Multiplexing is the Database function. Before the actual task, first you need to search for primers or probes, then open a new database and import the search results to its window. In this example a search for PCR primers was performed and all PCR primer sets were imported to the Oligo database.With primers in the database, choose "Minimize Reaction #" from the Analyze-Multiplex All menu.
After this automatic multiplexing the database window displays groups of compatible with each other primers at the bottom of the window. You may select any multiplex group by clicking on the right or left - pointing triangle, indicated by the red arrow below. When you choose a group, click the "Select" button to highlight all the primers in given group (number 1 in this example):
If you find that there are too many small groups, you may decrease "Acceptable 3'-Dimer Delta G" (in the example below to -3.5 kcal/mol; use the Change-Options menu) and repeat the multiplexing. In this case you will get less groups, and more primers in each group. The First group is the largest.