Over the past few releases of MacVector, we have been adding a lot of functionality to the Quicktest Primer and Primer Design/Test Pairs interfaces and slowly removing the old outdated primer design functions. The general strategy is that anything you need to do with a single primer, you can accomplish using the Quicktest Primer interface. Any manipulations to handle pairs of primers should be run through the Primer Design/Test Pairs interface.
MacVector 13 made some changes to the Primer Design/Test Pairs interface to allow it to completely substitute for the old Test PCR Primer Pairs algorithm that has now been removed from the Primers sub-menu. It’s pretty simple to test primers using the Primer Design/Test Pairs interface: Open the target sequence, choose Analyze | Primers | Primer Design/Test Pairs and select Use this primer for both the left and right primer. This will let you type/paste sequence data into each of the primer edit boxes and will also change the mode to Test Primer Pair.
When you click on the Test button, MacVector bypasses the normal Primer3 analysis and instead runs an updated variant of the original Test PCR Primer Pair algorithm. The results are presented in a very similar format to the old algorithm, listing the potential problems in red text. The characteristics of the potential product are listed in the Spreadsheet result view, including the recommended annealing temperature to use for the reaction. For more details on using this functionality, please check out this blog post.