Binding parameters

This opens the dialog displayed in figure 17.18:

Image primersearchstep2
Figure 17.18: Search parameters for finding primer binding sites.

At the top, select one or more primers by clicking the browse (Image browse) button. In CLC Genomics Workbench, primers are just DNA sequences like any other, but there is a filter on the length of the sequence. Only sequences up to 400 bp can be added.

The Match criteria for matching a primer to a sequence are:

Note that the number of mismatches is reported in the output, so you will be able to filter on this afterwards (see Results - binding sites and fragments).

Below the match settings, you can adjust Concentrations concerning the reaction mixture. This is used when reporting melting temperatures for the primers.