Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024206.1 Corchorus olitorius cultivar O-4 contig24239, 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: 49579
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33


Found at i:209 original size:29 final size:31

Alignment explanation

Indices: 135--201 Score: 102 Period size: 31 Copynumber: 2.2 Consensus size: 31 125 CCTGACGGAC 135 TATATCCTTAATTGCTCGTTTTTCGTAACAT 1 TATATCCTTAATTGCTCGTTTTTCGTAACAT * * 166 TATATCCTTAATTGCTTG-TTTT-GTAACGT 1 TATATCCTTAATTGCTCGTTTTTCGTAACAT 195 TATATCC 1 TATATCC 202 CAAATTGCAT Statistics Matches: 34, Mismatches: 2, Indels: 2 0.89 0.05 0.05 Matches are distributed among these distances: 29 13 0.38 30 4 0.12 31 17 0.50 ACGTcount: A:0.22, C:0.18, G:0.10, T:0.49 Consensus pattern (31 bp): TATATCCTTAATTGCTCGTTTTTCGTAACAT Found at i:496 original size:15 final size:17 Alignment explanation

Indices: 471--503 Score: 52 Period size: 16 Copynumber: 2.1 Consensus size: 17 461 TAAAAAGTGA 471 TTTAAATAAAA-TATTT 1 TTTAAATAAAATTATTT 487 TTTAAA-AAAATTATTT 1 TTTAAATAAAATTATTT 503 T 1 T 504 CTTCTGAATA Statistics Matches: 16, Mismatches: 0, Indels: 2 0.89 0.00 0.11 Matches are distributed among these distances: 15 4 0.25 16 12 0.75 ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52 Consensus pattern (17 bp): TTTAAATAAAATTATTT Found at i:633 original size:31 final size:31 Alignment explanation

Indices: 534--673 Score: 133 Period size: 31 Copynumber: 4.6 Consensus size: 31 524 AGATGATAAG * * *** 534 CAAGCAATTTAGGATATAATGTTTTCTG-CCG 1 CAAGCAATTAAGGATATAACGTTTTC-GATTT * *** 565 CAAGCAATTAAGGATATAACG-TTAC-AAAA 1 CAAGCAATTAAGGATATAACGTTTTCGATTT * 594 CAAGCAATTAAGGATATAACGTTTTTGATTT 1 CAAGCAATTAAGGATATAACGTTTTCGATTT * * * 625 TAAGCAATTAAGGATATGATGTTTTCGATTT 1 CAAGCAATTAAGGATATAACGTTTTCGATTT 656 CAAGCAATTAAGGATATA 1 CAAGCAATTAAGGATATA 674 GACATATAGT Statistics Matches: 89, Mismatches: 17, Indels: 6 0.79 0.15 0.05 Matches are distributed among these distances: 29 21 0.24 30 5 0.06 31 63 0.71 ACGTcount: A:0.39, C:0.11, G:0.17, T:0.33 Consensus pattern (31 bp): CAAGCAATTAAGGATATAACGTTTTCGATTT Found at i:886 original size:29 final size:31 Alignment explanation

Indices: 812--878 Score: 111 Period size: 31 Copynumber: 2.2 Consensus size: 31 802 CCTGACGGAC 812 TATATCCTTAATTGCTCGTTTTTCGTAACGT 1 TATATCCTTAATTGCTCGTTTTTCGTAACGT * 843 TATATCCTTAATTGCTTG-TTTT-GTAACGT 1 TATATCCTTAATTGCTCGTTTTTCGTAACGT 872 TATATCC 1 TATATCC 879 CAAATTGCAT Statistics Matches: 35, Mismatches: 1, Indels: 2 0.92 0.03 0.05 Matches are distributed among these distances: 29 14 0.40 30 4 0.11 31 17 0.49 ACGTcount: A:0.21, C:0.18, G:0.12, T:0.49 Consensus pattern (31 bp): TATATCCTTAATTGCTCGTTTTTCGTAACGT Found at i:4663 original size:128 final size:119 Alignment explanation

Indices: 4390--4705 Score: 343 Period size: 128 Copynumber: 2.6 Consensus size: 119 4380 ATGTAGCTAG * * 4390 TGCCTCGTTAAAAACCTTAAG-CTGGAAAACCCAATGGGACAAAACC-AGTCATAAGGAAAAAAG 1 TGCCTCATTAAAAACCTTAAGTC-GGAAAACCCAATGGGACAAAACCGA-TCATAAGGGAAAAAG ** * * * 4453 AGTGCAGCATATCAAGTCCATTTGTCTTCTGGACAAATATTACATGTGCTCTTTAT 64 AGTGCAGCATATCAAGTCCATTTGTCTTCAAGACAAACATTAAATGTGCTCATTAT ** * * 4509 TGCCTCATTAAAAACCTTGTGTCGGAAAACCCAATGGGACAAAACCGAACAGAAGGGAAAAAGAG 1 TGCCTCATTAAAAACCTTAAGTCGGAAAACCCAATGGGACAAAACCGATCATAAGGGAAAAAGAG * * 4574 TGCTAGAGCA-ATTTAAGTCCATGTAAATGTCTTCAAGACAATTACATCTAAATGTGCT-ATTGT 66 TGC---AGCATA-TCAAGTCCAT-T---TGTCTTCAAGACAA--ACAT-TAAATGTGCTCATTAT * ** 4637 TGTCTCATTAAAAACCTTAAGTCGGAAAACCCTGTGGGACAAAACCGATCATAAGGGAAAAAGAG 1 TGCCTCATTAAAAACCTTAAGTCGGAAAACCCAATGGGACAAAACCGATCATAAGGGAAAAAGAG 4702 TGCA 66 TGCA 4706 ACGCACTTTA Statistics Matches: 164, Mismatches: 20, Indels: 20 0.80 0.10 0.10 Matches are distributed among these distances: 119 58 0.35 120 2 0.01 121 1 0.01 122 13 0.08 123 1 0.01 125 1 0.01 126 12 0.07 128 67 0.41 129 9 0.05 ACGTcount: A:0.38, C:0.19, G:0.19, T:0.24 Consensus pattern (119 bp): TGCCTCATTAAAAACCTTAAGTCGGAAAACCCAATGGGACAAAACCGATCATAAGGGAAAAAGAG TGCAGCATATCAAGTCCATTTGTCTTCAAGACAAACATTAAATGTGCTCATTAT Found at i:8704 original size:90 final size:90 Alignment explanation

Indices: 8474--8807 Score: 389 Period size: 90 Copynumber: 3.6 Consensus size: 90 8464 ATTTTGAAAG * * * * *** * * 8474 GTAAAATCATGACAACTTCTGGTGTCAATTGAATAAAATTATGACATCTTCAAATGTCTATTGGA 1 GTAAAATCATGACAACTTCTGGTGTCAATTG--CAAGATCATGACAACTTCTGGTGTCAATT-GC * 8539 AATTTATCATGACAACTTCTGGTGTCAATT 63 AA--CATCATGACAACTTCTGGTGTCAATT * * ** * 8569 GAATAAAATTATGACATCTTCAAGTATCAATTGCAAGATCATGACAACTTCTGGTGTCAATTGCA 1 G--TAAAATCATGACAACTTCTGGTGTCAATTGCAAGATCATGACAACTTCTGGTGTCAATTGCA 8634 ACATCATGACAACTTCTGGTGTCAATT 64 ACATCATGACAACTTCTGGTGTCAATT * * * 8661 GCAACATCATGACAACTTCTGGTGTCAATTGCAAGATCATGACAACTTCTGGTGTCAATTGCAAG 1 GTAAAATCATGACAACTTCTGGTGTCAATTGCAAGATCATGACAACTTCTGGTGTCAATTGCAAC * * 8726 ATTATGACAACTTCTGGTGTCATTT 66 ATCATGACAACTTCTGGTGTCAATT * * * * 8751 GTAAGACCATGACAACTTCTGGTGTCAATTGTAAGACCATGACAACTTCTGGTGTCA 1 GTAAAATCATGACAACTTCTGGTGTCAATTGCAAGATCATGACAACTTCTGGTGTCA 8808 TTTGTAAGTA Statistics Matches: 207, Mismatches: 30, Indels: 9 0.84 0.12 0.04 Matches are distributed among these distances: 90 131 0.63 92 26 0.13 94 3 0.01 95 22 0.11 97 25 0.12 ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32 Consensus pattern (90 bp): GTAAAATCATGACAACTTCTGGTGTCAATTGCAAGATCATGACAACTTCTGGTGTCAATTGCAAC ATCATGACAACTTCTGGTGTCAATT Found at i:8808 original size:60 final size:60 Alignment explanation

Indices: 8479--8815 Score: 386 Period size: 60 Copynumber: 5.5 Consensus size: 60 8469 GAAAGGTAAA * * * *** * * * 8479 ATCATGACAACTTCTGGTGTCAATTGAATAAAATTATGACATCTTCAAATGTCTATTGGAAATTT 1 ATCATGACAACTTCTGGTGTCAATTG--TAAGATCATGACAACTTCTGGTGTCAATT-GCAA--G * * * ** * 8544 ATCATGACAACTTCTGGTGTCAATTGAATAAAATTATGACATCTTCAAGTATCAATTGCAAG 1 ATCATGACAACTTCTGGTGTCAATTG--TAAGATCATGACAACTTCTGGTGTCAATTGCAAG * * * 8606 ATCATGACAACTTCTGGTGTCAATTGCAACATCATGACAACTTCTGGTGTCAATTGCAAC 1 ATCATGACAACTTCTGGTGTCAATTGTAAGATCATGACAACTTCTGGTGTCAATTGCAAG * 8666 ATCATGACAACTTCTGGTGTCAATTGCAAGATCATGACAACTTCTGGTGTCAATTGCAAG 1 ATCATGACAACTTCTGGTGTCAATTGTAAGATCATGACAACTTCTGGTGTCAATTGCAAG * * * * 8726 ATTATGACAACTTCTGGTGTCATTTGTAAGACCATGACAACTTCTGGTGTCAATTGTAAG 1 ATCATGACAACTTCTGGTGTCAATTGTAAGATCATGACAACTTCTGGTGTCAATTGCAAG * * 8786 ACCATGACAACTTCTGGTGTCATTTGTAAG 1 ATCATGACAACTTCTGGTGTCAATTGTAAG 8816 TAGAGTAAAT Statistics Matches: 250, Mismatches: 22, Indels: 5 0.90 0.08 0.02 Matches are distributed among these distances: 60 167 0.67 62 26 0.10 64 3 0.01 65 54 0.22 ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33 Consensus pattern (60 bp): ATCATGACAACTTCTGGTGTCAATTGTAAGATCATGACAACTTCTGGTGTCAATTGCAAG Found at i:8815 original size:30 final size:30 Alignment explanation

Indices: 8544--8807 Score: 375 Period size: 30 Copynumber: 8.7 Consensus size: 30 8534 TTGGAAATTT * * 8544 ATCATGACAACTTCTGGTGTCAATTGAATAAA 1 ATCATGACAACTTCTGGTGTCAATTG--CAAG * * ** * 8576 ATTATGACATCTTCAAGTATCAATTGCAAG 1 ATCATGACAACTTCTGGTGTCAATTGCAAG * 8606 ATCATGACAACTTCTGGTGTCAATTGCAAC 1 ATCATGACAACTTCTGGTGTCAATTGCAAG * 8636 ATCATGACAACTTCTGGTGTCAATTGCAAC 1 ATCATGACAACTTCTGGTGTCAATTGCAAG 8666 ATCATGACAACTTCTGGTGTCAATTGCAAG 1 ATCATGACAACTTCTGGTGTCAATTGCAAG 8696 ATCATGACAACTTCTGGTGTCAATTGCAAG 1 ATCATGACAACTTCTGGTGTCAATTGCAAG * * * 8726 ATTATGACAACTTCTGGTGTCATTTGTAAG 1 ATCATGACAACTTCTGGTGTCAATTGCAAG * * 8756 ACCATGACAACTTCTGGTGTCAATTGTAAG 1 ATCATGACAACTTCTGGTGTCAATTGCAAG * 8786 ACCATGACAACTTCTGGTGTCA 1 ATCATGACAACTTCTGGTGTCA 8808 TTTGTAAGTA Statistics Matches: 212, Mismatches: 20, Indels: 2 0.91 0.09 0.01 Matches are distributed among these distances: 30 191 0.90 32 21 0.10 ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31 Consensus pattern (30 bp): ATCATGACAACTTCTGGTGTCAATTGCAAG Found at i:14222 original size:16 final size:16 Alignment explanation

Indices: 14201--14235 Score: 54 Period size: 16 Copynumber: 2.2 Consensus size: 16 14191 AGTTACTCAG 14201 TTAGGAG-TGGAGCATC 1 TTAGGAGTTGG-GCATC 14217 TTAGGAGTTGGGCATC 1 TTAGGAGTTGGGCATC 14233 TTA 1 TTA 14236 TATGTGCTTG Statistics Matches: 18, Mismatches: 0, Indels: 2 0.90 0.00 0.10 Matches are distributed among these distances: 16 15 0.83 17 3 0.17 ACGTcount: A:0.23, C:0.11, G:0.34, T:0.31 Consensus pattern (16 bp): TTAGGAGTTGGGCATC Found at i:19100 original size:20 final size:20 Alignment explanation

Indices: 19039--19106 Score: 63 Period size: 20 Copynumber: 3.5 Consensus size: 20 19029 TTAAACTAAA 19039 ACTCGATAATTTATATTTCT 1 ACTCGATAATTTATATTTCT * * 19059 A-T--TTCATTTA-ACTTTGCT 1 ACTCGATAATTTATA-TTT-CT 19077 ACTCGATAATTTATATTTCT 1 ACTCGATAATTTATATTTCT * 19097 ACTCTATAAT 1 ACTCGATAAT 19107 CTTAAATAAT Statistics Matches: 37, Mismatches: 5, Indels: 12 0.69 0.09 0.22 Matches are distributed among these distances: 16 1 0.03 17 9 0.24 18 3 0.08 19 2 0.05 20 12 0.32 21 9 0.24 22 1 0.03 ACGTcount: A:0.29, C:0.16, G:0.04, T:0.50 Consensus pattern (20 bp): ACTCGATAATTTATATTTCT Found at i:20452 original size:18 final size:18 Alignment explanation

Indices: 20413--20474 Score: 54 Period size: 18 Copynumber: 3.2 Consensus size: 18 20403 TTATATTACA * 20413 TATAAAAATAAAACGTATAT 1 TATAAACATAAAA--TATAT 20433 ATATTAAACATAAAATATAT 1 -TA-TAAACATAAAATATAT * 20453 TATAAATATAAAA-ATTAT 1 TATAAACATAAAATA-TAT 20471 TATA 1 TATA 20475 TTATATATAT Statistics Matches: 37, Mismatches: 2, Indels: 7 0.80 0.04 0.15 Matches are distributed among these distances: 17 1 0.03 18 17 0.46 19 2 0.05 20 5 0.14 21 2 0.05 22 10 0.27 ACGTcount: A:0.60, C:0.03, G:0.02, T:0.35 Consensus pattern (18 bp): TATAAACATAAAATATAT Found at i:23504 original size:6 final size:6 Alignment explanation

Indices: 23493--23546 Score: 108 Period size: 6 Copynumber: 9.0 Consensus size: 6 23483 TGCTTCGTCG 23493 CCGCAT CCGCAT CCGCAT CCGCAT CCGCAT CCGCAT CCGCAT CCGCAT 1 CCGCAT CCGCAT CCGCAT CCGCAT CCGCAT CCGCAT CCGCAT CCGCAT 23541 CCGCAT 1 CCGCAT 23547 ACCAGGGTGG Statistics Matches: 48, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 6 48 1.00 ACGTcount: A:0.17, C:0.50, G:0.17, T:0.17 Consensus pattern (6 bp): CCGCAT Found at i:32155 original size:20 final size:20 Alignment explanation

Indices: 32112--32151 Score: 55 Period size: 20 Copynumber: 2.0 Consensus size: 20 32102 TCTGTTAAAC * * 32112 GTTGCTTTGTTGTTATTTTT 1 GTTGCTTTGTGGTTATTTTG 32132 GTTGCTTTGTGGTT-TTTTG 1 GTTGCTTTGTGGTTATTTTG 32151 G 1 G 32152 GTTGAATCCA Statistics Matches: 18, Mismatches: 2, Indels: 1 0.86 0.10 0.05 Matches are distributed among these distances: 19 5 0.28 20 13 0.72 ACGTcount: A:0.03, C:0.05, G:0.28, T:0.65 Consensus pattern (20 bp): GTTGCTTTGTGGTTATTTTG Found at i:36468 original size:18 final size:19 Alignment explanation

Indices: 36431--36469 Score: 53 Period size: 18 Copynumber: 2.1 Consensus size: 19 36421 TTCCAAATCC 36431 CTGTTGTTTACCTCTATTT 1 CTGTTGTTTACCTCTATTT * * 36450 CTGTTTTTTA-CTTTATTT 1 CTGTTGTTTACCTCTATTT 36468 CT 1 CT 36470 CTCAAACAGT Statistics Matches: 18, Mismatches: 2, Indels: 1 0.86 0.10 0.05 Matches are distributed among these distances: 18 9 0.50 19 9 0.50 ACGTcount: A:0.10, C:0.18, G:0.08, T:0.64 Consensus pattern (19 bp): CTGTTGTTTACCTCTATTT Found at i:38951 original size:15 final size:14 Alignment explanation

Indices: 38926--38955 Score: 51 Period size: 15 Copynumber: 2.1 Consensus size: 14 38916 AATAAAAACA 38926 AATATTTTTATTTT 1 AATATTTTTATTTT 38940 AATATATTTTATTTT 1 AATAT-TTTTATTTT 38955 A 1 A 38956 TTTGAAAATT Statistics Matches: 15, Mismatches: 0, Indels: 1 0.94 0.00 0.06 Matches are distributed among these distances: 14 5 0.33 15 10 0.67 ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67 Consensus pattern (14 bp): AATATTTTTATTTT Found at i:39955 original size:15 final size:14 Alignment explanation

Indices: 39935--39964 Score: 51 Period size: 15 Copynumber: 2.1 Consensus size: 14 39925 AATTTTCGAA 39935 TAAAATAAAATATAT 1 TAAAATAAAA-ATAT 39950 TAAAATAAAAATAT 1 TAAAATAAAAATAT 39964 T 1 T 39965 TATTTTTATT Statistics Matches: 15, Mismatches: 0, Indels: 1 0.94 0.00 0.06 Matches are distributed among these distances: 14 5 0.33 15 10 0.67 ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33 Consensus pattern (14 bp): TAAAATAAAAATAT Found at i:42032 original size:30 final size:30 Alignment explanation

Indices: 41923--42130 Score: 166 Period size: 33 Copynumber: 6.6 Consensus size: 30 41913 ACTCTCCAAA * * * * 41923 TGACACCAGAAATTGTCATGATAAATCTCCAAA 1 TGACACCAGAAGTTGTCATGAT--CT-TACAAT * * * * 41956 TGGCACCAGAAGTTGTCATGATGAATCTCCAAA 1 TGACACCAGAAGTTGTCATGAT--CT-TACAAT * * 41989 TAACACCATAAGTTGTCATGATCTTACAAT 1 TGACACCAGAAGTTGTCATGATCTTACAAT * 42019 TGACACCAGAAGTTGTCAATGTTCTTACAAT 1 TGACACCAGAAGTTGTC-ATGATCTTACAAT * 42050 TGACACCAGAAGTTGTCAATGTTCTTACAA- 1 TGACACCAGAAGTTGTC-ATGATCTTACAAT * * * 42080 TGACACCGGAAGTTGTCATAATTTTATTCAAT 1 TGACACCAGAAGTTGTCATGATCTTA--CAAT * * 42112 TGACACAAGATGTTGTCAT 1 TGACACCAGAAGTTGTCAT 42131 ATACACTATT Statistics Matches: 152, Mismatches: 19, Indels: 9 0.84 0.11 0.05 Matches are distributed among these distances: 29 6 0.04 30 35 0.23 31 46 0.30 32 16 0.11 33 49 0.32 ACGTcount: A:0.35, C:0.19, G:0.16, T:0.30 Consensus pattern (30 bp): TGACACCAGAAGTTGTCATGATCTTACAAT Found at i:42048 original size:31 final size:31 Alignment explanation

Indices: 41991--42129 Score: 176 Period size: 31 Copynumber: 4.5 Consensus size: 31 41981 TCTCCAAATA * * 41991 ACACCATAAGTTGTC-ATGATCTTACAATTG 1 ACACCAGAAGTTGTCAATGTTCTTACAATTG 42021 ACACCAGAAGTTGTCAATGTTCTTACAATTG 1 ACACCAGAAGTTGTCAATGTTCTTACAATTG 42052 ACACCAGAAGTTGTCAATGTTCTTACAA-TG 1 ACACCAGAAGTTGTCAATGTTCTTACAATTG * * * 42082 ACACCGGAAGTTGTCATAATTTTATT-CAATTG 1 ACACCAGAAGTTGTC--AATGTTCTTACAATTG * * 42114 ACACAAGATGTTGTCA 1 ACACCAGAAGTTGTCA 42130 TATACACTAT Statistics Matches: 97, Mismatches: 8, Indels: 8 0.86 0.07 0.07 Matches are distributed among these distances: 30 31 0.32 31 45 0.46 32 21 0.22 ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32 Consensus pattern (31 bp): ACACCAGAAGTTGTCAATGTTCTTACAATTG Found at i:42067 original size:61 final size:60 Alignment explanation

Indices: 41991--42130 Score: 174 Period size: 61 Copynumber: 2.3 Consensus size: 60 41981 TCTCCAAATA * * 41991 ACACCATAAGTTGTCATGATCTTACAATTGACACCAGAAGTTGTC-AATGTTCTTACAATTG 1 ACACCAGAAGTTGTCATGATCTTACAA-TGACACCAGAAGTTGTCAAATGTTATT-CAATTG * * * 42052 ACACCAGAAGTTGTCAATGTTCTTACAATGACACCGGAAGTTGTCATAATTTTATTCAATTG 1 ACACCAGAAGTTGTC-ATGATCTTACAATGACACCAGAAGTTGTCA-AATGTTATTCAATTG * * 42114 ACACAAGATGTTGTCAT 1 ACACCAGAAGTTGTCAT 42131 ATACACTATT Statistics Matches: 69, Mismatches: 7, Indels: 6 0.84 0.09 0.07 Matches are distributed among these distances: 61 32 0.46 62 30 0.43 63 7 0.10 ACGTcount: A:0.33, C:0.19, G:0.16, T:0.33 Consensus pattern (60 bp): ACACCAGAAGTTGTCATGATCTTACAATGACACCAGAAGTTGTCAAATGTTATTCAATTG Found at i:44246 original size:33 final size:33 Alignment explanation

Indices: 44183--44246 Score: 83 Period size: 33 Copynumber: 1.9 Consensus size: 33 44173 ATCTTGATTA * ** 44183 ATATTGCCCTTGAAGAGGCACAAATGCATGAGC 1 ATATTGCCCCTGAAGAGGCACAAACCCATGAGC * * 44216 ATATTGCCCCTGTAGTGGCACAAACCCATGA 1 ATATTGCCCCTGAAGAGGCACAAACCCATGA 44247 AAAGATCACC Statistics Matches: 26, Mismatches: 5, Indels: 0 0.84 0.16 0.00 Matches are distributed among these distances: 33 26 1.00 ACGTcount: A:0.31, C:0.25, G:0.22, T:0.22 Consensus pattern (33 bp): ATATTGCCCCTGAAGAGGCACAAACCCATGAGC Done.