Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013135.1 Corchorus capsularis cultivar CVL-1 contig13156, 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: 26930
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32
Found at i:395 original size:20 final size:20
Alignment explanation
Indices: 366--438 Score: 58
Period size: 20 Copynumber: 3.4 Consensus size: 20
356 ATCAAAACCC
366 TTTG-AAAACCATGACTCTT
1 TTTGAAAAACCATGACTCTT
* *
385 TTTGAAAAACCATTTTATCAAAACTT
1 TTTGAAAAACCA--TGA-C---TCTT
*
411 TTTGCAAAACCATGACTCTT
1 TTTGAAAAACCATGACTCTT
431 TTTGAAAA
1 TTTGAAAA
439 CCTTTTTGAA
Statistics
Matches: 41, Mismatches: 6, Indels: 13
0.68 0.10 0.22
Matches are distributed among these distances:
19 4 0.10
20 17 0.41
22 2 0.05
23 2 0.05
24 2 0.05
26 14 0.34
ACGTcount: A:0.37, C:0.18, G:0.08, T:0.37
Consensus pattern (20 bp):
TTTGAAAAACCATGACTCTT
Found at i:440 original size:45 final size:45
Alignment explanation
Indices: 293--438 Score: 238
Period size: 45 Copynumber: 3.2 Consensus size: 45
283 TTTGAAATCA
* * *
293 TTTTTGGAAAATCATTTTATCCAAACCTTTTGAAAACCATGACTC
1 TTTTTGAAAAACCATTTTATCAAAACCTTTTGAAAACCATGACTC
*
338 TTTTTGAAAAACCATTTTATCAAAACCCTTTGAAAACCATGACTC
1 TTTTTGAAAAACCATTTTATCAAAACCTTTTGAAAACCATGACTC
*
383 TTTTTGAAAAACCATTTTATCAAAACTTTTTGCAAAACCATGACTC
1 TTTTTGAAAAACCATTTTATCAAAACCTTTTG-AAAACCATGACTC
429 TTTTTGAAAA
1 TTTTTGAAAA
439 CCTTTTTGAA
Statistics
Matches: 94, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
45 71 0.76
46 23 0.24
ACGTcount: A:0.36, C:0.19, G:0.08, T:0.37
Consensus pattern (45 bp):
TTTTTGAAAAACCATTTTATCAAAACCTTTTGAAAACCATGACTC
Found at i:445 original size:12 final size:12
Alignment explanation
Indices: 428--452 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
418 AACCATGACT
428 CTTTTTGAAAAC
1 CTTTTTGAAAAC
440 CTTTTTGAAAAC
1 CTTTTTGAAAAC
452 C
1 C
453 ATGACTTTTT
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:0.32, C:0.20, G:0.08, T:0.40
Consensus pattern (12 bp):
CTTTTTGAAAAC
Found at i:451 original size:31 final size:32
Alignment explanation
Indices: 404--471 Score: 113
Period size: 31 Copynumber: 2.2 Consensus size: 32
394 CCATTTTATC
404 AAAA-CTTTTTGCAAAACCATGACTCTTTTTG
1 AAAACCTTTTTGCAAAACCATGACTCTTTTTG
*
435 AAAACCTTTTTG-AAAACCATGACTTTTTTTG
1 AAAACCTTTTTGCAAAACCATGACTCTTTTTG
466 AAAACC
1 AAAACC
472 ATCGTTGCTT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
31 28 0.80
32 7 0.20
ACGTcount: A:0.35, C:0.19, G:0.09, T:0.37
Consensus pattern (32 bp):
AAAACCTTTTTGCAAAACCATGACTCTTTTTG
Found at i:519 original size:17 final size:17
Alignment explanation
Indices: 480--522 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
470 CCATCGTTGC
* *
480 TTTTTTTCTCTTTTCCC
1 TTTTTTTTTCTTTTCCA
* *
497 TCTTTTTTTCTTTTTCA
1 TTTTTTTTTCTTTTCCA
514 TTTTTTTTT
1 TTTTTTTTT
523 TCATTTTTTC
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTTTTTTTCTTTTCCA
Found at i:520 original size:18 final size:18
Alignment explanation
Indices: 479--530 Score: 59
Period size: 19 Copynumber: 2.8 Consensus size: 18
469 ACCATCGTTG
*
479 CTTTTTTTCTCTTTTCCCT
1 CTTTTTTTCT-TTTTCACT
*
498 CTTTTTTTCTTTTTCATT
1 CTTTTTTTCTTTTTCACT
*
516 TTTTTTTTCATTTTT
1 CTTTTTTTC-TTTTT
531 TCCACTTATC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
18 14 0.48
19 15 0.52
ACGTcount: A:0.04, C:0.19, G:0.00, T:0.77
Consensus pattern (18 bp):
CTTTTTTTCTTTTTCACT
Found at i:530 original size:12 final size:12
Alignment explanation
Indices: 501--531 Score: 53
Period size: 12 Copynumber: 2.5 Consensus size: 12
491 TTTCCCTCTT
501 TTTTTCTTTTTCA
1 TTTTT-TTTTTCA
514 TTTTTTTTTTCA
1 TTTTTTTTTTCA
526 TTTTTT
1 TTTTTT
532 CCACTTATCC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 13 0.72
13 5 0.28
ACGTcount: A:0.06, C:0.10, G:0.00, T:0.84
Consensus pattern (12 bp):
TTTTTTTTTTCA
Found at i:8848 original size:27 final size:28
Alignment explanation
Indices: 8779--8858 Score: 99
Period size: 27 Copynumber: 2.9 Consensus size: 28
8769 TAAAAATGGA
* * *
8779 CTAAAAATGACCAAAATGCTCCTTTAATG
1 CTAAAAATGACCAAAATAC-CCCTAAATG
* *
8808 CAAAAAAAGACCAAAATACCCCTAAATG
1 CTAAAAATGACCAAAATACCCCTAAATG
8836 -TAAAAATGACCAAAATACCCCTA
1 CTAAAAATGACCAAAATACCCCTA
8859 TGTGACCTTA
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
27 21 0.48
28 7 0.16
29 16 0.36
ACGTcount: A:0.50, C:0.24, G:0.07, T:0.19
Consensus pattern (28 bp):
CTAAAAATGACCAAAATACCCCTAAATG
Found at i:9341 original size:36 final size:36
Alignment explanation
Indices: 9273--9346 Score: 123
Period size: 37 Copynumber: 2.1 Consensus size: 36
9263 TTGCTTGAAT
*
9273 GTTTGTTTACTGGAAACTGAGACAGATAGAAAACGA
1 GTTTGTTTAATGGAAACTGAGACAGATAGAAAACGA
9309 GTTTGTTTTAATGGAAACTGAGACAGAT-GAAAACGA
1 GTTTG-TTTAATGGAAACTGAGACAGATAGAAAACGA
9345 GT
1 GT
9347 GGAAAGGCAC
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
36 15 0.42
37 21 0.58
ACGTcount: A:0.38, C:0.09, G:0.26, T:0.27
Consensus pattern (36 bp):
GTTTGTTTAATGGAAACTGAGACAGATAGAAAACGA
Found at i:10263 original size:28 final size:29
Alignment explanation
Indices: 10209--10265 Score: 89
Period size: 28 Copynumber: 2.0 Consensus size: 29
10199 GGTTAGACAC
*
10209 ATACAGCAAGGTTTTTTTTTTTTGGGTAAT
1 ATACAGCAAGG-TTTTTTTTTTGGGGTAAT
10239 ATACAGCAAGG-TTTTTTTTTGGGGTAA
1 ATACAGCAAGGTTTTTTTTTTGGGGTAA
10266 AGAATAAAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 15 0.58
30 11 0.42
ACGTcount: A:0.25, C:0.07, G:0.23, T:0.46
Consensus pattern (29 bp):
ATACAGCAAGGTTTTTTTTTTGGGGTAAT
Found at i:14994 original size:19 final size:19
Alignment explanation
Indices: 14983--15019 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
14973 AATTTTTAAG
14983 TAAAAATATAATATATAAA
1 TAAAAATATAATATATAAA
*
15002 TAAAAATTTAATAT-TAAA
1 TAAAAATATAATATATAAA
15020 ACAATTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
TAAAAATATAATATATAAA
Found at i:15579 original size:15 final size:14
Alignment explanation
Indices: 15555--15586 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
15545 GGAATAAAAA
15555 TTAAATATTTTATT
1 TTAAATATTTTATT
15569 TTAATATATTTTATT
1 TTAA-ATATTTTATT
15584 TTA
1 TTA
15587 TTGAAATTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (14 bp):
TTAAATATTTTATT
Found at i:15598 original size:20 final size:20
Alignment explanation
Indices: 15560--15598 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
15550 AAAAATTAAA
**
15560 TATTTTATTTTAATATATTT
1 TATTTTATTGAAATATATTT
*
15580 TATTTTATTGAAATTTATT
1 TATTTTATTGAAATATATT
15599 CTTAAAAAAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (20 bp):
TATTTTATTGAAATATATTT
Found at i:23023 original size:1 final size:1
Alignment explanation
Indices: 23017--23045 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
23007 AGTTTCACGG
23017 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
23046 CTCGTTCCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:23516 original size:84 final size:84
Alignment explanation
Indices: 23375--23543 Score: 338
Period size: 84 Copynumber: 2.0 Consensus size: 84
23365 CATATTGTAA
23375 TTTCTAGTTACTATTTTATAATTTCATTTATATATAGATGAAAATTACAATATTTTTCTTTCAAA
1 TTTCTAGTTACTATTTTATAATTTCATTTATATATAGATGAAAATTACAATATTTTTCTTTCAAA
23440 AAAAAATATGAGACCTTTT
66 AAAAAATATGAGACCTTTT
23459 TTTCTAGTTACTATTTTATAATTTCATTTATATATAGATGAAAATTACAATATTTTTCTTTCAAA
1 TTTCTAGTTACTATTTTATAATTTCATTTATATATAGATGAAAATTACAATATTTTTCTTTCAAA
23524 AAAAAATATGAGACCTTTT
66 AAAAAATATGAGACCTTTT
23543 T
1 T
23544 CTTACGAGAA
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
84 85 1.00
ACGTcount: A:0.38, C:0.09, G:0.06, T:0.47
Consensus pattern (84 bp):
TTTCTAGTTACTATTTTATAATTTCATTTATATATAGATGAAAATTACAATATTTTTCTTTCAAA
AAAAAATATGAGACCTTTT
Found at i:24693 original size:16 final size:16
Alignment explanation
Indices: 24662--24716 Score: 60
Period size: 16 Copynumber: 3.4 Consensus size: 16
24652 CTCAAATGTC
*
24662 GGGTCA-TTTGGGTTT
1 GGGTCATTTTTGGTTT
24677 GGGTCATTTTTGGTTT
1 GGGTCATTTTTGGTTT
*
24693 GGGT-GTTTTTCGGTTTT
1 GGGTCATTTTT-GG-TTT
24710 GGGTCAT
1 GGGTCAT
24717 ATGGTTCCAA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
15 11 0.33
16 14 0.42
17 7 0.21
18 1 0.03
ACGTcount: A:0.05, C:0.07, G:0.36, T:0.51
Consensus pattern (16 bp):
GGGTCATTTTTGGTTT
Found at i:25296 original size:3 final size:3
Alignment explanation
Indices: 25288--25313 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
25278 CGAAAATTAT
25288 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
25314 CAAAATCAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:25996 original size:2 final size:2
Alignment explanation
Indices: 25989--26013 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
25979 ATTACATGAG
25989 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
26014 GAAGTATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.