Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018477.1 Corchorus olitorius cultivar O-4 contig18510, 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: 1771
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.29
Found at i:264 original size:22 final size:22
Alignment explanation
Indices: 239--344 Score: 99
Period size: 22 Copynumber: 4.8 Consensus size: 22
229 GAAAGATTAT
* *
239 CAAAATTTCGTAGTGTGGTTAC
1 CAAAATTTCATAGTGAGGTTAC
* *
261 CAAAATTTCATA-TAGAGATTAT
1 CAAAATTTCATAGT-GAGGTTAC
* *
283 CAAAACTTCATAGTGTA-GTTAT
1 CAAAATTTCATAGTG-AGGTTAC
**
305 CAAAATTTCATACAGAGGTTAC
1 CAAAATTTCATAGTGAGGTTAC
*
327 CAAAATTTCATAGGGAGG
1 CAAAATTTCATAGTGAGG
345 GAGGTTACCA
Statistics
Matches: 68, Mismatches: 12, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
21 2 0.03
22 64 0.94
23 2 0.03
ACGTcount: A:0.38, C:0.13, G:0.17, T:0.32
Consensus pattern (22 bp):
CAAAATTTCATAGTGAGGTTAC
Found at i:280 original size:44 final size:44
Alignment explanation
Indices: 215--339 Score: 155
Period size: 44 Copynumber: 2.8 Consensus size: 44
205 TGACAATCAA
* *
215 ACCAAAA-TT-ATATAGAAAGATTATCAAAATTTCGTAGTGTGGTT
1 ACCAAAATTTCATATAG--AGATTATCAAAATTTCATAGTGTAGTT
*
259 ACCAAAATTTCATATAGAGATTATCAAAACTTCATAGTGTAGTT
1 ACCAAAATTTCATATAGAGATTATCAAAATTTCATAGTGTAGTT
* * * *
303 ATCAAAATTTCATACAGAGGTTACCAAAATTTCATAG
1 ACCAAAATTTCATATAGAGATTATCAAAATTTCATAG
340 GGAGGGAGGT
Statistics
Matches: 71, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
44 63 0.89
45 2 0.03
46 6 0.08
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.33
Consensus pattern (44 bp):
ACCAAAATTTCATATAGAGATTATCAAAATTTCATAGTGTAGTT
Found at i:408 original size:22 final size:22
Alignment explanation
Indices: 369--428 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
359 TTGTGTTTAT
**
369 CAAAATTTCCTAGAGAGGTTAA
1 CAAAATTTTATAGAGAGGTTAA
* *
391 CAAAATTTTATAGGGAGGTTAT
1 CAAAATTTTATAGAGAGGTTAA
* *
413 GAAAATTTTATGGAGA
1 CAAAATTTTATAGAGA
429 TTTTATCGAA
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.40, C:0.07, G:0.22, T:0.32
Consensus pattern (22 bp):
CAAAATTTTATAGAGAGGTTAA
Found at i:434 original size:22 final size:23
Alignment explanation
Indices: 365--441 Score: 63
Period size: 22 Copynumber: 3.5 Consensus size: 23
355 AAATTTGTGT
** *
365 TTATC-AAAATTTCCTAGAGAGG
1 TTATCGAAAATTTTATAGGGAGG
*
387 TTAAC-AAAATTTTATAGGGAGG
1 TTATCGAAAATTTTATAGGGAGG
**
409 TTAT-GAAAATTTTAT-GGAGATT
1 TTATCGAAAATTTTATAGG-GAGG
431 TTATCGAAAAT
1 TTATCGAAAAT
442 ACATAGAGAG
Statistics
Matches: 45, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
21 2 0.04
22 37 0.82
23 6 0.13
ACGTcount: A:0.39, C:0.06, G:0.18, T:0.36
Consensus pattern (23 bp):
TTATCGAAAATTTTATAGGGAGG
Found at i:513 original size:22 final size:23
Alignment explanation
Indices: 490--685 Score: 78
Period size: 22 Copynumber: 8.9 Consensus size: 23
480 GTTATCGGAA
* *
490 TTTCATGGTGTGGTTATCAAAAT
1 TTTCATAGTGCGGTTATCAAAAT
*
513 TTTCATAGTGCGGTTA-C-CAAT
1 TTTCATAGTGCGGTTATCAAAAT
* * *
534 TTT-ATTTAGTGTGATTATTAAAAT
1 TTTCA--TAGTGCGGTTATCAAAAT
*
558 TTT-ATAG-GCAGATTATCAAAA-
1 TTTCATAGTGC-GGTTATCAAAAT
* * * * *
579 TTTCACACTGAGATTATCGAAA-
1 TTTCATAGTGCGGTTATCAAAAT
* *
601 TTTCATAGTGTC-GTTACCCAAA-
1 TTTCATAGTG-CGGTTATCAAAAT
* **
623 TTTCATAGTGTGGTTAT-TGAAT
1 TTTCATAGTGCGGTTATCAAAAT
* *
645 TTTCATAG-GAGGTTATCGAAA-
1 TTTCATAGTGCGGTTATCAAAAT
666 TTTCATA-T-CAGGTTATCAAA
1 TTTCATAGTGC-GGTTATCAAA
686 TTTGCAAAAT
Statistics
Matches: 132, Mismatches: 28, Indels: 28
0.70 0.15 0.15
Matches are distributed among these distances:
20 1 0.01
21 35 0.27
22 74 0.56
23 15 0.11
24 7 0.05
ACGTcount: A:0.31, C:0.12, G:0.17, T:0.40
Consensus pattern (23 bp):
TTTCATAGTGCGGTTATCAAAAT
Found at i:658 original size:21 final size:21
Alignment explanation
Indices: 554--688 Score: 92
Period size: 22 Copynumber: 6.3 Consensus size: 21
544 GTGATTATTA
* * *
554 AAATTTTATAGGCAGATTATCA
1 AAATTTCATAGG-AGGTTATCG
* * *
576 AAATTTCACACTGAGATTATCG
1 AAATTTCATA-GGAGGTTATCG
** * *
598 AAATTTCATAGTGTCGTTACCC
1 AAATTTCATAG-GAGGTTATCG
* *
620 AAATTTCATAGTGTGGTTATTG
1 AAATTTCATAG-GAGGTTATCG
*
642 AATTTTCATAGGAGGTTATCG
1 AAATTTCATAGGAGGTTATCG
**
663 AAATTTCATATCAGGTTATC-
1 AAATTTCATAGGAGGTTATCG
683 AAATTT
1 AAATTT
689 GCAAAATGTG
Statistics
Matches: 90, Mismatches: 21, Indels: 6
0.77 0.18 0.05
Matches are distributed among these distances:
20 6 0.07
21 25 0.28
22 58 0.64
23 1 0.01
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.39
Consensus pattern (21 bp):
AAATTTCATAGGAGGTTATCG
Done.