Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016202.1 Corchorus capsularis cultivar CVL-1 contig16223, 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: 4831
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.33
Found at i:3800 original size:26 final size:26
Alignment explanation
Indices: 3770--3954 Score: 123
Period size: 26 Copynumber: 7.0 Consensus size: 26
3760 TATCTCTTGA
3770 TTACTAATTACCATTTTTTACTCTTT
1 TTACTAATTACCATTTTTTACTCTTT
* * *
3796 GTACTGATTACCATATTTTACT-TTGT
1 TTACTAATTACCATTTTTTACTCTT-T
* * * *
3822 TTACTGATTACCCCTTTTCATACTGTTT
1 TTACTAATTA-CCATTTT-TTACTCTTT
**
3850 TTACTGAA-TATTATTTTTTACTCTTT
1 TTACT-AATTACCATTTTTTACTCTTT
3876 TTACTTAATTACC-TTTTTTACTCTCTTT
1 TTAC-TAATTACCATTTTTTA--CTCTTT
*
3904 TTACTTAA-TA--ATATTTTTACCCCTTT
1 TTAC-TAATTACCAT-TTTTTA-CTCTTT
*
3930 TTACTGAA-TACCACTTTTTACTCTT
1 TTACT-AATTACCATTTTTTACTCTT
3955 CTTCTTTTTC
Statistics
Matches: 126, Mismatches: 19, Indels: 28
0.73 0.11 0.16
Matches are distributed among these distances:
25 3 0.02
26 67 0.53
27 26 0.21
28 27 0.21
29 3 0.02
ACGTcount: A:0.22, C:0.19, G:0.04, T:0.55
Consensus pattern (26 bp):
TTACTAATTACCATTTTTTACTCTTT
Found at i:3879 original size:54 final size:53
Alignment explanation
Indices: 3811--3953 Score: 130
Period size: 54 Copynumber: 2.7 Consensus size: 53
3801 GATTACCATA
* *
3811 TTTTACT-TTGTTTACTGATTACCCCTTTTCA-TACTGTTTTTACTGAATATTATT
1 TTTTACTCTT-TTTACTGATTACCCCTTTTCACT-CTCTTTTTACTGAATAATA-T
* * * *
3865 TTTTACTCTTTTTACTTAATTA-CCTTTTTTACTCTCTTTTTACTTAATAATAT
1 TTTTACTCTTTTTAC-TGATTACCCCTTTTCACTCTCTTTTTACTGAATAATAT
* * * *
3918 TTTTACCCCTTTTTACTGAATACCACTTTTTACTCT
1 TTTTA-CTCTTTTTACTGATTACCCCTTTTCACTCT
3954 TCTTCTTTTT
Statistics
Matches: 73, Mismatches: 11, Indels: 10
0.78 0.12 0.11
Matches are distributed among these distances:
53 10 0.14
54 55 0.75
55 8 0.11
ACGTcount: A:0.21, C:0.20, G:0.03, T:0.56
Consensus pattern (53 bp):
TTTTACTCTTTTTACTGATTACCCCTTTTCACTCTCTTTTTACTGAATAATAT
Found at i:4219 original size:22 final size:22
Alignment explanation
Indices: 4118--4456 Score: 161
Period size: 22 Copynumber: 15.9 Consensus size: 22
4108 TTTAACTAGA
*
4118 TTACTGATTACCCTTTTAC-TT
1 TTACTGATTACCTTTTTACTTT
*
4139 TTACTGATTACCATTTTACTCTT
1 TTACTGATTACCTTTTTACT-TT
* * * **
4162 TTGCTAATTACCATTTTACCCT
1 TTACTGATTACCTTTTTACTTT
4184 TTAC--ATATACCTTTTTACTTT
1 TTACTGAT-TACCTTTTTACTTT
4205 TTACTGATTACCTTTTTACTTT
1 TTACTGATTACCTTTTTACTTT
* ** * *
4227 TTATTG-TTTGC-TATTACTTC
1 TTACTGATTACCTTTTTACTTT
* * *
4247 TTACTGATT-TC-TATTACTCT
1 TTACTGATTACCTTTTTACTTT
**
4267 TTACTGATTA--TTACTTTACTCC
1 TTACTGATTACCTT--TTTACTTT
* * * ***
4289 TTACTAATTACCATTGTACCCA
1 TTACTGATTACCTTTTTACTTT
*
4311 TTACTGACTACCTTTTTACTTT
1 TTACTGATTACCTTTTTACTTT
* *
4333 TTACTGATTACC--ATTACTTC
1 TTACTGATTACCTTTTTACTTT
* *
4353 TTACTGATTA-C-TATTACTCT
1 TTACTGATTACCTTTTTACTTT
* * * * * *
4373 CTACTAATTACCATATTGCTCT
1 TTACTGATTACCTTTTTACTTT
* * *
4395 TTACTAATTACCATTTTACCTT
1 TTACTGATTACCTTTTTACTTT
** *
4417 TTACTGATTA--TCATTATTTT
1 TTACTGATTACCTTTTTACTTT
4437 TTACTGATTA-CTATTTTACT
1 TTACTGATTACCT-TTTTACT
4457 ATATGAATTT
Statistics
Matches: 247, Mismatches: 54, Indels: 33
0.74 0.16 0.10
Matches are distributed among these distances:
19 1 0.00
20 77 0.31
21 40 0.16
22 107 0.43
23 21 0.09
24 1 0.00
ACGTcount: A:0.23, C:0.21, G:0.04, T:0.51
Consensus pattern (22 bp):
TTACTGATTACCTTTTTACTTT
Found at i:4245 original size:20 final size:20
Alignment explanation
Indices: 4198--4275 Score: 77
Period size: 20 Copynumber: 3.8 Consensus size: 20
4188 ATATACCTTT
* *
4198 TTACTTTTTACTGATTACCTTT
1 TTACTTTTTACTGATT-TC-TA
*
4220 TTACTTTTTATTG-TTTGCTA
1 TTACTTTTTACTGATTT-CTA
*
4240 TTACTTCTTACTGATTTCTA
1 TTACTTTTTACTGATTTCTA
*
4260 TTACTCTTTACTGATT
1 TTACTTTTTACTGATT
4276 ATTACTTTAC
Statistics
Matches: 47, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
20 29 0.62
21 6 0.13
22 12 0.26
ACGTcount: A:0.18, C:0.17, G:0.06, T:0.59
Consensus pattern (20 bp):
TTACTTTTTACTGATTTCTA
Found at i:4419 original size:84 final size:84
Alignment explanation
Indices: 4247--4451 Score: 227
Period size: 84 Copynumber: 2.4 Consensus size: 84
4237 CTATTACTTC
* * *
4247 TTACTGATTTCTATTAC-TCTTTACTGATTATTACTTTACTCCTTACTAATTACCATTGTACCCA
1 TTACTGATTACCATTACTTC-TTACTGATTACTA--TTACTCCTTACTAATTACCATTGTACCCA
* * *
4311 TTACTGACTACCTTTTTACTTT
63 TTACTAACTACCATTTTACCTT
* * *
4333 TTACTGATTACCATTACTTCTTACTGATTACTATTACT-CTCTACTAATTACCATAT-TGCTCTT
1 TTACTGATTACCATTACTTCTTACTGATTACTATTACTCCT-TACTAATTACCAT-TGTACCCAT
*
4396 TACTAATTACCATTTTACCTT
64 TACTAACTACCATTTTACCTT
* * *
4417 TTACTGATTATCATTATTTTTTACTGATTACTATT
1 TTACTGATTACCATTACTTCTTACTGATTACTATT
4452 TTACTATATG
Statistics
Matches: 103, Mismatches: 13, Indels: 8
0.83 0.10 0.06
Matches are distributed among these distances:
83 2 0.02
84 71 0.69
85 1 0.01
86 27 0.26
87 2 0.02
ACGTcount: A:0.25, C:0.21, G:0.04, T:0.49
Consensus pattern (84 bp):
TTACTGATTACCATTACTTCTTACTGATTACTATTACTCCTTACTAATTACCATTGTACCCATTA
CTAACTACCATTTTACCTT
Found at i:4456 original size:106 final size:104
Alignment explanation
Indices: 4118--4447 Score: 317
Period size: 106 Copynumber: 3.1 Consensus size: 104
4108 TTTAACTAGA
* * * *
4118 TTACTGATTACCCTTTTACTT-TTACTGATTACCATTTTACTCTTTTGCTAATTACCATTTTACC
1 TTACTGATTA-CC-ATTACTTCTTACTGATTA-C-TATTACTC-TTTACTAATTACCA-TTTACT
* *
4182 CTTTAC--ATATACCTTTTTACTTTTTACTGATTACCTTTTTACTTT
60 CTTTACTAAT-TACCATTTTACCTTTTACTGATTA-CTTTTTACTTT
* * * * * * ** *
4227 TTATTGTTTGCTATTACTTCTTACTGATTTCTATTACTCTTTACTGATTATTACTTTACTCCTTA
1 TTACTGATTACCATTACTTCTTACTGATTACTATTACTCTTTACTAATTACCA-TTTACTCTTTA
* ** *
4292 CTAATTACCATTGTACCCATTACTGACTACCTTTTTACTTT
65 CTAATTACCATTTTACCTTTTACTGATTA-CTTTTTACTTT
* *
4333 TTACTGATTACCATTACTTCTTACTGATTACTATTACTCTCTACTAATTACCATATTGCTCTTTA
1 TTACTGATTACCATTACTTCTTACTGATTACTATTACTCTTTACTAATTACCAT-TTACTCTTTA
** *
4398 CTAATTACCATTTTACCTTTTACTGATTA-TCATTATTTT
65 CTAATTACCATTTTACCTTTTACTGATTACTTTTTACTTT
4437 TTACTGATTAC
1 TTACTGATTAC
4448 TATTTTACTA
Statistics
Matches: 179, Mismatches: 38, Indels: 13
0.78 0.17 0.06
Matches are distributed among these distances:
104 18 0.10
105 21 0.12
106 114 0.64
107 9 0.05
108 10 0.06
109 7 0.04
ACGTcount: A:0.23, C:0.22, G:0.05, T:0.51
Consensus pattern (104 bp):
TTACTGATTACCATTACTTCTTACTGATTACTATTACTCTTTACTAATTACCATTTACTCTTTAC
TAATTACCATTTTACCTTTTACTGATTACTTTTTACTTT
Found at i:4531 original size:30 final size:30
Alignment explanation
Indices: 4495--4590 Score: 120
Period size: 30 Copynumber: 3.1 Consensus size: 30
4485 TTTACTCTTT
4495 ACTGATTGTTTTTTCTTATTGAACTTAATC
1 ACTGATTGTTTTTTCTTATTGAACTTAATC
** *
4525 ACTGATTACTTTTTCTTATTGAACTTAATT
1 ACTGATTGTTTTTTCTTATTGAACTTAATC
* *
4555 ACTGATTGCCTTTTTGCTTTTTGGAACTTAATC
1 ACTGATTG--TTTTTTCTTATT-GAACTTAATC
4588 ACT
1 ACT
4591 CTGATCACCC
Statistics
Matches: 55, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
30 34 0.62
32 9 0.16
33 12 0.22
ACGTcount: A:0.23, C:0.16, G:0.10, T:0.51
Consensus pattern (30 bp):
ACTGATTGTTTTTTCTTATTGAACTTAATC
Done.