My November blog posts discussing the BLAST+ tools behaviour with an alignment limit setting (see What BLAST's max-target-sequences doesn't do, and the links from it), touched on database order, which comes into play as a tie breaker.
Well, how is the BLAST database order defined? It turns out to be the reverse of the FASTA file used with makeblastdb, or in other words: Last-in, First-out (LIFO).
