In the NCBI/local BLAST dialogs, you need to add a checkbox "BLAST selected primer pairs", which should appear (and be checked by default) only if primers/parent groups of primers that were found using Primer3 are selected (at least one pair of primers from the same group ). We define the menu item “Create PCR Product...” in a same way, if you want to see how this is done there.
Run BLAST for each primer pair. One primer - one BLAST. Only the results that both primers have are shown (check by accession number) and are marked with a pair of joined annotations adjacent to the primers (ATTENTION: if possible, run one blast per pair of primers, I’m not sure if this is possible or easy) .
Need to edit qualifiers. Either one qualifier contains information for both primers (if it can be combined), or save both qualifiers with postfixes like _forward and _reverse.
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UGENE-8043 Help: Add description in Remote Blast paragraph for "BLAST selected primer pairs" option
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