View Single Post
Old 10-22-2015, 01:55 AM   #2
WhatsOEver
Senior Member
 
Location: Germany

Join Date: Apr 2012
Posts: 215
Default

Though I'm not familiar with NCBI primer-blast, it seems to be a megablast/blastn related problem. When you are running a standard nucleotide blast, megablast is selected by default, but it doesn't work (well) with short input sequences (like primers). Under "program selection", choose "Somewhat similar sequences (blastn)" and try again.
WhatsOEver is offline   Reply With Quote