Figure 8
From: Designing multiple degenerate primers via consecutive pairwise alignments
Three steps of merging and refining two aligned sequences in PAMPS: (1) Aligned sequences are merged. The regions that occur in a gap are replaced with split points (circles) prior to merging. (2) A window of length l min slides through the merged sequence. Once the sequence that occurs within this window possesses degeneracy less than d max and has no split points, all nucleotides of that sequence are marked to be retained (solid lines). (3) Regions that their nucleotides are not marked (dotted lines) are replaced with new split points.