Tandem Repeats Finder Program written by: Gary Benson Program in Bioinformatics Boston University Version 4.09 Sequence: AWUE01017621.1 Corchorus olitorius cultivar O-4 contig17654, whole genome shotgun sequence 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: 41987 ACGTcount: A:0.32, C:0.16, G:0.17, T:0.34 Found at i:2820 original size:21 final size:21 Alignment explanation
Indices: 2796--2868 Score: 65 Period size: 21 Copynumber: 3.4 Consensus size: 21 2786 GGCACTGAAT * 2796 GGTGATGGCACGGGCATAGCC 1 GGTGATGGCACGGGCATAACC * * 2817 GGTGGTGGCACGGGCTTAACC 1 GGTGATGGCACGGGCATAACC * * * * 2838 GGTGGTGTCACGGTGAATACCC 1 GGTGATGGCACGG-GCATAACC * 2860 GGTAATGGC 1 GGTGATGGC 2869 TTGGTAGTGG Statistics Matches: 41, Mismatches: 10, Indels: 1 0.79 0.19 0.02 Matches are distributed among these distances: 21 30 0.73 22 11 0.27 ACGTcount: A:0.18, C:0.22, G:0.41, T:0.19 Consensus pattern (21 bp): GGTGATGGCACGGGCATAACC Found at i:5985 original size:29 final size:28 Alignment explanation
Indices: 5952--6028 Score: 95 Period size: 29 Copynumber: 2.8 Consensus size: 28 5942 AAAATATATA * 5952 TTTTTTTAAAAAAACGCAAGAACAAGTTT 1 TTTTTTTAAAAAAACGCAA-AACAAATTT * * 5981 TTTTTTTTAGAAAACGCAAAACAAA-TT 1 TTTTTTTAAAAAAACGCAAAACAAATTT * 6008 TTTTTTT-CAAAAACGCAAAAC 1 TTTTTTTAAAAAAACGCAAAAC 6029 TAATAAATTA Statistics Matches: 43, Mismatches: 5, Indels: 3 0.84 0.10 0.06 Matches are distributed among these distances: 26 12 0.28 27 9 0.21 28 5 0.12 29 17 0.40 ACGTcount: A:0.44, C:0.13, G:0.08, T:0.35 Consensus pattern (28 bp): TTTTTTTAAAAAAACGCAAAACAAATTT Found at i:6009 original size:26 final size:26 Alignment explanation
Indices: 5951--6028 Score: 86 Period size: 26 Copynumber: 2.9 Consensus size: 26 5941 AAAAATATAT ** 5951 ATTTTTTTAAAAAAACGCAAGAACAAG 1 ATTTTTTTTTAAAAACGCAA-AACAAG * 5978 TTTTTTTTTTTAGAAAACGCAAAACAA- 1 -ATTTTTTTTTA-AAAACGCAAAACAAG 6005 ATTTTTTTTTCAAAAACGCAAAAC 1 ATTTTTTTTT-AAAAACGCAAAAC 6029 TAATAAATTA Statistics Matches: 44, Mismatches: 4, Indels: 6 0.81 0.07 0.11 Matches are distributed among these distances: 26 21 0.48 27 1 0.02 28 13 0.30 29 9 0.20 ACGTcount: A:0.45, C:0.13, G:0.08, T:0.35 Consensus pattern (26 bp): ATTTTTTTTTAAAAACGCAAAACAAG Found at i:6098 original size:26 final size:26 Alignment explanation
Indices: 6042--6127 Score: 88 Period size: 24 Copynumber: 3.3 Consensus size: 26 6032 TAAATTAAAA * ** * 6042 ACGCAAGAAAACTTTTTTTTTATGAAAG 1 ACGCAA-AAAGCTTTTTTTTT-TTTATG 6070 ACGCAAAAAGCTTTTTTTTTTTTATG 1 ACGCAAAAAGCTTTTTTTTTTTTATG 6096 ACGC-AAAAG-TTTTTTTTTTTT-TCG 1 ACGCAAAAAGCTTTTTTTTTTTTAT-G 6120 ACGCAAAA 1 ACGCAAAA 6128 CACAAAACAA Statistics Matches: 52, Mismatches: 4, Indels: 7 0.83 0.06 0.11 Matches are distributed among these distances: 23 1 0.02 24 17 0.33 25 8 0.15 26 7 0.13 27 13 0.25 28 6 0.12 ACGTcount: A:0.33, C:0.13, G:0.13, T:0.42 Consensus pattern (26 bp): ACGCAAAAAGCTTTTTTTTTTTTATG Found at i:12750 original size:82 final size:82 Alignment explanation
Indices: 12648--12809 Score: 272 Period size: 82 Copynumber: 2.0 Consensus size: 82 12638 CTCAATTTAC * 12648 AATTGAGGGTAAATTGGTCTTCA-CATAAATAATATTAAGATGTGTGGTCAAGAATTGATTAAAA 1 AATTGAGGATAAATTGGTCTT-ATCATAAATAATATTAAGATGTGTGGTCAAGAATTGATTAAAA * 12712 ATCCTGGTGAAACATGTA 65 ATCCTAGTGAAACATGTA * 12730 AATTGAGGATAAATTGGTCTTATCATAAATAATATTAAGATGTGTGGTCAAGATTTGATTAAAAA 1 AATTGAGGATAAATTGGTCTTATCATAAATAATATTAAGATGTGTGGTCAAGAATTGATTAAAAA * 12795 TTCTAGTGAAACATG 66 TCCTAGTGAAACATG 12810 GTTTCTGCAC Statistics Matches: 75, Mismatches: 4, Indels: 2 0.93 0.05 0.02 Matches are distributed among these distances: 81 1 0.01 82 74 0.99 ACGTcount: A:0.40, C:0.07, G:0.20, T:0.33 Consensus pattern (82 bp): AATTGAGGATAAATTGGTCTTATCATAAATAATATTAAGATGTGTGGTCAAGAATTGATTAAAAA TCCTAGTGAAACATGTA Found at i:12916 original size:19 final size:18 Alignment explanation
Indices: 12881--12925 Score: 54 Period size: 19 Copynumber: 2.4 Consensus size: 18 12871 TAAAATTAAT * 12881 TAATTAATTATTAAATAA 1 TAATTATTTATTAAATAA * 12899 TAATTATTTTTTAGAATAA 1 TAATTATTTATTA-AATAA * 12918 TTATTATT 1 TAATTATT 12926 AAAATTCCCT Statistics Matches: 23, Mismatches: 3, Indels: 1 0.85 0.11 0.04 Matches are distributed among these distances: 18 11 0.48 19 12 0.52 ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53 Consensus pattern (18 bp): TAATTATTTATTAAATAA Found at i:20246 original size:122 final size:127 Alignment explanation
Indices: 20102--20352 Score: 377 Period size: 131 Copynumber: 2.0 Consensus size: 127 20092 CATTGTTTAA * * 20102 ACTTTTATAGGTTTATTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATAT-C-T-TA-T 1 ACTTTTACAGGTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATATCCTTATACT 20163 A-ATTTTTACCATTTTAATATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATAT 66 ATATTTTTACCATTTTAATATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATAT * * 20224 ACTTTTACAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATACC 1 ACTTTTACAGGTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATATCCTTATA-C * * 20289 TATTTTATTTTTACCATTTTACTATTTTATTTAAAAAACTTATATATATTAGAATTTTTTAAAT 65 TA---TATTTTTACCATTTTAATATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAAT 20353 TTTACAATTT Statistics Matches: 114, Mismatches: 6, Indels: 9 0.88 0.05 0.07 Matches are distributed among these distances: 122 52 0.46 123 1 0.01 124 1 0.01 125 2 0.02 127 2 0.02 131 56 0.49 ACGTcount: A:0.38, C:0.10, G:0.02, T:0.50 Consensus pattern (127 bp): ACTTTTACAGGTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATATCCTTATACT ATATTTTTACCATTTTAATATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATAT Found at i:21478 original size:316 final size:315 Alignment explanation
Indices: 20905--21528 Score: 1160 Period size: 316 Copynumber: 2.0 Consensus size: 315 20895 AGACTAGTAC 20905 TATTAAAAAGTACGTTCACCTGTAAAACTTTTGAATCGCCCATTATACCCTTATTTTTCGAATAT 1 TATTAAAAAGTACGTTCACCTGTAAAACTTTTGAATCGCCCATTATACCCTTATTTTTCGAATAT * 20970 ATTTCTTAAATGCCATTGTTTAAACTTTTATAGTTTTACTCAACTAAAAGCTCTAATGTTATTTA 66 ATTTCTTAAATGCCATTGTTTAAACTTTTATAGTTTTACTCAACTAAAAACTCTAATGTTATTTA 21035 ATTAAATCTAATATCTTTATAATTTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATT 131 ATTAAATCTAATATCTTTATAATTTTTACCATTTTACTATTTTAATTAAAAAAC-TATATATATT 21100 AGAATTTTTTAAATATACTTTTACAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAAT 195 AGAATTTTTTAAATATACTTTTACAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAAT * 21165 CTAATATCCTTATACCTATTTTATTTTTACCATTTTACTATTTTATTTCTACACTA 260 ATAATATCCTTATACCTATTTTATTTTTACCATTTTACTATTTTATTTCTACACTA * * 21221 TATTAAAAAGTATGTTCACCTGTAAAACTTTTGAATCGTCCATTATACCCTTATTTTTCGAATAT 1 TATTAAAAAGTACGTTCACCTGTAAAACTTTTGAATCGCCCATTATACCCTTATTTTTCGAATAT * 21286 ATTTCTTAAATGTCATTGTTTAAACTTTTATAGTTTTACTCAACTAAAAACTCTAATGTTATTTA 66 ATTTCTTAAATGCCATTGTTTAAACTTTTATAGTTTTACTCAACTAAAAACTCTAATGTTATTTA 21351 ATTAAATCTAATATCTTTATAATTTTTACCATTTTACTATTTTAATTAAAAAAAC-ATATATATT 131 ATTAAATCTAATATCTTTATAATTTTTACCATTTTACTATTTTAATT-AAAAAACTATATATATT * 21415 AGAATTTTTTTAAATATACTTTTACTGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAA 195 AGAA-TTTTTTAAATATACTTTTACAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAA 21480 TATAATATCCTTATACCTATTTTATTTTTACCATTTTACTATTTTATTT 259 TATAATATCCTTATACCTATTTTATTTTTACCATTTTACTATTTTATTT 21529 TAAAAAACTT Statistics Matches: 300, Mismatches: 6, Indels: 4 0.97 0.02 0.01 Matches are distributed among these distances: 315 13 0.04 316 280 0.93 317 7 0.02 ACGTcount: A:0.34, C:0.14, G:0.04, T:0.48 Consensus pattern (315 bp): TATTAAAAAGTACGTTCACCTGTAAAACTTTTGAATCGCCCATTATACCCTTATTTTTCGAATAT ATTTCTTAAATGCCATTGTTTAAACTTTTATAGTTTTACTCAACTAAAAACTCTAATGTTATTTA ATTAAATCTAATATCTTTATAATTTTTACCATTTTACTATTTTAATTAAAAAACTATATATATTA GAATTTTTTAAATATACTTTTACAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATA TAATATCCTTATACCTATTTTATTTTTACCATTTTACTATTTTATTTCTACACTA Found at i:21586 original size:14 final size:13 Alignment explanation
Indices: 21550--21588 Score: 51 Period size: 14 Copynumber: 2.9 Consensus size: 13 21540 TATATATTAG 21550 AATTTTTTAAATA 1 AATTTTTTAAATA * * 21563 TATTTCTTAAATGA 1 AATTTTTTAAAT-A 21577 AATTTTTTAAAT 1 AATTTTTTAAAT 21589 TTTACAATTT Statistics Matches: 21, Mismatches: 4, Indels: 1 0.81 0.15 0.04 Matches are distributed among these distances: 13 10 0.48 14 11 0.52 ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54 Consensus pattern (13 bp): AATTTTTTAAATA Found at i:22760 original size:188 final size:188 Alignment explanation
Indices: 22446--23011 Score: 976 Period size: 188 Copynumber: 3.0 Consensus size: 188 22436 GACATTAGAG * * * * 22446 TGAATAACCCAATATGGCAGAGAAATGCCGTGGTAA-T-TAAGGA-TTTCTTATGATTGAGCACC 1 TGAATAACCCAATCTGACAGAGAAATGCCCTAGTAATTATAAGGATTTTCTTATGATTGAGCACC * * * 22508 CAAAGTAACTGTTGAACTTTGAGAAAGGTTGGTGTTTGCCATATCCACTTCCAACTTGTCACAAG 66 CAAAGTAACTGTCGGACTTTGAGAAAGGTTGGTGTTTTCCATATCCACTTCCAACTTGTCACAAG 22573 TTCAAAGGCCTTTAGCAATCGGTTTAATAGACATTTTGACCCTTGAACTTGTAAGAAA 131 TTCAAAGGCCTTTAGCAATCGGTTTAATAGACATTTTGACCCTTGAACTTGTAAGAAA 22631 TGAATAACCCAATCTGACAGAGAAATGCCCTAGTAATTATAAGGATTTTCTTATGATTGAGCACC 1 TGAATAACCCAATCTGACAGAGAAATGCCCTAGTAATTATAAGGATTTTCTTATGATTGAGCACC 22696 CAAAGTAACTGTCGGACTTTGAGAAAGGTTGGTGTTTTCCATATCCACTTCCAACTTGTCACAAG 66 CAAAGTAACTGTCGGACTTTGAGAAAGGTTGGTGTTTTCCATATCCACTTCCAACTTGTCACAAG * 22761 TTCAAAGGTCTTTAGCAATCGGTTTAATAGACATTTTGACCCTTGAACTTGTAAGAAA 131 TTCAAAGGCCTTTAGCAATCGGTTTAATAGACATTTTGACCCTTGAACTTGTAAGAAA * * 22819 TGAATAACTCAATCTGACAGAAAAATGCCCTAGTAATTATAAGGATTTTCTTATGATTGAGCACC 1 TGAATAACCCAATCTGACAGAGAAATGCCCTAGTAATTATAAGGATTTTCTTATGATTGAGCACC ** * 22884 CAAAGTCTCATCTCGGACTTTGAGAAAGGTTGGTGTTTTCCATATCCACTTCCAACTTGTCACAA 66 CAAAGTAAC-TGTCGGACTTTGAGAAAGGTTGGTGTTTTCCATATCCACTTCCAACTTGTCACAA * 22949 GTTCAAAGGCCTTTAGCAATCGGTTTAATAGACATTTTGACCATTGAACTTGTAAGAAA 130 GTTCAAAGGCCTTTAGCAATCGGTTTAATAGACATTTTGACCCTTGAACTTGTAAGAAA 23008 TGAA 1 TGAA 23012 CAATTTAATC Statistics Matches: 362, Mismatches: 15, Indels: 4 0.95 0.04 0.01 Matches are distributed among these distances: 185 32 0.09 186 1 0.00 187 6 0.02 188 208 0.57 189 115 0.32 ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31 Consensus pattern (188 bp): TGAATAACCCAATCTGACAGAGAAATGCCCTAGTAATTATAAGGATTTTCTTATGATTGAGCACC CAAAGTAACTGTCGGACTTTGAGAAAGGTTGGTGTTTTCCATATCCACTTCCAACTTGTCACAAG TTCAAAGGCCTTTAGCAATCGGTTTAATAGACATTTTGACCCTTGAACTTGTAAGAAA Found at i:26412 original size:13 final size:14 Alignment explanation
Indices: 26394--26429 Score: 58 Period size: 13 Copynumber: 2.7 Consensus size: 14 26384 TTTTATTTTA 26394 TTTTGTATTTT-GT 1 TTTTGTATTTTCGT 26407 TTTTGT-TTTTCGT 1 TTTTGTATTTTCGT 26420 TTTTGTATTT 1 TTTTGTATTT 26430 CATTAGGTGC Statistics Matches: 21, Mismatches: 0, Indels: 3 0.88 0.00 0.12 Matches are distributed among these distances: 12 4 0.19 13 14 0.67 14 3 0.14 ACGTcount: A:0.06, C:0.03, G:0.14, T:0.78 Consensus pattern (14 bp): TTTTGTATTTTCGT Found at i:29422 original size:11 final size:10 Alignment explanation
Indices: 29397--29421 Score: 50 Period size: 10 Copynumber: 2.5 Consensus size: 10 29387 TTCAAAAGGA 29397 TTTTTAATTT 1 TTTTTAATTT 29407 TTTTTAATTT 1 TTTTTAATTT 29417 TTTTT 1 TTTTT 29422 TTTTTGCTTT Statistics Matches: 15, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 10 15 1.00 ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84 Consensus pattern (10 bp): TTTTTAATTT Found at i:36233 original size:21 final size:21 Alignment explanation
Indices: 36201--36292 Score: 68 Period size: 22 Copynumber: 4.4 Consensus size: 21 36191 GAAATATTTA * 36201 TATGAAACTATGATAACCTCC 1 TATGAAATTATGATAACCTCC * 36222 TATTAAATTATGATAA-CTACAC 1 TATGAAATTATGATAACCT-C-C * * 36244 TAT----TTTTGATGACCTCC 1 TATGAAATTATGATAACCTCC * 36261 TTATGAAATTTTGATAACCTTCC 1 -TATGAAATTATGATAACC-TCC 36284 TATGAAATT 1 TATGAAATT 36293 TTAATAACGA Statistics Matches: 57, Mismatches: 5, Indels: 17 0.72 0.06 0.22 Matches are distributed among these distances: 17 1 0.02 18 11 0.19 19 2 0.04 20 2 0.04 21 15 0.26 22 23 0.40 23 3 0.05 ACGTcount: A:0.35, C:0.17, G:0.09, T:0.39 Consensus pattern (21 bp): TATGAAATTATGATAACCTCC Found at i:36272 original size:22 final size:21 Alignment explanation
Indices: 36247--36952 Score: 374 Period size: 22 Copynumber: 32.3 Consensus size: 21 36237 ACTACACTAT * 36247 TTTTGATGACCTCCTTATGAAA 1 TTTTGATAACCTCC-TATGAAA 36269 TTTTGATAACCTTCCTATGAAA 1 TTTTGATAACC-TCCTATGAAA * * * * 36291 TTTTAATAACGATACTATGGAA 1 TTTTGATAAC-CTCCTATGAAA * * ** 36313 TTTCGAGAACCTTTTTAT-AAA 1 TTTTGATAACC-TCCTATGAAA ** * 36334 TTTTTTTTAACCTTCTTATGAAA 1 -TTTTGATAACC-TCCTATGAAA * * 36357 TTTTGTTAACCTCTCTAAGAAA 1 TTTTGATAACCTC-CTATGAAA * * 36379 TTTTGA-AGACTTCATTATGAAA 1 TTTTGATA-ACCTC-CTATGAAA * * 36401 TTTTGATAACTTCCCAATGAAA 1 TTTTGATAACCT-CCTATGAAA * * 36423 TTTTGATAACCAACACTATGAGA 1 TTTTGATAACC-TC-CTATGAAA * * 36446 TGTTGATAACCTCCATATGATA 1 TTTTGATAACCTCC-TATGAAA * * * 36468 TATTGATAACCACGTTATGAAA 1 TTTTGATAACCTC-CTATGAAA * * * * 36490 ATTTAAGAACCTCCATATG-GA 1 TTTTGATAACCTCC-TATGAAA * * * 36511 TTGTT-AGTAATCACACTCTGAAA 1 TT-TTGA-TAACCTC-CTATGAAA * * * 36534 TATTGATAATCACACTATGAAA 1 TTTTGATAACCTC-CTATGAAA * * 36556 TTGTCATAACCTCTCTATGAAA 1 TTTTGATAACCTC-CTATGAAA * 36578 TTTTGATAAACCTTCCTATAAAA 1 TTTTGAT-AACC-TCCTATGAAA * 36601 TTTTGATAAACCTCCCTATAAAA 1 TTTTGAT-AACCT-CCTATGAAA 36624 TTTTGATAACCTCCTTATGAAA 1 TTTTGATAACCTCC-TATGAAA * * 36646 TCTTGATAA----CTA-CAAA 1 TTTTGATAACCTCCTATGAAA * ** 36662 TTTTTATAACCTCCCTATGATT 1 TTTTGATAACCT-CCTATGAAA * ** 36684 TTTTTATAACCTCCCTATGATT 1 TTTTGATAACCT-CCTATGAAA * * 36706 TTTTTATAACCTCATTATGAAA 1 TTTTGATAACCTC-CTATGAAA * * 36728 TTTTGTTAATCTCCCTATGAAA 1 TTTTGATAACCT-CCTATGAAA * * * 36750 TTTTGATCTACATACTATGAAA 1 TTTTGAT-AACCTCCTATGAAA 36772 TTTTGATAATCCTCCTATGAAA 1 TTTTGATAA-CCTCCTATGAAA * * 36794 TTTTGA-AAACTAAGCTATGAAA 1 TTTTGATAACCT--CCTATGAAA * 36816 TTTTGATAACCTTCATATGAAA 1 TTTTGATAACC-TCCTATGAAA * * * * 36838 TTTTGATCTACATACTATAAAA 1 TTTTGAT-AACCTCCTATGAAA * 36860 TTTTGATAACCCTCTTATGAAA 1 TTTTGATAA-CCTCCTATGAAA * * 36882 TTTTGA-AAACTAAACTATGAAA 1 TTTTGATAACCT--CCTATGAAA * 36904 TTTTGATAACCTTCATATGAAA 1 TTTTGATAACC-TCCTATGAAA * * 36926 TTTTGATATCCTCC-CTGAAA 1 TTTTGATAACCTCCTATGAAA 36946 TTTTGAT 1 TTTTGAT 36953 TACTCCATAA Statistics Matches: 532, Mismatches: 109, Indels: 88 0.73 0.15 0.12 Matches are distributed among these distances: 16 10 0.02 17 2 0.00 18 1 0.00 20 16 0.03 21 23 0.04 22 398 0.75 23 78 0.15 24 4 0.01 ACGTcount: A:0.35, C:0.16, G:0.09, T:0.40 Consensus pattern (21 bp): TTTTGATAACCTCCTATGAAA Found at i:36625 original size:46 final size:45 Alignment explanation
Indices: 36563--36654 Score: 123 Period size: 46 Copynumber: 2.0 Consensus size: 45 36553 AAATTGTCAT * * * 36563 AACCTCTCTATGAAATTTTGATAAACCTTCC-TATAAAATTTTGATA 1 AACCTCCCTATAAAATTTTGAT-AACC-TCCTTATAAAATCTTGATA * 36609 AACCTCCCTATAAAATTTTGATAACCTCCTTATGAAATCTTGATA 1 AACCTCCCTATAAAATTTTGATAACCTCCTTATAAAATCTTGATA 36654 A 1 A 36655 CTACAAATTT Statistics Matches: 41, Mismatches: 4, Indels: 3 0.85 0.08 0.06 Matches are distributed among these distances: 44 3 0.07 45 18 0.44 46 20 0.49 ACGTcount: A:0.37, C:0.20, G:0.07, T:0.37 Consensus pattern (45 bp): AACCTCCCTATAAAATTTTGATAACCTCCTTATAAAATCTTGATA Found at i:37089 original size:22 final size:22 Alignment explanation
Indices: 37064--37285 Score: 107 Period size: 22 Copynumber: 10.0 Consensus size: 22 37054 AATGACATTT * 37064 TGAAAATTTGATAACCTCTTTA 1 TGAAAATTTGATAACCTCTCTA * 37086 TGAAATTTTGATAACCTCTCTA 1 TGAAAATTTGATAACCTCTCTA * * * 37108 T-AAAATTTTGTTGACCCCTCTA 1 TGAAAA-TTTGATAACCTCTCTA * * * 37130 TTAAAATTTTGATAATCACAT-TA 1 TGAAAA-TTTGATAACCTC-TCTA * * * * 37153 TGTAATTTTGATAACCTCGCTT 1 TGAAAATTTGATAACCTCTCTA * * ** * 37175 TGAAATTTTCATAACAACACTA 1 TGAAAATTTGATAACCTCTCTA * * 37197 TGAAATTTTGATAATCT-TCCTA 1 TGAAAATTTGATAACCTCT-CTA * * 37219 T-AAATTTTGATAATCCGATCTCTG 1 TGAAAATTTGATAA-CC--TCTCTA * * 37243 TG-AAATTTCGATAATCACTCTA 1 TGAAAATTT-GATAACCTCTCTA * 37265 TG-AGATTTGATAACCT-TCTA 1 TGAAAATTTGATAACCTCTCTA 37285 T 1 T 37286 CAAATGTTGG Statistics Matches: 152, Mismatches: 37, Indels: 24 0.71 0.17 0.11 Matches are distributed among these distances: 20 5 0.03 21 21 0.14 22 91 0.60 23 18 0.12 24 11 0.07 25 6 0.04 ACGTcount: A:0.33, C:0.16, G:0.09, T:0.41 Consensus pattern (22 bp): TGAAAATTTGATAACCTCTCTA Found at i:37204 original size:44 final size:42 Alignment explanation
Indices: 37064--37231 Score: 131 Period size: 44 Copynumber: 3.8 Consensus size: 42 37054 AATGACATTT * * * * 37064 TGAAAATTTGATAACCTCTTTATGAAATTTTGATAACCTCTCTA 1 TGAAATTTTGATAACCTCCTT-TGAAATTTTGATAA-CACACTA * * * * * * 37108 TAAAATTTTGTTGACCCCTCTATTAAAATTTTGATAATCACATTA 1 TGAAATTTTGATAACCTC-CT-TTGAAATTTTGATAA-CACACTA * * 37153 TGTAATTTTGATAACCTCGCTTTGAAATTTTCATAACAACACTA 1 TGAAATTTTGATAACCTC-CTTTGAAATTTTGATAAC-ACACTA * * 37197 TGAAATTTTGATAATCTTCCTAT-AAATTTTGATAA 1 TGAAATTTTGATAA-CCTCCTTTGAAATTTTGATAA 37232 TCCGATCTCT Statistics Matches: 96, Mismatches: 24, Indels: 9 0.74 0.19 0.07 Matches are distributed among these distances: 43 12 0.12 44 47 0.49 45 36 0.38 46 1 0.01 ACGTcount: A:0.35, C:0.15, G:0.08, T:0.42 Consensus pattern (42 bp): TGAAATTTTGATAACCTCCTTTGAAATTTTGATAACACACTA Found at i:37391 original size:22 final size:21 Alignment explanation
Indices: 37317--37473 Score: 97 Period size: 22 Copynumber: 7.1 Consensus size: 21 37307 AAATTGAGAC * 37317 TTTT-ATAACCTTCTTATGAAA 1 TTTTGATAACC-TCCTATGAAA * * 37338 TTTTGAAAACCTCCCCATGAAA 1 TTTTGATAACCT-CCTATGAAA * 37360 TATT-AGTAACCTCCTTATGAAA 1 TTTTGA-TAACCTCC-TATGAAA * * 37382 TTTTGTTAACCACACTATGAAA 1 TTTTGATAACCTC-CTATGAAA * 37404 TTCTT-ATAACCTCGCTATGACA 1 TT-TTGATAACCTC-CTATGAAA * * 37426 TTTTGATAATCTTTCTAT-AAA 1 TTTTGATAA-CCTCCTATGAAA * 37447 GTTTGTGATAACCACACTATGAAA 1 -TTT-TGATAACCTC-CTATGAAA 37471 TTT 1 TTT 37474 CAATCAGTAT Statistics Matches: 104, Mismatches: 19, Indels: 24 0.71 0.13 0.16 Matches are distributed among these distances: 21 12 0.12 22 71 0.68 23 18 0.17 24 3 0.03 ACGTcount: A:0.34, C:0.18, G:0.09, T:0.39 Consensus pattern (21 bp): TTTTGATAACCTCCTATGAAA Found at i:37402 original size:44 final size:44 Alignment explanation
Indices: 37319--37431 Score: 122 Period size: 44 Copynumber: 2.6 Consensus size: 44 37309 ATTGAGACTT * * * 37319 TTATAACCTTCTTATGAAATTTTGAAAACCTCCCCATGAAA-TA 1 TTATAACCTCCTTATGAAATTTTGAAAACCACACCATGAAATTA ** * * 37362 TTAGTAACCTCCTTATGAAATTTTGTTAACCACACTATGAAATTC 1 TTA-TAACCTCCTTATGAAATTTTGAAAACCACACCATGAAATTA * 37407 TTATAACCTCGC-TATGACATTTTGA 1 TTATAACCTC-CTTATGAAATTTTGA 37432 TAATCTTTCT Statistics Matches: 58, Mismatches: 9, Indels: 5 0.81 0.12 0.07 Matches are distributed among these distances: 43 3 0.05 44 50 0.86 45 5 0.09 ACGTcount: A:0.34, C:0.20, G:0.09, T:0.37 Consensus pattern (44 bp): TTATAACCTCCTTATGAAATTTTGAAAACCACACCATGAAATTA Found at i:41535 original size:16 final size:16 Alignment explanation
Indices: 41516--41559 Score: 61 Period size: 16 Copynumber: 2.8 Consensus size: 16 41506 ATCCGCCCGA * 41516 ACCCGAACCCGAAATT 1 ACCCGAACCCGAAAAT * * 41532 ACCCGAGCTCGAAAAT 1 ACCCGAACCCGAAAAT 41548 ACCCGAACCCGA 1 ACCCGAACCCGA 41560 GGCTGCCTGA Statistics Matches: 23, Mismatches: 5, Indels: 0 0.82 0.18 0.00 Matches are distributed among these distances: 16 23 1.00 ACGTcount: A:0.36, C:0.39, G:0.16, T:0.09 Consensus pattern (16 bp): ACCCGAACCCGAAAAT Done.