Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012500.1 Corchorus olitorius cultivar O-4 contig12533, 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: 23435
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:3582 original size:20 final size:20
Alignment explanation
Indices: 3529--3584 Score: 103
Period size: 20 Copynumber: 2.8 Consensus size: 20
3519 TCGGGTTAAT
*
3529 CCGGGTTTCAACGAGTCACA
1 CCGGGTTTCAACGGGTCACA
3549 CCGGGTTTCAACGGGTCACA
1 CCGGGTTTCAACGGGTCACA
3569 CCGGGTTTCAACGGGT
1 CCGGGTTTCAACGGGT
3585 TGTTTCCTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.20, C:0.29, G:0.30, T:0.21
Consensus pattern (20 bp):
CCGGGTTTCAACGGGTCACA
Found at i:3901 original size:26 final size:24
Alignment explanation
Indices: 3883--3928 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 24
3873 CACCACCGTG
3883 TAATCAATTCTAATCTCACCA-TA
1 TAATCAATTCTAATCTCACCACTA
*
3906 TAATCAATTCTAATCTCTCCACT
1 TAATCAATTCTAATCTCACCACT
3929 CAGTCATGGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 20 0.95
24 1 0.05
ACGTcount: A:0.35, C:0.28, G:0.00, T:0.37
Consensus pattern (24 bp):
TAATCAATTCTAATCTCACCACTA
Found at i:5814 original size:23 final size:23
Alignment explanation
Indices: 5788--5834 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
5778 ATAATTCGCA
5788 TATATAAAGCAAAACACATGACC
1 TATATAAAGCAAAACACATGACC
5811 TATATAAAGCAAAACACATGACC
1 TATATAAAGCAAAACACATGACC
5834 T
1 T
5835 CTCTTTCATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.51, C:0.21, G:0.09, T:0.19
Consensus pattern (23 bp):
TATATAAAGCAAAACACATGACC
Found at i:8394 original size:19 final size:18
Alignment explanation
Indices: 8357--8404 Score: 57
Period size: 16 Copynumber: 2.8 Consensus size: 18
8347 CGAAATTTAT
8357 TAATTATTTATTAAATAA
1 TAATTATTTATTAAATAA
* *
8375 TAATTATTT-TT-CAGAA
1 TAATTATTTATTAAATAA
8391 TAATTA-TTATTAAA
1 TAATTATTTATTAAA
8405 GTTTCCTTCT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
15 2 0.08
16 11 0.44
17 3 0.12
18 9 0.36
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (18 bp):
TAATTATTTATTAAATAA
Found at i:9636 original size:32 final size:32
Alignment explanation
Indices: 9595--9717 Score: 201
Period size: 32 Copynumber: 3.8 Consensus size: 32
9585 CTTAAATCAA
9595 ATATCACTCATCTCACAAACCATCTCCAACAG
1 ATATCACTCATCTCACAAACCATCTCCAACAG
*
9627 ATATCACTCATCTCACAAACTATCTCCAACAG
1 ATATCACTCATCTCACAAACCATCTCCAACAG
* *
9659 ATATCACTCATCTTACAAACCATCTCCAAGAG
1 ATATCACTCATCTCACAAACCATCTCCAACAG
* *
9691 ATATCACTCATCTCAAAAACCAGCTCC
1 ATATCACTCATCTCACAAACCATCTCC
9718 TGAAGCTACA
Statistics
Matches: 84, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 84 1.00
ACGTcount: A:0.37, C:0.35, G:0.04, T:0.24
Consensus pattern (32 bp):
ATATCACTCATCTCACAAACCATCTCCAACAG
Found at i:9640 original size:20 final size:20
Alignment explanation
Indices: 9615--9671 Score: 58
Period size: 20 Copynumber: 3.2 Consensus size: 20
9605 TCTCACAAAC
9615 CATCTCCAACAGATATCACT
1 CATCTCCAACAGATATCACT
9635 CATCT-C-AC--A-A--ACT
1 CATCTCCAACAGATATCACT
9648 -ATCTCCAACAGATATCACT
1 CATCTCCAACAGATATCACT
9667 CATCT
1 CATCT
9672 TACAAACCAT
Statistics
Matches: 29, Mismatches: 0, Indels: 16
0.64 0.00 0.36
Matches are distributed among these distances:
12 4 0.14
13 4 0.14
14 2 0.07
15 1 0.03
16 2 0.07
17 1 0.03
18 2 0.07
19 4 0.14
20 9 0.31
ACGTcount: A:0.35, C:0.35, G:0.04, T:0.26
Consensus pattern (20 bp):
CATCTCCAACAGATATCACT
Found at i:10689 original size:2 final size:2
Alignment explanation
Indices: 10682--10748 Score: 91
Period size: 2 Copynumber: 34.0 Consensus size: 2
10672 TTCTTTTCTT
* *
10682 TA TA TA TA TA TA TA TA CA TA TA TA TA TA TA TA TG TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
10724 TA TA TA TA TG TA TG TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
10749 CTTATGTTAC
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
1 1 0.02
2 55 0.98
ACGTcount: A:0.45, C:0.01, G:0.04, T:0.49
Consensus pattern (2 bp):
TA
Found at i:15267 original size:14 final size:14
Alignment explanation
Indices: 15248--15275 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
15238 GACACATACT
15248 CCACTTGATAATTA
1 CCACTTGATAATTA
15262 CCACTTGATAATTA
1 CCACTTGATAATTA
15276 ATTATGTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.21, G:0.07, T:0.36
Consensus pattern (14 bp):
CCACTTGATAATTA
Done.