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Define a "Hit" (based on some cutoff- evalue, score etc) Get output in the tabular format Count number of hits per query — it is usually given in the header; if you want to look for some selected hits (based on some cutoff, then you can parse the file and find out) Example file (header): # BLASTN 2.2.27+ # Query: TCONS_00036712 gene=XLOC_017996 # ...

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