[Genome] question about blat gfserver

[SaraH Chahrazed GUETTOUCHE]

hello
I have downloaded the executable blatSuite.34.zip (Linux vr).

I have 13930 files.fa (mouse seq gene) and I have more than 16000 files.fa of UTR_seq. How I must make to search where UTR_seq which match (occur) the best with the gene (using fgServer).
thanks
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