In the BLAST+ packages, you can align two sequences instead of searching a database:
tblastn -query seq1.fa -subject seq1.fa
The web BLAST documentation states that e-values are calculated from the nr database:
Because BLAST 2 Sequences uses the size of the current nucleotide or protein nr database to calculate Expect values, you may need to significantly increase the Expect threshold in order to see shorter alignments.
However, the command-line documentation explicitly states that you cannot provide both a database and a
-db <String> BLAST database name * Incompatible with: subject, subject_loc -subject <File_In> Subject sequence(s) to search * Incompatible with: db, gilist, seqidlist, negative_gilist, db_soft_mask, db_hard_mask
How is the e-value calculated when using BLAST-2-Sequences on the command line? (I am fairly certain I do not have the nr database downloaded.)