Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006975.1 Corchorus capsularis cultivar CVL-1 contig06996, 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: 17522
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.33
Found at i:1346 original size:18 final size:18
Alignment explanation
Indices: 1304--1339 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1294 ATGCGGGTTA
*
1304 GAATGATAATGCAATGTC
1 GAATGCTAATGCAATGTC
*
1322 GAATGCTAATGTAATGTC
1 GAATGCTAATGCAATGTC
1340 ATATGCTGAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.36, C:0.11, G:0.22, T:0.31
Consensus pattern (18 bp):
GAATGCTAATGCAATGTC
Found at i:9647 original size:16 final size:16
Alignment explanation
Indices: 9614--9648 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
9604 AAAGTCAAAA
* *
9614 ATTGTTATTATTTTTT
1 ATTGTTATTACTTATT
9630 ATTGTTATTACTTATT
1 ATTGTTATTACTTATT
9646 ATT
1 ATT
9649 ATCAATTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.23, C:0.03, G:0.06, T:0.69
Consensus pattern (16 bp):
ATTGTTATTACTTATT
Found at i:13555 original size:21 final size:21
Alignment explanation
Indices: 13531--13570 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
13521 ACTGATTACT
*
13531 CCTTGCTAATTACCATTTTGC
1 CCTTACTAATTACCATTTTGC
* *
13552 CCTTACTGATTACTATTTT
1 CCTTACTAATTACCATTTT
13571 ACTCTTTACC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.20, C:0.25, G:0.07, T:0.47
Consensus pattern (21 bp):
CCTTACTAATTACCATTTTGC
Found at i:13659 original size:14 final size:13
Alignment explanation
Indices: 13637--13668 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 13
13627 TTTGCCATTT
13637 TTACTTTTACTGA
1 TTACTTTTACTGA
13650 TTACTCTTTACTGA
1 TTACT-TTTACTGA
13664 TTACT
1 TTACT
13669 ATTTTACCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.22, C:0.19, G:0.06, T:0.53
Consensus pattern (13 bp):
TTACTTTTACTGA
Found at i:13709 original size:26 final size:27
Alignment explanation
Indices: 13663--13730 Score: 68
Period size: 26 Copynumber: 2.6 Consensus size: 27
13653 CTCTTTACTG
**
13663 ATTACTATTTT-ACCCTCTTGAACTTA
1 ATTACTATTTTCATTCTCTTGAACTTA
*
13689 ATTACTATTTTCATTCT-TTGAATTTA
1 ATTACTATTTTCATTCTCTTGAACTTA
* *
13715 ATCACCATTTATCATT
1 ATTACTATTT-TCATT
13731 TTACTCTTTG
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
26 27 0.77
27 8 0.23
ACGTcount: A:0.28, C:0.19, G:0.03, T:0.50
Consensus pattern (27 bp):
ATTACTATTTTCATTCTCTTGAACTTA
Found at i:13739 original size:32 final size:33
Alignment explanation
Indices: 13703--13773 Score: 92
Period size: 32 Copynumber: 2.2 Consensus size: 33
13693 CTATTTTCAT
13703 TCTTTGAATTTAA-TCACCATTTAT-CATTTTAC
1 TCTTTGAATTTAATTC-CCATTTATCCATTTTAC
* *
13735 TCTTTGGATTTAATTCCCATTTTTGCCATTTTAC
1 TCTTTGAATTTAATTCCCATTTAT-CCATTTTAC
13769 TCTTT
1 TCTTT
13774 ACTGATTACT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
32 19 0.56
33 2 0.06
34 13 0.38
ACGTcount: A:0.21, C:0.20, G:0.06, T:0.54
Consensus pattern (33 bp):
TCTTTGAATTTAATTCCCATTTATCCATTTTAC
Found at i:13894 original size:40 final size:38
Alignment explanation
Indices: 13808--13898 Score: 96
Period size: 40 Copynumber: 2.3 Consensus size: 38
13798 ATTTTTACCT
* *
13808 TTTTACCGATTTACTGATTACTTCTTTTACTCTTACTC
1 TTTTACCGATTTACCGATTACTTCCTTTACTCTTACTC
13846 TTGATTACC-ATTTTACCGATTACTTCCTTTACT-TTCACTCC
1 TT--TTACCGA-TTTACCGATTACTTCCTTTACTCTT-ACT-C
13887 ATTTTACCGATT
1 -TTTTACCGATT
13899 ACTTCTTCTA
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
38 2 0.05
39 3 0.07
40 35 0.80
41 2 0.05
42 2 0.05
ACGTcount: A:0.20, C:0.25, G:0.05, T:0.49
Consensus pattern (38 bp):
TTTTACCGATTTACCGATTACTTCCTTTACTCTTACTC
Found at i:13978 original size:36 final size:36
Alignment explanation
Indices: 13932--14000 Score: 102
Period size: 36 Copynumber: 1.9 Consensus size: 36
13922 TTGATTACCA
* *
13932 TTTTTCTGATTGCTTCCTTTACTTTTGACCTTTCAC
1 TTTTACTGATTACTTCCTTTACTTTTGACCTTTCAC
* *
13968 TTTTACTGATTACTTCTTTTACTTTTGCCCTTT
1 TTTTACTGATTACTTCCTTTACTTTTGACCTTT
14001 TGCTGATTAC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 29 1.00
ACGTcount: A:0.12, C:0.23, G:0.07, T:0.58
Consensus pattern (36 bp):
TTTTACTGATTACTTCCTTTACTTTTGACCTTTCAC
Found at i:13988 original size:16 final size:16
Alignment explanation
Indices: 13967--14030 Score: 53
Period size: 16 Copynumber: 4.1 Consensus size: 16
13957 TGACCTTTCA
13967 CTTTTACTGATTACTT
1 CTTTTACTGATTACTT
* * *
13983 CTTTTACT-TTTGC-C
1 CTTTTACTGATTACTT
*
13997 CTTTTGCTGATTACTT
1 CTTTTACTGATTACTT
*
14013 CCTTTA-TCGATTACTT
1 CTTTTACT-GATTACTT
14029 CT
1 CT
14031 CTTGGTTACC
Statistics
Matches: 35, Mismatches: 10, Indels: 6
0.69 0.20 0.12
Matches are distributed among these distances:
14 7 0.20
15 7 0.20
16 21 0.60
ACGTcount: A:0.14, C:0.23, G:0.08, T:0.55
Consensus pattern (16 bp):
CTTTTACTGATTACTT
Done.