Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010338.1 Corchorus capsularis cultivar CVL-1 contig10359, 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: 36880
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:7734 original size:29 final size:31
Alignment explanation
Indices: 7685--7755 Score: 85
Period size: 29 Copynumber: 2.3 Consensus size: 31
7675 GCTTGATCAG
*
7685 AGGGACTAAAATGACTCC-AAATTGCAAGTTTA
1 AGGGAC-AAAATGACTCCAAAATT-AAAGTTTA
7717 AGGGACAAAAT-A-TCCAAAATTAAAGTTTA
1 AGGGACAAAATGACTCCAAAATTAAAGTTTA
*
7746 TGGGACAAAA
1 AGGGACAAAA
7756 CGTTAAAATC
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
29 19 0.53
30 6 0.17
31 5 0.14
32 6 0.17
ACGTcount: A:0.46, C:0.13, G:0.18, T:0.23
Consensus pattern (31 bp):
AGGGACAAAATGACTCCAAAATTAAAGTTTA
Found at i:8709 original size:20 final size:20
Alignment explanation
Indices: 8684--8721 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
8674 AACCCTTTTG
*
8684 CAGTTTTCTCATAAATTTAA
1 CAGTTTTCTAATAAATTTAA
8704 CAGTTTTCTAATAAATTT
1 CAGTTTTCTAATAAATTT
8722 TTGTATATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.34, C:0.13, G:0.05, T:0.47
Consensus pattern (20 bp):
CAGTTTTCTAATAAATTTAA
Found at i:15204 original size:17 final size:18
Alignment explanation
Indices: 15184--15220 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
15174 AACAAATGCC
15184 TTCAATAAAC-AT-CAACA
1 TTCAA-AAACTATCCAACA
15201 TTCAAAAACTATCCAACA
1 TTCAAAAACTATCCAACA
15219 TT
1 TT
15221 AACAACTTCC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 4 0.22
17 7 0.39
18 7 0.39
ACGTcount: A:0.49, C:0.24, G:0.00, T:0.27
Consensus pattern (18 bp):
TTCAAAAACTATCCAACA
Found at i:16304 original size:112 final size:112
Alignment explanation
Indices: 16107--16335 Score: 449
Period size: 112 Copynumber: 2.0 Consensus size: 112
16097 GAAATTTTAT
16107 AAGGGTGGATAGGGCTTTGGGACTACTTTAATTAGAGCACAATCACTAATTACCCAAATTGTAAT
1 AAGGGTGGATAGGGCTTTGGGACTACTTTAATTAGAGCACAATCACTAATTACCCAAATTGTAAT
16172 TTATGGAGTACTATATAGTAATTTAAAGTCTTTAGGTATCACACAGG
66 TTATGGAGTACTATATAGTAATTTAAAGTCTTTAGGTATCACACAGG
*
16219 AAGGGTGGATAGGGTTTTGGGACTACTTTAATTAGAGCACAATCACTAATTACCCAAATTGTAAT
1 AAGGGTGGATAGGGCTTTGGGACTACTTTAATTAGAGCACAATCACTAATTACCCAAATTGTAAT
16284 TTATGGAGTACTATATAGTAATTTAAAGTCTTTAGGTATCACACAGG
66 TTATGGAGTACTATATAGTAATTTAAAGTCTTTAGGTATCACACAGG
16331 AAGGG
1 AAGGG
16336 CAGTTTAAGT
Statistics
Matches: 116, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
112 116 1.00
ACGTcount: A:0.34, C:0.13, G:0.21, T:0.32
Consensus pattern (112 bp):
AAGGGTGGATAGGGCTTTGGGACTACTTTAATTAGAGCACAATCACTAATTACCCAAATTGTAAT
TTATGGAGTACTATATAGTAATTTAAAGTCTTTAGGTATCACACAGG
Found at i:27728 original size:83 final size:84
Alignment explanation
Indices: 27588--27750 Score: 265
Period size: 83 Copynumber: 2.0 Consensus size: 84
27578 GTCTAAATGT
* * *
27588 TGGTTTAGCTATTACTGGATAATAAGCAATTGTAGTGAAGGGTAATAATTATGGTGCTCTTACTA
1 TGGTTTAGCTATTACTGAATAATAACCAATTGTAGTGAAGGGTAATAATGATGGTGCTCTTACTA
27653 GATTGAGAATTAATTGTGC
66 GATTGAGAATTAATTGTGC
* * *
27672 TGGTTTAGCTTTTACTGAATAA-ATCCAATTGTAGTGAAGGGTAATAATGATGGTGCTCTTTCTA
1 TGGTTTAGCTATTACTGAATAATAACCAATTGTAGTGAAGGGTAATAATGATGGTGCTCTTACTA
27736 GATTGAGAATTAATT
66 GATTGAGAATTAATT
27751 TAACTTTTCG
Statistics
Matches: 73, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
83 53 0.73
84 20 0.27
ACGTcount: A:0.31, C:0.09, G:0.23, T:0.38
Consensus pattern (84 bp):
TGGTTTAGCTATTACTGAATAATAACCAATTGTAGTGAAGGGTAATAATGATGGTGCTCTTACTA
GATTGAGAATTAATTGTGC
Found at i:30600 original size:33 final size:33
Alignment explanation
Indices: 30558--30715 Score: 163
Period size: 33 Copynumber: 4.7 Consensus size: 33
30548 AACCCATTGT
* *
30558 AGAGCCACCAAAGACCGAGGCAGCCGTCACGGC
1 AGAGCCACCAAAGACCGAGGCAGCAGCCACGGC
30591 AGAGCCACCAAAGACCGAGGCAGCAGCCACGGC
1 AGAGCCACCAAAGACCGAGGCAGCAGCCACGGC
* ** * *
30624 AGAGCCACCAAAGCCCGAGGCCGTAGTTGCCAAGGT
1 AGAGCCACCAAAGACCGAGG-C--AGCAGCCACGGC
* ** * *
30660 AGAGGCGGCAAAGCCCGAGGCAGCAGCCACGGA
1 AGAGCCACCAAAGACCGAGGCAGCAGCCACGGC
**
30693 AGAGCCGGCAAAGACCGAGGCAG
1 AGAGCCACCAAAGACCGAGGCAG
30716 TAGTAGCCAA
Statistics
Matches: 106, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
33 79 0.75
34 1 0.01
35 1 0.01
36 25 0.24
ACGTcount: A:0.31, C:0.32, G:0.34, T:0.03
Consensus pattern (33 bp):
AGAGCCACCAAAGACCGAGGCAGCAGCCACGGC
Found at i:30674 original size:36 final size:36
Alignment explanation
Indices: 30599--30758 Score: 134
Period size: 36 Copynumber: 4.6 Consensus size: 36
30589 GCAGAGCCAC
* * * **
30599 CAAAGACCGAGG-C--AGCAGCCACGGCAGAGCCAC
1 CAAAGACCGAGGCCGTAGTAGCCAAGGTAGAGCCGG
* * *
30632 CAAAGCCCGAGGCCGTAGTTGCCAAGGTAGAGGCGG
1 CAAAGACCGAGGCCGTAGTAGCCAAGGTAGAGCCGG
* * * *
30668 CAAAGCCCGAGG-C--AGCAGCCACGGAAGAGCCGG
1 CAAAGACCGAGGCCGTAGTAGCCAAGGTAGAGCCGG
*
30701 CAAAGACCGAGGCAGTAGTAGCCAAGGTAGAGCCGG
1 CAAAGACCGAGGCCGTAGTAGCCAAGGTAGAGCCGG
* * *
30737 TAAAGACCGAGGCGGCAGTAGC
1 CAAAGACCGAGGCCGTAGTAGC
30759 TGCCCCGGAG
Statistics
Matches: 100, Mismatches: 21, Indels: 9
0.77 0.16 0.07
Matches are distributed among these distances:
33 37 0.37
34 1 0.01
35 1 0.01
36 61 0.61
ACGTcount: A:0.31, C:0.28, G:0.36, T:0.06
Consensus pattern (36 bp):
CAAAGACCGAGGCCGTAGTAGCCAAGGTAGAGCCGG
Found at i:30697 original size:69 final size:69
Alignment explanation
Indices: 30558--30754 Score: 229
Period size: 69 Copynumber: 2.9 Consensus size: 69
30548 AACCCATTGT
** * * **
30558 AGAGCCACCAAAGACCGAGGCAGCCGT---CACGGCAGAGCCACCAAAGACCGAGGCAGCAGCCA
1 AGAGCCACCAAAGACCGAGGCAGTAGTAGCCAAGGTAGAGCCGGCAAAGACCGAGGCAGCAGCCA
*
30620 CGGC
66 CGGA
* * * * *
30624 AGAGCCACCAAAGCCCGAGGCCGTAGTTGCCAAGGTAGAGGCGGCAAAGCCCGAGGCAGCAGCCA
1 AGAGCCACCAAAGACCGAGGCAGTAGTAGCCAAGGTAGAGCCGGCAAAGACCGAGGCAGCAGCCA
30689 CGGA
66 CGGA
** * *
30693 AGAGCCGGCAAAGACCGAGGCAGTAGTAGCCAAGGTAGAGCCGGTAAAGACCGAGGCGGCAG
1 AGAGCCACCAAAGACCGAGGCAGTAGTAGCCAAGGTAGAGCCGGCAAAGACCGAGGCAGCAG
30755 TAGCTGCCCC
Statistics
Matches: 108, Mismatches: 20, Indels: 3
0.82 0.15 0.02
Matches are distributed among these distances:
66 23 0.21
69 85 0.79
ACGTcount: A:0.31, C:0.30, G:0.35, T:0.05
Consensus pattern (69 bp):
AGAGCCACCAAAGACCGAGGCAGTAGTAGCCAAGGTAGAGCCGGCAAAGACCGAGGCAGCAGCCA
CGGA
Found at i:33197 original size:21 final size:21
Alignment explanation
Indices: 33154--33199 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
33144 AAATCGAGGG
* *
33154 TTGCTAAATACCATCCTAGTT
1 TTGCTAAATACCATCCCACTT
*
33175 TTGCTAAATACCGTCCCACTT
1 TTGCTAAATACCATCCCACTT
33196 TTGC
1 TTGC
33200 CCTTTACCTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.24, C:0.28, G:0.11, T:0.37
Consensus pattern (21 bp):
TTGCTAAATACCATCCCACTT
Found at i:33299 original size:32 final size:32
Alignment explanation
Indices: 33251--33327 Score: 127
Period size: 32 Copynumber: 2.4 Consensus size: 32
33241 CCCACTAGGA
* *
33251 CGGTGGGACGGTTTTGCCAAGGCAGGCCGTCC
1 CGGTGGGGCGGCTTTGCCAAGGCAGGCCGTCC
*
33283 CGGTGGGGCGGCTTTGCCAGGGCAGGCCGTCC
1 CGGTGGGGCGGCTTTGCCAAGGCAGGCCGTCC
33315 CGGTGGGGCGGCT
1 CGGTGGGGCGGCT
33328 AGACCAAATT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 42 1.00
ACGTcount: A:0.08, C:0.29, G:0.47, T:0.17
Consensus pattern (32 bp):
CGGTGGGGCGGCTTTGCCAAGGCAGGCCGTCC
Found at i:33419 original size:32 final size:32
Alignment explanation
Indices: 33378--33534 Score: 233
Period size: 32 Copynumber: 4.9 Consensus size: 32
33368 AAAAAAATTA
33378 GCGAAGCCGCCCCACCGGTGCGGCCTGCCGTG
1 GCGAAGCCGCCCCACCGGTGCGGCCTGCCGTG
* *
33410 GCGAAGCCGCCCCACTGGTGCGGCCTTCCGTG
1 GCGAAGCCGCCCCACCGGTGCGGCCTGCCGTG
* *
33442 GCGAAGCCGCCCTACCGGTACGGCCTGCCGTG
1 GCGAAGCCGCCCCACCGGTGCGGCCTGCCGTG
* *
33474 GCGAAGCCGCCCCACCGGTGCTGCCTTCCGTG
1 GCGAAGCCGCCCCACCGGTGCGGCCTGCCGTG
** *
33506 GCGAAGCCGCCCCAGTGGGGCGGCCTGCC
1 GCGAAGCCGCCCCACCGGTGCGGCCTGCC
33535 CATGGTAAGC
Statistics
Matches: 110, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 110 1.00
ACGTcount: A:0.10, C:0.42, G:0.36, T:0.12
Consensus pattern (32 bp):
GCGAAGCCGCCCCACCGGTGCGGCCTGCCGTG
Found at i:36579 original size:2 final size:2
Alignment explanation
Indices: 36572--36606 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
36562 CTTAGTCCCC
36572 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
36607 GTTCAAGGGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.