primers dont match FASTA gene sequence... 'm confused - (Nov/20/2007 )
Exactly. Blast will match against the entire genome (or whatever is in Genbank). If it tells you it matches a gene, and you then go find that gene, then the gene sequence may not necessarily include the location bound by your primer. Blast is telling you exactly which sequence it matched, and which set of bases within that sequence match. If you download that exact sequence, and look at that exact location, you should find the matching bases. But if you download some gene, even one from the same organism, or perhaps even one as a subset of the specific sequence which matches, then there is a chance the match will be outside the exact boundaries of the gene.
I FOUND THE MATCHING SITES!! and also confirmed entire sequence for the PCR product! Thank you so much for your very usefull advice. I am gratefull. The binding site for the other member of the primer pair was indeed in an intron which was not part of the FASTA sequence of the gene. (Also lots of thanx for all the people who were nice enough to respond to my question)