Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013701.1 Corchorus capsularis cultivar CVL-1 contig13722, 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: 50068
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:522 original size:31 final size:31
Alignment explanation
Indices: 482--620 Score: 145
Period size: 31 Copynumber: 4.8 Consensus size: 31
472 GCATGTATCC
*
482 TTTT-GTACATGTGGCATGCCACGTGTCACT
1 TTTTGGTACATGTGGCGTGCCACGTGTCACT
* *
512 TTTTGGTACATGTGGCGTGACATGTGTCACT
1 TTTTGGTACATGTGGCGTGCCACGTGTCACT
*
543 TTTTTGTACATGT---G-G-CAC--G--ACT
1 TTTTGGTACATGTGGCGTGCCACGTGTCACT
*
565 TTTTGGTACATGTGGCGTGCCACATGTCACT
1 TTTTGGTACATGTGGCGTGCCACGTGTCACT
* *
596 TTTTGGTACACGTGACGTGCCACGT
1 TTTTGGTACATGTGGCGTGCCACGT
621 CGGACACCGT
Statistics
Matches: 90, Mismatches: 9, Indels: 19
0.76 0.08 0.16
Matches are distributed among these distances:
22 15 0.17
24 1 0.01
25 1 0.01
26 3 0.03
27 4 0.04
28 1 0.01
29 1 0.01
30 4 0.04
31 60 0.67
ACGTcount: A:0.17, C:0.21, G:0.26, T:0.37
Consensus pattern (31 bp):
TTTTGGTACATGTGGCGTGCCACGTGTCACT
Found at i:15710 original size:1 final size:1
Alignment explanation
Indices: 15704--15734 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
15694 CCTCTGAAGC
15704 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
15735 GAGGGGGGGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:20652 original size:2 final size:2
Alignment explanation
Indices: 20645--20678 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
20635 CTTGTCTTGA
20645 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20679 GCTTGCTATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:33432 original size:80 final size:80
Alignment explanation
Indices: 33292--33444 Score: 225
Period size: 80 Copynumber: 1.9 Consensus size: 80
33282 TCCAAATCCT
* * *
33292 ATCACATTTTCAAATATATATCATGTTTAGCACCTAATTAACCCCCAAATACACAACAAAAACAA
1 ATCACATTTTCAAATATATATCAGGTTTAGCACCTAATCAAACCCCAAATACACAACAAAAACAA
33357 ATTATTCAAGTTTCA
66 ATTATTCAAGTTTCA
* * * * * *
33372 ATCACATTTTCAAATATTTATCAGGTTTAGCACCTCATCAAACCGCAAATCCACACCAAAAACAG
1 ATCACATTTTCAAATATATATCAGGTTTAGCACCTAATCAAACCCCAAATACACAACAAAAACAA
33437 ATTATTCA
66 ATTATTCA
33445 TTTTGTTTTA
Statistics
Matches: 64, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
80 64 1.00
ACGTcount: A:0.42, C:0.24, G:0.05, T:0.29
Consensus pattern (80 bp):
ATCACATTTTCAAATATATATCAGGTTTAGCACCTAATCAAACCCCAAATACACAACAAAAACAA
ATTATTCAAGTTTCA
Found at i:35300 original size:110 final size:110
Alignment explanation
Indices: 35031--35300 Score: 411
Period size: 110 Copynumber: 2.4 Consensus size: 110
35021 ACTATTATAG
* * *
35031 TTTTATTCTACTAGAAACTCTATTTTTATTCAATTAAATTAAATCTAATATCTTTATAATTACTT
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAA-T---TCTAATATCTTTATAATTACTT
*
35096 TATTTTTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
62 TATTTTTACCAAAAAATTAGGATATACTAAAATTTTTTCTAATATACAA
35145 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAA-TCTAATATCTTTATAATTACTTTATT
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATTCTAATATCTTTATAATTACTTTATT
*
35209 TTTACCTAAAAAAATTAGGATATATTAAAA-TTTTTCTAATATACAA
66 TTTACC--AAAAAATTAGGATATACTAAAATTTTTTCTAATATACAA
*
35255 TTTTATTCTATTAAAAACTCTATTTTCATTTAATTAAATTC-AATAT
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATTCTAATAT
35301 TATATATATA
Statistics
Matches: 147, Mismatches: 6, Indels: 10
0.90 0.04 0.06
Matches are distributed among these distances:
109 32 0.22
110 58 0.39
111 22 0.15
114 35 0.24
ACGTcount: A:0.39, C:0.11, G:0.02, T:0.48
Consensus pattern (110 bp):
TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATTCTAATATCTTTATAATTACTTTATT
TTTACCAAAAAATTAGGATATACTAAAATTTTTTCTAATATACAA
Found at i:37875 original size:20 final size:21
Alignment explanation
Indices: 37840--37885 Score: 76
Period size: 20 Copynumber: 2.2 Consensus size: 21
37830 AAATATTATA
*
37840 TTTATCCTATAATGGGTAGTT
1 TTTATCCTAAAATGGGTAGTT
37861 TTTAT-CTAAAATGGGTAGTT
1 TTTATCCTAAAATGGGTAGTT
37881 TTTAT
1 TTTAT
37886 TTTATTTTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 19 0.79
21 5 0.21
ACGTcount: A:0.26, C:0.07, G:0.17, T:0.50
Consensus pattern (21 bp):
TTTATCCTAAAATGGGTAGTT
Found at i:38937 original size:10 final size:10
Alignment explanation
Indices: 38922--38946 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
38912 ATACTAATCA
38922 ATATACATAC
1 ATATACATAC
38932 ATATACATAC
1 ATATACATAC
38942 ATATA
1 ATATA
38947 GAAACTAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (10 bp):
ATATACATAC
Found at i:41953 original size:41 final size:41
Alignment explanation
Indices: 41896--41978 Score: 148
Period size: 41 Copynumber: 2.0 Consensus size: 41
41886 CTATCACGAA
* *
41896 CTCAAATCATTAATCATCATCTGTTGTTTTCGGAGCAAGGT
1 CTCAAATCATTAATCATCATCTGTTGTCTCCGGAGCAAGGT
41937 CTCAAATCATTAATCATCATCTGTTGTCTCCGGAGCAAGGT
1 CTCAAATCATTAATCATCATCTGTTGTCTCCGGAGCAAGGT
41978 C
1 C
41979 GGGAATATGA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.34
Consensus pattern (41 bp):
CTCAAATCATTAATCATCATCTGTTGTCTCCGGAGCAAGGT
Found at i:48409 original size:2 final size:2
Alignment explanation
Indices: 48402--48435 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
48392 CAGAAGAAAG
48402 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
48436 ACAGAGGGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Done.