[Genome] Relation between minMatch and score

[Jessica Wasserscheid]

Hi,

I am running gfClient v33 with tileSize 11 and stepSize 5 with the 
default minMatch 2.
I understand how 2 tiles will trigger an alignment, and the psl output 
could then report weak alignments with low scores along with a better 
and bigger alignment for the same sequence.
I know the tiles don't have to overlap, but could you explain how I can 
end up with *only one hit *for a sequence for which the score is 11 or 13 ?
I would expect the score to be at least 16, or if it is lower I would 
expect to have another hit for that sequence.

Thanks

Jessica Wasserscheid

-- 
Jessica Wasserscheid
Bioinformatician, Vervet Monkey Genomics Project
http://www.genomequebec.mcgill.ca/compgen/submit_db/vervet_project
McGill University & Genome Quebec Innovation Center
740 Dr. Penfield Avenue Room 7211
Montreal, Quebec Canada, H3A 1A4
 
Email : jessica.wasserscheid at mail.mcgill.ca
Phone : (001) 514-398-3311 #00476