#
# Transition probabilities and initial Probabilities for the overall HMM 
#
# number of states
3
#
# Transition probabilities of the Generalised Hidden-Markov Model
# Date: 10.06.2009

# Initial probabilities (a priori probs for a state ending at a
# certain position, e.g. the position before the first nucleotide in
# the sequence or the last position.
# only non-zero probabilities
[Initial]
# number of states where a start is possible
3
# state prob statename
0   .98    # intergenic region
1   .01    # single Exon
2   .01    # reverse single Exon

# 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
3
# state prob statename
0   .98    # intergenic region
1   .01    # single Exon
2   .01    # reverse single Exon

#
# Transition probabilities 
# only non-zero probabilities
[Transition]
#           -----  Igenic region  -----
# intergenic region
0 0     .99998
# single
0 1	.00001
# reverse single exon
0 2	.00001
#           -----  Single Exon  -----
# Intergenic region
1 0	1.0
#           -----  reverse Single Exon  -----
# Intergenic region
2 0	1.0