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. This is elaborated below. The Primer Parameters group in the Side Panel has the same options for specifying primer requirements, but differs by the following (see figure 17.12):

The work flow when designing alignment based primers and probes is as follows: