Tandem Repeats Finder Program written by: Gary Benson Program in Bioinformatics Boston University Version 4.09 Sequence: AWUE01011911.1 Corchorus olitorius cultivar O-4 contig11944, 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: 21538 ACGTcount: A:0.35, C:0.18, G:0.18, T:0.30 Warning! 1 characters in sequence are not A, C, G, or T Found at i:3631 original size:21 final size:21 Alignment explanation
Indices: 3570--3633 Score: 101 Period size: 21 Copynumber: 3.0 Consensus size: 21 3560 GGTATAACAT * 3570 GGTTTGACCATCAAAATTCGG 1 GGTTTGACCATCAAAATTTGG 3591 GGTTTGACCATCAAAATTTGG 1 GGTTTGACCATCAAAATTTGG * * 3612 GGTTTGACAATCAAACTTTGG 1 GGTTTGACCATCAAAATTTGG 3633 G 1 G 3634 CAGAAACACA Statistics Matches: 40, Mismatches: 3, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 21 40 1.00 ACGTcount: A:0.28, C:0.16, G:0.25, T:0.31 Consensus pattern (21 bp): GGTTTGACCATCAAAATTTGG Found at i:3727 original size:21 final size:21 Alignment explanation
Indices: 3692--3776 Score: 116 Period size: 21 Copynumber: 4.0 Consensus size: 21 3682 GGTTTAACAT * * 3692 GGTTTAACTATCAAAATTTGG 1 GGTTTGACCATCAAAATTTGG * * 3713 GGATTGACCATCAAAATTTGA 1 GGTTTGACCATCAAAATTTGG * * 3734 GGTTTGACTATCAAACTTTGG 1 GGTTTGACCATCAAAATTTGG 3755 GGTTTGACCATCAAAATTTGG 1 GGTTTGACCATCAAAATTTGG 3776 G 1 G 3777 CAAAAACACA Statistics Matches: 54, Mismatches: 10, Indels: 0 0.84 0.16 0.00 Matches are distributed among these distances: 21 54 1.00 ACGTcount: A:0.31, C:0.13, G:0.22, T:0.34 Consensus pattern (21 bp): GGTTTGACCATCAAAATTTGG Found at i:3744 original size:42 final size:42 Alignment explanation
Indices: 3692--3774 Score: 139 Period size: 42 Copynumber: 2.0 Consensus size: 42 3682 GGTTTAACAT 3692 GGTTTAACTATCAAAATTTGGGGATTGACCATCAAAATTTGA 1 GGTTTAACTATCAAAATTTGGGGATTGACCATCAAAATTTGA * * * 3734 GGTTTGACTATCAAACTTTGGGGTTTGACCATCAAAATTTG 1 GGTTTAACTATCAAAATTTGGGGATTGACCATCAAAATTTG 3775 GGCAAAAACA Statistics Matches: 38, Mismatches: 3, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 42 38 1.00 ACGTcount: A:0.31, C:0.13, G:0.20, T:0.35 Consensus pattern (42 bp): GGTTTAACTATCAAAATTTGGGGATTGACCATCAAAATTTGA Found at i:3858 original size:21 final size:21 Alignment explanation
Indices: 3834--3938 Score: 149 Period size: 21 Copynumber: 5.0 Consensus size: 21 3824 GGTTTAACAT * * 3834 GGTTTGACTATCAAACTTTGG 1 GGTTTGACCATCAAAATTTGG * 3855 GGTTTGACCATCAAAATTCGG 1 GGTTTGACCATCAAAATTTGG * 3876 GGTTTGACCATCAAAA-TTCG 1 GGTTTGACCATCAAAATTTGG * 3896 GTTTTGACCATCAAAATTTGG 1 GGTTTGACCATCAAAATTTGG * 3917 GGTTTGATCATCAAAATTTGG 1 GGTTTGACCATCAAAATTTGG 3938 G 1 G 3939 CAAAAACACA Statistics Matches: 74, Mismatches: 9, Indels: 2 0.87 0.11 0.02 Matches are distributed among these distances: 20 17 0.23 21 57 0.77 ACGTcount: A:0.28, C:0.15, G:0.23, T:0.34 Consensus pattern (21 bp): GGTTTGACCATCAAAATTTGG Found at i:3868 original size:142 final size:142 Alignment explanation
Indices: 3570--3917 Score: 536 Period size: 142 Copynumber: 2.4 Consensus size: 142 3560 GGTATAACAT * * 3570 GGTTTGACCATCAAAATTCGGGGTTTGACCATCAAAATTTGGGGTTTGACAATCAAACTTTGGGC 1 GGTTTGACCATCAAAATTCGGGGTTTGACCATC-AAATTTGGGGTTTGACCATCAAAATTTGGGC * 3635 AGAAACACAGTTTTGAGCAAAAATGTGGTGGGTGCTTCAATTGATAAGGTTTAACATGGTTTAAC 65 AAAAACACAGTTTTGAGCAAAAATGTGGTGGGTGCTTCAATTGATAAGGTTTAACATGGTTTAAC 3700 TATCAAAATTTGG 130 TATCAAAATTTGG * * * * 3713 GGATTGACCATCAAAATTTGAGGTTTGACTATCAAACTTTGGGGTTTGACCATCAAAATTTGGGC 1 GGTTTGACCATCAAAATTCGGGGTTTGACCATCAAA-TTTGGGGTTTGACCATCAAAATTTGGGC ** * * 3778 AAAAACACAGTTTTG-GGGAAAATGTTGTGGGTGCTTCAATTGATAAGGTTTAACATGGTTTGAC 65 AAAAACACAGTTTTGAGCAAAAATGTGGTGGGTGCTTCAATTGATAAGGTTTAACATGGTTTAAC * 3842 TATCAAACTTTGG 130 TATCAAAATTTGG * * * 3855 GGTTTGACCATCAAAATTCGGGGTTTGACCATCAAAATTCGGTTTTGACCATCAAAATTTGGG 1 GGTTTGACCATCAAAATTCGGGGTTTGACCATCAAATTTGGGGTTTGACCATCAAAATTTGGG 3918 GTTTGATCAT Statistics Matches: 185, Mismatches: 19, Indels: 4 0.89 0.09 0.02 Matches are distributed among these distances: 141 24 0.13 142 92 0.50 143 69 0.37 ACGTcount: A:0.30, C:0.14, G:0.24, T:0.32 Consensus pattern (142 bp): GGTTTGACCATCAAAATTCGGGGTTTGACCATCAAATTTGGGGTTTGACCATCAAAATTTGGGCA AAAACACAGTTTTGAGCAAAAATGTGGTGGGTGCTTCAATTGATAAGGTTTAACATGGTTTAACT ATCAAAATTTGG Found at i:3911 original size:41 final size:41 Alignment explanation
Indices: 3834--3934 Score: 139 Period size: 41 Copynumber: 2.4 Consensus size: 41 3824 GGTTTAACAT * * * 3834 GGTTTGACTATCAAACTTTGGGGTTTGACCATCAAAATTCGG 1 GGTTTGACCATCAAA-ATTCGGGTTTGACCATCAAAATTCGG * * 3876 GGTTTGACCATCAAAATTCGGTTTTGACCATCAAAATTTGG 1 GGTTTGACCATCAAAATTCGGGTTTGACCATCAAAATTCGG * 3917 GGTTTGATCATCAAAATT 1 GGTTTGACCATCAAAATT 3935 TGGGCAAAAA Statistics Matches: 53, Mismatches: 6, Indels: 1 0.88 0.10 0.02 Matches are distributed among these distances: 41 39 0.74 42 14 0.26 ACGTcount: A:0.29, C:0.16, G:0.21, T:0.35 Consensus pattern (41 bp): GGTTTGACCATCAAAATTCGGGTTTGACCATCAAAATTCGG Found at i:3978 original size:163 final size:163 Alignment explanation
Indices: 3692--4055 Score: 493 Period size: 163 Copynumber: 2.2 Consensus size: 163 3682 GGTTTAACAT * * * * 3692 GGTTTAACTATCAAAATTTGGGGATTGACCATCAAAATTTGAGGTTTGACTATCAAACTTTGGGG 1 GGTTTAACCATCAAAA-TTGGGGATTGACCATCAAAATTCGAGGTTTGACCATCAAAATTTGGGG * * * 3757 TTTGACCATCAAAATTTGGGCAAAAACACAGTTTTGGGGAAAATGTTGTGGGTGCTTCAATTGAT 65 TTTGACCATCAAAATTTGGGCAAAAACACAGTTTTAGGAAAAATGTTGTGGCTGCTTCAATTGAT * 3822 AAGGTTTAACATGGTTTGACTATCAAACTTT-GG 130 AAGGTTTAACATGATTTGACTATCAAACTTTAGG * * * 3855 GGTTTGACCATCAAAATTCGGGGTTTGACCATCAAAATTCG-GTTTTGACCATCAAAATTTGGGG 1 GGTTTAACCATCAAAATT-GGGGATTGACCATCAAAATTCGAGGTTTGACCATCAAAATTTGGGG * * * 3919 TTTGATCATCAAAATTTGGGCAAAAACACAATTTTTAGTAAAAATG-TGATGGCTGCTTCAATTG 65 TTTGACCATCAAAATTTGGGCAAAAACAC-AGTTTTAGGAAAAATGTTG-TGGCTGCTTCAATTG * * * 3983 ATAATGTTTGACATGATTTGATTATCAAACTTTAGG 128 ATAAGGTTTAACATGATTTGACTATCAAACTTTAGG * * 4019 GG-TTAACCATGAAAATTTGGGATTGACCATCAAAATT 1 GGTTTAACCATCAAAATTGGGGATTGACCATCAAAATT 4056 TGGGCAAAAT Statistics Matches: 176, Mismatches: 21, Indels: 9 0.85 0.10 0.04 Matches are distributed among these distances: 162 70 0.40 163 102 0.58 164 4 0.02 ACGTcount: A:0.32, C:0.13, G:0.21, T:0.34 Consensus pattern (163 bp): GGTTTAACCATCAAAATTGGGGATTGACCATCAAAATTCGAGGTTTGACCATCAAAATTTGGGGT TTGACCATCAAAATTTGGGCAAAAACACAGTTTTAGGAAAAATGTTGTGGCTGCTTCAATTGATA AGGTTTAACATGATTTGACTATCAAACTTTAGG Found at i:4097 original size:121 final size:122 Alignment explanation
Indices: 3902--4132 Score: 329 Period size: 121 Copynumber: 1.9 Consensus size: 122 3892 TTCGGTTTTG * * * * 3902 ACCATCAAAATTTGGGGTTTGATCATCAAAATTTGGGCAAAAACACAATTTTTAGTAAAAATGTG 1 ACCATCAAAATTTGGGGATTGACCATCAAAATTTGGGCAAAAACACAATTTTGAGCAAAAATGTG * * * 3967 ATGGCTGCTTCAATTGATAATGTTTGACATGATTTGATTATCAAACTTTAGGGGTTA 66 ATGGCTGCTTCAATTGATAAGGTTTAACATGATTTGACTATCAAACTTTAGGGGTTA * * * * 4024 ACCATGAAAATTT-GGGATTGACCATCAAAATTTGGGCAAAATCACAGTTTTGGGCAAAAATGTG 1 ACCATCAAAATTTGGGGATTGACCATCAAAATTTGGGCAAAAACACAATTTTGAGCAAAAATGTG * * * 4088 GTGGGTGCTTCAATTGATAAGGTTTAACATGGTTTGACTATCAAA 66 ATGGCTGCTTCAATTGATAAGGTTTAACATGATTTGACTATCAAA 4133 TTTTGTGATT Statistics Matches: 95, Mismatches: 14, Indels: 1 0.86 0.13 0.01 Matches are distributed among these distances: 121 83 0.87 122 12 0.13 ACGTcount: A:0.34, C:0.12, G:0.21, T:0.33 Consensus pattern (122 bp): ACCATCAAAATTTGGGGATTGACCATCAAAATTTGGGCAAAAACACAATTTTGAGCAAAAATGTG ATGGCTGCTTCAATTGATAAGGTTTAACATGATTTGACTATCAAACTTTAGGGGTTA Found at i:4221 original size:29 final size:31 Alignment explanation
Indices: 4163--4234 Score: 103 Period size: 29 Copynumber: 2.4 Consensus size: 31 4153 ATACCGTATA * 4163 GGTCCCTCTACTTTCAAAAAAGGATCAATTT 1 GGTCCCTCTACTATCAAAAAAGGATCAATTT ** 4194 GGTCCCTCTACTAT-AAAAACTG-TCAATTT 1 GGTCCCTCTACTATCAAAAAAGGATCAATTT 4223 GGTCCCTCTACT 1 GGTCCCTCTACT 4235 TACAATTTGG Statistics Matches: 38, Mismatches: 3, Indels: 2 0.88 0.07 0.05 Matches are distributed among these distances: 29 19 0.50 30 6 0.16 31 13 0.34 ACGTcount: A:0.28, C:0.26, G:0.12, T:0.33 Consensus pattern (31 bp): GGTCCCTCTACTATCAAAAAAGGATCAATTT Found at i:4655 original size:21 final size:20 Alignment explanation
Indices: 4629--4670 Score: 57 Period size: 21 Copynumber: 2.0 Consensus size: 20 4619 TTTGACCTGA * * 4629 TTTGACTATCAAACTTTAGGG 1 TTTGACCATCAAAATTT-GGG 4650 TTTGACCATCAAAATTTGGG 1 TTTGACCATCAAAATTTGGG 4670 T 1 T 4671 GACTGAAATG Statistics Matches: 19, Mismatches: 2, Indels: 1 0.86 0.09 0.05 Matches are distributed among these distances: 20 4 0.21 21 15 0.79 ACGTcount: A:0.29, C:0.14, G:0.19, T:0.38 Consensus pattern (20 bp): TTTGACCATCAAAATTTGGG Found at i:5025 original size:27 final size:27 Alignment explanation
Indices: 4987--5050 Score: 110 Period size: 27 Copynumber: 2.4 Consensus size: 27 4977 TCAACAAATT * * 4987 ATAAAGATTTTACATAGTATGGGTAAA 1 ATAAAGATTTTACAAAGTATGAGTAAA 5014 ATAAAGATTTTACAAAGTATGAGTAAA 1 ATAAAGATTTTACAAAGTATGAGTAAA 5041 ATAAAGATTT 1 ATAAAGATTT 5051 AGTAAAATGA Statistics Matches: 35, Mismatches: 2, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 27 35 1.00 ACGTcount: A:0.48, C:0.03, G:0.16, T:0.33 Consensus pattern (27 bp): ATAAAGATTTTACAAAGTATGAGTAAA Found at i:5069 original size:101 final size:101 Alignment explanation
Indices: 4943--5124 Score: 301 Period size: 101 Copynumber: 1.8 Consensus size: 101 4933 ATATTATGAT * * * 4943 AAGATTTAGTAAAATAAAAATTTAGTAATATTTTTCAACAAATTATAAAGATTTTACATAGTATG 1 AAGATTTAGTAAAATAAAAACTTAGTAATATTTTTCAACAAATTATAAAGATTTTACATAGAAAG 5008 GGTAAAATAAAGATTTTACAAAGTATGAGTAAAATA 66 GGTAAAATAAAGATTTTACAAAGTATGAGTAAAATA * * * 5044 AAGATTTAGTAAAATGAAAACTTAGTAATATTTTTCAACAAATTATAAAGGTTTTACATGGAAAG 1 AAGATTTAGTAAAATAAAAACTTAGTAATATTTTTCAACAAATTATAAAGATTTTACATAGAAAG * 5109 TGTAAAATAAAGATTT 66 GGTAAAATAAAGATTT 5125 AGTAATACTT Statistics Matches: 74, Mismatches: 7, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 101 74 1.00 ACGTcount: A:0.48, C:0.04, G:0.13, T:0.35 Consensus pattern (101 bp): AAGATTTAGTAAAATAAAAACTTAGTAATATTTTTCAACAAATTATAAAGATTTTACATAGAAAG GGTAAAATAAAGATTTTACAAAGTATGAGTAAAATA Found at i:5720 original size:25 final size:26 Alignment explanation
Indices: 5660--5720 Score: 63 Period size: 25 Copynumber: 2.4 Consensus size: 26 5650 TTTTAACTAT * 5660 TTCATTTTATTGTCTAATTGTTATATA 1 TTCATATT-TTGTCTAATTGTTATATA * * 5687 -TCACATTTTGTTTAATT-TTATATA 1 TTCATATTTTGTCTAATTGTTATATA * 5711 TTCATGTTTT 1 TTCATATTTT 5721 TTTTTTGAAA Statistics Matches: 28, Mismatches: 5, Indels: 4 0.76 0.14 0.11 Matches are distributed among these distances: 24 7 0.25 25 16 0.57 26 5 0.18 ACGTcount: A:0.25, C:0.08, G:0.07, T:0.61 Consensus pattern (26 bp): TTCATATTTTGTCTAATTGTTATATA Found at i:7848 original size:17 final size:17 Alignment explanation
Indices: 7826--7860 Score: 70 Period size: 17 Copynumber: 2.1 Consensus size: 17 7816 TTATACTATT 7826 AAATTTCACATTCTCCC 1 AAATTTCACATTCTCCC 7843 AAATTTCACATTCTCCC 1 AAATTTCACATTCTCCC 7860 A 1 A 7861 CTGACAATAT Statistics Matches: 18, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 17 18 1.00 ACGTcount: A:0.31, C:0.34, G:0.00, T:0.34 Consensus pattern (17 bp): AAATTTCACATTCTCCC Found at i:11111 original size:2 final size:2 Alignment explanation
Indices: 11100--11145 Score: 60 Period size: 2 Copynumber: 24.0 Consensus size: 2 11090 GAATCTTCTT * * 11100 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA AA GA -A TA TA 1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA 11140 TA TA TA 1 TA TA TA 11146 AGACATTGAA Statistics Matches: 40, Mismatches: 2, Indels: 4 0.87 0.04 0.09 Matches are distributed among these distances: 1 2 0.05 2 38 0.95 ACGTcount: A:0.54, C:0.00, G:0.02, T:0.43 Consensus pattern (2 bp): TA Found at i:12741 original size:31 final size:31 Alignment explanation
Indices: 12718--12784 Score: 82 Period size: 31 Copynumber: 2.1 Consensus size: 31 12708 CCGAACCTGC 12718 ATGACCCTAAATCCAGTAGACCCGAGACCCGA 1 ATGA-CCTAAATCCAGTAGACCCGAGACCCGA * * * 12750 ATGACCTGAATCCAG-ATGAGCCGAAACCCGA 1 ATGACCTAAATCCAGTA-GACCCGAGACCCGA 12781 ATGA 1 ATGA 12785 TCTGAGAAAA Statistics Matches: 31, Mismatches: 3, Indels: 3 0.84 0.08 0.08 Matches are distributed among these distances: 30 1 0.03 31 26 0.84 32 4 0.13 ACGTcount: A:0.36, C:0.30, G:0.21, T:0.13 Consensus pattern (31 bp): ATGACCTAAATCCAGTAGACCCGAGACCCGA Found at i:13632 original size:133 final size:133 Alignment explanation
Indices: 13465--13765 Score: 543 Period size: 132 Copynumber: 2.3 Consensus size: 133 13455 TTTTTTTGCC * * 13465 AAAAATTAGAGTTTTTAGTTGAATATAACTATAAAAATATATTTAAAAAATTCTAATATATATAA 1 AAAAA-TAGAGTTTTTAGTTGAGTAAAACTATAAAAATATATTTAAAAAATTCTAATATATATAA 13530 TTTTT-TAAGTTAAAATAGTAAAATGGTAAAAATTAAATAGTTATAAGGATATATTATATTTAAT 65 TTTTTCTAA-TTAAAATAGTAAAATGGTAAAAATTAAATAGTTATAAGGATATATTATATTTAAT 13594 TAAAT 129 TAAAT * 13599 AAAAATATAGTTTTTAGTTGAGTAAAACTAT-AAAATATATTTAAAAAATTCTAATATATATAAT 1 AAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAATATATTTAAAAAATTCTAATATATATAAT 13663 TTTTCTAATTAAAATAGTAAAATGGTAAAAATTAAATAGTTATAAGGATATATTATATTTAATTA 66 TTTTCTAATTAAAATAGTAAAATGGTAAAAATTAAATAGTTATAAGGATATATTATATTTAATTA 13728 AAT 131 AAT 13731 AAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAA 1 AAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAA 13766 GTCTAAACAA Statistics Matches: 161, Mismatches: 4, Indels: 5 0.95 0.02 0.03 Matches are distributed among these distances: 132 127 0.79 133 29 0.18 134 5 0.03 ACGTcount: A:0.50, C:0.02, G:0.09, T:0.39 Consensus pattern (133 bp): AAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAATATATTTAAAAAATTCTAATATATATAAT TTTTCTAATTAAAATAGTAAAATGGTAAAAATTAAATAGTTATAAGGATATATTATATTTAATTA AAT Found at i:15390 original size:27 final size:27 Alignment explanation
Indices: 15360--15411 Score: 70 Period size: 27 Copynumber: 1.9 Consensus size: 27 15350 TGGGAGACAA 15360 CCTCGAAA-ACACTTGGTTGAGAATGCT 1 CCTCGAAATA-ACTTGGTTGAGAATGCT * * 15387 CCTCGAAATAGCTTGGTTGATAATG 1 CCTCGAAATAACTTGGTTGAGAATG 15412 TCCCTCAAGA Statistics Matches: 22, Mismatches: 2, Indels: 2 0.85 0.08 0.08 Matches are distributed among these distances: 27 21 0.95 28 1 0.05 ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29 Consensus pattern (27 bp): CCTCGAAATAACTTGGTTGAGAATGCT Found at i:17123 original size:38 final size:38 Alignment explanation
Indices: 17076--17170 Score: 172 Period size: 38 Copynumber: 2.5 Consensus size: 38 17066 AGTCAACTTA * 17076 CTAACTAAATTTAAGAGATTTACTAGCCACAAAATCTG 1 CTAATTAAATTTAAGAGATTTACTAGCCACAAAATCTG * 17114 CTAATTAAATTTAAGAGATTTATTAGCCACAAAATCTG 1 CTAATTAAATTTAAGAGATTTACTAGCCACAAAATCTG 17152 CTAATTAAATTTAAGAGAT 1 CTAATTAAATTTAAGAGAT 17171 AATAATTAGC Statistics Matches: 55, Mismatches: 2, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 38 55 1.00 ACGTcount: A:0.43, C:0.14, G:0.11, T:0.33 Consensus pattern (38 bp): CTAATTAAATTTAAGAGATTTACTAGCCACAAAATCTG Found at i:17297 original size:8 final size:8 Alignment explanation
Indices: 17267--17299 Score: 50 Period size: 8 Copynumber: 4.1 Consensus size: 8 17257 CTAAATGATT 17267 TGTATATA 1 TGTATATA 17275 TGTAT-TA 1 TGTATATA 17282 TGTAATATA 1 TGT-ATATA 17291 TGTATATA 1 TGTATATA 17299 T 1 T 17300 ATACACTTTT Statistics Matches: 23, Mismatches: 0, Indels: 4 0.85 0.00 0.15 Matches are distributed among these distances: 7 5 0.22 8 13 0.57 9 5 0.22 ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52 Consensus pattern (8 bp): TGTATATA Done.