Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006133.1 Corchorus capsularis cultivar CVL-1 contig06151, 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: 23001
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:331 original size:31 final size:30
Alignment explanation
Indices: 287--378 Score: 105
Period size: 31 Copynumber: 3.0 Consensus size: 30
277 GGTATCCGAC
*
287 GTGGCATGCCACGTGCACTAAAAAGTGACAT
1 GTGGCACGCCACGTG-ACTAAAAAGTGACAT
*
318 GTGGCACGTCACGTGTAAC-AAAAAGTGACAT
1 GTGGCACGCCACGTG--ACTAAAAAGTGACAT
* *
349 GTGTCACGCCACGTGAATCAAAAAGTGACA
1 GTGGCACGCCACGTGACT-AAAAAGTGACA
379 CGTGTACCAA
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
29 1 0.02
31 49 0.94
32 2 0.04
ACGTcount: A:0.35, C:0.22, G:0.25, T:0.18
Consensus pattern (30 bp):
GTGGCACGCCACGTGACTAAAAAGTGACAT
Found at i:380 original size:19 final size:18
Alignment explanation
Indices: 358--401 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
348 TGTGTCACGC
358 CACGTGAATCAAAAAGTGA
1 CACGTGAA-CAAAAAGTGA
* *
377 CACGTGTACCAAAAGTGA
1 CACGTGAACAAAAAGTGA
*
395 CATGTGA
1 CACGTGA
402 CATGCTACGT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 14 0.67
19 7 0.33
ACGTcount: A:0.41, C:0.18, G:0.23, T:0.18
Consensus pattern (18 bp):
CACGTGAACAAAAAGTGA
Found at i:400 original size:49 final size:48
Alignment explanation
Indices: 327--426 Score: 130
Period size: 49 Copynumber: 2.1 Consensus size: 48
317 TGTGGCACGT
*
327 CACGTGTAACAAAAAGTGACATGTGTCACGCCACGTGAATCAAAAAGTGA
1 CACGTGTAACAAAAAGTGACATGTGACACGCCACGTGAA-CAAAAA-TGA
* * * *
377 CACGTGT-ACCAAAAGTGACATGTGACATGCTACGTGCACAAAAATGA
1 CACGTGTAACAAAAAGTGACATGTGACACGCCACGTGAACAAAAATGA
424 CAC
1 CAC
427 ATGCCACGTG
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
47 6 0.13
48 6 0.13
49 26 0.58
50 7 0.16
ACGTcount: A:0.39, C:0.22, G:0.21, T:0.18
Consensus pattern (48 bp):
CACGTGTAACAAAAAGTGACATGTGACACGCCACGTGAACAAAAATGA
Found at i:1204 original size:30 final size:30
Alignment explanation
Indices: 1168--1228 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
1158 ATAATACTCC
* * *
1168 CTCCGTCCCATATTATCTGTCCATTTCTAT
1 CTCCGTCCCATATTATATGCCCACTTCTAT
1198 CTCCGTCCCATATTATATGCCCACTTCTAT
1 CTCCGTCCCATATTATATGCCCACTTCTAT
1228 C
1 C
1229 AGGGGAAAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.18, C:0.36, G:0.07, T:0.39
Consensus pattern (30 bp):
CTCCGTCCCATATTATATGCCCACTTCTAT
Found at i:1391 original size:2 final size:2
Alignment explanation
Indices: 1384--1410 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1374 ATAAATAAAG
1384 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 A
1411 AGATTTCAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1439 original size:2 final size:2
Alignment explanation
Indices: 1432--1457 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1422 TCTTAAGGAA
1432 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
1458 CAAAATGATT
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:9690 original size:30 final size:30
Alignment explanation
Indices: 9654--9715 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
9644 GAAGAACCAG
9654 ATAAAGTTAGCCCAGAGCTTCATAATTCAT
1 ATAAAGTTAGCCCAGAGCTTCATAATTCAT
9684 ATAAAGTTAGCCCAGAGCTTCATAATTCAT
1 ATAAAGTTAGCCCAGAGCTTCATAATTCAT
9714 AT
1 AT
9716 CAGCTTCAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.37, C:0.19, G:0.13, T:0.31
Consensus pattern (30 bp):
ATAAAGTTAGCCCAGAGCTTCATAATTCAT
Found at i:21636 original size:17 final size:19
Alignment explanation
Indices: 21606--21641 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
21596 TTTTATTTGA
21606 GTTTGTTTTGAGTCAGTTT
1 GTTTGTTTTGAGTCAGTTT
21625 GTTT-TTTT-AGTCAGTTT
1 GTTTGTTTTGAGTCAGTTT
21642 CGAGTCTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
18 4 0.24
19 4 0.24
ACGTcount: A:0.11, C:0.06, G:0.22, T:0.61
Consensus pattern (19 bp):
GTTTGTTTTGAGTCAGTTT
Done.