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Table 2 The stemloc grammar, part 1 of 3: stem and loop structures.

From: Accelerated probabilistic inference of RNA structure evolution

L R (L → R)
Start Stem startInStem
  | LBulge (1 - startInStem) postStem [2]/ (2 postStem[i])
  | RBulge (1 - startInStem) postStem[2]/ (2 postStem[i])
  | LRBulge (1 - startInStem) postStem [3]/ ( postStem[i])
  | Multi (1 - startInStem) postStem [4]/ ( postStem[i])
Stem xyStemMatch 1 - stemGapOpen
  | yStemIns stemGapOpen/2
  | xStemDel stemGapOpen/2
StemMatch xyStemMatch (1 - stemGapOpen) stemExtend
  | yStemIns stemGapOpen/2
  | xStemDel stemGapOpen/2
  | StemExit (1 - stemGapOpen)(1 - stemExtend)
StemIns xyStemMatch (1 - stemGapExtend)(1 - stemGapSwap) stemExtend
  | yStemIns stemGapExtend
  | xStemDel (1 - stemGapExtend) stemGapSwap
  | StemExit (1 - stemGapExtend) (1 - stemGapSwap)(1 - stemExtend)
StemDel xyStemMatch (1 - stemGapExtend)(1 - stemGapSwap) stemExtend
  | xStemDel stemGapExtend
  | yStemIns (1 - stemGapExtend) stemGapSwap
  | StemExit (1 - stemGapExtend) stemGapSwap (1 - stemExtend)
StemExit Loop postStem [1]
  | LBulge postStem [2]/2
  | RBulge postStem [2]/2
  | LRBulge postStem [3]
  | Multi postStem [4]
Multi LMulti RMulti 1
LMulti LBulge multiBulgeOpen
  | Stem (1 - multiBulgeOpen)
RMulti Multi multiExtend
  | Stem (1 - multiExtend)(1 - multiBulgeOpen)2
  | LBulge (1 - multiExtend)(1 - multiBulgeOpen) multiBulgeOpen
  | RBulge (1 - multiExtend)(1 - multiBulgeOpen) multiBulgeOpen
  | LRBulge (1 - multiExtend) multiBulgeOpen2
Loop xyLoopMatch (1 - loopGapOpen)
  | yLoopIns loopGapOpen/2
  | xLoopDel loopGapOpen/2
LoopMatch xyLoopMatch (1 - loopGapOpen) loopExtend
  | yLoopIns loopGapOpen/2
  | xLoopDel loopGapOpen/2
  | ε (1 - loopGapOpen) (1 - loopExtend)
LoopIns xyLoopMatch (1 - loopGapExtend)(1 - loopGapSwap) loopExtend
  | yLoopIns loopGapExtend
  | xLoopDel (1 - loopGapExtend) loopGapSwap
  | ε (1 - loopGapExtend)(1 - loopGapSwap) (1 - loopExtend)
LoopDel xyLoopMatch (1 - loopGapExtend)(1 - loopGapSwap) loopExtend
  | xLoopDel loopGapExtend
  | yLoopIns (1 - loopGapExtend) loopGapSwap
  | ε (1 - loopGapExtend)(1 - loopGapSwap)(1 - loopExtend)