Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013433.1 Corchorus capsularis cultivar CVL-1 contig13454, 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: 13851
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35
Found at i:768 original size:13 final size:13
Alignment explanation
Indices: 738--780 Score: 72
Period size: 12 Copynumber: 3.5 Consensus size: 13
728 CATCGATACC
738 TCGATATATCCG-
1 TCGATATATCCGT
750 TCGATATATCCGT
1 TCGATATATCCGT
763 TCGATATATCCGT
1 TCGATATATCCGT
776 T-GATA
1 TCGATA
781 CCTGTATTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
12 16 0.53
13 14 0.47
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.37
Consensus pattern (13 bp):
TCGATATATCCGT
Found at i:6220 original size:90 final size:89
Alignment explanation
Indices: 6102--6342 Score: 302
Period size: 90 Copynumber: 2.7 Consensus size: 89
6092 AGGCAGATGA
* *
6102 TGATAAAACGGAACAAACTGCATCTGAAGAGTTATTAGATTCTGGCAGTCCAGAGCTTAAAAAAG
1 TGATAAAA-GGAACAAACTGCGTCTGAAGAGTTACTAGATTCTGGCAGTCCAGAGCTTAAAAAAG
*** *
6167 AAAGTGAGGTTGGAAACACGGAGGG
65 AAACCAAGGTTGGAAACACAGAGGG
* * * * *
6192 TGATACAAAGGAACAAACTGCGTCTGAAGAGTTAGTAGATTCTGACATTCCAGAGATTAAACAAG
1 TGATA-AAAGGAACAAACTGCGTCTGAAGAGTTACTAGATTCTGGCAGTCCAGAGCTTAAAAAAG
**
6257 AAACCAAGGTTGGAAATGCAGAGGG
65 AAACCAAGGTTGGAAACACAGAGGG
* * * *
6282 TGATAAAAAGGAACAAACTGTGTCTGAAGAGTTGCTAGATTCTGGAAGGCCAGAGCTTAAA
1 TGAT-AAAAGGAACAAACTGCGTCTGAAGAGTTACTAGATTCTGGCAGTCCAGAGCTTAAA
6343 GCTGAGCACT
Statistics
Matches: 129, Mismatches: 20, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
90 125 0.97
91 4 0.03
ACGTcount: A:0.39, C:0.14, G:0.27, T:0.21
Consensus pattern (89 bp):
TGATAAAAGGAACAAACTGCGTCTGAAGAGTTACTAGATTCTGGCAGTCCAGAGCTTAAAAAAGA
AACCAAGGTTGGAAACACAGAGGG
Found at i:9261 original size:86 final size:78
Alignment explanation
Indices: 9026--9280 Score: 314
Period size: 78 Copynumber: 3.2 Consensus size: 78
9016 TTGTTTAGGT
* * * * *
9026 TTTTA-TAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATATAACATCTTTATAACT
1 TTTTACTA-TTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATAACCTTATAACT
*
9090 ATTTTATTTTACCA
65 ATTATATTTTACCA
*
9104 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTA
1 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATAACCTTATAACTA
9169 TTATATTTTACCA
66 TTATATTTTACCA
* * *
9182 TTTTACTATTTTATTCAACTAAAAACTCTATTTTAATTTTATATGATTAAATCTATTAACCTTAT
1 TTTTACTATTTTACTCAACTAAAAACTCTA---T--TTTTATATAATTAAATCTAATAACC-T-T
**
9247 AATAACTATTATATTTTAATA
59 -ATAACTATTATATTTTACCA
9268 TTTTACTATTTTA
1 TTTTACTATTTTA
9281 ATTAAAAAAA
Statistics
Matches: 157, Mismatches: 11, Indels: 10
0.88 0.06 0.06
Matches are distributed among these distances:
78 99 0.63
79 2 0.01
81 1 0.01
83 22 0.14
84 1 0.01
85 1 0.01
86 31 0.20
ACGTcount: A:0.36, C:0.13, G:0.01, T:0.50
Consensus pattern (78 bp):
TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATAACCTTATAACTA
TTATATTTTACCA
Found at i:9401 original size:23 final size:23
Alignment explanation
Indices: 9373--9416 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
9363 AAACTTTTGC
*
9373 AATTGAAAACACTATTTTTATTT
1 AATTGAAAACAATATTTTTATTT
**
9396 AATTGAATTCAATATTTTTAT
1 AATTGAAAACAATATTTTTAT
9417 AATTATTTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.39, C:0.07, G:0.05, T:0.50
Consensus pattern (23 bp):
AATTGAAAACAATATTTTTATTT
Found at i:12734 original size:14 final size:14
Alignment explanation
Indices: 12715--12744 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
12705 CTTATTAGGG
12715 TTGAGGATTGTTGT
1 TTGAGGATTGTTGT
12729 TTGAGGATTGTTGT
1 TTGAGGATTGTTGT
12743 TT
1 TT
12745 TAGGCATATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.13, C:0.00, G:0.33, T:0.53
Consensus pattern (14 bp):
TTGAGGATTGTTGT
Found at i:12914 original size:12 final size:12
Alignment explanation
Indices: 12897--12923 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
12887 TTGTCATGAG
12897 AAGTTTAATTAA
1 AAGTTTAATTAA
12909 AAGTTTAATTAA
1 AAGTTTAATTAA
12921 AAG
1 AAG
12924 GATTCACCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.11, T:0.37
Consensus pattern (12 bp):
AAGTTTAATTAA
Found at i:13017 original size:21 final size:21
Alignment explanation
Indices: 12988--13029 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
12978 GCAACGGAAG
12988 TATACATATTTATATATAAAAA
1 TATACATATTTATATA-AAAAA
13010 TATA-ATATTTATATAAAAAA
1 TATACATATTTATATAAAAAA
13030 GGAATCTAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 5 0.25
21 11 0.55
22 4 0.20
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (21 bp):
TATACATATTTATATAAAAAA
Done.