I'm using blastn (https://anaconda.org/bioconda/blast) to find similar sequences of a target sequence against a FASTA file. But my read is quite short (68 bases). I realised that blastn won't report any hit. But there is actually a very good one in the FASTA file after checking manually.

Here is the query sequence:

$ cat query.fa
>query read
GGAGTAGGCGCGAGCGGCAGGAGGCGGGCAGGCGGAGGGCGAGGCAGGGAGGCGCCGCCTGGAGCGCA

And this is the "good one" that I found manually (I picked it out from the original FASTA file and save it as a single FASTA file and also created the BLAST database from it using makeblastdb):

$ cat db.fa
>database read
GAGTAGGCGCGAGCTAAGCAGGAGGCGGAGGCGGAGGCGGAGGGCGAGGGGCGGGGAGCGCCGCCTGGAGCGCGGCAG

And the command that I used is:

$ blastn -db db.fa -query query.fa -outfmt "6 qseqid sseqid evalue length pident bitscore ppos"

(then no hit was reported)

But they two can actually match very well:

database           1 -GAGTAGGCGCGAGCTAAGCAGGAGGCGGAGGCGGAGGCGGAGGGCGAGG     49
                      ||||||||||||||  .|||||||||||    |.|||||||||||||
query              1 GGAGTAGGCGCGAGC--GGCAGGAGGCGG----GCAGGCGGAGGGCGA--     42

database          50 GGCGGGGA-GCGCCGCCTGGAGCGCGGCAG     78
                     |||.|||| ||||||||||||||||.
query             43 GGCAGGGAGGCGCCGCCTGGAGCGCA----     68

(above is the alignment result by needle)

Is there any parameter of blastn that I can adjust to relax the BLAST requirement cutoff?