;; Produces exactly one structurally-conserved RNA annotation, flanked by
;; intergenic regions.
;;
;; A modified Pfold grammar with special states for closing (innermost basepairs)
;; is used for the RNA secondary structure model.  Note that this
;; grammar is ambiguous: closing loops can generated both in the "standard"
;; Pfold manner as well as with the new close states.
;;
;; Other features:
;;   - RNA SS annotation is a minimum length of 20 columns
;;   - "sum-from" modifier used to produce Inside score for Pfold sub-grammar
;;   - no transition state penalty into/out of Pfold sub-grammar, everything
;;     done using bifurcations 
;;
;; Notes:
;;   - Strand-symmetric nuc null model (see grammars/null_nuc_symmetric.eg).
;;     There are separate left and right-emitting intergenic nuc states.
;;     This is necessary because of how Xrate handles suffix subsequences.
;;     Note that intergenic scores (- and + strand) can be taken from /either/ 
;;     the lgInside(LEFT_INTERGENIC) or lgInside(RIGHT_INTERGENIC) score.
;;     This is a special feature of the strand-symmetric independent-sites model.
;;
;; Ian Holmes, Rob Bradley, and Andrew Uzilov wrote this grammar based on the
;; Pfold grammar as the starting point.  The intergenic sub-model was trained
;; on a subset of the Pecan 12fly alignments.


(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
 (parametric)
 (name ncRna_v22)
 (update-rates 0)  ;; turned off to prevent accidentally changing the grammar
 (update-rules 0)

 ;; up-front nonterminal declarations
 (nonterminal (name START))
 (nonterminal (name WINDOW))
 (nonterminal (name WINDOW_TAIL))
 (nonterminal (name HIT))
 (nonterminal (name FWD_SS) (gff (type ncRNA) (strand +)) (minlen 20) (infix))
 (nonterminal (name REV_SS) (gff (type ncRNA) (strand -)) (minlen 20) (infix))
 (nonterminal (name LEFT_INTERGENIC))
 (nonterminal (name LEFT_INTERGENIC_EMIT) (gaps-ok))
 (nonterminal (name RIGHT_INTERGENIC))
 (nonterminal (name RIGHT_INTERGENIC_EMIT) (gaps-ok))
 (nonterminal (name FWD_PFOLD_S) (sum-from))
 (nonterminal (name REV_PFOLD_S) (sum-from))
 (nonterminal (name FWD_PFOLD_F) (sum-from) (gaps-ok))
 (nonterminal (name REV_PFOLD_F) (sum-from) (gaps-ok))
 (nonterminal (name FWD_PFOLD_L) (sum-from))
 (nonterminal (name REV_PFOLD_L) (sum-from))
 (nonterminal (name FWD_PFOLD_B) (sum-from))
 (nonterminal (name REV_PFOLD_B) (sum-from))
 (nonterminal (name FWD_PFOLD_U) (sum-from) (gaps-ok))
 (nonterminal (name REV_PFOLD_U) (sum-from) (gaps-ok))

 (nonterminal (name FWD_PFOLD_CLOSE) (sum-from) (minlen 3) (gaps-ok))
 (nonterminal (name REV_PFOLD_CLOSE) (sum-from) (minlen 3) (gaps-ok))
 (nonterminal (name FWD_PFOLD_CLOSELOOP) (sum-from) (gaps-ok))
 (nonterminal (name REV_PFOLD_CLOSELOOP) (sum-from) (gaps-ok))

 ;; transformation rules
 ;; state 0: START
 (transform (from (START)) (to ()) (prob Trans_START2END))
 (transform (from (START)) (to (WINDOW)) (prob Trans_START2WINDOW))

 ;; two bifurcations to produce a conserved RNA secondary structure region
 ;; flanked by intergenic regions

 ;; state 1: WINDOW
 (transform (from (WINDOW)) (to (LEFT_INTERGENIC WINDOW_TAIL)))

 ;; state 2: WINDOW_TAIL
 (transform (from (WINDOW_TAIL)) (to (HIT RIGHT_INTERGENIC)))

 ;; state 3: HIT
 (transform (from (HIT)) (to (FWD_SS)) (prob Trans_HIT2FWD_SS))
 (transform (from (HIT)) (to (REV_SS)) (prob Trans_HIT2REV_SS))

 ;; state 4: FWD_SS
 ;; wraps the Pfold model (forward strand)
 (transform (from (FWD_SS)) (to (FWD_PFOLD_S)))

 ;; state 5: REV_SS
 ;; wraps the Pfold model (reverse strand)
 (transform (from (REV_SS)) (to (REV_PFOLD_S)))

 ;; intergenic model

 ;; NB: the intergenic model has a <1 transition probability to an end state,
 ;;     whereas the Pfold model doesn't, which will penalize the intergenic
 ;;     model and increase the log-odds ratio P(align|SS)/P(align|INTERGENIC);
 ;;     this is acceptable and even desired, as the end state penalty is part
 ;;     of the intergenic probabilistic sub-model, penalizing shorter features

 ;; state 6: LEFT_INTERGENIC
 (transform (from (LEFT_INTERGENIC)) (to (LEFT_INTERGENIC_EMIT)) (prob Trans_I2I))
 (transform (from (LEFT_INTERGENIC)) (to ()) (prob Trans_I2END))

 ;; state 7: LEFT_INTERGENIC_EMIT
 (transform (from (LEFT_INTERGENIC_EMIT)) (to (LEFT_INTERGENIC_EMIT* X))
            (annotate (row SS_cons) (column X) (label n)))
 (transform (from (LEFT_INTERGENIC_EMIT*)) (to (LEFT_INTERGENIC)) (prob 1))

 ;; state 8: RIGHT_INTERGENIC
 (transform (from (RIGHT_INTERGENIC)) (to (RIGHT_INTERGENIC_EMIT)) (prob Trans_I2I))
 (transform (from (RIGHT_INTERGENIC)) (to ()) (prob Trans_I2END))

 ;; state 9: RIGHT_INTERGENIC_EMIT
 (transform (from (RIGHT_INTERGENIC_EMIT)) (to (X RIGHT_INTERGENIC_EMIT*))
            (annotate (row SS_cons) (column X) (label n)))
 (transform (from (RIGHT_INTERGENIC_EMIT*)) (to (RIGHT_INTERGENIC)) (prob 1))

 ;; Pfold's conserved RNA secondary structure model

 ;; state 10: FWD_PFOLD_S = start state for FWD_PFOLD_ subgrammar (fwd)
 (transform (from (FWD_PFOLD_S)) (to (FWD_PFOLD_L)) (prob Trans_S2L))
 (transform (from (FWD_PFOLD_S)) (to (FWD_PFOLD_B)) (prob Trans_S2B))

 ;; state 11: REV_PFOLD_S = start state for REV_PFOLD_ subgrammar (rev)
 (transform (from (REV_PFOLD_S)) (to (REV_PFOLD_L)) (prob Trans_S2L))
 (transform (from (REV_PFOLD_S)) (to (REV_PFOLD_B)) (prob Trans_S2B))

 ;; state 12: FWD_PFOLD_F = emit state for paired bases (fwd)
 (transform (from (FWD_PFOLD_F)) (to (LNUC FWD_PFOLD_F* RNUC))
  (annotate (row SS_cons) (column LNUC) (label <))
  (annotate (row SS_cons) (column RNUC) (label >))
  (annotate (row STRAND) (column LNUC) (label +))
  (annotate (row STRAND) (column RNUC) (label +)))
 (transform (from (FWD_PFOLD_F*)) (to (FWD_PFOLD_F)) (prob Trans_F2F))
 (transform (from (FWD_PFOLD_F*)) (to (FWD_PFOLD_CLOSE)) (prob Trans_F2CLOSE))
 (transform (from (FWD_PFOLD_F*)) (to (FWD_PFOLD_B)) (prob Trans_F2B))

 ;; state 13: REV_PFOLD_F = emit state for paired bases (rev)
 (transform (from (REV_PFOLD_F)) (to (~RNUC REV_PFOLD_F* ~LNUC))
  (annotate (row SS_cons) (column RNUC) (label <))
  (annotate (row SS_cons) (column LNUC) (label >))
  (annotate (row STRAND) (column RNUC) (label -))
  (annotate (row STRAND) (column LNUC) (label -)))
 (transform (from (REV_PFOLD_F*)) (to (REV_PFOLD_F)) (prob Trans_F2F))
 (transform (from (REV_PFOLD_F*)) (to (REV_PFOLD_CLOSE)) (prob Trans_F2CLOSE))
 (transform (from (REV_PFOLD_F*)) (to (REV_PFOLD_B)) (prob Trans_F2B))

 ;; state 14: FWD_PFOLD_L = transition between paired and unpaired sites (fwd)
 (transform (from (FWD_PFOLD_L)) (to (FWD_PFOLD_F)) (prob Trans_L2F))
 (transform (from (FWD_PFOLD_L)) (to (FWD_PFOLD_U)) (prob Trans_L2U))

 ;; state 15: REV_PFOLD_L = transition between paired and unpaired sites (rev)
 (transform (from (REV_PFOLD_L)) (to (REV_PFOLD_F)) (prob Trans_L2F))
 (transform (from (REV_PFOLD_L)) (to (REV_PFOLD_U)) (prob Trans_L2U))

 ;; state 16: FWD_PFOLD_B = bifurcation (fwd)
 (transform (from (FWD_PFOLD_B)) (to (FWD_PFOLD_L FWD_PFOLD_S)))

 ;; state 17: REV_PFOLD_B = bifurcation (rev)
 (transform (from (REV_PFOLD_B)) (to (REV_PFOLD_S REV_PFOLD_L)))

 ;; state 18: FWD_PFOLD_U = emit state for unpaired bases (fwd)
 (transform (from (FWD_PFOLD_U)) (to (FWD_PFOLD_U* NUC))
  (annotate (row SS_cons) (column NUC) (label _))
  (annotate (row STRAND) (column NUC) (label +)))
 (transform (from (FWD_PFOLD_U*)) (to ()) (prob 1))

 ;; state 19: REV_PFOLD_U = emit state for unpaired bases (rev)
 (transform (from (REV_PFOLD_U)) (to (~NUC REV_PFOLD_U*))
  (annotate (row SS_cons) (column NUC) (label _))
  (annotate (row STRAND) (column NUC) (label -)))
 (transform (from (REV_PFOLD_U*)) (to ()) (prob 1))


 ;; Sub-model for closing basepair and subsequent loop emissions.
 ;; state FWD_PFOLD_CLOSE is the closing basepair state
 (transform (from (FWD_PFOLD_CLOSE)) (to (LCLOSE FWD_PFOLD_CLOSE* RCLOSE))
  (annotate (row SS_cons) (column LCLOSE) (label [))
  (annotate (row SS_cons) (column RCLOSE) (label ]))
  (annotate (row STRAND) (column LCLOSE) (label +))
  (annotate (row STRAND) (column RCLOSE) (label +)))
 (transform (from (FWD_PFOLD_CLOSE*)) (to (FWD_PFOLD_CLOSELOOP)) (prob 1))

 ;; state REV_PFOLD_CLOSE is the closing basepair state
 (transform (from (REV_PFOLD_CLOSE)) (to (~RCLOSE REV_PFOLD_CLOSE* ~LCLOSE))
  (annotate (row SS_cons) (column RCLOSE) (label [))
  (annotate (row SS_cons) (column LCLOSE) (label ]))
  (annotate (row STRAND) (column RCLOSE) (label -))
  (annotate (row STRAND) (column LCLOSE) (label -)))
 (transform (from (REV_PFOLD_CLOSE*)) (to (REV_PFOLD_CLOSELOOP)) (prob 1))

 ;; state FWD_PFOLD_CLOSELOOP is a dedicated left-emitting loop state
 (transform (from (FWD_PFOLD_CLOSELOOP)) (to (NUC FWD_PFOLD_CLOSELOOP*))
	    (annotate (row SS_cons) (column NUC) (label _))
	    (annotate (row STRAND) (column NUC) (label +)))
 (transform (from (FWD_PFOLD_CLOSELOOP*)) (to (FWD_PFOLD_CLOSELOOP)) (prob Trans_CLOSELOOP2CLOSELOOP))
 (transform (from (FWD_PFOLD_CLOSELOOP*)) (to ()) (prob Trans_CLOSELOOP2END))

 ;; state REV_PFOLD_CLOSELOOP is a dedicated left-emitting loop state
 (transform (from (REV_PFOLD_CLOSELOOP)) (to (REV_PFOLD_CLOSELOOP* ~NUC))
	    (annotate (row SS_cons) (column NUC) (label _))
	    (annotate (row STRAND) (column NUC) (label -)))
 (transform (from (REV_PFOLD_CLOSELOOP*)) (to (REV_PFOLD_CLOSELOOP)) (prob Trans_CLOSELOOP2CLOSELOOP))
 (transform (from (REV_PFOLD_CLOSELOOP*)) (to ()) (prob Trans_CLOSELOOP2END))



 ;; constant probability parameters
 (const-pgroup
   ;; transition probabilities
   ;; start state
   ((Trans_START2END 0.0001)
    (Trans_START2WINDOW 0.9999)
   )

   ;; strand selection for Pfold-submodel
   ;; unless you want a preference for hits on one strand vs the other, these should both be 0.5
   ((Trans_HIT2FWD_SS 0.5)
    (Trans_HIT2REV_SS 0.5)
   )

   ;; intergenic sub-model
   ((Trans_I2END 0.0001)
    (Trans_I2I   0.9999)
   )

   ;; Pfold sub-model
   ;; (these are "super-normalized", but it shouldn't pose a practical problem)
   ((Trans_S2L 0.252088)
    (Trans_S2B 0.747943)
   )
   ((Trans_F2F 0.670356)
    (Trans_F2B 0.270181)
    (Trans_F2CLOSE 0.059954)
   )
   ((Trans_L2F 0.226252)
    (Trans_L2U 0.774319)
   )

   ;; Closing-loop sub-model
   ((Trans_CLOSELOOP2CLOSELOOP 0.720465)
    (Trans_CLOSELOOP2END 0.280097)
   )

   ;; equilibria for Markov chains
   ;; stems (LNUC RNUC)
  ((LNUC_RNUC_aa 0.00311835)
   (LNUC_RNUC_ac 0.00296244)
   (LNUC_RNUC_ag 0.00210057)
   (LNUC_RNUC_au 0.154642)
   (LNUC_RNUC_ca 0.00325754)
   (LNUC_RNUC_cc 0.0011288)
   (LNUC_RNUC_cg 0.243332)
   (LNUC_RNUC_cu 0.0028457)
   (LNUC_RNUC_ga 0.00314876)
   (LNUC_RNUC_gc 0.265172)
   (LNUC_RNUC_gg 0.00369554)
   (LNUC_RNUC_gu 0.0673116)
   (LNUC_RNUC_ua 0.174222)
   (LNUC_RNUC_uc 0.00157985)
   (LNUC_RNUC_ug 0.0669394)
   (LNUC_RNUC_uu 0.00480583))

   ;; loops (NUC)
  ((NUC_a 0.389312)
   (NUC_c 0.166431)
   (NUC_g 0.207906)
   (NUC_u 0.236843))

   ;; closing basepair
  ((LCLOSE_RCLOSE_aa 0.0547499)
   (LCLOSE_RCLOSE_ac 0.066247)
   (LCLOSE_RCLOSE_ag 0.0596225)
   (LCLOSE_RCLOSE_au 0.0493434)
   (LCLOSE_RCLOSE_ca 0.0332385)
   (LCLOSE_RCLOSE_cc 0.0105034)
   (LCLOSE_RCLOSE_cg 0.067968)
   (LCLOSE_RCLOSE_cu 0.0185171)
   (LCLOSE_RCLOSE_ga 0.275667)
   (LCLOSE_RCLOSE_gc 0.0372659)
   (LCLOSE_RCLOSE_gg 0.027337)
   (LCLOSE_RCLOSE_gu 0.0158651)
   (LCLOSE_RCLOSE_ua 0.0721929)
   (LCLOSE_RCLOSE_uc 0.0554373)
   (LCLOSE_RCLOSE_ug 0.0727454)
   (LCLOSE_RCLOSE_uu 0.0836205))

   ;; null model (X)
  ((X_au 0.595016)
   (X_gc 0.405283))
   )

 ;; constant rate parameters
 (const-rate

  ;; stems (LNUC RNUC)
  (LNUC_RNUC_aa2ac 0.00786684)
  (LNUC_RNUC_aa2ag 0.0523016)
  (LNUC_RNUC_aa2au 0.364755)
  (LNUC_RNUC_aa2ca 0.0579519)
  (LNUC_RNUC_aa2cc 0.000513624)
  (LNUC_RNUC_aa2cg 0.170164)
  (LNUC_RNUC_aa2cu 0.00243139)
  (LNUC_RNUC_aa2ga 0.0512964)
  (LNUC_RNUC_aa2gc 0.204901)
  (LNUC_RNUC_aa2gg 0.0115097)
  (LNUC_RNUC_aa2gu 0.0980051)
  (LNUC_RNUC_aa2ua 0.68302)
  (LNUC_RNUC_aa2uc 0.00315094)
  (LNUC_RNUC_aa2ug 0.0685832)
  (LNUC_RNUC_aa2uu 0.0100198)
  (LNUC_RNUC_ac2aa 0.00828088)
  (LNUC_RNUC_ac2ag 0.00953204)
  (LNUC_RNUC_ac2au 2.15696)
  (LNUC_RNUC_ac2ca 0.0105472)
  (LNUC_RNUC_ac2cc 0.000227161)
  (LNUC_RNUC_ac2cg 0.143488)
  (LNUC_RNUC_ac2cu 0.00212106)
  (LNUC_RNUC_ac2ga 0.0148953)
  (LNUC_RNUC_ac2gc 0.737646)
  (LNUC_RNUC_ac2gg 0.00674484)
  (LNUC_RNUC_ac2gu 0.149581)
  (LNUC_RNUC_ac2ua 0.1009)
  (LNUC_RNUC_ac2uc 0.0368038)
  (LNUC_RNUC_ac2ug 0.0509773)
  (LNUC_RNUC_ac2uu 0.0514744)
  (LNUC_RNUC_ag2aa 0.077643)
  (LNUC_RNUC_ag2ac 0.013443)
  (LNUC_RNUC_ag2au 0.355273)
  (LNUC_RNUC_ag2ca 0.0151662)
  (LNUC_RNUC_ag2cc 0.00084486)
  (LNUC_RNUC_ag2cg 0.384752)
  (LNUC_RNUC_ag2cu 0.0144278)
  (LNUC_RNUC_ag2ga 0.0848466)
  (LNUC_RNUC_ag2gc 0.319968)
  (LNUC_RNUC_ag2gg 0.697372)
  (LNUC_RNUC_ag2gu 0.105623)
  (LNUC_RNUC_ag2ua 0.0955235)
  (LNUC_RNUC_ag2uc 0.058517)
  (LNUC_RNUC_ag2ug 0.133879)
  (LNUC_RNUC_ag2uu 0.00420698)
  (LNUC_RNUC_au2aa 0.0073502)
  (LNUC_RNUC_au2ac 0.0413491)
  (LNUC_RNUC_au2ag 0.00482251)
  (LNUC_RNUC_au2ca 0.00288343)
  (LNUC_RNUC_au2cc 0.00203748)
  (LNUC_RNUC_au2cg 0.232612)
  (LNUC_RNUC_au2cu 0.00274306)
  (LNUC_RNUC_au2ga 0.00198727)
  (LNUC_RNUC_au2gc 0.639493)
  (LNUC_RNUC_au2gg 0.00234045)
  (LNUC_RNUC_au2gu 0.189727)
  (LNUC_RNUC_au2ua 0.215835)
  (LNUC_RNUC_au2uc 0.00441308)
  (LNUC_RNUC_au2ug 0.0406106)
  (LNUC_RNUC_au2uu 0.0176645)
  (LNUC_RNUC_ca2aa 0.0554373)
  (LNUC_RNUC_ca2ac 0.00959169)
  (LNUC_RNUC_ca2ag 0.00977288)
  (LNUC_RNUC_ca2au 0.136787)
  (LNUC_RNUC_ca2cc 0.00901785)
  (LNUC_RNUC_ca2cg 1.35191)
  (LNUC_RNUC_ca2cu 0.0287758)
  (LNUC_RNUC_ca2ga 0.000438237)
  (LNUC_RNUC_ca2gc 0.0326449)
  (LNUC_RNUC_ca2gg 5.74235e-05)
  (LNUC_RNUC_ca2gu 0.0415214)
  (LNUC_RNUC_ca2ua 1.44693)
  (LNUC_RNUC_ca2uc 0.0435555)
  (LNUC_RNUC_ca2ug 0.136219)
  (LNUC_RNUC_ca2uu 0.0752586)
  (LNUC_RNUC_cc2aa 0.00141793)
  (LNUC_RNUC_cc2ac 0.000596165)
  (LNUC_RNUC_cc2ag 0.00157111)
  (LNUC_RNUC_cc2au 0.278935)
  (LNUC_RNUC_cc2ca 0.0260242)
  (LNUC_RNUC_cc2cg 0.783497)
  (LNUC_RNUC_cc2cu 0.284401)
  (LNUC_RNUC_cc2ga 7.95299e-07)
  (LNUC_RNUC_cc2gc 0.671752)
  (LNUC_RNUC_cc2gg 0.00160412)
  (LNUC_RNUC_cc2gu 0.00518299)
  (LNUC_RNUC_cc2ua 0.0373953)
  (LNUC_RNUC_cc2uc 0.000783923)
  (LNUC_RNUC_cc2ug 0.00206592)
  (LNUC_RNUC_cc2uu 0.387697)
  (LNUC_RNUC_cg2aa 0.00217918)
  (LNUC_RNUC_cg2ac 0.00174688)
  (LNUC_RNUC_cg2ag 0.00332138)
  (LNUC_RNUC_cg2au 0.147829)
  (LNUC_RNUC_cg2ca 0.0181109)
  (LNUC_RNUC_cg2cc 0.00363457)
  (LNUC_RNUC_cg2cu 0.00249975)
  (LNUC_RNUC_cg2ga 0.00385782)
  (LNUC_RNUC_cg2gc 0.177883)
  (LNUC_RNUC_cg2gg 0.00207166)
  (LNUC_RNUC_cg2gu 0.0388754)
  (LNUC_RNUC_cg2ua 0.422493)
  (LNUC_RNUC_cg2uc 0.00157111)
  (LNUC_RNUC_cg2ug 0.170046)
  (LNUC_RNUC_cg2uu 0.00360946)
  (LNUC_RNUC_cu2aa 0.00266435)
  (LNUC_RNUC_cu2ac 0.0022096)
  (LNUC_RNUC_cu2ag 0.0106574)
  (LNUC_RNUC_cu2au 0.149167)
  (LNUC_RNUC_cu2ca 0.0329632)
  (LNUC_RNUC_cu2cc 0.112891)
  (LNUC_RNUC_cu2cg 0.213899)
  (LNUC_RNUC_cu2ga 0.00878343)
  (LNUC_RNUC_cu2gc 0.0293804)
  (LNUC_RNUC_cu2gg 2.53401e-08)
  (LNUC_RNUC_cu2gu 0.0135835)
  (LNUC_RNUC_cu2ua 0.126833)
  (LNUC_RNUC_cu2uc 0.414085)
  (LNUC_RNUC_cu2ug 0.0144179)
  (LNUC_RNUC_cu2uu 0.117115)
  (LNUC_RNUC_ga2aa 0.050801)
  (LNUC_RNUC_ga2ac 0.0140236)
  (LNUC_RNUC_ga2ag 0.0566021)
  (LNUC_RNUC_ga2au 0.0975983)
  (LNUC_RNUC_ga2ca 0.000453692)
  (LNUC_RNUC_ga2cc 2.85303e-07)
  (LNUC_RNUC_ga2cg 0.298334)
  (LNUC_RNUC_ga2cu 0.00793805)
  (LNUC_RNUC_ga2gc 0.367038)
  (LNUC_RNUC_ga2gg 0.126482)
  (LNUC_RNUC_ga2gu 0.141709)
  (LNUC_RNUC_ga2ua 0.0706092)
  (LNUC_RNUC_ga2uc 0.0342204)
  (LNUC_RNUC_ga2ug 0.0263692)
  (LNUC_RNUC_ga2uu 0.00010649)
  (LNUC_RNUC_gc2aa 0.00240958)
  (LNUC_RNUC_gc2ac 0.0082408)
  (LNUC_RNUC_gc2ag 0.00253289)
  (LNUC_RNUC_gc2au 0.373195)
  (LNUC_RNUC_gc2ca 0.000401031)
  (LNUC_RNUC_gc2cc 0.00285954)
  (LNUC_RNUC_gc2cg 0.163232)
  (LNUC_RNUC_gc2cu 0.000315297)
  (LNUC_RNUC_gc2ga 0.00435836)
  (LNUC_RNUC_gc2gg 0.00462927)
  (LNUC_RNUC_gc2gu 0.148342)
  (LNUC_RNUC_gc2ua 0.110109)
  (LNUC_RNUC_gc2uc 0.00449021)
  (LNUC_RNUC_gc2ug 0.0375251)
  (LNUC_RNUC_gc2uu 0.00112022)
  (LNUC_RNUC_gg2aa 0.00971211)
  (LNUC_RNUC_gg2ac 0.00540683)
  (LNUC_RNUC_gg2ag 0.396392)
  (LNUC_RNUC_gg2au 0.0979371)
  (LNUC_RNUC_gg2ca 5.06527e-05)
  (LNUC_RNUC_gg2cc 0.000490316)
  (LNUC_RNUC_gg2cg 0.136503)
  (LNUC_RNUC_gg2cu 1.95129e-08)
  (LNUC_RNUC_gg2ga 0.107768)
  (LNUC_RNUC_gg2gc 0.332171)
  (LNUC_RNUC_gg2gu 0.102451)
  (LNUC_RNUC_gg2ua 0.0571541)
  (LNUC_RNUC_gg2uc 4.13716e-05)
  (LNUC_RNUC_gg2ug 0.238325)
  (LNUC_RNUC_gg2uu 0.000188781)
  (LNUC_RNUC_gu2aa 0.00454029)
  (LNUC_RNUC_gu2ac 0.00658318)
  (LNUC_RNUC_gu2ag 0.00329387)
  (LNUC_RNUC_gu2au 0.435879)
  (LNUC_RNUC_gu2ca 0.00200943)
  (LNUC_RNUC_gu2cc 8.69171e-05)
  (LNUC_RNUC_gu2cg 0.140535)
  (LNUC_RNUC_gu2cu 0.000573865)
  (LNUC_RNUC_gu2ga 0.00662437)
  (LNUC_RNUC_gu2gc 0.583984)
  (LNUC_RNUC_gu2gg 0.00562083)
  (LNUC_RNUC_gu2ua 0.122682)
  (LNUC_RNUC_gu2uc 0.0120652)
  (LNUC_RNUC_gu2ug 0.0493776)
  (LNUC_RNUC_gu2uu 0.0135647)
  (LNUC_RNUC_ua2aa 0.0122252)
  (LNUC_RNUC_ua2ac 0.00171568)
  (LNUC_RNUC_ua2ag 0.00115172)
  (LNUC_RNUC_ua2au 0.191577)
  (LNUC_RNUC_ua2ca 0.0270918)
  (LNUC_RNUC_ua2cc 0.000242286)
  (LNUC_RNUC_ua2cg 0.590496)
  (LNUC_RNUC_ua2cu 0.00207022)
  (LNUC_RNUC_ua2ga 0.00127525)
  (LNUC_RNUC_ua2gc 0.167589)
  (LNUC_RNUC_ua2gg 0.00121233)
  (LNUC_RNUC_ua2gu 0.0474319)
  (LNUC_RNUC_ua2uc 0.0152505)
  (LNUC_RNUC_ua2ug 0.180992)
  (LNUC_RNUC_ua2uu 0.00712448)
  (LNUC_RNUC_uc2aa 0.00621513)
  (LNUC_RNUC_uc2ac 0.0690124)
  (LNUC_RNUC_uc2ag 0.0777507)
  (LNUC_RNUC_uc2au 0.43167)
  (LNUC_RNUC_uc2ca 0.0898088)
  (LNUC_RNUC_uc2cc 0.000560111)
  (LNUC_RNUC_uc2cg 0.241987)
  (LNUC_RNUC_uc2cu 0.745355)
  (LNUC_RNUC_uc2ga 0.0681567)
  (LNUC_RNUC_uc2gc 0.753145)
  (LNUC_RNUC_uc2gg 9.67754e-05)
  (LNUC_RNUC_uc2gu 0.514057)
  (LNUC_RNUC_uc2ua 1.67946)
  (LNUC_RNUC_uc2ug 0.218393)
  (LNUC_RNUC_uc2uu 0.386891)
  (LNUC_RNUC_ug2aa 0.00319493)
  (LNUC_RNUC_ug2ac 0.00225603)
  (LNUC_RNUC_ug2ag 0.00420115)
  (LNUC_RNUC_ug2au 0.0938174)
  (LNUC_RNUC_ug2ca 0.00663356)
  (LNUC_RNUC_ug2cc 3.48375e-05)
  (LNUC_RNUC_ug2cg 0.618138)
  (LNUC_RNUC_ug2cu 0.000612501)
  (LNUC_RNUC_ug2ga 0.00123952)
  (LNUC_RNUC_ug2gc 0.148651)
  (LNUC_RNUC_ug2gg 0.0131572)
  (LNUC_RNUC_ug2gu 0.0496522)
  (LNUC_RNUC_ug2ua 0.471066)
  (LNUC_RNUC_ug2uc 0.00515433)
  (LNUC_RNUC_ug2uu 0.0180607)
  (LNUC_RNUC_uu2aa 0.00650155)
  (LNUC_RNUC_uu2ac 0.0317522)
  (LNUC_RNUC_uu2ag 0.00183883)
  (LNUC_RNUC_uu2au 0.568803)
  (LNUC_RNUC_uu2ca 0.0510481)
  (LNUC_RNUC_uu2cc 0.0911256)
  (LNUC_RNUC_uu2cg 0.182757)
  (LNUC_RNUC_uu2cu 0.0693)
  (LNUC_RNUC_uu2ga 6.97716e-05)
  (LNUC_RNUC_uu2gc 0.0618535)
  (LNUC_RNUC_uu2gg 0.000145167)
  (LNUC_RNUC_uu2gu 0.190122)
  (LNUC_RNUC_uu2ua 0.258279)
  (LNUC_RNUC_uu2uc 0.127185)
  (LNUC_RNUC_uu2ug 0.251564)

  ;; loops (NUC)
  (NUC_a2c 0.150622)
  (NUC_a2g 0.202361)
  (NUC_a2u 0.204192)
  (NUC_c2a 0.352086)
  (NUC_c2g 0.13167)
  (NUC_c2u 0.632878)
  (NUC_g2a 0.378667)
  (NUC_g2c 0.105404)
  (NUC_g2u 0.220523)
  (NUC_u2a 0.335643)
  (NUC_u2c 0.444729)
  (NUC_u2g 0.193714)

  ;; closing basepair (LCLOSE RCLOSE)
  (LCLOSE_RCLOSE_aa2ac 0.0595812)
  (LCLOSE_RCLOSE_aa2ag 0.0436765)
  (LCLOSE_RCLOSE_aa2au 0.730522)
  (LCLOSE_RCLOSE_aa2ca 0.231326)
  (LCLOSE_RCLOSE_aa2cc 0.029462)
  (LCLOSE_RCLOSE_aa2cg 0.0461668)
  (LCLOSE_RCLOSE_aa2cu 0.00576286)
  (LCLOSE_RCLOSE_aa2ga 0.393381)
  (LCLOSE_RCLOSE_aa2gc 0.0804368)
  (LCLOSE_RCLOSE_aa2gg 0.00595369)
  (LCLOSE_RCLOSE_aa2gu 0.0641681)
  (LCLOSE_RCLOSE_aa2ua 0.496891)
  (LCLOSE_RCLOSE_aa2uc 0.00130295)
  (LCLOSE_RCLOSE_aa2ug 0.019998)
  (LCLOSE_RCLOSE_aa2uu 0.0101456)
  (LCLOSE_RCLOSE_ac2aa 0.0492409)
  (LCLOSE_RCLOSE_ac2ag 0.162217)
  (LCLOSE_RCLOSE_ac2au 0.476319)
  (LCLOSE_RCLOSE_ac2ca 0.00553194)
  (LCLOSE_RCLOSE_ac2cc 0.156909)
  (LCLOSE_RCLOSE_ac2cg 0.0379962)
  (LCLOSE_RCLOSE_ac2cu 0.00679175)
  (LCLOSE_RCLOSE_ac2ga 0.00286153)
  (LCLOSE_RCLOSE_ac2gc 0.269433)
  (LCLOSE_RCLOSE_ac2gg 0.0020545)
  (LCLOSE_RCLOSE_ac2gu 0.0316862)
  (LCLOSE_RCLOSE_ac2ua 0.0331925)
  (LCLOSE_RCLOSE_ac2uc 0.118339)
  (LCLOSE_RCLOSE_ac2ug 0.0373694)
  (LCLOSE_RCLOSE_ac2uu 0.00499604)
  (LCLOSE_RCLOSE_ag2aa 0.0401071)
  (LCLOSE_RCLOSE_ag2ac 0.180241)
  (LCLOSE_RCLOSE_ag2au 0.252613)
  (LCLOSE_RCLOSE_ag2ca 0.00278521)
  (LCLOSE_RCLOSE_ag2cc 0.000565573)
  (LCLOSE_RCLOSE_ag2cg 0.152618)
  (LCLOSE_RCLOSE_ag2cu 0.00511872)
  (LCLOSE_RCLOSE_ag2ga 0.13167)
  (LCLOSE_RCLOSE_ag2gc 0.11415)
  (LCLOSE_RCLOSE_ag2gg 0.0426592)
  (LCLOSE_RCLOSE_ag2gu 0.0557455)
  (LCLOSE_RCLOSE_ag2ua 0.0697337)
  (LCLOSE_RCLOSE_ag2uc 1.72625e-05)
  (LCLOSE_RCLOSE_ag2ug 0.0899333)
  (LCLOSE_RCLOSE_ag2uu 0.00691047)
  (LCLOSE_RCLOSE_au2aa 0.810565)
  (LCLOSE_RCLOSE_au2ac 0.639493)
  (LCLOSE_RCLOSE_au2ag 0.305237)
  (LCLOSE_RCLOSE_au2ca 0.067968)
  (LCLOSE_RCLOSE_au2cc 0.133231)
  (LCLOSE_RCLOSE_au2cg 0.097666)
  (LCLOSE_RCLOSE_au2cu 0.257563)
  (LCLOSE_RCLOSE_au2ga 0.0520124)
  (LCLOSE_RCLOSE_au2gc 0.215088)
  (LCLOSE_RCLOSE_au2gg 0.0313585)
  (LCLOSE_RCLOSE_au2gu 0.204051)
  (LCLOSE_RCLOSE_au2ua 0.114626)
  (LCLOSE_RCLOSE_au2uc 0.134717)
  (LCLOSE_RCLOSE_au2ug 0.0442248)
  (LCLOSE_RCLOSE_au2uu 0.256672)
  (LCLOSE_RCLOSE_ca2aa 0.381036)
  (LCLOSE_RCLOSE_ca2ac 0.0110256)
  (LCLOSE_RCLOSE_ca2ag 0.00499604)
  (LCLOSE_RCLOSE_ca2au 0.1009)
  (LCLOSE_RCLOSE_ca2cc 0.144286)
  (LCLOSE_RCLOSE_ca2cg 0.434672)
  (LCLOSE_RCLOSE_ca2cu 0.173259)
  (LCLOSE_RCLOSE_ca2ga 0.106137)
  (LCLOSE_RCLOSE_ca2gc 0.137452)
  (LCLOSE_RCLOSE_ca2gg 0.00655586)
  (LCLOSE_RCLOSE_ca2gu 0.0655618)
  (LCLOSE_RCLOSE_ca2ua 0.742776)
  (LCLOSE_RCLOSE_ca2uc 0.0337259)
  (LCLOSE_RCLOSE_ca2ug 0.065109)
  (LCLOSE_RCLOSE_ca2uu 0.0267373)
  (LCLOSE_RCLOSE_cc2aa 0.15368)
  (LCLOSE_RCLOSE_cc2ac 0.989657)
  (LCLOSE_RCLOSE_cc2ag 0.0032127)
  (LCLOSE_RCLOSE_cc2au 0.625898)
  (LCLOSE_RCLOSE_cc2ca 0.456599)
  (LCLOSE_RCLOSE_cc2cg 0.450001)
  (LCLOSE_RCLOSE_cc2cu 1.12896)
  (LCLOSE_RCLOSE_cc2ga 0.00538813)
  (LCLOSE_RCLOSE_cc2gc 1.04102)
  (LCLOSE_RCLOSE_cc2gg 0.00657406)
  (LCLOSE_RCLOSE_cc2gu 0.255253)
  (LCLOSE_RCLOSE_cc2ua 0.572759)
  (LCLOSE_RCLOSE_cc2uc 0.932386)
  (LCLOSE_RCLOSE_cc2ug 0.217638)
  (LCLOSE_RCLOSE_cc2uu 0.174585)
  (LCLOSE_RCLOSE_cg2aa 0.0371885)
  (LCLOSE_RCLOSE_cg2ac 0.0370341)
  (LCLOSE_RCLOSE_cg2ag 0.133879)
  (LCLOSE_RCLOSE_cg2au 0.0709035)
  (LCLOSE_RCLOSE_cg2ca 0.212569)
  (LCLOSE_RCLOSE_cg2cc 0.0695406)
  (LCLOSE_RCLOSE_cg2cu 0.176165)
  (LCLOSE_RCLOSE_cg2ga 0.103092)
  (LCLOSE_RCLOSE_cg2gc 0.0422472)
  (LCLOSE_RCLOSE_cg2gg 0.0682986)
  (LCLOSE_RCLOSE_cg2gu 0.0590467)
  (LCLOSE_RCLOSE_cg2ua 0.050485)
  (LCLOSE_RCLOSE_cg2uc 0.0446561)
  (LCLOSE_RCLOSE_cg2ug 0.844986)
  (LCLOSE_RCLOSE_cg2uu 0.20208)
  (LCLOSE_RCLOSE_cu2aa 0.0170392)
  (LCLOSE_RCLOSE_cu2ac 0.0242983)
  (LCLOSE_RCLOSE_cu2ag 0.0164816)
  (LCLOSE_RCLOSE_cu2au 0.686342)
  (LCLOSE_RCLOSE_cu2ca 0.311003)
  (LCLOSE_RCLOSE_cu2cc 0.640824)
  (LCLOSE_RCLOSE_cu2cg 0.646624)
  (LCLOSE_RCLOSE_cu2ga 0.00284373)
  (LCLOSE_RCLOSE_cu2gc 0.378142)
  (LCLOSE_RCLOSE_cu2gg 0.00444685)
  (LCLOSE_RCLOSE_cu2gu 0.271119)
  (LCLOSE_RCLOSE_cu2ua 0.636839)
  (LCLOSE_RCLOSE_cu2uc 0.0421887)
  (LCLOSE_RCLOSE_cu2ug 0.176165)
  (LCLOSE_RCLOSE_cu2uu 0.576343)
  (LCLOSE_RCLOSE_ga2aa 0.0781289)
  (LCLOSE_RCLOSE_ga2ac 0.000688145)
  (LCLOSE_RCLOSE_ga2ag 0.0284782)
  (LCLOSE_RCLOSE_ga2au 0.00931002)
  (LCLOSE_RCLOSE_ga2ca 0.0128063)
  (LCLOSE_RCLOSE_ga2cc 0.000205439)
  (LCLOSE_RCLOSE_ga2cg 0.0254357)
  (LCLOSE_RCLOSE_ga2cu 0.000191151)
  (LCLOSE_RCLOSE_ga2gc 0.0355009)
  (LCLOSE_RCLOSE_ga2gg 0.0612138)
  (LCLOSE_RCLOSE_ga2gu 0.01888)
  (LCLOSE_RCLOSE_ga2ua 0.050485)
  (LCLOSE_RCLOSE_ga2uc 0.0301646)
  (LCLOSE_RCLOSE_ga2ug 0.0276036)
  (LCLOSE_RCLOSE_ga2uu 0.00599926)
  (LCLOSE_RCLOSE_gc2aa 0.118175)
  (LCLOSE_RCLOSE_gc2ac 0.478968)
  (LCLOSE_RCLOSE_gc2ag 0.182504)
  (LCLOSE_RCLOSE_gc2au 0.284796)
  (LCLOSE_RCLOSE_gc2ca 0.122597)
  (LCLOSE_RCLOSE_gc2cc 0.293615)
  (LCLOSE_RCLOSE_gc2cg 0.0770533)
  (LCLOSE_RCLOSE_gc2cu 0.187895)
  (LCLOSE_RCLOSE_gc2ga 0.262429)
  (LCLOSE_RCLOSE_gc2gg 0.125608)
  (LCLOSE_RCLOSE_gc2gu 0.242827)
  (LCLOSE_RCLOSE_gc2ua 0.0779126)
  (LCLOSE_RCLOSE_gc2uc 0.169341)
  (LCLOSE_RCLOSE_gc2ug 0.0315985)
  (LCLOSE_RCLOSE_gc2uu 0.408384)
  (LCLOSE_RCLOSE_gg2aa 0.0119239)
  (LCLOSE_RCLOSE_gg2ac 0.00497875)
  (LCLOSE_RCLOSE_gg2ag 0.0931048)
  (LCLOSE_RCLOSE_gg2au 0.0566021)
  (LCLOSE_RCLOSE_gg2ca 0.00797113)
  (LCLOSE_RCLOSE_gg2cc 0.00252588)
  (LCLOSE_RCLOSE_gg2cg 0.169811)
  (LCLOSE_RCLOSE_gg2cu 0.00301213)
  (LCLOSE_RCLOSE_gg2ga 0.617281)
  (LCLOSE_RCLOSE_gg2gc 0.171348)
  (LCLOSE_RCLOSE_gg2gu 0.0797153)
  (LCLOSE_RCLOSE_gg2ua 0.0414352)
  (LCLOSE_RCLOSE_gg2uc 0.0441024)
  (LCLOSE_RCLOSE_gg2ug 0.0840855)
  (LCLOSE_RCLOSE_gg2uu 0.00648805)
  (LCLOSE_RCLOSE_gu2aa 0.221595)
  (LCLOSE_RCLOSE_gu2ac 0.132402)
  (LCLOSE_RCLOSE_gu2ag 0.209642)
  (LCLOSE_RCLOSE_gu2au 0.634635)
  (LCLOSE_RCLOSE_gu2ca 0.137357)
  (LCLOSE_RCLOSE_gu2cc 0.168989)
  (LCLOSE_RCLOSE_gu2cg 0.253139)
  (LCLOSE_RCLOSE_gu2cu 0.316659)
  (LCLOSE_RCLOSE_gu2ga 0.328053)
  (LCLOSE_RCLOSE_gu2gc 0.570777)
  (LCLOSE_RCLOSE_gu2gg 0.137452)
  (LCLOSE_RCLOSE_gu2ua 0.442577)
  (LCLOSE_RCLOSE_gu2uc 0.176409)
  (LCLOSE_RCLOSE_gu2ug 0.339622)
  (LCLOSE_RCLOSE_gu2uu 0.354289)
  (LCLOSE_RCLOSE_ua2aa 0.376834)
  (LCLOSE_RCLOSE_ua2ac 0.0304587)
  (LCLOSE_RCLOSE_ua2ag 0.0575915)
  (LCLOSE_RCLOSE_ua2au 0.0782915)
  (LCLOSE_RCLOSE_ua2ca 0.341984)
  (LCLOSE_RCLOSE_ua2cc 0.0832734)
  (LCLOSE_RCLOSE_ua2cg 0.0475306)
  (LCLOSE_RCLOSE_ua2cu 0.163346)
  (LCLOSE_RCLOSE_ua2ga 0.192776)
  (LCLOSE_RCLOSE_ua2gc 0.0402184)
  (LCLOSE_RCLOSE_ua2gg 0.0156792)
  (LCLOSE_RCLOSE_ua2gu 0.0971933)
  (LCLOSE_RCLOSE_ua2uc 0.122428)
  (LCLOSE_RCLOSE_ua2ug 0.284599)
  (LCLOSE_RCLOSE_ua2uu 0.142497)
  (LCLOSE_RCLOSE_uc2aa 0.00128769)
  (LCLOSE_RCLOSE_uc2ac 0.141512)
  (LCLOSE_RCLOSE_uc2ag 1.85657e-05)
  (LCLOSE_RCLOSE_uc2au 0.119908)
  (LCLOSE_RCLOSE_uc2ca 0.020221)
  (LCLOSE_RCLOSE_uc2cc 0.176654)
  (LCLOSE_RCLOSE_uc2cg 0.0547499)
  (LCLOSE_RCLOSE_uc2cu 0.0141016)
  (LCLOSE_RCLOSE_uc2ga 0.149996)
  (LCLOSE_RCLOSE_uc2gc 0.113913)
  (LCLOSE_RCLOSE_uc2gg 0.0217476)
  (LCLOSE_RCLOSE_uc2gu 0.050485)
  (LCLOSE_RCLOSE_uc2ua 0.159431)
  (LCLOSE_RCLOSE_uc2ug 0.0578315)
  (LCLOSE_RCLOSE_uc2uu 0.104676)
  (LCLOSE_RCLOSE_ug2aa 0.0150614)
  (LCLOSE_RCLOSE_ug2ac 0.0340312)
  (LCLOSE_RCLOSE_ug2ag 0.0737609)
  (LCLOSE_RCLOSE_ug2au 0.0300186)
  (LCLOSE_RCLOSE_ug2ca 0.0297699)
  (LCLOSE_RCLOSE_ug2cc 0.0314456)
  (LCLOSE_RCLOSE_ug2cg 0.790041)
  (LCLOSE_RCLOSE_ug2cu 0.0448733)
  (LCLOSE_RCLOSE_ug2ga 0.104676)
  (LCLOSE_RCLOSE_ug2gc 0.0161872)
  (LCLOSE_RCLOSE_ug2gg 0.0315985)
  (LCLOSE_RCLOSE_ug2gu 0.0740683)
  (LCLOSE_RCLOSE_ug2ua 0.282633)
  (LCLOSE_RCLOSE_ug2uc 0.0440718)
  (LCLOSE_RCLOSE_ug2uu 0.113361)
  (LCLOSE_RCLOSE_uu2aa 0.00664277)
  (LCLOSE_RCLOSE_uu2ac 0.00395803)
  (LCLOSE_RCLOSE_uu2ag 0.00492726)
  (LCLOSE_RCLOSE_uu2au 0.151459)
  (LCLOSE_RCLOSE_uu2ca 0.0106279)
  (LCLOSE_RCLOSE_uu2cc 0.0219292)
  (LCLOSE_RCLOSE_uu2cg 0.164368)
  (LCLOSE_RCLOSE_uu2cu 0.127627)
  (LCLOSE_RCLOSE_uu2ga 0.0197774)
  (LCLOSE_RCLOSE_uu2gc 0.181999)
  (LCLOSE_RCLOSE_uu2gg 0.00212106)
  (LCLOSE_RCLOSE_uu2gu 0.0671718)
  (LCLOSE_RCLOSE_uu2ua 0.123023)
  (LCLOSE_RCLOSE_uu2uc 0.0693962)
  (LCLOSE_RCLOSE_uu2ug 0.0986184)

  ;; strand-symmetric null model (X)
  (X_a2c_u2g 0.176654)
  (X_a2g_u2c 0.352086)
  (X_a2u_u2a 0.247414)
  (X_c2a_g2u 0.265908)
  (X_c2g_g2c 0.2111)
  (X_c2u_g2a 0.529976)
 )


;; Markov chain substitution models

;; Basepairs
 (chain
  (update-policy parametric)
  (terminal (LNUC RNUC))

  ;; initial probability distribution
  (initial (state (a a)) (prob LNUC_RNUC_aa))
  (initial (state (c a)) (prob LNUC_RNUC_ca))
  (initial (state (g a)) (prob LNUC_RNUC_ga))
  (initial (state (u a)) (prob LNUC_RNUC_ua))
  (initial (state (a c)) (prob LNUC_RNUC_ac))
  (initial (state (c c)) (prob LNUC_RNUC_cc))
  (initial (state (g c)) (prob LNUC_RNUC_gc))
  (initial (state (u c)) (prob LNUC_RNUC_uc))
  (initial (state (a g)) (prob LNUC_RNUC_ag))
  (initial (state (c g)) (prob LNUC_RNUC_cg))
  (initial (state (g g)) (prob LNUC_RNUC_gg))
  (initial (state (u g)) (prob LNUC_RNUC_ug))
  (initial (state (a u)) (prob LNUC_RNUC_au))
  (initial (state (c u)) (prob LNUC_RNUC_cu))
  (initial (state (g u)) (prob LNUC_RNUC_gu))
  (initial (state (u u)) (prob LNUC_RNUC_uu))

  ;; mutation rates
  (mutate (from (a a)) (to (c a)) (rate LNUC_RNUC_aa2ca))
  (mutate (from (a a)) (to (g a)) (rate LNUC_RNUC_aa2ga))
  (mutate (from (a a)) (to (u a)) (rate LNUC_RNUC_aa2ua))
  (mutate (from (a a)) (to (a c)) (rate LNUC_RNUC_aa2ac))
  (mutate (from (a a)) (to (g c)) (rate LNUC_RNUC_aa2gc))
  (mutate (from (a a)) (to (u c)) (rate LNUC_RNUC_aa2uc))
  (mutate (from (a a)) (to (a g)) (rate LNUC_RNUC_aa2ag))
  (mutate (from (a a)) (to (c g)) (rate LNUC_RNUC_aa2cg))
  (mutate (from (a a)) (to (u g)) (rate LNUC_RNUC_aa2ug))
  (mutate (from (a a)) (to (a u)) (rate LNUC_RNUC_aa2au))
  (mutate (from (a a)) (to (c u)) (rate LNUC_RNUC_aa2cu))
  (mutate (from (a a)) (to (g u)) (rate LNUC_RNUC_aa2gu))
  (mutate (from (c a)) (to (a a)) (rate LNUC_RNUC_ca2aa))
  (mutate (from (c a)) (to (g a)) (rate LNUC_RNUC_ca2ga))
  (mutate (from (c a)) (to (u a)) (rate LNUC_RNUC_ca2ua))
  (mutate (from (c a)) (to (a c)) (rate LNUC_RNUC_ca2ac))
  (mutate (from (c a)) (to (c c)) (rate LNUC_RNUC_ca2cc))
  (mutate (from (c a)) (to (g c)) (rate LNUC_RNUC_ca2gc))
  (mutate (from (c a)) (to (u c)) (rate LNUC_RNUC_ca2uc))
  (mutate (from (c a)) (to (a g)) (rate LNUC_RNUC_ca2ag))
  (mutate (from (c a)) (to (c g)) (rate LNUC_RNUC_ca2cg))
  (mutate (from (c a)) (to (u g)) (rate LNUC_RNUC_ca2ug))
  (mutate (from (c a)) (to (a u)) (rate LNUC_RNUC_ca2au))
  (mutate (from (c a)) (to (c u)) (rate LNUC_RNUC_ca2cu))
  (mutate (from (c a)) (to (g u)) (rate LNUC_RNUC_ca2gu))
  (mutate (from (c a)) (to (u u)) (rate LNUC_RNUC_ca2uu))
  (mutate (from (g a)) (to (a a)) (rate LNUC_RNUC_ga2aa))
  (mutate (from (g a)) (to (c a)) (rate LNUC_RNUC_ga2ca))
  (mutate (from (g a)) (to (u a)) (rate LNUC_RNUC_ga2ua))
  (mutate (from (g a)) (to (a c)) (rate LNUC_RNUC_ga2ac))
  (mutate (from (g a)) (to (g c)) (rate LNUC_RNUC_ga2gc))
  (mutate (from (g a)) (to (a g)) (rate LNUC_RNUC_ga2ag))
  (mutate (from (g a)) (to (c g)) (rate LNUC_RNUC_ga2cg))
  (mutate (from (g a)) (to (u g)) (rate LNUC_RNUC_ga2ug))
  (mutate (from (g a)) (to (a u)) (rate LNUC_RNUC_ga2au))
  (mutate (from (g a)) (to (c u)) (rate LNUC_RNUC_ga2cu))
  (mutate (from (g a)) (to (g u)) (rate LNUC_RNUC_ga2gu))
  (mutate (from (u a)) (to (a a)) (rate LNUC_RNUC_ua2aa))
  (mutate (from (u a)) (to (c a)) (rate LNUC_RNUC_ua2ca))
  (mutate (from (u a)) (to (g a)) (rate LNUC_RNUC_ua2ga))
  (mutate (from (u a)) (to (a c)) (rate LNUC_RNUC_ua2ac))
  (mutate (from (u a)) (to (c c)) (rate LNUC_RNUC_ua2cc))
  (mutate (from (u a)) (to (g c)) (rate LNUC_RNUC_ua2gc))
  (mutate (from (u a)) (to (u c)) (rate LNUC_RNUC_ua2uc))
  (mutate (from (u a)) (to (a g)) (rate LNUC_RNUC_ua2ag))
  (mutate (from (u a)) (to (c g)) (rate LNUC_RNUC_ua2cg))
  (mutate (from (u a)) (to (g g)) (rate LNUC_RNUC_ua2gg))
  (mutate (from (u a)) (to (u g)) (rate LNUC_RNUC_ua2ug))
  (mutate (from (u a)) (to (a u)) (rate LNUC_RNUC_ua2au))
  (mutate (from (u a)) (to (c u)) (rate LNUC_RNUC_ua2cu))
  (mutate (from (u a)) (to (g u)) (rate LNUC_RNUC_ua2gu))
  (mutate (from (u a)) (to (u u)) (rate LNUC_RNUC_ua2uu))
  (mutate (from (a c)) (to (a a)) (rate LNUC_RNUC_ac2aa))
  (mutate (from (a c)) (to (c a)) (rate LNUC_RNUC_ac2ca))
  (mutate (from (a c)) (to (g a)) (rate LNUC_RNUC_ac2ga))
  (mutate (from (a c)) (to (u a)) (rate LNUC_RNUC_ac2ua))
  (mutate (from (a c)) (to (c c)) (rate LNUC_RNUC_ac2cc))
  (mutate (from (a c)) (to (g c)) (rate LNUC_RNUC_ac2gc))
  (mutate (from (a c)) (to (u c)) (rate LNUC_RNUC_ac2uc))
  (mutate (from (a c)) (to (a g)) (rate LNUC_RNUC_ac2ag))
  (mutate (from (a c)) (to (c g)) (rate LNUC_RNUC_ac2cg))
  (mutate (from (a c)) (to (u g)) (rate LNUC_RNUC_ac2ug))
  (mutate (from (a c)) (to (a u)) (rate LNUC_RNUC_ac2au))
  (mutate (from (a c)) (to (c u)) (rate LNUC_RNUC_ac2cu))
  (mutate (from (a c)) (to (g u)) (rate LNUC_RNUC_ac2gu))
  (mutate (from (a c)) (to (u u)) (rate LNUC_RNUC_ac2uu))
  (mutate (from (c c)) (to (c a)) (rate LNUC_RNUC_cc2ca))
  (mutate (from (c c)) (to (u a)) (rate LNUC_RNUC_cc2ua))
  (mutate (from (c c)) (to (a c)) (rate LNUC_RNUC_cc2ac))
  (mutate (from (c c)) (to (g c)) (rate LNUC_RNUC_cc2gc))
  (mutate (from (c c)) (to (u c)) (rate LNUC_RNUC_cc2uc))
  (mutate (from (c c)) (to (c g)) (rate LNUC_RNUC_cc2cg))
  (mutate (from (c c)) (to (u g)) (rate LNUC_RNUC_cc2ug))
  (mutate (from (c c)) (to (a u)) (rate LNUC_RNUC_cc2au))
  (mutate (from (c c)) (to (c u)) (rate LNUC_RNUC_cc2cu))
  (mutate (from (c c)) (to (g u)) (rate LNUC_RNUC_cc2gu))
  (mutate (from (c c)) (to (u u)) (rate LNUC_RNUC_cc2uu))
  (mutate (from (g c)) (to (a a)) (rate LNUC_RNUC_gc2aa))
  (mutate (from (g c)) (to (g a)) (rate LNUC_RNUC_gc2ga))
  (mutate (from (g c)) (to (u a)) (rate LNUC_RNUC_gc2ua))
  (mutate (from (g c)) (to (a c)) (rate LNUC_RNUC_gc2ac))
  (mutate (from (g c)) (to (c c)) (rate LNUC_RNUC_gc2cc))
  (mutate (from (g c)) (to (u c)) (rate LNUC_RNUC_gc2uc))
  (mutate (from (g c)) (to (c g)) (rate LNUC_RNUC_gc2cg))
  (mutate (from (g c)) (to (g g)) (rate LNUC_RNUC_gc2gg))
  (mutate (from (g c)) (to (u g)) (rate LNUC_RNUC_gc2ug))
  (mutate (from (g c)) (to (a u)) (rate LNUC_RNUC_gc2au))
  (mutate (from (g c)) (to (c u)) (rate LNUC_RNUC_gc2cu))
  (mutate (from (g c)) (to (g u)) (rate LNUC_RNUC_gc2gu))
  (mutate (from (g c)) (to (u u)) (rate LNUC_RNUC_gc2uu))
  (mutate (from (u c)) (to (a a)) (rate LNUC_RNUC_uc2aa))
  (mutate (from (u c)) (to (c a)) (rate LNUC_RNUC_uc2ca))
  (mutate (from (u c)) (to (u a)) (rate LNUC_RNUC_uc2ua))
  (mutate (from (u c)) (to (a c)) (rate LNUC_RNUC_uc2ac))
  (mutate (from (u c)) (to (c c)) (rate LNUC_RNUC_uc2cc))
  (mutate (from (u c)) (to (g c)) (rate LNUC_RNUC_uc2gc))
  (mutate (from (u c)) (to (a g)) (rate LNUC_RNUC_uc2ag))
  (mutate (from (u c)) (to (c g)) (rate LNUC_RNUC_uc2cg))
  (mutate (from (u c)) (to (u g)) (rate LNUC_RNUC_uc2ug))
  (mutate (from (u c)) (to (a u)) (rate LNUC_RNUC_uc2au))
  (mutate (from (u c)) (to (c u)) (rate LNUC_RNUC_uc2cu))
  (mutate (from (u c)) (to (g u)) (rate LNUC_RNUC_uc2gu))
  (mutate (from (u c)) (to (u u)) (rate LNUC_RNUC_uc2uu))
  (mutate (from (a g)) (to (a a)) (rate LNUC_RNUC_ag2aa))
  (mutate (from (a g)) (to (c a)) (rate LNUC_RNUC_ag2ca))
  (mutate (from (a g)) (to (g a)) (rate LNUC_RNUC_ag2ga))
  (mutate (from (a g)) (to (u a)) (rate LNUC_RNUC_ag2ua))
  (mutate (from (a g)) (to (a c)) (rate LNUC_RNUC_ag2ac))
  (mutate (from (a g)) (to (g c)) (rate LNUC_RNUC_ag2gc))
  (mutate (from (a g)) (to (u c)) (rate LNUC_RNUC_ag2uc))
  (mutate (from (a g)) (to (c g)) (rate LNUC_RNUC_ag2cg))
  (mutate (from (a g)) (to (u g)) (rate LNUC_RNUC_ag2ug))
  (mutate (from (a g)) (to (a u)) (rate LNUC_RNUC_ag2au))
  (mutate (from (a g)) (to (g u)) (rate LNUC_RNUC_ag2gu))
  (mutate (from (c g)) (to (a a)) (rate LNUC_RNUC_cg2aa))
  (mutate (from (c g)) (to (c a)) (rate LNUC_RNUC_cg2ca))
  (mutate (from (c g)) (to (u a)) (rate LNUC_RNUC_cg2ua))
  (mutate (from (c g)) (to (c c)) (rate LNUC_RNUC_cg2cc))
  (mutate (from (c g)) (to (g c)) (rate LNUC_RNUC_cg2gc))
  (mutate (from (c g)) (to (u c)) (rate LNUC_RNUC_cg2uc))
  (mutate (from (c g)) (to (a g)) (rate LNUC_RNUC_cg2ag))
  (mutate (from (c g)) (to (g g)) (rate LNUC_RNUC_cg2gg))
  (mutate (from (c g)) (to (u g)) (rate LNUC_RNUC_cg2ug))
  (mutate (from (c g)) (to (a u)) (rate LNUC_RNUC_cg2au))
  (mutate (from (c g)) (to (c u)) (rate LNUC_RNUC_cg2cu))
  (mutate (from (c g)) (to (g u)) (rate LNUC_RNUC_cg2gu))
  (mutate (from (c g)) (to (u u)) (rate LNUC_RNUC_cg2uu))
  (mutate (from (g g)) (to (u a)) (rate LNUC_RNUC_gg2ua))
  (mutate (from (g g)) (to (g c)) (rate LNUC_RNUC_gg2gc))
  (mutate (from (g g)) (to (c g)) (rate LNUC_RNUC_gg2cg))
  (mutate (from (g g)) (to (u g)) (rate LNUC_RNUC_gg2ug))
  (mutate (from (g g)) (to (a u)) (rate LNUC_RNUC_gg2au))
  (mutate (from (g g)) (to (g u)) (rate LNUC_RNUC_gg2gu))
  (mutate (from (g g)) (to (u u)) (rate LNUC_RNUC_gg2uu))
  (mutate (from (u g)) (to (a a)) (rate LNUC_RNUC_ug2aa))
  (mutate (from (u g)) (to (c a)) (rate LNUC_RNUC_ug2ca))
  (mutate (from (u g)) (to (g a)) (rate LNUC_RNUC_ug2ga))
  (mutate (from (u g)) (to (u a)) (rate LNUC_RNUC_ug2ua))
  (mutate (from (u g)) (to (a c)) (rate LNUC_RNUC_ug2ac))
  (mutate (from (u g)) (to (c c)) (rate LNUC_RNUC_ug2cc))
  (mutate (from (u g)) (to (g c)) (rate LNUC_RNUC_ug2gc))
  (mutate (from (u g)) (to (u c)) (rate LNUC_RNUC_ug2uc))
  (mutate (from (u g)) (to (a g)) (rate LNUC_RNUC_ug2ag))
  (mutate (from (u g)) (to (c g)) (rate LNUC_RNUC_ug2cg))
  (mutate (from (u g)) (to (g g)) (rate LNUC_RNUC_ug2gg))
  (mutate (from (u g)) (to (a u)) (rate LNUC_RNUC_ug2au))
  (mutate (from (u g)) (to (c u)) (rate LNUC_RNUC_ug2cu))
  (mutate (from (u g)) (to (g u)) (rate LNUC_RNUC_ug2gu))
  (mutate (from (u g)) (to (u u)) (rate LNUC_RNUC_ug2uu))
  (mutate (from (a u)) (to (a a)) (rate LNUC_RNUC_au2aa))
  (mutate (from (a u)) (to (c a)) (rate LNUC_RNUC_au2ca))
  (mutate (from (a u)) (to (g a)) (rate LNUC_RNUC_au2ga))
  (mutate (from (a u)) (to (u a)) (rate LNUC_RNUC_au2ua))
  (mutate (from (a u)) (to (a c)) (rate LNUC_RNUC_au2ac))
  (mutate (from (a u)) (to (c c)) (rate LNUC_RNUC_au2cc))
  (mutate (from (a u)) (to (g c)) (rate LNUC_RNUC_au2gc))
  (mutate (from (a u)) (to (u c)) (rate LNUC_RNUC_au2uc))
  (mutate (from (a u)) (to (a g)) (rate LNUC_RNUC_au2ag))
  (mutate (from (a u)) (to (c g)) (rate LNUC_RNUC_au2cg))
  (mutate (from (a u)) (to (g g)) (rate LNUC_RNUC_au2gg))
  (mutate (from (a u)) (to (u g)) (rate LNUC_RNUC_au2ug))
  (mutate (from (a u)) (to (c u)) (rate LNUC_RNUC_au2cu))
  (mutate (from (a u)) (to (g u)) (rate LNUC_RNUC_au2gu))
  (mutate (from (a u)) (to (u u)) (rate LNUC_RNUC_au2uu))
  (mutate (from (c u)) (to (a a)) (rate LNUC_RNUC_cu2aa))
  (mutate (from (c u)) (to (c a)) (rate LNUC_RNUC_cu2ca))
  (mutate (from (c u)) (to (g a)) (rate LNUC_RNUC_cu2ga))
  (mutate (from (c u)) (to (u a)) (rate LNUC_RNUC_cu2ua))
  (mutate (from (c u)) (to (a c)) (rate LNUC_RNUC_cu2ac))
  (mutate (from (c u)) (to (c c)) (rate LNUC_RNUC_cu2cc))
  (mutate (from (c u)) (to (g c)) (rate LNUC_RNUC_cu2gc))
  (mutate (from (c u)) (to (u c)) (rate LNUC_RNUC_cu2uc))
  (mutate (from (c u)) (to (c g)) (rate LNUC_RNUC_cu2cg))
  (mutate (from (c u)) (to (u g)) (rate LNUC_RNUC_cu2ug))
  (mutate (from (c u)) (to (a u)) (rate LNUC_RNUC_cu2au))
  (mutate (from (c u)) (to (g u)) (rate LNUC_RNUC_cu2gu))
  (mutate (from (c u)) (to (u u)) (rate LNUC_RNUC_cu2uu))
  (mutate (from (g u)) (to (a a)) (rate LNUC_RNUC_gu2aa))
  (mutate (from (g u)) (to (c a)) (rate LNUC_RNUC_gu2ca))
  (mutate (from (g u)) (to (g a)) (rate LNUC_RNUC_gu2ga))
  (mutate (from (g u)) (to (u a)) (rate LNUC_RNUC_gu2ua))
  (mutate (from (g u)) (to (a c)) (rate LNUC_RNUC_gu2ac))
  (mutate (from (g u)) (to (c c)) (rate LNUC_RNUC_gu2cc))
  (mutate (from (g u)) (to (g c)) (rate LNUC_RNUC_gu2gc))
  (mutate (from (g u)) (to (u c)) (rate LNUC_RNUC_gu2uc))
  (mutate (from (g u)) (to (a g)) (rate LNUC_RNUC_gu2ag))
  (mutate (from (g u)) (to (c g)) (rate LNUC_RNUC_gu2cg))
  (mutate (from (g u)) (to (g g)) (rate LNUC_RNUC_gu2gg))
  (mutate (from (g u)) (to (u g)) (rate LNUC_RNUC_gu2ug))
  (mutate (from (g u)) (to (a u)) (rate LNUC_RNUC_gu2au))
  (mutate (from (g u)) (to (c u)) (rate LNUC_RNUC_gu2cu))
  (mutate (from (g u)) (to (u u)) (rate LNUC_RNUC_gu2uu))
  (mutate (from (u u)) (to (c a)) (rate LNUC_RNUC_uu2ca))
  (mutate (from (u u)) (to (u a)) (rate LNUC_RNUC_uu2ua))
  (mutate (from (u u)) (to (a c)) (rate LNUC_RNUC_uu2ac))
  (mutate (from (u u)) (to (c c)) (rate LNUC_RNUC_uu2cc))
  (mutate (from (u u)) (to (g c)) (rate LNUC_RNUC_uu2gc))
  (mutate (from (u u)) (to (u c)) (rate LNUC_RNUC_uu2uc))
  (mutate (from (u u)) (to (c g)) (rate LNUC_RNUC_uu2cg))
  (mutate (from (u u)) (to (g g)) (rate LNUC_RNUC_uu2gg))
  (mutate (from (u u)) (to (u g)) (rate LNUC_RNUC_uu2ug))
  (mutate (from (u u)) (to (a u)) (rate LNUC_RNUC_uu2au))
  (mutate (from (u u)) (to (c u)) (rate LNUC_RNUC_uu2cu))
  (mutate (from (u u)) (to (g u)) (rate LNUC_RNUC_uu2gu))
 )  ;; end chain LNUC RNUC

;; Unpaired bases
 (chain
  (update-policy parametric)
  (terminal (NUC))

  ;; initial probability distribution
  (initial (state (a)) (prob NUC_a))
  (initial (state (c)) (prob NUC_c))
  (initial (state (g)) (prob NUC_g))
  (initial (state (u)) (prob NUC_u))

  ;; mutation rates
  (mutate (from (a)) (to (c)) (rate NUC_a2c))
  (mutate (from (a)) (to (g)) (rate NUC_a2g))
  (mutate (from (a)) (to (u)) (rate NUC_a2u))
  (mutate (from (c)) (to (a)) (rate NUC_c2a))
  (mutate (from (c)) (to (g)) (rate NUC_c2g))
  (mutate (from (c)) (to (u)) (rate NUC_c2u))
  (mutate (from (g)) (to (a)) (rate NUC_g2a))
  (mutate (from (g)) (to (c)) (rate NUC_g2c))
  (mutate (from (g)) (to (u)) (rate NUC_g2u))
  (mutate (from (u)) (to (a)) (rate NUC_u2a))
  (mutate (from (u)) (to (c)) (rate NUC_u2c))
  (mutate (from (u)) (to (g)) (rate NUC_u2g))
 )  ;; end chain NUC

;; Closing basepair
 (chain
  (update-policy parametric)
  (terminal (LCLOSE RCLOSE))

  ;; initial probability distribution
  (initial (state (a a)) (prob LCLOSE_RCLOSE_aa))
  (initial (state (c a)) (prob LCLOSE_RCLOSE_ca))
  (initial (state (g a)) (prob LCLOSE_RCLOSE_ga))
  (initial (state (u a)) (prob LCLOSE_RCLOSE_ua))
  (initial (state (a c)) (prob LCLOSE_RCLOSE_ac))
  (initial (state (c c)) (prob LCLOSE_RCLOSE_cc))
  (initial (state (g c)) (prob LCLOSE_RCLOSE_gc))
  (initial (state (u c)) (prob LCLOSE_RCLOSE_uc))
  (initial (state (a g)) (prob LCLOSE_RCLOSE_ag))
  (initial (state (c g)) (prob LCLOSE_RCLOSE_cg))
  (initial (state (g g)) (prob LCLOSE_RCLOSE_gg))
  (initial (state (u g)) (prob LCLOSE_RCLOSE_ug))
  (initial (state (a u)) (prob LCLOSE_RCLOSE_au))
  (initial (state (c u)) (prob LCLOSE_RCLOSE_cu))
  (initial (state (g u)) (prob LCLOSE_RCLOSE_gu))
  (initial (state (u u)) (prob LCLOSE_RCLOSE_uu))

  ;; mutation rates
  (mutate (from (a a)) (to (c a)) (rate LCLOSE_RCLOSE_aa2ca))
  (mutate (from (a a)) (to (g a)) (rate LCLOSE_RCLOSE_aa2ga))
  (mutate (from (a a)) (to (u a)) (rate LCLOSE_RCLOSE_aa2ua))
  (mutate (from (a a)) (to (a c)) (rate LCLOSE_RCLOSE_aa2ac))
  (mutate (from (a a)) (to (c c)) (rate LCLOSE_RCLOSE_aa2cc))
  (mutate (from (a a)) (to (g c)) (rate LCLOSE_RCLOSE_aa2gc))
  (mutate (from (a a)) (to (u c)) (rate LCLOSE_RCLOSE_aa2uc))
  (mutate (from (a a)) (to (a g)) (rate LCLOSE_RCLOSE_aa2ag))
  (mutate (from (a a)) (to (c g)) (rate LCLOSE_RCLOSE_aa2cg))
  (mutate (from (a a)) (to (g g)) (rate LCLOSE_RCLOSE_aa2gg))
  (mutate (from (a a)) (to (u g)) (rate LCLOSE_RCLOSE_aa2ug))
  (mutate (from (a a)) (to (a u)) (rate LCLOSE_RCLOSE_aa2au))
  (mutate (from (a a)) (to (c u)) (rate LCLOSE_RCLOSE_aa2cu))
  (mutate (from (a a)) (to (g u)) (rate LCLOSE_RCLOSE_aa2gu))
  (mutate (from (a a)) (to (u u)) (rate LCLOSE_RCLOSE_aa2uu))
  (mutate (from (c a)) (to (a a)) (rate LCLOSE_RCLOSE_ca2aa))
  (mutate (from (c a)) (to (g a)) (rate LCLOSE_RCLOSE_ca2ga))
  (mutate (from (c a)) (to (u a)) (rate LCLOSE_RCLOSE_ca2ua))
  (mutate (from (c a)) (to (a c)) (rate LCLOSE_RCLOSE_ca2ac))
  (mutate (from (c a)) (to (c c)) (rate LCLOSE_RCLOSE_ca2cc))
  (mutate (from (c a)) (to (g c)) (rate LCLOSE_RCLOSE_ca2gc))
  (mutate (from (c a)) (to (u c)) (rate LCLOSE_RCLOSE_ca2uc))
  (mutate (from (c a)) (to (a g)) (rate LCLOSE_RCLOSE_ca2ag))
  (mutate (from (c a)) (to (c g)) (rate LCLOSE_RCLOSE_ca2cg))
  (mutate (from (c a)) (to (g g)) (rate LCLOSE_RCLOSE_ca2gg))
  (mutate (from (c a)) (to (u g)) (rate LCLOSE_RCLOSE_ca2ug))
  (mutate (from (c a)) (to (a u)) (rate LCLOSE_RCLOSE_ca2au))
  (mutate (from (c a)) (to (c u)) (rate LCLOSE_RCLOSE_ca2cu))
  (mutate (from (c a)) (to (g u)) (rate LCLOSE_RCLOSE_ca2gu))
  (mutate (from (c a)) (to (u u)) (rate LCLOSE_RCLOSE_ca2uu))
  (mutate (from (g a)) (to (a a)) (rate LCLOSE_RCLOSE_ga2aa))
  (mutate (from (g a)) (to (c a)) (rate LCLOSE_RCLOSE_ga2ca))
  (mutate (from (g a)) (to (u a)) (rate LCLOSE_RCLOSE_ga2ua))
  (mutate (from (g a)) (to (a c)) (rate LCLOSE_RCLOSE_ga2ac))
  (mutate (from (g a)) (to (c c)) (rate LCLOSE_RCLOSE_ga2cc))
  (mutate (from (g a)) (to (g c)) (rate LCLOSE_RCLOSE_ga2gc))
  (mutate (from (g a)) (to (u c)) (rate LCLOSE_RCLOSE_ga2uc))
  (mutate (from (g a)) (to (a g)) (rate LCLOSE_RCLOSE_ga2ag))
  (mutate (from (g a)) (to (c g)) (rate LCLOSE_RCLOSE_ga2cg))
  (mutate (from (g a)) (to (g g)) (rate LCLOSE_RCLOSE_ga2gg))
  (mutate (from (g a)) (to (u g)) (rate LCLOSE_RCLOSE_ga2ug))
  (mutate (from (g a)) (to (a u)) (rate LCLOSE_RCLOSE_ga2au))
  (mutate (from (g a)) (to (c u)) (rate LCLOSE_RCLOSE_ga2cu))
  (mutate (from (g a)) (to (g u)) (rate LCLOSE_RCLOSE_ga2gu))
  (mutate (from (g a)) (to (u u)) (rate LCLOSE_RCLOSE_ga2uu))
  (mutate (from (u a)) (to (a a)) (rate LCLOSE_RCLOSE_ua2aa))
  (mutate (from (u a)) (to (c a)) (rate LCLOSE_RCLOSE_ua2ca))
  (mutate (from (u a)) (to (g a)) (rate LCLOSE_RCLOSE_ua2ga))
  (mutate (from (u a)) (to (a c)) (rate LCLOSE_RCLOSE_ua2ac))
  (mutate (from (u a)) (to (c c)) (rate LCLOSE_RCLOSE_ua2cc))
  (mutate (from (u a)) (to (g c)) (rate LCLOSE_RCLOSE_ua2gc))
  (mutate (from (u a)) (to (u c)) (rate LCLOSE_RCLOSE_ua2uc))
  (mutate (from (u a)) (to (a g)) (rate LCLOSE_RCLOSE_ua2ag))
  (mutate (from (u a)) (to (c g)) (rate LCLOSE_RCLOSE_ua2cg))
  (mutate (from (u a)) (to (g g)) (rate LCLOSE_RCLOSE_ua2gg))
  (mutate (from (u a)) (to (u g)) (rate LCLOSE_RCLOSE_ua2ug))
  (mutate (from (u a)) (to (a u)) (rate LCLOSE_RCLOSE_ua2au))
  (mutate (from (u a)) (to (c u)) (rate LCLOSE_RCLOSE_ua2cu))
  (mutate (from (u a)) (to (g u)) (rate LCLOSE_RCLOSE_ua2gu))
  (mutate (from (u a)) (to (u u)) (rate LCLOSE_RCLOSE_ua2uu))
  (mutate (from (a c)) (to (a a)) (rate LCLOSE_RCLOSE_ac2aa))
  (mutate (from (a c)) (to (c a)) (rate LCLOSE_RCLOSE_ac2ca))
  (mutate (from (a c)) (to (g a)) (rate LCLOSE_RCLOSE_ac2ga))
  (mutate (from (a c)) (to (u a)) (rate LCLOSE_RCLOSE_ac2ua))
  (mutate (from (a c)) (to (c c)) (rate LCLOSE_RCLOSE_ac2cc))
  (mutate (from (a c)) (to (g c)) (rate LCLOSE_RCLOSE_ac2gc))
  (mutate (from (a c)) (to (u c)) (rate LCLOSE_RCLOSE_ac2uc))
  (mutate (from (a c)) (to (a g)) (rate LCLOSE_RCLOSE_ac2ag))
  (mutate (from (a c)) (to (c g)) (rate LCLOSE_RCLOSE_ac2cg))
  (mutate (from (a c)) (to (g g)) (rate LCLOSE_RCLOSE_ac2gg))
  (mutate (from (a c)) (to (u g)) (rate LCLOSE_RCLOSE_ac2ug))
  (mutate (from (a c)) (to (a u)) (rate LCLOSE_RCLOSE_ac2au))
  (mutate (from (a c)) (to (c u)) (rate LCLOSE_RCLOSE_ac2cu))
  (mutate (from (a c)) (to (g u)) (rate LCLOSE_RCLOSE_ac2gu))
  (mutate (from (a c)) (to (u u)) (rate LCLOSE_RCLOSE_ac2uu))
  (mutate (from (c c)) (to (a a)) (rate LCLOSE_RCLOSE_cc2aa))
  (mutate (from (c c)) (to (c a)) (rate LCLOSE_RCLOSE_cc2ca))
  (mutate (from (c c)) (to (g a)) (rate LCLOSE_RCLOSE_cc2ga))
  (mutate (from (c c)) (to (u a)) (rate LCLOSE_RCLOSE_cc2ua))
  (mutate (from (c c)) (to (a c)) (rate LCLOSE_RCLOSE_cc2ac))
  (mutate (from (c c)) (to (g c)) (rate LCLOSE_RCLOSE_cc2gc))
  (mutate (from (c c)) (to (u c)) (rate LCLOSE_RCLOSE_cc2uc))
  (mutate (from (c c)) (to (a g)) (rate LCLOSE_RCLOSE_cc2ag))
  (mutate (from (c c)) (to (c g)) (rate LCLOSE_RCLOSE_cc2cg))
  (mutate (from (c c)) (to (g g)) (rate LCLOSE_RCLOSE_cc2gg))
  (mutate (from (c c)) (to (u g)) (rate LCLOSE_RCLOSE_cc2ug))
  (mutate (from (c c)) (to (a u)) (rate LCLOSE_RCLOSE_cc2au))
  (mutate (from (c c)) (to (c u)) (rate LCLOSE_RCLOSE_cc2cu))
  (mutate (from (c c)) (to (g u)) (rate LCLOSE_RCLOSE_cc2gu))
  (mutate (from (c c)) (to (u u)) (rate LCLOSE_RCLOSE_cc2uu))
  (mutate (from (g c)) (to (a a)) (rate LCLOSE_RCLOSE_gc2aa))
  (mutate (from (g c)) (to (c a)) (rate LCLOSE_RCLOSE_gc2ca))
  (mutate (from (g c)) (to (g a)) (rate LCLOSE_RCLOSE_gc2ga))
  (mutate (from (g c)) (to (u a)) (rate LCLOSE_RCLOSE_gc2ua))
  (mutate (from (g c)) (to (a c)) (rate LCLOSE_RCLOSE_gc2ac))
  (mutate (from (g c)) (to (c c)) (rate LCLOSE_RCLOSE_gc2cc))
  (mutate (from (g c)) (to (u c)) (rate LCLOSE_RCLOSE_gc2uc))
  (mutate (from (g c)) (to (a g)) (rate LCLOSE_RCLOSE_gc2ag))
  (mutate (from (g c)) (to (c g)) (rate LCLOSE_RCLOSE_gc2cg))
  (mutate (from (g c)) (to (g g)) (rate LCLOSE_RCLOSE_gc2gg))
  (mutate (from (g c)) (to (u g)) (rate LCLOSE_RCLOSE_gc2ug))
  (mutate (from (g c)) (to (a u)) (rate LCLOSE_RCLOSE_gc2au))
  (mutate (from (g c)) (to (c u)) (rate LCLOSE_RCLOSE_gc2cu))
  (mutate (from (g c)) (to (g u)) (rate LCLOSE_RCLOSE_gc2gu))
  (mutate (from (g c)) (to (u u)) (rate LCLOSE_RCLOSE_gc2uu))
  (mutate (from (u c)) (to (a a)) (rate LCLOSE_RCLOSE_uc2aa))
  (mutate (from (u c)) (to (c a)) (rate LCLOSE_RCLOSE_uc2ca))
  (mutate (from (u c)) (to (g a)) (rate LCLOSE_RCLOSE_uc2ga))
  (mutate (from (u c)) (to (u a)) (rate LCLOSE_RCLOSE_uc2ua))
  (mutate (from (u c)) (to (a c)) (rate LCLOSE_RCLOSE_uc2ac))
  (mutate (from (u c)) (to (c c)) (rate LCLOSE_RCLOSE_uc2cc))
  (mutate (from (u c)) (to (g c)) (rate LCLOSE_RCLOSE_uc2gc))
  (mutate (from (u c)) (to (a g)) (rate LCLOSE_RCLOSE_uc2ag))
  (mutate (from (u c)) (to (c g)) (rate LCLOSE_RCLOSE_uc2cg))
  (mutate (from (u c)) (to (g g)) (rate LCLOSE_RCLOSE_uc2gg))
  (mutate (from (u c)) (to (u g)) (rate LCLOSE_RCLOSE_uc2ug))
  (mutate (from (u c)) (to (a u)) (rate LCLOSE_RCLOSE_uc2au))
  (mutate (from (u c)) (to (c u)) (rate LCLOSE_RCLOSE_uc2cu))
  (mutate (from (u c)) (to (g u)) (rate LCLOSE_RCLOSE_uc2gu))
  (mutate (from (u c)) (to (u u)) (rate LCLOSE_RCLOSE_uc2uu))
  (mutate (from (a g)) (to (a a)) (rate LCLOSE_RCLOSE_ag2aa))
  (mutate (from (a g)) (to (c a)) (rate LCLOSE_RCLOSE_ag2ca))
  (mutate (from (a g)) (to (g a)) (rate LCLOSE_RCLOSE_ag2ga))
  (mutate (from (a g)) (to (u a)) (rate LCLOSE_RCLOSE_ag2ua))
  (mutate (from (a g)) (to (a c)) (rate LCLOSE_RCLOSE_ag2ac))
  (mutate (from (a g)) (to (c c)) (rate LCLOSE_RCLOSE_ag2cc))
  (mutate (from (a g)) (to (g c)) (rate LCLOSE_RCLOSE_ag2gc))
  (mutate (from (a g)) (to (u c)) (rate LCLOSE_RCLOSE_ag2uc))
  (mutate (from (a g)) (to (c g)) (rate LCLOSE_RCLOSE_ag2cg))
  (mutate (from (a g)) (to (g g)) (rate LCLOSE_RCLOSE_ag2gg))
  (mutate (from (a g)) (to (u g)) (rate LCLOSE_RCLOSE_ag2ug))
  (mutate (from (a g)) (to (a u)) (rate LCLOSE_RCLOSE_ag2au))
  (mutate (from (a g)) (to (c u)) (rate LCLOSE_RCLOSE_ag2cu))
  (mutate (from (a g)) (to (g u)) (rate LCLOSE_RCLOSE_ag2gu))
  (mutate (from (a g)) (to (u u)) (rate LCLOSE_RCLOSE_ag2uu))
  (mutate (from (c g)) (to (a a)) (rate LCLOSE_RCLOSE_cg2aa))
  (mutate (from (c g)) (to (c a)) (rate LCLOSE_RCLOSE_cg2ca))
  (mutate (from (c g)) (to (g a)) (rate LCLOSE_RCLOSE_cg2ga))
  (mutate (from (c g)) (to (u a)) (rate LCLOSE_RCLOSE_cg2ua))
  (mutate (from (c g)) (to (a c)) (rate LCLOSE_RCLOSE_cg2ac))
  (mutate (from (c g)) (to (c c)) (rate LCLOSE_RCLOSE_cg2cc))
  (mutate (from (c g)) (to (g c)) (rate LCLOSE_RCLOSE_cg2gc))
  (mutate (from (c g)) (to (u c)) (rate LCLOSE_RCLOSE_cg2uc))
  (mutate (from (c g)) (to (a g)) (rate LCLOSE_RCLOSE_cg2ag))
  (mutate (from (c g)) (to (g g)) (rate LCLOSE_RCLOSE_cg2gg))
  (mutate (from (c g)) (to (u g)) (rate LCLOSE_RCLOSE_cg2ug))
  (mutate (from (c g)) (to (a u)) (rate LCLOSE_RCLOSE_cg2au))
  (mutate (from (c g)) (to (c u)) (rate LCLOSE_RCLOSE_cg2cu))
  (mutate (from (c g)) (to (g u)) (rate LCLOSE_RCLOSE_cg2gu))
  (mutate (from (c g)) (to (u u)) (rate LCLOSE_RCLOSE_cg2uu))
  (mutate (from (g g)) (to (a a)) (rate LCLOSE_RCLOSE_gg2aa))
  (mutate (from (g g)) (to (c a)) (rate LCLOSE_RCLOSE_gg2ca))
  (mutate (from (g g)) (to (g a)) (rate LCLOSE_RCLOSE_gg2ga))
  (mutate (from (g g)) (to (u a)) (rate LCLOSE_RCLOSE_gg2ua))
  (mutate (from (g g)) (to (a c)) (rate LCLOSE_RCLOSE_gg2ac))
  (mutate (from (g g)) (to (c c)) (rate LCLOSE_RCLOSE_gg2cc))
  (mutate (from (g g)) (to (g c)) (rate LCLOSE_RCLOSE_gg2gc))
  (mutate (from (g g)) (to (u c)) (rate LCLOSE_RCLOSE_gg2uc))
  (mutate (from (g g)) (to (a g)) (rate LCLOSE_RCLOSE_gg2ag))
  (mutate (from (g g)) (to (c g)) (rate LCLOSE_RCLOSE_gg2cg))
  (mutate (from (g g)) (to (u g)) (rate LCLOSE_RCLOSE_gg2ug))
  (mutate (from (g g)) (to (a u)) (rate LCLOSE_RCLOSE_gg2au))
  (mutate (from (g g)) (to (c u)) (rate LCLOSE_RCLOSE_gg2cu))
  (mutate (from (g g)) (to (g u)) (rate LCLOSE_RCLOSE_gg2gu))
  (mutate (from (g g)) (to (u u)) (rate LCLOSE_RCLOSE_gg2uu))
  (mutate (from (u g)) (to (a a)) (rate LCLOSE_RCLOSE_ug2aa))
  (mutate (from (u g)) (to (c a)) (rate LCLOSE_RCLOSE_ug2ca))
  (mutate (from (u g)) (to (g a)) (rate LCLOSE_RCLOSE_ug2ga))
  (mutate (from (u g)) (to (u a)) (rate LCLOSE_RCLOSE_ug2ua))
  (mutate (from (u g)) (to (a c)) (rate LCLOSE_RCLOSE_ug2ac))
  (mutate (from (u g)) (to (c c)) (rate LCLOSE_RCLOSE_ug2cc))
  (mutate (from (u g)) (to (g c)) (rate LCLOSE_RCLOSE_ug2gc))
  (mutate (from (u g)) (to (u c)) (rate LCLOSE_RCLOSE_ug2uc))
  (mutate (from (u g)) (to (a g)) (rate LCLOSE_RCLOSE_ug2ag))
  (mutate (from (u g)) (to (c g)) (rate LCLOSE_RCLOSE_ug2cg))
  (mutate (from (u g)) (to (g g)) (rate LCLOSE_RCLOSE_ug2gg))
  (mutate (from (u g)) (to (a u)) (rate LCLOSE_RCLOSE_ug2au))
  (mutate (from (u g)) (to (c u)) (rate LCLOSE_RCLOSE_ug2cu))
  (mutate (from (u g)) (to (g u)) (rate LCLOSE_RCLOSE_ug2gu))
  (mutate (from (u g)) (to (u u)) (rate LCLOSE_RCLOSE_ug2uu))
  (mutate (from (a u)) (to (a a)) (rate LCLOSE_RCLOSE_au2aa))
  (mutate (from (a u)) (to (c a)) (rate LCLOSE_RCLOSE_au2ca))
  (mutate (from (a u)) (to (g a)) (rate LCLOSE_RCLOSE_au2ga))
  (mutate (from (a u)) (to (u a)) (rate LCLOSE_RCLOSE_au2ua))
  (mutate (from (a u)) (to (a c)) (rate LCLOSE_RCLOSE_au2ac))
  (mutate (from (a u)) (to (c c)) (rate LCLOSE_RCLOSE_au2cc))
  (mutate (from (a u)) (to (g c)) (rate LCLOSE_RCLOSE_au2gc))
  (mutate (from (a u)) (to (u c)) (rate LCLOSE_RCLOSE_au2uc))
  (mutate (from (a u)) (to (a g)) (rate LCLOSE_RCLOSE_au2ag))
  (mutate (from (a u)) (to (c g)) (rate LCLOSE_RCLOSE_au2cg))
  (mutate (from (a u)) (to (g g)) (rate LCLOSE_RCLOSE_au2gg))
  (mutate (from (a u)) (to (u g)) (rate LCLOSE_RCLOSE_au2ug))
  (mutate (from (a u)) (to (c u)) (rate LCLOSE_RCLOSE_au2cu))
  (mutate (from (a u)) (to (g u)) (rate LCLOSE_RCLOSE_au2gu))
  (mutate (from (a u)) (to (u u)) (rate LCLOSE_RCLOSE_au2uu))
  (mutate (from (c u)) (to (a a)) (rate LCLOSE_RCLOSE_cu2aa))
  (mutate (from (c u)) (to (c a)) (rate LCLOSE_RCLOSE_cu2ca))
  (mutate (from (c u)) (to (g a)) (rate LCLOSE_RCLOSE_cu2ga))
  (mutate (from (c u)) (to (u a)) (rate LCLOSE_RCLOSE_cu2ua))
  (mutate (from (c u)) (to (a c)) (rate LCLOSE_RCLOSE_cu2ac))
  (mutate (from (c u)) (to (c c)) (rate LCLOSE_RCLOSE_cu2cc))
  (mutate (from (c u)) (to (g c)) (rate LCLOSE_RCLOSE_cu2gc))
  (mutate (from (c u)) (to (u c)) (rate LCLOSE_RCLOSE_cu2uc))
  (mutate (from (c u)) (to (a g)) (rate LCLOSE_RCLOSE_cu2ag))
  (mutate (from (c u)) (to (c g)) (rate LCLOSE_RCLOSE_cu2cg))
  (mutate (from (c u)) (to (g g)) (rate LCLOSE_RCLOSE_cu2gg))
  (mutate (from (c u)) (to (u g)) (rate LCLOSE_RCLOSE_cu2ug))
  (mutate (from (c u)) (to (a u)) (rate LCLOSE_RCLOSE_cu2au))
  (mutate (from (c u)) (to (g u)) (rate LCLOSE_RCLOSE_cu2gu))
  (mutate (from (c u)) (to (u u)) (rate LCLOSE_RCLOSE_cu2uu))
  (mutate (from (g u)) (to (a a)) (rate LCLOSE_RCLOSE_gu2aa))
  (mutate (from (g u)) (to (c a)) (rate LCLOSE_RCLOSE_gu2ca))
  (mutate (from (g u)) (to (g a)) (rate LCLOSE_RCLOSE_gu2ga))
  (mutate (from (g u)) (to (u a)) (rate LCLOSE_RCLOSE_gu2ua))
  (mutate (from (g u)) (to (a c)) (rate LCLOSE_RCLOSE_gu2ac))
  (mutate (from (g u)) (to (c c)) (rate LCLOSE_RCLOSE_gu2cc))
  (mutate (from (g u)) (to (g c)) (rate LCLOSE_RCLOSE_gu2gc))
  (mutate (from (g u)) (to (u c)) (rate LCLOSE_RCLOSE_gu2uc))
  (mutate (from (g u)) (to (a g)) (rate LCLOSE_RCLOSE_gu2ag))
  (mutate (from (g u)) (to (c g)) (rate LCLOSE_RCLOSE_gu2cg))
  (mutate (from (g u)) (to (g g)) (rate LCLOSE_RCLOSE_gu2gg))
  (mutate (from (g u)) (to (u g)) (rate LCLOSE_RCLOSE_gu2ug))
  (mutate (from (g u)) (to (a u)) (rate LCLOSE_RCLOSE_gu2au))
  (mutate (from (g u)) (to (c u)) (rate LCLOSE_RCLOSE_gu2cu))
  (mutate (from (g u)) (to (u u)) (rate LCLOSE_RCLOSE_gu2uu))
  (mutate (from (u u)) (to (a a)) (rate LCLOSE_RCLOSE_uu2aa))
  (mutate (from (u u)) (to (c a)) (rate LCLOSE_RCLOSE_uu2ca))
  (mutate (from (u u)) (to (g a)) (rate LCLOSE_RCLOSE_uu2ga))
  (mutate (from (u u)) (to (u a)) (rate LCLOSE_RCLOSE_uu2ua))
  (mutate (from (u u)) (to (a c)) (rate LCLOSE_RCLOSE_uu2ac))
  (mutate (from (u u)) (to (c c)) (rate LCLOSE_RCLOSE_uu2cc))
  (mutate (from (u u)) (to (g c)) (rate LCLOSE_RCLOSE_uu2gc))
  (mutate (from (u u)) (to (u c)) (rate LCLOSE_RCLOSE_uu2uc))
  (mutate (from (u u)) (to (a g)) (rate LCLOSE_RCLOSE_uu2ag))
  (mutate (from (u u)) (to (c g)) (rate LCLOSE_RCLOSE_uu2cg))
  (mutate (from (u u)) (to (g g)) (rate LCLOSE_RCLOSE_uu2gg))
  (mutate (from (u u)) (to (u g)) (rate LCLOSE_RCLOSE_uu2ug))
  (mutate (from (u u)) (to (a u)) (rate LCLOSE_RCLOSE_uu2au))
  (mutate (from (u u)) (to (c u)) (rate LCLOSE_RCLOSE_uu2cu))
  (mutate (from (u u)) (to (g u)) (rate LCLOSE_RCLOSE_uu2gu))
 )  ;; end chain LCLOSE RCLOSE

;; Intergenic sites
 (chain
  (update-policy parametric)
  (terminal (X))

  ;; initial probability distribution
  (initial (state (a)) (prob (X_au / 2)))
  (initial (state (c)) (prob (X_gc / 2)))
  (initial (state (g)) (prob (X_gc / 2)))
  (initial (state (u)) (prob (X_au / 2)))

  ;; mutation rates
  (mutate (from (a)) (to (c)) (rate X_a2c_u2g))
  (mutate (from (a)) (to (g)) (rate X_a2g_u2c))
  (mutate (from (a)) (to (u)) (rate X_a2u_u2a))
  (mutate (from (c)) (to (a)) (rate X_c2a_g2u))
  (mutate (from (c)) (to (g)) (rate X_c2g_g2c))
  (mutate (from (c)) (to (u)) (rate X_c2u_g2a))
  (mutate (from (g)) (to (a)) (rate X_c2u_g2a))
  (mutate (from (g)) (to (c)) (rate X_c2g_g2c))
  (mutate (from (g)) (to (u)) (rate X_c2a_g2u))
  (mutate (from (u)) (to (a)) (rate X_a2u_u2a))
  (mutate (from (u)) (to (c)) (rate X_a2g_u2c))
  (mutate (from (u)) (to (g)) (rate X_a2c_u2g))
 )  ;; end chain X

)  ;; end grammar ncRnaDualStrand