Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014225.1 Corchorus capsularis cultivar CVL-1 contig14246, 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: 11143
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.33
Found at i:633 original size:5 final size:5
Alignment explanation
Indices: 623--655 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
613 ACAAGTTTTT
623 TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTT
1 TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTT
656 TCCTAGAACT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (5 bp):
TTTAA
Found at i:3825 original size:12 final size:12
Alignment explanation
Indices: 3808--3832 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3798 ATTATTCAGA
3808 AGACTTGAACTT
1 AGACTTGAACTT
3820 AGACTTGAACTT
1 AGACTTGAACTT
3832 A
1 A
3833 ATTCACCAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (12 bp):
AGACTTGAACTT
Found at i:5434 original size:11 final size:11
Alignment explanation
Indices: 5410--5444 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
5400 TTGACAGTAC
5410 AACAAAAACAA
1 AACAAAAACAA
* *
5421 AACGAAAACGA
1 AACAAAAACAA
5432 AACAAAAACAA
1 AACAAAAACAA
5443 AA
1 AA
5445 AACAGAAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.77, C:0.17, G:0.06, T:0.00
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:5487 original size:9 final size:9
Alignment explanation
Indices: 5473--5508 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
5463 ATGGCTTCCG
5473 TTTTTTGTT
1 TTTTTTGTT
5482 TTTTTTGTT
1 TTTTTTGTT
5491 TTTTTT-TT
1 TTTTTTGTT
*
5499 GTTTTTGTT
1 TTTTTTGTT
5508 T
1 T
5509 CGTTTTCAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
8 7 0.29
9 17 0.71
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (9 bp):
TTTTTTGTT
Found at i:5494 original size:11 final size:11
Alignment explanation
Indices: 5480--5514 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
5470 CCGTTTTTTG
5480 TTTTTTTTGTT
1 TTTTTTTTGTT
5491 TTTTTTTTGTT
1 TTTTTTTTGTT
* *
5502 TTTGTTTCGTT
1 TTTTTTTTGTT
5513 TT
1 TT
5515 CAATTTTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.00, C:0.03, G:0.11, T:0.86
Consensus pattern (11 bp):
TTTTTTTTGTT
Found at i:5495 original size:17 final size:17
Alignment explanation
Indices: 5472--5508 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
5462 GATGGCTTCC
*
5472 GTTTTTTGTTT-TTTTT
1 GTTTTTTTTTTGTTTTT
5488 GTTTTTTTTTTGTTTTT
1 GTTTTTTTTTTGTTTTT
5505 GTTT
1 GTTT
5509 CGTTTTCAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (17 bp):
GTTTTTTTTTTGTTTTT
Found at i:5498 original size:20 final size:22
Alignment explanation
Indices: 5473--5514 Score: 70
Period size: 20 Copynumber: 2.0 Consensus size: 22
5463 ATGGCTTCCG
5473 TTTTTTGTTTTT-TTT-GTTTT
1 TTTTTTGTTTTTGTTTCGTTTT
5493 TTTTTTGTTTTTGTTTCGTTTT
1 TTTTTTGTTTTTGTTTCGTTTT
5515 CAATTTTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 12 0.60
21 3 0.15
22 5 0.25
ACGTcount: A:0.00, C:0.02, G:0.12, T:0.86
Consensus pattern (22 bp):
TTTTTTGTTTTTGTTTCGTTTT
Found at i:6063 original size:2 final size:2
Alignment explanation
Indices: 6056--6084 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
6046 AACATTAAAC
6056 CA CA CA CA CA CA CA CA CA CA CA CA CA CA C
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA C
6085 CCATGAGGAC
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:0.48, C:0.52, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:6832 original size:2 final size:2
Alignment explanation
Indices: 6827--6867 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
6817 AACCGAAAAG
6827 AT AT AT AT AT 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 AT AT AT AT AT A
6868 ATTAGCTTTG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:7440 original size:26 final size:26
Alignment explanation
Indices: 7411--7462 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
7401 ACATACATAC
7411 ATATATATATATATATAATAGAAGCT
1 ATATATATATATATATAATAGAAGCT
7437 ATATATATATATATATAATAGAAGCT
1 ATATATATATATATATAATAGAAGCT
7463 TAACTTTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.50, C:0.04, G:0.08, T:0.38
Consensus pattern (26 bp):
ATATATATATATATATAATAGAAGCT
Found at i:8465 original size:3 final size:3
Alignment explanation
Indices: 8457--8497 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
8447 CTTATATTAT
8457 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
8498 GAGGTAATGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:9387 original size:12 final size:12
Alignment explanation
Indices: 9370--9412 Score: 68
Period size: 12 Copynumber: 3.5 Consensus size: 12
9360 TTAATACAGG
*
9370 TATCGATGGATA
1 TATCGACGGATA
9382 TATCGAACGGATA
1 TATCG-ACGGATA
9395 TATCGACGGATA
1 TATCGACGGATA
9407 TATCGA
1 TATCGA
9413 GGTATCGATG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
12 18 0.62
13 11 0.38
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Consensus pattern (12 bp):
TATCGACGGATA
Done.