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UGENE provides the In silico PCR feature only for nucleic sequences. To use it in UGENE open a DNA sequence and go to the In Silico silico PCR tab of the Options Panel: 

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Type two primers for running In Silico PCR. If the primers pair is invalid for running the PCR process then the warning is shown. Also, primers for the running In Silico silico PCR can be chosen from a primers library. Click the following button to choose a primer from the primers library: 

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