Design Primers (Primer3) allows you to quickly design primers in as little as three mouse clicks. It is meant to work interactively from the Map view of the Single Sequence editor. This module is based on Primer3, and as well as being easy to use, it also allows the knowledgeable user to use the full power of the Primer3 algorithm. As well as designing primer pairs, this module can also test pairs of primers, can design matching primers for a known primer, and can also design hybridization primers for use in realtime PCR analyzes and similar techniques.
You can also use primers direct from your own Primer Database
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.
Alternatively, you can specify a region within which the amplified product should lie. Simply choose the size of product you want and Primer3 will design primers to amplify products of that size, from anywhere in that region.
Finally, you can design primers by specifying two flanking regions and selecting left and right primers from these. This is similar to the Amplify Feature/Region method but it is much more flexible, as you can specify more precisely the region that each primer is selected from.
You can also use the primer design module to test primer sequences. You can test existing primer pairs to ensure that they match and produce the expected product. Alternatively, you can provide one primer and use the primer design module to design a suitable matching primer again for a specified region or sequence.
Many real time PCR techniques use a third oligonucleotide that will anneal inside the desired product. This makes is possible to track the progress of the PCR amplification using one of the many proprietary technologies available. The primer design module enables you to design these. You can design an internal primer suitable for use with a pair of existing primers, design external primers to suit an existing internal primer, or design all three primers from scratch.
How to design primers with tails and mismatches.