Tandem Repeats Finder Program written by: Gary Benson Program in Bioinformatics Boston University Version 4.09 Sequence: AWWV01006767.1 Corchorus capsularis cultivar CVL-1 contig06788, 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: 64976 ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31 Found at i:579 original size:19 final size:18 Alignment explanation
Indices: 555--590 Score: 54 Period size: 19 Copynumber: 1.9 Consensus size: 18 545 TGAAGATTTC 555 TTGAAGATAATTTGAAGAT 1 TTGAAGATAA-TTGAAGAT * 574 TTGAAGATCATTGAAGA 1 TTGAAGATAATTGAAGA 591 ATTATTTCAA Statistics Matches: 16, Mismatches: 1, Indels: 1 0.89 0.06 0.06 Matches are distributed among these distances: 18 7 0.44 19 9 0.56 ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33 Consensus pattern (18 bp): TTGAAGATAATTGAAGAT Found at i:3327 original size:19 final size:18 Alignment explanation
Indices: 3295--3330 Score: 54 Period size: 19 Copynumber: 1.9 Consensus size: 18 3285 TTGAATTAAT * 3295 TCTTCAATTGTCTTCAAA 1 TCTTCAATTATCTTCAAA 3313 TCTTCAAATTATCTTCAA 1 TCTTC-AATTATCTTCAA 3331 GAAATCTTCA Statistics Matches: 16, Mismatches: 1, Indels: 1 0.89 0.06 0.06 Matches are distributed among these distances: 18 5 0.31 19 11 0.69 ACGTcount: A:0.31, C:0.22, G:0.03, T:0.44 Consensus pattern (18 bp): TCTTCAATTATCTTCAAA Found at i:6215 original size:24 final size:24 Alignment explanation
Indices: 6196--6250 Score: 92 Period size: 24 Copynumber: 2.3 Consensus size: 24 6186 CCATTCAACG * 6196 GCAGAAGCCAACCACTATTCTACC 1 GCAGAAGCCAACCACAATTCTACC * 6220 GCAGAAGCCAACTACAATTCTACC 1 GCAGAAGCCAACCACAATTCTACC 6244 GCAGAAG 1 GCAGAAG 6251 TCAGTTTAAT Statistics Matches: 29, Mismatches: 2, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 24 29 1.00 ACGTcount: A:0.36, C:0.33, G:0.16, T:0.15 Consensus pattern (24 bp): GCAGAAGCCAACCACAATTCTACC Found at i:11799 original size:27 final size:26 Alignment explanation
Indices: 11743--11831 Score: 128 Period size: 27 Copynumber: 3.4 Consensus size: 26 11733 GGTGGCGTTG 11743 GCATGAGTCCCATA-TG-GGAGCTTCA 1 GCATGAGTCCCA-ACTGCGGAGCTTCA 11768 GCATGAGTCCCAACTGCGGAAGCTTCA 1 GCATGAGTCCCAACTGCGG-AGCTTCA * 11795 GCATGAGTCCCAACTGCGGGAGCTTCG 1 GCATGAGTCCCAACTGC-GGAGCTTCA 11822 GCATGAGTCC 1 GCATGAGTCC 11832 TTCAGCATAA Statistics Matches: 59, Mismatches: 1, Indels: 6 0.89 0.02 0.09 Matches are distributed among these distances: 24 1 0.02 25 14 0.24 26 2 0.03 27 40 0.68 28 2 0.03 ACGTcount: A:0.22, C:0.28, G:0.29, T:0.20 Consensus pattern (26 bp): GCATGAGTCCCAACTGCGGAGCTTCA Found at i:11847 original size:41 final size:41 Alignment explanation
Indices: 11790--11872 Score: 123 Period size: 41 Copynumber: 2.0 Consensus size: 41 11780 ACTGCGGAAG * * 11790 CTTCAGCATGAGTCCCAACTGCGG-GAGCTTCGGCATGAGTC 1 CTTCAGCATAAGTCCCAACTACGGAG-GCTTCGGCATGAGTC * 11831 CTTCAGCATAAGTCCCAACTACGGAGGCTTTGGCATGAGTC 1 CTTCAGCATAAGTCCCAACTACGGAGGCTTCGGCATGAGTC 11872 C 1 C 11873 CAACCGCGGG Statistics Matches: 38, Mismatches: 3, Indels: 2 0.88 0.07 0.05 Matches are distributed among these distances: 41 37 0.97 42 1 0.03 ACGTcount: A:0.22, C:0.29, G:0.27, T:0.23 Consensus pattern (41 bp): CTTCAGCATAAGTCCCAACTACGGAGGCTTCGGCATGAGTC Found at i:11874 original size:27 final size:27 Alignment explanation
Indices: 11836--11935 Score: 94 Period size: 27 Copynumber: 3.7 Consensus size: 27 11826 GAGTCCTTCA * * 11836 GCATAAGTCCCAACTACGGAGGCTTTG 1 GCATGAGTCCCAACTGCGGAGGCTTTG * * ** 11863 GCATGAGTCCCAACCGCGG-GAGCCTCA 1 GCATGAGTCCCAACTGCGGAG-GCTTTG * * 11890 ACATGAGTGCCAACTGCGGAGGCTTTG 1 GCATGAGTCCCAACTGCGGAGGCTTTG * * 11917 GCGTGAGTCTCAACTGCGG 1 GCATGAGTCCCAACTGCGG 11936 GAATTTTAGT Statistics Matches: 55, Mismatches: 16, Indels: 4 0.73 0.21 0.05 Matches are distributed among these distances: 26 1 0.02 27 53 0.96 28 1 0.02 ACGTcount: A:0.22, C:0.28, G:0.31, T:0.19 Consensus pattern (27 bp): GCATGAGTCCCAACTGCGGAGGCTTTG Found at i:11895 original size:68 final size:68 Alignment explanation
Indices: 11763--11897 Score: 189 Period size: 68 Copynumber: 2.0 Consensus size: 68 11753 CATATGGGAG * * * * ** 11763 CTTCAGCATGAGTCCCAACTGCGGAAGCTTCAGCATGAGTCCCAACTGCGGGAGCTTCGGCATGA 1 CTTCAGCATAAGTCCCAACTACGGAAGCTTCAGCATGAGTCCCAACCGCGGGAGCCTCAACATGA 11828 GTC 66 GTC * ** 11831 CTTCAGCATAAGTCCCAACTACGGAGGCTTTGGCATGAGTCCCAACCGCGGGAGCCTCAACATGA 1 CTTCAGCATAAGTCCCAACTACGGAAGCTTCAGCATGAGTCCCAACCGCGGGAGCCTCAACATGA 11896 GT 66 GT 11898 GCCAACTGCG Statistics Matches: 58, Mismatches: 9, Indels: 0 0.87 0.13 0.00 Matches are distributed among these distances: 68 58 1.00 ACGTcount: A:0.24, C:0.30, G:0.27, T:0.20 Consensus pattern (68 bp): CTTCAGCATAAGTCCCAACTACGGAAGCTTCAGCATGAGTCCCAACCGCGGGAGCCTCAACATGA GTC Found at i:12741 original size:24 final size:24 Alignment explanation
Indices: 12696--12741 Score: 65 Period size: 24 Copynumber: 1.9 Consensus size: 24 12686 ATTCAACGGC * 12696 AGAAGCCAACCACTATTATACCGT 1 AGAAGCCAACCACAATTATACCGT * * 12720 AGAAGCCAACTACAATTCTACC 1 AGAAGCCAACCACAATTATACC 12742 CCAGAAGTCA Statistics Matches: 19, Mismatches: 3, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 24 19 1.00 ACGTcount: A:0.39, C:0.30, G:0.11, T:0.20 Consensus pattern (24 bp): AGAAGCCAACCACAATTATACCGT Found at i:12747 original size:24 final size:24 Alignment explanation
Indices: 12695--12748 Score: 63 Period size: 24 Copynumber: 2.2 Consensus size: 24 12685 CATTCAACGG * * 12695 CAGAAGCCAACCACTATTATACCG 1 CAGAAGCCAACCACAATTATACCC * * * 12719 TAGAAGCCAACTACAATTCTACCC 1 CAGAAGCCAACCACAATTATACCC 12743 CAGAAG 1 CAGAAG 12749 TCAGTTTAAT Statistics Matches: 24, Mismatches: 6, Indels: 0 0.80 0.20 0.00 Matches are distributed among these distances: 24 24 1.00 ACGTcount: A:0.39, C:0.31, G:0.13, T:0.17 Consensus pattern (24 bp): CAGAAGCCAACCACAATTATACCC Found at i:22493 original size:31 final size:30 Alignment explanation
Indices: 22457--22515 Score: 75 Period size: 30 Copynumber: 1.9 Consensus size: 30 22447 ATATAAAATA 22457 AAAAACAGAAAAAG-AAAATATTTTTTTTAGG 1 AAAAAC-GAAAAAGCAAAA-ATTTTTTTTAGG * * 22488 AAAAACGGAAAAGCAAAACTTTTTTTTA 1 AAAAACGAAAAAGCAAAAATTTTTTTTA 22516 AAAAAAAAAT Statistics Matches: 25, Mismatches: 2, Indels: 3 0.83 0.07 0.10 Matches are distributed among these distances: 30 15 0.60 31 10 0.40 ACGTcount: A:0.53, C:0.07, G:0.12, T:0.29 Consensus pattern (30 bp): AAAAACGAAAAAGCAAAAATTTTTTTTAGG Found at i:24237 original size:19 final size:18 Alignment explanation
Indices: 24205--24241 Score: 56 Period size: 19 Copynumber: 2.0 Consensus size: 18 24195 TTGAATTAAT * 24205 TCTTCAATTGTCTTCAAA 1 TCTTCAATTATCTTCAAA 24223 TCTTCAAATTATCTTCAAA 1 TCTTC-AATTATCTTCAAA 24242 ACACGAACTT Statistics Matches: 17, Mismatches: 1, Indels: 1 0.89 0.05 0.05 Matches are distributed among these distances: 18 5 0.29 19 12 0.71 ACGTcount: A:0.32, C:0.22, G:0.03, T:0.43 Consensus pattern (18 bp): TCTTCAATTATCTTCAAA Found at i:32255 original size:21 final size:21 Alignment explanation
Indices: 32189--32255 Score: 66 Period size: 21 Copynumber: 3.2 Consensus size: 21 32179 ATGTGCATAA * 32189 CTTGGAATCGGTTGGAATATT 1 CTTGGAATCGATTGGAATATT * * * 32210 CCTAGAATCGATTGTGAGA-A-G 1 CTTGGAATCGATTG-GA-ATATT 32231 CTTGGAATCGATTGGAATATT 1 CTTGGAATCGATTGGAATATT 32252 CTTG 1 CTTG 32256 CTCAAAACAT Statistics Matches: 35, Mismatches: 7, Indels: 8 0.70 0.14 0.16 Matches are distributed among these distances: 19 1 0.03 20 3 0.09 21 27 0.77 22 3 0.09 23 1 0.03 ACGTcount: A:0.27, C:0.12, G:0.27, T:0.34 Consensus pattern (21 bp): CTTGGAATCGATTGGAATATT Found at i:35805 original size:32 final size:32 Alignment explanation
Indices: 35769--35870 Score: 84 Period size: 32 Copynumber: 3.2 Consensus size: 32 35759 TCGGGTTTCA * 35769 GGTCATACAGGTCTCGGATCACTCT-GGTTACT 1 GGTCATACAGGTCTCGGATCA-TCTGGGTTACG * * * * 35801 GGTCATTCGGGTTTCGGGTCATCTGGGTTACG 1 GGTCATACAGGTCTCGGATCATCTGGGTTACG * * * 35833 GGTCATTC-GAGTCTC-GAGTCTTCTGGGTTAAG 1 GGTCATACAG-GTCTCGGA-TCATCTGGGTTACG 35865 GGTCAT 1 GGTCAT 35871 TTGGGTAGCG Statistics Matches: 58, Mismatches: 9, Indels: 6 0.79 0.12 0.08 Matches are distributed among these distances: 31 5 0.09 32 53 0.91 ACGTcount: A:0.15, C:0.21, G:0.31, T:0.33 Consensus pattern (32 bp): GGTCATACAGGTCTCGGATCATCTGGGTTACG Found at i:35820 original size:16 final size:16 Alignment explanation
Indices: 35750--35841 Score: 69 Period size: 16 Copynumber: 5.8 Consensus size: 16 35740 GGTTAATTTC * 35750 TCGGGTTATTCGGGTT 1 TCGGGTCATTCGGGTT * * * * 35766 TCAGGTCATACAGGTC 1 TCGGGTCATTCGGGTT * * * 35782 TCGGATCACTCTGGTT 1 TCGGGTCATTCGGGTT * * 35798 ACTGGTCATTCGGGTT 1 TCGGGTCATTCGGGTT 35814 TCGGGTCA-TCTGGGTT 1 TCGGGTCATTC-GGGTT * 35830 ACGGGTCATTCG 1 TCGGGTCATTCG 35842 AGTCTCGAGT Statistics Matches: 55, Mismatches: 19, Indels: 4 0.71 0.24 0.05 Matches are distributed among these distances: 15 2 0.04 16 51 0.93 17 2 0.04 ACGTcount: A:0.13, C:0.21, G:0.32, T:0.35 Consensus pattern (16 bp): TCGGGTCATTCGGGTT Found at i:35871 original size:32 final size:32 Alignment explanation
Indices: 35801--35871 Score: 97 Period size: 32 Copynumber: 2.2 Consensus size: 32 35791 TCTGGTTACT * * * * 35801 GGTCATTCGGGTTTCGGGTCATCTGGGTTACG 1 GGTCATTCGAGTCTCGAGTCATCTGGGTTAAG * 35833 GGTCATTCGAGTCTCGAGTCTTCTGGGTTAAG 1 GGTCATTCGAGTCTCGAGTCATCTGGGTTAAG 35865 GGTCATT 1 GGTCATT 35872 TGGGTAGCGA Statistics Matches: 34, Mismatches: 5, Indels: 0 0.87 0.13 0.00 Matches are distributed among these distances: 32 34 1.00 ACGTcount: A:0.13, C:0.18, G:0.34, T:0.35 Consensus pattern (32 bp): GGTCATTCGAGTCTCGAGTCATCTGGGTTAAG Found at i:35883 original size:32 final size:32 Alignment explanation
Indices: 35822--35884 Score: 81 Period size: 32 Copynumber: 2.0 Consensus size: 32 35812 TTTCGGGTCA * ** 35822 TCTGGGTTACGGGTCATTCGAGTCTCGAGTCT 1 TCTGGGTTAAGGGTCATTCGAGTAGCGAGTCT * * 35854 TCTGGGTTAAGGGTCATTTGGGTAGCGAGTC 1 TCTGGGTTAAGGGTCATTCGAGTAGCGAGTC 35885 AGGCGGGTTT Statistics Matches: 26, Mismatches: 5, Indels: 0 0.84 0.16 0.00 Matches are distributed among these distances: 32 26 1.00 ACGTcount: A:0.14, C:0.17, G:0.35, T:0.33 Consensus pattern (32 bp): TCTGGGTTAAGGGTCATTCGAGTAGCGAGTCT Found at i:36338 original size:18 final size:18 Alignment explanation
Indices: 36310--36371 Score: 69 Period size: 18 Copynumber: 3.6 Consensus size: 18 36300 GCTGACGTGG * 36310 AATTTAATATAT-TTAA- 1 AATTTAAAATATATTAAT 36326 AATTTAAAATATA-TAATT 1 AATTTAAAATATATTAA-T 36344 AATTTAAAATATA-TAATT 1 AATTTAAAATATATTAA-T 36362 AATTTAAAAT 1 AATTTAAAAT 36372 CTAAAAACTA Statistics Matches: 42, Mismatches: 1, Indels: 4 0.89 0.02 0.09 Matches are distributed among these distances: 16 14 0.33 18 28 0.67 ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45 Consensus pattern (18 bp): AATTTAAAATATATTAAT Found at i:36474 original size:3 final size:3 Alignment explanation
Indices: 36466--36497 Score: 55 Period size: 3 Copynumber: 10.3 Consensus size: 3 36456 GTCTTTTATT 36466 TTC TTC TTC TTC TTCC TTC TTC TTC TTC TTC T 1 TTC TTC TTC TTC TT-C TTC TTC TTC TTC TTC T 36498 CTACCCAAAA Statistics Matches: 28, Mismatches: 0, Indels: 2 0.93 0.00 0.07 Matches are distributed among these distances: 3 25 0.89 4 3 0.11 ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66 Consensus pattern (3 bp): TTC Found at i:39426 original size:3 final size:3 Alignment explanation
Indices: 39411--39441 Score: 53 Period size: 3 Copynumber: 10.0 Consensus size: 3 39401 TATATATATA 39411 TAT TAT ATAT TAT TAT TAT TAT TAT TAT TAT 1 TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT 39442 ATACAAAAAG Statistics Matches: 27, Mismatches: 0, Indels: 2 0.93 0.00 0.07 Matches are distributed among these distances: 3 24 0.89 4 3 0.11 ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65 Consensus pattern (3 bp): TAT Found at i:39567 original size:15 final size:16 Alignment explanation
Indices: 39533--39576 Score: 63 Period size: 15 Copynumber: 2.8 Consensus size: 16 39523 TTCGAGCGGG 39533 TTCGGGTATTTTCAGA 1 TTCGGGTATTTTCAGA * 39549 TTCGGGTATTTT-GGA 1 TTCGGGTATTTTCAGA * 39564 TTCGCGTATTTTC 1 TTCGGGTATTTTC 39577 GGGTTTGACC Statistics Matches: 25, Mismatches: 2, Indels: 2 0.86 0.07 0.07 Matches are distributed among these distances: 15 13 0.52 16 12 0.48 ACGTcount: A:0.14, C:0.14, G:0.25, T:0.48 Consensus pattern (16 bp): TTCGGGTATTTTCAGA Found at i:40143 original size:31 final size:31 Alignment explanation
Indices: 40108--40179 Score: 74 Period size: 31 Copynumber: 2.3 Consensus size: 31 40098 TAAATTGTAG * 40108 CAAATTAAAACAAAT-TAAGTATTAGATTAAA 1 CAAATTAAAA-AAATGCAAGTATTAGATTAAA * ** * * 40139 CAAATCATCAAAATGCAAGTCTTAGGTTAAA 1 CAAATTAAAAAAATGCAAGTATTAGATTAAA 40170 CAAATTAAAA 1 CAAATTAAAA 40180 GCTAATGTAC Statistics Matches: 31, Mismatches: 9, Indels: 2 0.74 0.21 0.05 Matches are distributed among these distances: 30 4 0.13 31 27 0.87 ACGTcount: A:0.54, C:0.11, G:0.08, T:0.26 Consensus pattern (31 bp): CAAATTAAAAAAATGCAAGTATTAGATTAAA Found at i:40409 original size:16 final size:16 Alignment explanation
Indices: 40364--40409 Score: 58 Period size: 16 Copynumber: 2.9 Consensus size: 16 40354 CAGGTTCGGT * 40364 TTCGGGTTCGGGTGGA 1 TTCGGGTTCGGGTTGA * 40380 TTCGGGCTCGGGTTG- 1 TTCGGGTTCGGGTTGA 40395 TCTCGGGTTCGGGTT 1 T-TCGGGTTCGGGTT 40410 CGGACGGATT Statistics Matches: 26, Mismatches: 3, Indels: 2 0.84 0.10 0.06 Matches are distributed among these distances: 15 1 0.04 16 25 0.96 ACGTcount: A:0.02, C:0.17, G:0.46, T:0.35 Consensus pattern (16 bp): TTCGGGTTCGGGTTGA Found at i:40419 original size:38 final size:38 Alignment explanation
Indices: 40342--40419 Score: 95 Period size: 38 Copynumber: 2.0 Consensus size: 38 40332 TATTTTGATC * ** 40342 TCGGGCTCGGGTCAGGTTCGGTTTCGGGTTCGGGTGGAT 1 TCGGGCTCGGGT-AGGTTCGGGTTCGGGTTCGGACGGAT * 40381 TCGGGCTCGGGT-TGTCTCGGGTTCGGGTTCGGACGGAT 1 TCGGGCTCGGGTAGGT-TCGGGTTCGGGTTCGGACGGAT 40419 T 1 T 40420 TAGGATGTTG Statistics Matches: 34, Mismatches: 4, Indels: 3 0.83 0.10 0.07 Matches are distributed among these distances: 37 2 0.06 38 20 0.59 39 12 0.35 ACGTcount: A:0.05, C:0.19, G:0.45, T:0.31 Consensus pattern (38 bp): TCGGGCTCGGGTAGGTTCGGGTTCGGGTTCGGACGGAT Found at i:42057 original size:16 final size:16 Alignment explanation
Indices: 42022--42063 Score: 50 Period size: 16 Copynumber: 2.7 Consensus size: 16 42012 GGGTAATTCG * * * 42022 GATTTCGGGTCATTTG 1 GATTTCGGGTTATCTA 42038 GATTTCGGGTTATCTA 1 GATTTCGGGTTATCTA 42054 GA-TTCGGGTT 1 GATTTCGGGTT 42064 TCGGGTCAAT Statistics Matches: 23, Mismatches: 3, Indels: 1 0.85 0.11 0.04 Matches are distributed among these distances: 15 8 0.35 16 15 0.65 ACGTcount: A:0.14, C:0.12, G:0.31, T:0.43 Consensus pattern (16 bp): GATTTCGGGTTATCTA Found at i:42076 original size:16 final size:17 Alignment explanation
Indices: 42057--42097 Score: 59 Period size: 16 Copynumber: 2.5 Consensus size: 17 42047 TTATCTAGAT 42057 TCGGGTTTCGGGTCA-A 1 TCGGGTTTCGGGTCATA * 42073 TCGGGTCTCGGGTCATA 1 TCGGGTTTCGGGTCATA 42090 T-GGGTTTC 1 TCGGGTTTC 42098 TAGTCATTTG Statistics Matches: 22, Mismatches: 2, Indels: 2 0.85 0.08 0.08 Matches are distributed among these distances: 16 20 0.91 17 2 0.09 ACGTcount: A:0.10, C:0.20, G:0.37, T:0.34 Consensus pattern (17 bp): TCGGGTTTCGGGTCATA Found at i:42950 original size:16 final size:16 Alignment explanation
Indices: 42929--42973 Score: 63 Period size: 16 Copynumber: 2.8 Consensus size: 16 42919 TATAATATTC 42929 TCGGGTCATTCGGATT 1 TCGGGTCATTCGGATT * * 42945 TCGGGTCATACGGGTT 1 TCGGGTCATTCGGATT * 42961 TCGGGTCACTCGG 1 TCGGGTCATTCGG 42974 GTTACAAGTT Statistics Matches: 25, Mismatches: 4, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 16 25 1.00 ACGTcount: A:0.11, C:0.22, G:0.36, T:0.31 Consensus pattern (16 bp): TCGGGTCATTCGGATT Found at i:43061 original size:16 final size:16 Alignment explanation
Indices: 43013--43063 Score: 61 Period size: 16 Copynumber: 3.2 Consensus size: 16 43003 TGGGATACGA * 43013 GTCATTCGGGTCTCAA 1 GTCATTCGGGTCTCAG 43029 GTCA-TCTGGGT-TGCAG 1 GTCATTC-GGGTCT-CAG 43045 GTCATTCGGGTCTCAG 1 GTCATTCGGGTCTCAG 43061 GTC 1 GTC 43064 GGGCAGGTTC Statistics Matches: 30, Mismatches: 1, Indels: 8 0.77 0.03 0.21 Matches are distributed among these distances: 15 3 0.10 16 24 0.80 17 3 0.10 ACGTcount: A:0.14, C:0.24, G:0.31, T:0.31 Consensus pattern (16 bp): GTCATTCGGGTCTCAG Found at i:44875 original size:87 final size:87 Alignment explanation
Indices: 44779--44999 Score: 356 Period size: 86 Copynumber: 2.6 Consensus size: 87 44769 AATATTTTCC * 44779 AAATCTCCCACAATCTGGCAAGATTTAGAGAAATATTCTCATTACTATTCAATCTTTATTATTTA 1 AAATCTCCCACAATTTGGCAAGATTTAGAGAAATATTCTCATTACTATTCAATCTTTATTATTTA 44844 TTTATTTCTTAAAACATCTCCT 66 TTTATTTCTTAAAACATCTCCT * * * 44866 AAATCTCCCACAATTTGGCAAGATTTAGA-AAATATGCTTATTACTATGCAATCTTTATTATTTA 1 AAATCTCCCACAATTTGGCAAGATTTAGAGAAATATTCTCATTACTATTCAATCTTTATTATTTA * * 44930 TTTATTTCTTAAAATATCTCTT 66 TTTATTTCTTAAAACATCTCCT * * 44952 AAATCTCCCACAATTTGGCAAGATTTAGAG-AATACTCTCATTATTATT 1 AAATCTCCCACAATTTGGCAAGATTTAGAGAAATATTCTCATTACTATT 45000 TTAATGATTT Statistics Matches: 122, Mismatches: 11, Indels: 3 0.90 0.08 0.02 Matches are distributed among these distances: 86 94 0.77 87 28 0.23 ACGTcount: A:0.34, C:0.18, G:0.07, T:0.41 Consensus pattern (87 bp): AAATCTCCCACAATTTGGCAAGATTTAGAGAAATATTCTCATTACTATTCAATCTTTATTATTTA TTTATTTCTTAAAACATCTCCT Found at i:46390 original size:35 final size:35 Alignment explanation
Indices: 46335--46450 Score: 119 Period size: 35 Copynumber: 3.3 Consensus size: 35 46325 ACTCCCCTGG * * * * 46335 ATCAATTCTGATCATCGGAAATTTCTTG-AAATGAC 1 ATCAACTCTGATCGTTGGAAACTTC-TGAAAATGAC * * * 46370 ATCACCTCTGATTGTTGGAAACTACTGAAAATG-C 1 ATCAACTCTGATCGTTGGAAACTTCTGAAAATGAC * * 46404 GATCAATTCTGATCGTTGGAAACTTCTGAAAATGAG 1 -ATCAACTCTGATCGTTGGAAACTTCTGAAAATGAC 46440 ATCAACTCTGA 1 ATCAACTCTGA 46451 CCTCTGAACC Statistics Matches: 65, Mismatches: 13, Indels: 6 0.77 0.15 0.07 Matches are distributed among these distances: 34 3 0.05 35 62 0.95 ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31 Consensus pattern (35 bp): ATCAACTCTGATCGTTGGAAACTTCTGAAAATGAC Found at i:46456 original size:25 final size:25 Alignment explanation
Indices: 46428--46483 Score: 94 Period size: 25 Copynumber: 2.2 Consensus size: 25 46418 GTTGGAAACT 46428 TCTGAAAATGAGATCAACTCTGACC 1 TCTGAAAATGAGATCAACTCTGACC ** 46453 TCTGAACCTGAGATCAACTCTGACC 1 TCTGAAAATGAGATCAACTCTGACC 46478 TCTGAA 1 TCTGAA 46484 CTTCTTGGAA Statistics Matches: 29, Mismatches: 2, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 25 29 1.00 ACGTcount: A:0.32, C:0.27, G:0.16, T:0.25 Consensus pattern (25 bp): TCTGAAAATGAGATCAACTCTGACC Found at i:46484 original size:25 final size:25 Alignment explanation
Indices: 46436--46484 Score: 98 Period size: 25 Copynumber: 2.0 Consensus size: 25 46426 CTTCTGAAAA 46436 TGAGATCAACTCTGACCTCTGAACC 1 TGAGATCAACTCTGACCTCTGAACC 46461 TGAGATCAACTCTGACCTCTGAAC 1 TGAGATCAACTCTGACCTCTGAAC 46485 TTCTTGGAAT Statistics Matches: 24, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 25 24 1.00 ACGTcount: A:0.29, C:0.31, G:0.16, T:0.24 Consensus pattern (25 bp): TGAGATCAACTCTGACCTCTGAACC Found at i:46562 original size:35 final size:35 Alignment explanation
Indices: 46461--46872 Score: 657 Period size: 35 Copynumber: 11.8 Consensus size: 35 46451 CCTCTGAACC * 46461 TGAGATCAACTCTGACCTCTG--AACTTCTTGGAA 1 TGAGATCAACTCTGACCTCTGAAAACTTCTTGAAA 46494 TGAGATCAACTCTGACCTCTGAAAAACTTCTTGAAA 1 TGAGATCAACTCTGACCTCTG-AAAACTTCTTGAAA 46530 TGAGATCAACTCTGACCTCTGAAAACTTCTTGAAA 1 TGAGATCAACTCTGACCTCTGAAAACTTCTTGAAA * * * 46565 TGTGATCAACTCTGACCTCTAAAAACTACTTGAAA 1 TGAGATCAACTCTGACCTCTGAAAACTTCTTGAAA * * * 46600 TGAGATAAACTCTGACCTCTGGAAACTACTTGAAA 1 TGAGATCAACTCTGACCTCTGAAAACTTCTTGAAA * 46635 TGAGATCAACTCTGACCTCTGAAAACTACTTGAAA 1 TGAGATCAACTCTGACCTCTGAAAACTTCTTGAAA 46670 TGAGATCAACTCTGACCTCTGAAAACTTCTTGAAA 1 TGAGATCAACTCTGACCTCTGAAAACTTCTTGAAA * 46705 TGAGATCAACTCTGACCTCTGAAAACTTCTTGGAA 1 TGAGATCAACTCTGACCTCTGAAAACTTCTTGAAA * 46740 TGAGATCAACTCTGACCTCTGAAAACTTCTTGGAA 1 TGAGATCAACTCTGACCTCTGAAAACTTCTTGAAA ** 46775 TGAGATCAACTCTGACCTCTGAAAACTTCTTGGGA 1 TGAGATCAACTCTGACCTCTGAAAACTTCTTGAAA * ** 46810 TGAGATCAACTCTGACCTCTGACAACTTCTTGGGA 1 TGAGATCAACTCTGACCTCTGAAAACTTCTTGAAA * 46845 TGAGATCAACTCTGACCTCTGGAAACTT 1 TGAGATCAACTCTGACCTCTGAAAACTT 46873 TTATGCAAGA Statistics Matches: 360, Mismatches: 16, Indels: 4 0.95 0.04 0.01 Matches are distributed among these distances: 33 21 0.06 35 307 0.85 36 32 0.09 ACGTcount: A:0.33, C:0.23, G:0.16, T:0.28 Consensus pattern (35 bp): TGAGATCAACTCTGACCTCTGAAAACTTCTTGAAA Found at i:46954 original size:35 final size:35 Alignment explanation
Indices: 46879--47133 Score: 309 Period size: 35 Copynumber: 7.3 Consensus size: 35 46869 ACTTTTATGC * 46879 AAGACCGCCCTGGGTCAACTG-AATAAACTGGAGA 1 AAGACCGCCCTGGGTCAACTGAAATAAACTGAAGA * * 46913 ATGACCGCCCTGGGTCAACTGAAATAAGCTGAAGA 1 AAGACCGCCCTGGGTCAACTGAAATAAACTGAAGA * * * 46948 AAGACCGCCTTGGGCCAACTTAAATAAACTGAAGA 1 AAGACCGCCCTGGGTCAACTGAAATAAACTGAAGA * * * * * 46983 ATGATCGCCCTGGATCGAA-TCAAATATACTGAAGA 1 AAGACCGCCCTGGGTC-AACTGAAATAAACTGAAGA * * * 47018 AAGACCACCCTGGGTTAACTGAAATAAACTTAAGA 1 AAGACCGCCCTGGGTCAACTGAAATAAACTGAAGA * * 47053 ATGACCGCTCTGGGTCAACTG-AATAAACTGAAGA 1 AAGACCGCCCTGGGTCAACTGAAATAAACTGAAGA * * * 47087 AAGACCACCCTGGGTCAACTGAAATAAACTAAAGC 1 AAGACCGCCCTGGGTCAACTGAAATAAACTGAAGA 47122 AAGACCGCCCTG 1 AAGACCGCCCTG 47134 TACTTGACTC Statistics Matches: 183, Mismatches: 34, Indels: 7 0.82 0.15 0.03 Matches are distributed among these distances: 34 52 0.28 35 129 0.70 36 2 0.01 ACGTcount: A:0.38, C:0.23, G:0.22, T:0.18 Consensus pattern (35 bp): AAGACCGCCCTGGGTCAACTGAAATAAACTGAAGA Found at i:48142 original size:15 final size:14 Alignment explanation
Indices: 48112--48167 Score: 76 Period size: 15 Copynumber: 3.9 Consensus size: 14 48102 AGCCTTATCA * 48112 TTTCTTTTTTTTTT 1 TTTCTTTTTTTCTT 48126 TTTCTTTCTTTTCTT 1 TTTCTTT-TTTTCTT * 48141 TTTCTTTCTTTTTTT 1 TTTCTTT-TTTTCTT 48156 TTTCTTTTTTTC 1 TTTCTTTTTTTC 48168 GTCATGCATT Statistics Matches: 38, Mismatches: 3, Indels: 2 0.88 0.07 0.05 Matches are distributed among these distances: 14 11 0.29 15 27 0.71 ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86 Consensus pattern (14 bp): TTTCTTTTTTTCTT Found at i:48144 original size:29 final size:29 Alignment explanation
Indices: 48112--48167 Score: 96 Period size: 30 Copynumber: 1.9 Consensus size: 29 48102 AGCCTTATCA 48112 TTTCTTT-TTTTTTTTTTCTTTCTTTTCTT 1 TTTCTTTCTTTTTTTTTTCTTT-TTTTCTT 48141 TTTCTTTCTTTTTTTTTTCTTTTTTTC 1 TTTCTTTCTTTTTTTTTTCTTTTTTTC 48168 GTCATGCATT Statistics Matches: 26, Mismatches: 0, Indels: 2 0.93 0.00 0.07 Matches are distributed among these distances: 29 12 0.46 30 14 0.54 ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86 Consensus pattern (29 bp): TTTCTTTCTTTTTTTTTTCTTTTTTTCTT Found at i:48165 original size:11 final size:11 Alignment explanation
Indices: 48112--48166 Score: 69 Period size: 11 Copynumber: 5.0 Consensus size: 11 48102 AGCCTTATCA 48112 TTTCTTTTTTT 1 TTTCTTTTTTT 48123 TTT-TTTCTTTCT 1 TTTCTTT-TTT-T * 48135 TTTC-TTTTTC 1 TTTCTTTTTTT 48145 TTTCTTTTTTT 1 TTTCTTTTTTT 48156 TTTCTTTTTTT 1 TTTCTTTTTTT 48167 CGTCATGCAT Statistics Matches: 38, Mismatches: 2, Indels: 8 0.79 0.04 0.17 Matches are distributed among these distances: 10 7 0.18 11 25 0.66 12 6 0.16 ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87 Consensus pattern (11 bp): TTTCTTTTTTT Found at i:48527 original size:21 final size:22 Alignment explanation
Indices: 48481--48523 Score: 72 Period size: 21 Copynumber: 2.0 Consensus size: 22 48471 CTTTCCTCCA 48481 TCTTTTGCTTTTTCAACTTCTT 1 TCTTTTGCTTTTTCAACTTCTT 48503 TCTTTT-CTTTTTCAA-TTCTT 1 TCTTTTGCTTTTTCAACTTCTT 48523 T 1 T 48524 TCTTCATTTT Statistics Matches: 21, Mismatches: 0, Indels: 2 0.91 0.00 0.09 Matches are distributed among these distances: 20 6 0.29 21 9 0.43 22 6 0.29 ACGTcount: A:0.09, C:0.21, G:0.02, T:0.67 Consensus pattern (22 bp): TCTTTTGCTTTTTCAACTTCTT Found at i:48533 original size:20 final size:21 Alignment explanation
Indices: 48488--48534 Score: 62 Period size: 20 Copynumber: 2.3 Consensus size: 21 48478 CCATCTTTTG * 48488 CTTTTTCAACTTCTTTCTTTT 1 CTTTTTCAACTTCTTTCTCTT 48509 CTTTTTCAA-TTCTTT-TCTT 1 CTTTTTCAACTTCTTTCTCTT 48528 CATTTTT 1 C-TTTTT 48535 TTCTTCTCCT Statistics Matches: 24, Mismatches: 1, Indels: 3 0.86 0.04 0.11 Matches are distributed among these distances: 19 4 0.17 20 11 0.46 21 9 0.38 ACGTcount: A:0.11, C:0.21, G:0.00, T:0.68 Consensus pattern (21 bp): CTTTTTCAACTTCTTTCTCTT Found at i:48534 original size:21 final size:21 Alignment explanation
Indices: 48488--48537 Score: 57 Period size: 21 Copynumber: 2.3 Consensus size: 21 48478 CCATCTTTTG * 48488 CTTTTTCAACTTCTTTCTTTT 1 CTTTTTCAACTTCTTTCTTAT 48509 CTTTTTCAA-TTCTTTTCTTCAT 1 CTTTTTCAACTTC-TTTCTT-AT * 48531 TTTTTTC 1 CTTTTTC 48538 TTCTCCTTCT Statistics Matches: 25, Mismatches: 2, Indels: 3 0.83 0.07 0.10 Matches are distributed among these distances: 20 3 0.12 21 15 0.60 22 7 0.28 ACGTcount: A:0.10, C:0.22, G:0.00, T:0.68 Consensus pattern (21 bp): CTTTTTCAACTTCTTTCTTAT Found at i:49014 original size:9 final size:9 Alignment explanation
Indices: 49000--49036 Score: 56 Period size: 10 Copynumber: 3.9 Consensus size: 9 48990 TTCTTTCACA 49000 TTTTTTTCT 1 TTTTTTTCT 49009 TTTTTTTCCT 1 TTTTTTT-CT 49019 TTTTTTCTCT 1 TTTTTT-TCT 49029 TTTTTTTC 1 TTTTTTTC 49037 ACTTGATTTT Statistics Matches: 26, Mismatches: 0, Indels: 4 0.87 0.00 0.13 Matches are distributed among these distances: 9 9 0.35 10 16 0.62 11 1 0.04 ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84 Consensus pattern (9 bp): TTTTTTTCT Found at i:49049 original size:20 final size:19 Alignment explanation
Indices: 49003--49053 Score: 66 Period size: 20 Copynumber: 2.6 Consensus size: 19 48993 TTTCACATTT ** 49003 TTTTCTTTTTTTTCCTTTT 1 TTTTCTTTTTTTTCCTTGA 49022 TTTCTCTTTTTTTTCACTTGA 1 TTT-TCTTTTTTTTC-CTTGA 49043 TTTTCTTTTTT 1 TTTTCTTTTTT 49054 CTTTTGCTGA Statistics Matches: 28, Mismatches: 2, Indels: 3 0.85 0.06 0.09 Matches are distributed among these distances: 19 3 0.11 20 19 0.68 21 6 0.21 ACGTcount: A:0.04, C:0.16, G:0.02, T:0.78 Consensus pattern (19 bp): TTTTCTTTTTTTTCCTTGA Found at i:52756 original size:86 final size:86 Alignment explanation
Indices: 52617--52837 Score: 388 Period size: 86 Copynumber: 2.6 Consensus size: 86 52607 AATATTTTCC * 52617 AAATCTCCCACAATCTGGCAAGATTTAGAGAAATATTCTCATTACTATTCAATCTTTATTATTTA 1 AAATCTCCCACAATTTGGCAAGATTTAGAG-AATATTCTCATTACTATTCAATCTTTATTATTTA 52682 TTTATTTCTTAAAATATCTCCT 65 TTTATTTCTTAAAATATCTCCT * 52704 AAATCTCCCACAATTTGGCAAGATTTAGAGAATATTCTTATTACTATTCAATCTTTATTATTTAT 1 AAATCTCCCACAATTTGGCAAGATTTAGAGAATATTCTCATTACTATTCAATCTTTATTATTTAT * 52769 TTATTTCTTAAAATATCTCTT 66 TTATTTCTTAAAATATCTCCT * * 52790 AAATCTCCCACAATTTGGCAAGATTTAGAGAATACTCTCATTATTATT 1 AAATCTCCCACAATTTGGCAAGATTTAGAGAATATTCTCATTACTATT 52838 TTAATGATTT Statistics Matches: 128, Mismatches: 6, Indels: 1 0.95 0.04 0.01 Matches are distributed among these distances: 86 99 0.77 87 29 0.23 ACGTcount: A:0.33, C:0.17, G:0.07, T:0.43 Consensus pattern (86 bp): AAATCTCCCACAATTTGGCAAGATTTAGAGAATATTCTCATTACTATTCAATCTTTATTATTTAT TTATTTCTTAAAATATCTCCT Found at i:53024 original size:16 final size:17 Alignment explanation
Indices: 53005--53038 Score: 52 Period size: 16 Copynumber: 2.1 Consensus size: 17 52995 TATTTGGAAA 53005 TCTTTTAT-TTTGATTT 1 TCTTTTATATTTGATTT * 53021 TCTTTTATATTTTATTT 1 TCTTTTATATTTGATTT 53038 T 1 T 53039 AATCAATTTC Statistics Matches: 16, Mismatches: 1, Indels: 1 0.89 0.06 0.06 Matches are distributed among these distances: 16 8 0.50 17 8 0.50 ACGTcount: A:0.15, C:0.06, G:0.03, T:0.76 Consensus pattern (17 bp): TCTTTTATATTTGATTT Found at i:60309 original size:21 final size:21 Alignment explanation
Indices: 60256--60315 Score: 66 Period size: 21 Copynumber: 2.9 Consensus size: 21 60246 CTTGGAGCAA * 60256 GAATATTCCAATCGATTCTAT 1 GAATATTCCAATCGATTCTAG ** * * * 60277 GTCTACTACAATCGATTTTAG 1 GAATATTCCAATCGATTCTAG 60298 GAATATTCCAATCGATTC 1 GAATATTCCAATCGATTC 60316 CAAGTTATGC Statistics Matches: 28, Mismatches: 11, Indels: 0 0.72 0.28 0.00 Matches are distributed among these distances: 21 28 1.00 ACGTcount: A:0.32, C:0.20, G:0.12, T:0.37 Consensus pattern (21 bp): GAATATTCCAATCGATTCTAG Done.