Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013551.1 Corchorus capsularis cultivar CVL-1 contig13572, 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: 18544
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.36
Found at i:530 original size:23 final size:23
Alignment explanation
Indices: 504--563 Score: 86
Period size: 23 Copynumber: 2.6 Consensus size: 23
494 TGTCTAAAAT
504 AAATGAAT-ATTATAAAAGAATTA
1 AAAT-AATAATTATAAAAGAATTA
*
527 AAATATTAATTATAAAAGAATTA
1 AAATAATAATTATAAAAGAATTA
*
550 AAATATTAATTATA
1 AAATAATAATTATA
564 CAATGGTATT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
22 2 0.06
23 33 0.94
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (23 bp):
AAATAATAATTATAAAAGAATTA
Found at i:14772 original size:23 final size:22
Alignment explanation
Indices: 14738--14785 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 22
14728 TACTGATGAC
14738 TTTGTTTGTTTGTTTGTTTTGTT
1 TTTGTTTGTTTGTTT-TTTTGTT
* *
14761 TTTGTTTTTTTGTTTTTTTTTT
1 TTTGTTTGTTTGTTTTTTTGTT
14783 TTT
1 TTT
14786 AAATTTGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 9 0.39
23 14 0.61
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (22 bp):
TTTGTTTGTTTGTTTTTTTGTT
Found at i:14773 original size:14 final size:14
Alignment explanation
Indices: 14746--14784 Score: 62
Period size: 14 Copynumber: 2.8 Consensus size: 14
14736 ACTTTGTTTG
14746 TTTGTTTGTTTTGTT
1 TTTGTTT-TTTTGTT
14761 TTTGTTTTTTTGTT
1 TTTGTTTTTTTGTT
14775 TTT-TTTTTTT
1 TTTGTTTTTTT
14785 TAAATTTGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 7 0.29
14 10 0.42
15 7 0.29
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (14 bp):
TTTGTTTTTTTGTT
Found at i:14776 original size:8 final size:8
Alignment explanation
Indices: 14738--14785 Score: 57
Period size: 8 Copynumber: 6.2 Consensus size: 8
14728 TACTGATGAC
*
14738 TTTGTTTG
1 TTTGTTTT
14746 TTTGTTTGT
1 TTTGTTT-T
14755 TTTG--TT
1 TTTGTTTT
14761 TTTGTTTT
1 TTTGTTTT
14769 TTTGTTTT
1 TTTGTTTT
14777 TTT-TTTT
1 TTTGTTTT
14784 TT
1 TT
14786 AAATTTGAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
6 5 0.14
7 7 0.19
8 20 0.56
9 4 0.11
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (8 bp):
TTTGTTTT
Found at i:14782 original size:19 final size:19
Alignment explanation
Indices: 14742--14781 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
14732 GATGACTTTG
14742 TTTGTTTGTTTGTTTTGTT
1 TTTGTTTGTTTGTTTTGTT
*
14761 TTTGTTTTTTTGTTTT-TT
1 TTTGTTTGTTTGTTTTGTT
14779 TTT
1 TTT
14782 TTTTAAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (19 bp):
TTTGTTTGTTTGTTTTGTT
Found at i:17782 original size:7 final size:7
Alignment explanation
Indices: 17770--17809 Score: 55
Period size: 7 Copynumber: 5.9 Consensus size: 7
17760 TATTAGCTAG
17770 TTTTTAT
1 TTTTTAT
17777 TTTTTA-
1 TTTTTAT
17783 TTTTTAT
1 TTTTTAT
17790 TTTTTAT
1 TTTTTAT
* *
17797 TTTGTAG
1 TTTTTAT
17804 TTTTTA
1 TTTTTA
17810 CGTACTAAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
6 6 0.21
7 23 0.79
ACGTcount: A:0.15, C:0.00, G:0.05, T:0.80
Consensus pattern (7 bp):
TTTTTAT
Found at i:17788 original size:13 final size:13
Alignment explanation
Indices: 17770--17809 Score: 62
Period size: 13 Copynumber: 3.0 Consensus size: 13
17760 TATTAGCTAG
17770 TTTTTATTTTTTA
1 TTTTTATTTTTTA
17783 TTTTTATTTTTTA
1 TTTTTATTTTTTA
*
17796 TTTTGTAGTTTTTA
1 TTTT-TATTTTTTA
17810 CGTACTAAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
13 17 0.68
14 8 0.32
ACGTcount: A:0.15, C:0.00, G:0.05, T:0.80
Consensus pattern (13 bp):
TTTTTATTTTTTA
Found at i:17807 original size:20 final size:20
Alignment explanation
Indices: 17770--17807 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
17760 TATTAGCTAG
* *
17770 TTTTTATTTTTTATTTTTAT
1 TTTTTATTTTGTAGTTTTAT
17790 TTTTTATTTTGTAGTTTT
1 TTTTTATTTTGTAGTTTT
17808 TACGTACTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.00, G:0.05, T:0.82
Consensus pattern (20 bp):
TTTTTATTTTGTAGTTTTAT
Done.