Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005774.1 Corchorus capsularis cultivar CVL-1 contig05792, 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: 2347
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.35
Found at i:184 original size:25 final size:26
Alignment explanation
Indices: 156--207 Score: 81
Period size: 25 Copynumber: 2.0 Consensus size: 26
146 TTTATCACTT
156 TGACTCTTAATTA-TCGA-TTTACTGA
1 TGACTCTTAATTACT-GACTTTACTGA
181 TGACTCTTAATTACTGACTTTACTGA
1 TGACTCTTAATTACTGACTTTACTGA
207 T
1 T
208 TACTATTACC
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
25 15 0.60
26 10 0.40
ACGTcount: A:0.27, C:0.17, G:0.12, T:0.44
Consensus pattern (26 bp):
TGACTCTTAATTACTGACTTTACTGA
Found at i:367 original size:135 final size:126
Alignment explanation
Indices: 160--469 Score: 349
Period size: 135 Copynumber: 2.4 Consensus size: 126
150 TCACTTTGAC
* * * * * *
160 TCTTAATTATCGATTTACTGATGACTCTTAATTAC-TGACTTTACTGA-TTACT-ATTACCT-TG
1 TCTTAATTATCAATATACTGATTACTCTT-TTTACTTAAC--TACTGATTTACTGATTA-CTATT
* *
221 ACTCTTAATTATCAACTTACTGATTAATCTCTTTTTACTTAATTACTGATTTACTGATTATTACT
62 AC-CTTAATTATCAACTTACTGATTAATATCTTTTTACTTAATTACTGATTTACTGATTACTA--
286 TTT
124 TTT
*
289 ACTCCCTTAATTATCAATATACTTGATTAATCTCTTTTTACTTTACTACTGATTTACTGATTACT
1 --T--CTTAATTATCAATATAC-TGATT-A-CTCTTTTTACTTAACTACTGATTTACTGATTACT
* *
354 ATTACCTTAATTATCAATTTACTGATTAATATCTTTTTACTTAATTACTGATTTACTGATTGCTA
59 ATTACCTTAATTATCAACTTACTGATTAATATCTTTTTACTTAATTACTGATTTACTGATTACTA
419 TTT
124 TTT
* *
422 TCTTAATTATCAATTTACTGATTACTCTTTTTACTTAATTACTGATTT
1 TCTTAATTATCAATATACTGATTACTCTTTTTACTTAACTACTGATTT
470 GCCCTTGATG
Statistics
Matches: 157, Mismatches: 13, Indels: 23
0.81 0.07 0.12
Matches are distributed among these distances:
126 22 0.14
127 1 0.01
128 5 0.03
129 16 0.10
131 2 0.01
133 18 0.11
134 10 0.06
135 68 0.43
136 15 0.10
ACGTcount: A:0.28, C:0.16, G:0.06, T:0.50
Consensus pattern (126 bp):
TCTTAATTATCAATATACTGATTACTCTTTTTACTTAACTACTGATTTACTGATTACTATTACCT
TAATTATCAACTTACTGATTAATATCTTTTTACTTAATTACTGATTTACTGATTACTATTT
Found at i:374 original size:30 final size:29
Alignment explanation
Indices: 340--447 Score: 101
Period size: 30 Copynumber: 3.5 Consensus size: 29
330 TTTACTACTG
340 ATTTACTGATTACTATTACCTTAATTATCA
1 ATTTACTGATTACTATTA-CTTAATTATCA
* *
370 ATTTACTGATTAATATCTTTTTACTTAATTA-CTG
1 ATTTACTGA-T--TA-C-TATTACTTAATTATC-A
* *
404 ATTTACTGATTGCTATTTTCTTAATTATCA
1 ATTTACTGATTACTA-TTACTTAATTATCA
434 ATTTACTGATTACT
1 ATTTACTGATTACT
448 CTTTTTACTT
Statistics
Matches: 63, Mismatches: 7, Indels: 16
0.73 0.08 0.19
Matches are distributed among these distances:
29 1 0.02
30 33 0.52
31 3 0.05
33 4 0.06
34 18 0.29
35 4 0.06
ACGTcount: A:0.30, C:0.14, G:0.06, T:0.51
Consensus pattern (29 bp):
ATTTACTGATTACTATTACTTAATTATCA
Found at i:390 original size:64 final size:64
Alignment explanation
Indices: 186--469 Score: 338
Period size: 64 Copynumber: 4.2 Consensus size: 64
176 ACTGATGACT
*
186 CTTAATTACTGACTTTACTGATTACTATTACCTTGACTCTTAATTATCAACTTACTGATTAATCT
1 CTTAATTACTGA-TTTACTGATTAC---TA--TT-AC-CTTAATTATCAATTTACTGATTAATCT
251 CTTTTTA
58 CTTTTTA
* *
258 CTTAATTACTGATTTACTGATTATTACTTTTACTCCCTTAATTATCAATATACTTGATTAATCTC
1 CTTAATTACTGATTTACTG---ATTACTATTA---CCTTAATTATCAATTTAC-TGATTAATCTC
323 TTTTTA
59 TTTTTA
* * *
329 CTTTACTACTGATTTACTGATTACTATTACCTTAATTATCAATTTACTGATTAATATCTTTTTA
1 CTTAATTACTGATTTACTGATTACTATTACCTTAATTATCAATTTACTGATTAATCTCTTTTTA
* **
393 CTTAATTACTGATTTACTGATTGCTATTTTCTTAATTATCAATTTACTGATT-A-CTCTTTTTA
1 CTTAATTACTGATTTACTGATTACTATTACCTTAATTATCAATTTACTGATTAATCTCTTTTTA
455 CTTAATTACTGATTT
1 CTTAATTACTGATTT
470 GCCCTTGATG
Statistics
Matches: 191, Mismatches: 14, Indels: 24
0.83 0.06 0.10
Matches are distributed among these distances:
62 23 0.12
63 1 0.01
64 63 0.33
65 17 0.09
68 10 0.05
69 2 0.01
70 15 0.08
71 43 0.23
72 12 0.06
74 5 0.03
ACGTcount: A:0.28, C:0.17, G:0.05, T:0.50
Consensus pattern (64 bp):
CTTAATTACTGATTTACTGATTACTATTACCTTAATTATCAATTTACTGATTAATCTCTTTTTA
Found at i:2290 original size:11 final size:12
Alignment explanation
Indices: 2263--2287 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2253 AAAAAGAAGG
2263 TTAGGGTTTTTT
1 TTAGGGTTTTTT
2275 TTAGGGTTTTTT
1 TTAGGGTTTTTT
2287 T
1 T
2288 AGGTAATTCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.00, G:0.24, T:0.68
Consensus pattern (12 bp):
TTAGGGTTTTTT
Done.