Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014602.1 Corchorus capsularis cultivar CVL-1 contig14623, 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, 811
Length: 1352
ACGTcount: A:0.26, C:0.19, G:0.08, T:0.46
Found at i:248 original size:21 final size:21
Alignment explanation
Indices: 167--591 Score: 74
Period size: 21 Copynumber: 19.9 Consensus size: 21
157 CTCTTTACCA
*
167 TTTTTCTTTACTGATTACTCT
1 TTTTTCTTTACTGATTACTAT
* * *
188 TTATCCTTTACCAT-TTTACTGAT
1 TTTTTCTTTA-C-TGATTACT-AT
* * **
211 TTCTTC-TCACTCCTTACTAT
1 TTTTTCTTTACTGATTACTAT
231 TTTTTCTTTACTGATTACT-T
1 TTTTTCTTTACTGATTACTAT
* ** *
251 TTTACTCTTTACTCTTTACTCT
1 TTT-TTCTTTACTGATTACTAT
** ** **
273 TTACTGATTACTCTTTACTATTT
1 TTTTTCTTTACTGATTACTA--T
*
296 TTTTTCTTTACTGATTACTCT
1 TTTTTCTTTACTGATTACTAT
* * *
317 TTACTT-TTTACTAATTACCAT
1 TT-TTTCTTTACTGATTACTAT
* *
338 TTTACTT-TTCAGTGATTACCT-T
1 TTT--TTCTTTACTGATTA-CTAT
*
360 TTTACTT-TTTACTGATTACCAT
1 TTT--TTCTTTACTGATTACTAT
**
382 TACTTC-TTACTGATTACTACT
1 TTTTTCTTTACTGATTACTA-T
** * * *
403 TTACTCTTTGCTAATTACCAT
1 TTTTTCTTTACTGATTACTAT
** *
424 TTTACCCTTACTGA-TACCT-T
1 TTTTTCTTTACTGATTA-CTAT
444 TTTACTT-TTTACTGATTACCT-T
1 TTT--TTCTTTACTGATTA-CTAT
*
466 TTTACTTTTTTACTG-TGTACTAT
1 TTT--TTCTTTACTGAT-TACTAT
**
489 TACTT-TTTACTGACTT-CTA-
1 TTTTTCTTTACTGA-TTACTAT
** *
508 TTACTCTTTACTGATTACCACT
1 TTTTTCTTTACTGATTACTA-T
** * *
530 TTACTCTTTACTGATTATTTT
1 TTTTTCTTTACTGATTACTAT
* *
551 TTACTTTTTTTATTGATTACTA-
1 TT--TTTCTTTACTGATTACTAT
*
573 TTTTACTCTTACTGATTAC
1 TTTTTCT-TTACTGATTAC
592 CATTACTTTC
Statistics
Matches: 296, Mismatches: 75, Indels: 66
0.68 0.17 0.15
Matches are distributed among these distances:
19 4 0.01
20 55 0.19
21 105 0.35
22 88 0.30
23 44 0.15
ACGTcount: A:0.20, C:0.20, G:0.04, T:0.55
Consensus pattern (21 bp):
TTTTTCTTTACTGATTACTAT
Found at i:255 original size:7 final size:7
Alignment explanation
Indices: 245--372 Score: 58
Period size: 7 Copynumber: 17.7 Consensus size: 7
235 TCTTTACTGA
245 TTACTTT
1 TTACTTT
*
252 TTACTCT
1 TTACTTT
*
259 TTACTCT
1 TTACTTT
*
266 TTACTCT
1 TTACTTT
**
273 TTACTGA
1 TTACTTT
*
280 TTACTCT
1 TTACTTT
287 TTACTATT
1 TTACT-TT
**
295 TTTTTTCT
1 TTACTT-T
**
303 TTACTGA
1 TTACTTT
*
310 TTACTCT
1 TTACTTT
317 TTACTTT
1 TTACTTT
**
324 TTACTAA
1 TTACTTT
*
331 TTACCATT
1 TTA-CTTT
339 TTACTTT
1 TTACTTT
* * **
346 TCAGTGA
1 TTACTTT
353 TTACCTTT
1 TTA-CTTT
361 TTACTTT
1 TTACTTT
368 TTACT
1 TTACT
373 GATTACCATT
Statistics
Matches: 88, Mismatches: 29, Indels: 8
0.70 0.23 0.06
Matches are distributed among these distances:
7 72 0.82
8 16 0.18
ACGTcount: A:0.19, C:0.20, G:0.03, T:0.59
Consensus pattern (7 bp):
TTACTTT
Found at i:306 original size:30 final size:29
Alignment explanation
Indices: 252--325 Score: 105
Period size: 30 Copynumber: 2.6 Consensus size: 29
242 TGATTACTTT
* **
252 TTACTCTTTAC-TCTTTACTCTTTACTGA
1 TTACTCTTTACTTTTTTTTTCTTTACTGA
280 TTACTCTTTACTATTTTTTTTCTTTACTGA
1 TTACTCTTTACT-TTTTTTTTCTTTACTGA
310 TTACTCTTTACTTTTT
1 TTACTCTTTACTTTTT
326 ACTAATTACC
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
28 11 0.27
29 4 0.10
30 26 0.63
ACGTcount: A:0.16, C:0.20, G:0.03, T:0.61
Consensus pattern (29 bp):
TTACTCTTTACTTTTTTTTTCTTTACTGA
Found at i:327 original size:14 final size:14
Alignment explanation
Indices: 245--328 Score: 87
Period size: 14 Copynumber: 5.9 Consensus size: 14
235 TCTTTACTGA
245 TTACTTTTTACTCT
1 TTACTTTTTACTCT
*
259 TTACTCTTTACTCT
1 TTACTTTTTACTCT
**
273 TTACTGATTACTCT
1 TTACTTTTTACTCT
**
287 TTACTATTTTTTTTCT
1 TTAC--TTTTTACTCT
**
303 TTACTGATTACTCT
1 TTACTTTTTACTCT
317 TTACTTTTTACT
1 TTACTTTTTACT
329 AATTACCATT
Statistics
Matches: 55, Mismatches: 13, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
14 45 0.82
16 10 0.18
ACGTcount: A:0.17, C:0.20, G:0.02, T:0.61
Consensus pattern (14 bp):
TTACTTTTTACTCT
Found at i:328 original size:44 final size:44
Alignment explanation
Indices: 237--764 Score: 219
Period size: 44 Copynumber: 12.1 Consensus size: 44
227 CTATTTTTTC
* * ** *
237 TTTACTGATTA-CTTTTTAC-TCTTTACTCTTTACTCTTTACTG
1 TTTACTAATTACCATTTTACTTCTTTACTGATTACTCTTTACTT
* ** * **
279 ATTACTCTTTACTATTTTTTTTCTTTACTGATTACTCTTTACTT
1 TTTACTAATTACCATTTTACTTCTTTACTGATTACTCTTTACTT
* * *
323 TTTACTAATTACCATTTTACTT-TTCAGTGATTACCTTTTTACTT
1 TTTACTAATTACCATTTTACTTCTTTACTGATTA-CTCTTTACTT
* *
367 TTTACTGATTACCA--TTACTTC-TTACTGATTACTACTTTACTC
1 TTTACTAATTACCATTTTACTTCTTTACTGATTACT-CTTTACTT
* * *
409 TTTGCTAATTACCATTTTAC--CCTTACTGA-TACCTTTTTACTT
1 TTTACTAATTACCATTTTACTTCTTTACTGATTA-CTCTTTACTT
* * * *
451 TTTACTGATTACCTTTTTACTTTTTTACTG-TGTACT-ATTACTT
1 TTTACTAATTACCATTTTACTTCTTTACTGAT-TACTCTTTACTT
* * * *
494 TTTACTGACTT--C-TATTAC-TCTTTACTGATTACCACTTTACTC
1 TTTACT-AATTACCATTTTACTTCTTTACTGATTA-CTCTTTACTT
* ** * * *
536 TTTACTGATTA-TTTTTTACTTTTTTTATTGATTACTATTTTAC-T
1 TTTACTAATTACCATTTTAC-TTCTTTACTGATTACT-CTTTACTT
* * * *
580 CTTACTGATTACCATTACTTTCTGAATCTTGATTACTGATTAGCCTTTTTAC-T
1 TTTACTAATTACCATT--TTACT---TC-T--TTACTGATTA--CTCTTTACTT
** * * *
633 TTTACTGTTTA-C-TATTACTTC-TTACTGATTACT-ATTACTC
1 TTTACTAATTACCATTTTACTTCTTTACTGATTACTCTTTACTT
* * * * *
673 TTTACTGATTATCACTTTAC-TCTTTACTAATTAC-CATTTTACTC
1 TTTACTAATTACCATTTTACTTCTTTACTGATTACTC--TTTACTT
* *
717 TTTAC-AGA-TACCTTTTTACTT-TTTACTGATTTATCTTTTTACTT
1 TTTACTA-ATTACCATTTTACTTCTTTACTGA-TTA-CTCTTTACTT
761 TTTA
1 TTTA
765 TTATTTGCTA
Statistics
Matches: 367, Mismatches: 74, Indels: 88
0.69 0.14 0.17
Matches are distributed among these distances:
39 4 0.01
40 22 0.06
41 14 0.04
42 102 0.28
43 54 0.15
44 109 0.30
45 21 0.06
46 3 0.01
47 3 0.01
49 5 0.01
50 1 0.00
51 1 0.00
52 10 0.03
53 16 0.04
54 2 0.01
ACGTcount: A:0.21, C:0.20, G:0.05, T:0.54
Consensus pattern (44 bp):
TTTACTAATTACCATTTTACTTCTTTACTGATTACTCTTTACTT
Found at i:344 original size:22 final size:22
Alignment explanation
Indices: 302--764 Score: 241
Period size: 22 Copynumber: 21.2 Consensus size: 22
292 ATTTTTTTTC
302 TTTACTGATTA-C-TCTTTACTT
1 TTTACTGATTACCAT-TTTACTT
*
323 TTTACTAATTACCATTTTACTT
1 TTTACTGATTACCATTTTACTT
* * *
345 TTCAGTGATTACCTTTTTACTT
1 TTTACTGATTACCATTTTACTT
367 TTTACTGATTACCA--TTACTT
1 TTTACTGATTACCATTTTACTT
* * * *
387 CTTACTGATTACTACTTTACTC
1 TTTACTGATTACCATTTTACTT
* * *
409 TTTGCTAATTACCATTTTAC-C
1 TTTACTGATTACCATTTTACTT
* *
430 CTTACTGA-TACCTTTTTACTT
1 TTTACTGATTACCATTTTACTT
*
451 TTTACTGATTACCTTTTTACTTT
1 TTTACTGATTACCATTTTAC-TT
*
474 TTTACTG-TGTA-C-TATTACTT
1 TTTACTGAT-TACCATTTTACTT
* *
494 TTTACTGACTT--C-TATTACTC
1 TTTACTGA-TTACCATTTTACTT
* *
514 TTTACTGATTACCACTTTACTC
1 TTTACTGATTACCATTTTACTT
**
536 TTTACTGATTA-TTTTTTACTTTT
1 TTTACTGATTACCATTTTAC--TT
* *
559 TTTATTGATTACTATTTTAC-T
1 TTTACTGATTACCATTTTACTT
*
580 CTTACTGATTACCA--TTACTT
1 TTTACTGATTACCATTTTACTT
* *
600 TCTGAATCTTGATTACTGATTAGCCTTTTTAC-T
1 T-T-TA-C-TGATTAC-------CATTT-TACTT
* *
633 TTTACTGTTTA-C-TATTACTT
1 TTTACTGATTACCATTTTACTT
* * *
653 CTTACTGATTA-C-TATTACTC
1 TTTACTGATTACCATTTTACTT
* * *
673 TTTACTGATTATCACTTTACTC
1 TTTACTGATTACCATTTTACTT
* *
695 TTTACTAATTACCATTTTACTC
1 TTTACTGATTACCATTTTACTT
* *
717 TTTACAGA-TACCTTTTTACTT
1 TTTACTGATTACCATTTTACTT
* *
738 TTTACTGATTTATCTTTTTACTT
1 TTTACTGA-TTACCATTTTACTT
761 TTTA
1 TTTA
765 TTATTTGCTA
Statistics
Matches: 350, Mismatches: 56, Indels: 70
0.74 0.12 0.15
Matches are distributed among these distances:
19 9 0.03
20 84 0.24
21 68 0.19
22 120 0.34
23 40 0.11
24 14 0.04
29 5 0.01
30 1 0.00
31 2 0.01
32 1 0.00
33 3 0.01
34 3 0.01
ACGTcount: A:0.22, C:0.19, G:0.05, T:0.54
Consensus pattern (22 bp):
TTTACTGATTACCATTTTACTT
Found at i:398 original size:42 final size:41
Alignment explanation
Indices: 303--764 Score: 192
Period size: 42 Copynumber: 10.6 Consensus size: 41
293 TTTTTTTTCT
* *
303 TTACTGATTACTCTTTACTTTTTACTAATTACCATTTTACTT-
1 TTACTGATTACTTTTTACTTTTTACTGATTACCA--TTACTTC
*
345 TTCAGTGATTACCTTTTTACTTTTTACTGATTACCATTACTTC
1 TT-ACTGATTA-CTTTTTACTTTTTACTGATTACCATTACTTC
* * * * *
388 TTACTGATTACTACTTTACTCTTTGCTAATTACCATTTTAC-CC
1 TTACTGATTACT-TTTTACTTTTTACTGATTACCA--TTACTTC
* *
431 TTACTGA-TACCTTTTTACTTTTTACTGATTACCTTTTTACTTTT
1 TTACTGATTA-CTTTTTACTTTTTACTGATTACC--ATTAC-TTC
* *
475 TTACTG-TGTAC-TATTACTTTTTACTGACTT-CTATTAC-TC
1 TTACTGAT-TACTTTTTACTTTTTACTGA-TTACCATTACTTC
** * *** *
514 TTTACTGATTACCACTTTACTCTTTACTGATTATTTTTTACTTTTT
1 -TTACTGATTA-CTTTTTACTTTTTACTGATTA-CCATTAC--TTC
* *
560 TTATTGATTACTATTTTAC-TCTTACTGATTACCATTACTTTCTGAATC
1 TTACTGATTACT-TTTTACTTTTTACTGATTACCATTA----CT---TC
* *
608 TTGATTACTGATTAGCCTTTTTAC-TTTTACTGTTTACTATTACTTC
1 ----TTACTGATTA--CTTTTTACTTTTTACTGATTACCATTACTTC
* * *
654 TTACTGATTAC-TATTACTCTTTACTGATTATCACTTTAC-TC
1 TTACTGATTACTTTTTACTTTTTACTGATTA-C-CATTACTTC
* * * * * *
695 TTTACTAATTACCATTTTACTCTTTACAGA-TACCTTTTTACTTT
1 -TTACTGATTA-CTTTTTACTTTTTACTGATTACC--ATTACTTC
739 TTACTGATTTATCTTTTTACTTTTTA
1 TTACTGA-TTA-CTTTTTACTTTTTA
765 TTATTTGCTA
Statistics
Matches: 321, Mismatches: 52, Indels: 92
0.69 0.11 0.20
Matches are distributed among these distances:
39 6 0.02
40 19 0.06
41 14 0.04
42 93 0.29
43 57 0.18
44 76 0.24
45 17 0.05
46 3 0.01
47 1 0.00
48 1 0.00
49 2 0.01
52 9 0.03
53 21 0.07
54 2 0.01
ACGTcount: A:0.22, C:0.19, G:0.05, T:0.53
Consensus pattern (41 bp):
TTACTGATTACTTTTTACTTTTTACTGATTACCATTACTTC
Done.