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#
#
# Ok - something hacked around for the Transmembrane model
#
# This is an example of a Brown-Haussler mixture Dirichlet prior.
#

Mix   # Strategy (mixture Dirichlet)
Amino # type of prior (Amino or Nucleic)

# Transitions
2                   # 2 component - first component an ungappy region.
0.3                 #   with probability = 1.0
10.    0.015 0.015   # m->m, m->i, m->d alpha's
10.    1.170 0.060   # i->m, i->i, i->d alpha's
10.    0.060 0.300   # d->m, d->i, d->d alpha's
0.7                 #   with probability = 1.0
2.970 0.015 0.015   # m->m, m->i, m->d alpha's
1.770 1.170 0.060   # i->m, i->i, i->d alpha's
2.640 0.060 0.300   # d->m, d->i, d->d alpha's

# A C   D   E   F G H I   K   L  M  N P Q R S  T  V  W  Y 

# ok 
#
# 1st column meant to be a pretty heavy hyrdophobic prior thing.
#
# Match emissions
# A C D E F G H I K L M N P Q R S T V W Y 
#
11	# 11 components
0.031
# A     C     D     E     F    G     H      I      K    L      M    N     P    Q      R    S      T     V     W    Y 
20.    15.   0.2   0.2   20.   4.    4.    20.    0.2   20.   20.   20.   4.   1.    0.2   4.     4.   20.   15.   15.
0.001
22.379 0.175 0.818 1.110 0.292 1.928 0.175 0.234 0.467 0.409 0.117 0.643 0.993 0.351 0.292 25.184 1.811 0.643 0.117 0.292 
0.025 
4.468 0.194 1.632 7.266 0.466 13.443 0.272 0.583 1.049 1.243 0.194 0.622 0.777 2.487 0.466 1.399 0.699 0.932 0.117 0.505 
0.091 
0.788 0.158 0.158 0.237 6.150 0.237 0.079 16.873 0.237 27.991 2.917 0.237 0.237 0.237 0.237 0.237 0.473 20.421 0.158 0.788 
0.024 
1.313 0.303 0.808 0.707 0.606 0.808 0.303 0.707 0.606 1.717 0.303 0.505 87.087 0.606 0.505 1.515 0.909 1.010 0.202 0.505 
0.701 
0.160 0.042 0.126 0.146 0.070 0.120 0.054 0.094 0.166 0.138 0.056 0.090 0.062 0.094 0.080 0.150 0.126 0.122 0.038 0.070 
0.015 
1.017 0.113 87.577 16.950 0.565 0.565 0.113 0.452 0.791 0.339 0.226 1.017 0.565 0.452 0.339 0.565 0.339 0.452 0.001 0.791 
0.041 
0.994 0.339 2.031 1.185 0.804 1.269 1.016 0.402 0.741 0.592 0.444 4.401 0.529 0.592 0.508 1.502 1.164 0.571 0.360 1.671 
0.024 
26.730 0.286 0.800 1.885 0.800 0.971 0.228 1.142 2.056 3.770 0.343 0.742 1.142 0.685 0.571 1.199 1.713 11.252 0.171 0.514 
0.017 
1.170 0.177 1.489 0.745 1.028 0.957 0.177 0.674 2.092 1.347 0.142 1.170 0.603 0.496 17.053 2.801 0.957 1.560 0.177 0.638 
0.030 
0.001 0.001 0.001 0.001 0.001 5793.873 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 

## Insert emissions
1                   # Single component
1.0                 #    with probability 1.0
17430 6690 9370 9910 7950 17720 6720 7380 16100 17070 2950 8090 10140 7650 8180 13920 11710 12940 2100 5980