Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014292.1 Corchorus capsularis cultivar CVL-1 contig14313, 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: 9688
ACGTcount: A:0.26, C:0.23, G:0.17, T:0.33
Found at i:5019 original size:16 final size:16
Alignment explanation
Indices: 4986--5020 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
4976 AAGGTCAAAA
* *
4986 ATTGTTATTATTTCTT
1 ATTGTTATTACTTATT
5002 ATTGTTATTACTTATT
1 ATTGTTATTACTTATT
5018 ATT
1 ATT
5021 ATCATTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.23, C:0.06, G:0.06, T:0.66
Consensus pattern (16 bp):
ATTGTTATTACTTATT
Found at i:7600 original size:17 final size:19
Alignment explanation
Indices: 7568--7605 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
7558 TGTAAAATGC
*
7568 AAAGCGAAAGAAC-AAAGA
1 AAAGCGAAACAACAAAAGA
7586 AAAGC-AAACAACAAAAGA
1 AAAGCGAAACAACAAAAGA
7604 AA
1 AA
7606 TTAGTTAGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.71, C:0.13, G:0.16, T:0.00
Consensus pattern (19 bp):
AAAGCGAAACAACAAAAGA
Found at i:9000 original size:22 final size:21
Alignment explanation
Indices: 8986--9166 Score: 97
Period size: 22 Copynumber: 8.4 Consensus size: 21
8976 TTTTTGCTCT
*
8986 TACTGATTAC-TATTTTACCTTT
1 TACTGATTACAT-TTTTA-CTCT
*
9008 TACTGATTAC-TTTTTACTATT
1 TACTGATTACATTTTTACT-CT
* * * * *
9029 TACTAATAACCTTCTTACTTTT
1 TACTGATTACATTTTTAC-TCT
9051 TACTGATTAC-TATTTTACTCTT
1 TACTGATTACAT-TTTTACTC-T
*
9073 TACTGATTACCA-TTTTGCTCT
1 TACTGATTA-CATTTTTACTCT
* *
9094 TACTGATTAC-CTTTTACCCTT
1 TACTGATTACATTTTTACTC-T
* *
9115 TACTGGTTACCA-TTTTGCTCT
1 TACTGATTA-CATTTTTACTCT
*
9136 TACTGATTACCA-TTTTACCTTT
1 TACTGATTA-CATTTTTA-CTCT
9158 TACTGATTA
1 TACTGATTA
9167 TTATAACTTT
Statistics
Matches: 131, Mismatches: 16, Indels: 24
0.77 0.09 0.14
Matches are distributed among these distances:
20 9 0.07
21 52 0.40
22 68 0.52
23 2 0.02
ACGTcount: A:0.22, C:0.21, G:0.06, T:0.51
Consensus pattern (21 bp):
TACTGATTACATTTTTACTCT
Found at i:9010 original size:65 final size:65
Alignment explanation
Indices: 8937--9082 Score: 181
Period size: 65 Copynumber: 2.2 Consensus size: 65
8927 ATCACCTTTC
* * * * *
8937 ACTCTTTACAGATTACTATCTTATTCTTT-CTAATAACCATTTTTGC-TCTTACTGATTACTATT
1 ACTCTTTACTGATTACT-TCTTACTATTTACTAATAACC-TTCTTACTTCTTACTGATTACTATT
9000 TT
64 TT
* *
9002 AC-CTTTTACTGATTACTTTTTACTATTTACTAATAACCTTCTTACTTTTTACTGATTACTATTT
1 ACTC-TTTACTGATTACTTCTTACTATTTACTAATAACCTTCTTACTTCTTACTGATTACTATTT
9066 T
65 T
9067 ACTCTTTACTGATTAC
1 ACTCTTTACTGATTAC
9083 CATTTTGCTC
Statistics
Matches: 70, Mismatches: 7, Indels: 8
0.82 0.08 0.09
Matches are distributed among these distances:
64 14 0.20
65 55 0.79
66 1 0.01
ACGTcount: A:0.25, C:0.20, G:0.04, T:0.51
Consensus pattern (65 bp):
ACTCTTTACTGATTACTTCTTACTATTTACTAATAACCTTCTTACTTCTTACTGATTACTATTTT
Found at i:9018 original size:29 final size:29
Alignment explanation
Indices: 8985--9082 Score: 81
Period size: 29 Copynumber: 3.1 Consensus size: 29
8975 ATTTTTGCTC
8985 TTACTGATTACTATTTTACCTTTTACTGA
1 TTACTGATTACTATTTTACCTTTTACTGA
** **
9014 TTACTTTTTACTATTTACTAATAACCTTCTTACTTT
1 TTACTGATTACTA-TT--T--T-ACCTT-TTACTGA
9050 TTACTGATTACTATTTTA-CTCTTTACTGA
1 TTACTGATTACTATTTTACCT-TTTACTGA
9079 TTAC
1 TTAC
9083 CATTTTGCTC
Statistics
Matches: 53, Mismatches: 8, Indels: 16
0.69 0.10 0.21
Matches are distributed among these distances:
29 22 0.42
30 4 0.08
31 1 0.02
32 1 0.02
33 1 0.02
34 1 0.02
35 7 0.13
36 16 0.30
ACGTcount: A:0.24, C:0.18, G:0.04, T:0.53
Consensus pattern (29 bp):
TTACTGATTACTATTTTACCTTTTACTGA
Found at i:9022 original size:14 final size:14
Alignment explanation
Indices: 9000--9069 Score: 52
Period size: 14 Copynumber: 4.9 Consensus size: 14
8990 GATTACTATT
*
9000 TTACCTTTTACTGA
1 TTACTTTTTACTGA
9014 TTACTTTTTACT-A
1 TTACTTTTTACTGA
** * **
9027 TTTACTAATAACCTTC
1 -TTACTTTTTA-CTGA
9043 TTACTTTTTACTGA
1 TTACTTTTTACTGA
9057 TTACTATTTTACT
1 TTACT-TTTTACT
9070 CTTTACTGAT
Statistics
Matches: 42, Mismatches: 10, Indels: 7
0.71 0.17 0.12
Matches are distributed among these distances:
13 1 0.02
14 25 0.60
15 16 0.38
ACGTcount: A:0.24, C:0.19, G:0.03, T:0.54
Consensus pattern (14 bp):
TTACTTTTTACTGA
Found at i:9202 original size:22 final size:22
Alignment explanation
Indices: 9177--9300 Score: 101
Period size: 22 Copynumber: 6.1 Consensus size: 22
9167 TTATAACTTT
*
9177 TTACGATTTTACTCTTTACTGA
1 TTACCATTTTACTCTTTACTGA
*
9199 TTACCATTTTGCTC-TTACTGA
1 TTACCATTTTACTCTTTACTGA
9220 TTACCATTTTAC-CTTTTACTGA
1 TTACCATTTTACTC-TTTACTGA
* *
9242 TT---ATTATCACTTTTTAC-GA
1 TTACCATT-TTACTCTTTACTGA
9261 TT----T--TACTCTTTACTGA
1 TTACCATTTTACTCTTTACTGA
*
9277 TTACCATTTTACTTTTTACTGA
1 TTACCATTTTACTCTTTACTGA
9299 TT
1 TT
9301 TTTACTCTTT
Statistics
Matches: 83, Mismatches: 8, Indels: 22
0.73 0.07 0.19
Matches are distributed among these distances:
15 8 0.10
16 4 0.05
18 1 0.01
19 7 0.08
20 10 0.12
21 18 0.22
22 35 0.42
ACGTcount: A:0.22, C:0.19, G:0.06, T:0.52
Consensus pattern (22 bp):
TTACCATTTTACTCTTTACTGA
Found at i:9203 original size:78 final size:78
Alignment explanation
Indices: 9105--9300 Score: 338
Period size: 78 Copynumber: 2.5 Consensus size: 78
9095 ACTGATTACC
* *
9105 TTTTACCCTTTACTGGTTACCATTTTGCTCTTACTGATTACCATTTTACCTTTTACTGATTATTA
1 TTTTACTCTTTACTGATTACCATTTTGCTCTTACTGATTACCATTTTACCTTTTACTGATTATTA
9170 TAACTTTTTACGA
66 TAACTTTTTACGA
9183 TTTTACTCTTTACTGATTACCATTTTGCTCTTACTGATTACCATTTTACCTTTTACTGATTATTA
1 TTTTACTCTTTACTGATTACCATTTTGCTCTTACTGATTACCATTTTACCTTTTACTGATTATTA
*
9248 TCACTTTTTACGA
66 TAACTTTTTACGA
* *
9261 TTTTACTCTTTACTGATTACCATTTTACTTTTTACTGATT
1 TTTTACTCTTTACTGATTACCATTTTGC-TCTTACTGATT
9301 TTTACTCTTT
Statistics
Matches: 112, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
78 102 0.91
79 10 0.09
ACGTcount: A:0.21, C:0.20, G:0.07, T:0.52
Consensus pattern (78 bp):
TTTTACTCTTTACTGATTACCATTTTGCTCTTACTGATTACCATTTTACCTTTTACTGATTATTA
TAACTTTTTACGA
Found at i:9327 original size:15 final size:16
Alignment explanation
Indices: 9269--9327 Score: 50
Period size: 15 Copynumber: 3.8 Consensus size: 16
9259 GATTTTACTC
9269 TTTACTGATTACC-AT
1 TTTACTGATTACCGAT
** *
9284 TTTACTTTTTACTGATT
1 TTTACTGATTACCGA-T
**
9301 TTTACTCTTTACCGA-
1 TTTACTGATTACCGAT
9316 TTTACTGATTAC
1 TTTACTGATTAC
9328 TTCTTTTACT
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
15 20 0.57
16 1 0.03
17 14 0.40
ACGTcount: A:0.22, C:0.19, G:0.07, T:0.53
Consensus pattern (16 bp):
TTTACTGATTACCGAT
Found at i:9336 original size:78 final size:77
Alignment explanation
Indices: 9105--9328 Score: 286
Period size: 78 Copynumber: 2.8 Consensus size: 77
9095 ACTGATTACC
* * * * *
9105 TTTTACCCTTTACTGGTTACCATTTTGCTCTTACTGATTACCATTTTACCTTTTACTGATTATTA
1 TTTTACTCTTTACTGATTACCATTTTACTCTTACTGATTACCATTTTACCATTTACTGATTACTA
9170 TAACTTTTTACGA
66 T-ACTTTTTACGA
* * *
9183 TTTTACTCTTTACTGATTACCATTTTGCTCTTACTGATTACCATTTTACCTTTTACTGATTATTA
1 TTTTACTCTTTACTGATTACCATTTTACTCTTACTGATTACCATTTTACCATTTACTGATTACTA
9248 TCACTTTTTACGA
66 T-ACTTTTTACGA
* ***
9261 TTTTACTCTTTACTGATTACCATTTTACTTTTTACTGATTTTTACTCTTTACCGATTTACTGATT
1 TTTTACTCTTTACTGATTACCATTTTAC-TCTTACTGATTACCA-T-TTTACC-ATTTACTGATT
9326 ACT
62 ACT
9329 TCTTTTACTC
Statistics
Matches: 132, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
78 102 0.77
79 11 0.08
80 1 0.01
81 6 0.05
82 12 0.09
ACGTcount: A:0.21, C:0.20, G:0.07, T:0.52
Consensus pattern (77 bp):
TTTTACTCTTTACTGATTACCATTTTACTCTTACTGATTACCATTTTACCATTTACTGATTACTA
TACTTTTTACGA
Found at i:9360 original size:40 final size:42
Alignment explanation
Indices: 9316--9447 Score: 141
Period size: 40 Copynumber: 3.3 Consensus size: 42
9306 TCTTTACCGA
9316 TTTACTGATTACTTCTTTTACTCTT-ACTC-TTAATTAC-CAT
1 TTTACTGATTACTTCTTTTACT-TTGACTCTTTAATTACTCAT
*
9356 TTTACTGATTACTTCTTTTACTTTGACTCTTTAATTACTGAT
1 TTTACTGATTACTTCTTTTACTTTGACTCTTTAATTACTCAT
* * * * * *
9398 TTCACTGATTA-ATCTCTTACCTTGAC-CTTTGATTA-TCAA
1 TTTACTGATTACTTCTTTTACTTTGACTCTTTAATTACTCAT
*
9437 ATTACTGATTA
1 TTTACTGATTA
9448 ATCCCTTTTA
Statistics
Matches: 79, Mismatches: 10, Indels: 7
0.82 0.10 0.07
Matches are distributed among these distances:
39 13 0.16
40 34 0.43
41 20 0.25
42 12 0.15
ACGTcount: A:0.24, C:0.20, G:0.06, T:0.50
Consensus pattern (42 bp):
TTTACTGATTACTTCTTTTACTTTGACTCTTTAATTACTCAT
Done.