SIV Alignment uncertainty plot. We annotate the joint maximum a posteriori alignment estimate to indicate the approximate probability that each letter aligns to the root taxon in its column . The 8 gaps in the alignment are a result of only 4 indel events under the joint model, whereas the Clustal W alignment requires at least 5 indel events. Colors other than red indicates that letters or gaps may shift to adjacent positions. The high frequency of the CAA triplet is partially responsible for the level of alignment uncertainty.