Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015452.1 Corchorus capsularis cultivar CVL-1 contig15473, 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: 30843
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.31
Found at i:8372 original size:1 final size:1
Alignment explanation
Indices: 8366--8402 Score: 74
Period size: 1 Copynumber: 37.0 Consensus size: 1
8356 ATGGCAACTG
8366 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
8403 CCTCATTTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 36 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:11041 original size:78 final size:77
Alignment explanation
Indices: 10952--11338 Score: 534
Period size: 78 Copynumber: 5.2 Consensus size: 77
10942 TTTTTTAAAC
*
10952 TAAAATAGTAAAATTGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATTGA
1 TAAAATAGTAAAA-TGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
11017 GTTTTTAGTTGAG
65 GTTTTTAGTTGAG
*
11030 TAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATATA
1 TAAAATAGTAAAAT-GTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
11095 GTTTTTAGTTGAG
65 GTTTTTAGTTGAG
* * *
11108 TAAAATAGTAAAA--T-AAA-AT-A-A-TTATAAAGATATTATATTTAATTAAATAAAAATAGAG
1 TAAAATAGTAAAATGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAG
11166 TTTTTAGTTGAG
66 TTTTTAGTTGAG
11178 TAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
1 TAAAATAGTAAAAT-GTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
11243 GTTTTTAGTTGAG
65 GTTTTTAGTTGAG
* * * * * *
11256 TAAAATAGTAAAA--T-AAA-AT-A-A-TTATAAAGATATTATATTTATTTAAATGAAAATAGAT
1 TAAAATAGTAAAATGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAG
11314 TTTTTAGTTGAG
66 TTTTTAGTTGAG
11326 TAAAACTA-TAAAA
1 TAAAA-TAGTAAAA
11339 ACCTAAACAA
Statistics
Matches: 284, Mismatches: 15, Indels: 28
0.87 0.05 0.09
Matches are distributed among these distances:
70 111 0.39
71 4 0.01
72 2 0.01
73 5 0.02
74 9 0.03
75 4 0.01
76 1 0.00
77 2 0.01
78 146 0.51
ACGTcount: A:0.49, C:0.00, G:0.12, T:0.38
Consensus pattern (77 bp):
TAAAATAGTAAAATGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAG
TTTTTAGTTGAG
Found at i:11112 original size:70 final size:70
Alignment explanation
Indices: 11036--11338 Score: 401
Period size: 70 Copynumber: 4.2 Consensus size: 70
11026 TGAGTAAAAT
* * * * * *
11036 AGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATATAGTTTTT
1 AGTAAAATAGTAAAATAAAATAATTATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTTT
11101 AGTTG
66 AGTTG
*
11106 AGTAAAATAGTAAAATAAAATAATTATAAAGATATTATATTTAATTAAATAAAAATAGAGTTTTT
1 AGTAAAATAGTAAAATAAAATAATTATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTTT
11171 AGTTG
66 AGTTG
* *
11176 AGTAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATA
1 AGTAAAATAGTAAAA---T-AAA-AT-A-A-TTATAAAGATATTAGATTTAATTAAATAAAAATA
11241 GAGTTTTTAGTTG
58 GAGTTTTTAGTTG
* * * *
11254 AGTAAAATAGTAAAATAAAATAATTATAAAGATATTATATTTATTTAAATGAAAATAGATTTTTT
1 AGTAAAATAGTAAAATAAAATAATTATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTTT
11319 AGTTG
66 AGTTG
11324 AGTAAAACTA-TAAAA
1 AGTAAAA-TAGTAAAA
11339 ACCTAAACAA
Statistics
Matches: 208, Mismatches: 16, Indels: 18
0.86 0.07 0.07
Matches are distributed among these distances:
70 131 0.63
71 3 0.01
72 1 0.00
73 3 0.01
74 6 0.03
75 3 0.01
76 1 0.00
77 1 0.00
78 59 0.28
ACGTcount: A:0.50, C:0.00, G:0.12, T:0.38
Consensus pattern (70 bp):
AGTAAAATAGTAAAATAAAATAATTATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTTT
AGTTG
Found at i:11140 original size:148 final size:148
Alignment explanation
Indices: 10958--11338 Score: 647
Period size: 148 Copynumber: 2.6 Consensus size: 148
10948 AAACTAAAAT
* * * * * * *
10958 AGTAAAATTGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATTGAGTTTTT
1 AGTAAAATAGTAAAATAAAATAATTATAAAGATATTATATTTAATTAAATAAAAATAGAGTTTTT
11023 AGTTGAGTAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAA
66 AGTTGAGTAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAA
*
11088 AAATATAGTTTTTAGTTG
131 AAATAGAGTTTTTAGTTG
11106 AGTAAAATAGTAAAATAAAATAATTATAAAGATATTATATTTAATTAAATAAAAATAGAGTTTTT
1 AGTAAAATAGTAAAATAAAATAATTATAAAGATATTATATTTAATTAAATAAAAATAGAGTTTTT
11171 AGTTGAGTAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAA
66 AGTTGAGTAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAA
11236 AAATAGAGTTTTTAGTTG
131 AAATAGAGTTTTTAGTTG
* * *
11254 AGTAAAATAGTAAAATAAAATAATTATAAAGATATTATATTTATTTAAATGAAAATAGATTTTTT
1 AGTAAAATAGTAAAATAAAATAATTATAAAGATATTATATTTAATTAAATAAAAATAGAGTTTTT
11319 AGTTGAGTAAAACTA-TAAAA
66 AGTTGAGTAAAA-TAGTAAAA
11339 ACCTAAACAA
Statistics
Matches: 221, Mismatches: 11, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
148 219 0.99
149 2 0.01
ACGTcount: A:0.49, C:0.00, G:0.13, T:0.38
Consensus pattern (148 bp):
AGTAAAATAGTAAAATAAAATAATTATAAAGATATTATATTTAATTAAATAAAAATAGAGTTTTT
AGTTGAGTAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAA
AAATAGAGTTTTTAGTTG
Found at i:11443 original size:6 final size:6
Alignment explanation
Indices: 11426--11462 Score: 67
Period size: 6 Copynumber: 6.3 Consensus size: 6
11416 GTACATTTTA
11426 ATATAG -TATAG ATATAG ATATAG ATATAG ATATAG AT
1 ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG AT
11463 TAAGCGAACC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 5 0.17
6 25 0.83
ACGTcount: A:0.49, C:0.00, G:0.16, T:0.35
Consensus pattern (6 bp):
ATATAG
Found at i:11709 original size:19 final size:19
Alignment explanation
Indices: 11669--11710 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
11659 TTACATACTA
11669 AAAAACTTAAATAAAAAGT
1 AAAAACTTAAATAAAAAGT
* *
11688 AAAAA-TTAATATAGAAATT
1 AAAAACTTAA-ATAAAAAGT
11707 AAAA
1 AAAA
11711 GAAATGTAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.69, C:0.02, G:0.05, T:0.24
Consensus pattern (19 bp):
AAAAACTTAAATAAAAAGT
Found at i:13851 original size:12 final size:12
Alignment explanation
Indices: 13834--13859 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
13824 AACTTTGGAA
13834 ATTTTATTTTAT
1 ATTTTATTTTAT
13846 ATTTTATTTTAT
1 ATTTTATTTTAT
13858 AT
1 AT
13860 ATAAAGAGTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (12 bp):
ATTTTATTTTAT
Found at i:18698 original size:51 final size:51
Alignment explanation
Indices: 18617--18734 Score: 200
Period size: 51 Copynumber: 2.3 Consensus size: 51
18607 GTGGAAAAGT
* *
18617 AAAGACTCATAATATTTGGCCTTGCTATCTAATTATTTATTTATATATGGC
1 AAAGGCTCATAATATTTGGCCTTGCTATCTAATTATTTATTTATACATGGC
18668 AAAGGCTCATAATATTTGGCCTTGCTATCTAATTATTTATTTATACATGGC
1 AAAGGCTCATAATATTTGGCCTTGCTATCTAATTATTTATTTATACATGGC
*
18719 AAAGGCCCATATATAT
1 AAAGGCTCATA-ATAT
18735 ATAAACAAAA
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
51 59 0.94
52 4 0.06
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.40
Consensus pattern (51 bp):
AAAGGCTCATAATATTTGGCCTTGCTATCTAATTATTTATTTATACATGGC
Found at i:27436 original size:31 final size:31
Alignment explanation
Indices: 27401--27462 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
27391 GGTTCTTCTG
27401 GAACTTTTCCTTTCATCTTGCTGTCTGCAAA
1 GAACTTTTCCTTTCATCTTGCTGTCTGCAAA
27432 GAACTTTTCCTTTCATCTTGCTGTCTGCAAA
1 GAACTTTTCCTTTCATCTTGCTGTCTGCAAA
27463 TTGGCGAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.19, C:0.26, G:0.13, T:0.42
Consensus pattern (31 bp):
GAACTTTTCCTTTCATCTTGCTGTCTGCAAA
Found at i:29369 original size:18 final size:18
Alignment explanation
Indices: 29346--29388 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
29336 GTGCTTGGAA
29346 CATGCTCATCAAT-ATCTC
1 CATGCTCATC-ATCATCTC
*
29364 CATGCTCTTCATGCATCTC
1 CATGCTCATCAT-CATCTC
29383 CATGCT
1 CATGCT
29389 TCCTTGCAGC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 2 0.09
18 9 0.41
19 11 0.50
ACGTcount: A:0.21, C:0.35, G:0.09, T:0.35
Consensus pattern (18 bp):
CATGCTCATCATCATCTC
Done.