SeqBuilder Pro assigns a quality score for each primer pair it identifies. These scores are displayed in the Alternate Pairs pane of the Primer Design view.

The following considerations are made when determining the primer pair quality score:

  • The distance of each primer from its respective end.
  • Each primer’s melting temperature in relation to the Target Tm.
  • The number of false priming sites for each primer.
  • Whether or not a primer is located in a repeated region.
  • Uniqueness at the 3’ end of the primer.
  • Internal repetitiveness of the primer.
  • The stability profile of the primer.
  • The length of most stable dimer.
  • The length of most stable hairpin.

Each of the above characteristics is assigned a score. The individual scores are then combined and normalized to a range from 0 to 1, where 1 is the best possible score. The primer pairs are sorted from highest to lowest by score and displayed in the Alternate Pairs Pane.

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