Alphabet: ACGT
###############################################
##################
State BEGIN  
	E:   0.25  0.25  0.25  0.25   
	T:   BG 0.9959 Bs1 0.001 rBo1 0.001 aBo8 0.001 arBs7 0.001  END 0.0001
##################
State BG  
	E:   0.25  0.25  0.25  0.25   
	T:   BG 0.9959 Bs1 0.001 rBo1 0.001 aBo8 0.001 arBs7 0.001  END 0.0001
##################
##################
State Bs1  
	E:   0.02  0.94  0.02  0.02   
	T:   Bs2 1 
State aBs1  
	E:   0.02  0.02  0.94  0.02   
	T:   BG 0.9999  END 0.0001 
State Bs2  
	E:   0.49  0.01  0.01  0.49   
	T:   Bs3 1 
State aBs2  
	E:   0.49  0.01  0.01  0.49   
	T:   aBs1 1 
State Bs3  
	E:   0.02  0.02  0.02  0.94   
	T:   Bs4 1 
State aBs3  
	E:   0.94  0.02  0.02  0.02   
	T:   aBs2 1 
State Bs4  
	E:   0.02  0.02  0.02  0.94   
	T:   Bs5 1 
State aBs4  
	E:   0.94  0.02  0.02  0.02   
	T:   aBs3 1 
State Bs5  
	E:   0.02  0.02  0.94  0.02    
	T:   Bs6 1 
State aBs5  
	E:   0.02  0.94  0.02  0.02    
	T:   aBs4 1 
State Bs6  
	E:   0.02  0.02  0.02  0.94     
	T:   Bs7 1
State aBs6  
	E:   0.94  0.02  0.02  0.02     
	T:   aBs5 1
State Bs7  
	E:   0.25  0.25  0.25  0.25   
	T:   Bo1 0.5  SP1 0.5  
State aBs7  
	E:   0.25  0.25  0.25  0.25   
	T:   aBs6 1  
##################
State Bo1  
	E:   0.94  0.02  0.02  0.02   
	T:   Bo2 1 
State aBo1  
	E:   0.02  0.02  0.02  0.94   
	T:   aBs7 0.5  aSP1 0.5 
State Bo2  
	E:   0.02  0.02  0.02  0.94
	T:   Bo3 1 
State aBo2  
	E:   0.94  0.02  0.02  0.02
	T:   aBo1 1 
State Bo3  
	E:   0.02  0.02  0.94  0.02   
	T:   Bo4 1 
State aBo3  
	E:   0.02  0.94  0.02  0.02   
	T:   aBo2 1 
State Bo4  
	E:   0.02  0.94  0.02  0.02   
	T:   Bo5 1 
State aBo4  
	E:   0.02  0.02  0.94  0.02   
	T:   aBo3 1 
State Bo5  
	E:   0.47  0.03  0.03  0.47    
	T:   Bo6 1 
State aBo5  
	E:   0.47  0.03  0.03  0.47    
	T:   aBo4 1 
State Bo6  
	E:   0.47  0.03  0.03  0.47 
	T:   Bo7 1 
State aBo6  
	E:   0.47  0.03  0.03  0.47 
	T:   aBo5 1 
State Bo7  
	E:   0.47  0.03  0.03  0.47   
	T:   Bo8 1 
State aBo7  
	E:   0.47  0.03  0.03  0.47   
	T:   aBo6 1 
State Bo8  
	E:   0.47  0.03  0.03  0.47   
	T:   BG 0.9999  END 0.0001 
State aBo8  
	E:   0.47  0.03  0.03  0.47   
	T:   aBo7 1  
##################
State SP1  
	E:   0.25  0.25  0.25  0.25    
	T:   SP2 1
State SP2  
	E:   0.25  0.25  0.25  0.25    
	T:   SP3 1
State SP3  
	E:   0.25  0.25  0.25  0.25    
	T:   Bo1 0.5  SP4 0.5
State SP4  
	E:   0.25  0.25  0.25  0.25    
	T:   SP5 1
State SP5  
	E:   0.25  0.25  0.25  0.25    
	T:   SP6 1
State SP6  
	E:   0.25  0.25  0.25  0.25    
	T:   Bo1 1  
State aSP1  
	E:   0.25  0.25  0.25  0.25    
	T:   aSP2 1
State aSP2  
	E:   0.25  0.25  0.25  0.25    
	T:   aSP3 1
State aSP3  
	E:   0.25  0.25  0.25  0.25    
	T:   aBs7 0.5   aSP4 0.5
State aSP4  
	E:   0.25  0.25  0.25  0.25    
	T:   aSP5 1
State aSP5  
	E:   0.25  0.25  0.25  0.25    
	T:   aSP6 1
State aSP6  
	E:   0.25  0.25  0.25  0.25    
	T:   aBs7 1   
##################
State END  
	E:   0.25  0.25  0.25  0.25   
	T:   END 0
##################
##################
State rBs1  
	E:   0.02  0.94  0.02  0.02   
	T:   rBs2 1 
State arBs1  
	E:   0.02  0.02  0.94  0.02   
	T:   arBo8 0.5  arSP1 0.5  
State rBs2  
	E:   0.49  0.01  0.01  0.49   
	T:   rBs3 1 
State arBs2  
	E:   0.49  0.01  0.01  0.49   
	T:   arBs1 1 
State rBs3  
	E:   0.02  0.02  0.02  0.94   
	T:   rBs4 1 
State arBs3  
	E:   0.94  0.02  0.02  0.02   
	T:   arBs2 1 
State rBs4  
	E:   0.02  0.02  0.02  0.94   
	T:   rBs5 1 
State arBs4  
	E:   0.94  0.02  0.02  0.02   
	T:   arBs3 1 
State rBs5  
	E:   0.02  0.02  0.94  0.02    
	T:   rBs6 1 
State arBs5  
	E:   0.02  0.94  0.02  0.02    
	T:   arBs4 1 
State rBs6  
	E:   0.02  0.02  0.02  0.94     
	T:   rBs7 1
State arBs6  
	E:   0.94  0.02  0.02  0.02     
	T:   arBs5 1
State rBs7  
	E:   0.25  0.25  0.25  0.25   
	T:   BG 0.9999  END 0.0001  
State arBs7  
	E:   0.25  0.25  0.25  0.25   
	T:   arBs6 1  
##################
State rBo1  
	E:   0.94  0.02  0.02  0.02   
	T:   rBo2 1 
State arBo1  
	E:   0.02  0.02  0.02  0.94   
	T:   BG 0.9999  END 0.0001 
State rBo2  
	E:   0.02  0.02  0.02  0.94
	T:   rBo3 1 
State arBo2  
	E:   0.94  0.02  0.02  0.02
	T:   arBo1 1 
State rBo3  
	E:   0.02  0.02  0.94  0.02   
	T:   rBo4 1 
State arBo3  
	E:   0.02  0.94  0.02  0.02   
	T:   arBo2 1 
State rBo4  
	E:   0.02  0.94  0.02  0.02   
	T:   rBo5 1 
State arBo4  
	E:   0.02  0.02  0.94  0.02   
	T:   arBo3 1 
State rBo5  
	E:   0.47  0.03  0.03  0.47    
	T:   rBo6 1 
State arBo5  
	E:   0.47  0.03  0.03  0.47    
	T:   arBo4 1 
State rBo6  
	E:   0.47  0.03  0.03  0.47 
	T:   rBo7 1 
State arBo6  
	E:   0.47  0.03  0.03  0.47 
	T:   arBo5 1 
State rBo7  
	E:   0.47  0.03  0.03  0.47   
	T:   rBo8 1 
State arBo7  
	E:   0.47  0.03  0.03  0.47   
	T:   arBo6 1 
State rBo8  
	E:   0.47  0.03  0.03  0.47   
	T:   rBs1 0.5  rSP1 0.5 
State arBo8  
	E:   0.47  0.03  0.03  0.47   
	T:   arBo7 1  
##################
State rSP1  
	E:   0.25  0.25  0.25  0.25    
	T:   rSP2 1
State rSP2  
	E:   0.25  0.25  0.25  0.25    
	T:   rSP3 1
State rSP3  
	E:   0.25  0.25  0.25  0.25    
	T:   rBs1 0.5  rSP4 0.5
State rSP4  
	E:   0.25  0.25  0.25  0.25    
	T:   rSP5 1
State rSP5  
	E:   0.25  0.25  0.25  0.25    
	T:   rSP6 1
State rSP6  
	E:   0.25  0.25  0.25  0.25    
	T:   rBs1 1  
State arSP1  
	E:   0.25  0.25  0.25  0.25    
	T:   arSP2 1
State arSP2  
	E:   0.25  0.25  0.25  0.25    
	T:   arSP3 1
State arSP3  
	E:   0.25  0.25  0.25  0.25    
	T:   arBo8 0.5   arSP4 0.5
State arSP4  
	E:   0.25  0.25  0.25  0.25    
	T:   arSP5 1
State arSP5  
	E:   0.25  0.25  0.25  0.25    
	T:   arSP6 1
State arSP6  
	E:   0.25  0.25  0.25  0.25    
	T:   arBo8 1
################################################
#
NULLMODEL:  0.25  0.25  0.25  0.25  
#
compl_em:    Bo1 aBo1
compl_em:    Bo2 aBo2
compl_em:    Bo3 aBo3
compl_em:    Bo4 aBo4
compl_em:    Bo5 aBo5
compl_em:    Bo6 aBo6
compl_em:    Bo7 aBo7
compl_em:    Bo8 aBo8
compl_em:    Bs1 aBs1
compl_em:    Bs2 aBs2
compl_em:    Bs3 aBs3
compl_em:    Bs4 aBs4
compl_em:    Bs5 aBs5
compl_em:    Bs6 aBs6
compl_em:    Bs7 aBs7
############
compl_em:    rBo1 arBo1
compl_em:    rBo2 arBo2
compl_em:    rBo3 arBo3
compl_em:    rBo4 arBo4
compl_em:    rBo5 arBo5
compl_em:    rBo6 arBo6
compl_em:    rBo7 arBo7
compl_em:    rBo8 arBo8
compl_em:    rBs1 arBs1
compl_em:    rBs2 arBs2
compl_em:    rBs3 arBs3
compl_em:    rBs4 arBs4
compl_em:    rBs5 arBs5
compl_em:    rBs6 arBs6
compl_em:    rBs7 arBs7
############
#avoid states being in more than one tie group!
tie_em:      Bo1 rBo1   
tie_em:      Bo2 rBo2   
tie_em:      Bo3 rBo3   
tie_em:      Bo4 rBo4   
tie_em:      Bo5 rBo5   
tie_em:      Bo6 rBo6   
tie_em:      Bo7 rBo7   
tie_em:      Bo8 rBo8   
tie_em:    Bs1 rBs1
tie_em:    Bs2 rBs2
tie_em:    Bs3 rBs3
tie_em:    Bs4 rBs4
tie_em:    Bs5 rBs5
tie_em:    Bs6 rBs6
tie_em:    Bs7 rBs7
############
tie_em:      aBo1 arBo1   
tie_em:      aBo2 arBo2   
tie_em:      aBo3 arBo3   
tie_em:      aBo4 arBo4   
tie_em:      aBo5 arBo5   
tie_em:      aBo6 arBo6   
tie_em:      aBo7 arBo7   
tie_em:      aBo8 arBo8   
tie_em:    aBs1 arBs1
tie_em:    aBs2 arBs2
tie_em:    aBs3 arBs3
tie_em:    aBs4 arBs4
tie_em:    aBs5 arBs5
tie_em:    aBs6 arBs6
tie_em:    aBs7 arBs7
############
fix_em:  BEGIN  END  BG
fix_em:  SP1 SP2 SP3 SP4 SP5 SP6 aSP1 aSP2 aSP3 aSP4 aSP5 aSP6
fix_em:  rSP1 rSP2 rSP3 rSP4 rSP5 rSP6 arSP1 arSP2 arSP3 arSP4 arSP5 arSP6
#######