I agree with cliffbeall - it will list multiple hits if they exist.
Perhaps use the -out=blast option to get a traditional BLAST output file.
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In my hands it gives multiple hits, if they exist. Maybe your query only matches one sequence in the target?Leave a comment:
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Multiple hits from BLAT?
Hi guys,
Is there any option of BLAT to find multiple hits of one query? The name of BLAT is 'blast like alignment tool' so I thought it would produce multiple hits.
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