Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007744.1 Corchorus capsularis cultivar CVL-1 contig07765, 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: 18084
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Found at i:9913 original size:47 final size:47
Alignment explanation
Indices: 9844--9937 Score: 188
Period size: 47 Copynumber: 2.0 Consensus size: 47
9834 ATCTAACTTA
9844 AATACGTTATACTCTTTTGCTAAAATTTTGCTTTAGCCCCGAAAGTT
1 AATACGTTATACTCTTTTGCTAAAATTTTGCTTTAGCCCCGAAAGTT
9891 AATACGTTATACTCTTTTGCTAAAATTTTGCTTTAGCCCCGAAAGTT
1 AATACGTTATACTCTTTTGCTAAAATTTTGCTTTAGCCCCGAAAGTT
9938 GTAAATTTTG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.28, C:0.19, G:0.13, T:0.40
Consensus pattern (47 bp):
AATACGTTATACTCTTTTGCTAAAATTTTGCTTTAGCCCCGAAAGTT
Found at i:10626 original size:26 final size:25
Alignment explanation
Indices: 10595--10645 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 25
10585 TTTTTCAAAT
10595 ATATTTCTAAATTA-TCATTATTAAAA
1 ATATTT-T-AATTATTCATTATTAAAA
10621 ATATTTTAATTATTTCATTATTAAA
1 ATATTTTAATTA-TTCATTATTAAA
10646 TTAATGGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 5 0.22
25 1 0.04
26 17 0.74
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (25 bp):
ATATTTTAATTATTCATTATTAAAA
Found at i:11579 original size:10 final size:10
Alignment explanation
Indices: 11564--11588 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
11554 TAGAAATATA
11564 CTATATCTAT
1 CTATATCTAT
11574 CTATATCTAT
1 CTATATCTAT
11584 CTATA
1 CTATA
11589 ATATATATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.32, C:0.20, G:0.00, T:0.48
Consensus pattern (10 bp):
CTATATCTAT
Found at i:11882 original size:26 final size:26
Alignment explanation
Indices: 11833--11883 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
11823 ATTATTAAAA
*
11833 TATTTTATTTAGAAAAACTCAATTTT
1 TATTTTATTTAGAAAAACTAAATTTT
* *
11859 TATTTTATTTCGAAAAATTAAATTT
1 TATTTTATTTAGAAAAACTAAATTT
11884 ACAGTACCAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.39, C:0.06, G:0.04, T:0.51
Consensus pattern (26 bp):
TATTTTATTTAGAAAAACTAAATTTT
Found at i:18057 original size:75 final size:75
Alignment explanation
Indices: 17934--18084 Score: 275
Period size: 75 Copynumber: 2.0 Consensus size: 75
17924 TCCGTTCGAC
17934 TCTGCGGGTGACGTCTGCTTGGACGTTCGACCTCACTTATGATTTATACAGGGCACCAGTCTAGG
1 TCTGCGGGTGACGTCTGCTTGGACGTTCGACCTCACTTATGATTTATACAGGGCACCAGTCTAGG
17999 CGCTCAGCCG
66 CGCTCAGCCG
* * *
18009 TCTGCGGGTGATGTCTGCTTGGACGTTCGACCTCGCTTATGATTTATACGGGGCACCAGTCTAGG
1 TCTGCGGGTGACGTCTGCTTGGACGTTCGACCTCACTTATGATTTATACAGGGCACCAGTCTAGG
18074 CGCTCAGCCG
66 CGCTCAGCCG
18084 T
1 T
Statistics
Matches: 73, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
75 73 1.00
ACGTcount: A:0.16, C:0.27, G:0.29, T:0.28
Consensus pattern (75 bp):
TCTGCGGGTGACGTCTGCTTGGACGTTCGACCTCACTTATGATTTATACAGGGCACCAGTCTAGG
CGCTCAGCCG
Done.