Scoring primers

CLC Main Workbench employs a proprietary algorithm to rank primer and probe solutions. The algorithm considers both the parameters pertaining to single oligos, such as e.g. the secondary structure score and parameters pertaining to oligo-pairs such as e.g. the oligo pair-annealing score. The ideal score for a solution is 100 and solutions are thus ranked in descending order. Each parameter is assigned an ideal value and a tolerance. Consider for example oligo self-annealing, here the ideal value of the annealing score is 0 and the tolerance corresponds to the maximum value specified in the side panel. The contribution to the final score is determined by how much the parameter deviates from the ideal value and is scaled by the specified tolerance. Hence, a large deviation from the ideal and a small tolerance will give a large deduction in the final score and a small deviation from the ideal and a high tolerance will give a small deduction in the final score.