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Table 1 A stochastic context-free grammar for generating pairwise alignments of RNA structures.

From: Accelerated probabilistic inference of RNA structure evolution

L R (L → R)
Stem stemExtend (1 - stemGap) basepairSubstitution [AC, BD]
  | stemExtend (stemGap/2) basepairIndel [AC]
  | stemExtend (stemGap/2) basepairIndel [BD]
  | (1 - stemExtend)(1 - bifurcate) baseSubstitution [AB]
  | Stem Stem (1 - stemExtend) bifurcate
Loop loopExtend (1 - loopGap) baseSubstitution [AB]
  | loopExtend (loopGap/2) baseIndel [A]
  | loopExtend (loopGap/2) baseIndel [B]
  | ε 1 - loopExtend