Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009226.1 Corchorus capsularis cultivar CVL-1 contig09247, 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: 22884
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:2579 original size:2 final size:2
Alignment explanation
Indices: 2572--2605 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2562 AATGATTTGA
2572 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
2606 GTACGTGTTA
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:5333 original size:6 final size:7
Alignment explanation
Indices: 5316--5342 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
5306 TTCTTCTTAT
5316 TTTTTCA
1 TTTTTCA
5323 TTTTTCA
1 TTTTTCA
5330 TTTTTCA
1 TTTTTCA
5337 TTTTTC
1 TTTTTC
5343 CGTTTTTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.11, C:0.15, G:0.00, T:0.74
Consensus pattern (7 bp):
TTTTTCA
Found at i:6013 original size:1 final size:1
Alignment explanation
Indices: 6007--6035 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
5997 ATAAATATGG
6007 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
6036 CCAACCCCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:15819 original size:26 final size:27
Alignment explanation
Indices: 15766--15825 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 27
15756 TAATGCACCC
* * *
15766 AAAACATTTTAATAAAAATCATTTATA
1 AAAACAATTTAATAAAAATCAGTAATA
*
15793 AAAACAATTTATTAAAAAT-AGTAATA
1 AAAACAATTTAATAAAAATCAGTAATA
15819 AAAACAA
1 AAAACAA
15826 GTCCCTCAAC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 12 0.41
27 17 0.59
ACGTcount: A:0.62, C:0.07, G:0.02, T:0.30
Consensus pattern (27 bp):
AAAACAATTTAATAAAAATCAGTAATA
Found at i:17047 original size:17 final size:18
Alignment explanation
Indices: 17013--17052 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
17003 TCCTTCTTTA
* *
17013 TTTTCCTTTTTCTCTTCT
1 TTTTCCTATTCCTCTTCT
17031 TTTTCCTATTCCT-TTCT
1 TTTTCCTATTCCTCTTCT
17048 TTTTC
1 TTTTC
17053 TTCTCTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.03, C:0.28, G:0.00, T:0.70
Consensus pattern (18 bp):
TTTTCCTATTCCTCTTCT
Found at i:22483 original size:20 final size:20
Alignment explanation
Indices: 22458--22496 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
22448 ATAAAGCAGT
*
22458 CTTAATAAAGTTATTAAAAG
1 CTTAATAAAGTTACTAAAAG
*
22478 CTTAATAATGTTACTAAAA
1 CTTAATAAAGTTACTAAAA
22497 AGGCATAATA
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:0.49, C:0.08, G:0.08, T:0.36
Consensus pattern (20 bp):
CTTAATAAAGTTACTAAAAG
Found at i:22559 original size:20 final size:21
Alignment explanation
Indices: 22534--22573 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
22524 ATGCAAAAGA
22534 AAATCACGAAAA-AGTTTAAT
1 AAATCACGAAAATAGTTTAAT
*
22554 AAATCACTAAAATAGTTTAA
1 AAATCACGAAAATAGTTTAA
22574 GATTATTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.55, C:0.10, G:0.07, T:0.28
Consensus pattern (21 bp):
AAATCACGAAAATAGTTTAAT
Done.