#Read in the possible transitions
exon stop,1
exon_i0 donor_0,1
exon_i1 donor_1,1
exon_i2 donor_2,1
exon_m0 donor_0,1
exon_m1 donor_1,1
exon_m2 donor_2,1
exon_t stop,1
start spep,0.97 spep_i0,0.01 spep_i1,0.01 spep_i2,0.01
stop intergenic,1
donor_0 spacer5_0,1
donor_1 spacer5_1,1
donor_2 spacer5_2,1
acceptor_0 exon_t,0.38 exon_m0,0.21 exon_m1,0.21 exon_m2,0.21
acceptor_1 exon_t,0.38 exon_m0,0.21 exon_m1,0.21 exon_m2,0.21
acceptor_2 exon_t,0.38 exon_m0,0.21 exon_m1,0.21 exon_m2,0.21
branch_0 spacer3_0,1
branch_1 spacer3_1,1
branch_2 spacer3_2,1
spacer3_0 acceptor_0,1
spacer3_1 acceptor_1,1
spacer3_2 acceptor_2,1
spacer5_0 branch_0,1
spacer5_1 branch_1,1
spacer5_2 branch_2,1
r_spep_m0 r_acceptor2_0,1
r_spep_m1 r_acceptor2_1,1
r_spep_m2 r_acceptor2_2,1
r_exon r_spep,.4 r_spep_m0,.2 r_spep_m1,.2 r_spep_m2,.2
r_exon_i r_spep,.97 r_spep_m0,.01 r_spep_m1,.01 r_spep_m2,.01
r_exon_m0 r_acceptor_0,1
r_exon_m1 r_acceptor_1,1
r_exon_m2 r_acceptor_2,1
r_exon_t0 r_acceptor_0,1
r_exon_t1 r_acceptor_1,1
r_exon_t2 r_acceptor_2,1
r_start intergenic,1
r_stop r_exon,0.33 r_exon_t0,0.21 r_exon_t1,0.21 r_exon_t2,0.21
r_donor_0 r_exon_i,0.38 r_exon_m0,0.21 r_exon_m1,0.21 r_exon_m2,0.21
r_donor_1 r_exon_i,0.38 r_exon_m0,0.21 r_exon_m1,0.21 r_exon_m2,0.21
r_donor_2 r_exon_i,0.38 r_exon_m0,0.21 r_exon_m1,0.21 r_exon_m2,0.21
r_acceptor_0 r_spacer3_0,1
r_acceptor_1 r_spacer3_1,1
r_acceptor_2 r_spacer3_2,1
r_branch_0 r_spacer5_0,1
r_branch_1 r_spacer5_1,1
r_branch_2 r_spacer5_2,1
r_spacer3_0 r_branch_0,1
r_spacer3_1 r_branch_1,1
r_spacer3_2 r_branch_2,1
r_spacer5_0 r_donor_0,1
r_spacer5_1 r_donor_1,1
r_spacer5_2 r_donor_2,1
intergenic start,0.5 r_stop,0.5
contig intergenic,1
spep exon,.4 exon_i0,.2 exon_i1,.2 exon_i2,.2
spep_i0 donor2_0,1
spep_i1 donor2_1,1
spep_i2 donor2_2,1
spep_m exon_i0,.2 exon_i1,.2 exon_i2,.2 exon,.4 
r_spep r_start,1
r_spep_i r_start,1
donor2_0 spacer52_0,1
donor2_1 spacer52_1,1
donor2_2 spacer52_2,1
acceptor2_0 spep_m,1
acceptor2_1 spep_m,1
acceptor2_2 spep_m,1
branch2_0 spacer32_0,1
branch2_1 spacer32_1,1
branch2_2 spacer32_2,1
spacer32_0 acceptor2_0,1
spacer32_1 acceptor2_1,1
spacer32_2 acceptor2_2,1
spacer52_0 branch2_0,1
spacer52_1 branch2_1,1
spacer52_2 branch2_2,1
r_donor2_0 r_spep_i,1
r_donor2_1 r_spep_i,1
r_donor2_2 r_spep_i,1
r_acceptor2_0 r_spacer32_0,1
r_acceptor2_1 r_spacer32_1,1
r_acceptor2_2 r_spacer32_2,1
r_branch2_0 r_spacer52_0,1
r_branch2_1 r_spacer52_1,1
r_branch2_2 r_spacer52_2,1
r_spacer32_0 r_branch2_0,1
r_spacer32_1 r_branch2_1,1
r_spacer32_2 r_branch2_2,1
r_spacer52_0 r_donor2_0,1
r_spacer52_1 r_donor2_1,1
r_spacer52_2 r_donor2_2,1
