FIGURE 2.
Two secondary structures for the 5S rRNA from the Archaeon, Haloarcula japonica. (Left) The accepted secondary structure computed by phylogenetic methods. (Right) A computed structure comprising base pairs that have probabilities >50%, computed by UNAFold (Markham and Zuker 2008). The coloring scheme is identical to that used in Figure 1, as is the total number of red (24) and green (11) circled base pairs. The BP distance between this pair of structures is 35, the same as the corresponding distance from Figure 1.
