Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011571.1 Corchorus capsularis cultivar CVL-1 contig11592, 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: 14229
ACGTcount: A:0.37, C:0.18, G:0.15, T:0.29
Found at i:2755 original size:29 final size:31
Alignment explanation
Indices: 2690--2756 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
2680 GGGCATCCGG
* *
2690 CGTGGCATGCCACGTGTACCAAAAAATGCCA
1 CGTGGCATGCCACGTGTACCAAAAAAGGACA
*
2721 CATGGCATGCCACGTGTA-C-AAAAAGGACA
1 CGTGGCATGCCACGTGTACCAAAAAAGGACA
*
2750 TGTGGCA
1 CGTGGCA
2757 CACCACATGT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
29 13 0.42
30 1 0.03
31 17 0.55
ACGTcount: A:0.33, C:0.25, G:0.25, T:0.16
Consensus pattern (31 bp):
CGTGGCATGCCACGTGTACCAAAAAAGGACA
Found at i:4561 original size:21 final size:21
Alignment explanation
Indices: 4536--4577 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
4526 TTCTAAACAT
4536 CAATTGCTACTCAAAAAGAAA
1 CAATTGCTACTCAAAAAGAAA
*
4557 CAATTGCTACTCAAAACGAAA
1 CAATTGCTACTCAAAAAGAAA
4578 GGGAAAAGGG
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:0.50, C:0.21, G:0.10, T:0.19
Consensus pattern (21 bp):
CAATTGCTACTCAAAAAGAAA
Found at i:4741 original size:250 final size:250
Alignment explanation
Indices: 4300--4787 Score: 841
Period size: 250 Copynumber: 2.0 Consensus size: 250
4290 AAGAAAAAAG
*
4300 AAAGAAACAATTGCTACTCAAAACGAAAGGGAAAAGTGCCCATAAAAAACACCTGGCTTCCCATG
1 AAAGAAACAATTGCTACTCAAAACGAAAGGGAAAAGGGCCCATAAAAAACACCTGGCTTCCCATG
*
4365 TAATTAAAAGACGAAATGAAATTCTTCAAAATGAACCTTAACCCACCCAAAAATCAGAAACAAAA
66 TAATTAAAAGACGAAACGAAATTCTTCAAAATGAACCTTAACCCACCCAAAAATCAGAAACAAAA
* * *
4430 AGACAAGGAGACTAAAACTACTTTCTCACATAAACAAAAAGTACATCCCTCAAGAACTAAACCTT
131 ACACAAGGAGACTAAAACTACTTTCCCACATAAACAAAAAGTACATCCCTCAAAAACTAAACCTT
* * *
4495 CACCATCCAATTCTGGTTGAGCTTGGAACTTTTCTAAACATCAATTGCTACTCAA
196 CACCATCCAATTCCGGTTGAGCTTGAAACTTTTCCAAACATCAATTGCTACTCAA
*
4550 AAAGAAACAATTGCTACTCAAAACGAAAGGGAAAAGGGCCCATCAAAAACACCTGGCTTCCCATG
1 AAAGAAACAATTGCTACTCAAAACGAAAGGGAAAAGGGCCCATAAAAAACACCTGGCTTCCCATG
*
4615 TAATTAAAAGGCGAAACGAAATTCTTCAAAATGAACCTTAACCCACCCAAAAATCAGAAACAAAA
66 TAATTAAAAGACGAAACGAAATTCTTCAAAATGAACCTTAACCCACCCAAAAATCAGAAACAAAA
* * *
4680 ACACAAGGAGACTAAAACTACTTTCCCAGATAAACTAATAGTACATCCCTCAAAAACTAAACCTT
131 ACACAAGGAGACTAAAACTACTTTCCCACATAAACAAAAAGTACATCCCTCAAAAACTAAACCTT
* *
4745 TAGCATCCAATTCCGGTTGAGCTTGAAACTTTTCCAAACATCA
196 CACCATCCAATTCCGGTTGAGCTTGAAACTTTTCCAAACATCA
4788 GCAACATATT
Statistics
Matches: 223, Mismatches: 15, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
250 223 1.00
ACGTcount: A:0.44, C:0.24, G:0.12, T:0.20
Consensus pattern (250 bp):
AAAGAAACAATTGCTACTCAAAACGAAAGGGAAAAGGGCCCATAAAAAACACCTGGCTTCCCATG
TAATTAAAAGACGAAACGAAATTCTTCAAAATGAACCTTAACCCACCCAAAAATCAGAAACAAAA
ACACAAGGAGACTAAAACTACTTTCCCACATAAACAAAAAGTACATCCCTCAAAAACTAAACCTT
CACCATCCAATTCCGGTTGAGCTTGAAACTTTTCCAAACATCAATTGCTACTCAA
Found at i:6653 original size:18 final size:18
Alignment explanation
Indices: 6620--6654 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
6610 TCACCAAAAA
*
6620 GAAAAAAAAATGTTTATT
1 GAAAAAAAAATCTTTATT
*
6638 GAAAAAAATATCTTTAT
1 GAAAAAAAAATCTTTAT
6655 GATTGGTTTC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.03, G:0.09, T:0.34
Consensus pattern (18 bp):
GAAAAAAAAATCTTTATT
Found at i:13344 original size:70 final size:70
Alignment explanation
Indices: 13270--13494 Score: 306
Period size: 70 Copynumber: 3.1 Consensus size: 70
13260 TAACTAAAAT
*
13270 AGTAAAATTGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATTGAGTTTTT
1 AGTAAAATTGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAGTTTTT
13335 AGTTG
66 AGTTG
13340 AGTAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATA
1 AGT-AAA-A-T----T-GTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATA
13405 GAGTTTTTAGTTG
58 GAGTTTTTAGTTG
* * * * * *
13418 AGTAAAATAGTAAAATAAAATAATTATAAAGATATTATATTTAATTAAATAAAAATAGAGTTTTT
1 AGTAAAATTGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAGTTTTT
*
13483 AGTCG
66 AGTTG
13488 AGTAAAA
1 AGTAAAA
13495 CTATAAAAAC
Statistics
Matches: 139, Mismatches: 8, Indels: 16
0.85 0.05 0.10
Matches are distributed among these distances:
70 65 0.47
71 3 0.02
72 1 0.01
73 1 0.01
75 1 0.01
76 1 0.01
77 4 0.03
78 63 0.45
ACGTcount: A:0.49, C:0.00, G:0.13, T:0.37
Consensus pattern (70 bp):
AGTAAAATTGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAGTTTTT
AGTTG
Found at i:13353 original size:78 final size:77
Alignment explanation
Indices: 13264--13502 Score: 350
Period size: 78 Copynumber: 3.2 Consensus size: 77
13254 TTTTTTTAAC
*
13264 TAAAATAGTAAAATTGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATTGA
1 TAAAATAGTAAAA-TGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
13329 GTTTTTAGTTGAG
65 GTTTTTAGTTGAG
13342 TAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
1 TAAAATAGTAAAAT-GTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
13407 GTTTTTAGTTGAG
65 GTTTTTAGTTGAG
* * *
13420 TAAAATAGTAAAA--T-AAA-AT-A-A-TTATAAAGATATTATATTTAATTAAATAAAAATAGAG
1 TAAAATAGTAAAATGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAG
*
13478 TTTTTAGTCGAG
66 TTTTTAGTTGAG
13490 TAAAACTA-TAAAA
1 TAAAA-TAGTAAAA
13503 ACCTAAACAA
Statistics
Matches: 154, Mismatches: 5, Indels: 12
0.90 0.03 0.07
Matches are distributed among these distances:
70 55 0.36
71 3 0.02
72 1 0.01
73 2 0.01
74 3 0.02
75 1 0.01
77 1 0.01
78 88 0.57
ACGTcount: A:0.50, C:0.01, G:0.13, T:0.37
Consensus pattern (77 bp):
TAAAATAGTAAAATGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAG
TTTTTAGTTGAG
Done.