Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020719.1 Corchorus olitorius cultivar O-4 contig20752, 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: 18531
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Found at i:670 original size:6 final size:6
Alignment explanation
Indices: 646--694 Score: 71
Period size: 6 Copynumber: 7.7 Consensus size: 6
636 GTTTAGACTT
646 ATATAG TATATAG ATATATAG ATATAG ATATAG ATATAG ATATAG ATAT
1 ATATAG -ATATAG --ATATAG ATATAG ATATAG ATATAG ATATAG ATAT
695 TTGATCTGAT
Statistics
Matches: 41, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
6 28 0.68
7 6 0.15
8 7 0.17
ACGTcount: A:0.49, C:0.00, G:0.14, T:0.37
Consensus pattern (6 bp):
ATATAG
Found at i:6715 original size:21 final size:20
Alignment explanation
Indices: 6689--6733 Score: 72
Period size: 21 Copynumber: 2.2 Consensus size: 20
6679 TATCCTCCAG
*
6689 CACCACAGCCAAACCCCAACA
1 CACCACAACCAAACCCCAA-A
6710 CACCACAACCAAACCCCAAA
1 CACCACAACCAAACCCCAAA
6730 CACC
1 CACC
6734 CCCCAATATG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 5 0.22
21 18 0.78
ACGTcount: A:0.44, C:0.53, G:0.02, T:0.00
Consensus pattern (20 bp):
CACCACAACCAAACCCCAAA
Found at i:10937 original size:27 final size:24
Alignment explanation
Indices: 10907--10961 Score: 65
Period size: 27 Copynumber: 2.2 Consensus size: 24
10897 AATAATTCAG
* *
10907 AATATCATATATTACTTTATAATAAA
1 AATATAATATA-TAATTTA-AATAAA
10933 TAATATAATATATAATTTAAATAAA
1 -AATATAATATATAATTTAAATAAA
10958 AATA
1 AATA
10962 AAAATACTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
24 4 0.15
25 6 0.23
26 6 0.23
27 10 0.38
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (24 bp):
AATATAATATATAATTTAAATAAA
Found at i:11398 original size:45 final size:45
Alignment explanation
Indices: 11343--11439 Score: 124
Period size: 45 Copynumber: 2.2 Consensus size: 45
11333 CGTTAATTAC
* * ** *
11343 CTAA-ATTCTACTATTCCGTCTCTAGGTAATTCATTAAAATAAAG
1 CTAATATTCTACTACTCCATCTCTAAATAATTCATCAAAATAAAG
*
11387 CTAATATTCTACTCCTCCATCTCTAAATAATTCATCAAAATAAAG
1 CTAATATTCTACTACTCCATCTCTAAATAATTCATCAAAATAAAG
*
11432 TTAATATT
1 CTAATATT
11440 AATTGTTGCT
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 4 0.09
45 41 0.91
ACGTcount: A:0.38, C:0.20, G:0.05, T:0.37
Consensus pattern (45 bp):
CTAATATTCTACTACTCCATCTCTAAATAATTCATCAAAATAAAG
Found at i:12515 original size:7 final size:7
Alignment explanation
Indices: 12499--12554 Score: 53
Period size: 7 Copynumber: 7.6 Consensus size: 7
12489 TAAAGCACAT
12499 TTTTTCTC
1 TTTTT-TC
12507 TTTTTTC
1 TTTTTTC
12514 TTTTTT-
1 TTTTTTC
12520 TTTCCCTTTC
1 TTT---TTTC
12530 TTTTTTC
1 TTTTTTC
12537 -TTTTTC
1 TTTTTTC
12543 TCTTTTTC
1 T-TTTTTC
12551 TTTT
1 TTTT
12555 CTACTCTCTT
Statistics
Matches: 42, Mismatches: 0, Indels: 13
0.76 0.00 0.24
Matches are distributed among these distances:
6 9 0.21
7 15 0.36
8 12 0.29
9 3 0.07
10 3 0.07
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (7 bp):
TTTTTTC
Found at i:12555 original size:19 final size:19
Alignment explanation
Indices: 12499--12556 Score: 75
Period size: 19 Copynumber: 3.1 Consensus size: 19
12489 TAAAGCACAT
12499 TTTTTCTCTTTTTTCTTTT-
1 TTTTTCTC-TTTTTCTTTTC
*
12518 TTTTTCCCTTTCTT-TTTTC
1 TTTTTCTCTTT-TTCTTTTC
12537 TTTTTCTCTTTTTCTTTTC
1 TTTTTCTCTTTTTCTTTTC
12556 T
1 T
12557 ACTCTCTTCC
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
18 9 0.26
19 25 0.74
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (19 bp):
TTTTTCTCTTTTTCTTTTC
Found at i:17548 original size:17 final size:17
Alignment explanation
Indices: 17526--17558 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
17516 AGACAATCTT
*
17526 GGGCTTGGGCTTAAGGA
1 GGGCTTGAGCTTAAGGA
17543 GGGCTTGAGCTTAAGG
1 GGGCTTGAGCTTAAGG
17559 GAAGCCTAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.18, C:0.12, G:0.45, T:0.24
Consensus pattern (17 bp):
GGGCTTGAGCTTAAGGA
Done.