nohup /home/shah/local_progs/blat_dir/blat -fine -repMatch=1000000 -minIdentity=100 /home/shah/drosophila_annotations/dmel3_apr_2006/dmel3_apr_2006.fasta agilent_dm2_probe_sequences_5_215453.fasta agilent_dm2_probe_sequences_5_215453.psl &
explanation :
-fine
-repMatch=1000000 - number when tiles are considered overused
-minIdentity=100 - pick identical matches
e.g. for mapping probes to the reference genomes.
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