There is no direct option like that but you can set percentage identity filter with
However, this is only for reporting. BLAST will still perform all the alignments. That is why I suggested you to use bowtie.
EDIT-1 (getting long for comment)
If you want a word type of search then use the
-n option. But it always starts from the 5'end which is quite justified in case of miRNA because the seed region is in the 5'.
0 means no mismatch in seed region.
-l option defines the seed length; I would advise that you use something like
-e refers to maximum mismatches in the non seed region but it is not the number of mismatches; it means maximum tolerated sum of phred score of mismatches (fasta files are assigned a default phred score of 40 at all residues. So, for 2 mismatches you have to mention
Yes. Increasing mismatch and gap penalties would make the search more stringent if you have already specified a cutoff on score.