Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008041.1 Corchorus capsularis cultivar CVL-1 contig08062, 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: 60119
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:9502 original size:23 final size:23
Alignment explanation
Indices: 9472--9517 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
9462 CAAACAATCT
9472 TGAGCACTCTCGCTAGGTCTCTA
1 TGAGCACTCTCGCTAGGTCTCTA
*
9495 TGAGCACTCTCGCTCGGTCTCTA
1 TGAGCACTCTCGCTAGGTCTCTA
9518 CAAACTAACA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.15, C:0.33, G:0.22, T:0.30
Consensus pattern (23 bp):
TGAGCACTCTCGCTAGGTCTCTA
Found at i:10410 original size:23 final size:23
Alignment explanation
Indices: 10380--10448 Score: 120
Period size: 23 Copynumber: 3.0 Consensus size: 23
10370 CAAACAATCT
10380 TGAGCACTCTCGCTCGGTCTCTA
1 TGAGCACTCTCGCTCGGTCTCTA
*
10403 TGAGCACTCTCGCTCGGTTTCTA
1 TGAGCACTCTCGCTCGGTCTCTA
*
10426 TGAGCACTCTCGCTCAGTCTCTA
1 TGAGCACTCTCGCTCGGTCTCTA
10449 CAAACTAACA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 43 1.00
ACGTcount: A:0.14, C:0.33, G:0.20, T:0.32
Consensus pattern (23 bp):
TGAGCACTCTCGCTCGGTCTCTA
Found at i:10662 original size:23 final size:23
Alignment explanation
Indices: 10632--10677 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
10622 CAAACAATCT
*
10632 TGAGCACTCTCGCTCGGTCTCTA
1 TGAGCACTCTCGCTCAGTCTCTA
10655 TGAGCACTCTCGCTCAGTCTCTA
1 TGAGCACTCTCGCTCAGTCTCTA
10678 CAAACTAACA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.15, C:0.35, G:0.20, T:0.30
Consensus pattern (23 bp):
TGAGCACTCTCGCTCAGTCTCTA
Found at i:18169 original size:21 final size:22
Alignment explanation
Indices: 18143--18183 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
18133 AAGTAGCCCT
18143 TGCGAACAATAAAT-TGTCATA
1 TGCGAACAATAAATGTGTCATA
* *
18164 TGCGAATAGTAAATGTGTCA
1 TGCGAACAATAAATGTGTCA
18184 CCCTTGGAGC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.39, C:0.12, G:0.20, T:0.29
Consensus pattern (22 bp):
TGCGAACAATAAATGTGTCATA
Found at i:21780 original size:12 final size:12
Alignment explanation
Indices: 21765--21789 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
21755 AAAAACTCGG
21765 AAAAAAAATAAA
1 AAAAAAAATAAA
21777 AAAAAAAATAAA
1 AAAAAAAATAAA
21789 A
1 A
21790 CTCAGTGGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (12 bp):
AAAAAAAATAAA
Found at i:29993 original size:13 final size:13
Alignment explanation
Indices: 29975--30003 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
29965 ATATTAAAGT
29975 TTATTTGATCAAC
1 TTATTTGATCAAC
29988 TTATTTGATCAAC
1 TTATTTGATCAAC
30001 TTA
1 TTA
30004 AAGATAGTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.31, C:0.14, G:0.07, T:0.48
Consensus pattern (13 bp):
TTATTTGATCAAC
Found at i:36499 original size:2 final size:2
Alignment explanation
Indices: 36492--36525 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
36482 AGCTATGCAT
36492 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
36526 CAATCTATGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:42549 original size:113 final size:111
Alignment explanation
Indices: 42369--42587 Score: 282
Period size: 113 Copynumber: 2.0 Consensus size: 111
42359 ATGTATTTAT
* * *
42369 TTATAGGGTAAGTCTTATAATTTAATTTTATTATTAATAGGGTTTTAGTTTCTAAAATTAAAAAC
1 TTATAGGGTAAGTCTTATAATTTAAATTTATTATTAATAAGGTTTTAATTTCTAAAATTAAAAAC
** * *
42434 AAATTAAAAATAAGGTTTAGCCCAAATAAAATATAT-TTTTGTTAC
66 AAACAAAAAAGAAGATTTAGCCCAAATAAAATATATATTTTGTTAC
*
42479 TTATAGGGTTTAGTCTTATAATTTGAGACATTTATTATT-ATAAGGTTTTAATTTCTAAAA-TAA
1 TTATAGGG-TAAGTCTTATAATTT-A-A-ATTTATTATTAATAAGGTTTTAATTTCTAAAATTAA
**
42542 AATACAAACAAAAAAGAAGATTTAGCCTGAATAAAATATATATTTT
62 AA-ACAAACAAAAAAGAAGATTTAGCCCAAATAAAATATATATTTT
42588 TACAGGGTAA
Statistics
Matches: 93, Mismatches: 10, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
110 8 0.09
111 14 0.15
112 6 0.06
113 52 0.56
114 13 0.14
ACGTcount: A:0.42, C:0.06, G:0.11, T:0.41
Consensus pattern (111 bp):
TTATAGGGTAAGTCTTATAATTTAAATTTATTATTAATAAGGTTTTAATTTCTAAAATTAAAAAC
AAACAAAAAAGAAGATTTAGCCCAAATAAAATATATATTTTGTTAC
Found at i:43730 original size:5 final size:5
Alignment explanation
Indices: 43720--43757 Score: 69
Period size: 5 Copynumber: 7.8 Consensus size: 5
43710 TCGGGCGTCT
43720 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT- TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
43758 GCTCTTCGTG
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 4 0.12
5 29 0.88
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (5 bp):
TTTTA
Found at i:44587 original size:11 final size:11
Alignment explanation
Indices: 44571--44606 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
44561 ATTTATTCAT
44571 TATTAATTA-A
1 TATTAATTAGA
44581 CTATTAATTAGA
1 -TATTAATTAGA
44593 TATTAATTAGA
1 TATTAATTAGA
44604 TAT
1 TAT
44607 AGTATAATGG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 23 0.96
12 1 0.04
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (11 bp):
TATTAATTAGA
Done.