[Genome] 2 questions about BLAT

[Christian Arnold]

Hello,

I am using BLAT for research and I have two questions regarding the 
configuration of BLAT

1) Is there a way to define that the entered sequence has to be found in 
the whole length? Often, I have alignments where the first X bases are 
ignored because they did not had an significant alignment. But the 
identity score ignores these parts which is not what I want to have. The 
Identity number should include the whole sequence.

2) Is there an easy way to get the aligned sequence (not the one which I 
typed in) as a fasta file in its complete length?

I read the Manual but I didn't found anything, so it would be nice if 
you can help me with these issues...


best
Christian