The simplest way to design primers with MacVector is to select a particular feature or region of a sequence and design primers either side of it, to amplify the selection.
To design a primer using the Amplify Feature/Region method:1. Open the sequence file you want to analyze.
2. Select a feature of the sequence in the Map tab or the Features tab. Alternatively, select a region of the sequence in the Editor tab. Primers will be chosen from a 200 bp long region on either side of the feature or region selected.
3. Choose Analyze | Primers | Primer Design (Primer3) from the menu.
Note. When the Primer Design (Primer3) dialog box opens it is populated with information about the feature or region you selected in the active sequence window. You can populate the dialog box with information about an alternative feature in the active sequence using the feature selector drop-down menu, or you can specify an alternative region by providing residue numbers manually.
4. Ensure that Amplify Feature/Region is selected from the design method drop-down list.
5. Click OK.
The default primer design settings will be used to design the new primer. These will produce a ranked list and graphical map of the top five primer pairs that will amplify the selected feature or region, using the optimum values for the primer Tm and %GC. However, by modifying the Advanced Options it is possible to tune these, and other values, to obtain the best primers for non-standard situations.