Hi all,

I've designed primers to identify a strain of interest.

Just to be sure that the primers matche only the genome of this strain and no other genomes, I am using blastn analysis.

My input file is :

    >Seq_1 
    ATGTGCTAGCTATGGCG
    >Seq_2 
    GTCGGTAATCGATTCGA

And my database is a multifasta file containing several genomes including the genome of my strain of interest.

My command line is the following :

    > blastn -query Sequences.fasta -db genomes.fasta -out Results_blastn.txt -outfmt 6 -evalue 0.1

**The results file is blank.**

I do not understand how I've got no results even on the genome of my strain of interest ...

Do someone have an idea on how I should proceed to fix this issue?

Thank you so much in advance for your much appreciated help!

Audrey
Just add `-task blastn-short` to your command. By default, blastn uses megablast (optimized for highly similar long sequences).