Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold3821
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, 388
Length: 648
ACGTcount: A:0.38, C:0.27, G:0.02, T:0.33
Found at i:228 original size:7 final size:7
Alignment explanation
Indices: 222--268 Score: 76
Period size: 7 Copynumber: 6.6 Consensus size: 7
212 AAAACATAAA
222 CCCTAAAC
1 CCCT-AAC
230 CCCTAAC
1 CCCTAAC
237 CCCTAAC
1 CCCTAAC
*
244 CTCTAAC
1 CCCTAAC
251 CCCTAAC
1 CCCTAAC
258 CCCTAAC
1 CCCTAAC
265 CCCT
1 CCCT
269 CTTTTACAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
7 33 0.89
8 4 0.11
ACGTcount: A:0.28, C:0.55, G:0.00, T:0.17
Consensus pattern (7 bp):
CCCTAAC
Found at i:391 original size:7 final size:7
Alignment explanation
Indices: 381--449 Score: 59
Period size: 7 Copynumber: 9.9 Consensus size: 7
371 CACTAACTCT
*
381 TAACCTC
1 TAACCCC
*
388 TAACCTC
1 TAACCCC
395 TAACCCC
1 TAACCCC
402 TAACCCC
1 TAACCCC
*
409 TAACCCT
1 TAACCCC
**
416 TAACTAC
1 TAACCCC
423 TAACCCC
1 TAACCCC
*
430 CAACCCC
1 TAACCCC
*
437 CAACACCC
1 TAAC-CCC
445 -AACCC
1 TAACCC
450 TTAAACATTA
Statistics
Matches: 53, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
6 2 0.04
7 48 0.91
8 3 0.06
ACGTcount: A:0.32, C:0.52, G:0.00, T:0.16
Consensus pattern (7 bp):
TAACCCC
Done.