Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011368.1 Corchorus capsularis cultivar CVL-1 contig11389, 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: 5381
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.35
Found at i:2399 original size:25 final size:26
Alignment explanation
Indices: 2353--2414 Score: 72
Period size: 25 Copynumber: 2.3 Consensus size: 26
2343 TCTTACCGAT
*
2353 TACCATTTTTGCTTTTGCTAC-TGAA
1 TACCATTTTTACTTTTGCTACTTGAA
**
2378 TACCATTTTTACTTTTTTTACTATTGAA
1 TACCATTTTTACTTTTGCTAC--TTGAA
2406 TACCATTTT
1 TACCATTTT
2415 GATCCTTTTC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
25 18 0.58
28 13 0.42
ACGTcount: A:0.23, C:0.18, G:0.06, T:0.53
Consensus pattern (26 bp):
TACCATTTTTACTTTTGCTACTTGAA
Found at i:2423 original size:28 final size:28
Alignment explanation
Indices: 2365--2429 Score: 69
Period size: 28 Copynumber: 2.4 Consensus size: 28
2355 CCATTTTTGC
* * *
2365 TTTTGCTACTGAATACCATTTTTACTTT
1 TTTTACTACTGAATACCATTTTGACTCT
* *
2393 TTTTACTATTGAATACCATTTTGA-TCC
1 TTTTACTACTGAATACCATTTTGACTCT
*
2420 TTTTCCTACT
1 TTTTACTACT
2430 TACCATTTAC
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
27 9 0.30
28 21 0.70
ACGTcount: A:0.22, C:0.20, G:0.06, T:0.52
Consensus pattern (28 bp):
TTTTACTACTGAATACCATTTTGACTCT
Found at i:2574 original size:7 final size:7
Alignment explanation
Indices: 2504--2621 Score: 55
Period size: 7 Copynumber: 16.1 Consensus size: 7
2494 TTCTCTCTAA
2504 TTACTCT
1 TTACTCT
2511 TTAC-CTT
1 TTACTC-T
2518 TTAC-CATT
1 TTACTC--T
2526 TTACTCTT
1 TTACTC-T
**
2534 TTACTGA
1 TTACTCT
2541 TTACTCT
1 TTACTCT
* *
2548 GTACTTT
1 TTACTCT
2555 TTAC-CATT
1 TTACTC--T
2563 TTACTCT
1 TTACTCT
**
2570 TTACTGA
1 TTACTCT
2577 TTACTCT
1 TTACTCT
*
2584 TTACTTT
1 TTACTCT
2591 TTA-TCAT
1 TTACTC-T
2598 CTTACTCT
1 -TTACTCT
*
2606 TTACTATT
1 TTACT-CT
2614 TTACTCT
1 TTACTCT
2621 T
1 T
2622 ACTAGTTACC
Statistics
Matches: 85, Mismatches: 16, Indels: 20
0.70 0.13 0.17
Matches are distributed among these distances:
6 2 0.02
7 51 0.60
8 28 0.33
9 4 0.05
ACGTcount: A:0.19, C:0.23, G:0.03, T:0.56
Consensus pattern (7 bp):
TTACTCT
Found at i:2605 original size:22 final size:21
Alignment explanation
Indices: 2577--2624 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 21
2567 TCTTTACTGA
2577 TTACTCTTTACT-TTTTATCATC
1 TTACTCTTTACTATTTTA-C-TC
2599 TTACTCTTTACTATTTTACTC
1 TTACTCTTTACTATTTTACTC
2620 TTACT
1 TTACT
2625 AGTTACCTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
21 7 0.28
22 13 0.52
23 5 0.20
ACGTcount: A:0.19, C:0.23, G:0.00, T:0.58
Consensus pattern (21 bp):
TTACTCTTTACTATTTTACTC
Found at i:2624 original size:36 final size:36
Alignment explanation
Indices: 2503--2610 Score: 171
Period size: 36 Copynumber: 3.0 Consensus size: 36
2493 TTTCTCTCTA
*
2503 ATTACTCTTTACCTTTTACCATTTTACTCTTTTACTG
1 ATTACTCTTTACTTTTTACCATTTTACTC-TTTACTG
*
2540 ATTACTCTGTACTTTTTACCATTTTACTCTTTACTG
1 ATTACTCTTTACTTTTTACCATTTTACTCTTTACTG
* *
2576 ATTACTCTTTACTTTTTATCATCTTACTCTTTACT
1 ATTACTCTTTACTTTTTACCATTTTACTCTTTACT
2611 ATTTTACTCT
Statistics
Matches: 66, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
36 39 0.59
37 27 0.41
ACGTcount: A:0.19, C:0.23, G:0.03, T:0.55
Consensus pattern (36 bp):
ATTACTCTTTACTTTTTACCATTTTACTCTTTACTG
Found at i:2645 original size:35 final size:34
Alignment explanation
Indices: 2606--2718 Score: 118
Period size: 35 Copynumber: 3.2 Consensus size: 34
2596 ATCTTACTCT
2606 TTACTATTTTACTCTTACTAGTTACCTTTTACTGA
1 TTACTATTTTACTCTTAC-AGTTACCTTTTACTGA
* * * ** *
2641 TTACTATTTTATTATTACCACTTTGCTCTTACTGA
1 TTACTATTTTACTCTTA-CAGTTACCTTTTACTGA
* * *
2676 TTATTATTTTACTCTTACCGATTACTTTTTACTGA
1 TTACTATTTTACTCTTACAG-TTACCTTTTACTGA
2711 TTACTATT
1 TTACTATT
2719 ATCCAATTAC
Statistics
Matches: 60, Mismatches: 16, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
34 1 0.02
35 58 0.97
36 1 0.02
ACGTcount: A:0.23, C:0.19, G:0.05, T:0.53
Consensus pattern (34 bp):
TTACTATTTTACTCTTACAGTTACCTTTTACTGA
Found at i:2690 original size:21 final size:20
Alignment explanation
Indices: 2666--2708 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
2656 TACCACTTTG
* *
2666 CTCTTACTGATTATTATTTTA
1 CTCTTACCGATTACT-TTTTA
2687 CTCTTACCGATTACTTTTTA
1 CTCTTACCGATTACTTTTTA
2707 CT
1 CT
2709 GATTACTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.21, C:0.21, G:0.05, T:0.53
Consensus pattern (20 bp):
CTCTTACCGATTACTTTTTA
Done.