Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016376.1 Corchorus capsularis cultivar CVL-1 contig16397, 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: 9636
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.31
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:2896 original size:13 final size:13
Alignment explanation
Indices: 2878--2909 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
2868 TGACACGTCA
*
2878 GGAGGGACAATTT
1 GGAGGGACAAGTT
2891 GGAGGGACAAGTT
1 GGAGGGACAAGTT
2904 GGAGGG
1 GGAGGG
2910 TCATGTATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.28, C:0.06, G:0.50, T:0.16
Consensus pattern (13 bp):
GGAGGGACAAGTT
Found at i:3477 original size:16 final size:16
Alignment explanation
Indices: 3458--3547 Score: 83
Period size: 16 Copynumber: 5.6 Consensus size: 16
3448 CGGTCTCGGA
*
3458 TCATTTAGGTTACGGG
1 TCATTTGGGTTACGGG
* *
3474 TCATTCGGGTTTCGGG
1 TCATTTGGGTTACGGG
* *
3490 TCATCTGGGTTATGGG
1 TCATTTGGGTTACGGG
3506 TCATTTGGG-TATCGGG
1 TCATTTGGGTTA-CGGG
* * *
3522 TCATCTGCGTTGCGGG
1 TCATTTGGGTTACGGG
*
3538 TCATTCGGGT
1 TCATTTGGGT
3548 CTCGGATCGG
Statistics
Matches: 57, Mismatches: 15, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
15 2 0.04
16 54 0.95
17 1 0.02
ACGTcount: A:0.11, C:0.17, G:0.36, T:0.37
Consensus pattern (16 bp):
TCATTTGGGTTACGGG
Found at i:3501 original size:32 final size:32
Alignment explanation
Indices: 3465--3552 Score: 122
Period size: 32 Copynumber: 2.8 Consensus size: 32
3455 GGATCATTTA
*
3465 GGTTACGGGTCATTCGGGTTTCGGGTCATCTG
1 GGTTACGGGTCATTCGGGTATCGGGTCATCTG
* *
3497 GGTTATGGGTCATTTGGGTATCGGGTCATCTG
1 GGTTACGGGTCATTCGGGTATCGGGTCATCTG
* * *
3529 CGTTGCGGGTCATTCGGGTCTCGG
1 GGTTACGGGTCATTCGGGTATCGG
3553 ATCGGGCGGC
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 48 1.00
ACGTcount: A:0.09, C:0.18, G:0.39, T:0.34
Consensus pattern (32 bp):
GGTTACGGGTCATTCGGGTATCGGGTCATCTG
Found at i:8852 original size:10 final size:10
Alignment explanation
Indices: 8837--8862 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
8827 GAGGACTCTA
8837 GAATTTTCTG
1 GAATTTTCTG
8847 GAATTTTCTG
1 GAATTTTCTG
8857 GAATTT
1 GAATTT
8863 GGCAGCAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.23, C:0.08, G:0.19, T:0.50
Consensus pattern (10 bp):
GAATTTTCTG
Found at i:9466 original size:20 final size:20
Alignment explanation
Indices: 9443--9481 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
9433 AAAATAGGGT
9443 AAAAACACATAAAAATAGCA
1 AAAAACACATAAAAATAGCA
* *
9463 AAAAATATATAAAAATAGC
1 AAAAACACATAAAAATAGC
9482 TATAAAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.69, C:0.10, G:0.05, T:0.15
Consensus pattern (20 bp):
AAAAACACATAAAAATAGCA
Found at i:9492 original size:20 final size:20
Alignment explanation
Indices: 9451--9492 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
9441 GTAAAAACAC
9451 ATAAAAATAGCAAAAAATAT
1 ATAAAAATAGCAAAAAATAT
9471 ATAAAAATAGCTATAAAAATAT
1 ATAAAAATAGC-A-AAAAATAT
9493 GCATAATTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 11 0.55
21 1 0.05
22 8 0.40
ACGTcount: A:0.67, C:0.05, G:0.05, T:0.24
Consensus pattern (20 bp):
ATAAAAATAGCAAAAAATAT
Found at i:9498 original size:12 final size:11
Alignment explanation
Indices: 9450--9498 Score: 57
Period size: 10 Copynumber: 4.5 Consensus size: 11
9440 GGTAAAAACA
9450 CATAAAAATAG
1 CATAAAAATAG
9461 CA-AAAAATA-
1 CATAAAAATAG
*
9470 TATAAAAATAG
1 CATAAAAATAG
9481 CTATAAAAATATG
1 C-ATAAAAATA-G
9494 CATAA
1 CATAA
9499 TTTGAGCTCG
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
9 1 0.03
10 14 0.44
11 2 0.06
12 13 0.41
13 2 0.06
ACGTcount: A:0.63, C:0.08, G:0.06, T:0.22
Consensus pattern (11 bp):
CATAAAAATAG
Done.