Direct Comparison of Mfold 2.3 and Mfold 3.1 Folding Accuracy for Selected 16S and 23S rRNAs. Base-pairs marked in red are predicted correctly by both Mfold 2.3 and Mfold 3.1. Base-pairs marked in blue are predicted correctly only by Mfold 2.3, and base-pairs marked in green are predicted correctly only by Mfold 3.1. Black base-pairs are not predicted correctly by either version of Mfold. Only canonical base-pairs in the comparative models in the current study and previous Gutell Lab studies are considered. Non-canonical base-pairs in the comparative structure models are not counted. Full-sized versions of each annotated structure diagram are available at our website. A: Archaea 16S rRNA Haloferax volcanii. B.1: Archaea 23S rRNA, 5' half, Thermococcus celer. B.2: Archaea 23S rRNA, 3' half, Thermococcus celer. C: Eukaryotic Nuclear16S rRNA, Giardia intestinalis. D.1: Eukaryotic Nuclear 23S rRNA, 5' half, Giardia intestinalis. D.2: Eukaryotic Nuclear 23S rRNA, 3' half, Giardia intestinalis.