Announcement from BLAST product manager at NCBI. Cross-posting here since may be of general interest.

Primer-BLAST now has a “Primers common for a group of sequences” submission tab that allows you to design primers for a group of highly similar sequences. For example, you may want test for expression of any transcript of gene rather than a specific splice variant, so you want to design primers to cover all transcript variants.  Or you may want to design primers that will amplify the same gene in closely related bacteria strains. See the NCBI Insights post for an example search and more details.

If you have any questions or concerns, please email us at blast-help@ncbi.nlm.nih.gov