The Primer3 plugin is a port of the Primer3 tool, v. 2.6.1. It is intended to pick primers from a DNA sequence.
To use the Primer3, open a DNA sequence and select the Analyze ‣ Primer3 context menu item. The dialog will appear:
All available parameters are the same as in the original Primer3.
NOTE: The "Primer Designer" dialog has a detailed description of each parameter - just move the mouse cursor to the parameter you're interested about (or its name) and the tooltip appears. Due to this fact, there are no detailed description in this file.
However there is one additional feature available which is not originally a part of Primer3 tool. It allows user design primers for RT-PCR experiments by choosing which exons/introns to span with the primer product. This feature is described in detailed below. When you select the parameters you can save and load settings with a help of the corresponding buttons in the right corner of the dialog.