13.1.5 Primer Picking Weights

At the bottom of the Characteristics panel there is a Primer Picking Weights button. Clicking this brings up a second dialog containing many more options. The purpose of all of these options is to allow you to assign penalty weights to each of the parameters you can set in the options. The weight specified here determines how much of a penalty primers and probes get when they do not match the optimal options. The higher the value the less likely a primer or probe will be chosen if it does not meet the optimal value.

Some of the weights allow you to specify a “Less Than” and “Greater Than”. This is for options which allow you to specify an optimum score such as GC content. These weights are used when looking at primers whose value for this option falls below and above the optimum respectively. The other weights are applied no matter in which direction they vary.

For details on individual options in the Primer Picking Weights dialog, again hover your mouse over the option to see a short description.