##State name
##StartPhase EndPhase Duraration Prediodic Direction BurnLength
##State start conditions 
##State end conditions
##Parameter file names
#Single exon gene state
exon
coding 0 0 duration periodic forward 0 0
all,0
TAG,-1 TAA,-1 TGA,-1
exon_MC.mat exon_L.mat
#Initial exon states
exon_i0
coding 0 2 duration periodic forward 1 0
all,0
GT,-3
exon_MC.mat exon_i0_L.mat
#
exon_i1
coding 0 2 duration periodic forward 2 0
all,0
GT,-3
exon_MC.mat exon_i1_L.mat
#
exon_i2
coding 0 2 duration periodic forward 0 0
all,0
GT,-3
exon_MC.mat exon_i2_L.mat
#Middle exon states
exon_m0
coding -2 2 duration periodic forward 1
AG,4
GT,-3
exon_MC.mat exon_m0_L.mat
#
exon_m1
coding -2 2 duration periodic forward 2
AG,4
GT,-3
exon_MC.mat exon_m1_L.mat
#
exon_m2
coding -2 2 duration periodic forward 0
AG,4
GT,-3
exon_MC.mat exon_m2_L.mat
#Terminal exon states
exon_t
coding -2 0 duration periodic forward 0
AG,4
TAA,-1 TAG,-1 TGA,-1
exon_MC.mat exon_t_L.mat
#Start state
start
non-coding 0 0 fixed non-periodic forward 0
ATG,2
start_MC.mat 11
#Stop state
stop
non-coding 0 0 fixed non-periodic forward 0
TAA,2 TGA,2 TAG,2
stop_MC.mat 3
#Donor states
donor_0
non-coding 0 0 fixed non-periodic forward 0
GT,1
donor_0_MC.mat 4
#
donor_1
non-coding 0 0 fixed non-periodic forward 1
GT,1
donor_1_MC.mat 4
#
donor_2
non-coding 0 0 fixed non-periodic forward 2
GT,1
donor_2_MC.mat 4
#Acceptor states
acceptor_0
non-coding 0 0 fixed non-periodic forward 0
AG,3
acceptor_0_MC.mat 4
#
acceptor_1
non-coding 0 0 fixed non-periodic forward 1
AG,3
acceptor_1_MC.mat 4
#
acceptor_2
non-coding 0 0 fixed non-periodic forward 2
AG,3
acceptor_2_MC.mat 4
#Branch point states
branch_0
non-coding 0 0 fixed non-periodic forward 0 
A,2
branch_0_MC.mat 7
#
branch_1
non-coding 0 0 fixed non-periodic forward 1
A,2
branch_0_MC.mat 7
#
branch_2
non-coding 0 0 fixed non-periodic forward 2
A,2
branch_0_MC.mat 7
#Intron 3' spacer states
spacer3_0
non-coding 0 0 duration non-periodic forward 0
A,3
AG,-1
spacer3_0_MC.mat spacer3_0_L.mat
#
spacer3_1
non-coding 0 0 duration non-periodic forward 1
A,3
AG,-1
spacer3_0_MC.mat spacer3_0_L.mat
#
spacer3_2
non-coding 0 0 duration non-periodic forward 2
A,3
AG,-1
spacer3_0_MC.mat spacer3_0_L.mat
#Intron 5' spacer states
spacer5_0
non-coding 0 0 duration non-periodic forward 0
GT,2
A,-5
spacer5_0_MC.mat spacer5_0_L.mat
#
spacer5_1
non-coding 0 0 duration non-periodic forward 1
GT,2
A,-5
spacer5_0_MC.mat spacer5_0_L.mat
#     
spacer5_2
non-coding 0 0 duration non-periodic forward 2
GT,2
A,-5
spacer5_0_MC.mat spacer5_0_L.mat
#Reverse single exon gene state
r_exon
coding 0 0 duration periodic reverse 0 0
TTA,3 TCA,3 CTA,3
all,0
exon_MC.mat r_exon_L.mat
#Reverse initial exon state
r_exon_i
coding -2 0 duration periodic reverse 0 0
AC,4
all,0
exon_MC.mat r_exon_i_L.mat
#Reverse middle exon states
r_exon_m0
coding -2 2 duration periodic reverse 1
AC,4
CT,-3
exon_MC.mat r_exon_m0_L.mat
#
r_exon_m1
coding -2 2 duration periodic reverse 2
AC,4
CT,-3
exon_MC.mat exon_m1_L.mat
#
r_exon_m2
coding -2 2 duration periodic reverse 0
AC,4
CT,-3
exon_MC.mat exon_m2_L.mat
#
r_exon_t0
coding 0 2 duration periodic reverse 1
TTA,3 TCA,3 CTA,3
CT,-3
exon_MC.mat r_exon_t0_L.mat
#
r_exon_t1
coding 0 2 duration periodic reverse 2
TTA,3 TCA,3 CTA,3
CT,-3
exon_MC.mat r_exon_t1_L.mat
#
r_exon_t2
coding 0 2 duration periodic reverse 0
TTA,3 TCA,3 CTA,3
CT,-3
exon_MC.mat r_exon_t2_L.mat
#Reverse start
r_start
non-coding 0 0 fixed non-periodic reverse 0
CAT,10
start_MC.mat 11
#Reverse stop
r_stop
non-coding 0 0 fixed non-periodic reverse 0
TTA,2 TCA,2 CTA,2
stop_MC.mat 3
#Reverse donor site state
r_donor_0
non-coding 0 0 fixed non-periodic reverse 0
AC,3
donor_0_MC.mat 8
#
r_donor_1
non-coding 0 0 fixed non-periodic reverse 1
AC,3
donor_2_MC.mat 4
#
r_donor_2
non-coding 0 0 fixed non-periodic reverse 2
AC,3
donor_1_MC.mat 4
#Reverse acceptor site state
r_acceptor_0
non-coding 0 0 fixed non-periodic reverse 0
CT,1
acceptor_0_MC.mat 4
#
r_acceptor_1
non-coding 0 0 fixed non-periodic reverse 1
CT,1
acceptor_2_MC.mat 4
#
r_acceptor_2
non-coding 0 0 fixed non-periodic reverse 2
CT,1
acceptor_1_MC.mat 4
#Reverse branch point state
r_branch_0
non-coding 0 0 fixed non-periodic reverse 0
T,4
branch_0_MC.mat 7
#
r_branch_1
non-coding 0 0 fixed non-periodic reverse 1
T,4
branch_0_MC.mat 7
#
r_branch_2
non-coding 0 0 fixed non-periodic reverse 2
T,4
branch_0_MC.mat 7
#Reverse intron 3' spacer
r_spacer3_0
non-coding 0 0 duration non-periodic reverse 0
CT,2
T,-3
spacer3_0_MC.mat spacer3_0_L.mat
#
r_spacer3_1
non-coding 0 0 duration non-periodic reverse 1
CT,2
T,-3
spacer3_0_MC.mat spacer3_0_L.mat
#
r_spacer3_2
non-coding 0 0 duration non-periodic reverse 2
CT,2
T,-3
spacer3_0_MC.mat spacer3_0_L.mat
#Reverse intron 5' spacer
r_spacer5_0
non-coding 0 0 duration non-periodic reverse 0
T,5
AC,-1
spacer5_0_MC.mat spacer5_0_L.mat
#
r_spacer5_1
non-coding 0 0 duration non-periodic reverse 1
T,5
AC,-1
spacer5_0_MC.mat spacer5_0_L.mat
#
r_spacer5_2
non-coding 0 0 duration non-periodic reverse 2
T,5
AC,-1
spacer5_0_MC.mat spacer5_0_L.mat
#Intergenic region
intergenic
non-coding 0 0 duration non-periodic forward 0
TAA,3 TAG,3 TGA,3 CAT,11 contig,0
ATG,-9 TTA,-1 TCA,-1 CTA,-1 contig,0
intergenic_MC.mat intergenic_L.mat
#
spep
coding -3 0 duration periodic forward 0 0
ATG,3
all,0
spep_MC.mat spep_L.mat
#Initial spep states
spep_i0
coding -3 2 duration periodic forward 1 0
ATG,3
GT,-3
spep_MC.mat spep_i0_L.mat
#
spep_i1
coding -3 2 duration periodic forward 2 0
ATG,3
GT,-3
spep_MC.mat spep_i1_L.mat
#
spep_i2
coding -3 2 duration periodic forward 0 0
ATG,3
GT,-3
spep_MC.mat spep_i2_L.mat
#Middle spep states
spep_m
coding -2 0 duration periodic forward 0
AG,4
all,0
spep_MC.mat spep_m_L.mat
#Reverse single spep gene state
r_spep
coding 0 3 duration periodic reverse 0 0
all,0
CAT,-1
spep_MC.mat r_spep_L.mat
#Reverse initial spep state
r_spep_i
coding -2 3 duration periodic reverse 0 0
AC,4
CAT,-1
spep_MC.mat r_spep_i_L.mat
#Reverse middle spep states
r_spep_m0
coding 0 2 duration periodic reverse 1
all,0
CT,-3
spep_MC.mat r_spep_m0_L.mat
#
r_spep_m1
coding 0 2 duration periodic reverse 2
all,0
CT,-3
spep_MC.mat r_spep_m1_L.mat
#
r_spep_m2
coding 0 2 duration periodic reverse 0
all,0
CT,-3
spep_MC.mat r_spep_m2_L.mat
#Donor states
donor2_0
non-coding 0 0 fixed non-periodic forward 0
GT,1
donor_0_MC.mat 4
#
donor2_1
non-coding 0 0 fixed non-periodic forward 1
GT,1
donor_1_MC.mat 4
#
donor2_2
non-coding 0 0 fixed non-periodic forward 2
GT,1
donor_2_MC.mat 4
#Acceptor states
acceptor2_0
non-coding 0 0 fixed non-periodic forward 0
AG,3
acceptor_0_MC.mat 4
#
acceptor2_1
non-coding 0 0 fixed non-periodic forward 1
AG,3
acceptor_1_MC.mat 4
#
acceptor2_2
non-coding 0 0 fixed non-periodic forward 2
AG,3
acceptor_2_MC.mat 4
#Branch point states
branch2_0
non-coding 0 0 fixed non-periodic forward 0
A,2
branch_0_MC.mat 7
#
branch2_1
non-coding 0 0 fixed non-periodic forward 1
A,2
branch_0_MC.mat 7
#
branch2_2
non-coding 0 0 fixed non-periodic forward 2
A,2
branch_0_MC.mat 7
#Intron 3' spacer states
spacer32_0
non-coding 0 0 duration non-periodic forward 0
A,3
AG,-1
spacer3_0_MC.mat spacer3_0_L.mat
#
spacer32_1
non-coding 0 0 duration non-periodic forward 1
A,3
AG,-1
spacer3_0_MC.mat spacer3_0_L.mat
#
spacer32_2
non-coding 0 0 duration non-periodic forward 2
A,3
AG,-1
spacer3_0_MC.mat spacer3_0_L.mat
#Intron 5' spacer states
spacer52_0
non-coding 0 0 duration non-periodic forward 0
GT,2
A,-5
spacer5_0_MC.mat spacer5_0_L.mat
#
spacer52_1
non-coding 0 0 duration non-periodic forward 1
GT,2
A,-5
spacer5_0_MC.mat spacer5_0_L.mat
#
spacer52_2
non-coding 0 0 duration non-periodic forward 2
GT,2
A,-5
spacer5_0_MC.mat spacer5_0_L.mat
#
r_donor2_0
non-coding 0 0 fixed non-periodic reverse 0
AC,3
donor_0_MC.mat 8
#
r_donor2_1
non-coding 0 0 fixed non-periodic reverse 1
AC,3
donor_2_MC.mat 4
#
r_donor2_2
non-coding 0 0 fixed non-periodic reverse 2
AC,3
donor_1_MC.mat 4
#Reverse acceptor site state
r_acceptor2_0
non-coding 0 0 fixed non-periodic reverse 0
CT,1
acceptor_0_MC.mat 4
#
r_acceptor2_1
non-coding 0 0 fixed non-periodic reverse 1
CT,1
acceptor_2_MC.mat 4
#
r_acceptor2_2
non-coding 0 0 fixed non-periodic reverse 2
CT,1
acceptor_1_MC.mat 4
#Reverse branch point state
r_branch2_0
non-coding 0 0 fixed non-periodic reverse 0
T,4
branch_0_MC.mat 7
#
r_branch2_1
non-coding 0 0 fixed non-periodic reverse 1
T,4
branch_0_MC.mat 7
#
r_branch2_2
non-coding 0 0 fixed non-periodic reverse 2
T,4
branch_0_MC.mat 7
#Reverse intron 3' spacer
r_spacer32_0
non-coding 0 0 duration non-periodic reverse 0
CT,2
T,-3
spacer3_0_MC.mat spacer3_0_L.mat
#
r_spacer32_1
non-coding 0 0 duration non-periodic reverse 1
CT,2
T,-3
spacer3_0_MC.mat spacer3_0_L.mat
#
r_spacer32_2
non-coding 0 0 duration non-periodic reverse 2
CT,2
T,-3
spacer3_0_MC.mat spacer3_0_L.mat
#Reverse intron 5' spacer
r_spacer52_0
non-coding 0 0 duration non-periodic reverse 0
T,5
AC,-1
spacer5_0_MC.mat spacer5_0_L.mat
#
r_spacer52_1
non-coding 0 0 duration non-periodic reverse 1
T,5
AC,-1
spacer5_0_MC.mat spacer5_0_L.mat
#
r_spacer52_2
non-coding 0 0 duration non-periodic reverse 2
T,5
AC,-1
spacer5_0_MC.mat spacer5_0_L.mat
#####
