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Old 10-22-2015, 01:55 AM   #2
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Location: Germany

Join Date: Apr 2012
Posts: 215

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.
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