Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015637.1 Corchorus capsularis cultivar CVL-1 contig15658, 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: 19727
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.36
Found at i:455 original size:17 final size:17
Alignment explanation
Indices: 433--468 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
423 TTGACAGCGC
433 AACGAAA-ACAAAACAAA
1 AACGAAATA-AAAACAAA
450 AACGAAATAAAAACAAA
1 AACGAAATAAAAACAAA
467 AA
1 AA
469 ACAAAAAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 17 0.94
18 1 0.06
ACGTcount: A:0.78, C:0.14, G:0.06, T:0.03
Consensus pattern (17 bp):
AACGAAATAAAAACAAA
Found at i:1565 original size:41 final size:41
Alignment explanation
Indices: 1520--1602 Score: 166
Period size: 41 Copynumber: 2.0 Consensus size: 41
1510 TTTTCTATTA
1520 TATGCTAAATTGATGAATTTTCATTATGAATAGGACTTCGT
1 TATGCTAAATTGATGAATTTTCATTATGAATAGGACTTCGT
1561 TATGCTAAATTGATGAATTTTCATTATGAATAGGACTTCGT
1 TATGCTAAATTGATGAATTTTCATTATGAATAGGACTTCGT
1602 T
1 T
1603 CTTGTGAATA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.31, C:0.10, G:0.17, T:0.42
Consensus pattern (41 bp):
TATGCTAAATTGATGAATTTTCATTATGAATAGGACTTCGT
Found at i:2388 original size:14 final size:14
Alignment explanation
Indices: 2371--2423 Score: 60
Period size: 14 Copynumber: 4.1 Consensus size: 14
2361 AAACCATTGT
2371 ATTCAATAGTAACA
1 ATTCAATAGTAACA
*
2385 ATTC-TTA--AACA
1 ATTCAATAGTAACA
*
2396 A-TCTATAGTAACA
1 ATTCAATAGTAACA
2409 ATTCAATAGTAACA
1 ATTCAATAGTAACA
2423 A
1 A
2424 CGCCAGAGCC
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
10 2 0.06
11 7 0.22
13 7 0.22
14 16 0.50
ACGTcount: A:0.49, C:0.15, G:0.06, T:0.30
Consensus pattern (14 bp):
ATTCAATAGTAACA
Found at i:4205 original size:1 final size:1
Alignment explanation
Indices: 4199--4235 Score: 74
Period size: 1 Copynumber: 37.0 Consensus size: 1
4189 CCTGCACCGG
4199 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
4236 GCTGAGATTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 36 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:9609 original size:64 final size:64
Alignment explanation
Indices: 9530--9653 Score: 232
Period size: 64 Copynumber: 1.9 Consensus size: 64
9520 AGGGGGTATG
9530 CAGGTCAGTGTATGAAATAAATTTTCTATGTGGTGGG-TCAGCTTTTGATTTGTTTGTTTTACCC
1 CAGGTCAGTGTATGAAATAAATTTTCTATGTGGTGGGAT-AGCTTTTGATTTGTTTGTTTTACCC
9594 CAGGTCAGTGTATGAAATAAATTTTCTATGTGGTGGGATAGCTTTTGATTTGTTTGTTTT
1 CAGGTCAGTGTATGAAATAAATTTTCTATGTGGTGGGATAGCTTTTGATTTGTTTGTTTT
9654 CTGAATAGGT
Statistics
Matches: 59, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
64 58 0.98
65 1 0.02
ACGTcount: A:0.21, C:0.10, G:0.24, T:0.45
Consensus pattern (64 bp):
CAGGTCAGTGTATGAAATAAATTTTCTATGTGGTGGGATAGCTTTTGATTTGTTTGTTTTACCC
Found at i:12090 original size:24 final size:24
Alignment explanation
Indices: 12041--12090 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
12031 ACTGATGCTC
*
12041 AAAAGACAATTGAAGATGCAGCTG
1 AAAAGACAATTGAAGATGAAGCTG
* *
12065 AAAAGA-ATATTGAAGTTGAAGTTG
1 AAAAGACA-ATTGAAGATGAAGCTG
12089 AA
1 AA
12091 GTTGAAAATG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 1 0.05
24 21 0.95
ACGTcount: A:0.48, C:0.06, G:0.24, T:0.22
Consensus pattern (24 bp):
AAAAGACAATTGAAGATGAAGCTG
Found at i:18123 original size:2 final size:2
Alignment explanation
Indices: 18118--18146 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
18108 ACACACAAAC
18118 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 A
18147 ATACGTGCGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:19686 original size:19 final size:16
Alignment explanation
Indices: 19643--19691 Score: 62
Period size: 19 Copynumber: 2.8 Consensus size: 16
19633 ACGTCATATT
19643 TTTTTATTAAAAAATAA
1 TTTTT-TTAAAAAATAA
19660 TTTTTTTAAAAAATATA
1 TTTTTTTAAAAAATA-A
19677 TAATTTTTTAAAAAA
1 T--TTTTTTAAAAAA
19692 AATGGTGAGG
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
16 10 0.34
17 7 0.24
19 12 0.41
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
TTTTTTTAAAAAATAA
Done.