Specific options for alignment-based primer and probe design

Compared to the primer view of a single sequence, the most notable difference is that the alignment primer view has no available graphical information. Furthermore, the selection boxes found to the left of the names in the alignment play an important role in specifying the oligo design process.

The Primer Parameters group in the Side Panel has the same options as the ones defined for primers design based on single sequences, but differs by the following submenus(see figure 17.12):

The workflow when designing alignment based primers and probes is as follows (see figure 17.12):

Image primerview_alignments
Figure 17.13: The initial view of an alignment used for primer design.