Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01000271.1 Corchorus capsularis cultivar CVL-1 contig00271, 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, 658
Length: 1098
ACGTcount: A:0.22, C:0.20, G:0.08, T:0.49
Found at i:53 original size:22 final size:22
Alignment explanation
Indices: 2--276 Score: 186
Period size: 22 Copynumber: 12.9 Consensus size: 22
1 G
*
2 TACTGATTA-CTATTTTACTCTTG
1 TACTGATTACCT-TTTTACT-TTT
*
25 T--TGATTACCTTCTTACTTTT
1 TACTGATTACCTTTTTACTTTT
45 TACTGATTA-CTGTTTTACTCTTT
1 TACTGATTACCT-TTTTACT-TTT
*
68 TACTGATTA-CTCTTTACTATTT
1 TACTGATTACCTTTTTACT-TTT
*
90 T-CTG-CT-CC-TTTT--TTTT
1 TACTGATTACCTTTTTACTTTT
106 TACTGATTA-CTCTTTTACTTTT
1 TACTGATTACCT-TTTTACTTTT
* * *
128 TACTGATTGCGCCTTTTGCTTTT
1 TACTGATTAC-CTTTTTACTTTT
*
151 TACTGATTACCTTTTTACTTCT
1 TACTGATTACCTTTTTACTTTT
* * *
173 TGCTGATTAGCTTTTTACTCTT
1 TACTGATTACCTTTTTACTTTT
* *
195 TACTGATCACCTTTTTAC-TCT
1 TACTGATTACCTTTTTACTTTT
* * *
216 TACCGATTTCC-TTTTACTTCT
1 TACTGATTACCTTTTTACTTTT
* * **
237 TACTTATTACTTTTTTACTGAT
1 TACTGATTACCTTTTTACTTTT
259 TACT-ATTTA-CTTTTTACT
1 TACTGA-TTACCTTTTTACT
277 GACTACTATT
Statistics
Matches: 200, Mismatches: 34, Indels: 38
0.74 0.12 0.14
Matches are distributed among these distances:
16 4 0.02
17 4 0.02
18 2 0.01
19 3 0.01
20 15 0.08
21 45 0.22
22 93 0.47
23 33 0.17
24 1 0.00
ACGTcount: A:0.17, C:0.20, G:0.07, T:0.56
Consensus pattern (22 bp):
TACTGATTACCTTTTTACTTTT
Found at i:343 original size:23 final size:22
Alignment explanation
Indices: 243--354 Score: 124
Period size: 21 Copynumber: 5.1 Consensus size: 22
233 TTCTTACTTA
243 TTACTTTTTTACTGATTACTA-T
1 TTAC-TTTTTACTGATTACTATT
*
265 TTACTTTTTACTGACTACTATT
1 TTACTTTTTACTGATTACTATT
* *
287 TTACTCTTGT--TGATTACCT-TC
1 TTACT-TTTTACTGATTA-CTATT
308 TTACTTTTTACTGATTACTATT
1 TTACTTTTTACTGATTACTATT
*
330 TTACTCTTTTACTGATTACTCTT
1 TTACT-TTTTACTGATTACTATT
353 TT
1 TT
355 TACCCTTTCA
Statistics
Matches: 76, Mismatches: 7, Indels: 13
0.79 0.07 0.14
Matches are distributed among these distances:
20 3 0.04
21 28 0.37
22 24 0.32
23 21 0.28
ACGTcount: A:0.20, C:0.18, G:0.05, T:0.57
Consensus pattern (22 bp):
TTACTTTTTACTGATTACTATT
Found at i:383 original size:66 final size:64
Alignment explanation
Indices: 243--389 Score: 172
Period size: 66 Copynumber: 2.2 Consensus size: 64
233 TTCTTACTTA
* * *
243 TTACTTTTTTACTGATTACTATTTACTTTTTACTGACTACTATTTTACTCTTGTTGATTACCTTC
1 TTAC-TTTTTACTGATTACTATTTACTTTTTACTGACTACTATTTTACCCTTGTAGAGTACCTTC
* * *
308 TTACTTTTTACTGATTACTATTTTACTCTTTTACTGATTACTCTTTTTACCCTT-TCAG-GTATC
1 TTACTTTTTACTGATTACTA-TTTACT-TTTTACTGACTACT-ATTTTACCCTTGT-AGAGTACC
*
371 TTT
62 TTC
374 TTACTTTTTACTGATT
1 TTACTTTTTACTGATT
390 GCCTGCTATT
Statistics
Matches: 71, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
64 16 0.23
65 10 0.14
66 35 0.49
67 10 0.14
ACGTcount: A:0.19, C:0.18, G:0.06, T:0.56
Consensus pattern (64 bp):
TTACTTTTTACTGATTACTATTTACTTTTTACTGACTACTATTTTACCCTTGTAGAGTACCTTC
Found at i:697 original size:54 final size:53
Alignment explanation
Indices: 575--777 Score: 240
Period size: 54 Copynumber: 3.8 Consensus size: 53
565 CATTTTAACT
*
575 CTTAATTA-TCGATTTACTGATTACTATTACT-TTGACTCTGATTAATCTCTTTTTA
1 CTTAATTACT-GATTTACTGATTTCTATTACTCTTGAC-CTGATTAAT-TC-TTTTA
*
630 CTTAATTACTGATTTACTGATTTCTATTACTCTTTA-CTGATTAATTTCTTTTCA
1 CTTAATTACTGATTTACTGATTTCTATTACTCTTGACCTGATTAA-TTCTTTT-A
* *
684 CTTAATTATTGATTTACTGATTTCTATTAC-CTTGACTCTGGTTAA-T-TTTTA
1 CTTAATTACTGATTTACTGATTTCTATTACTCTTGAC-CTGATTAATTCTTTTA
* *
735 CTTAATTACTGATTTACTGATTTTTATTACTCTTTA-CTGATTA
1 CTTAATTACTGATTTACTGATTTCTATTACTCTTGACCTGATTA
778 TCACTTTAAT
Statistics
Matches: 132, Mismatches: 9, Indels: 19
0.82 0.06 0.12
Matches are distributed among these distances:
50 6 0.05
51 29 0.22
52 8 0.06
53 9 0.07
54 40 0.30
55 36 0.27
56 4 0.03
ACGTcount: A:0.25, C:0.15, G:0.07, T:0.53
Consensus pattern (53 bp):
CTTAATTACTGATTTACTGATTTCTATTACTCTTGACCTGATTAATTCTTTTA
Found at i:772 original size:105 final size:106
Alignment explanation
Indices: 575--777 Score: 327
Period size: 105 Copynumber: 1.9 Consensus size: 106
565 CATTTTAACT
*
575 CTTAATTATCGATTTACTGATTACTATTACTTTGACTCTGATTAATCTCTTTTTACTTAATTACT
1 CTTAATTATCGATTTACTGATTACTATTACCTTGACTCTGATTAA---CTTTTTACTTAATTACT
640 GATTTACTGATTTCTATTACTCTTTACTGATTAATTTCTTTTCA
63 GATTTACTGATTTCTATTACTCTTTACTGATTAATTTCTTTTCA
* * *
684 CTTAATTATTGATTTACTGATTTCTATTACCTTGACTCTGGTTAA-TTTTTACTTAATTACTGAT
1 CTTAATTATCGATTTACTGATTACTATTACCTTGACTCTGATTAACTTTTTACTTAATTACTGAT
*
748 TTACTGATTTTTATTACTCTTTACTGATTA
66 TTACTGATTTCTATTACTCTTTACTGATTA
778 TCACTTTAAT
Statistics
Matches: 89, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
105 48 0.54
109 41 0.46
ACGTcount: A:0.25, C:0.15, G:0.07, T:0.53
Consensus pattern (106 bp):
CTTAATTATCGATTTACTGATTACTATTACCTTGACTCTGATTAACTTTTTACTTAATTACTGAT
TTACTGATTTCTATTACTCTTTACTGATTAATTTCTTTTCA
Found at i:806 original size:22 final size:21
Alignment explanation
Indices: 765--822 Score: 62
Period size: 22 Copynumber: 2.7 Consensus size: 21
755 TTTTTATTAC
*
765 TCTTTACTGATTATCACTTTAA
1 TCTTTACTGATTACCACTTT-A
* *
787 TCTTTACTGATTGCCGCTTTA
1 TCTTTACTGATTACCACTTTA
*
808 CCTTTTACTGATTAC
1 TC-TTTACTGATTAC
823 ATCTTTCTTA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
21 2 0.07
22 28 0.93
ACGTcount: A:0.21, C:0.22, G:0.09, T:0.48
Consensus pattern (21 bp):
TCTTTACTGATTACCACTTTA
Done.