Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011678.1 Corchorus capsularis cultivar CVL-1 contig11699, 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: 15822
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.32
Found at i:489 original size:56 final size:56
Alignment explanation
Indices: 394--559 Score: 273
Period size: 56 Copynumber: 3.0 Consensus size: 56
384 TTTTCTTCTC
* * *
394 TTTTTATTATTGGTA--TTTTTGTAAACCCAAATGCAATAGTGTACTTATTAAGGA
1 TTTTTACTATTGGTATTTTTTTGCAAACACAAATGCAATAGTGTACTTATTAAGGA
448 TTTTTACTATTGGTATTTTTTTGCAAACACAAATGCAATAGTGTACTTATTAAGGA
1 TTTTTACTATTGGTATTTTTTTGCAAACACAAATGCAATAGTGTACTTATTAAGGA
* *
504 TTTTTACTATTGGTATTTTTTTGCAAACACAAATGCAATGGTGTACTTTTTAAGGA
1 TTTTTACTATTGGTATTTTTTTGCAAACACAAATGCAATAGTGTACTTATTAAGGA
560 AATTGGGCCA
Statistics
Matches: 105, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
54 14 0.13
56 91 0.87
ACGTcount: A:0.31, C:0.10, G:0.15, T:0.44
Consensus pattern (56 bp):
TTTTTACTATTGGTATTTTTTTGCAAACACAAATGCAATAGTGTACTTATTAAGGA
Found at i:763 original size:12 final size:12
Alignment explanation
Indices: 746--770 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
736 CTAACTTATT
746 GCTAAATTGAGA
1 GCTAAATTGAGA
758 GCTAAATTGAGA
1 GCTAAATTGAGA
770 G
1 G
771 TTAGTTAATC
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:0.40, C:0.08, G:0.28, T:0.24
Consensus pattern (12 bp):
GCTAAATTGAGA
Found at i:13727 original size:21 final size:21
Alignment explanation
Indices: 13653--13727 Score: 64
Period size: 21 Copynumber: 3.5 Consensus size: 21
13643 ACTCTTTGAA
* *
13653 TTACTGATCACC-TTTTACTC
1 TTACTGATTACCATTTGACTC
*
13673 TTTTACTGATTACTATTTGACTC
1 --TTACTGATTACCATTTGACTC
*
13696 TTACTAATTACCACTTTG-CTC
1 TTACTGATTACCA-TTTGACTC
*
13717 TTACTGGTTAC
1 TTACTGATTAC
13728 TGTTTTACCT
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
21 23 0.52
22 14 0.32
23 7 0.16
ACGTcount: A:0.21, C:0.24, G:0.08, T:0.47
Consensus pattern (21 bp):
TTACTGATTACCATTTGACTC
Found at i:13760 original size:20 final size:21
Alignment explanation
Indices: 13732--13772 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
13722 GGTTACTGTT
13732 TTAC-CTTTTACTGATTATCA
1 TTACTCTTTTACTGATTATCA
* *
13752 TTACTTTTTTATTGATTATCA
1 TTACTCTTTTACTGATTATCA
13773 AAGCCTTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.24, C:0.15, G:0.05, T:0.56
Consensus pattern (21 bp):
TTACTCTTTTACTGATTATCA
Found at i:14163 original size:50 final size:52
Alignment explanation
Indices: 14092--14336 Score: 274
Period size: 51 Copynumber: 4.8 Consensus size: 52
14082 AACCAATCAA
** * *
14092 TTTATTTACTAATGGC-CTAAAAGTTCACA-CTTCTAATTCCAAA-ATGACA-T
1 TTTATTTACTAATTACTCTAAAAATTCA-ATCTTCTTATT-CAAAGATGACATT
* * * * *
14142 TTTATTTACTAATTACT-TAAAAATTCAATCTTC-TATTAAAAGGTTAAATC
1 TTTATTTACTAATTACTCTAAAAATTCAATCTTCTTATTCAAAGATGACATT
* *
14192 TTTATTTACTAATTATTCTAAAAATTCAATC-TCTTACTCAAAGATGACATT
1 TTTATTTACTAATTACTCTAAAAATTCAATCTTCTTATTCAAAGATGACATT
**
14243 TTTATTTACTAATTACTCTAAAAATTCAATCTT-TTACCCAAAGATGACATT
1 TTTATTTACTAATTACTCTAAAAATTCAATCTTCTTATTCAAAGATGACATT
* *
14294 TTTATTTACTAATTACTCTAAAAATTCCATCTT-TTATCCAAAG
1 TTTATTTACTAATTACTCTAAAAATTCAATCTTCTTATTCAAAG
14337 GTTACATCTT
Statistics
Matches: 168, Mismatches: 20, Indels: 13
0.84 0.10 0.06
Matches are distributed among these distances:
48 3 0.02
49 7 0.04
50 45 0.27
51 112 0.67
52 1 0.01
ACGTcount: A:0.37, C:0.17, G:0.04, T:0.42
Consensus pattern (52 bp):
TTTATTTACTAATTACTCTAAAAATTCAATCTTCTTATTCAAAGATGACATT
Found at i:14328 original size:51 final size:51
Alignment explanation
Indices: 14130--14336 Score: 276
Period size: 51 Copynumber: 4.1 Consensus size: 51
14120 ACTTCTAATT
* *
14130 CCAAA-ATGACA-TTTTATTTACTAATTACT-TAAAAATTCAATCTTCTAT
1 CCAAAGATGACATTTTTATTTACTAATTACTCTAAAAATTCAATCTTTTAC
** * * * * * *
14178 TAAAAGGTTAAATCTTTATTTACTAATTATTCTAAAAATTCAATCTCTTAC
1 CCAAAGATGACATTTTTATTTACTAATTACTCTAAAAATTCAATCTTTTAC
*
14229 TCAAAGATGACATTTTTATTTACTAATTACTCTAAAAATTCAATCTTTTAC
1 CCAAAGATGACATTTTTATTTACTAATTACTCTAAAAATTCAATCTTTTAC
* *
14280 CCAAAGATGACATTTTTATTTACTAATTACTCTAAAAATTCCATCTTTTAT
1 CCAAAGATGACATTTTTATTTACTAATTACTCTAAAAATTCAATCTTTTAC
14331 CCAAAG
1 CCAAAG
14337 GTTACATCTT
Statistics
Matches: 136, Mismatches: 20, Indels: 3
0.86 0.13 0.02
Matches are distributed among these distances:
48 3 0.02
49 3 0.02
50 16 0.12
51 114 0.84
ACGTcount: A:0.38, C:0.16, G:0.04, T:0.42
Consensus pattern (51 bp):
CCAAAGATGACATTTTTATTTACTAATTACTCTAAAAATTCAATCTTTTAC
Done.