Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01003682.1 Corchorus capsularis cultivar CVL-1 contig03690, 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, 617
Length: 1029
ACGTcount: A:0.43, C:0.12, G:0.15, T:0.31
Found at i:329 original size:11 final size:11
Alignment explanation
Indices: 315--404 Score: 58
Period size: 11 Copynumber: 7.5 Consensus size: 11
305 GGAAAAAGAA
315 AAGAAAAAATT
1 AAGAAAAAATT
326 AAGAAAAAA--
1 AAGAAAAAATT
***
335 AAGGTTAAATT
1 AAGAAAAAATT
346 AAGAAAAAATTT
1 AAGAAAAAA-TT
358 AAGAAAAAATAT
1 AAGAAAAAAT-T
370 ACAACGTATAAAAACTT
1 --AA-G-A-AAAAA-TT
387 AAGAAAAAAATT
1 AAG-AAAAAATT
399 AAGAAA
1 AAGAAA
405 TTGGGGAAGA
Statistics
Matches: 62, Mismatches: 7, Indels: 20
0.70 0.08 0.22
Matches are distributed among these distances:
9 6 0.10
11 19 0.31
12 17 0.27
13 5 0.08
14 4 0.06
15 3 0.05
16 1 0.02
17 6 0.10
18 1 0.02
ACGTcount: A:0.68, C:0.03, G:0.10, T:0.19
Consensus pattern (11 bp):
AAGAAAAAATT
Found at i:342 original size:15 final size:16
Alignment explanation
Indices: 287--364 Score: 60
Period size: 16 Copynumber: 5.1 Consensus size: 16
277 AAATAAATTT
287 AAGAAAAAATTAAGAA
1 AAGAAAAAATTAAGAA
*
303 AAG--GAAA--AAGAA
1 AAGAAAAAATTAAGAA
315 AAGAAAAAATTAAGAA
1 AAGAAAAAATTAAGAA
** *
331 AA-AAAAGGTTAA-ATT
1 AAGAAAAAATTAAGA-A
346 AAGAAAAAATTTAAGAA
1 AAGAAAAAA-TTAAGAA
363 AA
1 AA
365 AATATACAAC
Statistics
Matches: 46, Mismatches: 8, Indels: 15
0.67 0.12 0.22
Matches are distributed among these distances:
12 8 0.17
14 7 0.15
15 10 0.22
16 14 0.30
17 6 0.13
18 1 0.02
ACGTcount: A:0.72, C:0.00, G:0.14, T:0.14
Consensus pattern (16 bp):
AAGAAAAAATTAAGAA
Found at i:361 original size:12 final size:12
Alignment explanation
Indices: 344--404 Score: 50
Period size: 12 Copynumber: 4.7 Consensus size: 12
334 AAAGGTTAAA
344 TTAAGAAAAAAT
1 TTAAGAAAAAAT
356 TTAAGAAAAAAT
1 TTAAGAAAAAAT
* *
368 ATACAACGTATAAAAAC
1 -T-TAA-G-A-AAAAAT
*
385 TTAAGAAAAAAA
1 TTAAGAAAAAAT
397 TTAAGAAA
1 TTAAGAAA
405 TTGGGGAAGA
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
12 25 0.62
13 2 0.05
14 3 0.08
15 3 0.08
16 2 0.05
17 5 0.12
ACGTcount: A:0.66, C:0.05, G:0.08, T:0.21
Consensus pattern (12 bp):
TTAAGAAAAAAT
Found at i:471 original size:45 final size:46
Alignment explanation
Indices: 419--523 Score: 135
Period size: 45 Copynumber: 2.3 Consensus size: 46
409 GGAAGAAGAA
*
419 AAGGAAAAAATTTAAGAAAAGAAATTGATAAAAACAGAAAACAGAG
1 AAGGAAAAAATTGAAGAAAAGAAATTGATAAAAACAGAAAACAGAG
* *
465 AA-GAAAAGGAA--GAAGAAAAGAAATTGATAAAAGCAGAAAACGGAG
1 AAGGAAAA--AATTGAAGAAAAGAAATTGATAAAAACAGAAAACAGAG
510 AAGGAAAGAAATTG
1 AAGGAAA-AAATTG
524 GGGAAAATAT
Statistics
Matches: 50, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
45 40 0.80
46 6 0.12
47 4 0.08
ACGTcount: A:0.63, C:0.04, G:0.23, T:0.10
Consensus pattern (46 bp):
AAGGAAAAAATTGAAGAAAAGAAATTGATAAAAACAGAAAACAGAG
Found at i:504 original size:21 final size:21
Alignment explanation
Indices: 433--504 Score: 58
Period size: 21 Copynumber: 3.3 Consensus size: 21
423 AAAAAATTTA
*
433 AGAAAAGAAATTGATAAAAAC
1 AGAAAAGAAATTGATAAAAGC
* *
454 AGAAAACAGAGAA--GAAAAGGAAGA
1 AG-AAA-AGA-AATTGATAA--AAGC
478 AGAAAAGAAATTGATAAAAGC
1 AGAAAAGAAATTGATAAAAGC
499 AGAAAA
1 AGAAAA
505 CGGAGAAGGA
Statistics
Matches: 39, Mismatches: 5, Indels: 14
0.67 0.09 0.24
Matches are distributed among these distances:
21 13 0.33
22 10 0.26
23 10 0.26
24 6 0.15
ACGTcount: A:0.67, C:0.04, G:0.21, T:0.08
Consensus pattern (21 bp):
AGAAAAGAAATTGATAAAAGC
Done.