Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012079.1 Corchorus olitorius cultivar O-4 contig12112, 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: 29157
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35


Found at i:3827 original size:14 final size:14

Alignment explanation

Indices: 3808--3836 Score: 58 Period size: 14 Copynumber: 2.1 Consensus size: 14 3798 TTATTGCTTG 3808 AATAATTGAGTCAT 1 AATAATTGAGTCAT 3822 AATAATTGAGTCAT 1 AATAATTGAGTCAT 3836 A 1 A 3837 TGCTAGTTAT Statistics Matches: 15, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 14 15 1.00 ACGTcount: A:0.45, C:0.07, G:0.14, T:0.34 Consensus pattern (14 bp): AATAATTGAGTCAT Found at i:4726 original size:15 final size:15 Alignment explanation

Indices: 4706--4735 Score: 51 Period size: 15 Copynumber: 2.0 Consensus size: 15 4696 GAATGGTAAG 4706 TGATTAAAGCTACTT 1 TGATTAAAGCTACTT * 4721 TGATTATAGCTACTT 1 TGATTAAAGCTACTT 4736 AAGAATGATG Statistics Matches: 14, Mismatches: 1, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 15 14 1.00 ACGTcount: A:0.30, C:0.13, G:0.13, T:0.43 Consensus pattern (15 bp): TGATTAAAGCTACTT Found at i:7444 original size:31 final size:31 Alignment explanation

Indices: 7365--7445 Score: 85 Period size: 29 Copynumber: 2.7 Consensus size: 31 7355 GTCCCTGTAC * 7365 TATTGAAAAAAGATCAATTTAATCCATCCAT 1 TATTGAAAAATGATCAATTTAATCCATCCAT * ** * * 7396 CA-TGAAATCT-ATCAATTTAATCCTTCTAT 1 TATTGAAAAATGATCAATTTAATCCATCCAT * 7425 TATTGAAAAGTGATCAATTTA 1 TATTGAAAAATGATCAATTTA 7446 GTCCCTCCGT Statistics Matches: 39, Mismatches: 9, Indels: 4 0.75 0.17 0.08 Matches are distributed among these distances: 29 18 0.46 30 11 0.28 31 10 0.26 ACGTcount: A:0.41, C:0.15, G:0.07, T:0.37 Consensus pattern (31 bp): TATTGAAAAATGATCAATTTAATCCATCCAT Found at i:8855 original size:18 final size:18 Alignment explanation

Indices: 8832--8869 Score: 67 Period size: 18 Copynumber: 2.1 Consensus size: 18 8822 ACGTCCTCTA * 8832 CCTCTTCTACATCTCAAT 1 CCTCTTCAACATCTCAAT 8850 CCTCTTCAACATCTCAAT 1 CCTCTTCAACATCTCAAT 8868 CC 1 CC 8870 AAATTACCTT Statistics Matches: 19, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 18 19 1.00 ACGTcount: A:0.24, C:0.42, G:0.00, T:0.34 Consensus pattern (18 bp): CCTCTTCAACATCTCAAT Found at i:13833 original size:21 final size:21 Alignment explanation

Indices: 13809--13884 Score: 116 Period size: 21 Copynumber: 3.6 Consensus size: 21 13799 TATATGAAAC * 13809 TTTGGGGTTTGACTATCAAAA 1 TTTGAGGTTTGACTATCAAAA * * 13830 TTTGAGGTTTGACCATCAAAC 1 TTTGAGGTTTGACTATCAAAA * 13851 TTTGGGGTTTGACTATCAAAA 1 TTTGAGGTTTGACTATCAAAA 13872 TTTGAGGTTTGAC 1 TTTGAGGTTTGAC 13885 CATAGTTTGA Statistics Matches: 48, Mismatches: 7, Indels: 0 0.87 0.13 0.00 Matches are distributed among these distances: 21 48 1.00 ACGTcount: A:0.26, C:0.12, G:0.24, T:0.38 Consensus pattern (21 bp): TTTGAGGTTTGACTATCAAAA Found at i:13864 original size:42 final size:42 Alignment explanation

Indices: 13805--13887 Score: 166 Period size: 42 Copynumber: 2.0 Consensus size: 42 13795 GAATTATATG 13805 AAACTTTGGGGTTTGACTATCAAAATTTGAGGTTTGACCATC 1 AAACTTTGGGGTTTGACTATCAAAATTTGAGGTTTGACCATC 13847 AAACTTTGGGGTTTGACTATCAAAATTTGAGGTTTGACCAT 1 AAACTTTGGGGTTTGACTATCAAAATTTGAGGTTTGACCAT 13888 AGTTTGACTA Statistics Matches: 41, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 42 41 1.00 ACGTcount: A:0.29, C:0.13, G:0.22, T:0.36 Consensus pattern (42 bp): AAACTTTGGGGTTTGACTATCAAAATTTGAGGTTTGACCATC Found at i:13893 original size:32 final size:32 Alignment explanation

Indices: 13857--13919 Score: 99 Period size: 32 Copynumber: 2.0 Consensus size: 32 13847 AAACTTTGGG 13857 GTTTGACTATCAAAATTTGAGGTTTGACCATA 1 GTTTGACTATCAAAATTTGAGGTTTGACCATA ** * 13889 GTTTGACTATCAAGCTTTGGGGTTTGACCAT 1 GTTTGACTATCAAAATTTGAGGTTTGACCAT 13920 TAATGACTAT Statistics Matches: 28, Mismatches: 3, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 32 28 1.00 ACGTcount: A:0.25, C:0.14, G:0.22, T:0.38 Consensus pattern (32 bp): GTTTGACTATCAAAATTTGAGGTTTGACCATA Found at i:13930 original size:31 final size:31 Alignment explanation

Indices: 13860--13932 Score: 85 Period size: 32 Copynumber: 2.3 Consensus size: 31 13850 CTTTGGGGTT * 13860 TGACTATCAAAATTTGAGGTTTGACCATAGTT 1 TGACTATCAAAATTTGAGGTTTGACCATAG-A ** * 13892 TGACTATCAAGCTTTGGGGTTTGACCATTA-A 1 TGACTATCAAAATTTGAGGTTTGACCA-TAGA 13923 TGACTATCAA 1 TGACTATCAA 13933 TAATAGATAT Statistics Matches: 36, Mismatches: 4, Indels: 3 0.84 0.09 0.07 Matches are distributed among these distances: 31 10 0.28 32 24 0.67 33 2 0.06 ACGTcount: A:0.30, C:0.15, G:0.19, T:0.36 Consensus pattern (31 bp): TGACTATCAAAATTTGAGGTTTGACCATAGA Found at i:16395 original size:28 final size:28 Alignment explanation

Indices: 16363--16433 Score: 142 Period size: 28 Copynumber: 2.5 Consensus size: 28 16353 ACATGGGCTA 16363 GCACGGCACGACCCATTAAAATGGCATG 1 GCACGGCACGACCCATTAAAATGGCATG 16391 GCACGGCACGACCCATTAAAATGGCATG 1 GCACGGCACGACCCATTAAAATGGCATG 16419 GCACGGCACGACCCA 1 GCACGGCACGACCCA 16434 CGTGCCGGCA Statistics Matches: 43, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 28 43 1.00 ACGTcount: A:0.31, C:0.32, G:0.25, T:0.11 Consensus pattern (28 bp): GCACGGCACGACCCATTAAAATGGCATG Found at i:16461 original size:22 final size:22 Alignment explanation

Indices: 16418--16462 Score: 63 Period size: 22 Copynumber: 2.0 Consensus size: 22 16408 AAAATGGCAT * * 16418 GGCACGGCACGACCCACGTGCC 1 GGCACAGCACGACCCACATGCC * 16440 GGCACAGCACGACCCATATGCC 1 GGCACAGCACGACCCACATGCC 16462 G 1 G 16463 ACGCAGCATG Statistics Matches: 20, Mismatches: 3, Indels: 0 0.87 0.13 0.00 Matches are distributed among these distances: 22 20 1.00 ACGTcount: A:0.22, C:0.42, G:0.29, T:0.07 Consensus pattern (22 bp): GGCACAGCACGACCCACATGCC Found at i:16469 original size:22 final size:22 Alignment explanation

Indices: 16424--16470 Score: 58 Period size: 22 Copynumber: 2.1 Consensus size: 22 16414 GCATGGCACG * * 16424 GCACGACCCACGTGCCGGCACA 1 GCACGACCCACATGCCGACACA * * 16446 GCACGACCCATATGCCGACGCA 1 GCACGACCCACATGCCGACACA 16468 GCA 1 GCA 16471 TGATCCATTT Statistics Matches: 21, Mismatches: 4, Indels: 0 0.84 0.16 0.00 Matches are distributed among these distances: 22 21 1.00 ACGTcount: A:0.26, C:0.43, G:0.26, T:0.06 Consensus pattern (22 bp): GCACGACCCACATGCCGACACA Found at i:17554 original size:31 final size:31 Alignment explanation

Indices: 17519--17603 Score: 86 Period size: 29 Copynumber: 2.8 Consensus size: 31 17509 TTTCACGGAG 17519 GGACTAAATTGATCGTTTTTCAATAATAAAA 1 GGACTAAATTGATCGTTTTTCAATAATAAAA * ** * 17550 GGACTAAATTGA-CAG-ATTTC-ATAATGGAG 1 GGACTAAATTGATC-GTTTTTCAATAATAAAA * * 17579 GGACTAAATTGATCTTTTTTTAATA 1 GGACTAAATTGATCGTTTTTCAATA 17604 GTACAGGGAC Statistics Matches: 43, Mismatches: 7, Indels: 8 0.74 0.12 0.14 Matches are distributed among these distances: 29 18 0.42 30 9 0.21 31 16 0.37 ACGTcount: A:0.38, C:0.09, G:0.16, T:0.36 Consensus pattern (31 bp): GGACTAAATTGATCGTTTTTCAATAATAAAA Found at i:17583 original size:29 final size:31 Alignment explanation

Indices: 17515--17592 Score: 90 Period size: 29 Copynumber: 2.6 Consensus size: 31 17505 CCCGTTTCAC * 17515 GGAGGGACTAAATTGATCGTTTTTCAATAAT 1 GGAGGGACTAAATTGATCGTATTTCAATAAT ** * 17546 AAAAGGACTAAATTGA-CAG-ATTTC-ATAAT 1 GGAGGGACTAAATTGATC-GTATTTCAATAAT 17575 GGAGGGACTAAATTGATC 1 GGAGGGACTAAATTGATC 17593 TTTTTTTAAT Statistics Matches: 38, Mismatches: 7, Indels: 5 0.76 0.14 0.10 Matches are distributed among these distances: 29 18 0.47 30 6 0.16 31 14 0.37 ACGTcount: A:0.38, C:0.10, G:0.22, T:0.29 Consensus pattern (31 bp): GGAGGGACTAAATTGATCGTATTTCAATAAT Found at i:19977 original size:22 final size:22 Alignment explanation

Indices: 19947--19988 Score: 66 Period size: 22 Copynumber: 1.9 Consensus size: 22 19937 GTTTATAATA * * 19947 TTCTTGGGTCATTCGGGTTAAC 1 TTCTCGGGTCATTCAGGTTAAC 19969 TTCTCGGGTCATTCAGGTTA 1 TTCTCGGGTCATTCAGGTTA 19989 CGGATTTGTC Statistics Matches: 18, Mismatches: 2, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 22 18 1.00 ACGTcount: A:0.14, C:0.19, G:0.26, T:0.40 Consensus pattern (22 bp): TTCTCGGGTCATTCAGGTTAAC Found at i:23092 original size:22 final size:22 Alignment explanation

Indices: 23033--23203 Score: 122 Period size: 22 Copynumber: 7.9 Consensus size: 22 23023 AAAAAATCGA * 23033 AGGTTA-CAAAATTTCATA-GAA 1 AGGTTATCAAAATTTCATATG-T * * * 23054 AGATTTATTAAAATTTCATATTT 1 AG-GTTATCAAAATTTCATATGT * * 23077 AGGTTATCAAAGTTTCATATGG 1 AGGTTATCAAAATTTCATATGT * * * 23099 AGTTTATCAAATTTTCATAGGT 1 AGGTTATCAAAATTTCATATGT * 23121 A-ATTATCAAAATTTCATA-GT 1 AGGTTATCAAAATTTCATATGT 23141 -GTGTTATCAAAATTTCATAGTGT 1 AG-GTTATCAAAATTTCATA-TGT * * * 23164 -GGTTATCAAAGTTTAATAGGGT 1 AGGTTATCAAAATTTCATA-TGT * 23186 A-ATTATCAAAATTTCATA 1 AGGTTATCAAAATTTCATA 23204 AAAATATTCA Statistics Matches: 120, Mismatches: 22, Indels: 15 0.76 0.14 0.10 Matches are distributed among these distances: 20 2 0.02 21 33 0.28 22 69 0.57 23 16 0.13 ACGTcount: A:0.38, C:0.08, G:0.13, T:0.40 Consensus pattern (22 bp): AGGTTATCAAAATTTCATATGT Found at i:23127 original size:43 final size:43 Alignment explanation

Indices: 23058--23203 Score: 145 Period size: 43 Copynumber: 3.4 Consensus size: 43 23048 ATAGAAAGAT * * * 23058 TTATTAAAATTTCATA-TTTAGGTTATCAAAGTTTCATATGGAGT- 1 TTATCAAAATTTCATAGTGTA-ATTATCAAAGTTTCATA-GG-GTA * * * * 23102 TTATCAAATTTTCATAG-GTAATTATCAAAATTTCATAGTGTG 1 TTATCAAAATTTCATAGTGTAATTATCAAAGTTTCATAGGGTA ** * 23144 TTATCAAAATTTCATAGTGTGGTTATCAAAGTTTAATAGGGTAA 1 TTATCAAAATTTCATAGTGTAATTATCAAAGTTTCATAGGGT-A 23188 TTATCAAAATTTCATA 1 TTATCAAAATTTCATA 23204 AAAATATTCA Statistics Matches: 85, Mismatches: 13, Indels: 8 0.80 0.12 0.08 Matches are distributed among these distances: 41 2 0.02 42 17 0.20 43 34 0.40 44 32 0.38 ACGTcount: A:0.36, C:0.08, G:0.13, T:0.42 Consensus pattern (43 bp): TTATCAAAATTTCATAGTGTAATTATCAAAGTTTCATAGGGTA Found at i:23299 original size:2 final size:2 Alignment explanation

Indices: 23292--23321 Score: 60 Period size: 2 Copynumber: 15.0 Consensus size: 2 23282 AGGGAAAATT 23292 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 23322 AAAGTACGAA Statistics Matches: 28, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 28 1.00 ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50 Consensus pattern (2 bp): TA Found at i:23415 original size:19 final size:19 Alignment explanation

Indices: 23387--23424 Score: 58 Period size: 19 Copynumber: 2.0 Consensus size: 19 23377 ATATTTCTAA * 23387 ATTTTCATTATTAAATTAT 1 ATTTTAATTATTAAATTAT * 23406 ATTTTAATTATTCAATTAT 1 ATTTTAATTATTAAATTAT 23425 TGAAATAATA Statistics Matches: 17, Mismatches: 2, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 19 17 1.00 ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58 Consensus pattern (19 bp): ATTTTAATTATTAAATTAT Found at i:23423 original size:27 final size:28 Alignment explanation

Indices: 23376--23430 Score: 71 Period size: 27 Copynumber: 2.0 Consensus size: 28 23366 TTTTTTCAAA 23376 TATATTTCTAAATTTTCATTATT-AAAT 1 TATATTTCTAAATTTTCATTATTGAAAT 23403 TATATTT-T-AATTATTCAATTATTGAAAT 1 TATATTTCTAAATT-TTC-ATTATTGAAAT 23431 AATAGGAATT Statistics Matches: 25, Mismatches: 0, Indels: 5 0.83 0.00 0.17 Matches are distributed among these distances: 25 4 0.16 26 4 0.16 27 13 0.52 28 4 0.16 ACGTcount: A:0.38, C:0.05, G:0.02, T:0.55 Consensus pattern (28 bp): TATATTTCTAAATTTTCATTATTGAAAT Found at i:25083 original size:22 final size:22 Alignment explanation

Indices: 25057--25111 Score: 58 Period size: 22 Copynumber: 2.5 Consensus size: 22 25047 ACTATAATAT * 25057 CAAAAAATTATAGGGAGATTAA 1 CAAAAAATCATAGGGAGATTAA ** * * 25079 CAAAATCTCATAGGGAGGTTAT 1 CAAAAAATCATAGGGAGATTAA 25101 C-AAAAATCATA 1 CAAAAAATCATA 25112 AGAAGGTTAC Statistics Matches: 26, Mismatches: 7, Indels: 1 0.76 0.21 0.03 Matches are distributed among these distances: 21 8 0.31 22 18 0.69 ACGTcount: A:0.49, C:0.11, G:0.16, T:0.24 Consensus pattern (22 bp): CAAAAAATCATAGGGAGATTAA Found at i:25141 original size:22 final size:21 Alignment explanation

Indices: 25078--25141 Score: 69 Period size: 21 Copynumber: 3.0 Consensus size: 21 25068 AGGGAGATTA * 25078 ACAAAATCTCAT-AGGGAGGTT 1 ACAAAAT-TCATAAGGAAGGTT * 25099 ATCAAAAATCATAA-GAAGGTT 1 A-CAAAATTCATAAGGAAGGTT 25120 ACAAATATTCATAAGGAAGGTT 1 ACAAA-ATTCATAAGGAAGGTT 25142 TATTAAAATT Statistics Matches: 36, Mismatches: 3, Indels: 7 0.78 0.07 0.15 Matches are distributed among these distances: 20 4 0.11 21 19 0.53 22 13 0.36 ACGTcount: A:0.45, C:0.11, G:0.19, T:0.25 Consensus pattern (21 bp): ACAAAATTCATAAGGAAGGTT Found at i:25188 original size:22 final size:22 Alignment explanation

Indices: 25070--25265 Score: 84 Period size: 22 Copynumber: 9.0 Consensus size: 22 25060 AAAATTATAG * * * * 25070 GGAGATTAACAAAATCTCATAG 1 GGAGTTTATCAAAATTTCATAT * * * 25092 GGAGGTTATCAAAA-ATCATAA 1 GGAGTTTATCAAAATTTCATAT * * * 25113 GAAGGTTA-C-AAATATTCATAA 1 GGAGTTTATCAAAAT-TTCATAT * 25134 GGAAGGTTTATTAAAATTTCATAT 1 GG-A-GTTTATCAAAATTTCATAT ** * * 25158 TTAGGTTATCAAAGTTTCATAT 1 GGAGTTTATCAAAATTTCATAT ** 25180 GGAGTTTATCATGATTTCATA- 1 GGAGTTTATCAAAATTTCATAT * 25201 GGTA-ATTATCAAAATTTCATA- 1 GG-AGTTTATCAAAATTTCATAT * * * 25222 GCGTGGTTATCAAAATTTAATA- 1 G-GAGTTTATCAAAATTTCATAT 25244 GG-GTAATTATCAAAATTTCATA 1 GGAGT--TTATCAAAATTTCATA 25266 AAAATATTCA Statistics Matches: 134, Mismatches: 29, Indels: 22 0.72 0.16 0.12 Matches are distributed among these distances: 19 3 0.02 20 2 0.01 21 37 0.28 22 77 0.57 23 5 0.04 24 6 0.04 25 4 0.03 ACGTcount: A:0.40, C:0.09, G:0.16, T:0.35 Consensus pattern (22 bp): GGAGTTTATCAAAATTTCATAT Found at i:25211 original size:21 final size:21 Alignment explanation

Indices: 25193--25265 Score: 101 Period size: 22 Copynumber: 3.4 Consensus size: 21 25183 GTTTATCATG 25193 ATTTCATAGGTAATTATCAAA 1 ATTTCATAGGTAATTATCAAA ** 25214 ATTTCATAGCGTGGTTATCAAA 1 ATTTCATAG-GTAATTATCAAA * 25236 ATTTAATAGGGTAATTATCAAA 1 ATTTCATA-GGTAATTATCAAA 25258 ATTTCATA 1 ATTTCATA 25266 AAAATATTCA Statistics Matches: 44, Mismatches: 6, Indels: 3 0.83 0.11 0.06 Matches are distributed among these distances: 21 9 0.20 22 34 0.77 23 1 0.02 ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38 Consensus pattern (21 bp): ATTTCATAGGTAATTATCAAA Found at i:25220 original size:43 final size:44 Alignment explanation

Indices: 25163--25265 Score: 129 Period size: 43 Copynumber: 2.4 Consensus size: 44 25153 CATATTTAGG * * ** * 25163 TTATCAAAGTTTCATATG-GAGTTTATCATGATTTCATA-GGTAA 1 TTATCAAAATTTCATA-GCGAGGTTATCAAAATTTAATAGGGTAA * 25206 TTATCAAAATTTCATAGCGTGGTTATCAAAATTTAATAGGGTAA 1 TTATCAAAATTTCATAGCGAGGTTATCAAAATTTAATAGGGTAA 25250 TTATCAAAATTTCATA 1 TTATCAAAATTTCATA 25266 AAAATATTCA Statistics Matches: 52, Mismatches: 6, Indels: 3 0.85 0.10 0.05 Matches are distributed among these distances: 42 1 0.02 43 30 0.58 44 21 0.40 ACGTcount: A:0.37, C:0.10, G:0.14, T:0.40 Consensus pattern (44 bp): TTATCAAAATTTCATAGCGAGGTTATCAAAATTTAATAGGGTAA Found at i:25330 original size:2 final size:2 Alignment explanation

Indices: 25323--25362 Score: 73 Period size: 2 Copynumber: 20.5 Consensus size: 2 25313 GTTAAAACTA 25323 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A 1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A 25363 AAATTTATGG Statistics Matches: 37, Mismatches: 0, Indels: 2 0.95 0.00 0.05 Matches are distributed among these distances: 1 1 0.03 2 36 0.97 ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50 Consensus pattern (2 bp): AT Found at i:29143 original size:15 final size:15 Alignment explanation

Indices: 29114--29154 Score: 73 Period size: 15 Copynumber: 2.7 Consensus size: 15 29104 TACTTTGCTC 29114 TGTTTTCTAGTTTAAT 1 TGTTTTCT-GTTTAAT 29130 TGTTTTCTGTTTAAT 1 TGTTTTCTGTTTAAT 29145 TGTTTTCTGT 1 TGTTTTCTGT 29155 CAA Statistics Matches: 25, Mismatches: 0, Indels: 1 0.96 0.00 0.04 Matches are distributed among these distances: 15 17 0.68 16 8 0.32 ACGTcount: A:0.12, C:0.07, G:0.15, T:0.66 Consensus pattern (15 bp): TGTTTTCTGTTTAAT Done.