Can I BLAST primers or short sequences?

You should be aware that there are issues with BLAST when searching for short sequences.  Blast is not guaranteed to find all occurrences of a short sequence in a database. Statistically, even with the word size set to 7 (the minimum for DNA searches) BLAST will typically miss 40% of possible hits when dealing with sequences of 20bp.   In addition to potentially missing a large percentage of possible matches, any matches Blast does produce will be local alignments rather than full length matches. 

If you want an alternative to Test with Saved Primers because ‘Test with Saved Primers’ is computationally intense, we recommend using the Map to Reference function rather than Blast.  The Map to Reference function is optimised for short sequence matching. 

Note that if the primer has a 5’ extension this should be annotated onto the sequence correctly and then Geneious will ignore that region when primer testing. If this isn’t done, the primer will not match. 

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