Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012186.1 Corchorus capsularis cultivar CVL-1 contig12207, 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: 19694
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Found at i:50 original size:32 final size:32
Alignment explanation
Indices: 8--101 Score: 125
Period size: 32 Copynumber: 2.9 Consensus size: 32
1 TTGGTCT
*
8 AGCCGTCCCACCGGGGCGGCCCGCCGTGGCAA
1 AGCCGCCCCACCGGGGCGGCCCGCCGTGGCAA
* * *
40 AGCCGCCCCACCAGGGCGGCCTGCCGTGGCGA
1 AGCCGCCCCACCGGGGCGGCCCGCCGTGGCAA
**
72 AGCCGCCCCAGTGGGGCGGCTCCGCCGTGG
1 AGCCGCCCCACCGGGGCGGC-CCGCCGTGG
102 TTAAGCCTCC
Statistics
Matches: 53, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
32 45 0.85
33 8 0.15
ACGTcount: A:0.11, C:0.43, G:0.39, T:0.07
Consensus pattern (32 bp):
AGCCGCCCCACCGGGGCGGCCCGCCGTGGCAA
Found at i:108 original size:33 final size:33
Alignment explanation
Indices: 20--158 Score: 138
Period size: 33 Copynumber: 4.3 Consensus size: 33
10 CCGTCCCACC
* **
20 GGGGCGGC-CCGCCGTGGCAAAGCCGCCCCACC
1 GGGGCGGCTCCGCCGTGGCTAAGCCGCCCCAGT
* * *
52 AGGGCGGC-CTGCCGTGGCGAAGCCGCCCCAGT
1 GGGGCGGCTCCGCCGTGGCTAAGCCGCCCCAGT
* *
84 GGGGCGGCTCCGCCGTGGTTAAGCCTCCCCAGT
1 GGGGCGGCTCCGCCGTGGCTAAGCCGCCCCAGT
* * * * *
117 GGAGAGGCTCCGCCGTGGCTGAGCCGTCCTAGT
1 GGGGCGGCTCCGCCGTGGCTAAGCCGCCCCAGT
*
150 GGGGAGGCT
1 GGGGCGGCT
159 AGTGTAAAAA
Statistics
Matches: 88, Mismatches: 18, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
32 34 0.39
33 54 0.61
ACGTcount: A:0.12, C:0.36, G:0.40, T:0.12
Consensus pattern (33 bp):
GGGGCGGCTCCGCCGTGGCTAAGCCGCCCCAGT
Found at i:6938 original size:2 final size:2
Alignment explanation
Indices: 6931--6956 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
6921 TTGTGAAACC
6931 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
6957 TGATAATAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9295 original size:20 final size:21
Alignment explanation
Indices: 9254--9295 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
9244 TTCTGGATTG
*
9254 CTAAATACTGCCTCCCTTTTA
1 CTAAATACCGCCTCCCTTTTA
*
9275 CTAAATACCGCC-CCTTTTTA
1 CTAAATACCGCCTCCCTTTTA
9295 C
1 C
9296 ATTTTTGCCC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.24, C:0.36, G:0.05, T:0.36
Consensus pattern (21 bp):
CTAAATACCGCCTCCCTTTTA
Found at i:9465 original size:11 final size:11
Alignment explanation
Indices: 9451--9497 Score: 58
Period size: 11 Copynumber: 3.9 Consensus size: 11
9441 TTAATCATAA
9451 ACTAATTAAAT
1 ACTAATTAAAT
9462 ACTAATTAATCAT
1 ACTAATTAA--AT
9475 AAACTAATTAAAT
1 --ACTAATTAAAT
9488 ACTAATTAAA
1 ACTAATTAAA
9498 CATAAACTGA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
11 19 0.59
13 4 0.12
15 9 0.28
ACGTcount: A:0.55, C:0.11, G:0.00, T:0.34
Consensus pattern (11 bp):
ACTAATTAAAT
Found at i:9470 original size:26 final size:26
Alignment explanation
Indices: 9441--9534 Score: 152
Period size: 26 Copynumber: 3.6 Consensus size: 26
9431 TTCCTTCATT
*
9441 TTAATCATAAACTAATTAAATACTAA
1 TTAAACATAAACTAATTAAATACTAA
*
9467 TTAATCATAAACTAATTAAATACTAA
1 TTAAACATAAACTAATTAAATACTAA
* *
9493 TTAAACATAAACTGACTAAATACTAA
1 TTAAACATAAACTAATTAAATACTAA
9519 TTAAACATAAACTAAT
1 TTAAACATAAACTAAT
9535 AAACAAAGTA
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 63 1.00
ACGTcount: A:0.54, C:0.13, G:0.01, T:0.32
Consensus pattern (26 bp):
TTAAACATAAACTAATTAAATACTAA
Found at i:9669 original size:10 final size:11
Alignment explanation
Indices: 9652--9676 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
9642 CTAGCCGGCC
9652 ATTTTTTTTAA
1 ATTTTTTTTAA
9663 ATTTTTTTTAA
1 ATTTTTTTTAA
9674 ATT
1 ATT
9677 CAAGTTTCAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (11 bp):
ATTTTTTTTAA
Found at i:19506 original size:9 final size:9
Alignment explanation
Indices: 19491--19525 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
19481 AAAAAAAAAC
19491 ATACTAATA
1 ATACTAATA
*
19500 CTACTAATTA
1 ATACTAA-TA
19510 ATACTAATA
1 ATACTAATA
19519 ATACTAA
1 ATACTAA
19526 ATTCTAGTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
9 15 0.65
10 8 0.35
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.34
Consensus pattern (9 bp):
ATACTAATA
Done.