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 |