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The Primer3 plugin is a port of the Primer3 tool. 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:

     <img src="/wiki/download/attachments/4227733/Primer3.png"/>

All available parameters are the same as in the original Primer3.

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.

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