My lab works with geminiviruses that have a circular genome. While testing previously published primers using the NCBI primer blast application, I realized that the software does not handle primer pairs where the forward primer is 'behind' the reverse primer when the sequence is linearized. The primer pair worked just fine when I used Primer 3 in Geneious with a local (but small) database. Is there a workaround, or is there something I am doing wrong, as I would like to see the entire scope of what the primer pair would bind to?

Many Thanks