- In the Mode submenu which specifies the reaction types the following options are found:
- Standard PCR. Used when the objective is to design primers, or primer pairs, for PCR amplification of a single DNA fragment.
- TaqMan. Used when the objective is to design a primer pair and a probe set for TaqMan quantitative PCR.
The work flow when designing alignment based primers and probes is as follows:
- Use selection boxes to specify groups of included and excluded sequences. To select all the sequences in the alignment, right-click one of the selection boxes and choose Mark All.
- Mark either a single forward primer region, a single reverse primer region or both on the sequence (and perhaps also a TaqMan region). Selections must cover all sequences in the included group. You can also specify that there should be no primers in a region (No Primers Here) or that a whole region should be amplified (Region to Amplify).
- Adjust parameters regarding single primers in the preference panel.
- Click the Calculate button.