Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold1608
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, 889
Length: 1483
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:358 original size:49 final size:49
Alignment explanation
Indices: 243--387 Score: 157
Period size: 49 Copynumber: 3.0 Consensus size: 49
233 ATTACATTGC
* * * * *
243 AACTCGGGCTCCCAATTCATAGTGGTTATACGGTCACAGGTTCAAGTAT
1 AACTCAGGCTCCCAATTGATGGTGGTTATGCGGTCATAGGTTCAAGTAT
* *
292 AACT-AGGGCTTCTAATTGATGGTGGTTATGCGGTCATAGGTTCAAGTAT
1 AACTCA-GGCTCCCAATTGATGGTGGTTATGCGGTCATAGGTTCAAGTAT
* * * * * *
341 AACTCAGGCCCCCAATTGACGGTGATTTTGCTGTCATGGGTTCAAGT
1 AACTCAGGCTCCCAATTGATGGTGGTTATGCGGTCATAGGTTCAAGT
388 TTCATGCCAC
Statistics
Matches: 79, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
49 78 0.99
50 1 0.01
ACGTcount: A:0.24, C:0.19, G:0.26, T:0.31
Consensus pattern (49 bp):
AACTCAGGCTCCCAATTGATGGTGGTTATGCGGTCATAGGTTCAAGTAT
Found at i:950 original size:49 final size:49
Alignment explanation
Indices: 863--962 Score: 137
Period size: 49 Copynumber: 2.0 Consensus size: 49
853 AGGGGTTTGA
*
863 TTATACTTGAACCCGTGATCGCATAACCACCATCAACTGGGAGCCCTAG
1 TTATACTTGAACCCGTGATCGCATAACCACCATCAACTGGGAGCCCAAG
* * *** *
912 TTATACTTGAATCCGTGATCGTATAACCATTTTGAACTGGGAGCCCAAG
1 TTATACTTGAACCCGTGATCGCATAACCACCATCAACTGGGAGCCCAAG
961 TT
1 TT
963 GCAATGCGAC
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
49 44 1.00
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (49 bp):
TTATACTTGAACCCGTGATCGCATAACCACCATCAACTGGGAGCCCAAG
Done.