Figure 2.

Output summary of the primer design and evaluation steps. (A) Shows the positions of the different amplicon sets mapped on the first sequence of the input alignment at the protein level. The nonredundant codon usage tables used for primer design are shown. All primer pair formulations and their thermodynamic properties can be downloaded using the TAB link. (B) The CODEHOP (bold) and the three codon-based primer formulations returned by the system (only the forward formulation is shown), aligned with the underlying codons. An ‘!’ sign denotes positions corrected by the system based on the codon alignment. (C) Output summary for the (forward) primer thermodynamic and phylogenetic quality evaluations.