Hello,
Sorry, I have another question about using blat for probe design. I have probes
with length ranging from 45 to 60, I am trying to find whether there are other
places in the genome with about 10% mismatch (the most) besides the 100% match
to exclude this probe from my list (it is not considered unique for
hybridization purposes). when using 95% min identity, I get a hit even with a
stretch of 8 mismatches (out of 60), since it is considered as a single gap ?
can I take these gaps into account as well when searching for a hit?
Thanks a lot,
Shlomit Amar-Farkash
The Hebrew university, Jerusalem
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