Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010053.1 Corchorus capsularis cultivar CVL-1 contig10074, 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: 39900
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.32
Found at i:1045 original size:41 final size:41
Alignment explanation
Indices: 995--1090 Score: 108
Period size: 41 Copynumber: 2.4 Consensus size: 41
985 ATTTATAACT
*
995 AGGGTTAAACTTGGATTTAATTTCTTAT-CTTAATTATCA-G
1 AGGGATAAACTTGGATTTAATTTCTT-TCCTTAATTATCAGG
* * * *
1035 AGGGACTAAACCTGAATTTAATTTGTTTCCTTAATTATTAGG
1 AGGGA-TAAACTTGGATTTAATTTCTTTCCTTAATTATCAGG
1077 AGGGATAAA-TTGGA
1 AGGGATAAACTTGGA
1091 GGGACAAATT
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
40 8 0.17
41 32 0.70
42 6 0.13
ACGTcount: A:0.32, C:0.09, G:0.19, T:0.40
Consensus pattern (41 bp):
AGGGATAAACTTGGATTTAATTTCTTTCCTTAATTATCAGG
Found at i:1093 original size:13 final size:13
Alignment explanation
Indices: 1075--1112 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
1065 TTAATTATTA
*
1075 GGAGGGATAAATT
1 GGAGGGACAAATT
1088 GGAGGGACAAATT
1 GGAGGGACAAATT
*
1101 GGAGGGTCAAAT
1 GGAGGGACAAAT
1113 AGAACTATCC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.37, C:0.05, G:0.39, T:0.18
Consensus pattern (13 bp):
GGAGGGACAAATT
Found at i:19391 original size:13 final size:13
Alignment explanation
Indices: 19373--19401 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
19363 ACAGAAAATC
19373 CAGAAGTGTTTTT
1 CAGAAGTGTTTTT
19386 CAGAAGTGTTTTT
1 CAGAAGTGTTTTT
19399 CAG
1 CAG
19402 CTGTTTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.24, C:0.10, G:0.24, T:0.41
Consensus pattern (13 bp):
CAGAAGTGTTTTT
Found at i:19615 original size:31 final size:31
Alignment explanation
Indices: 19580--19640 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
19570 AGAATATTTT
* *
19580 GTCCCCTGAACTTCC-AAATTCAAGACTATTA
1 GTCCCCTAAACTTCCTAAAGTCAAGA-TATTA
*
19611 GTCCCGTAAACTTCCTAAAGTCAAGATATT
1 GTCCCCTAAACTTCCTAAAGTCAAGATATT
19641 TTATCCTCTG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 17 0.65
32 9 0.35
ACGTcount: A:0.33, C:0.26, G:0.11, T:0.30
Consensus pattern (31 bp):
GTCCCCTAAACTTCCTAAAGTCAAGATATTA
Found at i:24018 original size:19 final size:19
Alignment explanation
Indices: 23984--24030 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
23974 AAAAACCCAG
23984 AAAGA-AATTAAGAAGGAA
1 AAAGAGAATTAAGAAGGAA
24002 AAAGAGAATTCAA-AAGGAA
1 AAAGAGAATT-AAGAAGGAA
* *
24021 GATGAGAATT
1 AAAGAGAATT
24031 TGAGGAGTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 5 0.20
19 18 0.72
20 2 0.08
ACGTcount: A:0.60, C:0.02, G:0.23, T:0.15
Consensus pattern (19 bp):
AAAGAGAATTAAGAAGGAA
Found at i:31562 original size:70 final size:70
Alignment explanation
Indices: 31487--31711 Score: 261
Period size: 70 Copynumber: 3.1 Consensus size: 70
31477 AAATTAAAAT
*
31487 AGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATTGAGTTTTT
1 AGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAGTTTTT
31552 AGTTGAG
66 AGTT--G
* * **
31559 TAAAATAGTAAAATGGTAAAATATAATAGTTCTAAGGATATTAGATTTAATTATATAGAAAGGGA
1 ------AGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
31624 GTTTTTAGTTG
60 GTTTTTAGTTG
* * * ** * * *
31635 AGTAAAATAGTAAAATAAAATAATTATAAACATATTATATTTAATTAAACAAAAATAGAGTTTTT
1 AGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAGTTTTT
31700 AGTTG
66 AGTTG
31705 AGTAAAA
1 AGTAAAA
31712 CTATAAAAAC
Statistics
Matches: 131, Mismatches: 16, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
70 65 0.50
76 1 0.01
78 65 0.50
ACGTcount: A:0.48, C:0.01, G:0.15, T:0.36
Consensus pattern (70 bp):
AGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAGTTTTT
AGTTG
Found at i:31569 original size:78 final size:78
Alignment explanation
Indices: 31481--31719 Score: 316
Period size: 78 Copynumber: 3.2 Consensus size: 78
31471 CTTTTTAAAT
*
31481 TAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATTGA
1 TAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
31546 GTTTTTAGTTGAG
66 GTTTTTAGTTGAG
* * **
31559 TAAAATAGTAAAATGGTAAAATATAATAGTTCTAAGGATATTAGATTTAATTATATAGAAAGGGA
1 TAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
31624 GTTTTTAGTTGAG
66 GTTTTTAGTTGAG
** * * *
31637 TAAAATAGTAAAA---T-AAA-AT-A-A-TTATAAACATATTATATTTAATTAAACAAAAATAGA
1 TAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
31694 GTTTTTAGTTGAG
66 GTTTTTAGTTGAG
31707 TAAAACTA-TAAAA
1 TAAAA-TAGTAAAA
31720 ACCTAAAAAA
Statistics
Matches: 147, Mismatches: 13, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
70 50 0.34
71 3 0.02
72 1 0.01
73 2 0.01
74 3 0.02
75 1 0.01
78 87 0.59
ACGTcount: A:0.49, C:0.02, G:0.14, T:0.36
Consensus pattern (78 bp):
TAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
GTTTTTAGTTGAG
Found at i:32432 original size:67 final size:67
Alignment explanation
Indices: 32321--32448 Score: 184
Period size: 67 Copynumber: 1.9 Consensus size: 67
32311 TATTTGACTT
**
32321 AATGGTAAGGTGTATGTTCTCTGGACTACGATGTCTCAGATTCAAATCTCACCGTTTCGATTGGC
1 AATGGTAAGGTACATGTTCTCTGGACTACGATGTCTCAGATTCAAATCTCACCGTTTCGATTGGC
32386 TC
66 TC
* * * * * *
32388 AATGGTAAGGTACATGTTCTTTGGACTGCGATGTCTCGGGTTCAAGTCTGACCGTTTCGAT
1 AATGGTAAGGTACATGTTCTCTGGACTACGATGTCTCAGATTCAAATCTCACCGTTTCGAT
32449 GTGTGTAGGT
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
67 53 1.00
ACGTcount: A:0.21, C:0.20, G:0.25, T:0.34
Consensus pattern (67 bp):
AATGGTAAGGTACATGTTCTCTGGACTACGATGTCTCAGATTCAAATCTCACCGTTTCGATTGGC
TC
Found at i:36415 original size:16 final size:16
Alignment explanation
Indices: 36396--36452 Score: 71
Period size: 16 Copynumber: 3.6 Consensus size: 16
36386 CCGTCTGAAT
* *
36396 CCGAACCTGAAATTAC
1 CCGAACCCGAAAATAC
36412 CCGAACCCGAAAATAC
1 CCGAACCCGAAAATAC
*
36428 CCGAACCCGAGACA-AC
1 CCGAACCCGA-AAATAC
36444 CCGAACCCG
1 CCGAACCCG
36453 TCCGAACCCG
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
16 35 0.95
17 2 0.05
ACGTcount: A:0.37, C:0.40, G:0.16, T:0.07
Consensus pattern (16 bp):
CCGAACCCGAAAATAC
Found at i:37260 original size:16 final size:16
Alignment explanation
Indices: 37239--37270 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
37229 CCCGACCCGG
37239 ACCCGAACCCGAAAAA
1 ACCCGAACCCGAAAAA
37255 ACCCGAACCCGAAAAA
1 ACCCGAACCCGAAAAA
37271 CTCATACCCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.38, G:0.12, T:0.00
Consensus pattern (16 bp):
ACCCGAACCCGAAAAA
Found at i:37984 original size:2 final size:2
Alignment explanation
Indices: 37977--38016 Score: 64
Period size: 2 Copynumber: 20.0 Consensus size: 2
37967 TTTGACCTTT
37977 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA TA CTA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
38017 CTTAAACCAT
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 1 0.03
2 33 0.92
3 2 0.06
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.