Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014524.1 Corchorus capsularis cultivar CVL-1 contig14545, 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: 28722
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:4803 original size:31 final size:30
Alignment explanation
Indices: 4768--4873 Score: 97
Period size: 31 Copynumber: 3.5 Consensus size: 30
4758 GTGGACCAAT
*
4768 TGCTCAAATAAGGGCTTAACATTTACCAAAA
1 TGCTCAAATAAGGGCTTAACATTTA-AAAAA
* * * * **
4799 TGCTCAAATAAAGGCTCAATATTT-TAATT
1 TGCTCAAATAAGGGCTTAACATTTAAAAAA
* * *
4828 TGGTCAAATAAGGGCCTAACGTTATAAAAAA
1 TGCTCAAATAAGGGCTTAACATT-TAAAAAA
4859 TGCTCAAATAAGGGC
1 TGCTCAAATAAGGGC
4874 CTGATCTTTT
Statistics
Matches: 57, Mismatches: 16, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
29 19 0.33
30 1 0.02
31 37 0.65
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.27
Consensus pattern (30 bp):
TGCTCAAATAAGGGCTTAACATTTAAAAAA
Found at i:4864 original size:60 final size:60
Alignment explanation
Indices: 4771--4935 Score: 181
Period size: 60 Copynumber: 2.8 Consensus size: 60
4761 GACCAATTGC
* * *
4771 TCAAATAAGGGCTTAACATT-TACCAAAATGCTCAAATAAAGG-CTCAATATTTTAATTTGG
1 TCAAATAAGGGCCTAACGTTATA-AAAAATGCTCAAATAAAGGCCT-AATATTTTAATTTGG
* * *
4831 TCAAATAAGGGCCTAACGTTATAAAAAATGCTCAAATAAGGGCCTGATCTTTTAATTTGG
1 TCAAATAAGGGCCTAACGTTATAAAAAATGCTCAAATAAAGGCCTAATATTTTAATTTGG
* * * *** *
4891 CCAAACAAGGGCCTAAAGTTATCGGAAATGCTCAAATAAGGGCCT
1 TCAAATAAGGGCCTAACGTTATAAAAAATGCTCAAATAAAGGCCT
4936 GACATCAGTT
Statistics
Matches: 91, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
60 87 0.96
61 4 0.04
ACGTcount: A:0.38, C:0.17, G:0.18, T:0.27
Consensus pattern (60 bp):
TCAAATAAGGGCCTAACGTTATAAAAAATGCTCAAATAAAGGCCTAATATTTTAATTTGG
Found at i:4936 original size:60 final size:60
Alignment explanation
Indices: 4795--4937 Score: 189
Period size: 60 Copynumber: 2.4 Consensus size: 60
4785 AACATTTACC
* * * * *
4795 AAAATGCTCAAATAAAGG-CTCAATATTTTAATTTGGTCAAATAAGGGCCTAACGTTATAA
1 AAAATGCTCAAATAAGGGCCT-GATATTTTAATTTGGCCAAACAAGGGCCTAAAGTTATAA
* **
4855 AAAATGCTCAAATAAGGGCCTGATCTTTTAATTTGGCCAAACAAGGGCCTAAAGTTATCG
1 AAAATGCTCAAATAAGGGCCTGATATTTTAATTTGGCCAAACAAGGGCCTAAAGTTATAA
*
4915 GAAATGCTCAAATAAGGGCCTGA
1 AAAATGCTCAAATAAGGGCCTGA
4938 CATCAGTTTG
Statistics
Matches: 73, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
60 71 0.97
61 2 0.03
ACGTcount: A:0.38, C:0.16, G:0.19, T:0.27
Consensus pattern (60 bp):
AAAATGCTCAAATAAGGGCCTGATATTTTAATTTGGCCAAACAAGGGCCTAAAGTTATAA
Found at i:9655 original size:66 final size:67
Alignment explanation
Indices: 9571--9703 Score: 178
Period size: 66 Copynumber: 2.0 Consensus size: 67
9561 CATTTGTTAT
* * *
9571 GTTTTAATTCTTTGATATTTTGAGTTGCTTGTTA-ATTAGATTCAATACTTTCCTTCTGCTTGTT
1 GTTTTAATTCTTTGATATTTTCAGTTGCTTGTGAGATTAGATTCAATACTTTCCCTCTGCTTGTT
9635 TC
66 TC
* * ** * *
9637 GTTTTAGTTCTTTGATATTTTCAGTTGTTTGTGAGATTAGATTTTATTCTTTCCCTCTGTTTGTT
1 GTTTTAATTCTTTGATATTTTCAGTTGCTTGTGAGATTAGATTCAATACTTTCCCTCTGCTTGTT
9702 TC
66 TC
9704 CTCGGAAACC
Statistics
Matches: 57, Mismatches: 9, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
66 30 0.53
67 27 0.47
ACGTcount: A:0.16, C:0.13, G:0.15, T:0.56
Consensus pattern (67 bp):
GTTTTAATTCTTTGATATTTTCAGTTGCTTGTGAGATTAGATTCAATACTTTCCCTCTGCTTGTT
TC
Found at i:18341 original size:83 final size:83
Alignment explanation
Indices: 18202--18369 Score: 318
Period size: 83 Copynumber: 2.0 Consensus size: 83
18192 GATTATATAT
* *
18202 CTTACTCTTATTCTACTGGATTGACTTTTCATTGTTGATAATGTTTTCTCAGTTGCAATGCTTCT
1 CTTACTCTTATTCTACTGGATTGACTTTTCAATGTTGATAATGTTTTCTCACTTGCAATGCTTCT
18267 TGACAATTGTTTTCACCA
66 TGACAATTGTTTTCACCA
18285 CTTACTCTTATTCTACTGGATTGACTTTTCAATGTTGATAATGTTTTCTCACTTGCAATGCTTCT
1 CTTACTCTTATTCTACTGGATTGACTTTTCAATGTTGATAATGTTTTCTCACTTGCAATGCTTCT
18350 TGACAATTGTTTTCACCA
66 TGACAATTGTTTTCACCA
18368 CT
1 CT
18370 AAATATGGTT
Statistics
Matches: 83, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
83 83 1.00
ACGTcount: A:0.21, C:0.20, G:0.12, T:0.46
Consensus pattern (83 bp):
CTTACTCTTATTCTACTGGATTGACTTTTCAATGTTGATAATGTTTTCTCACTTGCAATGCTTCT
TGACAATTGTTTTCACCA
Found at i:21668 original size:6 final size:6
Alignment explanation
Indices: 21657--21687 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
21647 AATCTCAAGG
21657 CTGCAT CTGCAT CTGCAT CTGCAT CTGCAT C
1 CTGCAT CTGCAT CTGCAT CTGCAT CTGCAT C
21688 AACATCTGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.16, C:0.35, G:0.16, T:0.32
Consensus pattern (6 bp):
CTGCAT
Found at i:21693 original size:18 final size:18
Alignment explanation
Indices: 21657--21699 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
21647 AATCTCAAGG
**
21657 CTGCATCTGCATCTGCAT
1 CTGCATCTGCATCAACAT
21675 CTGCATCTGCATCAACAT
1 CTGCATCTGCATCAACAT
21693 CTG-ATCT
1 CTGCATCT
21700 CAAGACAGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 4 0.17
18 19 0.83
ACGTcount: A:0.21, C:0.33, G:0.14, T:0.33
Consensus pattern (18 bp):
CTGCATCTGCATCAACAT
Found at i:28692 original size:2 final size:2
Alignment explanation
Indices: 28685--28722 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
28675 ATAAATAATG
28685 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Done.