Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013037.1 Corchorus olitorius cultivar O-4 contig13070, 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: 2486
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Found at i:252 original size:17 final size:16
Alignment explanation
Indices: 232--279 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 16
222 TTCGGGTTCA
232 GGCTCGGGTCGGGATCG
1 GGCTCGGGTCGGG-TCG
*
249 GGCTCGGACTCGGGTCG
1 GGCTCGG-GTCGGGTCG
*
266 GGTTCGGGCTCGGG
1 GGCTCGGG-TCGGG
280 CTGCCTCGGG
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 21 0.81
18 5 0.19
ACGTcount: A:0.04, C:0.25, G:0.52, T:0.19
Consensus pattern (16 bp):
GGCTCGGGTCGGGTCG
Found at i:260 original size:23 final size:23
Alignment explanation
Indices: 234--278 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
224 CGGGTTCAGG
234 CTCGGGTCGGGATCGGGCTCGGA
1 CTCGGGTCGGGATCGGGCTCGGA
*
257 CTCGGGTCGGGTTCGGGCTCGG
1 CTCGGGTCGGGATCGGGCTCGG
279 GCTGCCTCGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.04, C:0.27, G:0.49, T:0.20
Consensus pattern (23 bp):
CTCGGGTCGGGATCGGGCTCGGA
Found at i:296 original size:6 final size:6
Alignment explanation
Indices: 232--281 Score: 59
Period size: 6 Copynumber: 8.7 Consensus size: 6
222 TTCGGGTTCA
* * *
232 GGCTCG GG-TCG GGATCG GGCTCG GACTCG GG-TCG GGTTCG GGCTCG
1 GGCTCG GGCTCG GGCTCG GGCTCG GGCTCG GGCTCG GGCTCG GGCTCG
278 GGCT
1 GGCT
282 GCCTCGGGTT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
5 10 0.26
6 28 0.74
ACGTcount: A:0.04, C:0.26, G:0.50, T:0.20
Consensus pattern (6 bp):
GGCTCG
Found at i:304 original size:16 final size:16
Alignment explanation
Indices: 285--327 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
275 TCGGGCTGCC
*
285 TCGGGTTCGGGTATTT
1 TCGGGTTCGGGTAATT
* *
301 TCGGGCTCGGATAATT
1 TCGGGTTCGGGTAATT
317 TCGGGTTCGGG
1 TCGGGTTCGGG
328 CTCGGGCGGG
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.09, C:0.16, G:0.40, T:0.35
Consensus pattern (16 bp):
TCGGGTTCGGGTAATT
Found at i:341 original size:22 final size:22
Alignment explanation
Indices: 222--343 Score: 66
Period size: 23 Copynumber: 5.3 Consensus size: 22
212 TTCAAATTAT
*
222 TTCGGGTTCAGGCTCGGGTCGGG
1 TTCGGGTTCGGGCTCGGG-CGGG
* * *
245 ATCGGGCTCGGACTCGGGTCGGG
1 TTCGGGTTCGGGCTCGGG-CGGG
* **
268 TTCGGGCTCGGGCT-GCCTCGGG
1 TTCGGGTTCGGGCTCG-GGCGGG
*****
290 TTCGGGTATTTTCGGGCTCGGATAAT
1 TTCGGG----TTCGGGCTCGGGCGGG
316 TTCGGGTTCGGGCTCGGGCGGG
1 TTCGGGTTCGGGCTCGGGCGGG
338 TTCGGG
1 TTCGGG
344 ACGTTGACTT
Statistics
Matches: 73, Mismatches: 20, Indels: 13
0.69 0.19 0.12
Matches are distributed among these distances:
22 28 0.38
23 31 0.42
26 13 0.18
27 1 0.01
ACGTcount: A:0.06, C:0.23, G:0.45, T:0.26
Consensus pattern (22 bp):
TTCGGGTTCGGGCTCGGGCGGG
Found at i:520 original size:29 final size:27
Alignment explanation
Indices: 455--508 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
445 TATAGTATAG
*
455 ATTAATCCAATACTTTTTTTTATTCAA
1 ATTAATCCAATACTTTATTTTATTCAA
482 ATTAATCCAATACTTTATTTT-TTCAA
1 ATTAATCCAATACTTTATTTTATTCAA
508 A
1 A
509 AAATTATTCC
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
26 6 0.23
27 20 0.77
ACGTcount: A:0.35, C:0.15, G:0.00, T:0.50
Consensus pattern (27 bp):
ATTAATCCAATACTTTATTTTATTCAA
Found at i:1393 original size:34 final size:36
Alignment explanation
Indices: 1350--1423 Score: 107
Period size: 34 Copynumber: 2.1 Consensus size: 36
1340 GGCCTGCCTG
1350 GCGCGGCCCAAACG-ATAGGCCAGGCGC-CAGGCCA
1 GCGCGGCCCAAACGCATAGGCCAGGCGCACAGGCCA
* * *
1384 GCGCGGCCCAAGCGCCTAGGCCAGGCGCACGGGCCA
1 GCGCGGCCCAAACGCATAGGCCAGGCGCACAGGCCA
1420 GCGC
1 GCGC
1424 ATGGCCCAGC
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
34 13 0.37
35 12 0.34
36 10 0.29
ACGTcount: A:0.19, C:0.41, G:0.38, T:0.03
Consensus pattern (36 bp):
GCGCGGCCCAAACGCATAGGCCAGGCGCACAGGCCA
Found at i:1538 original size:5 final size:6
Alignment explanation
Indices: 1523--1557 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
1513 GCCCAATGTG
1523 AAATAA AAAT-A AAAT-A AAATAA AAATAA AAATAA A
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA A
1558 GAAAATAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 10 0.36
6 18 0.64
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
AAATAA
Found at i:1544 original size:16 final size:17
Alignment explanation
Indices: 1523--1557 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
1513 GCCCAATGTG
1523 AAATAAAAAT-AAAATA
1 AAATAAAAATAAAAATA
1539 AAATAAAAATAAAAATA
1 AAATAAAAATAAAAATA
1556 AA
1 AA
1558 GAAAATAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 10 0.56
17 8 0.44
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (17 bp):
AAATAAAAATAAAAATA
Done.