13.1.1 Generic primers

This option will design standard PCR primers according to the region input options you select. These options allow you to specify what part of a sequence you wish to amplify. Most options are optional and can be enabled or disabled with the associated check boxes beside them. If you have selected a region in the sequence before opening the primer dialog then this region will automatically be used for Included Region and Target Region. All of these are expressed in base pairs from the beginning of the sequence and are as follows:

• Included Region: Specifies the region of the sequence within which primers are allowed to fall. This must surround the target region and allows you to choose a small region on either side of the target in which primers must lie.
• Target Region: Specifies which region of the sequence you wish to amplify and unless the advanced options allow otherwise, the forward and reverse primers must fall somewhere outside this region.
• Product Size: Specifies the range of sizes which the product of a primer pair can have. The product size is the distance in bp between the beginning of the forward primer to the end of the reverse primer.
• Optimal Product Size: Specifies the preferred size of the product. Setting this will mean primer pairs that have a product size close to this will be chosen over those that do not. Warning: Setting these options can cause the primer design process to take considerably longer to complete.

The final option in this section is Number of Pairs to Generate which specifies how many candidate pairs of primers and DNA probes to generate and is compulsory. Setting this to 1 will give you only the primer pair which was considered best by the set parameters.

If you have chosen to return more than one pair of primers and you do not want the same primer used in different pairs, open the Characteristics panel and check Minimum Primer Distance. The number of bases specified here is the minimum distance between the 3^′ ends of primers of the same direction in different pairs. If this is on but set to zero, Geneious will not limit primer distances but will try not to reuse the same primer in different pairs.