Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008998.1 Corchorus capsularis cultivar CVL-1 contig09019, 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: 16856
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.34
Found at i:2141 original size:109 final size:110
Alignment explanation
Indices: 2009--2283 Score: 421
Period size: 109 Copynumber: 2.5 Consensus size: 110
1999 AAAAAAATTA
*
2009 TATAAA-ATATT-GAATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAG
1 TATAAAGATATTAGTATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAG
*
2072 AAAAAATTTTAATATATCCAATTTTTTTGGTAAAAATAAAGTAAT
66 AAAAAATTTTAATATATCCAAATTTTTTGGTAAAAATAAAGTAAT
2117 TATAAAGATATTAG-ATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAG
1 TATAAAGATATTAGTATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAG
*
2181 AAAAAATTTTAGTATATCCAAATTTTTTGGTAAAAATAAAGTAAT
66 AAAAAATTTTAATATATCCAAATTTTTTGGTAAAAATAAAGTAAT
* * * * *
2226 TATAAAGATGTTAGGTTTAATTTAATTGAATAAAAATATAGTTTCTAGTAGAATAAAA
1 TATAAAGATATTA-G--T-ATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAA
2284 CTATAATAGT
Statistics
Matches: 153, Mismatches: 7, Indels: 8
0.91 0.04 0.05
Matches are distributed among these distances:
108 6 0.04
109 110 0.72
110 2 0.01
114 35 0.23
ACGTcount: A:0.48, C:0.02, G:0.12, T:0.39
Consensus pattern (110 bp):
TATAAAGATATTAGTATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAG
AAAAAATTTTAATATATCCAAATTTTTTGGTAAAAATAAAGTAAT
Found at i:2456 original size:20 final size:19
Alignment explanation
Indices: 2421--2458 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 19
2411 ATGCCAAATA
2421 ATATTTTAATTAATATAAT
1 ATATTTTAATTAATATAAT
2440 ATATTTATAAGTT-ATATAA
1 ATATTT-TAA-TTAATATAA
2459 ATTTGAAGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 6 0.35
20 9 0.53
21 2 0.12
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (19 bp):
ATATTTTAATTAATATAAT
Found at i:6000 original size:22 final size:21
Alignment explanation
Indices: 5954--5994 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
5944 TTATATAACC
*
5954 AATTGATGCTATCATTGCTAT
1 AATTGATGCTATAATTGCTAT
*
5975 AATTGATGCTTTGAATTGCT
1 AATTGATGCTAT-AATTGCT
5995 TGAATTACTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.27, C:0.12, G:0.17, T:0.44
Consensus pattern (21 bp):
AATTGATGCTATAATTGCTAT
Found at i:13629 original size:15 final size:15
Alignment explanation
Indices: 13609--13653 Score: 63
Period size: 15 Copynumber: 3.0 Consensus size: 15
13599 TCCTATGACG
13609 GACTTCCTAGCCGTC
1 GACTTCCTAGCCGTC
* *
13624 GACTTCCTCGCAGTC
1 GACTTCCTAGCCGTC
*
13639 GACTTCCTTGCCGTC
1 GACTTCCTAGCCGTC
13654 TGACGGATAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.11, C:0.40, G:0.20, T:0.29
Consensus pattern (15 bp):
GACTTCCTAGCCGTC
Found at i:13781 original size:30 final size:30
Alignment explanation
Indices: 13738--13814 Score: 93
Period size: 30 Copynumber: 2.6 Consensus size: 30
13728 TGGAGGTTGT
* *
13738 GGATCAAAGTCCTCATCAGGATCCTCATCCA
1 GGATCAAAATCCTCATCAGGATCATCAT-CA
* *
13769 GG-TCAAAATCCTCGTCAGGATCATCATCT
1 GGATCAAAATCCTCATCAGGATCATCATCA
*
13798 GGATCAAAATCATCATC
1 GGATCAAAATCCTCATC
13815 TGGGTCAACA
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
29 3 0.08
30 34 0.87
31 2 0.05
ACGTcount: A:0.31, C:0.29, G:0.16, T:0.25
Consensus pattern (30 bp):
GGATCAAAATCCTCATCAGGATCATCATCA
Found at i:13811 original size:18 final size:18
Alignment explanation
Indices: 13788--13852 Score: 94
Period size: 18 Copynumber: 3.6 Consensus size: 18
13778 CCTCGTCAGG
* *
13788 ATCATCATCTGGATCAAA
1 ATCATCATCTGGGTCAAC
13806 ATCATCATCTGGGTCAAC
1 ATCATCATCTGGGTCAAC
*
13824 ACCATCATCTGGGTCAAC
1 ATCATCATCTGGGTCAAC
*
13842 ATCATCCTCTG
1 ATCATCATCTG
13853 AATCCGAATC
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 42 1.00
ACGTcount: A:0.29, C:0.29, G:0.14, T:0.28
Consensus pattern (18 bp):
ATCATCATCTGGGTCAAC
Found at i:15635 original size:42 final size:42
Alignment explanation
Indices: 15588--15735 Score: 168
Period size: 42 Copynumber: 3.6 Consensus size: 42
15578 TCTTTGAATC
* *
15588 ACTGATCACCTTTTACTCTTTACTGATTACTATTTTACTCTT
1 ACTGATTACCTTTTACTCTTTACTGATTAATATTTTACTCTT
*
15630 ACTGATTA-C-----CT-TTTACTGATTATTATTTTACTCGTT
1 ACTGATTACCTTTTACTCTTTACTGATTAATATTTTACTC-TT
*
15666 ACTGATTACCTTCTTACTTTTTACTGATTAATATTTTACT-TT
1 ACTGATTACCTT-TTACTCTTTACTGATTAATATTTTACTCTT
*
15708 ACTGATTACCATTTTGCTCTTTACTGAT
1 ACTGATTACC-TTTTACTCTTTACTGAT
15736 CTCTCTTTAC
Statistics
Matches: 91, Mismatches: 5, Indels: 20
0.78 0.04 0.17
Matches are distributed among these distances:
35 21 0.23
36 12 0.13
37 1 0.01
41 1 0.01
42 32 0.35
43 4 0.04
44 20 0.22
ACGTcount: A:0.22, C:0.20, G:0.07, T:0.51
Consensus pattern (42 bp):
ACTGATTACCTTTTACTCTTTACTGATTAATATTTTACTCTT
Found at i:15657 original size:35 final size:36
Alignment explanation
Indices: 15606--15683 Score: 131
Period size: 35 Copynumber: 2.2 Consensus size: 36
15596 CCTTTTACTC
15606 TTTACTGATTACTATTTTACTC-TTACTGATTACCT
1 TTTACTGATTACTATTTTACTCGTTACTGATTACCT
*
15641 TTTACTGATTATTATTTTACTCGTTACTGATTACCT
1 TTTACTGATTACTATTTTACTCGTTACTGATTACCT
15677 TCTTACT
1 T-TTACT
15684 TTTTACTGAT
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
35 21 0.52
36 14 0.35
37 5 0.12
ACGTcount: A:0.22, C:0.19, G:0.06, T:0.53
Consensus pattern (36 bp):
TTTACTGATTACTATTTTACTCGTTACTGATTACCT
Found at i:15667 original size:22 final size:22
Alignment explanation
Indices: 15641--15735 Score: 97
Period size: 22 Copynumber: 4.4 Consensus size: 22
15631 CTGATTACCT
*
15641 TTTACTGATTATTATTTTACTC
1 TTTACTGATTACTATTTTACTC
* * *
15663 GTTACTGATTACCT-TCTTACTT
1 TTTACTGATTA-CTATTTTACTC
*
15685 TTTACTGATTAATATTTTA--C
1 TTTACTGATTACTATTTTACTC
* *
15705 TTTACTGATTACCATTTTGCTC
1 TTTACTGATTACTATTTTACTC
15727 TTTACTGAT
1 TTTACTGAT
15736 CTCTCTTTAC
Statistics
Matches: 58, Mismatches: 11, Indels: 8
0.75 0.14 0.10
Matches are distributed among these distances:
20 16 0.28
21 1 0.02
22 40 0.69
23 1 0.02
ACGTcount: A:0.22, C:0.17, G:0.07, T:0.54
Consensus pattern (22 bp):
TTTACTGATTACTATTTTACTC
Found at i:15785 original size:21 final size:21
Alignment explanation
Indices: 15761--15824 Score: 50
Period size: 21 Copynumber: 3.3 Consensus size: 21
15751 ACCATTCTTC
15761 TTTTACTGATTACTCTTTACT
1 TTTTACTGATTACTCTTTACT
**
15782 TTTT--T-ACCA-T-TTTACT
1 TTTTACTGATTACTCTTTACT
*
15798 TTTTACCGATCT-CTCTTTACT
1 TTTTACTGAT-TACTCTTTACT
15819 TTTTAC
1 TTTTAC
15825 CACTTTACTG
Statistics
Matches: 32, Mismatches: 5, Indels: 12
0.65 0.10 0.24
Matches are distributed among these distances:
16 10 0.31
17 1 0.03
18 2 0.06
19 2 0.06
20 1 0.03
21 16 0.50
ACGTcount: A:0.17, C:0.22, G:0.03, T:0.58
Consensus pattern (21 bp):
TTTTACTGATTACTCTTTACT
Found at i:15832 original size:36 final size:36
Alignment explanation
Indices: 15704--15833 Score: 158
Period size: 36 Copynumber: 3.6 Consensus size: 36
15694 TAATATTTTA
** * *
15704 CTTTACTGATTACCATTTTGCTCTTTACTGATCTCT
1 CTTTACTTTTTACCATTTTACTTTTTACTGATCTCT
15740 CTTTACTTTTTACCATTCTT-C-TTTTACTGAT-TACT
1 CTTTACTTTTTACCATT-TTACTTTTTACTGATCT-CT
*
15775 CTTTACTTTTTTACCATTTTACTTTTTACCGATCTCT
1 CTTTAC-TTTTTACCATTTTACTTTTTACTGATCTCT
*
15812 CTTTACTTTTTACCACTTTACT
1 CTTTACTTTTTACCATTTTACT
15834 GATTACTATT
Statistics
Matches: 83, Mismatches: 5, Indels: 12
0.83 0.05 0.12
Matches are distributed among these distances:
34 1 0.01
35 19 0.23
36 43 0.52
37 19 0.23
38 1 0.01
ACGTcount: A:0.17, C:0.25, G:0.04, T:0.55
Consensus pattern (36 bp):
CTTTACTTTTTACCATTTTACTTTTTACTGATCTCT
Found at i:15865 original size:25 final size:26
Alignment explanation
Indices: 15835--15887 Score: 81
Period size: 25 Copynumber: 2.1 Consensus size: 26
15825 CACTTTACTG
*
15835 ATTACTATTTGCTCTC-TTGAATTTA
1 ATTACTATTTGCACTCTTTGAATTTA
*
15860 ATTACTATTTTCACTCTTTGAATTTA
1 ATTACTATTTGCACTCTTTGAATTTA
15886 AT
1 AT
15888 CACCATTTCG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 14 0.56
26 11 0.44
ACGTcount: A:0.26, C:0.15, G:0.06, T:0.53
Consensus pattern (26 bp):
ATTACTATTTGCACTCTTTGAATTTA
Found at i:15945 original size:35 final size:35
Alignment explanation
Indices: 15861--15946 Score: 106
Period size: 34 Copynumber: 2.5 Consensus size: 35
15851 TTGAATTTAA
*
15861 TTACTATTTTCACTCTTTGAATTTAATCACCATTTC
1 TTACCATTTT-ACTCTTTGAATTTAATCACCATTTC
* *
15897 GT--CATTTTACTCTTTGAATTTTAATTACCATTT-
1 TTACCATTTTACTCTTTGAA-TTTAATCACCATTTC
15930 TTACCATTTTACTCTTT
1 TTACCATTTTACTCTTT
15947 ACCGATTACT
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
33 11 0.26
34 18 0.42
35 13 0.30
36 1 0.02
ACGTcount: A:0.23, C:0.20, G:0.03, T:0.53
Consensus pattern (35 bp):
TTACCATTTTACTCTTTGAATTTAATCACCATTTC
Found at i:16096 original size:41 final size:41
Alignment explanation
Indices: 15982--16099 Score: 152
Period size: 40 Copynumber: 2.9 Consensus size: 41
15972 TTTTTATTCT
*
15982 TTACTGATTTACTGATTACTTCTTTTACTTTTACTC-TTAA
1 TTACTGATTTACTGATTACTTCTTTTACTTTGACTCTTTAA
*
16022 TTAC-CATTTTACTGATTACTTCTTTTACTTTGACTCTTTAA
1 TTACTGA-TTTACTGATTACTTCTTTTACTTTGACTCTTTAA
* * *
16063 TTACTGATTTCACTGATTA-ATCTCTTACCTTGACTCT
1 TTACTGATTT-ACTGATTACTTCTTTTACTTTGACTCT
16100 GGATTATCAA
Statistics
Matches: 68, Mismatches: 6, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
39 1 0.01
40 32 0.47
41 26 0.38
42 9 0.13
ACGTcount: A:0.22, C:0.20, G:0.06, T:0.52
Consensus pattern (41 bp):
TTACTGATTTACTGATTACTTCTTTTACTTTGACTCTTTAA
Done.