Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005490.1 Corchorus capsularis cultivar CVL-1 contig05508, 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: 9072
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.31
Found at i:8691 original size:13 final size:13
Alignment explanation
Indices: 8673--8719 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
8663 ATCATTTTTA
8673 CTCTTTTCTTACT
1 CTCTTTTCTTACT
* *
8686 CTCTTTAC-TATTT
1 CTCTTTTCTTA-CT
8699 ACTCTTTTCTTACT
1 -CTCTTTTCTTACT
8713 CTCTTTT
1 CTCTTTT
8720 ATTGATTACC
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
12 2 0.07
13 15 0.56
14 8 0.30
15 2 0.07
ACGTcount: A:0.11, C:0.28, G:0.00, T:0.62
Consensus pattern (13 bp):
CTCTTTTCTTACT
Found at i:8804 original size:21 final size:21
Alignment explanation
Indices: 8780--8882 Score: 95
Period size: 21 Copynumber: 4.9 Consensus size: 21
8770 ACTCTTTGAA
*
8780 TTACTGATCACCTTTTACTCT
1 TTACTGATTACCTTTTACTCT
*
8801 TTACTGATTACTATTTTACTC-
1 TTACTGATTAC-CTTTTACTCT
* * *
8822 TTACTAATTACCACTTTGCTC-
1 TTACTGATTACC-TTTTACTCT
*
8843 TTACTGATTACTATTTTACTC-
1 TTACTGATTAC-CTTTTACTCT
*
8864 TTACTGGTTACCTTTTACT
1 TTACTGATTACCTTTTACT
8883 GATTACTATT
Statistics
Matches: 67, Mismatches: 12, Indels: 7
0.78 0.14 0.08
Matches are distributed among these distances:
20 7 0.10
21 52 0.78
22 8 0.12
ACGTcount: A:0.21, C:0.23, G:0.06, T:0.50
Consensus pattern (21 bp):
TTACTGATTACCTTTTACTCT
Found at i:8847 original size:42 final size:41
Alignment explanation
Indices: 8799--8953 Score: 178
Period size: 42 Copynumber: 3.8 Consensus size: 41
8789 ACCTTTTACT
*
8799 CTTTACTGATTACTATTTTACTCTTACTAATTACCACTTTG
1 CTTTACTGATTACTATTTTACTCTTACTGATTACCACTTTG
*
8840 CTCTTACTGATTACTATTTTACTCTTACTGGTTA-C-C--T-
1 CT-TTACTGATTACTATTTTACTCTTACTGATTACCACTTTG
*
8877 -TTTACTGATTACTATTTTACTCTTTACTGATTACCATTTTTG
1 CTTTACTGATTACTATTTTACTC-TTACTGATTACCA-CTTTG
* * *
8919 CTTTTACTGATCACCATTTTGCTCTTACTGATTAC
1 C-TTTACTGATTACTATTTTACTCTTACTGATTAC
8954 TATTTTACCT
Statistics
Matches: 97, Mismatches: 7, Indels: 18
0.80 0.06 0.15
Matches are distributed among these distances:
35 21 0.22
36 10 0.10
37 1 0.01
38 1 0.01
40 1 0.01
41 4 0.04
42 29 0.30
43 11 0.11
44 19 0.20
ACGTcount: A:0.21, C:0.22, G:0.07, T:0.50
Consensus pattern (41 bp):
CTTTACTGATTACTATTTTACTCTTACTGATTACCACTTTG
Found at i:8902 original size:22 final size:22
Alignment explanation
Indices: 8877--9004 Score: 124
Period size: 22 Copynumber: 6.0 Consensus size: 22
8867 CTGGTTACCT
*
8877 TTTACTGATTACTATTTTACTC
1 TTTACTGATTACCATTTTACTC
*
8899 TTTACTGATTACCATTTTTGCT-
1 TTTACTGATTACCA-TTTTACTC
* *
8921 TTTACTGATCACCATTTTGCTC
1 TTTACTGATTACCATTTTACTC
*
8943 -TTACTGATTACTATTTTAC-C
1 TTTACTGATTACCATTTTACTC
* *
8963 TTTTACTGATTATCA--TTACTTT
1 -TTTACTGATTACCATTTTAC-TC
8985 TTTACTGATTACC-TTTTACT
1 TTTACTGATTACCATTTTACT
9005 ATTTTACTCT
Statistics
Matches: 88, Mismatches: 10, Indels: 17
0.77 0.09 0.15
Matches are distributed among these distances:
20 5 0.06
21 36 0.41
22 41 0.47
23 6 0.07
ACGTcount: A:0.21, C:0.20, G:0.06, T:0.53
Consensus pattern (22 bp):
TTTACTGATTACCATTTTACTC
Found at i:8966 original size:43 final size:44
Alignment explanation
Indices: 8871--9012 Score: 148
Period size: 43 Copynumber: 3.3 Consensus size: 44
8861 CTCTTACTGG
* *
8871 TTACCTTTTACTGATTACTATTTTACTCTTTACTGATTACCATT
1 TTACCTTTTACTGATCACCATTTTACTCTTTACTGATTACCATT
** * *
8915 TTTGCTTTTACTGATCACCATTTTGCTC-TTACTGATTACTATT
1 TTACCTTTTACTGATCACCATTTTACTCTTTACTGATTACCATT
* * *
8958 TTACCTTTTACTGATTATCA--TTACTTTTTTACTGATTACC-TT
1 TTACCTTTTACTGATCACCATTTTAC-TCTTTACTGATTACCATT
*
9000 TTACTATTTTACT
1 TTAC-CTTTTACT
9013 CTTTACTGAG
Statistics
Matches: 81, Mismatches: 14, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
41 3 0.04
42 7 0.09
43 48 0.59
44 23 0.28
ACGTcount: A:0.21, C:0.20, G:0.06, T:0.54
Consensus pattern (44 bp):
TTACCTTTTACTGATCACCATTTTACTCTTTACTGATTACCATT
Found at i:9001 original size:15 final size:15
Alignment explanation
Indices: 8977--9041 Score: 55
Period size: 15 Copynumber: 4.4 Consensus size: 15
8967 ACTGATTATC
*
8977 ATTACTTTTTTACTG
1 ATTACCTTTTTACTG
8992 ATTACC-TTTTACT-
1 ATTACCTTTTTACTG
*
9005 ATTTTA-CTCTTTACTG
1 A--TTACCTTTTTACTG
* *
9021 AGTATCTTTTTACTG
1 ATTACCTTTTTACTG
9036 ATTACC
1 ATTACC
9042 CTTTACTTTT
Statistics
Matches: 39, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
13 1 0.03
14 10 0.26
15 27 0.69
16 1 0.03
ACGTcount: A:0.22, C:0.18, G:0.06, T:0.54
Consensus pattern (15 bp):
ATTACCTTTTTACTG
Found at i:9004 original size:100 final size:98
Alignment explanation
Indices: 8779--8982 Score: 259
Period size: 100 Copynumber: 2.1 Consensus size: 98
8769 TACTCTTTGA
* * *
8779 ATTACTGATCACCT-TTTACTCTTTACTGATTACTATTTTACTCTTACTAATTACCACTTTGCTC
1 ATTACTGATTA-CTATTTACTCTTTACTGATTACCATTTTACTCTTACTAATCACCACTTTGCTC
*
8843 TTACTGATTACTATTTTACTCTTACTGGTTACCT
65 TTACTGATTACTATTTTACTCTTACTGATTACCT
* * * * *
8877 TTTACTGATTACTATTTTACTCTTTACTGATTACCATTTTTGCTTTTACTGATCACCATTTTGCT
1 ATTACTGATTACTA-TTTACTCTTTACTGATTACCA-TTTTACTCTTACTAATCACCACTTTGCT
* *
8942 CTTACTGATTACTATTTTACCTTTTACTGATTATC-
64 CTTACTGATTACTATTTTA-CTCTTACTGATTACCT
8977 ATTACT
1 ATTACT
8983 TTTTTACTGA
Statistics
Matches: 90, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
97 2 0.02
98 9 0.10
99 20 0.22
100 47 0.52
101 12 0.13
ACGTcount: A:0.22, C:0.22, G:0.06, T:0.50
Consensus pattern (98 bp):
ATTACTGATTACTATTTACTCTTTACTGATTACCATTTTACTCTTACTAATCACCACTTTGCTCT
TACTGATTACTATTTTACTCTTACTGATTACCT
Found at i:9009 original size:22 final size:21
Alignment explanation
Indices: 8871--9054 Score: 115
Period size: 22 Copynumber: 8.5 Consensus size: 21
8861 CTCTTACTGG
* *
8871 TTACCTTTTACTGATTACTATT
1 TTACTTTTTACTGATTAC-CTT
*
8893 TTACTCTTTACTGATTACCATTT
1 TTACTTTTTACTGATTACC--TT
* *
8916 TTGC-TTTTACTGATCACCATT
1 TTACTTTTTACTGATTACC-TT
* * *
8937 TTGC-TCTTACTGATTACTATT
1 TTACTTTTTACTGATTAC-CTT
* * *
8958 TTACCTTTTACTGATTATC-A
1 TTACTTTTTACTGATTACCTT
8978 TTACTTTTTTACTGATTACCTT
1 TTAC-TTTTTACTGATTACCTT
** *
9000 TTACTATTTTACTCTTTA-CTGA
1 TTACT-TTTTACTGATTACCT-T
* *
9022 GTATCTTTTTACTGATTACCCT
1 TTA-CTTTTTACTGATTACCTT
9044 TTACTTTTTAC
1 TTACTTTTTAC
9055 CGTTCTTCTT
Statistics
Matches: 125, Mismatches: 27, Indels: 21
0.72 0.16 0.12
Matches are distributed among these distances:
20 4 0.03
21 46 0.37
22 67 0.54
23 8 0.06
ACGTcount: A:0.21, C:0.20, G:0.06, T:0.53
Consensus pattern (21 bp):
TTACTTTTTACTGATTACCTT
Found at i:9019 original size:65 final size:64
Alignment explanation
Indices: 8875--9004 Score: 167
Period size: 65 Copynumber: 2.0 Consensus size: 64
8865 TACTGGTTAC
* *
8875 CTTTTACTGATTACTATTTTACTCTTTACTGATTACCATTTTTGCTTTTACTGATCACCATTTTG
1 CTTTTACTGATTACTATTTTACTCTTTACTGATTACCATTCTT-CTTTTACTGATCACCATTTTA
* * *
8940 CTCTTACTGATTACTATTTTAC-CTTTTACTGATTATCATTACTT-TTTTACTGATTACC-TTTT
1 CTTTTACTGATTACTATTTTACTC-TTTACTGATTACCATT-CTTCTTTTACTGATCACCATTTT
9002 A
64 A
9003 CT
1 CT
9005 ATTTTACTCT
Statistics
Matches: 58, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
63 6 0.10
64 14 0.24
65 36 0.62
66 2 0.03
ACGTcount: A:0.21, C:0.20, G:0.06, T:0.53
Consensus pattern (64 bp):
CTTTTACTGATTACTATTTTACTCTTTACTGATTACCATTCTTCTTTTACTGATCACCATTTTA
Done.