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;; Grammar nullprot3
;;
(grammar
(name nullprot3)
(update-rates 1)
(update-rules 1)
;; Transformation rules for grammar symbols
;; State Start
;;
(transform (from (Start)) (to (S2)) (prob 1))
;; State S0
;;
(transform (from (S0)) (to (A0 S0*)) (gaps-ok)
(annotate (row DSSP) (column A0) (label H))
(minlen 1))
(transform (from (S0*)) (to (S0)) (prob 0.873573))
(transform (from (S0*)) (to (S1)) (prob 0.00223424))
(transform (from (S0*)) (to (S2)) (prob 0.12474))
;; State S1
;;
(transform (from (S1)) (to (A1 S1*)) (gaps-ok)
(annotate (row DSSP) (column A1) (label E))
(minlen 1))
(transform (from (S1*)) (to (S0)) (prob 0.00794355))
(transform (from (S1*)) (to (S1)) (prob 0.754713))
(transform (from (S1*)) (to (S2)) (prob 0.237665))
;; State S2
;;
(transform (from (S2)) (to (A2 S2*)) (gaps-ok)
(annotate (row DSSP) (column A2) (label L))
(minlen 1))
(transform (from (S2*)) (to ()) (prob 0.00541809))
(transform (from (S2*)) (to (S0)) (prob 0.106137))
(transform (from (S2*)) (to (S1)) (prob 0.0615115))
(transform (from (S2*)) (to (S2)) (prob 0.827023))
;; Markov chain substitution models
(chain
(update-policy rev)
(terminal (A0))
;; initial probability distribution
(initial (state (a)) (prob 0.116481))
(initial (state (r)) (prob 0.0643491))
(initial (state (n)) (prob 0.0342123))
(initial (state (d)) (prob 0.0591351))
(initial (state (c)) (prob 0.00886682))
(initial (state (q)) (prob 0.0438141))
(initial (state (e)) (prob 0.0808752))
(initial (state (g)) (prob 0.0349772))
(initial (state (h)) (prob 0.0250475))
(initial (state (i)) (prob 0.058004))
(initial (state (l)) (prob 0.10566))
(initial (state (k)) (prob 0.0634016))
(initial (state (m)) (prob 0.0222641))
(initial (state (f)) (prob 0.0438022))
(initial (state (p)) (prob 0.0276675))
(initial (state (s)) (prob 0.04155))
(initial (state (t)) (prob 0.0381881))
(initial (state (w)) (prob 0.0231992))
(initial (state (y)) (prob 0.0443845))
(initial (state (v)) (prob 0.0641207))
;; mutation rates
(mutate (from (a)) (to (r)) (rate 0.0145634))
(mutate (from (a)) (to (n)) (rate 0.0165577))
(mutate (from (a)) (to (d)) (rate 0.017937))
(mutate (from (a)) (to (c)) (rate 0.012875))
(mutate (from (a)) (to (q)) (rate 0.0163673))
(mutate (from (a)) (to (e)) (rate 0.0828411))
(mutate (from (a)) (to (g)) (rate 0.0958752))
(mutate (from (a)) (to (h)) (rate 0.00225209))
(mutate (from (a)) (to (i)) (rate 0.00572919))
(mutate (from (a)) (to (l)) (rate 0.0244708))
(mutate (from (a)) (to (k)) (rate 0.013018))
(mutate (from (a)) (to (m)) (rate 0.00594066))
(mutate (from (a)) (to (f)) (rate 0.00834844))
(mutate (from (a)) (to (p)) (rate 0.0345727))
(mutate (from (a)) (to (s)) (rate 0.124224))
(mutate (from (a)) (to (t)) (rate 0.0788541))
(mutate (from (a)) (to (w)) (rate 0.000861798))
(mutate (from (a)) (to (y)) (rate 0.00803832))
(mutate (from (a)) (to (v)) (rate 0.0778705))
(mutate (from (r)) (to (a)) (rate 0.0263618))
(mutate (from (r)) (to (d)) (rate 0.0064252))
(mutate (from (r)) (to (c)) (rate 0.00151194))
(mutate (from (r)) (to (q)) (rate 0.0720089))
(mutate (from (r)) (to (e)) (rate 0.00690966))
(mutate (from (r)) (to (g)) (rate 0.00137018))
(mutate (from (r)) (to (h)) (rate 0.0307726))
(mutate (from (r)) (to (i)) (rate 0.0102194))
(mutate (from (r)) (to (l)) (rate 0.0101651))
(mutate (from (r)) (to (k)) (rate 0.233505))
(mutate (from (r)) (to (m)) (rate 0.00413908))
(mutate (from (r)) (to (f)) (rate 0.00253487))
(mutate (from (r)) (to (p)) (rate 0.00980488))
(mutate (from (r)) (to (s)) (rate 0.0486165))
(mutate (from (r)) (to (t)) (rate 0.00405395))
(mutate (from (r)) (to (w)) (rate 0.00410685))
(mutate (from (r)) (to (y)) (rate 0.00183991))
(mutate (from (r)) (to (v)) (rate 0.00788642))
(mutate (from (n)) (to (a)) (rate 0.0563732))
(mutate (from (n)) (to (d)) (rate 0.5676))
(mutate (from (n)) (to (c)) (rate 0.00175486))
(mutate (from (n)) (to (q)) (rate 0.0139114))
(mutate (from (n)) (to (e)) (rate 0.015027))
(mutate (from (n)) (to (g)) (rate 0.0490104))
(mutate (from (n)) (to (h)) (rate 0.118495))
(mutate (from (n)) (to (i)) (rate 0.0103199))
(mutate (from (n)) (to (l)) (rate 0.0141243))
(mutate (from (n)) (to (k)) (rate 0.285017))
(mutate (from (n)) (to (f)) (rate 0.00194658))
(mutate (from (n)) (to (p)) (rate 0.0101181))
(mutate (from (n)) (to (s)) (rate 0.222422))
(mutate (from (n)) (to (t)) (rate 0.0757107))
(mutate (from (n)) (to (w)) (rate 0.0127724))
(mutate (from (n)) (to (y)) (rate 0.0176516))
(mutate (from (n)) (to (v)) (rate 0.0112794))
(mutate (from (d)) (to (a)) (rate 0.0353313))
(mutate (from (d)) (to (r)) (rate 0.00699172))
(mutate (from (d)) (to (n)) (rate 0.328382))
(mutate (from (d)) (to (c)) (rate 0.000123038))
(mutate (from (d)) (to (q)) (rate 0.0203499))
(mutate (from (d)) (to (e)) (rate 0.864641))
(mutate (from (d)) (to (g)) (rate 0.0217009))
(mutate (from (d)) (to (h)) (rate 0.00210393))
(mutate (from (d)) (to (i)) (rate 0.00154927))
(mutate (from (d)) (to (l)) (rate 0.00214722))
(mutate (from (d)) (to (k)) (rate 0.0381508))
(mutate (from (d)) (to (m)) (rate 0.000402704))
(mutate (from (d)) (to (f)) (rate 0.00251304))
(mutate (from (d)) (to (p)) (rate 0.00533475))
(mutate (from (d)) (to (s)) (rate 0.0199909))
(mutate (from (d)) (to (t)) (rate 0.0128454))
(mutate (from (d)) (to (v)) (rate 0.00263461))
(mutate (from (c)) (to (a)) (rate 0.169136))
(mutate (from (c)) (to (r)) (rate 0.0109726))
(mutate (from (c)) (to (n)) (rate 0.00677105))
(mutate (from (c)) (to (d)) (rate 0.000820571))
(mutate (from (c)) (to (g)) (rate 0.0073272))
(mutate (from (c)) (to (h)) (rate 0.00608928))
(mutate (from (c)) (to (i)) (rate 0.0504272))
(mutate (from (c)) (to (l)) (rate 0.00134776))
(mutate (from (c)) (to (m)) (rate 0.0272607))
(mutate (from (c)) (to (p)) (rate 0.00677784))
(mutate (from (c)) (to (s)) (rate 0.092695))
(mutate (from (c)) (to (t)) (rate 0.0129726))
(mutate (from (c)) (to (w)) (rate 0.00660349))
(mutate (from (c)) (to (y)) (rate 0.0196696))
(mutate (from (c)) (to (v)) (rate 0.142792))
(mutate (from (q)) (to (a)) (rate 0.043513))
(mutate (from (q)) (to (r)) (rate 0.105758))
(mutate (from (q)) (to (n)) (rate 0.0108627))
(mutate (from (q)) (to (d)) (rate 0.0274658))
(mutate (from (q)) (to (e)) (rate 0.384753))
(mutate (from (q)) (to (g)) (rate 0.0140959))
(mutate (from (q)) (to (h)) (rate 0.101184))
(mutate (from (q)) (to (i)) (rate 0.000748309))
(mutate (from (q)) (to (l)) (rate 0.0264597))
(mutate (from (q)) (to (k)) (rate 0.126991))
(mutate (from (q)) (to (m)) (rate 0.00498793))
(mutate (from (q)) (to (p)) (rate 0.0125414))
(mutate (from (q)) (to (s)) (rate 0.037652))
(mutate (from (q)) (to (t)) (rate 0.0333896))
(mutate (from (q)) (to (v)) (rate 0.0160967))
(mutate (from (e)) (to (a)) (rate 0.119312))
(mutate (from (e)) (to (r)) (rate 0.00549774))
(mutate (from (e)) (to (n)) (rate 0.00635681))
(mutate (from (e)) (to (d)) (rate 0.632216))
(mutate (from (e)) (to (q)) (rate 0.20844))
(mutate (from (e)) (to (g)) (rate 0.0158983))
(mutate (from (e)) (to (h)) (rate 0.00546004))
(mutate (from (e)) (to (i)) (rate 0.00671843))
(mutate (from (e)) (to (l)) (rate 0.00349039))
(mutate (from (e)) (to (k)) (rate 0.0877983))
(mutate (from (e)) (to (m)) (rate 0.00127877))
(mutate (from (e)) (to (p)) (rate 0.00879693))
(mutate (from (e)) (to (s)) (rate 0.0411483))
(mutate (from (e)) (to (t)) (rate 0.0095502))
(mutate (from (e)) (to (w)) (rate 0.00249236))
(mutate (from (e)) (to (y)) (rate 0.0087831))
(mutate (from (e)) (to (v)) (rate 0.00516645))
(mutate (from (g)) (to (a)) (rate 0.319283))
(mutate (from (g)) (to (r)) (rate 0.00252078))
(mutate (from (g)) (to (n)) (rate 0.0479385))
(mutate (from (g)) (to (d)) (rate 0.0366891))
(mutate (from (g)) (to (c)) (rate 0.00185747))
(mutate (from (g)) (to (q)) (rate 0.0176572))
(mutate (from (g)) (to (e)) (rate 0.0367605))
(mutate (from (g)) (to (h)) (rate 0.00349566))
(mutate (from (g)) (to (i)) (rate 0.000444753))
(mutate (from (g)) (to (l)) (rate 0.00347221))
(mutate (from (g)) (to (k)) (rate 0.0387614))
(mutate (from (g)) (to (m)) (rate 0.00160203))
(mutate (from (g)) (to (f)) (rate 0.00211146))
(mutate (from (g)) (to (p)) (rate 0.0171846))
(mutate (from (g)) (to (s)) (rate 0.110634))
(mutate (from (g)) (to (t)) (rate 0.00855503))
(mutate (from (g)) (to (y)) (rate 0.000483698))
(mutate (from (g)) (to (v)) (rate 0.00734979))
(mutate (from (h)) (to (a)) (rate 0.0104731))
(mutate (from (h)) (to (r)) (rate 0.0790573))
(mutate (from (h)) (to (n)) (rate 0.161852))
(mutate (from (h)) (to (d)) (rate 0.0049672))
(mutate (from (h)) (to (c)) (rate 0.00215561))
(mutate (from (h)) (to (q)) (rate 0.176995))
(mutate (from (h)) (to (e)) (rate 0.0176298))
(mutate (from (h)) (to (g)) (rate 0.00488147))
(mutate (from (h)) (to (i)) (rate 0.00566332))
(mutate (from (h)) (to (l)) (rate 0.0198593))
(mutate (from (h)) (to (k)) (rate 0.00510643))
(mutate (from (h)) (to (m)) (rate 0.00132792))
(mutate (from (h)) (to (f)) (rate 0.0149743))
(mutate (from (h)) (to (p)) (rate 0.0114777))
(mutate (from (h)) (to (s)) (rate 0.0168629))
(mutate (from (h)) (to (t)) (rate 0.00372803))
(mutate (from (h)) (to (w)) (rate 0.00191508))
(mutate (from (h)) (to (y)) (rate 0.0473574))
(mutate (from (h)) (to (v)) (rate 0.0111936))
(mutate (from (i)) (to (a)) (rate 0.0115051))
(mutate (from (i)) (to (r)) (rate 0.0113373))
(mutate (from (i)) (to (n)) (rate 0.00608695))
(mutate (from (i)) (to (d)) (rate 0.00157948))
(mutate (from (i)) (to (c)) (rate 0.00770858))
(mutate (from (i)) (to (q)) (rate 0.000565246))
(mutate (from (i)) (to (e)) (rate 0.00936754))
(mutate (from (i)) (to (g)) (rate 0.000268193))
(mutate (from (i)) (to (h)) (rate 0.00244555))
(mutate (from (i)) (to (l)) (rate 0.22375))
(mutate (from (i)) (to (k)) (rate 0.0108282))
(mutate (from (i)) (to (m)) (rate 0.0567461))
(mutate (from (i)) (to (f)) (rate 0.0391299))
(mutate (from (i)) (to (p)) (rate 0.0029044))
(mutate (from (i)) (to (s)) (rate 0.00172578))
(mutate (from (i)) (to (t)) (rate 0.0360401))
(mutate (from (i)) (to (w)) (rate 0.00219908))
(mutate (from (i)) (to (y)) (rate 0.0111721))
(mutate (from (i)) (to (v)) (rate 0.384127))
(mutate (from (l)) (to (a)) (rate 0.0269771))
(mutate (from (l)) (to (r)) (rate 0.00619079))
(mutate (from (l)) (to (n)) (rate 0.0045734))
(mutate (from (l)) (to (d)) (rate 0.00120174))
(mutate (from (l)) (to (c)) (rate 0.000113102))
(mutate (from (l)) (to (q)) (rate 0.0109721))
(mutate (from (l)) (to (e)) (rate 0.00267165))
(mutate (from (l)) (to (g)) (rate 0.00114943))
(mutate (from (l)) (to (h)) (rate 0.00470781))
(mutate (from (l)) (to (i)) (rate 0.122832))
(mutate (from (l)) (to (k)) (rate 0.014824))
(mutate (from (l)) (to (m)) (rate 0.0730557))
(mutate (from (l)) (to (f)) (rate 0.0409705))
(mutate (from (l)) (to (p)) (rate 0.00363757))
(mutate (from (l)) (to (s)) (rate 0.00446089))
(mutate (from (l)) (to (t)) (rate 0.0107259))
(mutate (from (l)) (to (w)) (rate 0.00710254))
(mutate (from (l)) (to (y)) (rate 0.0071485))
(mutate (from (l)) (to (v)) (rate 0.0711286))
(mutate (from (k)) (to (a)) (rate 0.0239166))
(mutate (from (k)) (to (r)) (rate 0.236995))
(mutate (from (k)) (to (n)) (rate 0.153799))
(mutate (from (k)) (to (d)) (rate 0.0355835))
(mutate (from (k)) (to (q)) (rate 0.0877582))
(mutate (from (k)) (to (e)) (rate 0.111996))
(mutate (from (k)) (to (g)) (rate 0.0213838))
(mutate (from (k)) (to (h)) (rate 0.00201735))
(mutate (from (k)) (to (i)) (rate 0.00990633))
(mutate (from (k)) (to (l)) (rate 0.0247043))
(mutate (from (k)) (to (m)) (rate 0.0164198))
(mutate (from (k)) (to (f)) (rate 0.00197457))
(mutate (from (k)) (to (p)) (rate 0.0116859))
(mutate (from (k)) (to (s)) (rate 0.0627832))
(mutate (from (k)) (to (t)) (rate 0.0531804))
(mutate (from (k)) (to (y)) (rate 0.00528238))
(mutate (from (k)) (to (v)) (rate 0.00923359))
(mutate (from (m)) (to (a)) (rate 0.0310803))
(mutate (from (m)) (to (r)) (rate 0.011963))
(mutate (from (m)) (to (d)) (rate 0.00106961))
(mutate (from (m)) (to (c)) (rate 0.0108567))
(mutate (from (m)) (to (q)) (rate 0.00981588))
(mutate (from (m)) (to (e)) (rate 0.00464518))
(mutate (from (m)) (to (g)) (rate 0.00251681))
(mutate (from (m)) (to (h)) (rate 0.00149393))
(mutate (from (m)) (to (i)) (rate 0.147839))
(mutate (from (m)) (to (l)) (rate 0.346703))
(mutate (from (m)) (to (k)) (rate 0.0467587))
(mutate (from (m)) (to (f)) (rate 0.0480484))
(mutate (from (m)) (to (p)) (rate 0.00326304))
(mutate (from (m)) (to (s)) (rate 0.0088963))
(mutate (from (m)) (to (t)) (rate 0.0306607))
(mutate (from (m)) (to (w)) (rate 1.86914e-05))
(mutate (from (m)) (to (y)) (rate 0.00708952))
(mutate (from (m)) (to (v)) (rate 0.107744))
(mutate (from (f)) (to (a)) (rate 0.0222006))
(mutate (from (f)) (to (r)) (rate 0.00372394))
(mutate (from (f)) (to (n)) (rate 0.00152041))
(mutate (from (f)) (to (d)) (rate 0.00339273))
(mutate (from (f)) (to (g)) (rate 0.00168606))
(mutate (from (f)) (to (h)) (rate 0.0085628))
(mutate (from (f)) (to (i)) (rate 0.0518169))
(mutate (from (f)) (to (l)) (rate 0.098829))
(mutate (from (f)) (to (k)) (rate 0.0028581))
(mutate (from (f)) (to (m)) (rate 0.0244224))
(mutate (from (f)) (to (p)) (rate 0.000742357))
(mutate (from (f)) (to (s)) (rate 0.0139428))
(mutate (from (f)) (to (t)) (rate 0.000994385))
(mutate (from (f)) (to (w)) (rate 0.0173049))
(mutate (from (f)) (to (y)) (rate 0.151644))
(mutate (from (f)) (to (v)) (rate 0.0186645))
(mutate (from (p)) (to (a)) (rate 0.145552))
(mutate (from (p)) (to (r)) (rate 0.0228042))
(mutate (from (p)) (to (n)) (rate 0.0125115))
(mutate (from (p)) (to (d)) (rate 0.0114022))
(mutate (from (p)) (to (c)) (rate 0.00217215))
(mutate (from (p)) (to (q)) (rate 0.0198604))
(mutate (from (p)) (to (e)) (rate 0.0257144))
(mutate (from (p)) (to (g)) (rate 0.0217247))
(mutate (from (p)) (to (h)) (rate 0.0103908))
(mutate (from (p)) (to (i)) (rate 0.00608897))
(mutate (from (p)) (to (l)) (rate 0.0138916))
(mutate (from (p)) (to (k)) (rate 0.0267789))
(mutate (from (p)) (to (m)) (rate 0.00262577))
(mutate (from (p)) (to (f)) (rate 0.00117527))
(mutate (from (p)) (to (s)) (rate 0.0588983))
(mutate (from (p)) (to (t)) (rate 0.0252697))
(mutate (from (p)) (to (w)) (rate 0.00128108))
(mutate (from (p)) (to (v)) (rate 0.0126242))
(mutate (from (s)) (to (a)) (rate 0.348248))
(mutate (from (s)) (to (r)) (rate 0.0752931))
(mutate (from (s)) (to (n)) (rate 0.183142))
(mutate (from (s)) (to (d)) (rate 0.0284516))
(mutate (from (s)) (to (c)) (rate 0.0197812))
(mutate (from (s)) (to (q)) (rate 0.0397038))
(mutate (from (s)) (to (e)) (rate 0.0800933))
(mutate (from (s)) (to (g)) (rate 0.0931327))
(mutate (from (s)) (to (h)) (rate 0.0101654))
(mutate (from (s)) (to (i)) (rate 0.0024092))
(mutate (from (s)) (to (l)) (rate 0.0113438))
(mutate (from (s)) (to (k)) (rate 0.0958014))
(mutate (from (s)) (to (m)) (rate 0.00476698))
(mutate (from (s)) (to (f)) (rate 0.0146986))
(mutate (from (s)) (to (p)) (rate 0.0392194))
(mutate (from (s)) (to (t)) (rate 0.329776))
(mutate (from (s)) (to (w)) (rate 0.0122455))
(mutate (from (s)) (to (y)) (rate 0.00606956))
(mutate (from (s)) (to (v)) (rate 0.0180673))
(mutate (from (t)) (to (a)) (rate 0.24052))
(mutate (from (t)) (to (r)) (rate 0.00683114))
(mutate (from (t)) (to (n)) (rate 0.0678284))
(mutate (from (t)) (to (d)) (rate 0.0198914))
(mutate (from (t)) (to (c)) (rate 0.00301208))
(mutate (from (t)) (to (q)) (rate 0.0383087))
(mutate (from (t)) (to (e)) (rate 0.0202256))
(mutate (from (t)) (to (g)) (rate 0.00783572))
(mutate (from (t)) (to (h)) (rate 0.00244521))
(mutate (from (t)) (to (i)) (rate 0.0547415))
(mutate (from (t)) (to (l)) (rate 0.0296766))
(mutate (from (t)) (to (k)) (rate 0.0882926))
(mutate (from (t)) (to (m)) (rate 0.0178756))
(mutate (from (t)) (to (f)) (rate 0.00114057))
(mutate (from (t)) (to (p)) (rate 0.018308))
(mutate (from (t)) (to (s)) (rate 0.358808))
(mutate (from (t)) (to (y)) (rate 0.00839391))
(mutate (from (t)) (to (v)) (rate 0.105168))
(mutate (from (w)) (to (a)) (rate 0.00432702))
(mutate (from (w)) (to (r)) (rate 0.0113915))
(mutate (from (w)) (to (n)) (rate 0.0188358))
(mutate (from (w)) (to (c)) (rate 0.00252388))
(mutate (from (w)) (to (e)) (rate 0.00868868))
(mutate (from (w)) (to (h)) (rate 0.00206766))
(mutate (from (w)) (to (i)) (rate 0.00549827))
(mutate (from (w)) (to (l)) (rate 0.0323482))
(mutate (from (w)) (to (m)) (rate 1.79381e-05))
(mutate (from (w)) (to (f)) (rate 0.0326733))
(mutate (from (w)) (to (p)) (rate 0.00152783))
(mutate (from (w)) (to (s)) (rate 0.0219319))
(mutate (from (w)) (to (y)) (rate 0.0366642))
(mutate (from (y)) (to (a)) (rate 0.0210955))
(mutate (from (y)) (to (r)) (rate 0.00266752))
(mutate (from (y)) (to (n)) (rate 0.0136061))
(mutate (from (y)) (to (c)) (rate 0.00392946))
(mutate (from (y)) (to (e)) (rate 0.0160041))
(mutate (from (y)) (to (g)) (rate 0.000381178))
(mutate (from (y)) (to (h)) (rate 0.0267252))
(mutate (from (y)) (to (i)) (rate 0.0146003))
(mutate (from (y)) (to (l)) (rate 0.0170174))
(mutate (from (y)) (to (k)) (rate 0.00754569))
(mutate (from (y)) (to (m)) (rate 0.00355624))
(mutate (from (y)) (to (f)) (rate 0.149654))
(mutate (from (y)) (to (s)) (rate 0.00568194))
(mutate (from (y)) (to (t)) (rate 0.00722205))
(mutate (from (y)) (to (w)) (rate 0.0191638))
(mutate (from (y)) (to (v)) (rate 0.0178017))
(mutate (from (v)) (to (a)) (rate 0.141459))
(mutate (from (v)) (to (r)) (rate 0.00791452))
(mutate (from (v)) (to (n)) (rate 0.00601826))
(mutate (from (v)) (to (d)) (rate 0.00242976))
(mutate (from (v)) (to (c)) (rate 0.0197457))
(mutate (from (v)) (to (q)) (rate 0.010999))
(mutate (from (v)) (to (e)) (rate 0.00651643))
(mutate (from (v)) (to (g)) (rate 0.00400924))
(mutate (from (v)) (to (h)) (rate 0.00437256))
(mutate (from (v)) (to (i)) (rate 0.347484))
(mutate (from (v)) (to (l)) (rate 0.117207))
(mutate (from (v)) (to (k)) (rate 0.00913003))
(mutate (from (v)) (to (m)) (rate 0.0374109))
(mutate (from (v)) (to (f)) (rate 0.0127501))
(mutate (from (v)) (to (p)) (rate 0.00544721))
(mutate (from (v)) (to (s)) (rate 0.0117076))
(mutate (from (v)) (to (t)) (rate 0.0626345))
(mutate (from (v)) (to (y)) (rate 0.0123224))
) ;; end chain A0
(chain
(update-policy rev)
(terminal (A1))
;; initial probability distribution
(initial (state (a)) (prob 0.06764))
(initial (state (r)) (prob 0.0309357))
(initial (state (n)) (prob 0.0271373))
(initial (state (d)) (prob 0.0418616))
(initial (state (c)) (prob 0.0125181))
(initial (state (q)) (prob 0.0255913))
(initial (state (e)) (prob 0.02345))
(initial (state (g)) (prob 0.0690053))
(initial (state (h)) (prob 0.028271))
(initial (state (i)) (prob 0.112129))
(initial (state (l)) (prob 0.103525))
(initial (state (k)) (prob 0.030769))
(initial (state (m)) (prob 0.0266334))
(initial (state (f)) (prob 0.0679078))
(initial (state (p)) (prob 0.0304796))
(initial (state (s)) (prob 0.0359005))
(initial (state (t)) (prob 0.0561979))
(initial (state (w)) (prob 0.0240638))
(initial (state (y)) (prob 0.0572549))
(initial (state (v)) (prob 0.128729))
;; mutation rates
(mutate (from (a)) (to (r)) (rate 0.00105697))
(mutate (from (a)) (to (n)) (rate 0.00402287))
(mutate (from (a)) (to (d)) (rate 0.00263398))
(mutate (from (a)) (to (c)) (rate 0.0160415))
(mutate (from (a)) (to (q)) (rate 0.00869924))
(mutate (from (a)) (to (e)) (rate 0.01149))
(mutate (from (a)) (to (g)) (rate 0.0587835))
(mutate (from (a)) (to (h)) (rate 0.00212349))
(mutate (from (a)) (to (i)) (rate 0.0068465))
(mutate (from (a)) (to (l)) (rate 0.018426))
(mutate (from (a)) (to (k)) (rate 0.0038844))
(mutate (from (a)) (to (m)) (rate 0.00908531))
(mutate (from (a)) (to (f)) (rate 0.0131282))
(mutate (from (a)) (to (p)) (rate 0.0151742))
(mutate (from (a)) (to (s)) (rate 0.130343))
(mutate (from (a)) (to (t)) (rate 0.0773536))
(mutate (from (a)) (to (w)) (rate 0.000770829))
(mutate (from (a)) (to (y)) (rate 0.0069365))
(mutate (from (a)) (to (v)) (rate 0.102327))
(mutate (from (r)) (to (a)) (rate 0.00231103))
(mutate (from (r)) (to (d)) (rate 0.00113752))
(mutate (from (r)) (to (c)) (rate 0.00577936))
(mutate (from (r)) (to (q)) (rate 0.0239439))
(mutate (from (r)) (to (e)) (rate 0.00486194))
(mutate (from (r)) (to (g)) (rate 7.22515e-05))
(mutate (from (r)) (to (h)) (rate 0.00487005))
(mutate (from (r)) (to (i)) (rate 0.00163084))
(mutate (from (r)) (to (l)) (rate 0.000261925))
(mutate (from (r)) (to (k)) (rate 0.0864589))
(mutate (from (r)) (to (m)) (rate 0.00231455))
(mutate (from (r)) (to (f)) (rate 0.015589))
(mutate (from (r)) (to (p)) (rate 0.00134331))
(mutate (from (r)) (to (s)) (rate 0.0107036))
(mutate (from (r)) (to (t)) (rate 0.0049772))
(mutate (from (r)) (to (w)) (rate 0.000520206))
(mutate (from (r)) (to (y)) (rate 0.00765902))
(mutate (from (r)) (to (v)) (rate 0.0068575))
(mutate (from (n)) (to (a)) (rate 0.0100271))
(mutate (from (n)) (to (d)) (rate 0.164635))
(mutate (from (n)) (to (c)) (rate 4.04972e-05))
(mutate (from (n)) (to (q)) (rate 0.000895228))
(mutate (from (n)) (to (e)) (rate 0.00257612))
(mutate (from (n)) (to (g)) (rate 0.00293078))
(mutate (from (n)) (to (h)) (rate 0.0347109))
(mutate (from (n)) (to (i)) (rate 0.00480554))
(mutate (from (n)) (to (l)) (rate 0.00756849))
(mutate (from (n)) (to (k)) (rate 0.0427189))
(mutate (from (n)) (to (f)) (rate 0.00838278))
(mutate (from (n)) (to (p)) (rate 0.00432423))
(mutate (from (n)) (to (s)) (rate 0.0700827))
(mutate (from (n)) (to (t)) (rate 0.0338223))
(mutate (from (n)) (to (w)) (rate 0.000989092))
(mutate (from (n)) (to (y)) (rate 0.00710042))
(mutate (from (n)) (to (v)) (rate 0.00541239))
(mutate (from (d)) (to (a)) (rate 0.00425599))
(mutate (from (d)) (to (r)) (rate 0.00084063))
(mutate (from (d)) (to (n)) (rate 0.106727))
(mutate (from (d)) (to (c)) (rate 9.4282e-06))
(mutate (from (d)) (to (q)) (rate 0.00155109))
(mutate (from (d)) (to (e)) (rate 0.398509))
(mutate (from (d)) (to (g)) (rate 0.000784692))
(mutate (from (d)) (to (h)) (rate 0.000483701))
(mutate (from (d)) (to (i)) (rate 0.000260961))
(mutate (from (d)) (to (l)) (rate 9.58689e-05))
(mutate (from (d)) (to (k)) (rate 0.00400663))
(mutate (from (d)) (to (m)) (rate 2.58993e-05))
(mutate (from (d)) (to (f)) (rate 0.000644104))
(mutate (from (d)) (to (p)) (rate 0.000371615))
(mutate (from (d)) (to (s)) (rate 0.00424033))
(mutate (from (d)) (to (t)) (rate 0.00258968))
(mutate (from (d)) (to (v)) (rate 0.0018495))
(mutate (from (c)) (to (a)) (rate 0.0866785))
(mutate (from (c)) (to (r)) (rate 0.0142824))
(mutate (from (c)) (to (n)) (rate 8.77917e-05))
(mutate (from (c)) (to (d)) (rate 3.15287e-05))
(mutate (from (c)) (to (g)) (rate 0.0163053))
(mutate (from (c)) (to (h)) (rate 0.000593287))
(mutate (from (c)) (to (i)) (rate 0.0767899))
(mutate (from (c)) (to (l)) (rate 1.54116e-05))
(mutate (from (c)) (to (m)) (rate 0.027047))
(mutate (from (c)) (to (p)) (rate 0.00279413))
(mutate (from (c)) (to (s)) (rate 0.112093))
(mutate (from (c)) (to (t)) (rate 0.0151796))
(mutate (from (c)) (to (w)) (rate 6.98428e-06))
(mutate (from (c)) (to (y)) (rate 0.00785418))
(mutate (from (c)) (to (v)) (rate 0.202225))
(mutate (from (q)) (to (a)) (rate 0.0229929))
(mutate (from (q)) (to (r)) (rate 0.0289443))
(mutate (from (q)) (to (n)) (rate 0.000949309))
(mutate (from (q)) (to (d)) (rate 0.00253723))
(mutate (from (q)) (to (e)) (rate 0.0810246))
(mutate (from (q)) (to (g)) (rate 0.00159175))
(mutate (from (q)) (to (h)) (rate 0.0325247))
(mutate (from (q)) (to (i)) (rate 0.000246297))
(mutate (from (q)) (to (l)) (rate 0.0291358))
(mutate (from (q)) (to (k)) (rate 0.0299125))
(mutate (from (q)) (to (m)) (rate 0.0248673))
(mutate (from (q)) (to (p)) (rate 0.00544016))
(mutate (from (q)) (to (s)) (rate 0.00655049))
(mutate (from (q)) (to (t)) (rate 0.0186762))
(mutate (from (q)) (to (v)) (rate 0.0363421))
(mutate (from (e)) (to (a)) (rate 0.0331422))
(mutate (from (e)) (to (r)) (rate 0.00641395))
(mutate (from (e)) (to (n)) (rate 0.00298119))
(mutate (from (e)) (to (d)) (rate 0.711394))
(mutate (from (e)) (to (q)) (rate 0.0884231))
(mutate (from (e)) (to (g)) (rate 0.0050693))
(mutate (from (e)) (to (h)) (rate 0.00483594))
(mutate (from (e)) (to (i)) (rate 0.00673725))
(mutate (from (e)) (to (l)) (rate 0.0117417))
(mutate (from (e)) (to (k)) (rate 0.0205674))
(mutate (from (e)) (to (m)) (rate 0.0005037))
(mutate (from (e)) (to (p)) (rate 0.00336869))
(mutate (from (e)) (to (s)) (rate 0.0397626))
(mutate (from (e)) (to (t)) (rate 0.00644606))
(mutate (from (e)) (to (w)) (rate 0.00169613))
(mutate (from (e)) (to (y)) (rate 0.0091913))
(mutate (from (e)) (to (v)) (rate 0.00613587))
(mutate (from (g)) (to (a)) (rate 0.0576204))
(mutate (from (g)) (to (r)) (rate 3.2391e-05))
(mutate (from (g)) (to (n)) (rate 0.00115257))
(mutate (from (g)) (to (d)) (rate 0.000476027))
(mutate (from (g)) (to (c)) (rate 0.0029579))
(mutate (from (g)) (to (q)) (rate 0.000590314))
(mutate (from (g)) (to (e)) (rate 0.0017227))
(mutate (from (g)) (to (h)) (rate 0.000474265))
(mutate (from (g)) (to (i)) (rate 0.00144865))
(mutate (from (g)) (to (l)) (rate 0.0012758))
(mutate (from (g)) (to (k)) (rate 0.00236))
(mutate (from (g)) (to (m)) (rate 0.00318449))
(mutate (from (g)) (to (f)) (rate 0.00472736))
(mutate (from (g)) (to (p)) (rate 0.00076558))
(mutate (from (g)) (to (s)) (rate 0.0281826))
(mutate (from (g)) (to (t)) (rate 0.000769539))
(mutate (from (g)) (to (y)) (rate 0.00253749))
(mutate (from (g)) (to (v)) (rate 0.00216094))
(mutate (from (h)) (to (a)) (rate 0.00508059))
(mutate (from (h)) (to (r)) (rate 0.00532909))
(mutate (from (h)) (to (n)) (rate 0.0333189))
(mutate (from (h)) (to (d)) (rate 0.000716228))
(mutate (from (h)) (to (c)) (rate 0.000262702))
(mutate (from (h)) (to (q)) (rate 0.0294419))
(mutate (from (h)) (to (e)) (rate 0.00401129))
(mutate (from (h)) (to (g)) (rate 0.00115761))
(mutate (from (h)) (to (i)) (rate 0.00101528))
(mutate (from (h)) (to (l)) (rate 0.0103105))
(mutate (from (h)) (to (k)) (rate 0.00283326))
(mutate (from (h)) (to (m)) (rate 0.000909496))
(mutate (from (h)) (to (f)) (rate 0.00891077))
(mutate (from (h)) (to (p)) (rate 0.000127994))
(mutate (from (h)) (to (s)) (rate 0.00522133))
(mutate (from (h)) (to (t)) (rate 0.00401957))
(mutate (from (h)) (to (w)) (rate 0.000525767))
(mutate (from (h)) (to (y)) (rate 0.0434304))
(mutate (from (h)) (to (v)) (rate 0.0210324))
(mutate (from (i)) (to (a)) (rate 0.00413002))
(mutate (from (i)) (to (r)) (rate 0.000449936))
(mutate (from (i)) (to (n)) (rate 0.00116302))
(mutate (from (i)) (to (d)) (rate 9.7425e-05))
(mutate (from (i)) (to (c)) (rate 0.00857279))
(mutate (from (i)) (to (q)) (rate 5.62122e-05))
(mutate (from (i)) (to (e)) (rate 0.00140898))
(mutate (from (i)) (to (g)) (rate 0.000891511))
(mutate (from (i)) (to (h)) (rate 0.000255981))
(mutate (from (i)) (to (l)) (rate 0.154256))
(mutate (from (i)) (to (k)) (rate 0.00359427))
(mutate (from (i)) (to (m)) (rate 0.0186278))
(mutate (from (i)) (to (f)) (rate 0.0341179))
(mutate (from (i)) (to (p)) (rate 0.000297993))
(mutate (from (i)) (to (s)) (rate 0.00124202))
(mutate (from (i)) (to (t)) (rate 0.023085))
(mutate (from (i)) (to (w)) (rate 0.00741596))
(mutate (from (i)) (to (y)) (rate 0.00358808))
(mutate (from (i)) (to (v)) (rate 0.391227))
(mutate (from (l)) (to (a)) (rate 0.012039))
(mutate (from (l)) (to (r)) (rate 7.82695e-05))
(mutate (from (l)) (to (n)) (rate 0.00198395))
(mutate (from (l)) (to (d)) (rate 3.87658e-05))
(mutate (from (l)) (to (c)) (rate 1.86356e-06))
(mutate (from (l)) (to (q)) (rate 0.00720236))
(mutate (from (l)) (to (e)) (rate 0.00265968))
(mutate (from (l)) (to (g)) (rate 0.000850395))
(mutate (from (l)) (to (h)) (rate 0.00281563))
(mutate (from (l)) (to (i)) (rate 0.167077))
(mutate (from (l)) (to (k)) (rate 0.000465649))
(mutate (from (l)) (to (m)) (rate 0.0619236))
(mutate (from (l)) (to (f)) (rate 0.0365111))
(mutate (from (l)) (to (p)) (rate 0.00594405))
(mutate (from (l)) (to (s)) (rate 0.00244147))
(mutate (from (l)) (to (t)) (rate 0.00327511))
(mutate (from (l)) (to (w)) (rate 0.00105184))
(mutate (from (l)) (to (y)) (rate 0.00540887))
(mutate (from (l)) (to (v)) (rate 0.110572))
(mutate (from (k)) (to (a)) (rate 0.00853914))
(mutate (from (k)) (to (r)) (rate 0.0869274))
(mutate (from (k)) (to (n)) (rate 0.0376767))
(mutate (from (k)) (to (d)) (rate 0.00545106))
(mutate (from (k)) (to (q)) (rate 0.0248789))
(mutate (from (k)) (to (e)) (rate 0.015675))
(mutate (from (k)) (to (g)) (rate 0.00529276))
(mutate (from (k)) (to (h)) (rate 0.00260324))
(mutate (from (k)) (to (i)) (rate 0.0130984))
(mutate (from (k)) (to (l)) (rate 0.00156671))
(mutate (from (k)) (to (m)) (rate 0.0127697))
(mutate (from (k)) (to (f)) (rate 0.00062502))
(mutate (from (k)) (to (p)) (rate 0.000177031))
(mutate (from (k)) (to (s)) (rate 0.0225302))
(mutate (from (k)) (to (t)) (rate 0.0575171))
(mutate (from (k)) (to (y)) (rate 0.00430633))
(mutate (from (k)) (to (v)) (rate 0.00331328))
(mutate (from (m)) (to (a)) (rate 0.0230737))
(mutate (from (m)) (to (r)) (rate 0.00268844))
(mutate (from (m)) (to (d)) (rate 4.07077e-05))
(mutate (from (m)) (to (c)) (rate 0.0127125))
(mutate (from (m)) (to (q)) (rate 0.0238943))
(mutate (from (m)) (to (e)) (rate 0.000443495))
(mutate (from (m)) (to (g)) (rate 0.00825079))
(mutate (from (m)) (to (h)) (rate 0.000965415))
(mutate (from (m)) (to (i)) (rate 0.078425))
(mutate (from (m)) (to (l)) (rate 0.240698))
(mutate (from (m)) (to (k)) (rate 0.0147526))
(mutate (from (m)) (to (f)) (rate 0.0692845))
(mutate (from (m)) (to (p)) (rate 0.00862335))
(mutate (from (m)) (to (s)) (rate 0.00232362))
(mutate (from (m)) (to (t)) (rate 0.026809))
(mutate (from (m)) (to (w)) (rate 1.65602e-05))
(mutate (from (m)) (to (y)) (rate 0.000273554))
(mutate (from (m)) (to (v)) (rate 0.0969081))
(mutate (from (f)) (to (a)) (rate 0.0130764))
(mutate (from (f)) (to (r)) (rate 0.00710163))
(mutate (from (f)) (to (n)) (rate 0.00334992))
(mutate (from (f)) (to (d)) (rate 0.000397056))
(mutate (from (f)) (to (g)) (rate 0.00480376))
(mutate (from (f)) (to (h)) (rate 0.00370968))
(mutate (from (f)) (to (i)) (rate 0.0563355))
(mutate (from (f)) (to (l)) (rate 0.0556609))
(mutate (from (f)) (to (k)) (rate 0.000283196))
(mutate (from (f)) (to (m)) (rate 0.0271734))
(mutate (from (f)) (to (p)) (rate 0.000621688))
(mutate (from (f)) (to (s)) (rate 0.0102073))
(mutate (from (f)) (to (t)) (rate 0.00106579))
(mutate (from (f)) (to (w)) (rate 0.0196133))
(mutate (from (f)) (to (y)) (rate 0.0974149))
(mutate (from (f)) (to (v)) (rate 0.0185972))
(mutate (from (p)) (to (a)) (rate 0.0336744))
(mutate (from (p)) (to (r)) (rate 0.00136342))
(mutate (from (p)) (to (n)) (rate 0.00385005))
(mutate (from (p)) (to (d)) (rate 0.000510387))
(mutate (from (p)) (to (c)) (rate 0.00114756))
(mutate (from (p)) (to (q)) (rate 0.00456767))
(mutate (from (p)) (to (e)) (rate 0.00259176))
(mutate (from (p)) (to (g)) (rate 0.00173326))
(mutate (from (p)) (to (h)) (rate 0.000118719))
(mutate (from (p)) (to (i)) (rate 0.00109627))
(mutate (from (p)) (to (l)) (rate 0.0201891))
(mutate (from (p)) (to (k)) (rate 0.000178712))
(mutate (from (p)) (to (m)) (rate 0.00753518))
(mutate (from (p)) (to (f)) (rate 0.00138511))
(mutate (from (p)) (to (s)) (rate 0.00612211))
(mutate (from (p)) (to (t)) (rate 0.0023922))
(mutate (from (p)) (to (w)) (rate 1.0756e-06))
(mutate (from (p)) (to (v)) (rate 0.000977503))
(mutate (from (s)) (to (a)) (rate 0.245579))
(mutate (from (s)) (to (r)) (rate 0.00922339))
(mutate (from (s)) (to (n)) (rate 0.0529757))
(mutate (from (s)) (to (d)) (rate 0.00494441))
(mutate (from (s)) (to (c)) (rate 0.0390856))
(mutate (from (s)) (to (q)) (rate 0.00466945))
(mutate (from (s)) (to (e)) (rate 0.0259728))
(mutate (from (s)) (to (g)) (rate 0.0541707))
(mutate (from (s)) (to (h)) (rate 0.0041117))
(mutate (from (s)) (to (i)) (rate 0.00387926))
(mutate (from (s)) (to (l)) (rate 0.00704038))
(mutate (from (s)) (to (k)) (rate 0.0193098))
(mutate (from (s)) (to (m)) (rate 0.00172382))
(mutate (from (s)) (to (f)) (rate 0.0193077))
(mutate (from (s)) (to (p)) (rate 0.00519768))
(mutate (from (s)) (to (t)) (rate 0.28661))
(mutate (from (s)) (to (w)) (rate 0.00357401))
(mutate (from (s)) (to (y)) (rate 0.00438623))
(mutate (from (s)) (to (v)) (rate 0.0217094))
(mutate (from (t)) (to (a)) (rate 0.0931031))
(mutate (from (t)) (to (r)) (rate 0.00273984))
(mutate (from (t)) (to (n)) (rate 0.0163324))
(mutate (from (t)) (to (d)) (rate 0.00192904))
(mutate (from (t)) (to (c)) (rate 0.00338127))
(mutate (from (t)) (to (q)) (rate 0.00850475))
(mutate (from (t)) (to (e)) (rate 0.00268979))
(mutate (from (t)) (to (g)) (rate 0.000944917))
(mutate (from (t)) (to (h)) (rate 0.00202209))
(mutate (from (t)) (to (i)) (rate 0.0460606))
(mutate (from (t)) (to (l)) (rate 0.00603324))
(mutate (from (t)) (to (k)) (rate 0.0314913))
(mutate (from (t)) (to (m)) (rate 0.0127054))
(mutate (from (t)) (to (f)) (rate 0.00128787))
(mutate (from (t)) (to (p)) (rate 0.00129744))
(mutate (from (t)) (to (s)) (rate 0.183093))
(mutate (from (t)) (to (y)) (rate 0.00490771))
(mutate (from (t)) (to (v)) (rate 0.0666011))
(mutate (from (w)) (to (a)) (rate 0.00216669))
(mutate (from (w)) (to (r)) (rate 0.00066876))
(mutate (from (w)) (to (n)) (rate 0.00111542))
(mutate (from (w)) (to (c)) (rate 3.63325e-06))
(mutate (from (w)) (to (e)) (rate 0.00165287))
(mutate (from (w)) (to (h)) (rate 0.000617688))
(mutate (from (w)) (to (i)) (rate 0.0345559))
(mutate (from (w)) (to (l)) (rate 0.00452512))
(mutate (from (w)) (to (m)) (rate 1.83285e-05))
(mutate (from (w)) (to (f)) (rate 0.0553484))
(mutate (from (w)) (to (p)) (rate 1.36236e-06))
(mutate (from (w)) (to (s)) (rate 0.00533201))
(mutate (from (w)) (to (y)) (rate 0.00779906))
(mutate (from (y)) (to (a)) (rate 0.00819467))
(mutate (from (y)) (to (r)) (rate 0.00413829))
(mutate (from (y)) (to (n)) (rate 0.00336541))
(mutate (from (y)) (to (c)) (rate 0.00171722))
(mutate (from (y)) (to (e)) (rate 0.0037645))
(mutate (from (y)) (to (g)) (rate 0.00305826))
(mutate (from (y)) (to (h)) (rate 0.0214448))
(mutate (from (y)) (to (i)) (rate 0.00702699))
(mutate (from (y)) (to (l)) (rate 0.00977998))
(mutate (from (y)) (to (k)) (rate 0.00231424))
(mutate (from (y)) (to (m)) (rate 0.00012725))
(mutate (from (y)) (to (f)) (rate 0.11554))
(mutate (from (y)) (to (s)) (rate 0.00275029))
(mutate (from (y)) (to (t)) (rate 0.00481711))
(mutate (from (y)) (to (w)) (rate 0.00327789))
(mutate (from (y)) (to (v)) (rate 0.00962187))
(mutate (from (v)) (to (a)) (rate 0.0537672))
(mutate (from (v)) (to (r)) (rate 0.00164798))
(mutate (from (v)) (to (n)) (rate 0.00114099))
(mutate (from (v)) (to (d)) (rate 0.000601445))
(mutate (from (v)) (to (c)) (rate 0.0196652))
(mutate (from (v)) (to (q)) (rate 0.00722482))
(mutate (from (v)) (to (e)) (rate 0.00111775))
(mutate (from (v)) (to (g)) (rate 0.00115838))
(mutate (from (v)) (to (h)) (rate 0.00461907))
(mutate (from (v)) (to (i)) (rate 0.34078))
(mutate (from (v)) (to (l)) (rate 0.0889227))
(mutate (from (v)) (to (k)) (rate 0.000791947))
(mutate (from (v)) (to (m)) (rate 0.0200499))
(mutate (from (v)) (to (f)) (rate 0.00981054))
(mutate (from (v)) (to (p)) (rate 0.000231447))
(mutate (from (v)) (to (s)) (rate 0.00605444))
(mutate (from (v)) (to (t)) (rate 0.0290755))
(mutate (from (v)) (to (y)) (rate 0.00427954))
) ;; end chain A1
(chain
(update-policy rev)
(terminal (A2))
;; initial probability distribution
(initial (state (a)) (prob 0.0612873))
(initial (state (r)) (prob 0.0404616))
(initial (state (n)) (prob 0.0684408))
(initial (state (d)) (prob 0.0856228))
(initial (state (c)) (prob 0.00999889))
(initial (state (q)) (prob 0.030173))
(initial (state (e)) (prob 0.0531515))
(initial (state (g)) (prob 0.12202))
(initial (state (h)) (prob 0.0275494))
(initial (state (i)) (prob 0.0351163))
(initial (state (l)) (prob 0.0559547))
(initial (state (k)) (prob 0.0490547))
(initial (state (m)) (prob 0.0168358))
(initial (state (f)) (prob 0.0439447))
(initial (state (p)) (prob 0.065496))
(initial (state (s)) (prob 0.0644602))
(initial (state (t)) (prob 0.0599512))
(initial (state (w)) (prob 0.0196872))
(initial (state (y)) (prob 0.0456412))
(initial (state (v)) (prob 0.0451528))
;; mutation rates
(mutate (from (a)) (to (r)) (rate 0.0182449))
(mutate (from (a)) (to (n)) (rate 0.0384616))
(mutate (from (a)) (to (d)) (rate 0.0335167))
(mutate (from (a)) (to (c)) (rate 0.0123656))
(mutate (from (a)) (to (q)) (rate 0.0199987))
(mutate (from (a)) (to (e)) (rate 0.108545))
(mutate (from (a)) (to (g)) (rate 0.186869))
(mutate (from (a)) (to (h)) (rate 0.00882591))
(mutate (from (a)) (to (i)) (rate 0.00868838))
(mutate (from (a)) (to (l)) (rate 0.0308438))
(mutate (from (a)) (to (k)) (rate 0.013074))
(mutate (from (a)) (to (m)) (rate 0.00904765))
(mutate (from (a)) (to (f)) (rate 0.00616719))
(mutate (from (a)) (to (p)) (rate 0.122979))
(mutate (from (a)) (to (s)) (rate 0.246538))
(mutate (from (a)) (to (t)) (rate 0.179858))
(mutate (from (a)) (to (w)) (rate 0.00135186))
(mutate (from (a)) (to (y)) (rate 0.011726))
(mutate (from (a)) (to (v)) (rate 0.114726))
(mutate (from (r)) (to (a)) (rate 0.0276356))
(mutate (from (r)) (to (d)) (rate 0.00417632))
(mutate (from (r)) (to (c)) (rate 0.0016324))
(mutate (from (r)) (to (q)) (rate 0.0818772))
(mutate (from (r)) (to (e)) (rate 0.00344714))
(mutate (from (r)) (to (g)) (rate 0.00412287))
(mutate (from (r)) (to (h)) (rate 0.0543826))
(mutate (from (r)) (to (i)) (rate 0.0104614))
(mutate (from (r)) (to (l)) (rate 0.0050916))
(mutate (from (r)) (to (k)) (rate 0.240907))
(mutate (from (r)) (to (m)) (rate 0.0146708))
(mutate (from (r)) (to (f)) (rate 0.00321947))
(mutate (from (r)) (to (p)) (rate 0.0430467))
(mutate (from (r)) (to (s)) (rate 0.0800018))
(mutate (from (r)) (to (t)) (rate 0.00661173))
(mutate (from (r)) (to (w)) (rate 0.0149116))
(mutate (from (r)) (to (y)) (rate 0.00514994))
(mutate (from (r)) (to (v)) (rate 0.00820741))
(mutate (from (n)) (to (a)) (rate 0.0344415))
(mutate (from (n)) (to (d)) (rate 0.519018))
(mutate (from (n)) (to (c)) (rate 0.000850605))
(mutate (from (n)) (to (q)) (rate 0.00482991))
(mutate (from (n)) (to (e)) (rate 0.00884966))
(mutate (from (n)) (to (g)) (rate 0.0442515))
(mutate (from (n)) (to (h)) (rate 0.11041))
(mutate (from (n)) (to (i)) (rate 0.00623101))
(mutate (from (n)) (to (l)) (rate 0.00991489))
(mutate (from (n)) (to (k)) (rate 0.136917))
(mutate (from (n)) (to (f)) (rate 0.00297315))
(mutate (from (n)) (to (p)) (rate 0.0116629))
(mutate (from (n)) (to (s)) (rate 0.188592))
(mutate (from (n)) (to (t)) (rate 0.0636077))
(mutate (from (n)) (to (w)) (rate 0.00202152))
(mutate (from (n)) (to (y)) (rate 0.0179308))
(mutate (from (n)) (to (v)) (rate 0.00683127))
(mutate (from (d)) (to (a)) (rate 0.0239907))
(mutate (from (d)) (to (r)) (rate 0.00197354))
(mutate (from (d)) (to (n)) (rate 0.414866))
(mutate (from (d)) (to (c)) (rate 0.00123532))
(mutate (from (d)) (to (q)) (rate 0.00975637))
(mutate (from (d)) (to (e)) (rate 0.6087))
(mutate (from (d)) (to (g)) (rate 0.0370843))
(mutate (from (d)) (to (h)) (rate 0.00277657))
(mutate (from (d)) (to (i)) (rate 0.0014078))
(mutate (from (d)) (to (l)) (rate 0.000906031))
(mutate (from (d)) (to (k)) (rate 0.0216051))
(mutate (from (d)) (to (m)) (rate 0.000702508))
(mutate (from (d)) (to (f)) (rate 0.000611939))
(mutate (from (d)) (to (p)) (rate 0.00648652))
(mutate (from (d)) (to (s)) (rate 0.0194057))
(mutate (from (d)) (to (t)) (rate 0.0125994))
(mutate (from (d)) (to (v)) (rate 0.00263967))
(mutate (from (c)) (to (a)) (rate 0.0757939))
(mutate (from (c)) (to (r)) (rate 0.0066057))
(mutate (from (c)) (to (n)) (rate 0.00582226))
(mutate (from (c)) (to (d)) (rate 0.0105784))
(mutate (from (c)) (to (g)) (rate 0.0123724))
(mutate (from (c)) (to (h)) (rate 0.0187696))
(mutate (from (c)) (to (i)) (rate 0.0386524))
(mutate (from (c)) (to (l)) (rate 0.000743658))
(mutate (from (c)) (to (m)) (rate 0.00193765))
(mutate (from (c)) (to (p)) (rate 0.00968853))
(mutate (from (c)) (to (s)) (rate 0.105453))
(mutate (from (c)) (to (t)) (rate 0.00536494))
(mutate (from (c)) (to (w)) (rate 0.000301335))
(mutate (from (c)) (to (y)) (rate 0.0394814))
(mutate (from (c)) (to (v)) (rate 0.0530106))
(mutate (from (q)) (to (a)) (rate 0.0406213))
(mutate (from (q)) (to (r)) (rate 0.109796))
(mutate (from (q)) (to (n)) (rate 0.0109556))
(mutate (from (q)) (to (d)) (rate 0.027686))
(mutate (from (q)) (to (e)) (rate 0.340163))
(mutate (from (q)) (to (g)) (rate 0.0246278))
(mutate (from (q)) (to (h)) (rate 0.208214))
(mutate (from (q)) (to (i)) (rate 0.00129305))
(mutate (from (q)) (to (l)) (rate 0.0447169))
(mutate (from (q)) (to (k)) (rate 0.149499))
(mutate (from (q)) (to (m)) (rate 0.0130958))
(mutate (from (q)) (to (p)) (rate 0.040737))
(mutate (from (q)) (to (s)) (rate 0.0390129))
(mutate (from (q)) (to (t)) (rate 0.046631))
(mutate (from (q)) (to (v)) (rate 0.0188273))
(mutate (from (e)) (to (a)) (rate 0.12516))
(mutate (from (e)) (to (r)) (rate 0.00262413))
(mutate (from (e)) (to (n)) (rate 0.0113953))
(mutate (from (e)) (to (d)) (rate 0.980568))
(mutate (from (e)) (to (q)) (rate 0.193103))
(mutate (from (e)) (to (g)) (rate 0.0422495))
(mutate (from (e)) (to (h)) (rate 0.011016))
(mutate (from (e)) (to (i)) (rate 0.0099399))
(mutate (from (e)) (to (l)) (rate 0.00289579))
(mutate (from (e)) (to (k)) (rate 0.0645648))
(mutate (from (e)) (to (m)) (rate 0.00145734))
(mutate (from (e)) (to (p)) (rate 0.0197161))
(mutate (from (e)) (to (s)) (rate 0.0567696))
(mutate (from (e)) (to (t)) (rate 0.012854))
(mutate (from (e)) (to (w)) (rate 0.000124526))
(mutate (from (e)) (to (y)) (rate 0.00656081))
(mutate (from (e)) (to (v)) (rate 0.0104277))
(mutate (from (g)) (to (a)) (rate 0.0938591))
(mutate (from (g)) (to (r)) (rate 0.00136714))
(mutate (from (g)) (to (n)) (rate 0.0248206))
(mutate (from (g)) (to (d)) (rate 0.0260225))
(mutate (from (g)) (to (c)) (rate 0.00101385))
(mutate (from (g)) (to (q)) (rate 0.00608993))
(mutate (from (g)) (to (e)) (rate 0.0184038))
(mutate (from (g)) (to (h)) (rate 0.00213681))
(mutate (from (g)) (to (i)) (rate 0.000816356))
(mutate (from (g)) (to (l)) (rate 0.00104636))
(mutate (from (g)) (to (k)) (rate 0.0134965))
(mutate (from (g)) (to (m)) (rate 0.00160974))
(mutate (from (g)) (to (f)) (rate 0.00175278))
(mutate (from (g)) (to (p)) (rate 0.0064077))
(mutate (from (g)) (to (s)) (rate 0.0534253))
(mutate (from (g)) (to (t)) (rate 0.00368086))
(mutate (from (g)) (to (y)) (rate 0.00025808))
(mutate (from (g)) (to (v)) (rate 0.00427942))
(mutate (from (h)) (to (a)) (rate 0.0196344))
(mutate (from (h)) (to (r)) (rate 0.0798712))
(mutate (from (h)) (to (n)) (rate 0.274291))
(mutate (from (h)) (to (d)) (rate 0.00862951))
(mutate (from (h)) (to (c)) (rate 0.00681229))
(mutate (from (h)) (to (q)) (rate 0.228042))
(mutate (from (h)) (to (e)) (rate 0.0212533))
(mutate (from (h)) (to (g)) (rate 0.00946421))
(mutate (from (h)) (to (i)) (rate 0.0030213))
(mutate (from (h)) (to (l)) (rate 0.0216943))
(mutate (from (h)) (to (k)) (rate 0.00412687))
(mutate (from (h)) (to (m)) (rate 0.00143789))
(mutate (from (h)) (to (f)) (rate 0.0222545))
(mutate (from (h)) (to (p)) (rate 0.0314417))
(mutate (from (h)) (to (s)) (rate 0.0209969))
(mutate (from (h)) (to (t)) (rate 0.00709363))
(mutate (from (h)) (to (w)) (rate 0.00365758))
(mutate (from (h)) (to (y)) (rate 0.0396231))
(mutate (from (h)) (to (v)) (rate 0.014402))
(mutate (from (i)) (to (a)) (rate 0.0151635))
(mutate (from (i)) (to (r)) (rate 0.0120538))
(mutate (from (i)) (to (n)) (rate 0.0121441))
(mutate (from (i)) (to (d)) (rate 0.00343259))
(mutate (from (i)) (to (c)) (rate 0.0110057))
(mutate (from (i)) (to (q)) (rate 0.00111102))
(mutate (from (i)) (to (e)) (rate 0.0150449))
(mutate (from (i)) (to (g)) (rate 0.00283662))
(mutate (from (i)) (to (h)) (rate 0.00237027))
(mutate (from (i)) (to (l)) (rate 0.164247))
(mutate (from (i)) (to (k)) (rate 0.0161118))
(mutate (from (i)) (to (m)) (rate 0.0370953))
(mutate (from (i)) (to (f)) (rate 0.0565019))
(mutate (from (i)) (to (p)) (rate 0.0128396))
(mutate (from (i)) (to (s)) (rate 0.00336566))
(mutate (from (i)) (to (t)) (rate 0.0737023))
(mutate (from (i)) (to (w)) (rate 0.000584735))
(mutate (from (i)) (to (y)) (rate 0.00935231))
(mutate (from (i)) (to (v)) (rate 0.451935))
(mutate (from (l)) (to (a)) (rate 0.0337833))
(mutate (from (l)) (to (r)) (rate 0.0036818))
(mutate (from (l)) (to (n)) (rate 0.0121274))
(mutate (from (l)) (to (d)) (rate 0.00138642))
(mutate (from (l)) (to (c)) (rate 0.000132889))
(mutate (from (l)) (to (q)) (rate 0.0241131))
(mutate (from (l)) (to (e)) (rate 0.00275072))
(mutate (from (l)) (to (g)) (rate 0.00228179))
(mutate (from (l)) (to (h)) (rate 0.0106812))
(mutate (from (l)) (to (i)) (rate 0.103079))
(mutate (from (l)) (to (k)) (rate 0.0104381))
(mutate (from (l)) (to (m)) (rate 0.103119))
(mutate (from (l)) (to (f)) (rate 0.0533429))
(mutate (from (l)) (to (p)) (rate 0.0123472))
(mutate (from (l)) (to (s)) (rate 0.0110644))
(mutate (from (l)) (to (t)) (rate 0.0122906))
(mutate (from (l)) (to (w)) (rate 0.00654383))
(mutate (from (l)) (to (y)) (rate 0.0123959))
(mutate (from (l)) (to (v)) (rate 0.0972163))
(mutate (from (k)) (to (a)) (rate 0.0163342))
(mutate (from (k)) (to (r)) (rate 0.198706))
(mutate (from (k)) (to (n)) (rate 0.191026))
(mutate (from (k)) (to (d)) (rate 0.0377107))
(mutate (from (k)) (to (q)) (rate 0.0919552))
(mutate (from (k)) (to (e)) (rate 0.0699569))
(mutate (from (k)) (to (g)) (rate 0.0335716))
(mutate (from (k)) (to (h)) (rate 0.00231768))
(mutate (from (k)) (to (i)) (rate 0.0115338))
(mutate (from (k)) (to (l)) (rate 0.0119063))
(mutate (from (k)) (to (m)) (rate 0.0254063))
(mutate (from (k)) (to (f)) (rate 0.00135257))
(mutate (from (k)) (to (p)) (rate 0.0200602))
(mutate (from (k)) (to (s)) (rate 0.0756336))
(mutate (from (k)) (to (t)) (rate 0.0736354))
(mutate (from (k)) (to (y)) (rate 0.00428512))
(mutate (from (k)) (to (v)) (rate 0.00828506))
(mutate (from (m)) (to (a)) (rate 0.0329362))
(mutate (from (m)) (to (r)) (rate 0.0352583))
(mutate (from (m)) (to (d)) (rate 0.00357279))
(mutate (from (m)) (to (c)) (rate 0.00115078))
(mutate (from (m)) (to (q)) (rate 0.0234702))
(mutate (from (m)) (to (e)) (rate 0.0046009))
(mutate (from (m)) (to (g)) (rate 0.0116668))
(mutate (from (m)) (to (h)) (rate 0.00235292))
(mutate (from (m)) (to (i)) (rate 0.0773739))
(mutate (from (m)) (to (l)) (rate 0.342722))
(mutate (from (m)) (to (k)) (rate 0.0740268))
(mutate (from (m)) (to (f)) (rate 0.0329774))
(mutate (from (m)) (to (p)) (rate 0.00475654))
(mutate (from (m)) (to (s)) (rate 0.00794126))
(mutate (from (m)) (to (t)) (rate 0.0421871))
(mutate (from (m)) (to (w)) (rate 0.000180272))
(mutate (from (m)) (to (y)) (rate 0.000162251))
(mutate (from (m)) (to (v)) (rate 0.112904))
(mutate (from (f)) (to (a)) (rate 0.00860105))
(mutate (from (f)) (to (r)) (rate 0.0029643))
(mutate (from (f)) (to (n)) (rate 0.00463047))
(mutate (from (f)) (to (d)) (rate 0.00119232))
(mutate (from (f)) (to (g)) (rate 0.00486689))
(mutate (from (f)) (to (h)) (rate 0.0139516))
(mutate (from (f)) (to (i)) (rate 0.0451508))
(mutate (from (f)) (to (l)) (rate 0.0679215))
(mutate (from (f)) (to (k)) (rate 0.00150986))
(mutate (from (f)) (to (m)) (rate 0.0126341))
(mutate (from (f)) (to (p)) (rate 0.00700877))
(mutate (from (f)) (to (s)) (rate 0.0182601))
(mutate (from (f)) (to (t)) (rate 0.00352006))
(mutate (from (f)) (to (w)) (rate 0.0131871))
(mutate (from (f)) (to (y)) (rate 0.175055))
(mutate (from (f)) (to (v)) (rate 0.0104028))
(mutate (from (p)) (to (a)) (rate 0.115076))
(mutate (from (p)) (to (r)) (rate 0.026593))
(mutate (from (p)) (to (n)) (rate 0.0121873))
(mutate (from (p)) (to (d)) (rate 0.00847982))
(mutate (from (p)) (to (c)) (rate 0.00147909))
(mutate (from (p)) (to (q)) (rate 0.0187669))
(mutate (from (p)) (to (e)) (rate 0.016))
(mutate (from (p)) (to (g)) (rate 0.0119376))
(mutate (from (p)) (to (h)) (rate 0.0132252))
(mutate (from (p)) (to (i)) (rate 0.00688408))
(mutate (from (p)) (to (l)) (rate 0.0105485))
(mutate (from (p)) (to (k)) (rate 0.0150245))
(mutate (from (p)) (to (m)) (rate 0.00122267))
(mutate (from (p)) (to (f)) (rate 0.00470255))
(mutate (from (p)) (to (s)) (rate 0.0584005))
(mutate (from (p)) (to (t)) (rate 0.0231076))
(mutate (from (p)) (to (w)) (rate 0.00102977))
(mutate (from (p)) (to (v)) (rate 0.00660594))
(mutate (from (s)) (to (a)) (rate 0.234403))
(mutate (from (s)) (to (r)) (rate 0.0502171))
(mutate (from (s)) (to (n)) (rate 0.200239))
(mutate (from (s)) (to (d)) (rate 0.0257767))
(mutate (from (s)) (to (c)) (rate 0.0163577))
(mutate (from (s)) (to (q)) (rate 0.0182614))
(mutate (from (s)) (to (e)) (rate 0.0468102))
(mutate (from (s)) (to (g)) (rate 0.101131))
(mutate (from (s)) (to (h)) (rate 0.00897381))
(mutate (from (s)) (to (i)) (rate 0.00183353))
(mutate (from (s)) (to (l)) (rate 0.00960444))
(mutate (from (s)) (to (k)) (rate 0.0575578))
(mutate (from (s)) (to (m)) (rate 0.00207411))
(mutate (from (s)) (to (f)) (rate 0.0124485))
(mutate (from (s)) (to (p)) (rate 0.059339))
(mutate (from (s)) (to (t)) (rate 0.331784))
(mutate (from (s)) (to (w)) (rate 0.0134895))
(mutate (from (s)) (to (y)) (rate 0.00577953))
(mutate (from (s)) (to (v)) (rate 0.0163584))
(mutate (from (t)) (to (a)) (rate 0.183866))
(mutate (from (t)) (to (r)) (rate 0.00446231))
(mutate (from (t)) (to (n)) (rate 0.0726151))
(mutate (from (t)) (to (d)) (rate 0.0179946))
(mutate (from (t)) (to (c)) (rate 0.000894784))
(mutate (from (t)) (to (q)) (rate 0.023469))
(mutate (from (t)) (to (e)) (rate 0.0113961))
(mutate (from (t)) (to (g)) (rate 0.00749172))
(mutate (from (t)) (to (h)) (rate 0.00325974))
(mutate (from (t)) (to (i)) (rate 0.043171))
(mutate (from (t)) (to (l)) (rate 0.0114713))
(mutate (from (t)) (to (k)) (rate 0.0602517))
(mutate (from (t)) (to (m)) (rate 0.0118472))
(mutate (from (t)) (to (f)) (rate 0.00258023))
(mutate (from (t)) (to (p)) (rate 0.0252448))
(mutate (from (t)) (to (s)) (rate 0.356738))
(mutate (from (t)) (to (y)) (rate 0.00815071))
(mutate (from (t)) (to (v)) (rate 0.0647513))
(mutate (from (w)) (to (a)) (rate 0.00420842))
(mutate (from (w)) (to (r)) (rate 0.0306467))
(mutate (from (w)) (to (n)) (rate 0.00702764))
(mutate (from (w)) (to (c)) (rate 0.000153044))
(mutate (from (w)) (to (e)) (rate 0.000336196))
(mutate (from (w)) (to (h)) (rate 0.00511827))
(mutate (from (w)) (to (i)) (rate 0.001043))
(mutate (from (w)) (to (l)) (rate 0.0185988))
(mutate (from (w)) (to (m)) (rate 0.000154162))
(mutate (from (w)) (to (f)) (rate 0.0294356))
(mutate (from (w)) (to (p)) (rate 0.00342587))
(mutate (from (w)) (to (s)) (rate 0.0441675))
(mutate (from (w)) (to (y)) (rate 0.0199409))
(mutate (from (y)) (to (a)) (rate 0.0157457))
(mutate (from (y)) (to (r)) (rate 0.0045655))
(mutate (from (y)) (to (n)) (rate 0.0268879))
(mutate (from (y)) (to (c)) (rate 0.00864942))
(mutate (from (y)) (to (e)) (rate 0.0076404))
(mutate (from (y)) (to (g)) (rate 0.000689968))
(mutate (from (y)) (to (h)) (rate 0.0239169))
(mutate (from (y)) (to (i)) (rate 0.00719566))
(mutate (from (y)) (to (l)) (rate 0.015197))
(mutate (from (y)) (to (k)) (rate 0.0046056))
(mutate (from (y)) (to (m)) (rate 5.98499e-05))
(mutate (from (y)) (to (f)) (rate 0.168549))
(mutate (from (y)) (to (s)) (rate 0.00816257))
(mutate (from (y)) (to (t)) (rate 0.0107062))
(mutate (from (y)) (to (w)) (rate 0.00860143))
(mutate (from (y)) (to (v)) (rate 0.00880061))
(mutate (from (v)) (to (a)) (rate 0.155722))
(mutate (from (v)) (to (r)) (rate 0.00735469))
(mutate (from (v)) (to (n)) (rate 0.0103546))
(mutate (from (v)) (to (d)) (rate 0.00500559))
(mutate (from (v)) (to (c)) (rate 0.011739))
(mutate (from (v)) (to (q)) (rate 0.0125812))
(mutate (from (v)) (to (e)) (rate 0.012275))
(mutate (from (v)) (to (g)) (rate 0.0115646))
(mutate (from (v)) (to (h)) (rate 0.00878719))
(mutate (from (v)) (to (i)) (rate 0.35148))
(mutate (from (v)) (to (l)) (rate 0.120473))
(mutate (from (v)) (to (k)) (rate 0.00900102))
(mutate (from (v)) (to (m)) (rate 0.0420976))
(mutate (from (v)) (to (f)) (rate 0.0101245))
(mutate (from (v)) (to (p)) (rate 0.00958219))
(mutate (from (v)) (to (s)) (rate 0.0233533))
(mutate (from (v)) (to (t)) (rate 0.0859729))
(mutate (from (v)) (to (y)) (rate 0.0088958))
) ;; end chain A2
) ;; end grammar nullprot3
;; Alphabet Protein
;;
(alphabet
(name Protein)
(token (a r n d c q e g h i l k m f p s t w y v))
(extend (to x) (from a) (from r) (from n) (from d) (from c) (from q) (from e) (from g) (from h) (from i) (from l) (from k) (from m) (from f) (from p) (from s) (from t) (from w) (from y) (from v))
(extend (to b) (from n) (from d))
(extend (to z) (from q) (from e))
(wildcard *)
) ;; end alphabet Protein