4) Parameters for Beacon design
The parameters specifically associated with Beacon designs are: Stem Length, Stem GC Content, Stem dG, Num Redundant Stems, Solution Distance Stems and Force Terminal GC Pair:
Stem Length - The length in nucleotides of both stems of the beacon to be designed
Stem GC Content (GCC) - The total percentage of G and C bases that the stems contain
Stem dG - The dG of the hybridized stems of the beacon to be designed
Num Redundant Stems - Refers to the amount of stems sent through each filtering process (increasing it wil increase the number of potential stems and computational time)
Solution Distance Stems - This is the minimum distance (in nucleotides) between different solutions (decreasing it will increase the number of potential stems and computational time)
Force Terminal GC Pair - When set to TRUE, the 5' and 3' end of the Beacon Probe will form a GC basepair
