Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011651.1 Corchorus olitorius cultivar O-4 contig11684, 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, 660
Length: 1101
ACGTcount: A:0.23, C:0.29, G:0.28, T:0.21
Found at i:30 original size:20 final size:20
Alignment explanation
Indices: 7--413 Score: 367
Period size: 20 Copynumber: 22.4 Consensus size: 20
1 AAGTGT
7 CGAGTGCCATCGGCAAGTCC
1 CGAGTGCCATCGGCAAGTCC
*
27 CGAGTG----C--CAAG-GC
1 CGAGTGCCATCGGCAAGTCC
*
40 CGAGTGCCATCGGCAAGTCT
1 CGAGTGCCATCGGCAAGTCC
60 CGAGTGCCATCGGCAAGTCC
1 CGAGTGCCATCGGCAAGTCC
*
80 CGAGTG----C--CAAG-GC
1 CGAGTGCCATCGGCAAGTCC
93 CGAGTGCCATCGGCAAGTCC
1 CGAGTGCCATCGGCAAGTCC
113 CGAGTGCCATCGGCAAGTCC
1 CGAGTGCCATCGGCAAGTCC
133 CGAGTGCCATCGGCAAGTCC
1 CGAGTGCCATCGGCAAGTCC
*
153 CGAGTGCCATCGGCAACTCC
1 CGAGTGCCATCGGCAAGTCC
*
173 CGAGTGCCATCGGCAACTCC
1 CGAGTGCCATCGGCAAGTCC
*
193 CGAGTG----C--CAAG-GC
1 CGAGTGCCATCGGCAAGTCC
* *
206 CTAGTGCCATCGGCAAGTGC
1 CGAGTGCCATCGGCAAGTCC
**
226 CGAGTGCCATCGGCAAGTGT
1 CGAGTGCCATCGGCAAGTCC
*
246 CGAGTGCCATCGGCAGGTCC
1 CGAGTGCCATCGGCAAGTCC
266 CGAGTGCCATCGGCAAGTCC
1 CGAGTGCCATCGGCAAGTCC
*
286 CGAGTG----C--CAA-TGC
1 CGAGTGCCATCGGCAAGTCC
* *
299 CGAGTGCCATCGGCAGGTGC
1 CGAGTGCCATCGGCAAGTCC
319 CGAGTGCCATCGGCAAGTCC
1 CGAGTGCCATCGGCAAGTCC
*
339 CGAGTG----C--CAAG-GC
1 CGAGTGCCATCGGCAAGTCC
*
352 CGAGTGCCATCAGCAAGTCC
1 CGAGTGCCATCGGCAAGTCC
*
372 CGAGTG----C--CAAG-GC
1 CGAGTGCCATCGGCAAGTCC
385 CGAGTGCCATCGGCAAGTCC
1 CGAGTGCCATCGGCAAGTCC
405 CGAGTGCCA
1 CGAGTGCCA
414 AGGCCGAGTG
Statistics
Matches: 321, Mismatches: 24, Indels: 84
0.75 0.06 0.20
Matches are distributed among these distances:
13 42 0.13
14 22 0.07
16 6 0.02
17 6 0.02
19 22 0.07
20 223 0.69
ACGTcount: A:0.20, C:0.33, G:0.32, T:0.14
Consensus pattern (20 bp):
CGAGTGCCATCGGCAAGTCC
Found at i:86 original size:53 final size:53
Alignment explanation
Indices: 7--446 Score: 413
Period size: 53 Copynumber: 8.2 Consensus size: 53
1 AAGTGT
*
7 CGAGTGCCATCGGCAAGTCCCGAGTGCCAAGGCCGAGTGCCATCGGCAAGTCT
1 CGAGTGCCATCGGCAAGTCCCGAGTGCCAAGGCCGAGTGCCATCGGCAAGTCC
60 CGAGTGCCATCGGCAAGTCCCGAGTGCCAAGGCCGAGTGCCATCGGCAAGTCC
1 CGAGTGCCATCGGCAAGTCCCGAGTGCCAAGGCCGAGTGCCATCGGCAAGTCC
* *
113 CGAGTGCCATCGGCAAGTCCCGAGTGCCATCGGCAAGTCCCGAGTGCCATCGGCAACTCC
1 CGAGTGCCATCGGCAAGTCCCGAGTG----C--CAAG-GCCGAGTGCCATCGGCAAGTCC
* * *
173 CGAGTGCCATCGGCAACTCCCGAGTGCCAAGGCCTAGTGCCATCGGCAAGTGC
1 CGAGTGCCATCGGCAAGTCCCGAGTGCCAAGGCCGAGTGCCATCGGCAAGTCC
**
226 CGAGTGCCATCGGCAAGTGTCGAGTGCCATCGGCAGGTCCCGAGTGCCATCGGCAAGTCC
1 CGAGTGCCATCGGCAAGTCCCGAGTGCCA-----AGG--CCGAGTGCCATCGGCAAGTCC
* * * * *
286 CGAGTGCCAAT-GCCGAGTGCC-A-TCGGCAGGTGCCGAGTGCCATCGGCAAGTCC
1 CGAGTGCC-ATCGGCAAGTCCCGAGT-GCCAAG-GCCGAGTGCCATCGGCAAGTCC
* * * * *
339 CGAGTG----C--CAAG-GCCGAGTGCCATCA-G-CAAGTCCCGAGT-GCCAAG-GC
1 CGAGTGCCATCGGCAAGTCCCGAGTGCCA--AGGCCGAGTGCC-A-TCGGCAAGTCC
* *
385 CGAGTGCCATCGGCAAGTCCCGAGTGCCAAGGCCGAGTGTCATCAGCAAGTCC
1 CGAGTGCCATCGGCAAGTCCCGAGTGCCAAGGCCGAGTGCCATCGGCAAGTCC
438 CGAGTGCCA
1 CGAGTGCCA
447 AGGCCGAGTG
Statistics
Matches: 320, Mismatches: 32, Indels: 70
0.76 0.08 0.17
Matches are distributed among these distances:
46 16 0.05
47 14 0.04
48 2 0.01
50 1 0.00
51 2 0.01
52 10 0.03
53 174 0.54
54 5 0.02
55 1 0.00
56 1 0.00
57 1 0.00
58 4 0.01
59 8 0.03
60 79 0.25
61 2 0.01
ACGTcount: A:0.21, C:0.33, G:0.32, T:0.15
Consensus pattern (53 bp):
CGAGTGCCATCGGCAAGTCCCGAGTGCCAAGGCCGAGTGCCATCGGCAAGTCC
Found at i:354 original size:33 final size:33
Alignment explanation
Indices: 317--492 Score: 325
Period size: 33 Copynumber: 5.3 Consensus size: 33
307 ATCGGCAGGT
317 GCCGAGTGCCATCGGCAAGTCCCGAGTGCCAAG
1 GCCGAGTGCCATCGGCAAGTCCCGAGTGCCAAG
*
350 GCCGAGTGCCATCAGCAAGTCCCGAGTGCCAAG
1 GCCGAGTGCCATCGGCAAGTCCCGAGTGCCAAG
383 GCCGAGTGCCATCGGCAAGTCCCGAGTGCCAAG
1 GCCGAGTGCCATCGGCAAGTCCCGAGTGCCAAG
* *
416 GCCGAGTGTCATCAGCAAGTCCCGAGTGCCAAG
1 GCCGAGTGCCATCGGCAAGTCCCGAGTGCCAAG
449 GCCGAGTGCCATCGGCAAGTCCCGAGTGCCAAG
1 GCCGAGTGCCATCGGCAAGTCCCGAGTGCCAAG
482 GCCGAGTGCCA
1 GCCGAGTGCCA
493 AGGCCCAGTG
Statistics
Matches: 137, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 137 1.00
ACGTcount: A:0.22, C:0.33, G:0.32, T:0.12
Consensus pattern (33 bp):
GCCGAGTGCCATCGGCAAGTCCCGAGTGCCAAG
Found at i:488 original size:13 final size:13
Alignment explanation
Indices: 470--505 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
460 TCGGCAAGTC
470 CCGAGTGCCAAGG
1 CCGAGTGCCAAGG
483 CCGAGTGCCAAGG
1 CCGAGTGCCAAGG
*
496 CCCAGTGCCA
1 CCGAGTGCCA
506 CCAAGTGCCG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.22, C:0.36, G:0.33, T:0.08
Consensus pattern (13 bp):
CCGAGTGCCAAGG
Done.