Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01006979.1 Corchorus olitorius cultivar O-4 contig07004, 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, 681
Length: 1136
ACGTcount: A:0.35, C:0.13, G:0.24, T:0.28
Found at i:474 original size:46 final size:46
Alignment explanation
Indices: 423--514 Score: 148
Period size: 46 Copynumber: 2.0 Consensus size: 46
413 GGCCAGCTAG
* *
423 GCAGGCCTGGCCAACGCTGGGCCGCACTGCTGCCAATGGGCAGCGT
1 GCAGGCCTAGCCAACGCTGGGCCACACTGCTGCCAATGGGCAGCGT
**
469 GCAGGCCTAGCCAGTGCTGGGCCACACTGCTGCCAATGGGCAGCGT
1 GCAGGCCTAGCCAACGCTGGGCCACACTGCTGCCAATGGGCAGCGT
515 TAGGTCCTAG
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 42 1.00
ACGTcount: A:0.16, C:0.34, G:0.36, T:0.14
Consensus pattern (46 bp):
GCAGGCCTAGCCAACGCTGGGCCACACTGCTGCCAATGGGCAGCGT
Found at i:642 original size:15 final size:14
Alignment explanation
Indices: 622--680 Score: 59
Period size: 14 Copynumber: 4.1 Consensus size: 14
612 CCCAAAGAGG
622 GAGAAAAAAGAAGAA
1 GAGAAAAAAGAA-AA
637 GAGAAAAATAGAAAA
1 GAGAAAAA-AGAAAA
* *
652 GA-AAAATAGAAAG
1 GAGAAAAAAGAAAA
665 GA-AAAGAAAGAAAA
1 GAGAAA-AAAGAAAA
679 GA
1 GA
681 AAAGGAAGGA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
13 10 0.26
14 12 0.32
15 12 0.32
16 4 0.11
ACGTcount: A:0.73, C:0.00, G:0.24, T:0.03
Consensus pattern (14 bp):
GAGAAAAAAGAAAA
Found at i:643 original size:13 final size:14
Alignment explanation
Indices: 627--684 Score: 68
Period size: 13 Copynumber: 4.4 Consensus size: 14
617 AGAGGGAGAA
*
627 AAAAGA-AGAAGAG
1 AAAAGATAGAAAAG
640 AAAA-ATAGAAAAG
1 AAAAGATAGAAAAG
*
653 AAAA-ATAGAAAGG
1 AAAAGATAGAAAAG
*
666 AAAAGAAAGAAAAG
1 AAAAGATAGAAAAG
680 AAAAG
1 AAAAG
685 GAAGGAAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
12 1 0.03
13 26 0.67
14 12 0.31
ACGTcount: A:0.74, C:0.00, G:0.22, T:0.03
Consensus pattern (14 bp):
AAAAGATAGAAAAG
Found at i:684 original size:14 final size:14
Alignment explanation
Indices: 627--699 Score: 62
Period size: 13 Copynumber: 5.4 Consensus size: 14
617 AGAGGGAGAA
*
627 AAAAG-AAGAAGAG
1 AAAAGAAAGAAAAG
*
640 AAAA-ATAGAAAAG
1 AAAAGAAAGAAAAG
* *
653 AAAA-ATAGAAAGG
1 AAAAGAAAGAAAAG
666 AAAAGAAAGAAAAG
1 AAAAGAAAGAAAAG
* *
680 AAAAGGAAGGAAAAA
1 AAAA-GAAAGAAAAG
695 AAAAG
1 AAAAG
700 GAAAATAAGG
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
13 26 0.52
14 12 0.24
15 12 0.24
ACGTcount: A:0.74, C:0.00, G:0.23, T:0.03
Consensus pattern (14 bp):
AAAAGAAAGAAAAG
Found at i:692 original size:15 final size:15
Alignment explanation
Indices: 646--703 Score: 59
Period size: 15 Copynumber: 4.1 Consensus size: 15
636 AGAGAAAAAT
*
646 AGAAAAGAAAA--AT
1 AGAAAAGAAAAGGAA
*
659 AGAAAGGAAAA-GAA
1 AGAAAAGAAAAGGAA
673 AGAAAAGAAAAGGAA
1 AGAAAAGAAAAGGAA
* *
688 GGAAAAAAAAAGGAA
1 AGAAAAGAAAAGGAA
703 A
1 A
704 ATAAGGAAAT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
13 10 0.27
14 11 0.30
15 16 0.43
ACGTcount: A:0.74, C:0.00, G:0.24, T:0.02
Consensus pattern (15 bp):
AGAAAAGAAAAGGAA
Found at i:844 original size:27 final size:27
Alignment explanation
Indices: 776--845 Score: 70
Period size: 27 Copynumber: 2.6 Consensus size: 27
766 TTACTATTTT
** *
776 ACCCTTTGATGGGTAAAGTACTAAATC
1 ACCCTTTGATGATTAAAGTACGAAATC
* * *
803 ACCC-TTAAGTTATTAAATTACGAAATC
1 ACCCTTTGA-TGATTAAAGTACGAAATC
830 ACCCTTTGATGATTAA
1 ACCCTTTGATGATTAA
846 TTTTAAGAAT
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
26 3 0.09
27 27 0.82
28 3 0.09
ACGTcount: A:0.36, C:0.19, G:0.13, T:0.33
Consensus pattern (27 bp):
ACCCTTTGATGATTAAAGTACGAAATC
Done.