#
# Transition probabilities and initial Probabilities for the overall HMM 
#
# number of states
25
#
# Transition probabilities of the Generalised Hidden-Markov Model
# Date: 19.05.2003

# Initial probabilities (a priori probs for a state ending at a
# certain position, e.g. the position before the first nukleotide in
# the sequence or the last position.
# only non-zero probabilities
[Initial]
# number of states where a start is possible
1
# state prob statename
0   1     # start intergenic region

# Terminal probabilities (a priori probs for a state ending at
# the last position.
# only non-zero probabilities neccessary
[Terminal]
# number of states where terminating is possible
1
# state prob statename
24  1     # end intergenic region

#
# Transition probabilities 
# only non-zero probabilities
[Transition]
#           -----  Igenic region  -----
# intergenic region
0 0     .9999
# single
0 1	.000017
# initial exon 0, 40% of the multi exon genes
0 2	.000028
# initial exon 1, 43% of the multi exon genes
0 3	.000028
# initial exon 2, 17% of the multi exon genes
0 4	.000027
#           -----  Single Exon  -----
# Final Intergenic region
1 24	1.0
#           -----  Initial Exon 0  -----
# longdss0 Intron
2 10	1.0
#           -----  Initial Exon 1  -----
# longdss1 Intron
3 15	1.0
#           -----  Initial Exon 2  -----
# longdss2 Intron
4 20	1.0
#           -----  Internal Exon 0  -----
# longdss0 Intron
5 10	   1.0
#           -----  Internal Exon 1  -----
# longdss1 Intron
6 15	   1.0
#           -----  Internal Exon 2  -----
# longdss2 Intron
7 20	   1.0
#           -----  Terminal Exon  -----
# intergenic region  
8 24	   1
#           -----  lessD0 Intron 0  -----
# longass0
9 13	   1.0
#           -----  longdss0 Intron 0    -----
# lessD0
10 9	.5
# equalD0
10 11	.5
#           -----  equalD0 Intron 0    -----
# geometric0
11 12	1.0
#           -----  geometric0 Intron 0  -----
# geometric0 intron
12 12	     .9997447
# longass0
12 13	     .0002553
#           -----  longass0 Intron 0     -----
# internal exon 0, 45% of all internal exons 
13 5	   .3
# internal exon 1, 33% of all internal exons 
13 6	   .3
# internal exon 2, 22% of all internal exons 
13 7	   .3
# terminal exon
13 8	   .1
#           -----  lessD1 Intron 1  -----
# longass1
14 18	   1.0
#           -----  longdss1 Intron 1    -----
# lessD1
15 14      .5
# equalD1
15 16      .5
#           -----  equalD1 Intron 1    -----
# geometric1
16 17      1.0
#           -----  geometric1 Intron 1  -----
# geometric1 intron
17 17	     .9997447
# longass1
17 18	     .0002553
#           -----  longass1 Intron 1  -----
# internal exon 0, 45% of all internal exons 
18 5	   .3
# internal exon 1, 33% of all internal exons 
18 6	   .3
# internal exon 2, 22% of all internal exons
18 7	   .3
# terminal exon
18 8	   .1
#           -----  lessD2 Intron 2  -----
# longass2
19 23	   1.0
#           -----  longdss2 Intron 2    -----
# lessD2
20 19      .5
# equalD2
20 21      .5
#           -----  equalD2 Intron 2    -----
# geometric0
21 22      1.0
#           -----  geometric2 Intron 2  -----
# geometric2 intron
22 22	     .9997447
# longass2
22 23	     .0002553
#           -----  longass2 Intron 2     -----
# internal exon 0, 45% of all internal exons 
23 5	   .3
# internal exon 1, 33% of all internal exons 
23 6	   .3
# internal exon 2, 22% of all internal exons 
23 7	   .3
# terminal exon
23 8	   .1
#           -----  Igenic region  -----
# intergenic region
24 24   1
