Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019921.1 Corchorus olitorius cultivar O-4 contig19954, 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: 49232
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:513 original size:16 final size:15
Alignment explanation
Indices: 494--526 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 15
484 TGTATGTATA
494 TCTTTTTTTTCTCTTT
1 TCTTTTTTTT-TCTTT
510 TCTTTTTTTTTCTTT
1 TCTTTTTTTTTCTTT
525 TC
1 TC
527 AACTATAGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (15 bp):
TCTTTTTTTTTCTTT
Found at i:517 original size:15 final size:15
Alignment explanation
Indices: 497--526 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
487 ATGTATATCT
497 TTTTTTTCTCTTTTC
1 TTTTTTTCTCTTTTC
*
512 TTTTTTTTTCTTTTC
1 TTTTTTTCTCTTTTC
527 AACTATAGGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (15 bp):
TTTTTTTCTCTTTTC
Found at i:1974 original size:7 final size:7
Alignment explanation
Indices: 1964--1988 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1954 TTAAAAATGA
1964 AAAAAAC
1 AAAAAAC
1971 AAAAAAC
1 AAAAAAC
1978 AAAAAAC
1 AAAAAAC
1985 AAAA
1 AAAA
1989 TTTGAATCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (7 bp):
AAAAAAC
Found at i:14664 original size:46 final size:46
Alignment explanation
Indices: 14594--14682 Score: 142
Period size: 46 Copynumber: 1.9 Consensus size: 46
14584 TCCAATTCGG
14594 TTCAAATCCGATCCAACCAAGTTTATCCGGTTATTAATCAAAGCGT
1 TTCAAATCCGATCCAACCAAGTTTATCCGGTTATTAATCAAAGCGT
* ** *
14640 TTCAAATCCGGTCCAACCGGGTTTATGCGGTTATTAATCAAAG
1 TTCAAATCCGATCCAACCAAGTTTATCCGGTTATTAATCAAAG
14683 TAAAAAGACA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.30
Consensus pattern (46 bp):
TTCAAATCCGATCCAACCAAGTTTATCCGGTTATTAATCAAAGCGT
Found at i:15058 original size:5 final size:5
Alignment explanation
Indices: 15048--15099 Score: 86
Period size: 5 Copynumber: 10.0 Consensus size: 5
15038 ATTAAACTAT
15048 ATATA ATATA ATATA ATATA ATATA ATATA ATATAA TATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATAT-A -ATATA ATATA ATATA
15100 CTAAATATTA
Statistics
Matches: 45, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
5 39 0.87
6 2 0.04
7 4 0.09
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATATA
Found at i:34949 original size:121 final size:127
Alignment explanation
Indices: 34711--34959 Score: 393
Period size: 121 Copynumber: 2.0 Consensus size: 127
34701 AAGAAATATG
*
34711 TTTAAAAAATTCTAATATATATAAGTTTTTAAATTAAAATAGTAAAATGGTAAAAATAAAATAGG
1 TTTAAAAAATTATAATATATATAAGTTTTTAAATTAAAATAGTAAAATGGTAAAAAT---ATA-G
*
34776 TATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTGTAAAAGTAT
62 TATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAGTAT
34841 A
127 A
*
34842 TTTAAAAAATTAT-A-ATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAAT-TA-TA-A
1 TTTAAAAAATTATAATATATATAAGTTTTTAAATTAAAATAGTAAAATGGTAAAAATATAGTATA
34902 A-GATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAGT
66 AGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAGT
34960 TTAAACAATG
Statistics
Matches: 115, Mismatches: 3, Indels: 10
0.90 0.02 0.08
Matches are distributed among these distances:
121 56 0.49
122 2 0.02
123 2 0.02
125 2 0.02
129 40 0.35
130 1 0.01
131 12 0.10
ACGTcount: A:0.51, C:0.01, G:0.11, T:0.37
Consensus pattern (127 bp):
TTTAAAAAATTATAATATATATAAGTTTTTAAATTAAAATAGTAAAATGGTAAAAATATAGTATA
AGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAGTATA
Found at i:36182 original size:42 final size:43
Alignment explanation
Indices: 36131--36218 Score: 133
Period size: 45 Copynumber: 2.0 Consensus size: 43
36121 TGCATTACCT
* *
36131 AAATTCTA-CTCCATCTCTAGGTAATTCATCAAAATAAAGCTA
1 AAATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAACTA
36173 AAATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAACTA
1 AAATTCTA--CCTCCATCTCTAGATAATTCATCAAAATAAAACTA
36218 A
1 A
36219 TATTAATTGT
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
42 8 0.20
45 33 0.80
ACGTcount: A:0.42, C:0.23, G:0.05, T:0.31
Consensus pattern (43 bp):
AAATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAACTA
Found at i:44567 original size:37 final size:35
Alignment explanation
Indices: 44515--44602 Score: 115
Period size: 37 Copynumber: 2.5 Consensus size: 35
44505 TCATGTTCTC
*
44515 AACTCATGCCTAAATT-CTGGGCAAAAAAAAAAAAA
1 AACTCATGCCTAAATTAGT-GGCAAAAAAAAAAAAA
* *
44550 AATTCTCATGCCTAAATTAGTTGCCAAAAAAAAAAAA
1 AA--CTCATGCCTAAATTAGTGGCAAAAAAAAAAAAA
44587 AACTCATGCCTAAATT
1 AACTCATGCCTAAATT
44603 TCTTAATATG
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
35 16 0.34
37 30 0.64
38 1 0.02
ACGTcount: A:0.50, C:0.18, G:0.09, T:0.23
Consensus pattern (35 bp):
AACTCATGCCTAAATTAGTGGCAAAAAAAAAAAAA
Found at i:45002 original size:15 final size:15
Alignment explanation
Indices: 44982--45012 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
44972 GGATCAGTAA
44982 GGGACGGGATAGGAT
1 GGGACGGGATAGGAT
*
44997 GGGACGGGATGGGAT
1 GGGACGGGATAGGAT
45012 G
1 G
45013 TCTTTTTAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.23, C:0.06, G:0.58, T:0.13
Consensus pattern (15 bp):
GGGACGGGATAGGAT
Done.