Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013379.1 Corchorus olitorius cultivar O-4 contig13412, 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: 34346
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31


Found at i:120 original size:22 final size:21

Alignment explanation

Indices: 95--148 Score: 60 Period size: 19 Copynumber: 2.6 Consensus size: 21 85 GAAGCTCATG 95 TTTGAAGACTTATTGAAGATAA 1 TTTGAAGA-TTATTGAAGATAA * 117 TTTGAAGA-T-TTGAAGATCA 1 TTTGAAGATTATTGAAGATAA 136 -TTGAAGAATTATT 1 TTTGAAG-ATTATT 149 TCAAGAAGCA Statistics Matches: 28, Mismatches: 1, Indels: 7 0.78 0.03 0.19 Matches are distributed among these distances: 18 6 0.21 19 10 0.36 20 2 0.07 21 2 0.07 22 8 0.29 ACGTcount: A:0.39, C:0.04, G:0.19, T:0.39 Consensus pattern (21 bp): TTTGAAGATTATTGAAGATAA Found at i:2697 original size:18 final size:18 Alignment explanation

Indices: 2674--2708 Score: 61 Period size: 18 Copynumber: 1.9 Consensus size: 18 2664 TTCTGAAATA 2674 TGGATTCTGAATTCTGAT 1 TGGATTCTGAATTCTGAT * 2692 TGGATTCTGATTTCTGA 1 TGGATTCTGAATTCTGA 2709 ATTCTGATTG Statistics Matches: 16, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 18 16 1.00 ACGTcount: A:0.20, C:0.11, G:0.23, T:0.46 Consensus pattern (18 bp): TGGATTCTGAATTCTGAT Found at i:2709 original size:25 final size:24 Alignment explanation

Indices: 2678--2728 Score: 84 Period size: 25 Copynumber: 2.1 Consensus size: 24 2668 GAAATATGGA 2678 TTCTGAATTCTGATTGGATTCTGAT 1 TTCTGAATTCTGATTGGATTCT-AT * 2703 TTCTGAATTCTGATTGGTTTCTAT 1 TTCTGAATTCTGATTGGATTCTAT 2727 TT 1 TT 2729 ATTTTGAAAA Statistics Matches: 25, Mismatches: 1, Indels: 1 0.93 0.04 0.04 Matches are distributed among these distances: 24 4 0.16 25 21 0.84 ACGTcount: A:0.18, C:0.12, G:0.18, T:0.53 Consensus pattern (24 bp): TTCTGAATTCTGATTGGATTCTAT Found at i:5507 original size:22 final size:22 Alignment explanation

Indices: 5482--5699 Score: 142 Period size: 22 Copynumber: 9.8 Consensus size: 22 5472 TCTTTGTGTG * 5482 GTTATCAAAATTTCATAAGATC 1 GTTATCAAAATTTCATAGGATC * * * 5504 GTTATTATAATTTCATGAGGA-G 1 GTTATCAAAATTTCAT-AGGATC * * 5526 GTTATCAAAATTCCATAGTG-TG 1 GTTATCAAAATTTCATAG-GATC * * 5548 GTTACCAAAATTTCATATGGA-A 1 GTTATCAAAATTTCATA-GGATC * 5570 GTTATCAAAATTTCATGGGA-C 1 GTTATCAAAATTTCATAGGATC * 5591 GGTTATCAAAATTTCATAGTG-TG 1 -GTTATCAAAATTTCATAG-GATC * 5614 GTTACCAAAATTTCATAGGATC 1 GTTATCAAAATTTCATAGGATC * * ** 5636 AGGTTATTAAAATTTCTTAGGAAG 1 --GTTATCAAAATTTCATAGGATC ** * 5660 GTTATTGAAATTTCATAGTG-TG 1 GTTATCAAAATTTCATAG-GATC * * 5682 GTTATCACAATTTTATAG 1 GTTATCAAAATTTCATAG 5700 AAAGGTTATC Statistics Matches: 155, Mismatches: 29, Indels: 24 0.75 0.14 0.12 Matches are distributed among these distances: 21 6 0.04 22 126 0.81 23 6 0.04 24 17 0.11 ACGTcount: A:0.34, C:0.11, G:0.17, T:0.38 Consensus pattern (22 bp): GTTATCAAAATTTCATAGGATC Found at i:5560 original size:44 final size:44 Alignment explanation

Indices: 5481--6044 Score: 227 Period size: 44 Copynumber: 13.0 Consensus size: 44 5471 ATCTTTGTGT * * * * 5481 GGTTATCAAAATTTCATA-AGATCGTTATTATAATTTCATGAGGA 1 GGTTATCAAAATTTCATAGTGATGGTTATCAAAATTTCAT-AGGA * * 5525 GGTTATCAAAATTCCATAGTG-TGGTTACCAAAATTTCATATGGA 1 GGTTATCAAAATTTCATAGTGATGGTTATCAAAATTTCATA-GGA * * * * 5569 AGTTATCAAAATTTCAT-GGGACGGTTATCAAAATTTCATAGTGT 1 GGTTATCAAAATTTCATAGTGATGGTTATCAAAATTTCATAG-GA * * * 5613 GGTTACCAAAATTTCATAG-GATCAGGTTATTAAAATTTCTTAGGAA 1 GGTTATCAAAATTTCATAGTGAT--GGTTATCAAAATTTCATAGG-A ** * * * 5659 GGTTATTGAAATTTCATAGTG-TGGTTATCACAATTTTATAGAAA 1 GGTTATCAAAATTTCATAGTGATGGTTATCAAAATTTCATAG-GA * * 5703 GGTTATC---A----A-A--GA-GATTATCAAAATGTCATAGCGA 1 GGTTATCAAAATTTCATAGTGATGGTTATCAAAATTTCATAG-GA * 5737 GGTTA-AAAGAATTTCATAGTG-TGGTTAAT-AAAATTTCATAAGGA 1 GGTTATCAA-AATTTCATAGTGATGGTT-ATCAAAATTTCAT-AGGA * * * * * * 5781 GGTTA-CTAATATTTTATGGGGA-GGTTATCAAAATTT-TTAGTGT 1 GGTTATC-AAAATTTCATAGTGATGGTTATCAAAATTTCATAG-GA * * * * 5824 GGTTACCAAAATTTCATA-TGAAGGTTATAAAAGTCTCAATTTCATA-AA 1 GGTTATCAAAATTTCATAGTGATGGTTAT-CAA-----AATTTCATAGGA * * * * * 5872 GAG-TACCAAAATTTGATA--GAAGGTTATC-AAATCTCATAGAA 1 G-GTTATCAAAATTTCATAGTGATGGTTATCAAAATTTCATAGGA * ** * ** 5913 TGATTATTGAAATTTCATAGAGATCCTATTATCAAAATTT-ATAGGA 1 -GGTTATCAAAATTTCATAGTGAT--GGTTATCAAAATTTCATAGGA * * * * * * 5959 TGATTATCAAAATTTCATAATG-TTGTCATCAAAATTTCAAAATGA 1 -GGTTATCAAAATTTCATAGTGATGGTTATCAAAATTTC-ATAGGA * * * 6004 GGTTATCAAAATTACATAATG-TGATTATCAAAATTTCATAG 1 GGTTATCAAAATTTCATAGTGATGGTTATCAAAATTTCATAG 6045 AGGGGTGTTG Statistics Matches: 392, Mismatches: 79, Indels: 99 0.69 0.14 0.17 Matches are distributed among these distances: 34 22 0.06 36 1 0.00 37 2 0.01 40 8 0.02 41 4 0.01 42 17 0.04 43 41 0.10 44 182 0.46 45 15 0.04 46 62 0.16 47 15 0.04 48 15 0.04 49 6 0.02 50 2 0.01 ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36 Consensus pattern (44 bp): GGTTATCAAAATTTCATAGTGATGGTTATCAAAATTTCATAGGA Found at i:5560 original size:66 final size:66 Alignment explanation

Indices: 5477--5699 Score: 272 Period size: 66 Copynumber: 3.3 Consensus size: 66 5467 GATCATCTTT * * * * 5477 GTGTGGTTATCAAAATTTCATAAGATCGTTATTATAATTTCATGAGGAGGTTATCAAAATTCCAT 1 GTGTGGTTACCAAAATTTCATAGGATCGTTATTAAAATTTCATGAGGAGGTTATCAAAATTTCAT 5542 A 66 A * * 5543 GTGTGGTTACCAAAATTTCATATGGA-AGTTATCAAAATTTCATG-GGACGGTTATCAAAATTTC 1 GTGTGGTTACCAAAATTTCATA-GGATCGTTATTAAAATTTCATGAGGA-GGTTATCAAAATTTC 5606 ATA 64 ATA * ** 5609 GTGTGGTTACCAAAATTTCATAGGATCAGGTTATTAAAATTTC-TTAGGAAGGTTATTGAAATTT 1 GTGTGGTTACCAAAATTTCATAGGATC--GTTATTAAAATTTCATGAGG-AGGTTATCAAAATTT 5673 CATA 63 CATA * * * 5677 GTGTGGTTATCACAATTTTATAG 1 GTGTGGTTACCAAAATTTCATAG 5700 AAAGGTTATC Statistics Matches: 136, Mismatches: 14, Indels: 12 0.84 0.09 0.07 Matches are distributed among these distances: 65 6 0.04 66 75 0.55 67 3 0.02 68 51 0.38 69 1 0.01 ACGTcount: A:0.34, C:0.10, G:0.18, T:0.38 Consensus pattern (66 bp): GTGTGGTTACCAAAATTTCATAGGATCGTTATTAAAATTTCATGAGGAGGTTATCAAAATTTCAT A Found at i:5753 original size:22 final size:21 Alignment explanation

Indices: 5722--5855 Score: 69 Period size: 22 Copynumber: 6.2 Consensus size: 21 5712 AGAGATTATC * 5722 AAAATGTCATAGCGAGGTTAA- 1 AAAATTTCATAG-GAGGTTAAT * 5743 AAGAATTTCATAGTGTGGTTAAT 1 AA-AATTTCATAG-GAGGTTAAT * 5766 AAAATTTCATAAGGAGGTTACT 1 AAAATTTCAT-AGGAGGTTAAT * * * 5788 AATATTTTATGGGGAGGTT-AT 1 AAAATTTCAT-AGGAGGTTAAT * * ** 5809 CAAAATTT-TTAGTGTGGTTACC 1 -AAAATTTCATAG-GAGGTTAAT * 5831 AAAATTTCATATGAAGGTT-AT 1 AAAATTTCATA-GGAGGTTAAT 5852 AAAA 1 AAAA 5856 GTCTCAATTT Statistics Matches: 84, Mismatches: 21, Indels: 16 0.69 0.17 0.13 Matches are distributed among these distances: 20 1 0.01 21 20 0.24 22 58 0.69 23 5 0.06 ACGTcount: A:0.38, C:0.07, G:0.20, T:0.35 Consensus pattern (21 bp): AAAATTTCATAGGAGGTTAAT Found at i:5930 original size:22 final size:22 Alignment explanation

Indices: 5861--6045 Score: 120 Period size: 22 Copynumber: 8.5 Consensus size: 22 5851 TAAAAGTCTC * * 5861 AATTTCATA-AA-GAGTACCAA 1 AATTTCATAGAATGATTATCAA * * 5881 AATTTGATAGAA-GGTTATC-A 1 AATTTCATAGAATGATTATCAA * ** 5901 AATCTCATAGAATGATTATTGA 1 AATTTCATAGAATGATTATCAA * 5923 AATTTCATAGAGATCCTATTATCAA 1 AATTTCATAGA-AT--GATTATCAA * 5948 AATTT-ATAGGATGATTATCAA 1 AATTTCATAGAATGATTATCAA * 5969 AATTTCAT--AATGTTGTCATCAA 1 AATTTCATAGAATGAT-T-ATCAA 5991 AATTTCA-A-AATGAGGTTATCAA 1 AATTTCATAGAATGA--TTATCAA * * 6013 AATTACATA-ATGTGATTATCAA 1 AATTTCATAGA-ATGATTATCAA 6035 AATTTCATAGA 1 AATTTCATAGA 6046 GGGGTGTTGC Statistics Matches: 130, Mismatches: 20, Indels: 27 0.73 0.11 0.15 Matches are distributed among these distances: 20 23 0.18 21 25 0.19 22 55 0.42 23 8 0.06 24 8 0.06 25 11 0.08 ACGTcount: A:0.43, C:0.10, G:0.12, T:0.35 Consensus pattern (22 bp): AATTTCATAGAATGATTATCAA Found at i:6544 original size:18 final size:18 Alignment explanation

Indices: 6502--6544 Score: 52 Period size: 18 Copynumber: 2.4 Consensus size: 18 6492 GCACCCACTA 6502 ATTAATAATAATTATTGT 1 ATTAATAATAATTATTGT ** 6520 AAAAATAATAATTATT-T 1 ATTAATAATAATTATTGT 6537 ATTTAATA 1 A-TTAATA 6545 CTTTCGGTCT Statistics Matches: 20, Mismatches: 4, Indels: 2 0.77 0.15 0.08 Matches are distributed among these distances: 17 2 0.10 18 18 0.90 ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47 Consensus pattern (18 bp): ATTAATAATAATTATTGT Found at i:6765 original size:21 final size:22 Alignment explanation

Indices: 6715--6792 Score: 86 Period size: 22 Copynumber: 3.5 Consensus size: 22 6705 AAGGGGTCAA * * 6715 CAAAATTTTATAGAGAGGTTAT 1 CAAAATTTCATAAAGAGGTTAT 6737 CAAAATTTCATAAAGAGGTTAT 1 CAAAATTTCATAAAGAGGTTAT * * * * 6759 CAAATTTTCA-AAATATGATTAC 1 CAAAATTTCATAAAGA-GGTTAT 6781 CAAAATTTCATA 1 CAAAATTTCATA 6793 GTGGTATTTC Statistics Matches: 47, Mismatches: 7, Indels: 3 0.82 0.12 0.05 Matches are distributed among these distances: 21 4 0.09 22 42 0.89 23 1 0.02 ACGTcount: A:0.45, C:0.10, G:0.10, T:0.35 Consensus pattern (22 bp): CAAAATTTCATAAAGAGGTTAT Found at i:7010 original size:44 final size:44 Alignment explanation

Indices: 6899--7345 Score: 301 Period size: 44 Copynumber: 10.2 Consensus size: 44 6889 GAATATTACA * * * * 6899 AAAATTTCATAGTTTA-GTTTTCAAAATTTCATA-AGAGGGTTGTC 1 AAAATTTCATAG-TGAGGTTATCAAAATTTCATAGGGA-GGTTATC * * * * 6943 GAAATTTCATAGT-ATGTAGATCAAAATTTCATAGGGAGATTCA-C 1 AAAATTTCATAGTGAGGT-TATCAAAATTTCATAGGGAGGTT-ATC * * * 6987 AAAATTTCATAATGAGGTTATCAAAAAATT-ATAGGAAGGTTATC 1 AAAATTTCATAGTGAGGTTATC-AAAATTTCATAGGGAGGTTATC * * 7031 AAAA-TT--T-GT-A-GTTATCAAGATTTCATAAGGAGGTTATC 1 AAAATTTCATAGTGAGGTTATCAAAATTTCATAGGGAGGTTATC * * * * 7069 AAAATTTTATAGGGAGGTTTATCAAAATTTTATAGGAAGGTTTATC 1 AAAATTTCATAGTGAGG-TTATCAAAATTTCATAGGGAGG-TTATC * * * * * * 7115 AAAATTTTATAGCGAGGTTATCACAATTTCATAGTGTGATTATC 1 AAAATTTCATAGTGAGGTTATCAAAATTTCATAGGGAGGTTATC * * * * * * * 7159 AAAATTTCAGAGTGTGATTA-CTAACAA-TTCATATGAAGGTTTTT 1 AAAATTTCATAGTGAGGTTATC-AA-AATTTCATAGGGAGGTTATC * ** * * * * 7203 AAATTTTCATAACGTGGTTATCAATATATCATATGGAGGTTATC 1 AAAATTTCATAGTGAGGTTATCAAAATTTCATAGGGAGGTTATC * * * * * 7247 AACATCTCATAGTGTTGGTTATCAAAATTTCATTGGGAAGTTATC 1 AAAATTTCATAGTG-AGGTTATCAAAATTTCATAGGGAGGTTATC * * 7292 AAAATTTCATAGTGAGG-TATTCAAAATTTCTTAGGGAGGTTAAC 1 AAAATTTCATAGTGAGGTTA-TCAAAATTTCATAGGGAGGTTATC 7336 AAAATTTCAT 1 AAAATTTCAT 7346 CTATAAGAAG Statistics Matches: 311, Mismatches: 70, Indels: 44 0.73 0.16 0.10 Matches are distributed among these distances: 37 5 0.02 38 22 0.07 39 3 0.01 40 1 0.00 41 2 0.01 42 2 0.01 43 11 0.04 44 159 0.51 45 85 0.27 46 21 0.07 ACGTcount: A:0.37, C:0.09, G:0.17, T:0.37 Consensus pattern (44 bp): AAAATTTCATAGTGAGGTTATCAAAATTTCATAGGGAGGTTATC Found at i:7011 original size:22 final size:22 Alignment explanation

Indices: 6874--7345 Score: 257 Period size: 22 Copynumber: 21.6 Consensus size: 22 6864 TTATGGAGTA ** 6874 ATCAAAATTTCATA-TGAATATT 1 ATCAAAATTTCATAGTG-AGGTT * 6896 A-CAAAAATTTCATAGTTTA-GTT 1 ATC-AAAATTTCATAG-TGAGGTT * * 6918 TTCAAAATTTCATA-AGAGGGTT 1 ATCAAAATTTCATAGTGA-GGTT * * * * 6940 GTCGAAATTTCATAGT-ATGTAG 1 ATCAAAATTTCATAGTGAGGT-T * * 6962 ATCAAAATTTCATAGGGAGATT 1 ATCAAAATTTCATAGTGAGGTT * 6984 CA-CAAAATTTCATAATGAGGTT 1 -ATCAAAATTTCATAGTGAGGTT * 7006 ATCAAAAAATT-ATAG-GAAGGTT 1 ATC-AAAATTTCATAGTG-AGGTT 7028 ATCAAAA-TT--T-GT-A-GTT 1 ATCAAAATTTCATAGTGAGGTT * 7044 ATCAAGATTTCATAAG-GAGGTT 1 ATCAAAATTTCAT-AGTGAGGTT * * 7066 ATCAAAATTTTATAGGGAGGTTT 1 ATCAAAATTTCATAGTGAGG-TT * 7089 ATCAAAATTTTATAG-GAAGGTTT 1 ATCAAAATTTCATAGTG-AGG-TT * * 7112 ATCAAAATTTTATAGCGAGGTT 1 ATCAAAATTTCATAGTGAGGTT * * * 7134 ATCACAATTTCATAGTGTGATT 1 ATCAAAATTTCATAGTGAGGTT * * * 7156 ATCAAAATTTCAGAGTGTGATT 1 ATCAAAATTTCATAGTGAGGTT 7178 A-CTAACAA-TTCATA-TGAAGGTT 1 ATC-AA-AATTTCATAGTG-AGGTT * * * ** * 7200 TTTAAATTTTCATAACGTGGTT 1 ATCAAAATTTCATAGTGAGGTT * * 7222 ATCAATATATCATA-TGGAGGTT 1 ATCAAAATTTCATAGT-GAGGTT * * * 7244 ATCAACATCTCATAGTGTTGGTT 1 ATCAAAATTTCATAGTG-AGGTT * * * 7267 ATCAAAATTTCATTGGGAAGTT 1 ATCAAAATTTCATAGTGAGGTT 7289 ATCAAAATTTCATAGTGAGG-T 1 ATCAAAATTTCATAGTGAGGTT * * 7310 ATTCAAAATTTCTTAGGGAGGTT 1 A-TCAAAATTTCATAGTGAGGTT * 7333 AACAAAATTTCAT 1 ATCAAAATTTCAT 7346 CTATAAGAAG Statistics Matches: 352, Mismatches: 62, Indels: 72 0.72 0.13 0.15 Matches are distributed among these distances: 16 9 0.03 17 3 0.01 18 1 0.00 19 2 0.01 20 3 0.01 21 19 0.05 22 238 0.68 23 75 0.21 24 2 0.01 ACGTcount: A:0.37, C:0.10, G:0.16, T:0.37 Consensus pattern (22 bp): ATCAAAATTTCATAGTGAGGTT Found at i:8690 original size:30 final size:31 Alignment explanation

Indices: 8650--8734 Score: 120 Period size: 30 Copynumber: 2.8 Consensus size: 31 8640 CCGTGCTTAT * 8650 TTTCTCTCAGGTCCTGCGCCACTTCACTTTC 1 TTTCTCTCAGGCCCTGCGCCACTTCACTTTC * * 8681 TTTCT-TCAGGCCCTGCACCACTTTACTTTC 1 TTTCTCTCAGGCCCTGCGCCACTTCACTTTC * 8711 -TTCTCTCAAGCCCTGCGCCACTTC 1 TTTCTCTCAGGCCCTGCGCCACTTC 8735 CTCCAGCAAC Statistics Matches: 47, Mismatches: 6, Indels: 3 0.84 0.11 0.05 Matches are distributed among these distances: 29 4 0.09 30 38 0.81 31 5 0.11 ACGTcount: A:0.12, C:0.40, G:0.12, T:0.36 Consensus pattern (31 bp): TTTCTCTCAGGCCCTGCGCCACTTCACTTTC Found at i:16561 original size:22 final size:21 Alignment explanation

Indices: 16530--16583 Score: 54 Period size: 22 Copynumber: 2.5 Consensus size: 21 16520 AAGGTTCTCG * * * 16530 AAATTCCATAGTATCGTTATTA 1 AAATTTCATAG-AACGTTATCA * 16552 AAATTTCATAAGAAGGTTATCA 1 AAATTTCAT-AGAACGTTATCA 16574 AAATTTCATA 1 AAATTTCATA 16584 AGGAAGTCAT Statistics Matches: 27, Mismatches: 4, Indels: 3 0.79 0.12 0.09 Matches are distributed among these distances: 21 1 0.04 22 24 0.89 23 2 0.07 ACGTcount: A:0.43, C:0.11, G:0.09, T:0.37 Consensus pattern (21 bp): AAATTTCATAGAACGTTATCA Found at i:16600 original size:23 final size:22 Alignment explanation

Indices: 16551--16600 Score: 66 Period size: 22 Copynumber: 2.2 Consensus size: 22 16541 TATCGTTATT * 16551 AAAATTTCATAAGAAGGTTATC 1 AAAATTTCATAAGAAGGTCATC 16573 AAAATTTCATAAGGAA-GTCATC 1 AAAATTTCATAA-GAAGGTCATC 16595 AGAAAT 1 A-AAAT 16601 AGTGTAATTA Statistics Matches: 25, Mismatches: 1, Indels: 3 0.86 0.03 0.10 Matches are distributed among these distances: 22 18 0.72 23 7 0.28 ACGTcount: A:0.48, C:0.10, G:0.14, T:0.28 Consensus pattern (22 bp): AAAATTTCATAAGAAGGTCATC Found at i:32502 original size:16 final size:15 Alignment explanation

Indices: 32464--32505 Score: 75 Period size: 15 Copynumber: 2.7 Consensus size: 15 32454 CAGAGGTTTG 32464 ACAGAAAACAATTAA 1 ACAGAAAACAATTAA 32479 ACAGAAAACAATTAA 1 ACAGAAAACAATTAA 32494 ACTAGAAAACAA 1 AC-AGAAAACAA 32506 AGTAGAGTAA Statistics Matches: 26, Mismatches: 0, Indels: 1 0.96 0.00 0.04 Matches are distributed among these distances: 15 17 0.65 16 9 0.35 ACGTcount: A:0.67, C:0.14, G:0.07, T:0.12 Consensus pattern (15 bp): ACAGAAAACAATTAA Done.