Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011475.1 Corchorus capsularis cultivar CVL-1 contig11496, 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: 18239
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.33
Found at i:5096 original size:2 final size:2
Alignment explanation
Indices: 5089--5116 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5079 TTTCTTTGCC
5089 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5117 TATTCTTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:14106 original size:2 final size:2
Alignment explanation
Indices: 14099--14123 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
14089 AGAGTGTATG
14099 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
14124 GTGTTATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:14689 original size:30 final size:33
Alignment explanation
Indices: 14647--14714 Score: 115
Period size: 32 Copynumber: 2.2 Consensus size: 33
14637 TGTAGATTTT
14647 ATTTTATTTTTTTGGTG-AA-ATGAAGTTGTAG
1 ATTTTATTTTTTTGGTGAAATATGAAGTTGTAG
14678 ATTTT-TTTTTTTGGTGAAATATGAAGTTGTAG
1 ATTTTATTTTTTTGGTGAAATATGAAGTTGTAG
14710 ATTTT
1 ATTTT
14715 GATGGAATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
30 11 0.31
31 7 0.20
32 17 0.49
ACGTcount: A:0.25, C:0.00, G:0.21, T:0.54
Consensus pattern (33 bp):
ATTTTATTTTTTTGGTGAAATATGAAGTTGTAG
Found at i:15606 original size:14 final size:14
Alignment explanation
Indices: 15587--15632 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
15577 TGGCCCAAGG
15587 GAAAAAAAAAAGAA
1 GAAAAAAAAAAGAA
15601 G-AAAAAAAAA-AA
1 GAAAAAAAAAAGAA
*
15613 GAGAAAAGAAAAGAA
1 GA-AAAAAAAAAGAA
15628 GAAAA
1 GAAAA
15633 GCCTTTGGAT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
12 3 0.11
13 9 0.32
14 12 0.43
15 4 0.14
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (14 bp):
GAAAAAAAAAAGAA
Found at i:15608 original size:15 final size:15
Alignment explanation
Indices: 15588--15630 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
15578 GGCCCAAGGG
15588 AAAAAAAAAAGAAGA
1 AAAAAAAAAAGAAGA
15603 AAAAAAAAAAG-AGA
1 AAAAAAAAAAGAAGA
*
15617 AAAGAAAAGAAGAA
1 AAA-AAAAAAAGAA
15631 AAGCCTTTGG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
14 6 0.24
15 18 0.72
16 1 0.04
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAGAAGA
Found at i:15633 original size:13 final size:13
Alignment explanation
Indices: 15589--15632 Score: 63
Period size: 13 Copynumber: 3.3 Consensus size: 13
15579 GCCCAAGGGA
15589 AAAAAAAAAGAAG
1 AAAAAAAAAGAAG
15602 AAAAAAAAA-AAG
1 AAAAAAAAAGAAG
15614 AGAAAAGAAAAGAAG
1 A-AAAA-AAAAGAAG
15629 AAAA
1 AAAA
15633 GCCTTTGGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
12 4 0.14
13 13 0.46
14 7 0.25
15 4 0.14
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAGAAG
Found at i:16763 original size:116 final size:113
Alignment explanation
Indices: 16526--16768 Score: 308
Period size: 116 Copynumber: 2.1 Consensus size: 113
16516 AAAAATAGTG
* *
16526 ATTTTCAGTCGACTATGCTTGGTGTTGAAACTGCAGTCGCGTGGTCGTCAATACTGACACTTTTT
1 ATTTTCAGTCGACTATCCTTGGTGTTGAAACTGCAGTCGCGTGGTCGTCAACACTGACACTTTTT
* *
16591 TGAAGGTCTGATTAAAATTTCAGTAGACTACAGAAAGTGTTGAAAATC
66 TGAAAGACTGATTAAAATTTCAGTAGACTACAGAAAGTGTTGAAAATC
* * * *
16639 ACTTTCAGTCGACTATCCTTGGTGTTGAAACTGCAGTCTCTTTGGTCGTCAACACTGCCACTTTT
1 ATTTTCAGTCGACTATCCTTGGTGTTGAAACTGCAGTCGC-GTGGTCGTCAACACTGACACTTTT
* * * * **
16704 CTTGAATAGACTGATTGAACTTTCAGTCGATTGTA-ACAAGTGTTGAAAATC
65 -TTGAA-AGACTGATTAAAATTTCAGTAGACTACAGA-AAGTGTTGAAAATC
*
16755 ATTTTCAGTTGACT
1 ATTTTCAGTCGACT
16769 GAAAATATTT
Statistics
Matches: 110, Mismatches: 16, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
113 37 0.34
114 21 0.19
115 6 0.05
116 46 0.42
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.35
Consensus pattern (113 bp):
ATTTTCAGTCGACTATCCTTGGTGTTGAAACTGCAGTCGCGTGGTCGTCAACACTGACACTTTTT
TGAAAGACTGATTAAAATTTCAGTAGACTACAGAAAGTGTTGAAAATC
Done.