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Secondary structure prediction of Escherichia coli 5S rRNA from our benchmark data set. (A) Structure reference, (B) prediction by RNAfold with default parameters and (C) prediction by RNAfold with guiding pseudo-energies obtained from SHAPE reactivity data using RNApvmin. Structure plots created using the forna Web server (Kerpedjiev et al., 2015). White nucleotides correspond to missing SHAPE reactivity data
