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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.

  • #2
    In my hands it gives multiple hits, if they exist. Maybe your query only matches one sequence in the target?

    Comment


    • #3
      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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