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Dear Sushim,

apologies for the slow reply.
No unfortunately I don’t think there is a way to retain only the best hit per region inside a large query. The filtering criteria apply only to the database sequences…
(it may be possible to program something using ruby or another scripting language)

kind regards,


Hi Sushim,

I once wrote a ruby script to do this, although for a different reason. Hopefully it should still work.


Note you’ll also need blast_mask.rb from the same place available in your $PATH.

Hope that helps.