Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015736.1 Corchorus capsularis cultivar CVL-1 contig15757, 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: 18614
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:500 original size:2 final size:2
Alignment explanation
Indices: 493--534 Score: 66
Period size: 2 Copynumber: 20.0 Consensus size: 2
483 ATTGTTTTAA
493 AT AT AT AT AT AT AT AT AT AT AT AT AT AT GAT AT AT GAT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT -AT AT AT
535 GATTTGATTT
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 34 0.89
3 4 0.11
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (2 bp):
AT
Found at i:731 original size:35 final size:35
Alignment explanation
Indices: 685--754 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
675 GTCTAGGTCT
685 CAGCTTGGAGACTCTGCGTACGCCACCCTCCGTTG
1 CAGCTTGGAGACTCTGCGTACGCCACCCTCCGTTG
720 CAGCTTGGAGACTCTGCGTACGCCACCCTCCGTTG
1 CAGCTTGGAGACTCTGCGTACGCCACCCTCCGTTG
755 ATTAAAGACT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.14, C:0.37, G:0.26, T:0.23
Consensus pattern (35 bp):
CAGCTTGGAGACTCTGCGTACGCCACCCTCCGTTG
Found at i:3122 original size:28 final size:28
Alignment explanation
Indices: 3085--3143 Score: 109
Period size: 28 Copynumber: 2.1 Consensus size: 28
3075 TTTTGGCCAG
3085 ATTAGTCCTTGCAATCCAATATGTACAA
1 ATTAGTCCTTGCAATCCAATATGTACAA
*
3113 ATTAGTCCTTGTAATCCAATATGTACAA
1 ATTAGTCCTTGCAATCCAATATGTACAA
3141 ATT
1 ATT
3144 GGTCTCTATA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.36, C:0.19, G:0.10, T:0.36
Consensus pattern (28 bp):
ATTAGTCCTTGCAATCCAATATGTACAA
Found at i:4831 original size:4 final size:4
Alignment explanation
Indices: 4815--4847 Score: 57
Period size: 4 Copynumber: 8.0 Consensus size: 4
4805 AAATGGAAAG
4815 AGAA AGCAA AGAA AGAA AGAA AGAA AGAA AGAA
1 AGAA AG-AA AGAA AGAA AGAA AGAA AGAA AGAA
4848 GAATTAGAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 24 0.86
5 4 0.14
ACGTcount: A:0.73, C:0.03, G:0.24, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:6347 original size:48 final size:48
Alignment explanation
Indices: 6286--6381 Score: 174
Period size: 48 Copynumber: 2.0 Consensus size: 48
6276 AATTTATACA
* *
6286 GGTGGCTATGAAAGCAGGAATGGAAGCCCTGAAATGGGATATCCTGCT
1 GGTGACTATGAAAGCAGGAATGGAAGCCCTGAAATGAGATATCCTGCT
6334 GGTGACTATGAAAGCAGGAATGGAAGCCCTGAAATGAGATATCCTGCT
1 GGTGACTATGAAAGCAGGAATGGAAGCCCTGAAATGAGATATCCTGCT
6382 TCTGAAGGCT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.31, C:0.17, G:0.31, T:0.21
Consensus pattern (48 bp):
GGTGACTATGAAAGCAGGAATGGAAGCCCTGAAATGAGATATCCTGCT
Found at i:9453 original size:2 final size:2
Alignment explanation
Indices: 9446--9475 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
9436 CAAAACCCAT
9446 TC TC TC TC TC T- TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
9476 ATATAGGCCT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
TC
Found at i:10806 original size:44 final size:47
Alignment explanation
Indices: 10724--10818 Score: 151
Period size: 44 Copynumber: 2.1 Consensus size: 47
10714 TCAATTTCTT
* *
10724 ATATCTCTCAATCAAATAGTAATCACTTGAAGATGATCCATCAACTA
1 ATATCTCTCAATCAAATAGTAATCACTTAAAGAGGATCCATCAACTA
10771 ATATCTCTCAATC-AA-A-TAATCACTTAAAGAGGATCCATCAACTA
1 ATATCTCTCAATCAAATAGTAATCACTTAAAGAGGATCCATCAACTA
10815 ATAT
1 ATAT
10819 ATATTAATAT
Statistics
Matches: 46, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
44 30 0.65
45 1 0.02
46 2 0.04
47 13 0.28
ACGTcount: A:0.42, C:0.21, G:0.07, T:0.29
Consensus pattern (47 bp):
ATATCTCTCAATCAAATAGTAATCACTTAAAGAGGATCCATCAACTA
Found at i:11342 original size:60 final size:61
Alignment explanation
Indices: 11249--11408 Score: 157
Period size: 60 Copynumber: 2.7 Consensus size: 61
11239 CTAATTGCTT
* * * * * ** *
11249 AAATAAAGGCCTAACGTT-TGCCAAAATACTCAAATAAGA-ATTTGATATTTTAATTTGGCC
1 AAATAAGGGCTTAACGTTAT-CAAAAATGCTCAAATAAGAGACTCAATATTTTAAGTTGGCC
* * * *
11309 AAATAAGGGCTTAACGTTATCGAAAATGCTCAAATAA-AGGCTCAATCTTTTTAGTTGGCC
1 AAATAAGGGCTTAACGTTATCAAAAATGCTCAAATAAGAGACTCAATATTTTAAGTTGGCC
*
11369 AGATAAGGG-TCTAACGTTATCAAAAATGCTCAAATAAGAG
1 AAATAAGGGCT-TAACGTTATCAAAAATGCTCAAATAAGAG
11409 CCTGGCGTCA
Statistics
Matches: 83, Mismatches: 13, Indels: 7
0.81 0.13 0.07
Matches are distributed among these distances:
59 2 0.02
60 78 0.94
61 3 0.04
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.29
Consensus pattern (61 bp):
AAATAAGGGCTTAACGTTATCAAAAATGCTCAAATAAGAGACTCAATATTTTAAGTTGGCC
Found at i:11488 original size:31 final size:31
Alignment explanation
Indices: 11450--11584 Score: 134
Period size: 31 Copynumber: 4.4 Consensus size: 31
11440 TTTCGATGCC
*
11450 AGGCTCTTATTTGAGCATTTTGGAAAAAGTT
1 AGGCCCTTATTTGAGCATTTTGGAAAAAGTT
* ** *
11481 AGGCTCTTATTTG-GCCAAATT--AAAAA-AT
1 AGGCCCTTATTTGAG-CATTTTGGAAAAAGTT
* *
11509 AGGGCCCTTATTTGAGCATTTTGGTAAATGTT
1 A-GGCCCTTATTTGAGCATTTTGGAAAAAGTT
* * *
11541 AGGCCCTTATTTGAACATTTTGGTAAATGTT
1 AGGCCCTTATTTGAGCATTTTGGAAAAAGTT
11572 AGGCCCTTATTTG
1 AGGCCCTTATTTG
11585 GCCAAATTAG
Statistics
Matches: 88, Mismatches: 10, Indels: 12
0.80 0.09 0.11
Matches are distributed among these distances:
28 2 0.02
29 20 0.23
30 2 0.02
31 62 0.70
32 2 0.02
ACGTcount: A:0.27, C:0.13, G:0.21, T:0.39
Consensus pattern (31 bp):
AGGCCCTTATTTGAGCATTTTGGAAAAAGTT
Found at i:11610 original size:91 final size:91
Alignment explanation
Indices: 11450--11648 Score: 265
Period size: 91 Copynumber: 2.2 Consensus size: 91
11440 TTTCGATGCC
* * * *
11450 AGGCTCTTATTTGAGCATTTTGGAAAAAGTTAGGCTCTTATTTGGCCAAATTAAAAAATAGGGCC
1 AGGCCCTTATTTGAACATTTTGGAAAAAGTTAGGCCCTTATTTGGCCAAATTAAAAAATAAGGCC
** *
11515 CTTATTTGAGCATTTTGGTAAATGTT
66 CTTATTTGAGCATTTTGCCAAACGTT
* * * *
11541 AGGCCCTTATTTGAACATTTTGGTAAATGTTAGGCCCTTATTTGGCCAAATTAGAAGATCAAGG-
1 AGGCCCTTATTTGAACATTTTGGAAAAAGTTAGGCCCTTATTTGGCCAAATTAAAAAAT-AAGGC
11605 CCTTATTTGAGCATTTTGCCAAACGTT
65 CCTTATTTGAGCATTTTGCCAAACGTT
* *
11632 AGACCTTTATTTGAACA
1 AGGCCCTTATTTGAACA
11649 ATTAGCAAAA
Statistics
Matches: 94, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
91 91 0.97
92 3 0.03
ACGTcount: A:0.29, C:0.15, G:0.20, T:0.36
Consensus pattern (91 bp):
AGGCCCTTATTTGAACATTTTGGAAAAAGTTAGGCCCTTATTTGGCCAAATTAAAAAATAAGGCC
CTTATTTGAGCATTTTGCCAAACGTT
Found at i:12030 original size:17 final size:17
Alignment explanation
Indices: 12008--12062 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
11998 AAATCATTTT
*
12008 TATTTTAATATGTAAAA
1 TATTTTAATATGTAATA
** **
12025 TATTTTGTTAAATAATA
1 TATTTTAATATGTAATA
12042 TATTATTAATATGTAATA
1 TATT-TTAATATGTAATA
12060 TAT
1 TAT
12063 ATGTGTAATA
Statistics
Matches: 28, Mismatches: 9, Indels: 1
0.74 0.24 0.03
Matches are distributed among these distances:
17 16 0.57
18 12 0.43
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (17 bp):
TATTTTAATATGTAATA
Done.