Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012833.1 Corchorus capsularis cultivar CVL-1 contig12854, 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: 25734
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:9612 original size:29 final size:30
Alignment explanation
Indices: 9557--9614 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
9547 CATAGCAGAA
*
9557 AGGTTTATCTGGGCAAAATTGATAGTTCAG
1 AGGTTTATCTGGCCAAAATTGATAGTTCAG
* *
9587 AGGTTTATTTGGCCAAATTTGA-AGTTCA
1 AGGTTTATCTGGCCAAAATTGATAGTTCA
9615 TGGGCCTATT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 6 0.24
30 19 0.76
ACGTcount: A:0.29, C:0.10, G:0.24, T:0.36
Consensus pattern (30 bp):
AGGTTTATCTGGCCAAAATTGATAGTTCAG
Found at i:9803 original size:95 final size:96
Alignment explanation
Indices: 9691--9874 Score: 334
Period size: 97 Copynumber: 1.9 Consensus size: 96
9681 AATTTCCGTA
9691 AATTTCCGTAC-TCTTTTTTGTCTTTGAGAGATTTTTGTTCATGCATCTTTCTAGAAATTAACAA
1 AATTTCCGTACTTCTTTTTTGTCTTTGAGAGATTTTTGTTCATGCATCTTTCTAGAAATTAACAA
9755 CTTAAACATTGATTACATGTAATCTTCCATG
66 CTTAAACATTGATTACATGTAATCTTCCATG
* *
9786 AATTTTCGTACTTTTTTTTTTGTCTTTGAGAGATTTTTGTTCATGCATCTTTCTAGAAATTAACA
1 AATTTCCGTAC-TTCTTTTTTGTCTTTGAGAGATTTTTGTTCATGCATCTTTCTAGAAATTAACA
9851 ACTTAAACATTGATTACATGTAAT
65 ACTTAAACATTGATTACATGTAAT
9875 GCCAAAAAAA
Statistics
Matches: 85, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
95 10 0.12
97 75 0.88
ACGTcount: A:0.28, C:0.15, G:0.11, T:0.46
Consensus pattern (96 bp):
AATTTCCGTACTTCTTTTTTGTCTTTGAGAGATTTTTGTTCATGCATCTTTCTAGAAATTAACAA
CTTAAACATTGATTACATGTAATCTTCCATG
Found at i:14341 original size:3 final size:3
Alignment explanation
Indices: 14329--14394 Score: 123
Period size: 3 Copynumber: 22.0 Consensus size: 3
14319 AAAAAAAAAA
*
14329 AAG AAA AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
14377 AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG
14395 TACCTCTGCA
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 61 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:19764 original size:14 final size:14
Alignment explanation
Indices: 19745--19771 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
19735 CAAGAAAAGA
19745 AAAATAAAATAAAT
1 AAAATAAAATAAAT
19759 AAAATAAAATAAA
1 AAAATAAAATAAA
19772 GAACAAAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (14 bp):
AAAATAAAATAAAT
Found at i:22466 original size:24 final size:24
Alignment explanation
Indices: 22439--22497 Score: 109
Period size: 24 Copynumber: 2.5 Consensus size: 24
22429 TATTTCACCT
*
22439 TATCTTTTCCTCCTAAGCATGGAA
1 TATCTTTCCCTCCTAAGCATGGAA
22463 TATCTTTCCCTCCTAAGCATGGAA
1 TATCTTTCCCTCCTAAGCATGGAA
22487 TATCTTTCCCT
1 TATCTTTCCCT
22498 TCTTATTGAG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.22, C:0.29, G:0.10, T:0.39
Consensus pattern (24 bp):
TATCTTTCCCTCCTAAGCATGGAA
Found at i:25549 original size:2 final size:2
Alignment explanation
Indices: 25542--25567 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
25532 GAGGACCATG
25542 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
25568 GAGTTACATG
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
Done.