Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008101.1 Corchorus capsularis cultivar CVL-1 contig08122, 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: 90815
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:2618 original size:33 final size:33

Alignment explanation

Indices: 2581--2743 Score: 162 Period size: 33 Copynumber: 4.9 Consensus size: 33 2571 GGCGGCTGAG 2581 CCATGGCCAAGCCGCCCTCCTGGGGCGGCACTA 1 CCATGGCCAAGCCGCCCTCCTGGGGCGGCACTA * * 2614 CCATGGCCAGGCCG-CCTCCCTGGGGCGGCCCTA 1 CCATGGCCAAGCCGCCCT-CCTGGGGCGGCACTA 2647 CCATGG--ATAGACCGCCC-CCTTGGGGCGGCACTA 1 CCATGGCCA-AG-CCGCCCTCC-TGGGGCGGCACTA * * 2680 CCATGGCCAGGCCG-CCTCCCTGGGGCGGCCCTA 1 CCATGGCCAAGCCGCCCT-CCTGGGGCGGCACTA 2713 CCATGG--ATAGACCGCCC-CCTTGGGGCGGCAC 1 CCATGGCCA-AG-CCGCCCTCC-TGGGGCGGCAC 2744 CGGTACTAAA Statistics Matches: 109, Mismatches: 8, Indels: 26 0.76 0.06 0.18 Matches are distributed among these distances: 31 2 0.02 32 11 0.10 33 88 0.81 34 7 0.06 35 1 0.01 ACGTcount: A:0.13, C:0.42, G:0.32, T:0.13 Consensus pattern (33 bp): CCATGGCCAAGCCGCCCTCCTGGGGCGGCACTA Found at i:2671 original size:66 final size:66 Alignment explanation

Indices: 2592--2743 Score: 288 Period size: 66 Copynumber: 2.3 Consensus size: 66 2582 CATGGCCAAG 2592 CCGCCCTCC-TGGGGCGGCACTACCATGGCCAGGCCGCCTCCCTGGGGCGGCCCTACCATGGATA 1 CCGCCC-CCTTGGGGCGGCACTACCATGGCCAGGCCGCCTCCCTGGGGCGGCCCTACCATGGATA 2656 GA 65 GA 2658 CCGCCCCCTTGGGGCGGCACTACCATGGCCAGGCCGCCTCCCTGGGGCGGCCCTACCATGGATAG 1 CCGCCCCCTTGGGGCGGCACTACCATGGCCAGGCCGCCTCCCTGGGGCGGCCCTACCATGGATAG 2723 A 66 A 2724 CCGCCCCCTTGGGGCGGCAC 1 CCGCCCCCTTGGGGCGGCAC 2744 CGGTACTAAA Statistics Matches: 85, Mismatches: 0, Indels: 2 0.98 0.00 0.02 Matches are distributed among these distances: 65 2 0.02 66 83 0.98 ACGTcount: A:0.12, C:0.42, G:0.32, T:0.13 Consensus pattern (66 bp): CCGCCCCCTTGGGGCGGCACTACCATGGCCAGGCCGCCTCCCTGGGGCGGCCCTACCATGGATAG A Found at i:2896 original size:32 final size:32 Alignment explanation

Indices: 2804--2887 Score: 125 Period size: 32 Copynumber: 2.6 Consensus size: 32 2794 AAAAAGCCTT * * 2804 GCCGCCCTAGTGGGGTGGCTAGCCGTGGCAGA 1 GCCGTCCTAGTGGGGAGGCTAGCCGTGGCAGA * 2836 GCCGTCCTAGT-GGGACGGCTAGCCGTGGCGGA 1 GCCGTCCTAGTGGGGA-GGCTAGCCGTGGCAGA 2868 GCCGTCCTAGTGGGGAGGCT 1 GCCGTCCTAGTGGGGAGGCT 2888 CCGCGTGGCT Statistics Matches: 47, Mismatches: 3, Indels: 4 0.87 0.06 0.07 Matches are distributed among these distances: 31 3 0.06 32 40 0.85 33 4 0.09 ACGTcount: A:0.12, C:0.27, G:0.44, T:0.17 Consensus pattern (32 bp): GCCGTCCTAGTGGGGAGGCTAGCCGTGGCAGA Found at i:4529 original size:2 final size:2 Alignment explanation

Indices: 4522--4557 Score: 54 Period size: 2 Copynumber: 18.0 Consensus size: 2 4512 CACAACACAA * * 4522 CT CT CT CT CT CT CT GT CT GT CT CT CT CT CT CT CT CT 1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT 4558 AATTTTCTCT Statistics Matches: 30, Mismatches: 4, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 2 30 1.00 ACGTcount: A:0.00, C:0.44, G:0.06, T:0.50 Consensus pattern (2 bp): CT Found at i:7125 original size:19 final size:19 Alignment explanation

Indices: 7101--7137 Score: 74 Period size: 19 Copynumber: 1.9 Consensus size: 19 7091 TGTTTAGTAC 7101 ACCGTTTCACCACCGTTTG 1 ACCGTTTCACCACCGTTTG 7120 ACCGTTTCACCACCGTTT 1 ACCGTTTCACCACCGTTT 7138 TGGGTCTAAA Statistics Matches: 18, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 19 18 1.00 ACGTcount: A:0.16, C:0.38, G:0.14, T:0.32 Consensus pattern (19 bp): ACCGTTTCACCACCGTTTG Found at i:18390 original size:28 final size:31 Alignment explanation

Indices: 18358--18438 Score: 87 Period size: 33 Copynumber: 2.6 Consensus size: 31 18348 TTCCCCCAAT 18358 ATCCTG-T-AACCGC-TTTGGGTCTCGACTA 1 ATCCTGTTGAACCGCGTTTGGGTCTCGACTA * 18386 ATCCTGAGTTGAGCCGCGTTTGGGTCTCGACTA 1 ATCCT--GTTGAACCGCGTTTGGGTCTCGACTA * 18419 ATCCTGAGTTGAGCCGCGTT 1 ATCCT--GTTGAACCGCGTT 18439 GAACCCCCAA Statistics Matches: 47, Mismatches: 1, Indels: 5 0.89 0.02 0.09 Matches are distributed among these distances: 28 5 0.11 30 1 0.02 31 1 0.02 32 5 0.11 33 35 0.74 ACGTcount: A:0.16, C:0.26, G:0.27, T:0.31 Consensus pattern (31 bp): ATCCTGTTGAACCGCGTTTGGGTCTCGACTA Found at i:18413 original size:33 final size:33 Alignment explanation

Indices: 18367--18438 Score: 137 Period size: 33 Copynumber: 2.2 Consensus size: 33 18357 TATCCTGTAA 18367 CCGC-TTTGGGTCTCGACTAATCCTGAGTTGAG 1 CCGCGTTTGGGTCTCGACTAATCCTGAGTTGAG 18399 CCGCGTTTGGGTCTCGACTAATCCTGAGTTGAG 1 CCGCGTTTGGGTCTCGACTAATCCTGAGTTGAG 18432 CCGCGTT 1 CCGCGTT 18439 GAACCCCCAA Statistics Matches: 39, Mismatches: 0, Indels: 1 0.98 0.00 0.03 Matches are distributed among these distances: 32 4 0.10 33 35 0.90 ACGTcount: A:0.14, C:0.26, G:0.29, T:0.31 Consensus pattern (33 bp): CCGCGTTTGGGTCTCGACTAATCCTGAGTTGAG Found at i:22840 original size:18 final size:18 Alignment explanation

Indices: 22817--22852 Score: 63 Period size: 18 Copynumber: 2.0 Consensus size: 18 22807 TTTGAGTACT 22817 CTACAGGCCCAGGTGATG 1 CTACAGGCCCAGGTGATG * 22835 CTACAGGTCCAGGTGATG 1 CTACAGGCCCAGGTGATG 22853 GTAAGCCAAG Statistics Matches: 17, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 18 17 1.00 ACGTcount: A:0.22, C:0.25, G:0.33, T:0.19 Consensus pattern (18 bp): CTACAGGCCCAGGTGATG Found at i:27591 original size:18 final size:18 Alignment explanation

Indices: 27558--27634 Score: 109 Period size: 19 Copynumber: 4.1 Consensus size: 18 27548 CATTCTCTAT 27558 TTTCCATCTCCAAAAATA 1 TTTCCATCTCCAAAAATA * 27576 TCTCCATTCTCCAAAAATA 1 TTTCCA-TCTCCAAAAATA 27595 TTTTCCATCTCCAAAAATA 1 -TTTCCATCTCCAAAAATA * 27614 TTTCCATTCTCTAAAAATA 1 TTTCCA-TCTCCAAAAATA 27633 TT 1 TT 27635 ATGCTTGTTT Statistics Matches: 53, Mismatches: 3, Indels: 5 0.87 0.05 0.08 Matches are distributed among these distances: 18 11 0.21 19 37 0.70 20 5 0.09 ACGTcount: A:0.36, C:0.26, G:0.00, T:0.38 Consensus pattern (18 bp): TTTCCATCTCCAAAAATA Found at i:27606 original size:38 final size:38 Alignment explanation

Indices: 27555--27634 Score: 142 Period size: 38 Copynumber: 2.1 Consensus size: 38 27545 GAACATTCTC 27555 TATTTTCCATCTCCAAAAATATCTCCATTCTCCAAAAA 1 TATTTTCCATCTCCAAAAATATCTCCATTCTCCAAAAA * * 27593 TATTTTCCATCTCCAAAAATATTTCCATTCTCTAAAAA 1 TATTTTCCATCTCCAAAAATATCTCCATTCTCCAAAAA 27631 TATT 1 TATT 27635 ATGCTTGTTT Statistics Matches: 40, Mismatches: 2, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 38 40 1.00 ACGTcount: A:0.36, C:0.25, G:0.00, T:0.39 Consensus pattern (38 bp): TATTTTCCATCTCCAAAAATATCTCCATTCTCCAAAAA Found at i:39944 original size:70 final size:70 Alignment explanation

Indices: 39862--40094 Score: 288 Period size: 70 Copynumber: 3.2 Consensus size: 70 39852 TTGTTTAGGT * * * 39862 TTTTA-TAGTTTTACTCAACTAAAAATTCTATTTTTATTTAATTAAATATAATATCTTTATAATT 1 TTTTACTA-TTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCTTTATAATT 39926 ATTTTA 65 ATTTTA * 39932 TTTTACTATTTTACTCAACTAAAAACTATATTTTTATATAATTAAATCTAATATCCTTATAGCTA 1 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATAT-CTT-TA--TA * 39997 TTATATTTTACCA 62 AT-TATTTT---A * * * 40010 TTTTACTATTTTACTCAACTAAAAACTCAATTTTTATATAATTAAATCTAATATCCTTATAACTA 1 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCTTTATAATTA * 40075 TTATA 66 TTTTA * 40080 TTTTACAATTTTACT 1 TTTTACTATTTTACT 40095 ATTTTAGTTA Statistics Matches: 142, Mismatches: 12, Indels: 18 0.83 0.07 0.10 Matches are distributed among these distances: 70 62 0.44 71 5 0.04 72 2 0.01 73 5 0.04 74 5 0.04 75 6 0.04 76 2 0.01 77 2 0.01 78 53 0.37 ACGTcount: A:0.37, C:0.12, G:0.01, T:0.50 Consensus pattern (70 bp): TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCTTTATAATTA TTTTA Found at i:39944 original size:78 final size:77 Alignment explanation

Indices: 39862--40100 Score: 332 Period size: 78 Copynumber: 3.2 Consensus size: 77 39852 TTGTTTAGGT * * * 39862 TTTTA-TAGTTTTACTCAACTAAAAATTCTATTTTTATTTAATTAAATATAATAT-CTT-T-A-T 1 TTTTACTA-TTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACT * 39922 AAT-TATTTT--A 65 ATTATATTTTACA * * 39932 TTTTACTATTTTACTCAACTAAAAACTATATTTTTATATAATTAAATCTAATATCCTTATAGCTA 1 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTA 39997 TTATATTTTACCA 66 TTATATTTTA-CA * 40010 TTTTACTATTTTACTCAACTAAAAACTCAATTTTTATATAATTAAATCTAATATCCTTATAACTA 1 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTA 40075 TTATATTTTACAA 66 TTATATTTTAC-A 40088 TTTTACTATTTTA 1 TTTTACTATTTTA 40101 GTTAAAAAAA Statistics Matches: 150, Mismatches: 9, Indels: 12 0.88 0.05 0.07 Matches are distributed among these distances: 70 47 0.31 71 5 0.03 72 1 0.01 74 3 0.02 75 6 0.04 77 1 0.01 78 87 0.58 ACGTcount: A:0.37, C:0.12, G:0.01, T:0.50 Consensus pattern (77 bp): TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTA TTATATTTTACA Found at i:41976 original size:5 final size:5 Alignment explanation

Indices: 41966--42005 Score: 80 Period size: 5 Copynumber: 8.0 Consensus size: 5 41956 ACTCTGCAGC 41966 ACAGA ACAGA ACAGA ACAGA ACAGA ACAGA ACAGA ACAGA 1 ACAGA ACAGA ACAGA ACAGA ACAGA ACAGA ACAGA ACAGA 42006 GCTTCCATGG Statistics Matches: 35, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 5 35 1.00 ACGTcount: A:0.60, C:0.20, G:0.20, T:0.00 Consensus pattern (5 bp): ACAGA Found at i:50111 original size:2 final size:2 Alignment explanation

Indices: 50058--50099 Score: 59 Period size: 2 Copynumber: 21.5 Consensus size: 2 50048 CCAAACCAAT * * 50058 TA TA CA TA TA TA T- TG 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 TA TA TA TA TA TA 50099 T 1 T 50100 GTACACATAT Statistics Matches: 36, Mismatches: 3, Indels: 2 0.88 0.07 0.05 Matches are distributed among these distances: 1 1 0.03 2 35 0.97 ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50 Consensus pattern (2 bp): TA Found at i:56770 original size:27 final size:28 Alignment explanation

Indices: 56740--56792 Score: 81 Period size: 27 Copynumber: 1.9 Consensus size: 28 56730 CGGTATTCAG * * 56740 GACTTTGTCTTGACTAATCC-GATCCAA 1 GACTTTGCCCTGACTAATCCGGATCCAA 56767 GACTTTGCCCTGACTAATCCGGATCC 1 GACTTTGCCCTGACTAATCCGGATCC 56793 GACCCGCGAT Statistics Matches: 23, Mismatches: 2, Indels: 1 0.88 0.08 0.04 Matches are distributed among these distances: 27 18 0.78 28 5 0.22 ACGTcount: A:0.23, C:0.30, G:0.17, T:0.30 Consensus pattern (28 bp): GACTTTGCCCTGACTAATCCGGATCCAA Found at i:58815 original size:138 final size:138 Alignment explanation

Indices: 58586--58845 Score: 448 Period size: 138 Copynumber: 1.9 Consensus size: 138 58576 CTAGGGGCAG ** * 58586 ATCAATCAGAAGTGAACCGCTCATGAACATTGTAGATAAAGGACAAGCACACCATCAACCATTCA 1 ATCAATCAGAAGTGAAAAGCTCATAAACATTGTAGATAAAGGACAAGCACACCATCAACCATTCA * * * * 58651 TATATGTCTAATGCCTTATAATCTCAAATTCTCATTTCATATTATCTCAAGACAACATCCGATCT 66 TACATGCCTAATGCCTCATAATCTCAAATTCTCATTTCATATTAACTCAAGACAACATCCGATCT 58716 AAAGGCGC 131 AAAGGCGC 58724 ATCAATCAGAAGTGAAAAGCTCATAAACATTGTAGATAAAGGACAAGCACACCATCAACCATTCA 1 ATCAATCAGAAGTGAAAAGCTCATAAACATTGTAGATAAAGGACAAGCACACCATCAACCATTCA * 58789 TACATGCCTAATGCCTCATAATCTCAAATTCTCGTTTCATATTAACTCAAGACAACA 66 TACATGCCTAATGCCTCATAATCTCAAATTCTCATTTCATATTAACTCAAGACAACA 58846 AAGTTCATAC Statistics Matches: 114, Mismatches: 8, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 138 114 1.00 ACGTcount: A:0.39, C:0.24, G:0.12, T:0.26 Consensus pattern (138 bp): ATCAATCAGAAGTGAAAAGCTCATAAACATTGTAGATAAAGGACAAGCACACCATCAACCATTCA TACATGCCTAATGCCTCATAATCTCAAATTCTCATTTCATATTAACTCAAGACAACATCCGATCT AAAGGCGC Found at i:63836 original size:51 final size:51 Alignment explanation

Indices: 63776--63878 Score: 206 Period size: 51 Copynumber: 2.0 Consensus size: 51 63766 TCTTTCTGCC 63776 TTTCCCCTGCAAGTAAACTGAAGATGATTAAAGTTCAATCTATCTTTGGCA 1 TTTCCCCTGCAAGTAAACTGAAGATGATTAAAGTTCAATCTATCTTTGGCA 63827 TTTCCCCTGCAAGTAAACTGAAGATGATTAAAGTTCAATCTATCTTTGGCA 1 TTTCCCCTGCAAGTAAACTGAAGATGATTAAAGTTCAATCTATCTTTGGCA 63878 T 1 T 63879 AATTGAATTT Statistics Matches: 52, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 51 52 1.00 ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34 Consensus pattern (51 bp): TTTCCCCTGCAAGTAAACTGAAGATGATTAAAGTTCAATCTATCTTTGGCA Found at i:66579 original size:5 final size:5 Alignment explanation

Indices: 66569--66602 Score: 68 Period size: 5 Copynumber: 6.8 Consensus size: 5 66559 GTGAAATTCT 66569 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT 1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT 66603 GAATGAAGAT Statistics Matches: 29, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 5 29 1.00 ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82 Consensus pattern (5 bp): TTTTA Found at i:67387 original size:94 final size:92 Alignment explanation

Indices: 67129--67396 Score: 321 Period size: 91 Copynumber: 2.9 Consensus size: 92 67119 CCACGTGTGT * * * * 67129 CTAGAAACATGGTCAACTATCGACTATCAAGAAATAAACCCTAAGTCGACATGGCATTTCCTAGT 1 CTAGAAACATGGCCAACTATC-ACTATCAAGAAATAAACACTAAGTTGACATGGCATTTTCTAGT * * 67194 CGCATAGCATGCTGATGTTGCCACGTGC 65 CACATAGCATGCTGATGTTGCCACGTAC * * 67222 CAAGAAACGTGGCCAA--AT---TATCAAGAAATAAACCTCACTCAAGTTGACATGGCATTTTCT 1 CTAGAAACATGGCCAACTATCACTATCAAGAAATAAA---CACT-AAGTTGACATGGCATTTTCT * 67282 AGTCACATAGCATGTTGATGTTGCCACGTAC 62 AGTCACATAGCATGCTGATGTTGCCACGTAC * * * 67313 CTAGAAACATAGCCAAACTATCACTATCAGGAAATAAACACTAAAGTTGACGTGGCATTTTCTAG 1 CTAGAAACATGGCC-AACTATCACTATCAAGAAATAAACACT-AAGTTGACATGGCATTTTCTAG * 67378 TCACATAGCAAGCTGATGT 64 TCACATAGCATGCTGATGT 67397 GGACCTTTTA Statistics Matches: 148, Mismatches: 17, Indels: 19 0.80 0.09 0.10 Matches are distributed among these distances: 87 14 0.09 90 3 0.02 91 59 0.40 92 2 0.01 93 13 0.09 94 44 0.30 97 13 0.09 ACGTcount: A:0.34, C:0.22, G:0.18, T:0.25 Consensus pattern (92 bp): CTAGAAACATGGCCAACTATCACTATCAAGAAATAAACACTAAGTTGACATGGCATTTTCTAGTC ACATAGCATGCTGATGTTGCCACGTAC Done.