Unipro UGENE User Manual
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UGENE provides the "PCR Primer Design for DNA Assembly" feature only for nucleic sequences with the "Standard DNA" alphabet. To use it in UGENE open a DNA sequence and go to the "PCR Primer Design for DNA Assembly" tab of the Options Panel: 

514px100The PCR Primer Design for DNA Assembly tab. Click on the picture to scale.

There are the following parameters:

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