Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023200.1 Corchorus olitorius cultivar O-4 contig23233, 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: 4273
ACGTcount: A:0.26, C:0.18, G:0.19, T:0.38
Found at i:411 original size:31 final size:31
Alignment explanation
Indices: 368--439 Score: 110
Period size: 31 Copynumber: 2.3 Consensus size: 31
358 ATTTATTTTT
*
368 TTTATTATTTTTTTAAACTATTATCTATTTA
1 TTTACTATTTTTTTAAACTATTATCTATTTA
*
399 TTTACTATTTTTTTTAACTATTATCTATTTA
1 TTTACTATTTTTTTAAACTATTATCTATTTA
430 -TTATCTATTT
1 TTTA-CTATTT
440 ATCTTTTTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
30 3 0.08
31 35 0.92
ACGTcount: A:0.26, C:0.08, G:0.00, T:0.65
Consensus pattern (31 bp):
TTTACTATTTTTTTAAACTATTATCTATTTA
Found at i:441 original size:8 final size:8
Alignment explanation
Indices: 430--690 Score: 88
Period size: 8 Copynumber: 33.8 Consensus size: 8
420 TATCTATTTA
430 TTATCTAT
1 TTATCTAT
*
438 TTATCTTT
1 TTATCTAT
*
446 TTATTTATTT
1 TTATCTA--T
*
456 TTAACTA-
1 TTATCTAT
463 TTATCTAT
1 TTATCTAT
471 TTATTTACTAT
1 TTA--T-CTAT
*
482 TTATCTTT
1 TTATCTAT
*
490 TTATTTAT
1 TTATCTAT
* * *
498 TAATTTAA
1 TTATCTAT
506 TTAT-TAT
1 TTATCTAT
* *
513 CTATTTAT
1 TTATCTAT
521 TTA-CTAT
1 TTATCTAT
*
528 TTATCTTT
1 TTATCTAT
*
536 TTATTTAT
1 TTATCTAT
* * *
544 TAATTTAA
1 TTATCTAT
552 TTAT-TAT
1 TTATCTAT
* *
559 CTATTTAT
1 TTATCTAT
567 TTA-CTAT
1 TTATCTAT
574 TTATCT-T
1 TTATCTAT
581 TT-TC--T
1 TTATCTAT
586 TTAT-TAAT
1 TTATCT-AT
594 TTAGT-TA-
1 TTA-TCTAT
601 TTATCTAT
1 TTATCTAT
*
609 TTATGTA-
1 TTATCTAT
616 TTAT-TA-
1 TTATCTAT
622 TTATCT-T
1 TTATCTAT
* * *
629 TTTTTTAG
1 TTATCTAT
* *
637 CTACCTAT
1 TTATCTAT
645 TTATCTA-
1 TTATCTAT
*
652 TTATTCTCT
1 TTA-TCTAT
*
661 GTATCTAT
1 TTATCTAT
*
669 TTATCTCT
1 TTATCTAT
*
677 ATATCTAT
1 TTATCTAT
685 TTATCT
1 TTATCT
691 TTTTTTATTA
Statistics
Matches: 186, Mismatches: 45, Indels: 44
0.68 0.16 0.16
Matches are distributed among these distances:
5 3 0.02
6 10 0.05
7 48 0.26
8 106 0.57
9 5 0.03
10 7 0.04
11 7 0.04
ACGTcount: A:0.25, C:0.10, G:0.02, T:0.64
Consensus pattern (8 bp):
TTATCTAT
Found at i:443 original size:19 final size:19
Alignment explanation
Indices: 341--622 Score: 98
Period size: 19 Copynumber: 15.8 Consensus size: 19
331 AAAATATTTT
341 TTTA-TTATTTATTCA-CTA
1 TTTATTTATTTATT-ATCTA
359 TTTATTT-TTT-TTAT-TA
1 TTTATTTATTTATTATCTA
** *
375 TTT-TTT-TAAACTAT-TA
1 TTTATTTATTTATTATCTA
* *
391 TCTATTTATTTACTAT-T-
1 TTTATTTATTTATTATCTA
**
408 TTT-TTTAACTATTATCTA
1 TTTATTTATTTATTATCTA
* *
426 TTTA-TTATCTATTTATCTT
1 TTTATTTATTTA-TTATCTA
*
445 TTTATTTATTT-TTAACTA
1 TTTATTTATTTATTATCTA
*
463 -TTATCTATTTATT-TACTA
1 TTTATTTATTTATTAT-CTA
481 TTTATCTT-TTTA-T-T-TA
1 TTTAT-TTATTTATTATCTA
* *
497 TTAATTTAATTATTATCTA
1 TTTATTTATTTATTATCTA
* *
516 TTTATTTA-CTATTTATCTT
1 TTTATTTATTTA-TTATCTA
*
535 TTTATTTATTAATTTAAT-TA
1 TTTATTTATTTA-TT-ATCTA
*
555 -TTATCTATTTATT-TACTA
1 TTTATTTATTTATTAT-CTA
*
573 TTTATCTT-TTT-CT-T-TA
1 TTTAT-TTATTTATTATCTA
* *
589 TTAATTTAGTTATTATCTA
1 TTTATTTATTTATTATCTA
*
608 TTTATGTA-TTATTAT
1 TTTATTTATTTATTAT
623 TATCTTTTTT
Statistics
Matches: 200, Mismatches: 35, Indels: 58
0.68 0.12 0.20
Matches are distributed among these distances:
15 8 0.04
16 40 0.20
17 19 0.09
18 52 0.26
19 67 0.34
20 12 0.06
21 2 0.01
ACGTcount: A:0.26, C:0.07, G:0.01, T:0.66
Consensus pattern (19 bp):
TTTATTTATTTATTATCTA
Found at i:449 original size:27 final size:27
Alignment explanation
Indices: 419--583 Score: 92
Period size: 27 Copynumber: 6.1 Consensus size: 27
409 TTTTTAACTA
419 TTATCTATTTATTATCTATTTATCTTT
1 TTATCTATTTATTATCTATTTATCTTT
* * *
446 TTATTTATTT-TTAACTA-TTATCTAT
1 TTATCTATTTATTATCTATTTATCTTT
* * *
471 TTATTTA-CTATTTATCTTTTTAT-TTAT
1 TTATCTATTTA-TTATCTATTTATCTT-T
* * * *
498 TAATTTAATTATTATCTATTTATTTACTAT
1 TTATCTATTTATTATCTATTTA--T-CTTT
* * *
528 TTATCTTTTTATTTAT-TAATTTA-ATTA
1 TTATCTATTTA-TTATCT-ATTTATCTTT
555 TTATCTATTTATT-TACTATTTATCTTT
1 TTATCTATTTATTAT-CTATTTATCTTT
582 TT
1 TT
584 CTTTATTAAT
Statistics
Matches: 103, Mismatches: 21, Indels: 28
0.68 0.14 0.18
Matches are distributed among these distances:
24 1 0.01
25 15 0.15
26 19 0.18
27 46 0.45
28 2 0.02
29 1 0.01
30 9 0.09
31 10 0.10
ACGTcount: A:0.26, C:0.08, G:0.00, T:0.66
Consensus pattern (27 bp):
TTATCTATTTATTATCTATTTATCTTT
Found at i:522 original size:46 final size:46
Alignment explanation
Indices: 411--635 Score: 341
Period size: 46 Copynumber: 4.9 Consensus size: 46
401 TACTATTTTT
*
411 TTTAACTATTATCTATTTA-TTATCTATTTATCTTTTTATTTATT--
1 TTTAATTATTATCTATTTATTTA-CTATTTATCTTTTTATTTATTAA
*
455 TTTAACTATTATCTATTTATTTACTATTTATCTTTTTATTTATTAA
1 TTTAATTATTATCTATTTATTTACTATTTATCTTTTTATTTATTAA
501 TTTAATTATTATCTATTTATTTACTATTTATCTTTTTATTTATTAA
1 TTTAATTATTATCTATTTATTTACTATTTATCTTTTTATTTATTAA
*
547 TTTAATTATTATCTATTTATTTACTATTTATCTTTTTCTTTATTAA
1 TTTAATTATTATCTATTTATTTACTATTTATCTTTTTATTTATTAA
* * *
593 TTTAGTTATTATCTATTTATGTATTATTATTATCTTTTT-TTTA
1 TTTAATTATTATCTATTTATTTACTA-T-TTATCTTTTTATTTA
636 GCTACCTATT
Statistics
Matches: 171, Mismatches: 5, Indels: 7
0.93 0.03 0.04
Matches are distributed among these distances:
44 40 0.23
45 3 0.02
46 113 0.66
47 5 0.03
48 10 0.06
ACGTcount: A:0.26, C:0.08, G:0.01, T:0.65
Consensus pattern (46 bp):
TTTAATTATTATCTATTTATTTACTATTTATCTTTTTATTTATTAA
Found at i:2663 original size:11 final size:13
Alignment explanation
Indices: 2638--2679 Score: 61
Period size: 13 Copynumber: 3.3 Consensus size: 13
2628 TTTATTACTA
2638 TTTTATTAAATTG
1 TTTTATTAAATTG
2651 TTTTA-TAAA-TG
1 TTTTATTAAATTG
2662 TTTTAATTAAATTG
1 TTTT-ATTAAATTG
2676 TTTT
1 TTTT
2680 GGGTGCATGA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
11 6 0.23
12 5 0.19
13 9 0.35
14 6 0.23
ACGTcount: A:0.31, C:0.00, G:0.07, T:0.62
Consensus pattern (13 bp):
TTTTATTAAATTG
Found at i:3092 original size:17 final size:17
Alignment explanation
Indices: 3070--3103 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
3060 TCAAATTGTT
3070 TCTTAATCCGTATCAGG
1 TCTTAATCCGTATCAGG
3087 TCTTAATCCGTATCAGG
1 TCTTAATCCGTATCAGG
3104 GTATTTTGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.24, G:0.18, T:0.35
Consensus pattern (17 bp):
TCTTAATCCGTATCAGG
Done.