Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013197.1 Corchorus olitorius cultivar O-4 contig13230, 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: 48384
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.31


Found at i:3568 original size:94 final size:94

Alignment explanation

Indices: 3369--3549 Score: 222 Period size: 94 Copynumber: 1.9 Consensus size: 94 3359 TAGTACCAAA * 3369 ATGAACTGAACTAGGATAAAGAAATGCTGATTTTTTTTTGGTATATTTATAAATTAATCTTGTTC 1 ATGAACTGAACTAGGATAAAGAAATGCTGA---TTTTTT-GTATATTTATAAATTAATCTTATTC ** * * 3434 AAATTAAGTCAGTCCATCATGAGATTCTAAAATG 62 AAATTAAGTCAACCCATCATGAGATGC-AAAAGG * * 3468 ATGAACTGAACTAAGGATAAAGAAATGCTGA-TTTTT-TATATTTATAAGTTAATCTTATTCGAA 1 ATGAACTGAACT-AGGATAAAGAAATGCTGATTTTTTGTATATTTATAAATTAATCTTATTCAAA * 3531 TTAAGTCAACCCATTATGA 65 TTAAGTCAACCCATCATGA 3550 CGTAGCAACG Statistics Matches: 75, Mismatches: 6, Indels: 7 0.85 0.07 0.08 Matches are distributed among these distances: 94 40 0.53 96 5 0.07 99 12 0.16 100 18 0.24 ACGTcount: A:0.38, C:0.10, G:0.14, T:0.38 Consensus pattern (94 bp): ATGAACTGAACTAGGATAAAGAAATGCTGATTTTTTGTATATTTATAAATTAATCTTATTCAAAT TAAGTCAACCCATCATGAGATGCAAAAGG Found at i:6568 original size:34 final size:33 Alignment explanation

Indices: 6485--6569 Score: 100 Period size: 33 Copynumber: 2.5 Consensus size: 33 6475 AATATGGCCG * * * 6485 GTCGCGACCGTATCGCGACCAGCCCGTGGTCAA 1 GTCGAGACCGGATCGCGACCAGCCCGTGGGCAA * * 6518 GTCGCGACCGGATCGCGACCGGCCCGTGGGCTAA 1 GTCGAGACCGGATCGCGACCAGCCCGTGGGC-AA 6552 -TCGAGACCCGGATCGCGA 1 GTCGAGA-CCGGATCGCGA 6570 TTAGCCCACG Statistics Matches: 46, Mismatches: 4, Indels: 3 0.87 0.08 0.06 Matches are distributed among these distances: 33 33 0.72 34 13 0.28 ACGTcount: A:0.18, C:0.35, G:0.34, T:0.13 Consensus pattern (33 bp): GTCGAGACCGGATCGCGACCAGCCCGTGGGCAA Found at i:6608 original size:20 final size:22 Alignment explanation

Indices: 6564--6612 Score: 75 Period size: 20 Copynumber: 2.3 Consensus size: 22 6554 GAGACCCGGA * 6564 TCGCGATTAGCCCACGGGCCAG 1 TCGCGACTAGCCCACGGGCCAG 6586 TCGCGACTA-CCCACGGG-CAG 1 TCGCGACTAGCCCACGGGCCAG 6606 TCGCGAC 1 TCGCGAC 6613 CCGATCCGGT Statistics Matches: 26, Mismatches: 1, Indels: 2 0.90 0.03 0.07 Matches are distributed among these distances: 20 10 0.38 21 8 0.31 22 8 0.31 ACGTcount: A:0.18, C:0.39, G:0.31, T:0.12 Consensus pattern (22 bp): TCGCGACTAGCCCACGGGCCAG Found at i:11107 original size:15 final size:16 Alignment explanation

Indices: 11077--11115 Score: 62 Period size: 16 Copynumber: 2.4 Consensus size: 16 11067 TTACTTTGCT 11077 TTGTTTTCTAGTTTAA 1 TTGTTTTCTAGTTTAA 11093 TTGTTTTCT-GTTTAA 1 TTGTTTTCTAGTTTAA 11108 TTGCTTTT 1 TTG-TTTT 11116 TGTCAACCTC Statistics Matches: 22, Mismatches: 0, Indels: 2 0.92 0.00 0.08 Matches are distributed among these distances: 15 9 0.41 16 13 0.59 ACGTcount: A:0.13, C:0.08, G:0.13, T:0.67 Consensus pattern (16 bp): TTGTTTTCTAGTTTAA Found at i:11406 original size:15 final size:15 Alignment explanation

Indices: 11386--11414 Score: 58 Period size: 15 Copynumber: 1.9 Consensus size: 15 11376 TAATTAGAAA 11386 AAATTAAAATACAAG 1 AAATTAAAATACAAG 11401 AAATTAAAATACAA 1 AAATTAAAATACAA 11415 ATCATTCGGC Statistics Matches: 14, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 15 14 1.00 ACGTcount: A:0.69, C:0.07, G:0.03, T:0.21 Consensus pattern (15 bp): AAATTAAAATACAAG Found at i:13793 original size:16 final size:15 Alignment explanation

Indices: 13769--13809 Score: 55 Period size: 16 Copynumber: 2.7 Consensus size: 15 13759 ATTGATTAAT 13769 TAATAATTAATGAAA 1 TAATAATTAATGAAA ** 13784 TAACTAATTAATTTAA 1 TAA-TAATTAATGAAA 13800 TAATAATTAA 1 TAATAATTAA 13810 ATCTATTAAT Statistics Matches: 23, Mismatches: 2, Indels: 2 0.85 0.07 0.07 Matches are distributed among these distances: 15 10 0.43 16 13 0.57 ACGTcount: A:0.56, C:0.02, G:0.02, T:0.39 Consensus pattern (15 bp): TAATAATTAATGAAA Found at i:13861 original size:22 final size:20 Alignment explanation

Indices: 13833--13873 Score: 64 Period size: 22 Copynumber: 1.9 Consensus size: 20 13823 TTTTCATATT 13833 TTAATAAAATTATAATTAATAA 1 TTAATAAAA-TAT-ATTAATAA 13855 TTAATAAAATATATTAATA 1 TTAATAAAATATATTAATA 13874 TATGAATACT Statistics Matches: 19, Mismatches: 0, Indels: 2 0.90 0.00 0.10 Matches are distributed among these distances: 20 7 0.37 21 3 0.16 22 9 0.47 ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41 Consensus pattern (20 bp): TTAATAAAATATATTAATAA Found at i:14072 original size:17 final size:17 Alignment explanation

Indices: 14043--14075 Score: 50 Period size: 17 Copynumber: 1.9 Consensus size: 17 14033 AATTATTTAG 14043 ATAATCTAAAAATAATA 1 ATAATCTAAAAATAATA 14060 ATAA-CTAATAAATAAT 1 ATAATCTAA-AAATAAT 14076 TAATTTAATT Statistics Matches: 15, Mismatches: 0, Indels: 2 0.88 0.00 0.12 Matches are distributed among these distances: 16 4 0.27 17 11 0.73 ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30 Consensus pattern (17 bp): ATAATCTAAAAATAATA Found at i:14758 original size:46 final size:44 Alignment explanation

Indices: 14661--14748 Score: 117 Period size: 46 Copynumber: 2.0 Consensus size: 44 14651 AGTAAAATTT * * * 14661 TTTTTATGTGTTTGATAATCCATTTTAAATTTCAATGGTTTGATAT 1 TTTTCATGTGTTTGATAATCCATTTTAAATTT--ATGGTTTAATAA 14707 TTTTCATGTGTTTGATAATCCATTTTAAATTT-T-GTTTAATAA 1 TTTTCATGTGTTTGATAATCCATTTTAAATTTATGGTTTAATAA 14749 AAAATTTTCA Statistics Matches: 39, Mismatches: 3, Indels: 4 0.85 0.07 0.09 Matches are distributed among these distances: 42 7 0.18 43 1 0.03 46 31 0.79 ACGTcount: A:0.27, C:0.07, G:0.11, T:0.55 Consensus pattern (44 bp): TTTTCATGTGTTTGATAATCCATTTTAAATTTATGGTTTAATAA Found at i:15733 original size:16 final size:16 Alignment explanation

Indices: 15712--15753 Score: 61 Period size: 14 Copynumber: 2.8 Consensus size: 16 15702 TTATAGTTTG * 15712 AATTCAGTACTTTTAA 1 AATTCAGTACTTTAAA 15728 AATTCAGTA--TTAAA 1 AATTCAGTACTTTAAA 15742 AATTCAGTACTT 1 AATTCAGTACTT 15754 AATCTTTCAG Statistics Matches: 23, Mismatches: 1, Indels: 4 0.82 0.04 0.14 Matches are distributed among these distances: 14 13 0.57 16 10 0.43 ACGTcount: A:0.40, C:0.12, G:0.07, T:0.40 Consensus pattern (16 bp): AATTCAGTACTTTAAA Found at i:15745 original size:14 final size:15 Alignment explanation

Indices: 15712--15770 Score: 66 Period size: 15 Copynumber: 3.9 Consensus size: 15 15702 TTATAGTTTG * 15712 AATTCAGTACTTTTAA 1 AATTCAGTAC-TTAAA 15728 AATTCAGTA-TTAAA 1 AATTCAGTACTTAAA * 15742 AATTCAGTACTTAAT 1 AATTCAGTACTTAAA ** 15757 CTTTCAGTACTTAA 1 AATTCAGTACTTAA 15771 TTTTCAGTTT Statistics Matches: 38, Mismatches: 4, Indels: 3 0.84 0.09 0.07 Matches are distributed among these distances: 14 13 0.34 15 16 0.42 16 9 0.24 ACGTcount: A:0.39, C:0.14, G:0.07, T:0.41 Consensus pattern (15 bp): AATTCAGTACTTAAA Found at i:15777 original size:14 final size:15 Alignment explanation

Indices: 15744--15778 Score: 63 Period size: 15 Copynumber: 2.4 Consensus size: 15 15734 GTATTAAAAA 15744 TTCAGTACTTAATCT 1 TTCAGTACTTAATCT 15759 TTCAGTACTTAAT-T 1 TTCAGTACTTAATCT 15773 TTCAGT 1 TTCAGT 15779 TTTATCAAAC Statistics Matches: 20, Mismatches: 0, Indels: 1 0.95 0.00 0.05 Matches are distributed among these distances: 14 7 0.35 15 13 0.65 ACGTcount: A:0.26, C:0.17, G:0.09, T:0.49 Consensus pattern (15 bp): TTCAGTACTTAATCT Found at i:17078 original size:65 final size:65 Alignment explanation

Indices: 16974--17102 Score: 258 Period size: 65 Copynumber: 2.0 Consensus size: 65 16964 CGTTATTAAC 16974 GGTAACGGCACAGTAACAGCGCCTGTGGTATACATCCAAAATTCCATCTGATTTAGGCCTGATTT 1 GGTAACGGCACAGTAACAGCGCCTGTGGTATACATCCAAAATTCCATCTGATTTAGGCCTGATTT 17039 GGTAACGGCACAGTAACAGCGCCTGTGGTATACATCCAAAATTCCATCTGATTTAGGCCTGATT 1 GGTAACGGCACAGTAACAGCGCCTGTGGTATACATCCAAAATTCCATCTGATTTAGGCCTGATT 17103 AGGTGTGTTT Statistics Matches: 64, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 65 64 1.00 ACGTcount: A:0.28, C:0.23, G:0.22, T:0.27 Consensus pattern (65 bp): GGTAACGGCACAGTAACAGCGCCTGTGGTATACATCCAAAATTCCATCTGATTTAGGCCTGATTT Found at i:17412 original size:27 final size:26 Alignment explanation

Indices: 17382--17443 Score: 81 Period size: 26 Copynumber: 2.3 Consensus size: 26 17372 TATTGTATAA 17382 TTTTCGA-TCCCCTTGTCCGATTGAAGT 1 TTTTCGAGT-CCC-TGTCCGATTGAAGT ** 17409 TTTTCGAGTGTCTGTCCGATTGAAGT 1 TTTTCGAGTCCCTGTCCGATTGAAGT 17435 TTTTCGAGT 1 TTTTCGAGT 17444 GTCGGTTAAG Statistics Matches: 32, Mismatches: 2, Indels: 3 0.86 0.05 0.08 Matches are distributed among these distances: 26 23 0.72 27 8 0.25 28 1 0.03 ACGTcount: A:0.15, C:0.19, G:0.23, T:0.44 Consensus pattern (26 bp): TTTTCGAGTCCCTGTCCGATTGAAGT Found at i:17444 original size:26 final size:26 Alignment explanation

Indices: 17395--17446 Score: 104 Period size: 26 Copynumber: 2.0 Consensus size: 26 17385 TCGATCCCCT 17395 TGTCCGATTGAAGTTTTTCGAGTGTC 1 TGTCCGATTGAAGTTTTTCGAGTGTC 17421 TGTCCGATTGAAGTTTTTCGAGTGTC 1 TGTCCGATTGAAGTTTTTCGAGTGTC 17447 GGTTAAGATG Statistics Matches: 26, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 26 26 1.00 ACGTcount: A:0.15, C:0.15, G:0.27, T:0.42 Consensus pattern (26 bp): TGTCCGATTGAAGTTTTTCGAGTGTC Found at i:17615 original size:9 final size:9 Alignment explanation

Indices: 17597--17630 Score: 50 Period size: 9 Copynumber: 3.7 Consensus size: 9 17587 ATCAATTCGA * 17597 TTATTGGTT 1 TTATTAGTT 17606 TTATTAGTT 1 TTATTAGTT 17615 TTATTAGTT 1 TTATTAGTT 17624 TCTATTA 1 T-TATTA 17631 AGAATTAATC Statistics Matches: 23, Mismatches: 1, Indels: 1 0.92 0.04 0.04 Matches are distributed among these distances: 9 18 0.78 10 5 0.22 ACGTcount: A:0.21, C:0.03, G:0.12, T:0.65 Consensus pattern (9 bp): TTATTAGTT Found at i:18802 original size:29 final size:30 Alignment explanation

Indices: 18760--18817 Score: 100 Period size: 29 Copynumber: 2.0 Consensus size: 30 18750 TAAATAAATC * 18760 AAATCATACATATACATCTCATTTTCACAA 1 AAATCATAAATATACATCTCATTTTCACAA 18790 AAAT-ATAAATATACATCTCATTTTCACA 1 AAATCATAAATATACATCTCATTTTCACA 18818 TTTATTTCCT Statistics Matches: 27, Mismatches: 1, Indels: 1 0.93 0.03 0.03 Matches are distributed among these distances: 29 23 0.85 30 4 0.15 ACGTcount: A:0.45, C:0.21, G:0.00, T:0.34 Consensus pattern (30 bp): AAATCATAAATATACATCTCATTTTCACAA Found at i:29331 original size:145 final size:145 Alignment explanation

Indices: 29063--29332 Score: 479 Period size: 145 Copynumber: 1.9 Consensus size: 145 29053 GTCAGGTGTC * * * 29063 AATGTTTTGTGAAGAATGCATTTTACACGGGAAGGAAACCTTAGGAAACAAATGCAGCATCCACT 1 AATGCTTTGTAAAGAATGCATTTTACACAGGAAGGAAACCTTAGGAAACAAATGCAGCATCCACT * 29128 GCATTCATCTATCATATTGCAAGGAAAATGGAAAAGACTAAAACCGATTTGCCAGATGCAGGAAG 66 CCATTCATCTATCATATTGCAAGGAAAATGGAAAAGACTAAAACCGATTTGCCAGATGCAGGAAG 29193 GAAACCTTAGGTCTG 131 GAAACCTTAGGTCTG 29208 AATGCTTTGTAAAGAATGCATTTTACACAGGAAGGAAACCTTAGGAAACAAATGCAAGCATCCAC 1 AATGCTTTGTAAAGAATGCATTTTACACAGGAAGGAAACCTTAGGAAACAAATGC-AGCATCCAC * 29273 TCCCTTCATCTATCATATTGCAAGGAAAATGGAAAAGACT-AAACCGATTTGCCAGATGCA 65 TCCATTCATCTATCATATTGCAAGGAAAATGGAAAAGACTAAAACCGATTTGCCAGATGCA 29333 TCCATACAAA Statistics Matches: 119, Mismatches: 5, Indels: 2 0.94 0.04 0.02 Matches are distributed among these distances: 145 72 0.61 146 47 0.39 ACGTcount: A:0.38, C:0.19, G:0.20, T:0.23 Consensus pattern (145 bp): AATGCTTTGTAAAGAATGCATTTTACACAGGAAGGAAACCTTAGGAAACAAATGCAGCATCCACT CCATTCATCTATCATATTGCAAGGAAAATGGAAAAGACTAAAACCGATTTGCCAGATGCAGGAAG GAAACCTTAGGTCTG Found at i:32086 original size:1 final size:1 Alignment explanation

Indices: 32080--32163 Score: 51 Period size: 1 Copynumber: 84.0 Consensus size: 1 32070 AAGAAAAGAG * * * * * * * * ** 32080 AAAAAAAAACAAAACAAAAAAAAACAAAAACAAAAACAAAAACAAAAACAAAAACAAAAACCAAA 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA * * * 32145 AACAAAAAACAAAACAAAA 1 AAAAAAAAAAAAAAAAAAA 32164 CAATACATAG Statistics Matches: 59, Mismatches: 24, Indels: 0 0.71 0.29 0.00 Matches are distributed among these distances: 1 59 1.00 ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00 Consensus pattern (1 bp): A Found at i:32099 original size:6 final size:6 Alignment explanation

Indices: 32080--32163 Score: 115 Period size: 6 Copynumber: 14.5 Consensus size: 6 32070 AAGAAAAGAG 32080 AAAA-A AAAAC- AAAAC- AAAA-A AAAACA AAAACA AAAACA AAAACA 1 AAAACA AAAACA AAAACA AAAACA AAAACA AAAACA AAAACA AAAACA 32124 AAAACA AAAACA AAAACCA AAAACA AAAA-A CAAAACA AAA 1 AAAACA AAAACA AAAA-CA AAAACA AAAACA -AAAACA AAA 32164 CAATACATAG Statistics Matches: 73, Mismatches: 0, Indels: 11 0.87 0.00 0.13 Matches are distributed among these distances: 5 18 0.25 6 48 0.66 7 7 0.10 ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00 Consensus pattern (6 bp): AAAACA Found at i:38581 original size:2 final size:2 Alignment explanation

Indices: 38576--38613 Score: 51 Period size: 2 Copynumber: 19.5 Consensus size: 2 38566 TAATGAAAAA * * 38576 AT AT AT AT AT AT AT AT GT AT AT AT GT AT AT AT A- AT AT A 1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A 38614 CCACTAACAG Statistics Matches: 31, Mismatches: 4, Indels: 2 0.84 0.11 0.05 Matches are distributed among these distances: 1 1 0.03 2 30 0.97 ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47 Consensus pattern (2 bp): AT Found at i:38783 original size:16 final size:17 Alignment explanation

Indices: 38762--38795 Score: 61 Period size: 16 Copynumber: 2.1 Consensus size: 17 38752 TTGATTTTTT 38762 TTTTTTATATATA-TAG 1 TTTTTTATATATACTAG 38778 TTTTTTATATATACTAG 1 TTTTTTATATATACTAG 38795 T 1 T 38796 CCTCACTTTC Statistics Matches: 17, Mismatches: 0, Indels: 1 0.94 0.00 0.06 Matches are distributed among these distances: 16 13 0.76 17 4 0.24 ACGTcount: A:0.29, C:0.03, G:0.06, T:0.62 Consensus pattern (17 bp): TTTTTTATATATACTAG Found at i:39834 original size:5 final size:5 Alignment explanation

Indices: 39834--39918 Score: 129 Period size: 5 Copynumber: 16.8 Consensus size: 5 39824 AAATAAAATA 39834 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT 1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT 39884 ATAAT ATAAT AT-AT AATAAT AATAA- ATAAAT ATAA 1 ATAAT ATAAT ATAAT -ATAAT -ATAAT AT-AAT ATAA 39919 GATTTGTATT Statistics Matches: 76, Mismatches: 0, Indels: 8 0.90 0.00 0.10 Matches are distributed among these distances: 4 4 0.05 5 63 0.83 6 9 0.12 ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38 Consensus pattern (5 bp): ATAAT Found at i:43865 original size:27 final size:26 Alignment explanation

Indices: 43820--43892 Score: 103 Period size: 27 Copynumber: 2.7 Consensus size: 26 43810 TGGGTAATCC 43820 TTGGGCTTTTAACTTATTTCATGTG-T 1 TTGGGCTTTTAACTTATTTCAT-TGAT * 43846 TTGGGTTTTTCAACTTATTTCATTGCAT 1 TTGGGCTTTT-AACTTATTTCATTG-AT 43874 TTGGGCTTTTAACTTATTT 1 TTGGGCTTTTAACTTATTT 43893 TTTCATGCAC Statistics Matches: 42, Mismatches: 2, Indels: 5 0.86 0.04 0.10 Matches are distributed among these distances: 26 11 0.26 27 21 0.50 28 10 0.24 ACGTcount: A:0.16, C:0.12, G:0.16, T:0.55 Consensus pattern (26 bp): TTGGGCTTTTAACTTATTTCATTGAT Found at i:43906 original size:29 final size:26 Alignment explanation

Indices: 43819--43910 Score: 94 Period size: 27 Copynumber: 3.3 Consensus size: 26 43809 TTGGGTAATC ** 43819 CTTGGGCTTTTAACTTATTTCATGTG 1 CTTGGGCTTTTAACTTATTTCATGCA * * 43845 TTTGGGTTTTTCAACTTATTTCATTGCA 1 CTTGGGCTTTT-AACTTATTTCA-TGCA * 43873 TTTGGGCTTTTAACTTATTTTTTCATGCA 1 CTTGGGCTTTTAACTTA---TTTCATGCA 43902 CTTGGGCTT 1 CTTGGGCTT 43911 GTTTTGTTAG Statistics Matches: 55, Mismatches: 6, Indels: 7 0.81 0.09 0.10 Matches are distributed among these distances: 26 9 0.16 27 17 0.31 28 12 0.22 29 12 0.22 30 5 0.09 ACGTcount: A:0.15, C:0.15, G:0.17, T:0.52 Consensus pattern (26 bp): CTTGGGCTTTTAACTTATTTCATGCA Found at i:47463 original size:21 final size:21 Alignment explanation

Indices: 47437--47478 Score: 75 Period size: 21 Copynumber: 2.0 Consensus size: 21 47427 GCATCTTAGG 47437 CAACTCCGATGAGCTTGAAAC 1 CAACTCCGATGAGCTTGAAAC * 47458 CAACTCTGATGAGCTTGAAAC 1 CAACTCCGATGAGCTTGAAAC 47479 TTCTTCCTTA Statistics Matches: 20, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 21 20 1.00 ACGTcount: A:0.33, C:0.26, G:0.19, T:0.21 Consensus pattern (21 bp): CAACTCCGATGAGCTTGAAAC Done.