Fig. 4

Binding region and match information for Assay A and Assay B. For each assay, the upper plots indicate the nucleotide distribution in the target alignment within the oligo binding regions (left: forward primer; middle: probe; right: reverse primer). The sequence is shown in the same direction as the oligo (i.e. in oligo 5′-3′ direction). The lower plots show the proportion of target sequences in the input alignment that matches perfectly, or with one, two, three or four or more mismatches to the oligo within the intended binding region (on-target match). They also show the proportion of target sequences that match (with maximum of two mismatches) to at least one sequence variant of the oligo outside the intended binding region (off-target match). Assay B was designed using the mixed strategy and the consensus and degenerate part of the primer is indicated. The plots were generated using the plotData function