 0.28 158 96 0.72 ACGTcount: A:0.39, C:0.16, G:0.13, T:0.32 Consensus pattern (157 bp): ACAACAAAAGATCATGCAATCAACCTAACACAACTAGATCACAAGTATATCATAAACACTTTTTC ATTCTCAAGTTCCAAAATATTTAAATATAATTTGGGGTTGTGATTTTATTCTCAATCTGATACAA GTACAAGAACTAGAAGCCAAAAAAAGA Found at i:42530666 original size:28 final size:28 Alignment explanation
Indices: 42530603--42530667 Score: 69 Period size: 29 Copynumber: 2.3 Consensus size: 28 42530593 CAAACCAGAT * ** 42530603 TGACCAAAAAAAACATTAGGTGGTAAAG 1 TGACCAAAAAAAACATAAGGTGCCAAAG * 42530631 TGCTCCAAAAAAAACATAAAGG-GCCAAAG 1 TG-ACCAAAAAAAACAT-AAGGTGCCAAAG 42530660 TGACCAAA 1 TGACCAAA 42530668 CATCCAAACG Statistics Matches: 30, Mismatches: 5, Indels: 4 0.77 0.13 0.10 Matches are distributed among these distances: 28 7 0.23 29 20 0.67 30 3 0.10 ACGTcount: A:0.51, C:0.17, G:0.18, T:0.14 Consensus pattern (28 bp): TGACCAAAAAAAACATAAGGTGCCAAAG Found at i:42532673 original size:16 final size:16 Alignment explanation
Indices: 42532648--42532682 Score: 54 Period size: 16 Copynumber: 2.2 Consensus size: 16 42532638 TAAAAGGAGC 42532648 TTTACAAAACA-AAGT 1 TTTACAAAACATAAGT 42532663 TTTATCAAAACATAAGT 1 TTTA-CAAAACATAAGT 42532680 TTT 1 TTT 42532683 TTATACAAAC Statistics Matches: 18, Mismatches: 0, Indels: 2 0.90 0.00 0.10 Matches are distributed among these distances: 15 4 0.22 16 7 0.39 17 7 0.39 ACGTcount: A:0.46, C:0.11, G:0.06, T:0.37 Consensus pattern (16 bp): TTTACAAAACATAAGT Found at i:42535107 original size:5 final size:5 Alignment explanation
Indices: 42535097--42535159 Score: 110 Period size: 5 Copynumber: 12.8 Consensus size: 5 42535087 TCATCACGAA * 42535097 ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC TTATC ATATC 1 ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC 42535147 ATATC ATA-C ATAT 1 ATATC ATATC ATAT 42535160 TAGAAGCAAA Statistics Matches: 55, Mismatches: 2, Indels: 2 0.93 0.03 0.03 Matches are distributed among these distances: 4 4 0.07 5 51 0.93 ACGTcount: A:0.40, C:0.19, G:0.00, T:0.41 Consensus pattern (5 bp): ATATC Found at i:42536726 original size:41 final size:41 Alignment explanation
Indices: 42536676--42536756 Score: 135 Period size: 41 Copynumber: 2.0 Consensus size: 41 42536666 TTAAACAGAT * * 42536676 TCACTGGCACTTAGCCTGCTAGGCTTAAAGCTTGATTCAGG 1 TCACCGGCACTTAGCCTGCTAGGCTTAAAGCCTGATTCAGG * 42536717 TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAG 1 TCACCGGCACTTAGCCTGCTAGGCTTAAAGCCTGATTCAG 42536757 TTCTAGCTTG Statistics Matches: 37, Mismatches: 3, Indels: 0 0.93 0.08 0.00 Matches are distributed among these distances: 41 37 1.00 ACGTcount: A:0.21, C:0.27, G:0.23, T:0.28 Consensus pattern (41 bp): TCACCGGCACTTAGCCTGCTAGGCTTAAAGCCTGATTCAGG Found at i:42542697 original size:25 final size:25 Alignment explanation
Indices: 42542669--42542731 Score: 76 Period size: 25 Copynumber: 2.5 Consensus size: 25 42542659 TTATGTGTTT * 42542669 TTAGTATAGT-CTATCTATAGTAGTC 1 TTAGTATA-TACTACCTATAGTAGTC 42542694 TTAGTATATACTACCTATAGTAGT- 1 TTAGTATATACTACCTATAGTAGTC * 42542718 TTCAGGATATACTA 1 TT-AGTATATACTA 42542732 TCAAACACAG Statistics Matches: 34, Mismatches: 2, Indels: 4 0.85 0.05 0.10 Matches are distributed among these distances: 24 3 0.09 25 31 0.91 ACGTcount: A:0.32, C:0.13, G:0.14, T:0.41 Consensus pattern (25 bp): TTAGTATATACTACCTATAGTAGTC Found at i:42555311 original size:40 final size:40 Alignment explanation
Indices: 42555108--42555311 Score: 211 Period size: 40 Copynumber: 5.1 Consensus size: 40 42555098 CGGAATTTAA ** * 42555108 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC 1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC * * * * 42555148 CCAGTTATAGTAACTCGCACAATTGCCTTCGGGACTTAAC 1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC * * 42555188 CCGAATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGC 1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC * * 42555227 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT 1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC * * * 42555267 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC 1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC 42555307 CCGGA 1 CCGGA 42555312 CATCATTCAA Statistics Matches: 135, Mismatches: 22, Indels: 14 0.79 0.13 0.08 Matches are distributed among these distances: 38 2 0.01 39 32 0.24 40 89 0.66 41 12 0.09 ACGTcount: A:0.25, C:0.27, G:0.22, T:0.25 Consensus pattern (40 bp): CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC Found at i:42558640 original size:36 final size:36 Alignment explanation
Indices: 42558593--42558664 Score: 144 Period size: 36 Copynumber: 2.0 Consensus size: 36 42558583 TCGGATCAAC 42558593 TACTCGTCAACTTTCGATTTCGCTCGATCTAAATCT 1 TACTCGTCAACTTTCGATTTCGCTCGATCTAAATCT 42558629 TACTCGTCAACTTTCGATTTCGCTCGATCTAAATCT 1 TACTCGTCAACTTTCGATTTCGCTCGATCTAAATCT 42558665 GACTTCTTTA Statistics Matches: 36, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 36 36 1.00 ACGTcount: A:0.22, C:0.28, G:0.11, T:0.39 Consensus pattern (36 bp): TACTCGTCAACTTTCGATTTCGCTCGATCTAAATCT Found at i:42564443 original size:27 final size:27 Alignment explanation
Indices: 42564412--42564589 Score: 196 Period size: 27 Copynumber: 6.6 Consensus size: 27 42564402 TAAATTGTAC * 42564412 AGCACTAAGTGTGCGATTTGACTATGT 1 AGCACTAAGTGTGCGAATTGACTATGT * * * 42564439 TGCACTAAGTGTGCGAAATGAATATG- 1 AGCACTAAGTGTGCGAATTGACTATGT * * 42564465 ATGCACTAAGTGTGCGAATTGACCATGC 1 A-GCACTAAGTGTGCGAATTGACTATGT * * 42564493 GGCACTAAGTGTGCGAGTTGACTATGT 1 AGCACTAAGTGTGCGAATTGACTATGT * * 42564520 AGCACTAAGTGTGCGAGTTTGATTATGT 1 AGCACTAAGTGTGCGA-ATTGACTATGT * * * * 42564548 GGCACTAAGTGTGCGAGTTGATTATAT 1 AGCACTAAGTGTGCGAATTGACTATGT * 42564575 AGCACTGAGTGTGCG 1 AGCACTAAGTGTGCG 42564590 GACTTAATAT Statistics Matches: 128, Mismatches: 20, Indels: 6 0.83 0.13 0.04 Matches are distributed among these distances: 27 104 0.81 28 24 0.19 ACGTcount: A:0.26, C:0.15, G:0.29, T:0.30 Consensus pattern (27 bp): AGCACTAAGTGTGCGAATTGACTATGT Found at i:42564475 original size:54 final size:55 Alignment explanation
Indices: 42564412--42564589 Score: 236 Period size: 54 Copynumber: 3.3 Consensus size: 55 42564402 TAAATTGTAC * ** 42564412 AGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGAT 1 AGCACTAAGTGTGCGATTTGACTATGTGGCACTAAGTGTGCGAGTTGAATATGAT * * * * 42564467 -GCACTAAGTGTGCGAATTGACCATGCGGCACTAAGTGTGCGAGTTGACTATG-T 1 AGCACTAAGTGTGCGATTTGACTATGTGGCACTAAGTGTGCGAGTTGAATATGAT * * 42564520 AGCACTAAGTGTGCGAGTTTGATTATGTGGCACTAAGTGTGCGAGTTGATTAT-AT 1 AGCACTAAGTGTGCGA-TTTGACTATGTGGCACTAAGTGTGCGAGTTGAATATGAT * 42564575 AGCACTGAGTGTGCG 1 AGCACTAAGTGTGCG 42564590 GACTTAATAT Statistics Matches: 107, Mismatches: 13, Indels: 6 0.85 0.10 0.05 Matches are distributed among these distances: 53 1 0.01 54 60 0.56 55 46 0.43 ACGTcount: A:0.26, C:0.15, G:0.29, T:0.30 Consensus pattern (55 bp): AGCACTAAGTGTGCGATTTGACTATGTGGCACTAAGTGTGCGAGTTGAATATGAT Found at i:42567275 original size:75 final size:75 Alignment explanation
Indices: 42567099--42567371 Score: 390 Period size: 75 Copynumber: 3.6 Consensus size: 75 42567089 TGGATTTAGC * * * * * * 42567099 ACTTAGTAACC-CCAGTGATTCGGGGAATCATCACTTAGCAACCCCTTTCACATTCAAAAATACG 1 ACTTAGCAACCACCAATAATTCGGGGAATCAACACTTAGCAACCCCTTTCAGATT-TAAAATACG * * 42567163 GTGGAATCAGC- 65 ATGGGATCA-CA * 42567174 ACTTAGCAACCACCAGTGAA-TCGGGGAATCAACACTTAGCAACCCCTTTCAGATTTAAAATACG 1 ACTTAGCAACCACCAAT-AATTCGGGGAATCAACACTTAGCAACCCCTTTCAGATTTAAAATACG 42567238 ATGGGATCACA 65 ATGGGATCACA * 42567249 ACTTAGCAACCACCAATAATTCGGGGAATCAGCACTTAGCAACCCCTTTCAGATTTAAAATACGA 1 ACTTAGCAACCACCAATAATTCGGGGAATCAACACTTAGCAACCCCTTTCAGATTTAAAATACGA 42567314 TGGGATCACA 66 TGGGATCACA * * 42567324 ACTTAGCAACCACCAATGATTCGAGGAATCAACACTTAGCAACCCCTT 1 ACTTAGCAACCACCAATAATTCGGGGAATCAACACTTAGCAACCCCTT 42567372 GGGGGAATCA Statistics Matches: 182, Mismatches: 12, Indels: 8 0.90 0.06 0.04 Matches are distributed among these distances: 74 3 0.02 75 140 0.77 76 38 0.21 77 1 0.01 ACGTcount: A:0.35, C:0.27, G:0.16, T:0.22 Consensus pattern (75 bp): ACTTAGCAACCACCAATAATTCGGGGAATCAACACTTAGCAACCCCTTTCAGATTTAAAATACGA TGGGATCACA Found at i:42569404 original size:26 final size:26 Alignment explanation
Indices: 42569337--42569408 Score: 76 Period size: 26 Copynumber: 2.8 Consensus size: 26 42569327 TCTCATCTCA * * * 42569337 ATTTTA-CTTCAGTAAAATTTTGACT 1 ATTTTACCTTAAGTAAAATTTTAACG * 42569362 ATTTTACCTTAACTAAAATTTTAACG 1 ATTTTACCTTAAGTAAAATTTTAACG * 42569388 ATTTTACCCTT-GGTAAAATTT 1 ATTTTA-CCTTAAGTAAAATTT 42569409 CGAGAAAATT Statistics Matches: 39, Mismatches: 6, Indels: 3 0.81 0.12 0.06 Matches are distributed among these distances: 25 6 0.15 26 29 0.74 27 4 0.10 ACGTcount: A:0.33, C:0.14, G:0.07, T:0.46 Consensus pattern (26 bp): ATTTTACCTTAAGTAAAATTTTAACG Found at i:42571011 original size:11 final size:11 Alignment explanation
Indices: 42570995--42571020 Score: 52 Period size: 11 Copynumber: 2.4 Consensus size: 11 42570985 TAGAAGAGAC 42570995 GAAACAGGGGA 1 GAAACAGGGGA 42571006 GAAACAGGGGA 1 GAAACAGGGGA 42571017 GAAA 1 GAAA 42571021 GAAGAAAAAG Statistics Matches: 15, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 11 15 1.00 ACGTcount: A:0.50, C:0.08, G:0.42, T:0.00 Consensus pattern (11 bp): GAAACAGGGGA Found at i:42578589 original size:138 final size:136 Alignment explanation
Indices: 42578287--42578705 Score: 635 Period size: 136 Copynumber: 3.1 Consensus size: 136 42578277 AAGAAAAAGG * 42578287 AATTATATTCTTTCCAAAAGAATATTAATTTCCATATCTTTTATATTTTGATCGAAATTAATTAA 1 AATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGATCGAAATTAATTAA * * 42578352 TATAACTATTTATATTAATAAATTTGGTAATATATATA-ATTAATATTTTGTATGAATCAAATTC 66 TATAACTGTTTATATTAATAAA-TTGGTAAAATATATACATTAATATTTTGTATGAATCAAATTC * 42578416 GTATATT 130 ATATATT * * * * * * 42578423 AATTATATTATTTCCAAAAGAAAATTAATTTTCACGTATTTTATATTTTGACCGAAATTAATTAA 1 AATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGATCGAAATTAATTAA * ** 42578488 TATAACTGTTTATATTAATAAAGTTGGTAAAATATTTACCATTAATATTTTAAATGAATCAAATT 66 TATAACTGTTTATATTAATAAA-TTGGTAAAATATATA-CATTAATATTTTGTATGAATCAAATT 42578553 CATATATT 129 CATATATT * 42578561 AATTATATTCTTTCTAAAAGAATATTAATTTCCATGTCTTTTATATTTTGATCGAAATTAATTAA 1 AATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGATCGAAATTAATTAA * * 42578626 TATAATTG-TTATATTAATAAATTCAGTAAAATATATACAATTAATATTTTGTATGAATCAAATT 66 TATAACTGTTTATATTAATAAATT-GGTAAAATATATAC-ATTAATATTTTGTATGAATCAAATT 42578690 CATATATT 129 CATATATT 42578698 AATTATAT 1 AATTATAT 42578706 CTACGATTAA Statistics Matches: 253, Mismatches: 26, Indels: 7 0.88 0.09 0.02 Matches are distributed among these distances: 136 95 0.38 137 63 0.25 138 95 0.38 ACGTcount: A:0.41, C:0.07, G:0.06, T:0.46 Consensus pattern (136 bp): AATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGATCGAAATTAATTAA TATAACTGTTTATATTAATAAATTGGTAAAATATATACATTAATATTTTGTATGAATCAAATTCA TATATT Found at i:42584817 original size:65 final size:63 Alignment explanation
Indices: 42584737--42584865 Score: 240 Period size: 65 Copynumber: 2.0 Consensus size: 63 42584727 CGGTAAGCCC 42584737 AAAGAGCGTCGTCTAAACCTAGGCTCCAATCCTTCCTACCCACATTTCACTTCTCTAAGTTCGAA 1 AAAGAGCGTCGTCTAAACCTAGGCTCCAATCCTTCCTACCCACATTTCACTTCTCT-A-TTCGAA 42584802 AAAGAGCGTCGTCTAAACCTAGGCTCCAATCCTTCCTACCCACATTTCACTTCTCTATTCGAA 1 AAAGAGCGTCGTCTAAACCTAGGCTCCAATCCTTCCTACCCACATTTCACTTCTCTATTCGAA 42584865 A 1 A 42584866 CTTCAGCTTG Statistics Matches: 64, Mismatches: 0, Indels: 2 0.97 0.00 0.03 Matches are distributed among these distances: 63 7 0.11 64 1 0.02 65 56 0.88 ACGTcount: A:0.28, C:0.33, G:0.12, T:0.28 Consensus pattern (63 bp): AAAGAGCGTCGTCTAAACCTAGGCTCCAATCCTTCCTACCCACATTTCACTTCTCTATTCGAA Found at i:42588236 original size:23 final size:23 Alignment explanation
Indices: 42588210--42588256 Score: 67 Period size: 23 Copynumber: 2.0 Consensus size: 23 42588200 CTGATATTAA 42588210 GCATGTATGATATATGCATTTTG 1 GCATGTATGATATATGCATTTTG * * * 42588233 GCATTTGTTATATATGCATTTTG 1 GCATGTATGATATATGCATTTTG 42588256 G 1 G 42588257 ATGAGATTGT Statistics Matches: 21, Mismatches: 3, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 23 21 1.00 ACGTcount: A:0.23, C:0.09, G:0.21, T:0.47 Consensus pattern (23 bp): GCATGTATGATATATGCATTTTG Found at i:42588269 original size:23 final size:23 Alignment explanation
Indices: 42588219--42588270 Score: 61 Period size: 23 Copynumber: 2.3 Consensus size: 23 42588209 AGCATGTATG ** 42588219 ATATATGCATTTTGGCATTTGTT 1 ATATATGCATTTTGGCATGAGTT 42588242 ATATATGCATTTTGG-ATGAGATT 1 ATATATGCATTTTGGCATGAG-TT * 42588265 GTATAT 1 ATATAT 42588271 ATGGAGGAAG Statistics Matches: 25, Mismatches: 3, Indels: 2 0.83 0.10 0.07 Matches are distributed among these distances: 22 3 0.12 23 22 0.88 ACGTcount: A:0.27, C:0.06, G:0.19, T:0.48 Consensus pattern (23 bp): ATATATGCATTTTGGCATGAGTT Found at i:42596164 original size:38 final size:38 Alignment explanation
Indices: 42596101--42596313 Score: 255 Period size: 38 Copynumber: 5.6 Consensus size: 38 42596091 ACACTGGCAA * * * * 42596101 TAAGCCTACTAGGCACTAAGCCTGAATAACACCAACAC 1 TAAGCCTGCTAGGCACAAAGCCTGAACAACACCGACAC * * * * 42596139 TAAGCCTACTAGGGACAAAGTCTGAATAACACCGACAC 1 TAAGCCTGCTAGGCACAAAGCCTGAACAACACCGACAC * 42596177 TAAGCCTGCTAGGCACAAAGCCTAAACAACACCGACAC 1 TAAGCCTGCTAGGCACAAAGCCTGAACAACACCGACAC * * * * 42596215 TAAGCATGCTAGGAACAAAGCCTGAACAACATCGGCAC 1 TAAGCCTGCTAGGCACAAAGCCTGAACAACACCGACAC * * * * 42596253 TATGCCTGCTAGGCACAAAGCCTAAACTACACCGGCAC 1 TAAGCCTGCTAGGCACAAAGCCTGAACAACACCGACAC ** 42596291 TGTGCCTGCTAGGCACAAAGCCT 1 TAAGCCTGCTAGGCACAAAGCCT 42596314 AAATAAGGGT Statistics Matches: 154, Mismatches: 21, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 38 154 1.00 ACGTcount: A:0.36, C:0.31, G:0.18, T:0.15 Consensus pattern (38 bp): TAAGCCTGCTAGGCACAAAGCCTGAACAACACCGACAC Found at i:42603309 original size:38 final size:38 Alignment explanation
Indices: 42603263--42603379 Score: 171 Period size: 38 Copynumber: 3.1 Consensus size: 38 42603253 AACTTTAATT * * * * 42603263 ACACCGGCAATAAGCCTACTAGGCACTAAGCCTGAATA 1 ACACCGGCACTAAGCCTGCTAGGCACAAAGCCTAAATA * 42603301 ACATCGGCACTAAGCCTGCTAGGCACAAAGCCTAAATA 1 ACACCGGCACTAAGCCTGCTAGGCACAAAGCCTAAATA * * 42603339 ACACCGACACTAAGCCTGCTAGGCACAAAACCTAAATA 1 ACACCGGCACTAAGCCTGCTAGGCACAAAGCCTAAATA 42603377 ACA 1 ACA 42603380 GTGTAACTCA Statistics Matches: 71, Mismatches: 8, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 38 71 1.00 ACGTcount: A:0.39, C:0.30, G:0.16, T:0.15 Consensus pattern (38 bp): ACACCGGCACTAAGCCTGCTAGGCACAAAGCCTAAATA Found at i:42607606 original size:3 final size:3 Alignment explanation
Indices: 42607598--42607632 Score: 70 Period size: 3 Copynumber: 11.7 Consensus size: 3 42607588 CACCCTTTTG 42607598 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA 1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA 42607633 GCTTAGCCAC Statistics Matches: 32, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 3 32 1.00 ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31 Consensus pattern (3 bp): AAT Found at i:42607698 original size:14 final size:14 Alignment explanation
Indices: 42607676--42607711 Score: 63 Period size: 14 Copynumber: 2.6 Consensus size: 14 42607666 AGTAATTGCT * 42607676 AATCATAGTAAAGA 1 AATCCTAGTAAAGA 42607690 AATCCTAGTAAAGA 1 AATCCTAGTAAAGA 42607704 AATCCTAG 1 AATCCTAG 42607712 CAAAACAAAA Statistics Matches: 21, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 14 21 1.00 ACGTcount: A:0.50, C:0.14, G:0.14, T:0.22 Consensus pattern (14 bp): AATCCTAGTAAAGA Found at i:42609313 original size:18 final size:19 Alignment explanation
Indices: 42609282--42609381 Score: 116 Period size: 18 Copynumber: 5.3 Consensus size: 19 42609272 AGAAATATAA * 42609282 ATTTTGGAATTTTTATAAA-T 1 ATTTT-GAA-TTTTAAAAATT * 42609302 ATTTTTAATTTTAAAAATT 1 ATTTTGAATTTTAAAAATT * 42609321 ATTTT-AAATTTAAAAATT 1 ATTTTGAATTTTAAAAATT 42609339 ATTTTGAA-TTTAAAAATT 1 ATTTTGAATTTTAAAAATT * 42609357 ATTTTGAATTTTTGAAAATT 1 ATTTTGAA-TTTTAAAAATT 42609377 ATTTT 1 ATTTT 42609382 ATTTTATTGT Statistics Matches: 72, Mismatches: 4, Indels: 8 0.86 0.05 0.10 Matches are distributed among these distances: 18 43 0.60 19 10 0.14 20 19 0.26 ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55 Consensus pattern (19 bp): ATTTTGAATTTTAAAAATT Found at i:42610082 original size:32 final size:32 Alignment explanation
Indices: 42610016--42610082 Score: 75 Period size: 32 Copynumber: 2.1 Consensus size: 32 42610006 TTAGGTTTTG ** * 42610016 ATTTCTAAATTTATTGCATTTCATTTGAATAT 1 ATTTCTAAATTTATTGCATTAAATTTGAAAAT 42610048 ATTTCTAAATTTATTTGCA-TAAATATT-AAAAT 1 ATTTCTAAATTTA-TTGCATTAAAT-TTGAAAAT 42610080 ATT 1 ATT 42610083 GTAATTATTT Statistics Matches: 30, Mismatches: 3, Indels: 4 0.81 0.08 0.11 Matches are distributed among these distances: 32 23 0.77 33 7 0.23 ACGTcount: A:0.37, C:0.07, G:0.04, T:0.51 Consensus pattern (32 bp): ATTTCTAAATTTATTGCATTAAATTTGAAAAT Found at i:42611483 original size:10 final size:9 Alignment explanation
Indices: 42611462--42611573 Score: 62 Period size: 9 Copynumber: 11.7 Consensus size: 9 42611452 TTTCTATACA 42611462 TTTTATAAT 1 TTTTATAAT * 42611471 TTTTATGAT 1 TTTTATAAT 42611480 TTTTATAATT 1 TTTTATAA-T * 42611490 TTTTCTAAT 1 TTTTATAAT * 42611499 TTTTAATAAA 1 TTTT-ATAAT ** * 42611509 AATTAAATAT 1 TTTTATA-AT * 42611519 TTCTTATATT 1 TT-TTATAAT * 42611529 TTTTATTAAAA 1 TTTTA-T-AAT * 42611540 TTTAATAAT 1 TTTTATAAT * 42611549 TTTTATAAC 1 TTTTATAAT * 42611558 TTTTATTTAT 1 TTTTA-TAAT 42611568 TTTTAT 1 TTTTAT 42611574 TTTTATCATT Statistics Matches: 75, Mismatches: 21, Indels: 14 0.68 0.19 0.13 Matches are distributed among these distances: 9 40 0.53 10 26 0.35 11 9 0.12 ACGTcount: A:0.34, C:0.03, G:0.01, T:0.62 Consensus pattern (9 bp): TTTTATAAT Found at i:42611530 original size:29 final size:29 Alignment explanation
Indices: 42611497--42611555 Score: 75 Period size: 29 Copynumber: 2.0 Consensus size: 29 42611487 ATTTTTTCTA 42611497 ATTTTTAATAAAAATTAAAT-ATTTCTTAT 1 ATTTTTAATAAAAATTAAATAATTT-TTAT * * * 42611526 ATTTTTTATTAAAATTTAATAATTTTTAT 1 ATTTTTAATAAAAATTAAATAATTTTTAT 42611555 A 1 A 42611556 ACTTTTATTT Statistics Matches: 26, Mismatches: 3, Indels: 2 0.84 0.10 0.06 Matches are distributed among these distances: 29 22 0.85 30 4 0.15 ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56 Consensus pattern (29 bp): ATTTTTAATAAAAATTAAATAATTTTTAT Found at i:42613496 original size:13 final size:14 Alignment explanation
Indices: 42613480--42613509 Score: 53 Period size: 13 Copynumber: 2.2 Consensus size: 14 42613470 CCATTTTTCA 42613480 TATTTTATTT-TTT 1 TATTTTATTTATTT 42613493 TATTTTATTTATTT 1 TATTTTATTTATTT 42613507 TAT 1 TAT 42613510 ATATATATTT Statistics Matches: 16, Mismatches: 0, Indels: 1 0.94 0.00 0.06 Matches are distributed among these distances: 13 10 0.62 14 6 0.38 ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80 Consensus pattern (14 bp): TATTTTATTTATTT Found at i:42613672 original size:6 final size:6 Alignment explanation
Indices: 42613631--42613665 Score: 63 Period size: 6 Copynumber: 6.0 Consensus size: 6 42613621 GCTTTAGCCC 42613631 ATTTTT ATTTTT ATTTTT ATTTTT A-TTTT ATTTTT 1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT 42613666 TTGTTTTCAT Statistics Matches: 28, Mismatches: 0, Indels: 2 0.93 0.00 0.07 Matches are distributed among these distances: 5 5 0.18 6 23 0.82 ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83 Consensus pattern (6 bp): ATTTTT Found at i:42613672 original size:18 final size:18 Alignment explanation
Indices: 42613631--42613665 Score: 63 Period size: 17 Copynumber: 2.0 Consensus size: 18 42613621 GCTTTAGCCC 42613631 ATTTTTATTTTTATTTTT 1 ATTTTTATTTTTATTTTT 42613649 ATTTTTA-TTTTATTTTT 1 ATTTTTATTTTTATTTTT 42613666 TTGTTTTCAT Statistics Matches: 17, Mismatches: 0, Indels: 1 0.94 0.00 0.06 Matches are distributed among these distances: 17 10 0.59 18 7 0.41 ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83 Consensus pattern (18 bp): ATTTTTATTTTTATTTTT Found at i:42613792 original size:29 final size:29 Alignment explanation
Indices: 42613739--42613835 Score: 81 Period size: 30 Copynumber: 3.3 Consensus size: 29 42613729 AATATATAAA * * * 42613739 TTACATTTTGGCCTCTAAACTTTTTCAAAT 1 TTACATTTTGACCCCT-AACATTTTCAAAT 42613769 TTACATTTTGACCCCTAACATTTTCTAAAAT 1 TTACATTTTGACCCCTAACATTTTC--AAAT * * * * 42613800 TT-CATCTTAACCCCTAATATTTTGTAAA- 1 TTACATTTTGACCCCTAACATTTT-CAAAT 42613828 TTACATTT 1 TTACATTT 42613836 GGGCCCTAAA Statistics Matches: 55, Mismatches: 8, Indels: 9 0.76 0.11 0.12 Matches are distributed among these distances: 28 2 0.04 29 15 0.27 30 32 0.58 31 6 0.11 ACGTcount: A:0.30, C:0.21, G:0.04, T:0.45 Consensus pattern (29 bp): TTACATTTTGACCCCTAACATTTTCAAAT Found at i:42613814 original size:30 final size:31 Alignment explanation
Indices: 42613765--42613827 Score: 83 Period size: 30 Copynumber: 2.1 Consensus size: 31 42613755 AAACTTTTTC * * 42613765 AAATTTACATTTTGACCCCTAACATTTTCTA 1 AAATTTACATCTTAACCCCTAACATTTTCTA * * 42613796 AAATTT-CATCTTAACCCCTAATATTTTGTA 1 AAATTTACATCTTAACCCCTAACATTTTCTA 42613826 AA 1 AA 42613828 TTACATTTGG Statistics Matches: 28, Mismatches: 4, Indels: 1 0.85 0.12 0.03 Matches are distributed among these distances: 30 22 0.79 31 6 0.21 ACGTcount: A:0.35, C:0.21, G:0.03, T:0.41 Consensus pattern (31 bp): AAATTTACATCTTAACCCCTAACATTTTCTA Found at i:42614443 original size:13 final size:13 Alignment explanation
Indices: 42614417--42614481 Score: 80 Period size: 13 Copynumber: 4.9 Consensus size: 13 42614407 GCCCCGAAGA 42614417 AGAAGAAGAAAAAG 1 AGAAGAA-AAAAAG 42614431 A-AAGGAAAAAAAG 1 AGAA-GAAAAAAAG 42614444 AGAAGAAAAAAGAG 1 AGAAGAAAAAA-AG * 42614458 AGAAGAAAAAGAG 1 AGAAGAAAAAAAG 42614471 A-AAGAAAAAAA 1 AGAAGAAAAAAA 42614482 TATCTTACAC Statistics Matches: 46, Mismatches: 2, Indels: 8 0.82 0.04 0.14 Matches are distributed among these distances: 12 9 0.20 13 19 0.41 14 18 0.39 ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00 Consensus pattern (13 bp): AGAAGAAAAAAAG Found at i:42614465 original size:27 final size:26 Alignment explanation
Indices: 42614417--42614481 Score: 80 Period size: 25 Copynumber: 2.5 Consensus size: 26 42614407 GCCCCGAAGA 42614417 AGAAGAAGAAAAAGAAAGGAAAAAAAG 1 AGAAGAA-AAAAAGAAAGGAAAAAAAG * 42614444 AGAAG-AAAAAAGAGA-GAAGAAAAAG 1 AGAAGAAAAAAAGAAAGGAA-AAAAAG 42614469 AGAAAGAAAAAAA 1 AG-AAGAAAAAAA 42614482 TATCTTACAC Statistics Matches: 34, Mismatches: 1, Indels: 6 0.83 0.02 0.15 Matches are distributed among these distances: 24 3 0.09 25 16 0.47 26 4 0.12 27 11 0.32 ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00 Consensus pattern (26 bp): AGAAGAAAAAAAGAAAGGAAAAAAAG Found at i:42614837 original size:13 final size:12 Alignment explanation
Indices: 42614809--42614847 Score: 51 Period size: 13 Copynumber: 3.0 Consensus size: 12 42614799 ACACCCAGCA 42614809 AAAAAAAAAAGAG 1 AAAAAAAAAAG-G 42614822 AAAGAAAAAAAGG 1 AAA-AAAAAAAGG 42614835 AAAAAAGAAAAGG 1 AAAAAA-AAAAGG 42614848 GCCCACAACT Statistics Matches: 24, Mismatches: 0, Indels: 4 0.86 0.00 0.14 Matches are distributed among these distances: 12 3 0.12 13 13 0.54 14 8 0.33 ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00 Consensus pattern (12 bp): AAAAAAAAAAGG Found at i:42615335 original size:18 final size:19 Alignment explanation
Indices: 42615290--42615337 Score: 57 Period size: 18 Copynumber: 2.6 Consensus size: 19 42615280 AAAATAAACA 42615290 ATCGTATTTCAAAAGTTTTC 1 ATCGT-TTTCAAAAGTTTTC 42615310 AT-GTTTTCAAAA-TTTTC 1 ATCGTTTTCAAAAGTTTTC 42615327 -TCGTGTTTCAA 1 ATCGT-TTTCAA 42615338 CAAAATAATA Statistics Matches: 26, Mismatches: 0, Indels: 6 0.81 0.00 0.19 Matches are distributed among these distances: 16 1 0.04 17 7 0.27 18 14 0.54 19 2 0.08 20 2 0.08 ACGTcount: A:0.27, C:0.15, G:0.10, T:0.48 Consensus pattern (19 bp): ATCGTTTTCAAAAGTTTTC Found at i:42615422 original size:15 final size:16 Alignment explanation
Indices: 42615398--42615430 Score: 50 Period size: 15 Copynumber: 2.1 Consensus size: 16 42615388 TTAAAAAAAC 42615398 AATTTCCGTG-TTTCA 1 AATTTCCGTGTTTTCA * 42615413 AATTTTCGTGTTTTCA 1 AATTTCCGTGTTTTCA 42615429 AA 1 AA 42615431 AAATTCTCGT Statistics Matches: 16, Mismatches: 1, Indels: 1 0.89 0.06 0.06 Matches are distributed among these distances: 15 9 0.56 16 7 0.44 ACGTcount: A:0.24, C:0.15, G:0.12, T:0.48 Consensus pattern (16 bp): AATTTCCGTGTTTTCA Found at i:42615447 original size:18 final size:19 Alignment explanation
Indices: 42615412--42615450 Score: 62 Period size: 19 Copynumber: 2.1 Consensus size: 19 42615402 TCCGTGTTTC * 42615412 AAATTTTCGTGTTTTCAAA 1 AAATTCTCGTGTTTTCAAA 42615431 AAATTCTCGTG-TTTCAAA 1 AAATTCTCGTGTTTTCAAA 42615449 AA 1 AA 42615451 TTTTCAAATT Statistics Matches: 19, Mismatches: 1, Indels: 1 0.90 0.05 0.05 Matches are distributed among these distances: 18 9 0.47 19 10 0.53 ACGTcount: A:0.36, C:0.13, G:0.10, T:0.41 Consensus pattern (19 bp): AAATTCTCGTGTTTTCAAA Done.