Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013136.1 Corchorus olitorius cultivar O-4 contig13169, 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: 30707
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:3381 original size:10 final size:10
Alignment explanation
Indices: 3368--3396 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
3358 TATGTGTGTT
3368 GGTATGTGAA
1 GGTATGTGAA
3378 GGTATGTGAA
1 GGTATGTGAA
3388 GGTATGTGA
1 GGTATGTGA
3397 TTTGTGTTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.28, C:0.00, G:0.41, T:0.31
Consensus pattern (10 bp):
GGTATGTGAA
Found at i:5752 original size:21 final size:21
Alignment explanation
Indices: 5724--5772 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
5714 TTGGAATGGC
*
5724 GATGGCACAGGCATAGCCGGT
1 GATGGCACAGGCATAACCGGT
* * *
5745 GGTGGCACGGGCTTAACCGGT
1 GATGGCACAGGCATAACCGGT
5766 GATGGCA
1 GATGGCA
5773 TGGTGAATGG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.20, C:0.22, G:0.41, T:0.16
Consensus pattern (21 bp):
GATGGCACAGGCATAACCGGT
Found at i:9411 original size:15 final size:16
Alignment explanation
Indices: 9387--9426 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
9377 AGAGGTTGAA
*
9387 AGAAAGCAATTAAAC-
1 AGAAAACAATTAAACT
*
9402 AGAAAACAATTATACT
1 AGAAAACAATTAAACT
9418 AGAAAACAA
1 AGAAAACAA
9427 AGCAAAGTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.62, C:0.12, G:0.10, T:0.15
Consensus pattern (16 bp):
AGAAAACAATTAAACT
Found at i:10248 original size:10 final size:10
Alignment explanation
Indices: 10235--10263 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
10225 TATGTGTGTT
10235 GGTATGTGAA
1 GGTATGTGAA
10245 GGTATGTGAA
1 GGTATGTGAA
10255 GGTATGTGA
1 GGTATGTGA
10264 TTTGTGTTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.28, C:0.00, G:0.41, T:0.31
Consensus pattern (10 bp):
GGTATGTGAA
Found at i:11916 original size:16 final size:15
Alignment explanation
Indices: 11878--11919 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
11868 ACAGAGATTG
*
11878 ACAGAAAGCAATTAA
1 ACAGAAAACAATTAA
11893 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
11908 ACTAGAAAACAA
1 AC-AGAAAACAA
11920 AGCAAAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.64, C:0.14, G:0.10, T:0.12
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Found at i:18424 original size:13 final size:13
Alignment explanation
Indices: 18406--18433 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
18396 AATTCCAACC
18406 TTTTTCTTTTTCT
1 TTTTTCTTTTTCT
18419 TTTTTCTTTTTCT
1 TTTTTCTTTTTCT
18432 TT
1 TT
18434 ATTACTCTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (13 bp):
TTTTTCTTTTTCT
Found at i:21181 original size:27 final size:27
Alignment explanation
Indices: 21107--21182 Score: 107
Period size: 27 Copynumber: 2.8 Consensus size: 27
21097 AGTGAACTTA
* * * *
21107 AAATGACCAAAATGTCTCTGAATGTGC
1 AAATGACCAAAATGCCCCTGGACGTGC
21134 AAATGACCAAAATGCCCCTGGACGTGC
1 AAATGACCAAAATGCCCCTGGACGTGC
*
21161 AAATGACTAAAATGCCCCTGGA
1 AAATGACCAAAATGCCCCTGGA
21183 TGTCCCCAAT
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 44 1.00
ACGTcount: A:0.37, C:0.24, G:0.20, T:0.20
Consensus pattern (27 bp):
AAATGACCAAAATGCCCCTGGACGTGC
Found at i:24004 original size:56 final size:56
Alignment explanation
Indices: 23930--24094 Score: 208
Period size: 56 Copynumber: 3.0 Consensus size: 56
23920 GTTAGTAACT
*
23930 CACGCGCTTCACGGCGTGTACTGTTGTTTGATCTTTTTAAGGATTTTAATTTGGAG
1 CACGCGCTTCACGACGTGTACTGTTGTTTGATCTTTTTAAGGATTTTAATTTGGAG
* * ** *
23986 TACGCGCTTCGCGACGTGTACTGTTGAATGATCTTTTTAAGGATTTTAATTTGGGG
1 CACGCGCTTCACGACGTGTACTGTTGTTTGATCTTTTTAAGGATTTTAATTTGGAG
* * * * *
24042 CAAGCGCTTCACAACATGTATTGTTGTTTGAT-TTTTTAA-AATTTTAATATTGG
1 CACGCGCTTCACGACGTGTACTGTTGTTTGATCTTTTTAAGGATTTTAAT-TTGG
24095 GTGTCTTATT
Statistics
Matches: 93, Mismatches: 15, Indels: 3
0.84 0.14 0.03
Matches are distributed among these distances:
54 8 0.09
55 11 0.12
56 74 0.80
ACGTcount: A:0.22, C:0.14, G:0.22, T:0.42
Consensus pattern (56 bp):
CACGCGCTTCACGACGTGTACTGTTGTTTGATCTTTTTAAGGATTTTAATTTGGAG
Found at i:26242 original size:1 final size:1
Alignment explanation
Indices: 26236--26274 Score: 78
Period size: 1 Copynumber: 39.0 Consensus size: 1
26226 TCTGACACAC
26236 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
26275 CTAAACACAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 38 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:30612 original size:21 final size:21
Alignment explanation
Indices: 30569--30612 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
30559 TGGAAAAATT
* *
30569 AATATATTAATTTCATAATTG
1 AATATATTAATTACATAAGTG
* *
30590 AATATATTGATTACATTAGTG
1 AATATATTAATTACATAAGTG
30611 AA
1 AA
30613 ATTATAATTA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.43, C:0.05, G:0.09, T:0.43
Consensus pattern (21 bp):
AATATATTAATTACATAAGTG
Done.