13.2 Manual primer design

It is possible to create PCR primers by adding a primer annotation directly onto a sequence. This is especially useful for cloning applications as generally the primers must bind to a specified set of bases at the beginning and end of the gene to be cloned. To manually add a primer, select the region of sequence where you wish the primer to bind and click Add Annotation. Make the annotation type primer bind and you will then see primer-specific options and characteristics as in Figure 13.5 . Changing the primer binding site position in the Add annotation window will automatically update the primer sequence and characteristics. A 5 extension can also be added directly onto a primer in this step by clicking the button next to “Extension”. See section 13.9 for more information on adding 5 extensions.


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Figure 13.5: Create a primer by adding a primer annotation