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(alphabet
(name RNA)
(token (a c g u))
(complement (u g c a))
(extend (to n) (from a) (from c) (from g) (from u))
(extend (to x) (from a) (from c) (from g) (from u))
(extend (to t) (from u))
(extend (to r) (from a) (from g))
(extend (to y) (from c) (from u))
(extend (to m) (from a) (from c))
(extend (to k) (from g) (from u))
(extend (to s) (from c) (from g))
(extend (to w) (from a) (from u))
(extend (to h) (from a) (from c) (from u))
(extend (to b) (from c) (from g) (from u))
(extend (to v) (from a) (from c) (from g))
(extend (to d) (from a) (from g) (from u))
(wildcard *)
) ;; end alphabet RNA
(grammar
(name codon)
(update-rates 1)
(update-rules 1)
(chain
(update-policy rev)
(terminal (NUC))
;; initial probability distribution
(initial (state (a)) (prob 0.25))
(initial (state (c)) (prob 0.25))
(initial (state (g)) (prob 0.25))
(initial (state (u)) (prob 0.25))
;; mutation rates
(mutate (from (a)) (to (c)) (rate 0.25))
(mutate (from (a)) (to (g)) (rate 0.25))
(mutate (from (a)) (to (u)) (rate 0.25))
(mutate (from (c)) (to (a)) (rate 0.25))
(mutate (from (c)) (to (g)) (rate 0.25))
(mutate (from (c)) (to (u)) (rate 0.25))
(mutate (from (g)) (to (a)) (rate 0.25))
(mutate (from (g)) (to (c)) (rate 0.25))
(mutate (from (g)) (to (u)) (rate 0.25))
(mutate (from (u)) (to (a)) (rate 0.25))
(mutate (from (u)) (to (c)) (rate 0.25))
(mutate (from (u)) (to (g)) (rate 0.25))
) ;; end chain NUC
(chain
(update-policy rev)
(terminal (POS1 POS2 POS3))
;; initial probability distribution
(initial (state (a a a)) (prob 0.015625))
(initial (state (c a a)) (prob 0.015625))
(initial (state (g a a)) (prob 0.015625))
(initial (state (u a a)) (prob 0.015625))
(initial (state (a c a)) (prob 0.015625))
(initial (state (c c a)) (prob 0.015625))
(initial (state (g c a)) (prob 0.015625))
(initial (state (u c a)) (prob 0.015625))
(initial (state (a g a)) (prob 0.015625))
(initial (state (c g a)) (prob 0.015625))
(initial (state (g g a)) (prob 0.015625))
(initial (state (u g a)) (prob 0.015625))
(initial (state (a u a)) (prob 0.015625))
(initial (state (c u a)) (prob 0.015625))
(initial (state (g u a)) (prob 0.015625))
(initial (state (u u a)) (prob 0.015625))
(initial (state (a a c)) (prob 0.015625))
(initial (state (c a c)) (prob 0.015625))
(initial (state (g a c)) (prob 0.015625))
(initial (state (u a c)) (prob 0.015625))
(initial (state (a c c)) (prob 0.015625))
(initial (state (c c c)) (prob 0.015625))
(initial (state (g c c)) (prob 0.015625))
(initial (state (u c c)) (prob 0.015625))
(initial (state (a g c)) (prob 0.015625))
(initial (state (c g c)) (prob 0.015625))
(initial (state (g g c)) (prob 0.015625))
(initial (state (u g c)) (prob 0.015625))
(initial (state (a u c)) (prob 0.015625))
(initial (state (c u c)) (prob 0.015625))
(initial (state (g u c)) (prob 0.015625))
(initial (state (u u c)) (prob 0.015625))
(initial (state (a a g)) (prob 0.015625))
(initial (state (c a g)) (prob 0.015625))
(initial (state (g a g)) (prob 0.015625))
(initial (state (u a g)) (prob 0.015625))
(initial (state (a c g)) (prob 0.015625))
(initial (state (c c g)) (prob 0.015625))
(initial (state (g c g)) (prob 0.015625))
(initial (state (u c g)) (prob 0.015625))
(initial (state (a g g)) (prob 0.015625))
(initial (state (c g g)) (prob 0.015625))
(initial (state (g g g)) (prob 0.015625))
(initial (state (u g g)) (prob 0.015625))
(initial (state (a u g)) (prob 0.015625))
(initial (state (c u g)) (prob 0.015625))
(initial (state (g u g)) (prob 0.015625))
(initial (state (u u g)) (prob 0.015625))
(initial (state (a a u)) (prob 0.015625))
(initial (state (c a u)) (prob 0.015625))
(initial (state (g a u)) (prob 0.015625))
(initial (state (u a u)) (prob 0.015625))
(initial (state (a c u)) (prob 0.015625))
(initial (state (c c u)) (prob 0.015625))
(initial (state (g c u)) (prob 0.015625))
(initial (state (u c u)) (prob 0.015625))
(initial (state (a g u)) (prob 0.015625))
(initial (state (c g u)) (prob 0.015625))
(initial (state (g g u)) (prob 0.015625))
(initial (state (u g u)) (prob 0.015625))
(initial (state (a u u)) (prob 0.015625))
(initial (state (c u u)) (prob 0.015625))
(initial (state (g u u)) (prob 0.015625))
(initial (state (u u u)) (prob 0.015625))
;; mutation rates
(mutate (from (a a a)) (to (c a a)) (rate 0.015625))
(mutate (from (a a a)) (to (g a a)) (rate 0.015625))
(mutate (from (a a a)) (to (u a a)) (rate 0.015625))
(mutate (from (a a a)) (to (a c a)) (rate 0.015625))
(mutate (from (a a a)) (to (c c a)) (rate 0.015625))
(mutate (from (a a a)) (to (g c a)) (rate 0.015625))
(mutate (from (a a a)) (to (u c a)) (rate 0.015625))
(mutate (from (a a a)) (to (a g a)) (rate 0.015625))
(mutate (from (a a a)) (to (c g a)) (rate 0.015625))
(mutate (from (a a a)) (to (g g a)) (rate 0.015625))
(mutate (from (a a a)) (to (u g a)) (rate 0.015625))
(mutate (from (a a a)) (to (a u a)) (rate 0.015625))
(mutate (from (a a a)) (to (c u a)) (rate 0.015625))
(mutate (from (a a a)) (to (g u a)) (rate 0.015625))
(mutate (from (a a a)) (to (u u a)) (rate 0.015625))
(mutate (from (a a a)) (to (a a c)) (rate 0.015625))
(mutate (from (a a a)) (to (c a c)) (rate 0.015625))
(mutate (from (a a a)) (to (g a c)) (rate 0.015625))
(mutate (from (a a a)) (to (u a c)) (rate 0.015625))
(mutate (from (a a a)) (to (a c c)) (rate 0.015625))
(mutate (from (a a a)) (to (c c c)) (rate 0.015625))
(mutate (from (a a a)) (to (g c c)) (rate 0.015625))
(mutate (from (a a a)) (to (u c c)) (rate 0.015625))
(mutate (from (a a a)) (to (a g c)) (rate 0.015625))
(mutate (from (a a a)) (to (c g c)) (rate 0.015625))
(mutate (from (a a a)) (to (g g c)) (rate 0.015625))
(mutate (from (a a a)) (to (u g c)) (rate 0.015625))
(mutate (from (a a a)) (to (a u c)) (rate 0.015625))
(mutate (from (a a a)) (to (c u c)) (rate 0.015625))
(mutate (from (a a a)) (to (g u c)) (rate 0.015625))
(mutate (from (a a a)) (to (u u c)) (rate 0.015625))
(mutate (from (a a a)) (to (a a g)) (rate 0.015625))
(mutate (from (a a a)) (to (c a g)) (rate 0.015625))
(mutate (from (a a a)) (to (g a g)) (rate 0.015625))
(mutate (from (a a a)) (to (u a g)) (rate 0.015625))
(mutate (from (a a a)) (to (a c g)) (rate 0.015625))
(mutate (from (a a a)) (to (c c g)) (rate 0.015625))
(mutate (from (a a a)) (to (g c g)) (rate 0.015625))
(mutate (from (a a a)) (to (u c g)) (rate 0.015625))
(mutate (from (a a a)) (to (a g g)) (rate 0.015625))
(mutate (from (a a a)) (to (c g g)) (rate 0.015625))
(mutate (from (a a a)) (to (g g g)) (rate 0.015625))
(mutate (from (a a a)) (to (u g g)) (rate 0.015625))
(mutate (from (a a a)) (to (a u g)) (rate 0.015625))
(mutate (from (a a a)) (to (c u g)) (rate 0.015625))
(mutate (from (a a a)) (to (g u g)) (rate 0.015625))
(mutate (from (a a a)) (to (u u g)) (rate 0.015625))
(mutate (from (a a a)) (to (a a u)) (rate 0.015625))
(mutate (from (a a a)) (to (c a u)) (rate 0.015625))
(mutate (from (a a a)) (to (g a u)) (rate 0.015625))
(mutate (from (a a a)) (to (u a u)) (rate 0.015625))
(mutate (from (a a a)) (to (a c u)) (rate 0.015625))
(mutate (from (a a a)) (to (c c u)) (rate 0.015625))
(mutate (from (a a a)) (to (g c u)) (rate 0.015625))
(mutate (from (a a a)) (to (u c u)) (rate 0.015625))
(mutate (from (a a a)) (to (a g u)) (rate 0.015625))
(mutate (from (a a a)) (to (c g u)) (rate 0.015625))
(mutate (from (a a a)) (to (g g u)) (rate 0.015625))
(mutate (from (a a a)) (to (u g u)) (rate 0.015625))
(mutate (from (a a a)) (to (a u u)) (rate 0.015625))
(mutate (from (a a a)) (to (c u u)) (rate 0.015625))
(mutate (from (a a a)) (to (g u u)) (rate 0.015625))
(mutate (from (a a a)) (to (u u u)) (rate 0.015625))
(mutate (from (c a a)) (to (a a a)) (rate 0.015625))
(mutate (from (c a a)) (to (g a a)) (rate 0.015625))
(mutate (from (c a a)) (to (u a a)) (rate 0.015625))
(mutate (from (c a a)) (to (a c a)) (rate 0.015625))
(mutate (from (c a a)) (to (c c a)) (rate 0.015625))
(mutate (from (c a a)) (to (g c a)) (rate 0.015625))
(mutate (from (c a a)) (to (u c a)) (rate 0.015625))
(mutate (from (c a a)) (to (a g a)) (rate 0.015625))
(mutate (from (c a a)) (to (c g a)) (rate 0.015625))
(mutate (from (c a a)) (to (g g a)) (rate 0.015625))
(mutate (from (c a a)) (to (u g a)) (rate 0.015625))
(mutate (from (c a a)) (to (a u a)) (rate 0.015625))
(mutate (from (c a a)) (to (c u a)) (rate 0.015625))
(mutate (from (c a a)) (to (g u a)) (rate 0.015625))
(mutate (from (c a a)) (to (u u a)) (rate 0.015625))
(mutate (from (c a a)) (to (a a c)) (rate 0.015625))
(mutate (from (c a a)) (to (c a c)) (rate 0.015625))
(mutate (from (c a a)) (to (g a c)) (rate 0.015625))
(mutate (from (c a a)) (to (u a c)) (rate 0.015625))
(mutate (from (c a a)) (to (a c c)) (rate 0.015625))
(mutate (from (c a a)) (to (c c c)) (rate 0.015625))
(mutate (from (c a a)) (to (g c c)) (rate 0.015625))
(mutate (from (c a a)) (to (u c c)) (rate 0.015625))
(mutate (from (c a a)) (to (a g c)) (rate 0.015625))
(mutate (from (c a a)) (to (c g c)) (rate 0.015625))
(mutate (from (c a a)) (to (g g c)) (rate 0.015625))
(mutate (from (c a a)) (to (u g c)) (rate 0.015625))
(mutate (from (c a a)) (to (a u c)) (rate 0.015625))
(mutate (from (c a a)) (to (c u c)) (rate 0.015625))
(mutate (from (c a a)) (to (g u c)) (rate 0.015625))
(mutate (from (c a a)) (to (u u c)) (rate 0.015625))
(mutate (from (c a a)) (to (a a g)) (rate 0.015625))
(mutate (from (c a a)) (to (c a g)) (rate 0.015625))
(mutate (from (c a a)) (to (g a g)) (rate 0.015625))
(mutate (from (c a a)) (to (u a g)) (rate 0.015625))
(mutate (from (c a a)) (to (a c g)) (rate 0.015625))
(mutate (from (c a a)) (to (c c g)) (rate 0.015625))
(mutate (from (c a a)) (to (g c g)) (rate 0.015625))
(mutate (from (c a a)) (to (u c g)) (rate 0.015625))
(mutate (from (c a a)) (to (a g g)) (rate 0.015625))
(mutate (from (c a a)) (to (c g g)) (rate 0.015625))
(mutate (from (c a a)) (to (g g g)) (rate 0.015625))
(mutate (from (c a a)) (to (u g g)) (rate 0.015625))
(mutate (from (c a a)) (to (a u g)) (rate 0.015625))
(mutate (from (c a a)) (to (c u g)) (rate 0.015625))
(mutate (from (c a a)) (to (g u g)) (rate 0.015625))
(mutate (from (c a a)) (to (u u g)) (rate 0.015625))
(mutate (from (c a a)) (to (a a u)) (rate 0.015625))
(mutate (from (c a a)) (to (c a u)) (rate 0.015625))
(mutate (from (c a a)) (to (g a u)) (rate 0.015625))
(mutate (from (c a a)) (to (u a u)) (rate 0.015625))
(mutate (from (c a a)) (to (a c u)) (rate 0.015625))
(mutate (from (c a a)) (to (c c u)) (rate 0.015625))
(mutate (from (c a a)) (to (g c u)) (rate 0.015625))
(mutate (from (c a a)) (to (u c u)) (rate 0.015625))
(mutate (from (c a a)) (to (a g u)) (rate 0.015625))
(mutate (from (c a a)) (to (c g u)) (rate 0.015625))
(mutate (from (c a a)) (to (g g u)) (rate 0.015625))
(mutate (from (c a a)) (to (u g u)) (rate 0.015625))
(mutate (from (c a a)) (to (a u u)) (rate 0.015625))
(mutate (from (c a a)) (to (c u u)) (rate 0.015625))
(mutate (from (c a a)) (to (g u u)) (rate 0.015625))
(mutate (from (c a a)) (to (u u u)) (rate 0.015625))
(mutate (from (g a a)) (to (a a a)) (rate 0.015625))
(mutate (from (g a a)) (to (c a a)) (rate 0.015625))
(mutate (from (g a a)) (to (u a a)) (rate 0.015625))
(mutate (from (g a a)) (to (a c a)) (rate 0.015625))
(mutate (from (g a a)) (to (c c a)) (rate 0.015625))
(mutate (from (g a a)) (to (g c a)) (rate 0.015625))
(mutate (from (g a a)) (to (u c a)) (rate 0.015625))
(mutate (from (g a a)) (to (a g a)) (rate 0.015625))
(mutate (from (g a a)) (to (c g a)) (rate 0.015625))
(mutate (from (g a a)) (to (g g a)) (rate 0.015625))
(mutate (from (g a a)) (to (u g a)) (rate 0.015625))
(mutate (from (g a a)) (to (a u a)) (rate 0.015625))
(mutate (from (g a a)) (to (c u a)) (rate 0.015625))
(mutate (from (g a a)) (to (g u a)) (rate 0.015625))
(mutate (from (g a a)) (to (u u a)) (rate 0.015625))
(mutate (from (g a a)) (to (a a c)) (rate 0.015625))
(mutate (from (g a a)) (to (c a c)) (rate 0.015625))
(mutate (from (g a a)) (to (g a c)) (rate 0.015625))
(mutate (from (g a a)) (to (u a c)) (rate 0.015625))
(mutate (from (g a a)) (to (a c c)) (rate 0.015625))
(mutate (from (g a a)) (to (c c c)) (rate 0.015625))
(mutate (from (g a a)) (to (g c c)) (rate 0.015625))
(mutate (from (g a a)) (to (u c c)) (rate 0.015625))
(mutate (from (g a a)) (to (a g c)) (rate 0.015625))
(mutate (from (g a a)) (to (c g c)) (rate 0.015625))
(mutate (from (g a a)) (to (g g c)) (rate 0.015625))
(mutate (from (g a a)) (to (u g c)) (rate 0.015625))
(mutate (from (g a a)) (to (a u c)) (rate 0.015625))
(mutate (from (g a a)) (to (c u c)) (rate 0.015625))
(mutate (from (g a a)) (to (g u c)) (rate 0.015625))
(mutate (from (g a a)) (to (u u c)) (rate 0.015625))
(mutate (from (g a a)) (to (a a g)) (rate 0.015625))
(mutate (from (g a a)) (to (c a g)) (rate 0.015625))
(mutate (from (g a a)) (to (g a g)) (rate 0.015625))
(mutate (from (g a a)) (to (u a g)) (rate 0.015625))
(mutate (from (g a a)) (to (a c g)) (rate 0.015625))
(mutate (from (g a a)) (to (c c g)) (rate 0.015625))
(mutate (from (g a a)) (to (g c g)) (rate 0.015625))
(mutate (from (g a a)) (to (u c g)) (rate 0.015625))
(mutate (from (g a a)) (to (a g g)) (rate 0.015625))
(mutate (from (g a a)) (to (c g g)) (rate 0.015625))
(mutate (from (g a a)) (to (g g g)) (rate 0.015625))
(mutate (from (g a a)) (to (u g g)) (rate 0.015625))
(mutate (from (g a a)) (to (a u g)) (rate 0.015625))
(mutate (from (g a a)) (to (c u g)) (rate 0.015625))
(mutate (from (g a a)) (to (g u g)) (rate 0.015625))
(mutate (from (g a a)) (to (u u g)) (rate 0.015625))
(mutate (from (g a a)) (to (a a u)) (rate 0.015625))
(mutate (from (g a a)) (to (c a u)) (rate 0.015625))
(mutate (from (g a a)) (to (g a u)) (rate 0.015625))
(mutate (from (g a a)) (to (u a u)) (rate 0.015625))
(mutate (from (g a a)) (to (a c u)) (rate 0.015625))
(mutate (from (g a a)) (to (c c u)) (rate 0.015625))
(mutate (from (g a a)) (to (g c u)) (rate 0.015625))
(mutate (from (g a a)) (to (u c u)) (rate 0.015625))
(mutate (from (g a a)) (to (a g u)) (rate 0.015625))
(mutate (from (g a a)) (to (c g u)) (rate 0.015625))
(mutate (from (g a a)) (to (g g u)) (rate 0.015625))
(mutate (from (g a a)) (to (u g u)) (rate 0.015625))
(mutate (from (g a a)) (to (a u u)) (rate 0.015625))
(mutate (from (g a a)) (to (c u u)) (rate 0.015625))
(mutate (from (g a a)) (to (g u u)) (rate 0.015625))
(mutate (from (g a a)) (to (u u u)) (rate 0.015625))
(mutate (from (u a a)) (to (a a a)) (rate 0.015625))
(mutate (from (u a a)) (to (c a a)) (rate 0.015625))
(mutate (from (u a a)) (to (g a a)) (rate 0.015625))
(mutate (from (u a a)) (to (a c a)) (rate 0.015625))
(mutate (from (u a a)) (to (c c a)) (rate 0.015625))
(mutate (from (u a a)) (to (g c a)) (rate 0.015625))
(mutate (from (u a a)) (to (u c a)) (rate 0.015625))
(mutate (from (u a a)) (to (a g a)) (rate 0.015625))
(mutate (from (u a a)) (to (c g a)) (rate 0.015625))
(mutate (from (u a a)) (to (g g a)) (rate 0.015625))
(mutate (from (u a a)) (to (u g a)) (rate 0.015625))
(mutate (from (u a a)) (to (a u a)) (rate 0.015625))
(mutate (from (u a a)) (to (c u a)) (rate 0.015625))
(mutate (from (u a a)) (to (g u a)) (rate 0.015625))
(mutate (from (u a a)) (to (u u a)) (rate 0.015625))
(mutate (from (u a a)) (to (a a c)) (rate 0.015625))
(mutate (from (u a a)) (to (c a c)) (rate 0.015625))
(mutate (from (u a a)) (to (g a c)) (rate 0.015625))
(mutate (from (u a a)) (to (u a c)) (rate 0.015625))
(mutate (from (u a a)) (to (a c c)) (rate 0.015625))
(mutate (from (u a a)) (to (c c c)) (rate 0.015625))
(mutate (from (u a a)) (to (g c c)) (rate 0.015625))
(mutate (from (u a a)) (to (u c c)) (rate 0.015625))
(mutate (from (u a a)) (to (a g c)) (rate 0.015625))
(mutate (from (u a a)) (to (c g c)) (rate 0.015625))
(mutate (from (u a a)) (to (g g c)) (rate 0.015625))
(mutate (from (u a a)) (to (u g c)) (rate 0.015625))
(mutate (from (u a a)) (to (a u c)) (rate 0.015625))
(mutate (from (u a a)) (to (c u c)) (rate 0.015625))
(mutate (from (u a a)) (to (g u c)) (rate 0.015625))
(mutate (from (u a a)) (to (u u c)) (rate 0.015625))
(mutate (from (u a a)) (to (a a g)) (rate 0.015625))
(mutate (from (u a a)) (to (c a g)) (rate 0.015625))
(mutate (from (u a a)) (to (g a g)) (rate 0.015625))
(mutate (from (u a a)) (to (u a g)) (rate 0.015625))
(mutate (from (u a a)) (to (a c g)) (rate 0.015625))
(mutate (from (u a a)) (to (c c g)) (rate 0.015625))
(mutate (from (u a a)) (to (g c g)) (rate 0.015625))
(mutate (from (u a a)) (to (u c g)) (rate 0.015625))
(mutate (from (u a a)) (to (a g g)) (rate 0.015625))
(mutate (from (u a a)) (to (c g g)) (rate 0.015625))
(mutate (from (u a a)) (to (g g g)) (rate 0.015625))
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(mutate (from (c u u)) (to (a a a)) (rate 0.015625))
(mutate (from (c u u)) (to (c a a)) (rate 0.015625))
(mutate (from (c u u)) (to (g a a)) (rate 0.015625))
(mutate (from (c u u)) (to (u a a)) (rate 0.015625))
(mutate (from (c u u)) (to (a c a)) (rate 0.015625))
(mutate (from (c u u)) (to (c c a)) (rate 0.015625))
(mutate (from (c u u)) (to (g c a)) (rate 0.015625))
(mutate (from (c u u)) (to (u c a)) (rate 0.015625))
(mutate (from (c u u)) (to (a g a)) (rate 0.015625))
(mutate (from (c u u)) (to (c g a)) (rate 0.015625))
(mutate (from (c u u)) (to (g g a)) (rate 0.015625))
(mutate (from (c u u)) (to (u g a)) (rate 0.015625))
(mutate (from (c u u)) (to (a u a)) (rate 0.015625))
(mutate (from (c u u)) (to (c u a)) (rate 0.015625))
(mutate (from (c u u)) (to (g u a)) (rate 0.015625))
(mutate (from (c u u)) (to (u u a)) (rate 0.015625))
(mutate (from (c u u)) (to (a a c)) (rate 0.015625))
(mutate (from (c u u)) (to (c a c)) (rate 0.015625))
(mutate (from (c u u)) (to (g a c)) (rate 0.015625))
(mutate (from (c u u)) (to (u a c)) (rate 0.015625))
(mutate (from (c u u)) (to (a c c)) (rate 0.015625))
(mutate (from (c u u)) (to (c c c)) (rate 0.015625))
(mutate (from (c u u)) (to (g c c)) (rate 0.015625))
(mutate (from (c u u)) (to (u c c)) (rate 0.015625))
(mutate (from (c u u)) (to (a g c)) (rate 0.015625))
(mutate (from (c u u)) (to (c g c)) (rate 0.015625))
(mutate (from (c u u)) (to (g g c)) (rate 0.015625))
(mutate (from (c u u)) (to (u g c)) (rate 0.015625))
(mutate (from (c u u)) (to (a u c)) (rate 0.015625))
(mutate (from (c u u)) (to (c u c)) (rate 0.015625))
(mutate (from (c u u)) (to (g u c)) (rate 0.015625))
(mutate (from (c u u)) (to (u u c)) (rate 0.015625))
(mutate (from (c u u)) (to (a a g)) (rate 0.015625))
(mutate (from (c u u)) (to (c a g)) (rate 0.015625))
(mutate (from (c u u)) (to (g a g)) (rate 0.015625))
(mutate (from (c u u)) (to (u a g)) (rate 0.015625))
(mutate (from (c u u)) (to (a c g)) (rate 0.015625))
(mutate (from (c u u)) (to (c c g)) (rate 0.015625))
(mutate (from (c u u)) (to (g c g)) (rate 0.015625))
(mutate (from (c u u)) (to (u c g)) (rate 0.015625))
(mutate (from (c u u)) (to (a g g)) (rate 0.015625))
(mutate (from (c u u)) (to (c g g)) (rate 0.015625))
(mutate (from (c u u)) (to (g g g)) (rate 0.015625))
(mutate (from (c u u)) (to (u g g)) (rate 0.015625))
(mutate (from (c u u)) (to (a u g)) (rate 0.015625))
(mutate (from (c u u)) (to (c u g)) (rate 0.015625))
(mutate (from (c u u)) (to (g u g)) (rate 0.015625))
(mutate (from (c u u)) (to (u u g)) (rate 0.015625))
(mutate (from (c u u)) (to (a a u)) (rate 0.015625))
(mutate (from (c u u)) (to (c a u)) (rate 0.015625))
(mutate (from (c u u)) (to (g a u)) (rate 0.015625))
(mutate (from (c u u)) (to (u a u)) (rate 0.015625))
(mutate (from (c u u)) (to (a c u)) (rate 0.015625))
(mutate (from (c u u)) (to (c c u)) (rate 0.015625))
(mutate (from (c u u)) (to (g c u)) (rate 0.015625))
(mutate (from (c u u)) (to (u c u)) (rate 0.015625))
(mutate (from (c u u)) (to (a g u)) (rate 0.015625))
(mutate (from (c u u)) (to (c g u)) (rate 0.015625))
(mutate (from (c u u)) (to (g g u)) (rate 0.015625))
(mutate (from (c u u)) (to (u g u)) (rate 0.015625))
(mutate (from (c u u)) (to (a u u)) (rate 0.015625))
(mutate (from (c u u)) (to (g u u)) (rate 0.015625))
(mutate (from (c u u)) (to (u u u)) (rate 0.015625))
(mutate (from (g u u)) (to (a a a)) (rate 0.015625))
(mutate (from (g u u)) (to (c a a)) (rate 0.015625))
(mutate (from (g u u)) (to (g a a)) (rate 0.015625))
(mutate (from (g u u)) (to (u a a)) (rate 0.015625))
(mutate (from (g u u)) (to (a c a)) (rate 0.015625))
(mutate (from (g u u)) (to (c c a)) (rate 0.015625))
(mutate (from (g u u)) (to (g c a)) (rate 0.015625))
(mutate (from (g u u)) (to (u c a)) (rate 0.015625))
(mutate (from (g u u)) (to (a g a)) (rate 0.015625))
(mutate (from (g u u)) (to (c g a)) (rate 0.015625))
(mutate (from (g u u)) (to (g g a)) (rate 0.015625))
(mutate (from (g u u)) (to (u g a)) (rate 0.015625))
(mutate (from (g u u)) (to (a u a)) (rate 0.015625))
(mutate (from (g u u)) (to (c u a)) (rate 0.015625))
(mutate (from (g u u)) (to (g u a)) (rate 0.015625))
(mutate (from (g u u)) (to (u u a)) (rate 0.015625))
(mutate (from (g u u)) (to (a a c)) (rate 0.015625))
(mutate (from (g u u)) (to (c a c)) (rate 0.015625))
(mutate (from (g u u)) (to (g a c)) (rate 0.015625))
(mutate (from (g u u)) (to (u a c)) (rate 0.015625))
(mutate (from (g u u)) (to (a c c)) (rate 0.015625))
(mutate (from (g u u)) (to (c c c)) (rate 0.015625))
(mutate (from (g u u)) (to (g c c)) (rate 0.015625))
(mutate (from (g u u)) (to (u c c)) (rate 0.015625))
(mutate (from (g u u)) (to (a g c)) (rate 0.015625))
(mutate (from (g u u)) (to (c g c)) (rate 0.015625))
(mutate (from (g u u)) (to (g g c)) (rate 0.015625))
(mutate (from (g u u)) (to (u g c)) (rate 0.015625))
(mutate (from (g u u)) (to (a u c)) (rate 0.015625))
(mutate (from (g u u)) (to (c u c)) (rate 0.015625))
(mutate (from (g u u)) (to (g u c)) (rate 0.015625))
(mutate (from (g u u)) (to (u u c)) (rate 0.015625))
(mutate (from (g u u)) (to (a a g)) (rate 0.015625))
(mutate (from (g u u)) (to (c a g)) (rate 0.015625))
(mutate (from (g u u)) (to (g a g)) (rate 0.015625))
(mutate (from (g u u)) (to (u a g)) (rate 0.015625))
(mutate (from (g u u)) (to (a c g)) (rate 0.015625))
(mutate (from (g u u)) (to (c c g)) (rate 0.015625))
(mutate (from (g u u)) (to (g c g)) (rate 0.015625))
(mutate (from (g u u)) (to (u c g)) (rate 0.015625))
(mutate (from (g u u)) (to (a g g)) (rate 0.015625))
(mutate (from (g u u)) (to (c g g)) (rate 0.015625))
(mutate (from (g u u)) (to (g g g)) (rate 0.015625))
(mutate (from (g u u)) (to (u g g)) (rate 0.015625))
(mutate (from (g u u)) (to (a u g)) (rate 0.015625))
(mutate (from (g u u)) (to (c u g)) (rate 0.015625))
(mutate (from (g u u)) (to (g u g)) (rate 0.015625))
(mutate (from (g u u)) (to (u u g)) (rate 0.015625))
(mutate (from (g u u)) (to (a a u)) (rate 0.015625))
(mutate (from (g u u)) (to (c a u)) (rate 0.015625))
(mutate (from (g u u)) (to (g a u)) (rate 0.015625))
(mutate (from (g u u)) (to (u a u)) (rate 0.015625))
(mutate (from (g u u)) (to (a c u)) (rate 0.015625))
(mutate (from (g u u)) (to (c c u)) (rate 0.015625))
(mutate (from (g u u)) (to (g c u)) (rate 0.015625))
(mutate (from (g u u)) (to (u c u)) (rate 0.015625))
(mutate (from (g u u)) (to (a g u)) (rate 0.015625))
(mutate (from (g u u)) (to (c g u)) (rate 0.015625))
(mutate (from (g u u)) (to (g g u)) (rate 0.015625))
(mutate (from (g u u)) (to (u g u)) (rate 0.015625))
(mutate (from (g u u)) (to (a u u)) (rate 0.015625))
(mutate (from (g u u)) (to (c u u)) (rate 0.015625))
(mutate (from (g u u)) (to (u u u)) (rate 0.015625))
(mutate (from (u u u)) (to (a a a)) (rate 0.015625))
(mutate (from (u u u)) (to (c a a)) (rate 0.015625))
(mutate (from (u u u)) (to (g a a)) (rate 0.015625))
(mutate (from (u u u)) (to (u a a)) (rate 0.015625))
(mutate (from (u u u)) (to (a c a)) (rate 0.015625))
(mutate (from (u u u)) (to (c c a)) (rate 0.015625))
(mutate (from (u u u)) (to (g c a)) (rate 0.015625))
(mutate (from (u u u)) (to (u c a)) (rate 0.015625))
(mutate (from (u u u)) (to (a g a)) (rate 0.015625))
(mutate (from (u u u)) (to (c g a)) (rate 0.015625))
(mutate (from (u u u)) (to (g g a)) (rate 0.015625))
(mutate (from (u u u)) (to (u g a)) (rate 0.015625))
(mutate (from (u u u)) (to (a u a)) (rate 0.015625))
(mutate (from (u u u)) (to (c u a)) (rate 0.015625))
(mutate (from (u u u)) (to (g u a)) (rate 0.015625))
(mutate (from (u u u)) (to (u u a)) (rate 0.015625))
(mutate (from (u u u)) (to (a a c)) (rate 0.015625))
(mutate (from (u u u)) (to (c a c)) (rate 0.015625))
(mutate (from (u u u)) (to (g a c)) (rate 0.015625))
(mutate (from (u u u)) (to (u a c)) (rate 0.015625))
(mutate (from (u u u)) (to (a c c)) (rate 0.015625))
(mutate (from (u u u)) (to (c c c)) (rate 0.015625))
(mutate (from (u u u)) (to (g c c)) (rate 0.015625))
(mutate (from (u u u)) (to (u c c)) (rate 0.015625))
(mutate (from (u u u)) (to (a g c)) (rate 0.015625))
(mutate (from (u u u)) (to (c g c)) (rate 0.015625))
(mutate (from (u u u)) (to (g g c)) (rate 0.015625))
(mutate (from (u u u)) (to (u g c)) (rate 0.015625))
(mutate (from (u u u)) (to (a u c)) (rate 0.015625))
(mutate (from (u u u)) (to (c u c)) (rate 0.015625))
(mutate (from (u u u)) (to (g u c)) (rate 0.015625))
(mutate (from (u u u)) (to (u u c)) (rate 0.015625))
(mutate (from (u u u)) (to (a a g)) (rate 0.015625))
(mutate (from (u u u)) (to (c a g)) (rate 0.015625))
(mutate (from (u u u)) (to (g a g)) (rate 0.015625))
(mutate (from (u u u)) (to (u a g)) (rate 0.015625))
(mutate (from (u u u)) (to (a c g)) (rate 0.015625))
(mutate (from (u u u)) (to (c c g)) (rate 0.015625))
(mutate (from (u u u)) (to (g c g)) (rate 0.015625))
(mutate (from (u u u)) (to (u c g)) (rate 0.015625))
(mutate (from (u u u)) (to (a g g)) (rate 0.015625))
(mutate (from (u u u)) (to (c g g)) (rate 0.015625))
(mutate (from (u u u)) (to (g g g)) (rate 0.015625))
(mutate (from (u u u)) (to (u g g)) (rate 0.015625))
(mutate (from (u u u)) (to (a u g)) (rate 0.015625))
(mutate (from (u u u)) (to (c u g)) (rate 0.015625))
(mutate (from (u u u)) (to (g u g)) (rate 0.015625))
(mutate (from (u u u)) (to (u u g)) (rate 0.015625))
(mutate (from (u u u)) (to (a a u)) (rate 0.015625))
(mutate (from (u u u)) (to (c a u)) (rate 0.015625))
(mutate (from (u u u)) (to (g a u)) (rate 0.015625))
(mutate (from (u u u)) (to (u a u)) (rate 0.015625))
(mutate (from (u u u)) (to (a c u)) (rate 0.015625))
(mutate (from (u u u)) (to (c c u)) (rate 0.015625))
(mutate (from (u u u)) (to (g c u)) (rate 0.015625))
(mutate (from (u u u)) (to (u c u)) (rate 0.015625))
(mutate (from (u u u)) (to (a g u)) (rate 0.015625))
(mutate (from (u u u)) (to (c g u)) (rate 0.015625))
(mutate (from (u u u)) (to (g g u)) (rate 0.015625))
(mutate (from (u u u)) (to (u g u)) (rate 0.015625))
(mutate (from (u u u)) (to (a u u)) (rate 0.015625))
(mutate (from (u u u)) (to (c u u)) (rate 0.015625))
(mutate (from (u u u)) (to (g u u)) (rate 0.015625))
) ;; end chain POS1 POS2 POS3
;; state Start
(transform (from (Start)) (to (Null)) (prob 0.25))
(transform (from (Start)) (to (Fwd)) (prob 0.25))
(transform (from (Start)) (to (Rev)) (prob 0.25))
;; state Null
(transform (from (Null)) (to (NUC Null*)) (gaps-ok))
(transform (from (Null*)) (to ()) (prob 0.25))
(transform (from (Null*)) (to (Null)) (prob 0.25))
(transform (from (Null*)) (to (Fwd)) (prob 0.25))
(transform (from (Null*)) (to (Rev)) (prob 0.25))
;; state Fwd
(transform (from (Fwd)) (to (POS1 POS2 POS3 Fwd*)) (gaps-ok)
(annotate (row Codon) (column POS1) (label 0))
(annotate (row Codon) (column POS2) (label 1))
(annotate (row Codon) (column POS3) (label 2)))
(transform (from (Fwd*)) (to ()) (prob 0.333556))
(transform (from (Fwd*)) (to (Null)) (prob 0.333556))
(transform (from (Fwd*)) (to (Fwd)) (prob 0.333556))
;; state Rev
(transform (from (Rev)) (to (~POS3 ~POS2 ~POS1 Rev*)) (gaps-ok)
(annotate (row Codon) (column POS3) (label 2))
(annotate (row Codon) (column POS2) (label 1))
(annotate (row Codon) (column POS1) (label 0)))
(transform (from (Rev*)) (to ()) (prob 0.333556))
(transform (from (Rev*)) (to (Null)) (prob 0.333556))
(transform (from (Rev*)) (to (Rev)) (prob 0.333556))
) ;; end grammar codon