Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010258.1 Corchorus capsularis cultivar CVL-1 contig10279, 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: 5700
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.32
Found at i:3484 original size:70 final size:71
Alignment explanation
Indices: 3401--3633 Score: 274
Period size: 70 Copynumber: 3.2 Consensus size: 71
3391 TTATTAAAAT
* *
3401 AGTAAAA-TTGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATTGAGTTTT
1 AGTAAAACTAGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAGTTTT
3465 TAGTTG
66 TAGTTG
*
3471 AGTAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATA
1 AGT-AAA-ACT---A--GTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATA
**
3536 GAAATTTTAGTTG
59 GAGTTTTTAGTTG
* * * * * *
3549 AGTAAAA-TAGTAAAATAAAATAATTATAAAGATATTATATTTAATTAAATAAAAATAAAGTTTT
1 AGTAAAACTAGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAGTTTT
*
3613 TAGTTA
66 TAGTTG
3619 AGTAAAACTA-TAAAA
1 AGTAAAACTAGTAAAA
3634 ACCTAAACAA
Statistics
Matches: 141, Mismatches: 13, Indels: 18
0.82 0.08 0.10
Matches are distributed among these distances:
70 67 0.48
71 5 0.04
72 2 0.01
73 1 0.01
75 1 0.01
76 1 0.01
77 3 0.02
78 61 0.43
ACGTcount: A:0.51, C:0.00, G:0.12, T:0.37
Consensus pattern (71 bp):
AGTAAAACTAGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAGTTTT
TAGTTG
Found at i:3484 original size:78 final size:77
Alignment explanation
Indices: 3395--3633 Score: 323
Period size: 78 Copynumber: 3.2 Consensus size: 77
3385 GTTTTTTTAT
*
3395 TAAAATAGTAAAATTGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATTGA
1 TAAAATAGTAAAA-TGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
3460 GTTTTTAGTTGAG
65 GTTTTTAGTTGAG
3473 TAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
1 TAAAATAGTAAAAT-GTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
**
3538 AATTTTAGTTGAG
65 GTTTTTAGTTGAG
* * * *
3551 TAAAATAGTAAAA--T-AAA-AT-A-A-TTATAAAGATATTATATTTAATTAAATAAAAATAAAG
1 TAAAATAGTAAAATGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAG
*
3609 TTTTTAGTTAAG
66 TTTTTAGTTGAG
3621 TAAAACTA-TAAAA
1 TAAAA-TAGTAAAA
3634 ACCTAAACAA
Statistics
Matches: 149, Mismatches: 10, Indels: 12
0.87 0.06 0.07
Matches are distributed among these distances:
70 52 0.35
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 86 0.58
ACGTcount: A:0.51, C:0.00, G:0.11, T:0.37
Consensus pattern (77 bp):
TAAAATAGTAAAATGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAG
TTTTTAGTTGAG
Found at i:4444 original size:70 final size:70
Alignment explanation
Indices: 4361--4592 Score: 304
Period size: 70 Copynumber: 3.2 Consensus size: 70
4351 TAACTAAAAT
* *
4361 AGTAAAATTGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATTGAGTTTTT
1 AGTAAAATAGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAGTTTTT
4426 AGTTG
66 AGTTG
4431 AGTAAAATAGTAAAATGGTAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAG
1 AGTAAAATAGT---A----AAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAG
4496 AGTTTTTAGTTG
59 AGTTTTTAGTTG
* * ** * * *
4508 AGTAAAATAGTAAAATAAAATAATTATAAAAATATTATATTTAATTAAATAAAAACAGAGTTTTT
1 AGTAAAATAGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAGTTTTT
4573 AGTTG
66 AGTTG
4578 AGTAAAACTA-TAAAA
1 AGTAAAA-TAGTAAAA
4593 ACCTAAACAA
Statistics
Matches: 145, Mismatches: 9, Indels: 16
0.85 0.05 0.09
Matches are distributed among these distances:
70 73 0.50
71 2 0.01
73 1 0.01
74 1 0.01
77 68 0.47
ACGTcount: A:0.50, C:0.01, G:0.12, T:0.37
Consensus pattern (70 bp):
AGTAAAATAGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAGTTTTT
AGTTG
Found at i:4467 original size:77 final size:76
Alignment explanation
Indices: 4355--4592 Score: 337
Period size: 77 Copynumber: 3.2 Consensus size: 76
4345 TTTTTTTAAC
*
4355 TAAAATAGTAAAATTGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATTGA
1 TAAAATAGTAAAA-TGT-AAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
4420 GTTTTTAGTTGAG
64 GTTTTTAGTTGAG
4433 TAAAATAGTAAAATGGTAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAG
1 TAAAATAGTAAAAT-GTAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAG
4498 TTTTTAGTTGAG
65 TTTTTAGTTGAG
** * * *
4510 TAAAATAGTAAAA--TAAA-AT-A-A-TTATAAAAATATTATATTTAATTAAATAAAAACAGAGT
1 TAAAATAGTAAAATGTAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAGT
4569 TTTTAGTTGAG
66 TTTTAGTTGAG
4580 TAAAACTA-TAAAA
1 TAAAA-TAGTAAAA
4593 ACCTAAACAA
Statistics
Matches: 152, Mismatches: 6, Indels: 12
0.89 0.04 0.07
Matches are distributed among these distances:
70 54 0.36
71 3 0.02
72 1 0.01
73 2 0.01
74 4 0.03
77 73 0.48
78 15 0.10
ACGTcount: A:0.50, C:0.01, G:0.12, T:0.37
Consensus pattern (76 bp):
TAAAATAGTAAAATGTAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAGT
TTTTAGTTGAG
Found at i:5427 original size:21 final size:21
Alignment explanation
Indices: 5398--5437 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
5388 ACTAGATTGT
5398 TAAACACCG-TCTCCCTTTTAC
1 TAAACACCGCTC-CCCTTTTAC
*
5419 TAAATACCGCTCCCCTTTT
1 TAAACACCGCTCCCCTTTT
5438 TACACTTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 15 0.88
22 2 0.12
ACGTcount: A:0.23, C:0.38, G:0.05, T:0.35
Consensus pattern (21 bp):
TAAACACCGCTCCCCTTTTAC
Found at i:5682 original size:32 final size:31
Alignment explanation
Indices: 5582--5691 Score: 114
Period size: 32 Copynumber: 3.4 Consensus size: 31
5572 TTGTTTTTAG
*
5582 GGCTATGCCGCCCAGCCTGGGCGGCTTGCCAT
1 GGCT-TGCCGCCCAGCGTGGGCGGCTTGCCAT
* **
5614 GGCCTTGCTGCCCAG-GCTGGGCGGCATACCCAT
1 GG-CTTGCCGCCCAGCG-TGGGCGGC-TTGCCAT
*
5647 GGCTTGACCGCCCTGCGTGGGCGGCTTGCCAT
1 GGCTTG-CCGCCCAGCGTGGGCGGCTTGCCAT
5679 GGCTGTGCCGCCC
1 GGCT-TGCCGCCC
5692 GGCTAGGGC
Statistics
Matches: 64, Mismatches: 8, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
32 38 0.59
33 25 0.39
34 1 0.02
ACGTcount: A:0.08, C:0.37, G:0.35, T:0.19
Consensus pattern (31 bp):
GGCTTGCCGCCCAGCGTGGGCGGCTTGCCAT
Done.