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Phylogenetic secondary structure, the predicted lowest free energy secondary structure, and the four suboptimal structures of E. coli 5S rRNA. Loops A–E are labeled in the phylogenetic structure. Base-paired regions that are predicted correctly in the suboptimal structures are shaded. Nucleotides cleaved by RNase H cleavage are circled. The lowest free energy structure only has 27% of the base pairs present in the phylogenetic structure.
