# Frederic.Schutz@isb-sib.ch
#
# Simple file to model simulated AT and CG rich regions 
#
Alphabet: ACGT
# only single letters in alphabet
# avoid the keywords 
#
# keep this order of lines: first the alphabet, then the states, 
# then the optional lines fix_tr and fix_em
State BEGIN 
	T: AT 0.8 CG 0.2
# T:   identifies line for transmission probabilities
# the state name is followed by a space and the probability value
State AT: 
	E: 0.4 0.1 0.1 0.4
	T: AT 0.949
	T: CG 0.05
        T: END 0.001
State CG: 
	E: 0.1 0.4 0.4 0.1
	T: AT 0.1 
	T: CG 0.9
State END:
# the states BEGIN and END must be listed and must carry this name
# emission null model used for pseudocounts
NULLMODEL: 0.25 0.25  0.25 0.25  
# 0 0  0 0 
# 0.25 0.25  0.25 0.25  
############################################################