##State name
##StartPhase EndPhase Duraration Prediodic Direction BurnLength
##State start conditions 
##State end conditions
##Parameter file names
#Single exon gene state
exon
coding -3 0 duration periodic forward 0 6
ATG,3
TAG,-1 TAA,-1 TGA,-1
exon_MC.mat exon_L.mat exon_introMC.mat
#Initial exon states
exon_i0
coding -3 2 duration periodic forward 1 6
ATG,3
GT,-3
exon_MC.mat exon_i0_L.mat exon_introMC.mat
#
exon_i1
coding -3 2 duration periodic forward 2 6
ATG,3
GT,-3
exon_MC.mat exon_i1_L.mat exon_introMC.mat
#
exon_i2
coding -3 2 duration periodic forward 0 6
ATG,3
GT,-3
exon_MC.mat exon_i2_L.mat exon_introMC.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
#
spacerFixed_0
non-coding 0 0 duration non-periodic forward 0
GT,2
all,0
spacer_0_MC.mat spacerFixed_0_L.mat
#
spacerFixed_1
non-coding 0 0 duration non-periodic forward 1
GT,2
all,0
spacer_0_MC.mat spacerFixed_1_L.mat
#
spacerFixed_2
non-coding 0 0 duration non-periodic forward 2
GT,2
all,0
spacer_0_MC.mat spacerFixed_2_L.mat
#
spacerExtender_0
non-coding 0 0 duration non-periodic forward 0
all,0
all,0
spacer_0_MC.mat spacerExtender_0_L.mat
#
spacerExtender_1
non-coding 0 0 duration non-periodic forward 1
all,0
all,0
spacer_0_MC.mat spacerExtender_1_L.mat
#
spacerExtender_2
non-coding 0 0 duration non-periodic forward 2
all,0
all,0
spacer_0_MC.mat spacerExtender_2_L.mat
#
spacer_0
non-coding 0 0 duration non-periodic forward 0
GT,2
AG,-1
spacer_0_MC.mat spacer_0_L.mat
#
spacer_1
non-coding 0 0 duration non-periodic forward 1
GT,2
AG,-1
spacer_0_MC.mat spacer_1_L.mat
#
spacer_2
non-coding 0 0 duration non-periodic forward 2
GT,2
AG,-1
spacer_0_MC.mat spacer_2_L.mat
#
r_exon
coding 0 3 duration periodic reverse 0 6
TTA,3 TCA,3 CTA,3
CAT,-1
exon_MC.mat exon_L.mat exon_introMC.mat
#Reverse initial exon state
r_exon_i
coding -2 3 duration periodic reverse 0 6
AC,4
CAT,-1
exon_MC.mat exon_i0_L.mat exon_introMC.mat
#Reverse middle exon states
r_exon_m0
coding -2 2 duration periodic reverse 1
AC,4
CT,-3
exon_MC.mat exon_m0_L.mat
#
r_exon_m1
coding -2 2 duration periodic reverse 2
AC,4
CT,-3
exon_MC.mat exon_m0_L.mat
#
r_exon_m2
coding -2 2 duration periodic reverse 0
AC,4
CT,-3
exon_MC.mat exon_m0_L.mat
#
r_exon_t0
coding 0 2 duration periodic reverse 1
TTA,3 TCA,3 CTA,3
CT,-3
exon_MC.mat exon_t_L.mat
#
r_exon_t1
coding 0 2 duration periodic reverse 2
TTA,3 TCA,3 CTA,3
CT,-3
exon_MC.mat exon_t_L.mat
#
r_exon_t2
coding 0 2 duration periodic reverse 0
TTA,3 TCA,3 CTA,3
CT,-3
exon_MC.mat exon_t_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
#
r_spacerFixed_0
non-coding 0 0 duration non-periodic forward 0
all,0
AC,-1
spacer_0_MC.mat spacerFixed_0_L.mat
#
r_spacerFixed_1
non-coding 0 0 duration non-periodic forward 1
all,0
AC,-1
spacer_0_MC.mat spacerFixed_1_L.mat
#
r_spacerFixed_2
non-coding 0 0 duration non-periodic forward 2
all,0
AC,-1
spacer_0_MC.mat spacerFixed_2_L.mat
#
r_spacerExtender_0
non-coding 0 0 duration non-periodic reverse 0
all,0
all,0
spacer_0_MC.mat spacerExtender_0_L.mat
#
r_spacerExtender_1
non-coding 0 0 duration non-periodic reverse 1
all,0
all,0
spacer_0_MC.mat spacerExtender_1_L.mat
#
r_spacerExtender_2
non-coding 0 0 duration non-periodic reverse 2
all,0
all,0
spacer_0_MC.mat spacerExtender_2_L.mat
#
r_spacer_0
non-coding 0 0 duration non-periodic reverse 0
CT,2
AC,-1
spacer_0_MC.mat spacer_0_L.mat
#
r_spacer_1
non-coding 0 0 duration non-periodic reverse 1
CT,2
AC,-1
spacer_0_MC.mat spacer_1_L.mat
#
r_spacer_2
non-coding 0 0 duration non-periodic reverse 2
CT,2
AC,-1
spacer_0_MC.mat spacer_2_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
#####