USEARCH v12
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Default index parameters


Default values of index parameters are determined from the command name and sequence type (nucleotide or protein). UBLAST parameters apply to the ublast command, USEARCH parameters apply to usearch_ and cluster_ commands.
Parameter UBLAST
protein 		USEARCH
protein 		UBLAST
nucleotide 		USEARCH
nucleotide
-wordlength (use pattern) 5 8 8
-pattern 10111011 (use kmers) (use kmers) (use kmers)
-alpha (see below) aa nt nt
- dbstep 1 1 1 1
-dbaccel 1.0 1.0 1.0 1.0
-slots (don't hash) (don't hash) (don't hash) (don't hash)

The default alphabet for protein ublast is A,KR,DENQ,C,G,H,ILVM,FYW,P,ST.