##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
ST1,5,0 ST ST_BRN,2,0
#Start state
start
non-coding 0 0 fixed non-periodic forward 0
ATG,2
ST2,2,11 11
#Stop state
stop
non-coding 0 0 fixed non-periodic forward 0
TAA,2 TGA,2 TAG,2
ST3,2,3 3
#Intergenic region
intergenic_i
non-coding 0 0 duration non-periodic forward 0
contig,0
ATG,-9
ST4,5,0 ST
#Intergenic region
intergenic_m
non-coding 0 0 duration non-periodic forward 0
TAA,3 TAG,3 TGA,3
ATG,-9
ST4,5,0 ST
#
intergenic_t
non-coding 0 0 duration non-periodic forward 0
TAA,3 TAG,3 TGA,3
contig,0
ST4,5,0 ST
#
nonCoding
non-coding 0 0 duration non-periodic forward 0
contig,0
contig,0
ST4,5,0 ST
#####