Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016514.1 Corchorus capsularis cultivar CVL-1 contig16535, 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: 8032
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.35
Found at i:3985 original size:22 final size:21
Alignment explanation
Indices: 3945--4029 Score: 79
Period size: 21 Copynumber: 4.0 Consensus size: 21
3935 AGCATCACTA
3945 TTTTACTGATTA-TATTTTAC
1 TTTTACTGATTACTATTTTAC
3965 TTTGTACTGATTACTATTTTAC
1 TTT-TACTGATTACTATTTTAC
*
3987 TCTTT-CAGA-TACCT-TTTTAC
1 T-TTTACTGATTA-CTATTTTAC
* *
4007 TTTTTAGTGATTACCATTTTAC
1 -TTTTACTGATTACTATTTTAC
4029 T
1 T
4030 CTTTTACTTT
Statistics
Matches: 53, Mismatches: 4, Indels: 15
0.74 0.06 0.21
Matches are distributed among these distances:
20 14 0.26
21 19 0.36
22 18 0.34
23 2 0.04
ACGTcount: A:0.22, C:0.15, G:0.07, T:0.55
Consensus pattern (21 bp):
TTTTACTGATTACTATTTTAC
Found at i:4035 original size:30 final size:29
Alignment explanation
Indices: 3999--4066 Score: 91
Period size: 30 Copynumber: 2.3 Consensus size: 29
3989 TTTCAGATAC
*
3999 CTTTTTACTTTTTAGTGATTACCATTTTA
1 CTTTTTACTTTTTACTGATTACCATTTTA
* * *
4028 CTCTTTTACTTTTTACTGATTGCCTTTTTG
1 CT-TTTTACTTTTTACTGATTACCATTTTA
4058 CTTTTTACT
1 CTTTTTACT
4067 GATTACCTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 9 0.26
30 25 0.74
ACGTcount: A:0.15, C:0.18, G:0.07, T:0.60
Consensus pattern (29 bp):
CTTTTTACTTTTTACTGATTACCATTTTA
Found at i:4061 original size:22 final size:22
Alignment explanation
Indices: 4031--4307 Score: 205
Period size: 22 Copynumber: 12.8 Consensus size: 22
4021 CATTTTACTC
*
4031 TTTTACTTTTTACTGATTGCCT
1 TTTTACTTTTTACTGATTACCT
*
4053 TTTTGCTTTTTACTGATTACCT
1 TTTTACTTTTTACTGATTACCT
* *
4075 TTTTACTTCTTGCTGATTAGCC-
1 TTTTACTTTTTACTGATTA-CCT
* *
4097 TTTTACTCTTTACTGATCACCT
1 TTTTACTTTTTACTGATTACCT
* *
4119 TTTTAC-TCTTACTGATTTCC-
1 TTTTACTTTTTACTGATTACCT
* * *
4139 TTTTACTTCTTACTTATTACTTT
1 TTTTACTTTTTACTGATTAC-CT
*
4162 TTTTAC-TCTTACTGATTA--T
1 TTTTACTTTTTACTGATTACCT
*
4181 TATTTACTTTTTACTGACTA-CT
1 T-TTTACTTTTTACTGATTACCT
* *
4203 ATTTTAC-TCTTATTGATTACCT
1 -TTTTACTTTTTACTGATTACCT
* * **
4225 TCTTACTTTTTACTTATTACAA
1 TTTTACTTTTTACTGATTACCT
* * *
4247 TTTTACTCTTTACTAATTTACCA
1 TTTTACTTTTTACTGA-TTACCT
* * *
4270 TTTTACCTTTT-C-AAATACCT
1 TTTTACTTTTTACTGATTACCT
*
4290 TTTTTCTTTTTACTGATT
1 TTTTACTTTTTACTGATT
4308 GCATGCTATT
Statistics
Matches: 201, Mismatches: 40, Indels: 28
0.75 0.15 0.10
Matches are distributed among these distances:
19 2 0.01
20 24 0.12
21 50 0.25
22 102 0.51
23 23 0.11
ACGTcount: A:0.19, C:0.20, G:0.05, T:0.56
Consensus pattern (22 bp):
TTTTACTTTTTACTGATTACCT
Found at i:4165 original size:43 final size:42
Alignment explanation
Indices: 4031--4280 Score: 209
Period size: 43 Copynumber: 5.7 Consensus size: 42
4021 CATTTTACTC
* * *
4031 TTTTACTTTTTACTGATTGCCTTTTTGCTTTTTACTGATTACCT
1 TTTTAC-TCTTACTGATTTCC-TTTTACTTTTTACTGATTACCT
* * * *
4075 TTTTACTTCTTGCTGATTAGCCTTTTACTCTTTACTGATCACCT
1 TTTTAC-TCTTACTGATT-TCCTTTTACTTTTTACTGATTACCT
* * *
4119 TTTTACTCTTACTGATTTCCTTTTACTTCTTACTTATTACTTT
1 TTTTACTCTTACTGATTTCCTTTTACTTTTTACTGATTAC-CT
*
4162 TTTTACTCTTACTGATTAT--TATTTACTTTTTACTGACTA-CT
1 TTTTACTCTTACTGATT-TCCT-TTTACTTTTTACTGATTACCT
* * * **
4203 ATTTTACTCTTATTGATTACCTTCTTACTTTTTACTTATTACAA
1 -TTTTACTCTTACTGATTTCCTT-TTACTTTTTACTGATTACCT
* *
4247 TTTTACTCTTTACTAATTTACCATTTTACCTTTT
1 TTTTACTC-TTACTGATTT-CC-TTTTACTTTTT
4281 CAAATACCTT
Statistics
Matches: 168, Mismatches: 26, Indels: 23
0.77 0.12 0.11
Matches are distributed among these distances:
41 1 0.01
42 36 0.21
43 67 0.40
44 49 0.29
45 13 0.08
46 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.05, T:0.56
Consensus pattern (42 bp):
TTTTACTCTTACTGATTTCCTTTTACTTTTTACTGATTACCT
Found at i:4534 original size:34 final size:34
Alignment explanation
Indices: 4491--4612 Score: 131
Period size: 34 Copynumber: 3.5 Consensus size: 34
4481 CTCTATTATC
4491 AATTTACTGATTACTATCTTTTTACTTAATTACT
1 AATTTACTGATTACTATCTTTTTACTTAATTACT
**
4525 AATTTACTGATTACTAT-TATCTGGACTCTTAATTA-T
1 AATTTACTGATTACTATCT-T-TTTA--CTTAATTACT
* *
4561 CAATTTACTGATTACTATCTTTTTACCTGATTACT
1 -AATTTACTGATTACTATCTTTTTACTTAATTACT
* *
4596 GATTTTCTGATTACTAT
1 AATTTACTGATTACTAT
4613 TACCTTGACT
Statistics
Matches: 73, Mismatches: 8, Indels: 14
0.77 0.08 0.15
Matches are distributed among these distances:
33 1 0.01
34 39 0.53
35 3 0.04
36 3 0.04
37 26 0.36
38 1 0.01
ACGTcount: A:0.28, C:0.16, G:0.07, T:0.50
Consensus pattern (34 bp):
AATTTACTGATTACTATCTTTTTACTTAATTACT
Found at i:4567 original size:71 final size:71
Alignment explanation
Indices: 4485--4624 Score: 226
Period size: 71 Copynumber: 2.0 Consensus size: 71
4475 TTAATTCTCT
* *
4485 ATTATCAATTTACTGATTACTATCTTTTTACTTAATTACTAATTTACTGATTACTATTATCTGGA
1 ATTATCAATTTACTGATTACTATCTTTTTACCTAATTACTAATTTACTGATTACTATTACCTGGA
4550 CTCTTA
66 CTCTTA
* * * *
4556 ATTATCAATTTACTGATTACTATCTTTTTACCTGATTACTGATTTTCTGATTACTATTACCTTGA
1 ATTATCAATTTACTGATTACTATCTTTTTACCTAATTACTAATTTACTGATTACTATTACCTGGA
4621 CTCT
66 CTCT
4625 GATTAATCTC
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
71 63 1.00
ACGTcount: A:0.27, C:0.17, G:0.06, T:0.49
Consensus pattern (71 bp):
ATTATCAATTTACTGATTACTATCTTTTTACCTAATTACTAATTTACTGATTACTATTACCTGGA
CTCTTA
Found at i:4698 original size:22 final size:21
Alignment explanation
Indices: 4670--5010 Score: 209
Period size: 22 Copynumber: 15.9 Consensus size: 21
4660 ATTACTATTA
4670 TTTTACTCTTTACTGATTACTC
1 TTTTACTCTTTACTGATTAC-C
*
4692 TTTTACT-TTGTACTGATTGCC
1 TTTTACTCTT-TACTGATTACC
* *
4713 ATTTTTGCTTTTTACTGA-TACC
1 --TTTTACTCTTTACTGATTACC
* *
4735 TTTTACT-TCTTATTGATTAGCT
1 TTTTACTCT-TTACTGATTA-CC
*
4757 TTTTACTCTTCACTGATTACC
1 TTTTACTCTTTACTGATTACC
*
4778 TTTATACTC-TTACTGTTTACC
1 TTT-TACTCTTTACTGATTACC
*
4799 TTTTACT-TCTTACTGATTACT
1 TTTTACTCT-TTACTGATTACC
* * * *
4820 TTTTACTTTTTGCCGATTACTA
1 TTTTACTCTTTACTGATTAC-C
4842 TTTTACTC-TTACTGATTACC
1 TTTTACTCTTTACTGATTACC
** * *
4862 ATTTTTGTTTCTTGACTAATTACC
1 --TTTT-ACTCTTTACTGATTACC
* *
4886 ATTTTTCTCTTTACTGATTGCC
1 -TTTTACTCTTTACTGATTACC
* *
4908 TTTTATTTTTTTACTGATTACC
1 TTTTA-CTCTTTACTGATTACC
* *
4930 TTTACTTCTCTTTACTAATTACC
1 TTT--TACTCTTTACTGATTACC
* *
4953 -TTTACT-TCTTACTGACTACTA
1 TTTTACTCT-TTACTGATTAC-C
*
4974 TTTTACTC-TTA-TGGATGACC
1 TTTTACTCTTTACT-GATTACC
4994 TTTTACTC-TTACTGATT
1 TTTTACTCTTTACTGATT
5011 TTACTGATTA
Statistics
Matches: 248, Mismatches: 45, Indels: 54
0.71 0.13 0.16
Matches are distributed among these distances:
19 2 0.01
20 43 0.17
21 69 0.28
22 89 0.36
23 32 0.13
24 13 0.05
ACGTcount: A:0.19, C:0.21, G:0.07, T:0.54
Consensus pattern (21 bp):
TTTTACTCTTTACTGATTACC
Found at i:4758 original size:21 final size:21
Alignment explanation
Indices: 4670--5010 Score: 220
Period size: 21 Copynumber: 15.9 Consensus size: 21
4660 ATTACTATTA
4670 TTTTAC-TCTTTACTGATTACTC
1 TTTTACTTC-TTACTGATTAC-C
*
4692 TTTTACTT-TGTACTGATTGCC
1 TTTTACTTCT-TACTGATTACC
* *
4713 ATTTTTGCTTTTTACTGA-TACC
1 --TTTTACTTCTTACTGATTACC
* *
4735 TTTTACTTCTTATTGATTAGCT
1 TTTTACTTCTTACTGATTA-CC
4757 TTTTAC-TCTTCACTGATTACC
1 TTTTACTTCTT-ACTGATTACC
*
4778 TTTATAC-TCTTACTGTTTACC
1 TTT-TACTTCTTACTGATTACC
*
4799 TTTTACTTCTTACTGATTACT
1 TTTTACTTCTTACTGATTACC
* * * *
4820 TTTTACTTTTTGCCGATTACTA
1 TTTTACTTCTTACTGATTAC-C
4842 TTTTAC-TCTTACTGATTACC
1 TTTTACTTCTTACTGATTACC
** *
4862 ATTTTTGTTTCTTGACTAATTACC
1 --TTTTACTTCTT-ACTGATTACC
* *
4886 ATTTTTC-TCTTTACTGATTGCC
1 -TTTTACTTC-TTACTGATTACC
* *
4908 TTTTATTTTTTTACTGATTACC
1 TTTTA-CTTCTTACTGATTACC
*
4930 -TTTACTTCTCTTTACTAATTACC
1 TTTTAC-T-TC-TTACTGATTACC
* *
4953 -TTTACTTCTTACTGACTACTA
1 TTTTACTTCTTACTGATTAC-C
*
4974 TTTTAC-TCTTA-TGGATGACC
1 TTTTACTTCTTACT-GATTACC
4994 TTTTAC-TCTTACTGATT
1 TTTTACTTCTTACTGATT
5011 TTACTGATTA
Statistics
Matches: 252, Mismatches: 42, Indels: 52
0.73 0.12 0.15
Matches are distributed among these distances:
20 40 0.16
21 84 0.33
22 77 0.31
23 41 0.16
24 10 0.04
ACGTcount: A:0.19, C:0.21, G:0.07, T:0.54
Consensus pattern (21 bp):
TTTTACTTCTTACTGATTACC
Done.