Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006303.1 Corchorus capsularis cultivar CVL-1 contig06324, 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: 25629
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:14 original size:7 final size:7
Alignment explanation
Indices: 3--431 Score: 772
Period size: 7 Copynumber: 62.7 Consensus size: 7
1 CT
3 ACCCTAA
1 ACCCTAA
10 ACCCTAA
1 ACCCTAA
17 ACCCTAA
1 ACCCTAA
24 ACCCTAA
1 ACCCTAA
31 ACCCTAA
1 ACCCTAA
38 ACCCTAA
1 ACCCTAA
45 ACCCTAA
1 ACCCTAA
52 ACCCTAA
1 ACCCTAA
59 ACCCTAA
1 ACCCTAA
66 ACCCT-A
1 ACCCTAA
72 ACCCT-A
1 ACCCTAA
78 ACCCTAA
1 ACCCTAA
85 ACCCTAA
1 ACCCTAA
92 ACCCT-A
1 ACCCTAA
98 ACCCTAA
1 ACCCTAA
105 ACCCTAA
1 ACCCTAA
112 ACCCTAA
1 ACCCTAA
119 ACCCTAA
1 ACCCTAA
126 ACCCTAA
1 ACCCTAA
133 ACCCTAA
1 ACCCTAA
140 ACCCTAA
1 ACCCTAA
147 ACCCTAA
1 ACCCTAA
154 ACCCT-A
1 ACCCTAA
160 ACCCTAA
1 ACCCTAA
167 ACCCTAA
1 ACCCTAA
174 ACCCTAA
1 ACCCTAA
181 ACCCTAA
1 ACCCTAA
188 ACCCTAA
1 ACCCTAA
195 ACCCTAA
1 ACCCTAA
202 ACCCTAA
1 ACCCTAA
209 ACCCTAA
1 ACCCTAA
216 ACCCTAA
1 ACCCTAA
223 ACCCTAA
1 ACCCTAA
230 ACCCTAAA
1 ACCCT-AA
238 ACCCTAA
1 ACCCTAA
245 ACCCTAA
1 ACCCTAA
252 ACCCTAA
1 ACCCTAA
259 ACCCTAA
1 ACCCTAA
266 ACCCTAA
1 ACCCTAA
273 ACCCTAA
1 ACCCTAA
280 ACCCTAA
1 ACCCTAA
287 ACCCTAA
1 ACCCTAA
294 ACCCTAA
1 ACCCTAA
301 ACCCTAA
1 ACCCTAA
308 ACCCTAA
1 ACCCTAA
315 ACCCTAA
1 ACCCTAA
322 ACCCTAA
1 ACCCTAA
329 ACCCTAA
1 ACCCTAA
336 ACCCTAA
1 ACCCTAA
343 ACCCTAA
1 ACCCTAA
350 ACCCT-A
1 ACCCTAA
356 A-CCTAA
1 ACCCTAA
362 ACCCTAA
1 ACCCTAA
369 ACCCT-A
1 ACCCTAA
375 ACCCT-A
1 ACCCTAA
381 ACCCTAA
1 ACCCTAA
388 ACCCTAA
1 ACCCTAA
395 ACCCT-A
1 ACCCTAA
401 ACCCT-A
1 ACCCTAA
407 ACCCTAA
1 ACCCTAA
414 ACCCT-A
1 ACCCTAA
420 ACCCTAA
1 ACCCTAA
427 ACCCT
1 ACCCT
432 GAGTGTCTTT
Statistics
Matches: 413, Mismatches: 0, Indels: 18
0.96 0.00 0.04
Matches are distributed among these distances:
5 3 0.01
6 58 0.14
7 345 0.84
8 7 0.02
ACGTcount: A:0.41, C:0.44, G:0.00, T:0.15
Consensus pattern (7 bp):
ACCCTAA
Found at i:2930 original size:29 final size:29
Alignment explanation
Indices: 2894--2951 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
2884 TCTCGTTTTT
2894 AAAAGTTAAGGGGCCAATTTGTCCCAAAA
1 AAAAGTTAAGGGGCCAATTTGTCCCAAAA
2923 AAAAGTTAAGGGGCCAATTTGTCCCAAAA
1 AAAAGTTAAGGGGCCAATTTGTCCCAAAA
2952 TGGATAATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.41, C:0.17, G:0.21, T:0.21
Consensus pattern (29 bp):
AAAAGTTAAGGGGCCAATTTGTCCCAAAA
Found at i:6699 original size:31 final size:31
Alignment explanation
Indices: 6661--6720 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
6651 AAAGTCATTA
*
6661 ATGAATATTGTGATTATTCATAAATCAAGAG
1 ATGAATATTGTAATTATTCATAAATCAAGAG
*
6692 ATGAATATTGTAATTATTCATGAATCAAG
1 ATGAATATTGTAATTATTCATAAATCAAG
6721 TGTTCTCTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.42, C:0.07, G:0.15, T:0.37
Consensus pattern (31 bp):
ATGAATATTGTAATTATTCATAAATCAAGAG
Found at i:16383 original size:120 final size:120
Alignment explanation
Indices: 16170--16417 Score: 496
Period size: 120 Copynumber: 2.1 Consensus size: 120
16160 CATTTTGATC
16170 CTCAGGCTTAAACTTGTCTGAAGTTTGAGTATGCAATCAAAAACTACATGGACAGATGCATTTAA
1 CTCAGGCTTAAACTTGTCTGAAGTTTGAGTATGCAATCAAAAACTACATGGACAGATGCATTTAA
16235 TGTTTTGTTACCCCCATTTTAAGAAAGGAATAATCTAAGAAACTCTATCTATTTT
66 TGTTTTGTTACCCCCATTTTAAGAAAGGAATAATCTAAGAAACTCTATCTATTTT
16290 CTCAGGCTTAAACTTGTCTGAAGTTTGAGTATGCAATCAAAAACTACATGGACAGATGCATTTAA
1 CTCAGGCTTAAACTTGTCTGAAGTTTGAGTATGCAATCAAAAACTACATGGACAGATGCATTTAA
16355 TGTTTTGTTACCCCCATTTTAAGAAAGGAATAATCTAAGAAACTCTATCTATTTT
66 TGTTTTGTTACCCCCATTTTAAGAAAGGAATAATCTAAGAAACTCTATCTATTTT
16410 CTCAGGCT
1 CTCAGGCT
16418 CCAGCTGAAA
Statistics
Matches: 128, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
120 128 1.00
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.34
Consensus pattern (120 bp):
CTCAGGCTTAAACTTGTCTGAAGTTTGAGTATGCAATCAAAAACTACATGGACAGATGCATTTAA
TGTTTTGTTACCCCCATTTTAAGAAAGGAATAATCTAAGAAACTCTATCTATTTT
Done.