Tandem Repeats Finder Program written by: Gary Benson Program in Bioinformatics Boston University Version 4.09 Sequence: AWUE01019949.1 Corchorus olitorius cultivar O-4 contig19982, 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: 94493 ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32 Found at i:4559 original size:52 final size:52 Alignment explanation
Indices: 4481--4586 Score: 203 Period size: 52 Copynumber: 2.0 Consensus size: 52 4471 AATCTGTAGA 4481 CAAACCTTCCATTGCTTCCATTGCTTCAATTGACTGGTTCTTTGCAGAAATT 1 CAAACCTTCCATTGCTTCCATTGCTTCAATTGACTGGTTCTTTGCAGAAATT * 4533 CAAACCTTCCATTGCTTCCATTGCTTCAATTGACTGGTTCTTTGTAGAAATT 1 CAAACCTTCCATTGCTTCCATTGCTTCAATTGACTGGTTCTTTGCAGAAATT 4585 CA 1 CA 4587 TTTGGGATAT Statistics Matches: 53, Mismatches: 1, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 52 53 1.00 ACGTcount: A:0.24, C:0.25, G:0.13, T:0.39 Consensus pattern (52 bp): CAAACCTTCCATTGCTTCCATTGCTTCAATTGACTGGTTCTTTGCAGAAATT Found at i:7820 original size:33 final size:33 Alignment explanation
Indices: 7758--7821 Score: 85 Period size: 33 Copynumber: 1.9 Consensus size: 33 7748 CTTTTGCCAA * 7758 TTGTATGACCGGATGCTGGACTTGGTTCGTAGG 1 TTGTATGACCGGATGCTGGACATGGTTCGTAGG * * 7791 TTGTATTACCTGATGCTGGA-ATGGTTTCGTA 1 TTGTATGACCGGATGCTGGACATGG-TTCGTA 7822 ATTTGGTAAT Statistics Matches: 27, Mismatches: 3, Indels: 2 0.84 0.09 0.06 Matches are distributed among these distances: 32 3 0.11 33 24 0.89 ACGTcount: A:0.17, C:0.14, G:0.31, T:0.38 Consensus pattern (33 bp): TTGTATGACCGGATGCTGGACATGGTTCGTAGG Found at i:18104 original size:123 final size:128 Alignment explanation
Indices: 17967--18222 Score: 414 Period size: 123 Copynumber: 2.0 Consensus size: 128 17957 CATTGTTTAA * 17967 ACTTTTATAATTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATATAATAT-CTT-TA-T 1 ACTTTTACAATTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATATAATATCCTTATACT 18029 A-ATTTTTACCATTTTACTATTTTAATT-AAAAAACTTATATATATTAGAATTTTTTAAATAT 66 ATATTTTTACCATTTTACTATTTTAATTAAAAAAACTTATATATATTAGAATTTTTTAAATAT * * 18090 ACTTTTACAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATACC 1 ACTTTTACAATTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATATAATATCCTTATA-C 18155 TATTTTATTTTTACCATTTTACTATTTTAATTAAAAAAACTTATATATATTAGAATTTTTTAAAT 65 TA---TATTTTTACCATTTTACTATTTTAATTAAAAAAACTTATATATATTAGAATTTTTTAAAT 18220 AT 127 AT 18222 A 1 A 18223 TTTCTTAAAT Statistics Matches: 121, Mismatches: 3, Indels: 9 0.91 0.02 0.07 Matches are distributed among these distances: 123 53 0.44 124 3 0.02 125 2 0.02 127 2 0.02 131 26 0.21 132 35 0.29 ACGTcount: A:0.39, C:0.11, G:0.01, T:0.50 Consensus pattern (128 bp): ACTTTTACAATTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATATAATATCCTTATACT ATATTTTTACCATTTTACTATTTTAATTAAAAAAACTTATATATATTAGAATTTTTTAAATAT Found at i:18244 original size:14 final size:13 Alignment explanation
Indices: 18208--18246 Score: 51 Period size: 14 Copynumber: 2.9 Consensus size: 13 18198 TATATATTAG 18208 AATTTTTTAAATA 1 AATTTTTTAAATA * * 18221 TATTTCTTAAATGA 1 AATTTTTTAAAT-A 18235 AATTTTTTAAAT 1 AATTTTTTAAAT 18247 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:24819 original size:2 final size:2 Alignment explanation
Indices: 24779--24810 Score: 64 Period size: 2 Copynumber: 16.0 Consensus size: 2 24769 TCAAGCCCAT 24779 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA 1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA 24811 CGGTATATAA Statistics Matches: 30, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 30 1.00 ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50 Consensus pattern (2 bp): TA Found at i:29303 original size:102 final size:102 Alignment explanation
Indices: 29150--29355 Score: 385 Period size: 102 Copynumber: 2.0 Consensus size: 102 29140 ATTGTTTGAG 29150 TTTAGAAATTTCTGCTTGTAAATATGTAGTTGCTGACTGATGAAGTGGTAGGTCTCTTCATTATG 1 TTTAGAAATTTCTGCTTGTAAATATGTAGTTGCTGACTGATGAAGTGGTAGGTCTCTTCATTATG * 29215 TAAATGTTTAGACAATTTGAGGTTTAGGGCAATGGAA 66 TAAATGTTCAGACAATTTGAGGTTTAGGGCAATGGAA * 29252 TTTAGAAATTTCTGCTTGTAAATATGTAGTTGCTGACTGATGAAGTGGTAGGTTTCTTCATTATG 1 TTTAGAAATTTCTGCTTGTAAATATGTAGTTGCTGACTGATGAAGTGGTAGGTCTCTTCATTATG * 29317 TAAATGTTCAGATAATTTGAGGTTTAGGGCAATGGAA 66 TAAATGTTCAGACAATTTGAGGTTTAGGGCAATGGAA 29354 TT 1 TT 29356 GAGGTTATTG Statistics Matches: 101, Mismatches: 3, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 102 101 1.00 ACGTcount: A:0.28, C:0.08, G:0.24, T:0.39 Consensus pattern (102 bp): TTTAGAAATTTCTGCTTGTAAATATGTAGTTGCTGACTGATGAAGTGGTAGGTCTCTTCATTATG TAAATGTTCAGACAATTTGAGGTTTAGGGCAATGGAA Found at i:35290 original size:21 final size:19 Alignment explanation
Indices: 35266--35314 Score: 53 Period size: 22 Copynumber: 2.4 Consensus size: 19 35256 GAGTAAAATT * 35266 AAAATTACCTTTTTATTACAA 1 AAAATTAACTTTTT-TTA-AA * 35287 AAAAGTAAACTTTTTTTAAA 1 AAAA-TTAACTTTTTTTAAA 35307 AAAATTAA 1 AAAATTAA 35315 AATTATTGAA Statistics Matches: 24, Mismatches: 3, Indels: 4 0.77 0.10 0.13 Matches are distributed among these distances: 19 3 0.12 20 6 0.25 21 7 0.29 22 8 0.33 ACGTcount: A:0.51, C:0.08, G:0.02, T:0.39 Consensus pattern (19 bp): AAAATTAACTTTTTTTAAA Found at i:35308 original size:20 final size:22 Alignment explanation
Indices: 35274--35315 Score: 61 Period size: 20 Copynumber: 2.0 Consensus size: 22 35264 TTAAAATTAC 35274 CTTTTTATTACAAAAAAGTAAA 1 CTTTTTATTACAAAAAAGTAAA * 35296 CTTTTT-TTA-AAAAAATTAAA 1 CTTTTTATTACAAAAAAGTAAA 35316 ATTATTGAAT Statistics Matches: 19, Mismatches: 1, Indels: 2 0.86 0.05 0.09 Matches are distributed among these distances: 20 10 0.53 21 3 0.16 22 6 0.32 ACGTcount: A:0.50, C:0.07, G:0.02, T:0.40 Consensus pattern (22 bp): CTTTTTATTACAAAAAAGTAAA Found at i:44263 original size:19 final size:20 Alignment explanation
Indices: 44233--44296 Score: 76 Period size: 21 Copynumber: 3.1 Consensus size: 20 44223 TTGACACTGT 44233 TTAGCAACTGTACAGATGAGA 1 TTAGC-ACTGTACAGATGAGA * 44254 TTA-CACTGTACAGATTAGA 1 TTAGCACTGTACAGATGAGA * * 44273 TTAGGTACTGTACATATGAGA 1 TTA-GCACTGTACAGATGAGA 44294 TTA 1 TTA 44297 TTAGAGCAGC Statistics Matches: 37, Mismatches: 4, Indels: 4 0.82 0.09 0.09 Matches are distributed among these distances: 19 17 0.46 20 1 0.03 21 19 0.51 ACGTcount: A:0.36, C:0.12, G:0.20, T:0.31 Consensus pattern (20 bp): TTAGCACTGTACAGATGAGA Found at i:44284 original size:21 final size:19 Alignment explanation
Indices: 44239--44296 Score: 71 Period size: 19 Copynumber: 2.9 Consensus size: 19 44229 CTGTTTAGCA 44239 ACTGTACAGATGAGATTAC 1 ACTGTACAGATGAGATTAC * * 44258 ACTGTACAGATTAGATTAGGT 1 ACTGTACAGATGAGATTA--C * 44279 ACTGTACATATGAGATTA 1 ACTGTACAGATGAGATTA 44297 TTAGAGCAGC Statistics Matches: 33, Mismatches: 4, Indels: 2 0.85 0.10 0.05 Matches are distributed among these distances: 19 17 0.52 21 16 0.48 ACGTcount: A:0.36, C:0.12, G:0.21, T:0.31 Consensus pattern (19 bp): ACTGTACAGATGAGATTAC Found at i:46290 original size:31 final size:31 Alignment explanation
Indices: 46255--46422 Score: 156 Period size: 31 Copynumber: 5.5 Consensus size: 31 46245 TTTGGCTAAT 46255 TGCTCAAATAAGGGCCTAACGTTTGCTAAAA 1 TGCTCAAATAAGGGCCTAACGTTTGCTAAAA * * ** 46286 TGCTCAACTAAGGGCCTGATC-TTT--TAATT 1 TGCTCAAATAAGGGCCT-AACGTTTGCTAAAA 46315 TGGC-CAAATAAGGGCCTAACGTTTGGC-AAAA 1 T-GCTCAAATAAGGGCCTAACGTTT-GCTAAAA * ** 46346 TGCTCAAATAAGGGCCTGATC-TTT--TAATT 1 TGCTCAAATAAGGGCCT-AACGTTTGCTAAAA * 46375 TGGC-CAAATAAGGGCCTAACGTTTGCCAAAA 1 T-GCTCAAATAAGGGCCTAACGTTTGCTAAAA 46406 TGCTCAAATAAGGGCCT 1 TGCTCAAATAAGGGCCT 46423 GGCGTCGAAA Statistics Matches: 108, Mismatches: 15, Indels: 28 0.72 0.10 0.19 Matches are distributed among these distances: 28 4 0.04 29 38 0.35 30 8 0.07 31 54 0.50 32 4 0.04 ACGTcount: A:0.32, C:0.20, G:0.21, T:0.27 Consensus pattern (31 bp): TGCTCAAATAAGGGCCTAACGTTTGCTAAAA Found at i:46331 original size:29 final size:29 Alignment explanation
Indices: 46294--46391 Score: 110 Period size: 29 Copynumber: 3.3 Consensus size: 29 46284 AATGCTCAAC 46294 TAAGGGCCTGATCTTTTAATTTGGCCAAA 1 TAAGGGCCTGATCTTTTAATTTGGCCAAA * * ** 46323 TAAGGGCCT-AACGTTTGGCAAAAT-GCTCAAA 1 TAAGGGCCTGATC-TTT--TAATTTGGC-CAAA 46354 TAAGGGCCTGATCTTTTAATTTGGCCAAA 1 TAAGGGCCTGATCTTTTAATTTGGCCAAA 46383 TAAGGGCCT 1 TAAGGGCCT 46392 AACGTTTGCC Statistics Matches: 55, Mismatches: 8, Indels: 12 0.73 0.11 0.16 Matches are distributed among these distances: 28 2 0.04 29 28 0.51 30 4 0.07 31 19 0.35 32 2 0.04 ACGTcount: A:0.30, C:0.18, G:0.22, T:0.30 Consensus pattern (29 bp): TAAGGGCCTGATCTTTTAATTTGGCCAAA Found at i:46352 original size:60 final size:60 Alignment explanation
Indices: 46259--46423 Score: 296 Period size: 60 Copynumber: 2.8 Consensus size: 60 46249 GCTAATTGCT * 46259 CAAATAAGGGCCTAACGTTT-GCTAAAATGCTCAACTAAGGGCCTGATCTTTTAATTTGGC 1 CAAATAAGGGCCTAACGTTTGGC-AAAATGCTCAAATAAGGGCCTGATCTTTTAATTTGGC 46319 CAAATAAGGGCCTAACGTTTGGCAAAATGCTCAAATAAGGGCCTGATCTTTTAATTTGGC 1 CAAATAAGGGCCTAACGTTTGGCAAAATGCTCAAATAAGGGCCTGATCTTTTAATTTGGC * 46379 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCTG 1 CAAATAAGGGCCTAACGTTTGGCAAAATGCTCAAATAAGGGCCTG 46424 GCGTCGAAAA Statistics Matches: 102, Mismatches: 2, Indels: 2 0.96 0.02 0.02 Matches are distributed among these distances: 60 100 0.98 61 2 0.02 ACGTcount: A:0.32, C:0.20, G:0.21, T:0.27 Consensus pattern (60 bp): CAAATAAGGGCCTAACGTTTGGCAAAATGCTCAAATAAGGGCCTGATCTTTTAATTTGGC Found at i:46539 original size:60 final size:60 Alignment explanation
Indices: 46465--46620 Score: 217 Period size: 60 Copynumber: 2.6 Consensus size: 60 46455 GACGCCAGAC ** * 46465 CCTTATTTGAGCATTTTTTATAACGTTAGGCCCTTATGTGGCCAAATTAAAAGATCGGAT 1 CCTTATTTGAGCATTTTCGATAACATTAGGCCCTTATGTGGCCAAATTAAAAGATCGGAT * * 46525 CCTTATTTGAGCATTTTCGATAACATTAGGCCCTTATTTGGCCAAATTAAAAGATCGGCT 1 CCTTATTTGAGCATTTTCGATAACATTAGGCCCTTATGTGGCCAAATTAAAAGATCGGAT * * * 46585 -CTTATTTGAACATTTTGGCA-AATATTAGGCCCTTAT 1 CCTTATTTGAGCATTTTCG-ATAACATTAGGCCCTTAT 46621 TTGAGCAATT Statistics Matches: 87, Mismatches: 8, Indels: 3 0.89 0.08 0.03 Matches are distributed among these distances: 59 31 0.36 60 56 0.64 ACGTcount: A:0.28, C:0.18, G:0.17, T:0.37 Consensus pattern (60 bp): CCTTATTTGAGCATTTTCGATAACATTAGGCCCTTATGTGGCCAAATTAAAAGATCGGAT Found at i:57080 original size:13 final size:13 Alignment explanation
Indices: 57062--57087 Score: 52 Period size: 13 Copynumber: 2.0 Consensus size: 13 57052 TAAATATGAC 57062 CTTAAAAAGAATA 1 CTTAAAAAGAATA 57075 CTTAAAAAGAATA 1 CTTAAAAAGAATA 57088 AAAGAAAAGG Statistics Matches: 13, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 13 1.00 ACGTcount: A:0.62, C:0.08, G:0.08, T:0.23 Consensus pattern (13 bp): CTTAAAAAGAATA Found at i:62785 original size:6 final size:6 Alignment explanation
Indices: 62774--62800 Score: 54 Period size: 6 Copynumber: 4.5 Consensus size: 6 62764 TATCTCATGA 62774 TTTTCT TTTTCT TTTTCT TTTTCT TTT 1 TTTTCT TTTTCT TTTTCT TTTTCT TTT 62801 GCTTCGTACT Statistics Matches: 21, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 6 21 1.00 ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85 Consensus pattern (6 bp): TTTTCT Found at i:68544 original size:18 final size:18 Alignment explanation
Indices: 68521--68556 Score: 72 Period size: 18 Copynumber: 2.0 Consensus size: 18 68511 CAAAATAAAA 68521 GAATGCTTATTTGAAGTT 1 GAATGCTTATTTGAAGTT 68539 GAATGCTTATTTGAAGTT 1 GAATGCTTATTTGAAGTT 68557 TTGTTCTTTG Statistics Matches: 18, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 18 18 1.00 ACGTcount: A:0.28, C:0.06, G:0.22, T:0.44 Consensus pattern (18 bp): GAATGCTTATTTGAAGTT Found at i:68585 original size:42 final size:42 Alignment explanation
Indices: 68535--68618 Score: 159 Period size: 42 Copynumber: 2.0 Consensus size: 42 68525 GCTTATTTGA 68535 AGTTGAATGCTTATTTGAAGTTTTGTTCTTTGTTTTGAATTC 1 AGTTGAATGCTTATTTGAAGTTTTGTTCTTTGTTTTGAATTC * 68577 AGTTGAATGCTTATTTGAATTTTTGTTCTTTGTTTTGAATTC 1 AGTTGAATGCTTATTTGAAGTTTTGTTCTTTGTTTTGAATTC 68619 TCTTTTGCTC Statistics Matches: 41, Mismatches: 1, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 42 41 1.00 ACGTcount: A:0.19, C:0.07, G:0.18, T:0.56 Consensus pattern (42 bp): AGTTGAATGCTTATTTGAAGTTTTGTTCTTTGTTTTGAATTC Found at i:80091 original size:11 final size:11 Alignment explanation
Indices: 80075--80104 Score: 51 Period size: 11 Copynumber: 2.7 Consensus size: 11 80065 AAGGGCTGAA 80075 ATTAATTAATT 1 ATTAATTAATT 80086 ATTAATTAATT 1 ATTAATTAATT * 80097 AATAATTA 1 ATTAATTA 80105 TTTTCTTGAA Statistics Matches: 18, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 11 18 1.00 ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50 Consensus pattern (11 bp): ATTAATTAATT Found at i:80092 original size:15 final size:15 Alignment explanation
Indices: 80074--80104 Score: 53 Period size: 15 Copynumber: 2.1 Consensus size: 15 80064 CAAGGGCTGA * 80074 AATTAATTAATTATT 1 AATTAATTAATAATT 80089 AATTAATTAATAATT 1 AATTAATTAATAATT 80104 A 1 A 80105 TTTTCTTGAA Statistics Matches: 15, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 15 15 1.00 ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48 Consensus pattern (15 bp): AATTAATTAATAATT Found at i:81557 original size:51 final size:50 Alignment explanation
Indices: 81456--81557 Score: 111 Period size: 51 Copynumber: 2.0 Consensus size: 50 81446 GTTCATCAAC * ** 81456 TTTTCCTTGTTTAGATCTTGTCTCAGGACAATCAAACACTTTTTTAGTGT 1 TTTTCCTTGTTTAGATCTTGTCTCAGGACAATCAAACACTTGTACAGTGT * 81506 TTTTCTCTTGTTTCA-ATCTTGTCTCCGGAC-ATACAAACAC-TGTACACGTGT 1 TTTTC-CTTGTTT-AGATCTTGTCTCAGGACAAT-CAAACACTTGTACA-GTGT 81557 T 1 T 81558 CTTAATTCAG Statistics Matches: 44, Mismatches: 4, Indels: 7 0.80 0.07 0.13 Matches are distributed among these distances: 50 10 0.23 51 33 0.75 52 1 0.02 ACGTcount: A:0.22, C:0.22, G:0.14, T:0.43 Consensus pattern (50 bp): TTTTCCTTGTTTAGATCTTGTCTCAGGACAATCAAACACTTGTACAGTGT Found at i:88988 original size:20 final size:19 Alignment explanation
Indices: 88950--88988 Score: 51 Period size: 19 Copynumber: 2.0 Consensus size: 19 88940 GTCTCTCTGC * 88950 TTTTGTTTTCTTCTTATTA 1 TTTTGTTTTCTTATTATTA * 88969 TTTTGTTTTATTTATTATTA 1 TTTTGTTTT-CTTATTATTA 88989 ATTATTTTAC Statistics Matches: 17, Mismatches: 2, Indels: 1 0.85 0.10 0.05 Matches are distributed among these distances: 19 9 0.53 20 8 0.47 ACGTcount: A:0.15, C:0.05, G:0.05, T:0.74 Consensus pattern (19 bp): TTTTGTTTTCTTATTATTA Found at i:92682 original size:42 final size:43 Alignment explanation
Indices: 92631--92724 Score: 138 Period size: 45 Copynumber: 2.2 Consensus size: 43 92621 GGTGCATTAC * * 92631 CTAA-ATTCTACT-CCATCTCTAGGTAATTCATCAAAATAAAT 1 CTAATATTCTACTCCCATCTCTAGATAATTCATCAAAATAAAG 92672 CTAATATTCTACTCCCCCATCTCTAGATAATTCATCAAAATAAAG 1 CTAATATTCTACT--CCCATCTCTAGATAATTCATCAAAATAAAG 92717 CTAATATT 1 CTAATATT 92725 GATTGTTGCT Statistics Matches: 47, Mismatches: 2, Indels: 4 0.89 0.04 0.08 Matches are distributed among these distances: 41 4 0.09 42 8 0.17 45 35 0.74 ACGTcount: A:0.38, C:0.23, G:0.04, T:0.34 Consensus pattern (43 bp): CTAATATTCTACTCCCATCTCTAGATAATTCATCAAAATAAAG Found at i:93903 original size:22 final size:23 Alignment explanation
Indices: 93878--93923 Score: 60 Period size: 22 Copynumber: 2.0 Consensus size: 23 93868 TAATATCCAC 93878 ACACAATTAAT-ATATAAT-TAAA 1 ACACAATTAATCATA-AATATAAA * 93900 ACACACTTAATCATAAATATAAA 1 ACACAATTAATCATAAATATAAA 93923 A 1 A 93924 ATAGTAAATT Statistics Matches: 21, Mismatches: 1, Indels: 3 0.84 0.04 0.12 Matches are distributed among these distances: 22 13 0.62 23 8 0.38 ACGTcount: A:0.59, C:0.13, G:0.00, T:0.28 Consensus pattern (23 bp): ACACAATTAATCATAAATATAAA Done.