#
# Transition probabilities and initial probabilities for the overall HMM 
#
# number of states
3
#
# Transition probabilities of the Semi-CRF
# Date: 8.3.2012

# 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   .3    # intergenic region
1   .4    # single Exon
2   .4    # reverse single Exon

# Terminal probabilities (a priori probs for a state ending at
# the last position.
# only non-zero probabilities necessary
[Terminal]
# number of states where terminating is possible
3
# state prob statename
0   .3    # intergenic region
1   .4    # single Exon
2   .4    # reverse single Exon

#
# Transition probabilities 
# only non-zero probabilities
[Transition]
#           -----  Igenic region  -----
# intergenic region
0 0     .992
# single
0 1	.004 # increase? maybe try 0.01, 0.03, 0.1, 0.3, 1, 10
# reverse single exon
0 2	.004
#           -----  Single Exon  -----
# intergenic region
1 0	.96
# single exon (usually overlapping)
1 1	.02
# reverse single exon (usually overlapping)
1 2	.02
#           -----  reverse Single Exon  -----
# intergenic region
2 0	.96
# single exon (usually overlapping)
2 1	.02
# reverse single exon (usually overlapping)
2 2	.02

