##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 0
ATG,3
TAG,-1 TAA,-1 TGA,-1
ST_exon_MC,5,0 ST_exon_L ST_BRN,2,6
#Initial exon states
exon_i0
coding -3 2 duration periodic forward 1 0
ATG,3
GT,-3
ST_exon_MC,5,0 ST_exon_L ST_BRN,2,6
#
exon_i1
coding -3 2 duration periodic forward 2 0
ATG,3
GT,-3
ST_exon_MC,5,0 ST_exon_L ST_BRN,2,6
#
exon_i2
coding -3 2 duration periodic forward 0 0
ATG,3
GT,-3
ST_exon_MC,5,0 ST_exon_L ST_BRN,2,6
#Middle exon states
exon_m0
coding -2 2 duration periodic forward 1
AG,4
GT,-3
ST_exon_MC,5,0 ST_exon_L
#
exon_m1
coding -2 2 duration periodic forward 2
AG,4
GT,-3
ST_exon_MC,5,0 ST_exon_L
#
exon_m2
coding -2 2 duration periodic forward 0
AG,4
GT,-3
ST_exon_MC,5,0 ST_exon_L
#Terminal exon states
exon_t
coding -2 0 duration periodic forward 0
AG,4
TAA,-1 TAG,-1 TGA,-1
ST_exon_MC,5,0 ST_exon_L
#Start state
start
non-coding 0 0 fixed non-periodic forward 0
ATG,2
ST_start_MC,2,11 11
#Stop state
stop
non-coding 0 0 fixed non-periodic forward 0
TAA,2 TGA,2 TAG,2
ST_stop_MC,2,3 3
#Donor states
donor_0
non-coding 0 0 fixed non-periodic forward 0
GT,1
ST_MC_DON0,1,4 4
#
donor_1
non-coding 0 0 fixed non-periodic forward 1
GT,1
ST_MC_DON1,1,4 4
#
donor_2
non-coding 0 0 fixed non-periodic forward 2
GT,1
ST_MC_DON2,1,4 4
#Acceptor states
acceptor_0
non-coding 0 0 fixed non-periodic forward 0
AG,3
ST_MC_ACC0,1,4 4
#
acceptor_1
non-coding 0 0 fixed non-periodic forward 1
AG,3
ST_MC_ACC1,1,4 4
#
acceptor_2
non-coding 0 0 fixed non-periodic forward 2
AG,3
ST_MC_ACC2,1,4 4
#Branch point states
branch_0
non-coding 0 0 fixed non-periodic forward 0 
A,2
ST_branch_MC,1,7 7
#
branch_1
non-coding 0 0 fixed non-periodic forward 1
A,2
ST_branch_MC,1,7 7
#
branch_2
non-coding 0 0 fixed non-periodic forward 2
A,2
ST_branch_MC,1,7 7
#Intron 3' spacer states
spacer3_0
non-coding 0 0 duration non-periodic forward 0
A,3
AG,-1
ST_spacer3_MC,2,0 ST_spacer3_L
#
spacer3_1
non-coding 0 0 duration non-periodic forward 1
A,3
AG,-1
ST_spacer3_MC,2,0 ST_spacer3_L
#
spacer3_2
non-coding 0 0 duration non-periodic forward 2
A,3
AG,-1
ST_spacer3_MC,2,0 ST_spacer3_L
#Intron 5' spacer states
spacer5_0
non-coding 0 0 duration non-periodic forward 0
GT,2
A,-5
ST_spacer5_MC,5,0 ST_spacer5_L
#
spacer5_1
non-coding 0 0 duration non-periodic forward 1
GT,2
A,-5
ST_spacer5_MC,5,0 ST_spacer5_L
#     
spacer5_2
non-coding 0 0 duration non-periodic forward 2
GT,2
A,-5
ST_spacer5_MC,5,0 ST_spacer5_L
#Reverse single exon gene state
r_exon
coding 0 3 duration periodic reverse 0 0
TTA,3 TCA,3 CTA,3
CAT,-1
ST_exon_MC,5,0 ST_exon_L ST_BRN,2,6
#Reverse initial exon state
r_exon_i
coding -2 3 duration periodic reverse 0 0
AC,4
CAT,-1
ST_exon_MC,5,0 ST_exon_L ST_BRN,2,6
#Reverse middle exon states
r_exon_m0
coding -2 2 duration periodic reverse 1
AC,4
CT,-3
ST_exon_MC,5,0 ST_exon_L
#
r_exon_m1
coding -2 2 duration periodic reverse 2
AC,4
CT,-3
ST_exon_MC,5,0 ST_exon_L
#
r_exon_m2
coding -2 2 duration periodic reverse 0
AC,4
CT,-3
ST_exon_MC,5,0 ST_exon_L
#
r_exon_t0
coding 0 2 duration periodic reverse 1
TTA,3 TCA,3 CTA,3
CT,-3
ST_exon_MC,5,0 ST_exon_L
#
r_exon_t1
coding 0 2 duration periodic reverse 2
TTA,3 TCA,3 CTA,3
CT,-3
ST_exon_MC,5,0 ST_exon_L
#
r_exon_t2
coding 0 2 duration periodic reverse 0
TTA,3 TCA,3 CTA,3
CT,-3
ST_exon_MC,5,0 ST_exon_L
#Reverse start
r_start
non-coding 0 0 fixed non-periodic reverse 0
CAT,10
ST_start_MC,2,11 11
#Reverse stop
r_stop
non-coding 0 0 fixed non-periodic reverse 0
TTA,2 TCA,2 CTA,2
ST_stop_MC,2,3 3
#Reverse donor site state
r_donor_0
non-coding 0 0 fixed non-periodic reverse 0
AC,3
ST_MC_DON0,1,4 4
#
r_donor_1
non-coding 0 0 fixed non-periodic reverse 1
AC,3
ST_MC_DON2,1,4 4
#
r_donor_2
non-coding 0 0 fixed non-periodic reverse 2
AC,3
ST_MC_DON1,1,4 4
#Reverse acceptor site state
r_acceptor_0
non-coding 0 0 fixed non-periodic reverse 0
CT,1
ST_MC_ACC0,1,4 4
#
r_acceptor_1
non-coding 0 0 fixed non-periodic reverse 1
CT,1
ST_MC_ACC2,1,4 4
#
r_acceptor_2
non-coding 0 0 fixed non-periodic reverse 2
CT,1
ST_MC_ACC1,1,4 4
#Reverse branch point state
r_branch_0
non-coding 0 0 fixed non-periodic reverse 0
T,4
ST_branch_MC,1,7 7
#
r_branch_1
non-coding 0 0 fixed non-periodic reverse 1
T,4
ST_branch_MC,1,7 7
#
r_branch_2
non-coding 0 0 fixed non-periodic reverse 2
T,4
ST_branch_MC,1,7 7
#Reverse intron 3' spacer
r_spacer3_0
non-coding 0 0 duration non-periodic reverse 0
CT,2
T,-3
ST_spacer3_MC,2,0 ST_spacer3_L
#
r_spacer3_1
non-coding 0 0 duration non-periodic reverse 1
CT,2
T,-3
ST_spacer3_MC,2,0 ST_spacer3_L
#
r_spacer3_2
non-coding 0 0 duration non-periodic reverse 2
CT,2
T,-3
ST_spacer3_MC,2,0 ST_spacer3_L
#Reverse intron 5' spacer
r_spacer5_0
non-coding 0 0 duration non-periodic reverse 0
T,5
AC,-1
ST_spacer5_MC,5,0 ST_spacer5_L
#
r_spacer5_1
non-coding 0 0 duration non-periodic reverse 1
T,5
AC,-1
ST_spacer5_MC,5,0 ST_spacer5_L
#
r_spacer5_2
non-coding 0 0 duration non-periodic reverse 2
T,5
AC,-1
ST_spacer5_MC,5,0 ST_spacer5_L
#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
ST_intergenic_MC,5,0 ST_intergenic_L
#####