Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015970.1 Corchorus capsularis cultivar CVL-1 contig15991, 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: 9624
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Found at i:328 original size:17 final size:18
Alignment explanation
Indices: 300--336 Score: 67
Period size: 17 Copynumber: 2.1 Consensus size: 18
290 CCTCCCCATA
300 GTACCTAGGTAGTATGAG
1 GTACCTAGGTAGTATGAG
318 GTACC-AGGTAGTATGAG
1 GTACCTAGGTAGTATGAG
335 GT
1 GT
337 GATAGGCTGC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.27, C:0.11, G:0.35, T:0.27
Consensus pattern (18 bp):
GTACCTAGGTAGTATGAG
Found at i:4063 original size:21 final size:21
Alignment explanation
Indices: 4039--4079 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
4029 AAATATTCTC
*
4039 ATCTGTACAGTAACAAATTTT
1 ATCTGTACAATAACAAATTTT
4060 ATCTGTACAATAACAAATTT
1 ATCTGTACAATAACAAATTT
4080 AACACGTACA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.41, C:0.15, G:0.07, T:0.37
Consensus pattern (21 bp):
ATCTGTACAATAACAAATTTT
Found at i:4609 original size:130 final size:130
Alignment explanation
Indices: 4376--4730 Score: 611
Period size: 130 Copynumber: 2.7 Consensus size: 130
4366 GCGGTTTTTG
4376 CGGTTTTTTTAGGAGGATATAATATTCAAATCTTATTACAATTAAATAATTCTTTATATGTTCAA
1 CGGTTTTTTTAGGAGGATATAATATTCAAATCTTATTACAATTAAATAATTCTTTATATGTTCAA
* * *
4441 ACATAGTGTGAAAAATGACCAAATAAACAATTAATTCGATACTTTATATTCTTAACCATGTAACA
66 ACATCGAGTGAAAAATGACCAAATAAACAATTAATTCGAAACTTTATATTCTTAACCATGTAACA
* *
4506 CGGTTTTTTTAGGAGGATATAATATTCAAATCTTATTACAATTAAACAATTTTTTATATGTTCAA
1 CGGTTTTTTTAGGAGGATATAATATTCAAATCTTATTACAATTAAATAATTCTTTATATGTTCAA
* * *
4571 ACATCGAGTGAAAAATGACCAAGTAAACAATTAATTCGAAATTTTATATTCTTAACCATGTAACG
66 ACATCGAGTGAAAAATGACCAAATAAACAATTAATTCGAAACTTTATATTCTTAACCATGTAACA
* * *
4636 CGGTTTTTTTAGAAGGATACAATATTTAAATCTTATTACAATTAAATAATTCTTTATATGTTCAA
1 CGGTTTTTTTAGGAGGATATAATATTCAAATCTTATTACAATTAAATAATTCTTTATATGTTCAA
4701 ACATCGAGTGAAAAATGACCAAATAAACAA
66 ACATCGAGTGAAAAATGACCAAATAAACAA
4731 ACTATATAAT
Statistics
Matches: 211, Mismatches: 14, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
130 211 1.00
ACGTcount: A:0.41, C:0.12, G:0.11, T:0.37
Consensus pattern (130 bp):
CGGTTTTTTTAGGAGGATATAATATTCAAATCTTATTACAATTAAATAATTCTTTATATGTTCAA
ACATCGAGTGAAAAATGACCAAATAAACAATTAATTCGAAACTTTATATTCTTAACCATGTAACA
Found at i:6862 original size:7 final size:7
Alignment explanation
Indices: 6847--6876 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
6837 TATTTCTGGC
*
6847 AAAACAA
1 AAAAGAA
6854 AAAAGAA
1 AAAAGAA
6861 AAAAGAA
1 AAAAGAA
6868 AAAAGAA
1 AAAAGAA
6875 AA
1 AA
6877 GCAAGGCTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.87, C:0.03, G:0.10, T:0.00
Consensus pattern (7 bp):
AAAAGAA
Found at i:7246 original size:13 final size:11
Alignment explanation
Indices: 7216--7254 Score: 51
Period size: 13 Copynumber: 3.3 Consensus size: 11
7206 TCATCTGAAC
7216 AAAAAGAAAAG
1 AAAAAGAAAAG
7227 AAAAAGAGAAAG
1 AAAAAGA-AAAG
7239 AAAGAAGAAGAAG
1 AAA-AAGAA-AAG
7252 AAA
1 AAA
7255 CCCTCTCTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 7 0.28
12 8 0.32
13 10 0.40
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAAG
Done.