Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01004356.1 Corchorus olitorius cultivar O-4 contig04370, 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, 622
Length: 1038
ACGTcount: A:0.38, C:0.17, G:0.19, T:0.25
Found at i:265 original size:29 final size:29
Alignment explanation
Indices: 205--383 Score: 189
Period size: 29 Copynumber: 6.1 Consensus size: 29
195 CCAAAGAGGA
* * *
205 CCTAGAGTATGCAAAAATGACCAAACTACC
1 CCTAGA-TGTGCAAAAATGACCAAAATGCC
* * * *
235 CCAAAATGTGTAAAAATGACCATAATGCC
1 CCTAGATGTGCAAAAATGACCAAAATGCC
* *
264 CCTGGATGGGCAAAAATGACCAAAATGCC
1 CCTAGATGTGCAAAAATGACCAAAATGCC
* *
293 CCTAGATGCGCAAAAATGACCATAATGCC
1 CCTAGATGTGCAAAAATGACCAAAATGCC
* *
322 CCTGGATGTGCAAAAATTACCAAAATGCC
1 CCTAGATGTGCAAAAATGACCAAAATGCC
* * *
351 CCT-GAGCGAGCAAAAATGACCGAAATGCC
1 CCTAGA-TGTGCAAAAATGACCAAAATGCC
380 CCTA
1 CCTA
384 TGAGAGTCAA
Statistics
Matches: 123, Mismatches: 24, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
28 2 0.02
29 117 0.95
30 4 0.03
ACGTcount: A:0.40, C:0.26, G:0.18, T:0.17
Consensus pattern (29 bp):
CCTAGATGTGCAAAAATGACCAAAATGCC
Found at i:353 original size:58 final size:58
Alignment explanation
Indices: 214--382 Score: 218
Period size: 58 Copynumber: 2.9 Consensus size: 58
204 ACCTAGAGTA
* * * * * *
214 TGCAAAAATGACCAAACTACCCCAAAATGTGTAAAAATGACCATAATGCCCCTGGATG
1 TGCAAAAATGACCAAAATGCCCCTAGATGCGCAAAAATGACCATAATGCCCCTGGATG
*
272 GGCAAAAATGACCAAAATGCCCCTAGATGCGCAAAAATGACCATAATGCCCCTGGATG
1 TGCAAAAATGACCAAAATGCCCCTAGATGCGCAAAAATGACCATAATGCCCCTGGATG
*
330 TGCAAAAATTACCAAAATGCCCCT-GA-GCGAGCAAAAATGACCGA-AATGCCCCT
1 TGCAAAAATGACCAAAATGCCCCTAGATGC--GCAAAAATGACC-ATAATGCCCCT
383 ATGAGAGTCA
Statistics
Matches: 99, Mismatches: 9, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
56 2 0.02
57 2 0.02
58 94 0.95
59 1 0.01
ACGTcount: A:0.40, C:0.26, G:0.18, T:0.17
Consensus pattern (58 bp):
TGCAAAAATGACCAAAATGCCCCTAGATGCGCAAAAATGACCATAATGCCCCTGGATG
Found at i:402 original size:58 final size:56
Alignment explanation
Indices: 246--412 Score: 191
Period size: 58 Copynumber: 2.9 Consensus size: 56
236 CAAAATGTGT
* *
246 AAAAATGACCATAATGCCCCTGGATGGGCAAAAATGACCAAAATGCCCCTAGATGCGC
1 AAAAATGACCATAATGCCCCTGGATGTGC-AAAATTACCAAAATGCCCCT-GATGCGC
304 AAAAATGACCATAATGCCCCTGGATGTGCAAAAATTACCAAAATGCCCCTGA-GCGAGC
1 AAAAATGACCATAATGCCCCTGGATGTGC-AAAATTACCAAAATGCCCCTGATGC--GC
362 AAAAATGACCGA-AATGCCCCTATGAGA-GT-C-AAATTAACCAAAATGCCCCTG
1 AAAAATGACC-ATAATGCCCC--TG-GATGTGCAAAATT-ACCAAAATGCCCCTG
413 GGCTTGCGAA
Statistics
Matches: 100, Mismatches: 2, Indels: 14
0.86 0.02 0.12
Matches are distributed among these distances:
56 2 0.02
57 7 0.07
58 83 0.83
59 2 0.02
60 4 0.04
61 2 0.02
ACGTcount: A:0.39, C:0.26, G:0.19, T:0.17
Consensus pattern (56 bp):
AAAAATGACCATAATGCCCCTGGATGTGCAAAATTACCAAAATGCCCCTGATGCGC
Found at i:405 original size:29 final size:28
Alignment explanation
Indices: 247--412 Score: 108
Period size: 29 Copynumber: 5.8 Consensus size: 28
237 AAAATGTGTA
* * *
247 AAAATGACCATAATGCCCCTG-GATGGGC
1 AAAATTACCAAAATGCCCCTGAGA-GAGC
* *
275 AAAAATGACCAAAATGCCCCT-AGATGCGC
1 -AAAATTACCAAAATGCCCCTGAGA-GAGC
* * *
304 AAAAATGACCATAATGCCCCTG-GATGTGC
1 -AAAATTACCAAAATGCCCCTGAGA-GAGC
*
333 AAAAATTACCAAAATGCCCCTGAGCGAGC
1 -AAAATTACCAAAATGCCCCTGAGAGAGC
* *
362 AAAAATGACCGAAATGCCCCT-ATGAGAGTC
1 -AAAATTACCAAAATGCCCCTGA-GAGAG-C
392 -AAATTAACCAAAATGCCCCTG
1 AAAATT-ACCAAAATGCCCCTG
413 GGCTTGCGAA
Statistics
Matches: 117, Mismatches: 13, Indels: 13
0.82 0.09 0.09
Matches are distributed among these distances:
28 5 0.04
29 110 0.94
30 2 0.02
ACGTcount: A:0.39, C:0.26, G:0.19, T:0.17
Consensus pattern (28 bp):
AAAATTACCAAAATGCCCCTGAGAGAGC
Found at i:407 original size:87 final size:87
Alignment explanation
Indices: 240--413 Score: 212
Period size: 87 Copynumber: 2.0 Consensus size: 87
230 CTACCCCAAA
* * *
240 ATGTGTAAAAATGACCATAATGCCCCTGGATGGGCAAAAATGACCAAAATGCCCCTAGATGCGCA
1 ATGTGCAAAAATGACCAAAATGCCCCTGGATGGGCAAAAATGACCAAAATGCCCCTAGATGAGCA
* *
305 AAAATGACCATAATGCCCCTGG
66 AAAATAACCAAAATGCCCCTGG
* *
327 ATGTGCAAAAATTACCAAAATGCCCCT-GA-GCGAGCAAAAATGACCGAAATGCCCCTATGA-GA
1 ATGTGCAAAAATGACCAAAATGCCCCTGGATG-G-GCAAAAATGACCAAAATGCCCCTA-GATGA
*
389 GTC-AAATTAACCAAAATGCCCCTGG
63 G-CAAAAATAACCAAAATGCCCCTGG
414 GCTTGCGAAT
Statistics
Matches: 75, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
85 1 0.01
86 3 0.04
87 68 0.91
88 3 0.04
ACGTcount: A:0.38, C:0.25, G:0.20, T:0.18
Consensus pattern (87 bp):
ATGTGCAAAAATGACCAAAATGCCCCTGGATGGGCAAAAATGACCAAAATGCCCCTAGATGAGCA
AAAATAACCAAAATGCCCCTGG
Done.