Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016427.1 Corchorus capsularis cultivar CVL-1 contig16448, 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: 28874
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.28
Found at i:12279 original size:1 final size:1
Alignment explanation
Indices: 12268--12355 Score: 77
Period size: 1 Copynumber: 88.0 Consensus size: 1
12258 GGACAACTCC
* ** * * * *
12268 AAAACAAAAAAATCAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAACAAAACAAAACAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * *
12333 ACAAACAAAACAAAACAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAA
12356 TTTCTTCAAA
Statistics
Matches: 66, Mismatches: 21, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 66 1.00
ACGTcount: A:0.88, C:0.11, G:0.00, T:0.01
Consensus pattern (1 bp):
A
Found at i:12288 original size:10 final size:9
Alignment explanation
Indices: 12268--12355 Score: 104
Period size: 9 Copynumber: 9.3 Consensus size: 9
12258 GGACAACTCC
12268 AAAACAAAA
1 AAAACAAAA
*
12277 AAATCAAAA
1 AAAACAAAA
*
12286 AAAAAAAAA
1 AAAACAAAA
*
12295 AAAAAAAAA
1 AAAACAAAA
12304 AAAACAAAAAA
1 AAAAC--AAAA
12315 AAAACAAAA
1 AAAACAAAA
12324 CAAAACAAAA
1 -AAAACAAAA
*
12334 CAAACAAAA
1 AAAACAAAA
12343 CAAAACAAAA
1 -AAAACAAAA
12353 AAA
1 AAA
12356 TTTCTTCAAA
Statistics
Matches: 69, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
9 43 0.62
10 17 0.25
11 9 0.13
ACGTcount: A:0.88, C:0.11, G:0.00, T:0.01
Consensus pattern (9 bp):
AAAACAAAA
Found at i:12290 original size:14 final size:13
Alignment explanation
Indices: 12267--12355 Score: 101
Period size: 13 Copynumber: 6.6 Consensus size: 13
12257 AGGACAACTC
*
12267 CAAAACAAAAAAAT
1 CAAAA-AAAAAAAA
12281 CAAAAAAAAAAAA
1 CAAAAAAAAAAAA
12294 -AAAAAAAAAAAA
1 CAAAAAAAAAAAA
12306 -AACAAAAAAAAAA
1 CAA-AAAAAAAAAA
12319 CAAAACAAAACAAAA
1 CAAAA-AAAA-AAAA
*
12334 CAAACAAAACAAAA
1 CAAA-AAAAAAAAA
12348 CAAAAAAA
1 CAAAAAAA
12356 TTTCTTCAAA
Statistics
Matches: 68, Mismatches: 2, Indels: 11
0.84 0.02 0.14
Matches are distributed among these distances:
12 14 0.21
13 23 0.34
14 19 0.28
15 11 0.16
16 1 0.01
ACGTcount: A:0.87, C:0.12, G:0.00, T:0.01
Consensus pattern (13 bp):
CAAAAAAAAAAAA
Found at i:26342 original size:6 final size:6
Alignment explanation
Indices: 26333--26358 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
26323 TTAAGTAGAT
26333 TGGGTG TGGGTG TGGGTG TGGGTG TG
1 TGGGTG TGGGTG TGGGTG TGGGTG TG
26359 AATGAGGTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.00, G:0.65, T:0.35
Consensus pattern (6 bp):
TGGGTG
Found at i:27448 original size:18 final size:18
Alignment explanation
Indices: 27425--27462 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
27415 ATCTATTTAA
27425 GAAATTACTCCTTGTGGT
1 GAAATTACTCCTTGTGGT
*
27443 GAAATTATTCCTTGTGGT
1 GAAATTACTCCTTGTGGT
27461 GA
1 GA
27463 GTGTGGCGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.24, C:0.13, G:0.24, T:0.39
Consensus pattern (18 bp):
GAAATTACTCCTTGTGGT
Done.