Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009736.1 Corchorus capsularis cultivar CVL-1 contig09757, 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: 24364
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Found at i:3440 original size:21 final size:21
Alignment explanation
Indices: 3382--3441 Score: 68
Period size: 25 Copynumber: 2.7 Consensus size: 21
3372 TGTATTAAAA
3382 ATAAAAAAAA-TTTATTAAGT
1 ATAAAAAAAACTTTATTAAGT
*
3402 ATAAAATTAAATTTCTTTATTAAGT
1 ATAAAA--AAA--ACTTTATTAAGT
3427 ATAAAAAAAACTTTA
1 ATAAAAAAAACTTTA
3442 GAAGTTATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
20 6 0.18
21 5 0.15
22 3 0.09
23 3 0.09
25 16 0.48
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.38
Consensus pattern (21 bp):
ATAAAAAAAACTTTATTAAGT
Found at i:8089 original size:16 final size:16
Alignment explanation
Indices: 8071--8100 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
8061 AAAAGAAAAA
8071 AAAAC-CTTAACACTT
1 AAAACACTTAACACTT
8086 AAAACACTTAACACT
1 AAAACACTTAACACT
8101 ATTAAACACA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.50, C:0.27, G:0.00, T:0.23
Consensus pattern (16 bp):
AAAACACTTAACACTT
Found at i:8380 original size:2 final size:2
Alignment explanation
Indices: 8373--8403 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
8363 ATAGATATTG
8373 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
8404 GAAATAGTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:9101 original size:18 final size:18
Alignment explanation
Indices: 9074--9108 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
9064 ACTTGGGGCA
* *
9074 CTTTAGTTTTTTCTAAGT
1 CTTTAATTTTTTATAAGT
9092 CTTTAATTTTTTATAAG
1 CTTTAATTTTTTATAAG
9109 CCTATAGGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.23, C:0.09, G:0.09, T:0.60
Consensus pattern (18 bp):
CTTTAATTTTTTATAAGT
Found at i:10198 original size:36 final size:36
Alignment explanation
Indices: 10158--10228 Score: 133
Period size: 36 Copynumber: 2.0 Consensus size: 36
10148 ATGATTTGGG
10158 CAATTCCGATCGACTTAAACCGAGCTCTGATACCAA
1 CAATTCCGATCGACTTAAACCGAGCTCTGATACCAA
*
10194 CAATTCCGATCGAGTTAAACCGAGCTCTGATACCA
1 CAATTCCGATCGACTTAAACCGAGCTCTGATACCA
10229 CTTATTGGGA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.32, C:0.30, G:0.15, T:0.23
Consensus pattern (36 bp):
CAATTCCGATCGACTTAAACCGAGCTCTGATACCAA
Found at i:15701 original size:14 final size:14
Alignment explanation
Indices: 15682--15712 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
15672 CTCTGTTATC
15682 TTTACTAGTATGAA
1 TTTACTAGTATGAA
*
15696 TTTACTGGTATGAA
1 TTTACTAGTATGAA
15710 TTT
1 TTT
15713 TTTAGACCCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.29, C:0.06, G:0.16, T:0.48
Consensus pattern (14 bp):
TTTACTAGTATGAA
Found at i:18476 original size:31 final size:31
Alignment explanation
Indices: 18441--18509 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
18431 AAAAAACTGT
* *
18441 AAAAGTTAAATAAGGATATAATAGGTATTTC
1 AAAAGTTAAATAAGGATATAATAAGCATTTC
* *
18472 AAAAGTTAAATAAGGGTATAATAAGCGTTTC
1 AAAAGTTAAATAAGGATATAATAAGCATTTC
18503 AAAAGTT
1 AAAAGTT
18510 TCTCGAAACT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.48, C:0.04, G:0.17, T:0.30
Consensus pattern (31 bp):
AAAAGTTAAATAAGGATATAATAAGCATTTC
Found at i:19153 original size:15 final size:16
Alignment explanation
Indices: 19122--19157 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
19112 ACTAGACTCG
19122 AAACTGACTAAAAAAC
1 AAACTGACTAAAAAAC
*
19138 AAACTGACT-CAAAAC
1 AAACTGACTAAAAAAC
19153 AAACT
1 AAACT
19158 CAAATAAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.53
16 9 0.47
ACGTcount: A:0.58, C:0.22, G:0.06, T:0.14
Consensus pattern (16 bp):
AAACTGACTAAAAAAC
Found at i:19863 original size:22 final size:23
Alignment explanation
Indices: 19835--19877 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
19825 TGTAATCAGA
19835 ACTCC-TTGTGAGAGCATTTGGG
1 ACTCCTTTGTGAGAGCATTTGGG
*
19857 ACTCCTTTGTGAGAGCTTTTG
1 ACTCCTTTGTGAGAGCATTTG
19878 TCTTGCTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.16, C:0.19, G:0.28, T:0.37
Consensus pattern (23 bp):
ACTCCTTTGTGAGAGCATTTGGG
Found at i:24261 original size:2 final size:2
Alignment explanation
Indices: 24254--24285 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
24244 CAATGCCCTA
24254 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
24286 TATTTGACAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.