File: //usr/share/snap/HMM/minimal.hmm
zoeHMM minimal.hmm 6 8 6 7
<STATES>
Einit 0 0 3 -1 explicit
Esngl 0 0 150 -1 explicit
Eterm 0 0 3 -1 explicit
Exon 0 0 6 -1 explicit
Inter 0.9 0.9 0 0 geometric
Intron 0.1 0.1 0 0 geometric
<STATE_TRANSITIONS>
Einit Intron 1
Esngl Inter 1
Eterm Inter 1
Exon Intron 1
Inter Einit 0.977636
Inter Esngl 0.022364
Intron Eterm 0.160251
Intron Exon 0.839749
<PHASE_PREFERENCES>
0.488562
0.297386
0.214052
0.594784
0.189567
0.215649
0.557522
0.222503
0.219975
0.582938
0.194313
0.222749
0.816676
0.183324
0.862282
0.137718
0.861538
0.138462
<STATE_DURATIONS>
Einit 2
DEFINED 0 249
-9.508 -9.398 -9.295 -9.200 -9.110
-9.026 -8.946 -8.870 -8.799 -8.730
-8.665 -8.609 -8.556 -8.504 -8.454
-8.406 -8.359 -8.314 -8.270 -8.227
-8.186 -8.141 -8.097 -8.055 -8.014
-7.974 -7.934 -7.897 -7.859 -7.823
-7.788 -7.759 -7.730 -7.702 -7.674
-7.647 -7.621 -7.594 -7.569 -7.544
-7.519 -7.493 -7.468 -7.444 -7.420
-7.396 -7.373 -7.350 -7.327 -7.305
-7.283 -7.266 -7.249 -7.232 -7.215
-7.199 -7.183 -7.167 -7.151 -7.135
-7.120 -7.125 -7.130 -7.134 -7.139
-7.144 -7.149 -7.154 -7.159 -7.164
-7.169 -7.183 -7.196 -7.210 -7.224
-7.238 -7.252 -7.266 -7.281 -7.295
-7.310 -7.321 -7.333 -7.344 -7.355
-7.367 -7.378 -7.390 -7.402 -7.414
-7.426 -7.441 -7.456 -7.471 -7.487
-7.503 -7.519 -7.535 -7.551 -7.568
-7.584 -7.590 -7.596 -7.601 -7.607
-7.613 -7.618 -7.624 -7.630 -7.636
-7.641 -7.655 -7.670 -7.684 -7.698
-7.713 -7.728 -7.743 -7.758 -7.773
-7.788 -7.804 -7.819 -7.835 -7.851
-7.868 -7.884 -7.901 -7.917 -7.934
-7.952 -7.972 -7.993 -8.014 -8.035
-8.056 -8.078 -8.101 -8.123 -8.146
-8.169 -8.186 -8.203 -8.221 -8.238
-8.256 -8.274 -8.292 -8.310 -8.329
-8.348 -8.376 -8.406 -8.436 -8.466
-8.498 -8.529 -8.562 -8.596 -8.630
-8.665 -8.677 -8.689 -8.701 -8.713
-8.725 -8.738 -8.750 -8.763 -8.775
-8.788 -8.806 -8.825 -8.843 -8.862
-8.881 -8.901 -8.920 -8.940 -8.960
-8.981 -8.990 -8.999 -9.008 -9.017
-9.026 -9.035 -9.044 -9.053 -9.063
-9.072 -9.078 -9.085 -9.091 -9.097
-9.104 -9.110 -9.117 -9.123 -9.130
-9.136 -9.173 -9.210 -9.249 -9.288
-9.329 -9.371 -9.414 -9.458 -9.504
-9.551 -9.551 -9.551 -9.551 -9.551
-9.551 -9.551 -9.551 -9.551 -9.551
-9.551 -9.573 -9.596 -9.618 -9.641
-9.665 -9.689 -9.713 -9.738 -9.763
-9.788 -9.793 -9.799 -9.804 -9.809
-9.814 -9.819 -9.825 -9.830 -9.835
-9.841 -9.846 -9.851 -9.857 -9.862
-9.868 -9.873 -9.879 -9.884 -9.890
GEOMETRIC 250 -1
127
Esngl 1
GEOMETRIC 0 -1
1000
Eterm 2
DEFINED 0 249
-11.438 -11.375 -11.315 -11.257 -11.202
-11.148 -11.097 -11.047 -10.999 -10.953
-10.907 -10.875 -10.842 -10.811 -10.780
-10.750 -10.720 -10.691 -10.663 -10.635
-10.608 -10.555 -10.504 -10.454 -10.406
-10.360 -10.315 -10.272 -10.229 -10.188
-10.148 -10.023 -9.907 -9.801 -9.701
-9.608 -9.520 -9.438 -9.360 -9.286
-9.216 -9.148 -9.084 -9.023 -8.964
-8.907 -8.853 -8.801 -8.750 -8.701
-8.654 -8.621 -8.590 -8.559 -8.529
-8.499 -8.470 -8.442 -8.414 -8.387
-8.360 -8.334 -8.308 -8.282 -8.257
-8.233 -8.209 -8.185 -8.162 -8.139
-8.116 -8.091 -8.066 -8.041 -8.017
-7.993 -7.970 -7.947 -7.924 -7.902
-7.880 -7.873 -7.866 -7.860 -7.853
-7.846 -7.840 -7.833 -7.827 -7.820
-7.813 -7.784 -7.755 -7.726 -7.699
-7.671 -7.644 -7.618 -7.592 -7.567
-7.542 -7.532 -7.523 -7.513 -7.504
-7.494 -7.485 -7.476 -7.466 -7.457
-7.448 -7.449 -7.450 -7.451 -7.452
-7.453 -7.454 -7.455 -7.456 -7.457
-7.458 -7.469 -7.481 -7.492 -7.504
-7.515 -7.527 -7.539 -7.550 -7.562
-7.574 -7.596 -7.617 -7.639 -7.661
-7.683 -7.706 -7.729 -7.752 -7.776
-7.801 -7.802 -7.803 -7.804 -7.806
-7.807 -7.808 -7.810 -7.811 -7.812
-7.813 -7.817 -7.821 -7.825 -7.829
-7.833 -7.837 -7.841 -7.845 -7.849
-7.853 -7.862 -7.872 -7.881 -7.891
-7.901 -7.910 -7.920 -7.930 -7.940
-7.950 -7.953 -7.955 -7.958 -7.961
-7.964 -7.967 -7.970 -7.973 -7.976
-7.979 -8.014 -8.050 -8.087 -8.126
-8.165 -8.205 -8.247 -8.290 -8.334
-8.379 -8.418 -8.458 -8.499 -8.542
-8.586 -8.631 -8.677 -8.725 -8.775
-8.827 -8.840 -8.853 -8.866 -8.880
-8.894 -8.907 -8.921 -8.935 -8.950
-8.964 -8.996 -9.029 -9.063 -9.097
-9.132 -9.168 -9.205 -9.243 -9.282
-9.322 -9.322 -9.322 -9.322 -9.322
-9.322 -9.322 -9.322 -9.322 -9.322
-9.322 -9.330 -9.337 -9.345 -9.352
-9.360 -9.368 -9.375 -9.383 -9.391
-9.398 -9.395 -9.391 -9.387 -9.383
-9.379 -9.375 -9.371 -9.368 -9.364
GEOMETRIC 250 -1
185
Exon 2
DEFINED 0 249
-17.003 -16.155 -15.625 -15.238 -14.933
-14.681 -14.467 -14.281 -14.116 -13.968
-13.833 -13.667 -13.518 -13.383 -13.259
-13.145 -13.040 -12.942 -12.850 -12.763
-12.681 -12.424 -12.206 -12.017 -11.850
-11.700 -11.564 -11.440 -11.325 -11.219
-11.121 -10.933 -10.767 -10.618 -10.483
-10.359 -10.246 -10.140 -10.042 -9.950
-9.864 -9.747 -9.639 -9.538 -9.444
-9.356 -9.273 -9.194 -9.119 -9.049
-8.981 -8.889 -8.803 -8.721 -8.644
-8.571 -8.501 -8.435 -8.371 -8.310
-8.252 -8.206 -8.162 -8.119 -8.078
-8.038 -7.998 -7.960 -7.923 -7.886
-7.851 -7.829 -7.808 -7.786 -7.765
-7.745 -7.724 -7.704 -7.685 -7.665
-7.646 -7.640 -7.635 -7.629 -7.624
-7.619 -7.613 -7.608 -7.602 -7.597
-7.592 -7.586 -7.579 -7.573 -7.567
-7.560 -7.554 -7.548 -7.542 -7.536
-7.530 -7.532 -7.535 -7.537 -7.539
-7.542 -7.544 -7.547 -7.549 -7.552
-7.554 -7.553 -7.553 -7.552 -7.551
-7.550 -7.549 -7.548 -7.548 -7.547
-7.546 -7.549 -7.552 -7.555 -7.558
-7.560 -7.563 -7.566 -7.569 -7.572
-7.575 -7.595 -7.615 -7.635 -7.656
-7.677 -7.698 -7.720 -7.742 -7.764
-7.787 -7.803 -7.819 -7.836 -7.853
-7.870 -7.888 -7.905 -7.923 -7.941
-7.959 -7.977 -7.995 -8.014 -8.033
-8.052 -8.071 -8.091 -8.111 -8.131
-8.152 -8.176 -8.200 -8.225 -8.250
-8.275 -8.302 -8.328 -8.355 -8.383
-8.411 -8.423 -8.436 -8.448 -8.461
-8.474 -8.487 -8.500 -8.513 -8.526
-8.540 -8.553 -8.567 -8.581 -8.595
-8.609 -8.623 -8.637 -8.652 -8.667
-8.681 -8.696 -8.711 -8.727 -8.742
-8.758 -8.774 -8.790 -8.806 -8.822
-8.838 -8.848 -8.857 -8.866 -8.875
-8.884 -8.894 -8.903 -8.913 -8.922
-8.932 -8.943 -8.954 -8.964 -8.975
-8.987 -8.998 -9.009 -9.020 -9.032
-9.043 -9.058 -9.074 -9.089 -9.105
-9.121 -9.137 -9.153 -9.169 -9.186
-9.202 -9.213 -9.225 -9.236 -9.247
-9.259 -9.270 -9.282 -9.293 -9.305
-9.317 -9.324 -9.331 -9.338 -9.345
-9.352 -9.359 -9.367 -9.374 -9.381
GEOMETRIC 250 -1
230
Inter 1
GEOMETRIC 0 -1
500
Intron 1
GEOMETRIC 0 -1
304
<SEQUENCE_MODELS>
Acceptor SDT 2 1 4 2 0.000
AG WMM 15 11 4 0 0.000
0.440 -0.800 -1.561 0.790
0.452 -0.664 -1.565 0.734
0.546 -0.660 -1.787 0.694
0.681 -1.267 -1.862 0.771
0.743 -1.716 -1.906 0.811
0.175 -1.667 -2.024 1.208
-2.278 -2.834 -4.043 1.845
-5.146 -4.228 -6.441 1.966
-1.458 -0.723 -1.433 1.411
-2.982 1.737 -7.579 -0.906
1.999 -9.900 -9.900 -9.900
-9.900 -9.900 1.999 -9.900
0.684 -0.753 0.351 -0.929
0.220 -0.506 -0.606 0.560
0.235 -0.166 -0.481 0.281
NN TRM 0 0 0 0 0.000
Coding CDS 3 2 4 3 0.000
frame0 LUT 3 2 4 0 0.000
0.379 -0.640 -0.031 0.110
0.457 -0.540 -0.680 0.395
0.648 -0.283 -1.481 0.325
-1.544 -0.140 0.263 0.632
0.737 -0.815 -0.173 -0.189
1.143 -1.640 -0.371 -0.521
0.564 -0.774 -0.859 0.470
-0.995 0.115 -0.292 0.677
0.427 -0.784 -0.317 0.347
0.299 -0.306 -1.001 0.547
1.304 -1.108 -1.874 -0.333
-0.717 -0.115 -0.212 0.682
. 0.818 . 1.162
0.461 -0.566 -0.273 0.164
. 0.219 0.486 0.521
-1.036 0.459 0.087 0.105
frame2 LUT 3 2 4 0 0.000
0.259 -0.386 0.370 -0.423
0.487 -0.960 0.318 -0.255
0.474 -0.032 -0.057 -0.576
-0.282 -0.071 0.514 -0.326
0.462 -0.358 -0.029 -0.215
0.488 -0.850 0.541 -0.766
0.543 -0.790 0.187 -0.275
-0.761 0.125 0.694 -0.512
0.508 -0.595 0.194 -0.373
0.406 -0.334 0.021 -0.205
0.515 -0.055 -0.122 -0.535
-0.505 -0.072 0.732 -0.550
0.176 -0.178 -0.133 0.104
0.509 -0.599 0.208 -0.393
0.496 -0.478 0.265 -0.577
-0.694 0.197 0.560 -0.393
frame2 LUT 3 2 4 0 0.000
0.535 -0.308 -0.915 0.278
0.336 -0.007 -0.556 0.087
0.665 -0.112 -0.753 -0.160
-0.844 0.367 -0.664 0.606
0.726 -0.195 -0.919 -0.084
0.329 -0.192 -0.150 -0.048
0.781 -0.468 -0.212 -0.525
-0.194 0.282 -0.631 0.338
0.819 -0.554 -0.870 0.011
0.392 -0.094 -1.027 0.333
0.917 -0.073 -0.982 -0.610
-0.646 0.084 -0.512 0.678
0.315 -0.237 -1.067 0.516
0.326 -0.006 -0.515 0.072
0.540 -0.255 -0.159 -0.300
-0.826 0.381 -0.700 0.602
Donor SDT 2 0 4 2 0.000
GT WMM 9 3 4 0 0.000
0.642 -0.079 -0.387 -0.458
1.179 -0.792 -1.242 -0.443
-0.391 -2.106 1.305 -0.903
-9.900 -9.900 1.999 -9.900
-9.900 -9.900 -9.900 1.999
1.187 -4.093 -0.012 -0.572
1.405 -1.657 -1.491 -0.558
-1.393 -2.561 1.584 -1.149
-0.325 -1.357 -1.615 1.313
NN TRM 0 0 0 0 0.000
Inter LUT 3 2 4 0 0.000
0.869 -0.885 -1.237 0.272
0.479 -0.437 -0.700 0.324
0.527 -0.486 -0.767 0.331
-0.141 -0.548 -0.825 0.884
0.550 -0.374 -0.699 0.199
0.326 -0.056 -0.533 0.129
0.336 -0.215 -0.465 0.204
-0.347 0.076 -0.529 0.552
0.779 -0.800 -0.579 0.057
0.335 -0.180 -0.497 0.198
0.339 -0.196 -0.450 0.176
-0.203 -0.470 -0.330 0.690
0.440 -0.610 -0.804 0.501
0.336 -0.345 -0.791 0.457
0.356 -0.406 -0.731 0.447
-0.660 -0.304 -0.758 0.975
Intron LUT 3 2 4 0 0.000
1.060 -1.253 -1.395 0.158
0.536 -0.477 -0.790 0.325
0.401 -0.513 -0.548 0.373
-0.121 -0.842 -0.836 0.973
0.740 -0.711 -0.395 -0.061
0.458 -0.315 -0.246 -0.031
0.465 -0.429 -0.153 -0.033
0.019 -0.349 -0.309 0.480
0.927 -1.032 -0.547 -0.112
0.402 -0.126 -0.565 0.120
0.280 -0.223 -0.448 0.259
0.036 -0.762 -0.295 0.651
0.611 -0.775 -0.573 0.282
0.528 -0.449 -0.537 0.184
0.501 -0.485 -0.504 0.220
-0.591 -0.542 -0.755 1.041
Start SDT 3 0 4 2 0.000
ATG WMM 12 6 4 0 0.000
0.078 -0.178 -0.583 0.478
0.138 -0.168 -0.464 0.361
0.410 0.227 -0.378 -0.451
1.203 -0.821 -0.253 -1.773
0.998 -0.477 -0.477 -0.821
1.016 -0.624 -0.275 -0.993
1.993 -7.297 -7.297 -7.297
-7.297 -7.297 -7.297 1.993
-7.297 -7.297 1.993 -7.297
0.296 -0.529 0.281 -0.209
0.025 0.561 -0.343 -0.477
-0.137 -0.147 -0.030 0.273
NNN TRM 0 0 0 0 0.000
Stop SDT 3 0 4 4 0.000
TAA WMM 9 6 4 0 0.000
0.419 -0.042 -0.025 -0.497
0.571 -0.385 -0.451 0.025
0.072 -0.042 -0.222 0.163
-0.111 -0.301 0.419 -0.111
0.768 -0.723 -1.322 0.369
0.317 -0.042 -1.059 0.382
-6.451 -6.451 -6.451 1.988
1.988 -6.451 -6.451 -6.451
1.988 -6.451 -6.451 -6.451
TAG WMM 9 6 4 0 0.000
0.481 0.033 -0.311 -0.367
0.512 -0.488 -0.204 -0.011
0.159 -0.204 -0.311 0.274
-0.011 -0.426 -0.057 0.381
0.603 -0.488 -1.552 0.512
-0.153 -0.204 0.159 0.159
-5.011 -5.011 -5.011 1.966
1.966 -5.011 -5.011 -5.011
-5.011 -5.011 1.966 -5.011
TGA WMM 9 6 4 0 0.000
0.388 -0.313 -0.143 -0.027
0.360 -0.143 -0.225 -0.065
0.009 -0.268 -0.225 0.388
0.272 -0.669 -0.065 0.272
0.494 -0.612 -0.728 0.415
-0.506 -0.225 -0.065 0.570
-5.313 -5.313 -5.313 1.973
-5.313 -5.313 1.973 -5.313
1.973 -5.313 -5.313 -5.313
NNN TRM 0 0 0 0 0.000