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SimulFold: Simultaneously Inferring RNA Structures Including Pseudoknots, Alignments, and Trees Using a Bayesian MCMC Framework

Figure 7

Clustal-X Alignment for the HDV Dataset Consisting of 15 Sequences of HDV Ribozymes

Some parts of the AB037948 and L22063 sequences are misaligned (red characters), which causes nonsense base-pairs (highlighted in green) when mapping the known reference structure onto these sequences.

Figure 7