#
# transition probabilities and initial probabilities for the overall HMM 
# toxoplasma version
# number of states
71
#
# Transition probabilities of the Generalised Hidden-Markov Model
# Date: 18.01.2007

# Initial probabilities (a priori probs for a state ending at a
# certain position, e.g. the position before the first nucleotide in
# the sequence
# only non-zero probabilities
[Initial]
# number of states where a start is possible
71
# state prob statename
0   .788    # start intergenic region
1   .001    # single Exon
2   .001    # initial Exon win 0
3   .001    # initial Exon win 1
4   .001    # initial Exon win 2
5   .001    # internal Exon win 0
6   .001    # internal Exon win 1
7   .001    # internal Exon win 2
8   .001    # terminal exon
9   .001    # lessD0 Intron win 0
10  .001    # 
11  .001    # 
12  .01     # geometric0 Intron win 0
13  .001    # 
14  .001    # 
15  .001    # 
16  .001    # 
17  .01     # geometric1 Intron win 1
18  .001    # 
19  .001    # 
20  .001    # 
21  .001    # 
22  .01     # geometric2 Intron win 2
23  .001    # 
24  .012    # 5' UTR single exon
25  .001    # 5' UTR initial exon
26  .02     # 5' UTR intron single base
27  .0      # 5' UTR intron variable length
28  .001    # 5' UTR internal exon
29  .006    # 5' UTR terminal exon
30  .024    # 3' UTR single exon
31  .000    # 3' UTR initial exon
32  .000    # 3' UTR intron single base
33  .0      # 3' UTR intron variable length
34  .000    # 3' UTR internal exon
35  .000    # 3' UTR terminal exon
36  .001    # reverse single Exon
37  .001    # reverse initial Exon
38  .001    # reverse internal Exon win 0
39  .001    # reverse internal Exon win 1
40  .001    # reverse internal Exon win 2
41  .001    # reverse terminal exon win 0
42  .001    # reverse terminal exon win 1
43  .001    # reverse terminal exon win 2
44  .001    # reverse lessD0 Intron win 0
45  .001    # reverse 
46  .001    # reverse 
47  .01     # reverse geometric0 Intron win 0
48  .001    # reverse 
49  .001    # reverse 
50  .001    # reverse 
51  .001    # reverse 
52  .01     # reverse geometric1 Intron win 1
53  .001    # reverse 
54  .001    # reverse 
55  .001    # reverse 
56  .001    # reverse 
57  .01     # reverse geometric2 Intron win 2
58  .001    # reverse
59  .001    # reverse 5' UTR single exon
60  .001    # reverse 5' UTR initial exon
61  .02     # reverse 5' UTR intron single base
62  .0      # reverse 5' UTR intron variable length
63  .001    # reverse 5' UTR internal exon
64  .001    # reverse 5' UTR terminal exon
65  .024    # reverse 3' UTR single exon
66  .000    # reverse 3' UTR initial exon
67  .000    # reverse 3' UTR intron single base
68  .0      # reverse 3' UTR intron variable length
69  .000    # reverse 3' UTR internal exon
70  .000    # reverse 3' UTR terminal 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
71
# state prob statename
0  .76     # start intergenic region
1  .003    # single Exon
2  .001    # initial Exon win 0
3  .001    # initial Exon win 1
4  .001    # initial Exon win 2
5  .001    # internal Exon win 0
6  .001    # internal Exon win 1
7  .001    # internal Exon win 2
8  .003    # terminal exon
9  .001    # lessD0 Intron win 0
10 .001    # 
11 .001    # 
12 .009    # geometric0 Intron win 0
13 .001    # 
14 .001    # 
15 .001    # 
16 .001    # 
17 .009    # geometric1 Intron win 1
18 .001    # 
19 .001    # 
20 .001    # 
21 .001    # 
22 .009    # geometric2 Intron win 2
23 .001    # 
24 .001    # 5' UTR single exon
25 .001    # 5' UTR initial exon
26 .02     # 5' UTR intron single base
27 .0      # 5' UTR intron variable length
28 .001    # 5' UTR internal exon
29 .001    # 5' UTR terminal exon
30 .042    # 3' UTR single exon
31 .000    # 3' UTR initial exon
32 .0      # 3' UTR intron single base
33 .0      # 3' UTR intron variable length
34 .000    # 3' UTR internal exon
35 .000    # 3' UTR terminal exon
36 .003    # reverse single Exon
37 .003    # reverse initial Exon
38 .001    # reverse internal Exon win 0
39 .001    # reverse internal Exon win 1
40 .001    # reverse internal Exon win 2
41 .001    # reverse terminal exon win 0
42 .001    # reverse terminal exon win 1
43 .001    # reverse terminal exon win 2
44 .001    # reverse lessD0 Intron win 0
45 .001    # reverse 
46 .001    # reverse 
47 .009    # reverse geometric0 Intron win 0
48 .001    # reverse 
49 .001    # reverse 
50 .001    # reverse 
51 .001    # reverse 
52 .009    # reverse geometric1 Intron win 1
53 .001    # reverse 
54 .001    # reverse 
55 .001    # reverse 
56 .001    # reverse 
57 .009    # reverse geometric2 Intron win 2
58 .001    # reverse
59 .012    # reverse 5' UTR single exon
60 .004    # reverse 5' UTR initial exon
61 .02     # reverse 5' UTR intron single base
62 .0      # reverse 5' UTR intron variable length
63 .003    # reverse 5' UTR internal exon
64 .001    # reverse 5' UTR terminal exon
65 .001    # reverse 3' UTR single exon
66 .001    # reverse 3' UTR initial exon
67 .01     # reverse 3' UTR intron single base
68 .0      # reverse 3' UTR intron variable length
69 .001    # reverse 3' UTR internal exon
70 .001    # reverse 3' UTR terminal exon

#
# Transition probabilities
# only non-zero probabilities
[Transition]
#           -----  Igenic region  -----
# intergenic region
0 0     .9994
# 5' UTR single exon
0 24	.00029
# 5' UTR initial exon
0 25    .00001
# reverse 3' UTR single exon
0 65	.00029
# reverse 3' UTR terminal exon
0 70    .00001
#           -----  Single Exon  -----
# intergenic region
#1 0	1.0
# 3' UTR single exon
1 30      0.98
# 3' UTR initial exon
1 31      0.02
#           -----  Initial Exon 0  -----
# longdss0 Intron
2 10	1.0
#           -----  Initial Exon 1  -----
# longdss1 Intron
3 15	1.0
#           -----  Initial Exon 2  -----
# longdss2 Intron
4 20	1.0
#           -----  Internal Exon 0  -----
# longdss0 Intron
5 10	   1.0
#           -----  Internal Exon 1  -----
# longdss1 Intron
6 15	   1.0
#           -----  Internal Exon 2  -----
# longdss2 Intron
7 20	   1.0
#           -----  Terminal Exon  -----
# 3' UTR single exon
8 30      0.98
# 3' UTR initial exon
8 31      0.02
#           -----  lessD0 Intron 0  -----
# longass0
9 13	   1.0
#           -----  longdss0 Intron 0    -----
# lessD0
10 9	.5
# equalD0
10 11	.5
#           -----  equalD0 Intron 0    -----
# geometric0
11 12	1.0
#           -----  geometric0 Intron 0  -----
# geometric0 intron
12 12	     .9997447
# longass0
12 13	     .0002553
#           -----  longass0 Intron 0     -----
# internal exon 0, 45% of all internal exons 
13 5	   .25
# internal exon 1, 33% of all internal exons 
13 6	   .25
# internal exon 2, 22% of all internal exons 
13 7	   .25
# terminal exon
13 8	   .25
#           -----  lessD1 Intron 1  -----
# longass1
14 18	   1.0
#           -----  longdss1 Intron 1    -----
# lessD1
15 14      .5
# equalD1
15 16      .5
#           -----  equalD1 Intron 1    -----
# geometric1
16 17      1.0
#           -----  geometric1 Intron 1  -----
# geometric1 intron
17 17	     .9997447
# longass1
17 18	     .0002553
#           -----  longass1 Intron 1  -----
# internal exon 0, 45% of all internal exons 
18 5	   .25
# internal exon 1, 33% of all internal exons 
18 6	   .25
# internal exon 2, 22% of all internal exons
18 7	   .25
# terminal exon
18 8	   .25
#           -----  lessD2 Intron 2  -----
# longass2
19 23	   1.0
#           -----  longdss2 Intron 2    -----
# lessD2
20 19      .5
# equalD2
20 21      .5
#           -----  equalD2 Intron 2    -----
# geometric0
21 22      1.0
#           -----  geometric2 Intron 2  -----
# geometric2 intron
22 22	     .9997447
# longass2
22 23	     .0002553
#           -----  longass2 Intron 2     -----
# internal exon 0, 45% of all internal exons 
23 5	   .25
# internal exon 1, 33% of all internal exons 
23 6	   .25
# internal exon 2, 22% of all internal exons 
23 7	   .25
# terminal exon
23 8	   .25
#           -----  5' UTR single exon  -----
# single
24 1     .18
# initial exon 0
24 2     .28
# initial exon 1
24 3     .28
# initial exon 2
24 4     .26
#           -----  5' UTR initial exon  -----
# 5' UTR intron single base
25 26    1.0
# 5' UTR intron variable length
25 27    1.0
#           -----  5' UTR intron single base -----
# 5' UTR intron
26 26    .995
# 5' UTR internal exon
26 28    .001
# 5' UTR terminal exon
26 29    .004
#           -----  5' UTR intron variable length ----
# 5' UTR internal exon
27 28    .2
# 5' UTR terminal exon
27 29    .8
#           -----  5' UTR internal exon  -----
# 5' UTR intron single base
28 26   1.0
# 5' UTR intron variable length
28 27   1.0
#           -----  5' UTR terminal exon  -----
# single
29 1     .18
# initial exon 0
29 2     .28
# initial exon 1
29 3     .28
# initial exon 2
29 4     .26
#           -----  3' UTR single exon  -----
# intergenic region
30 0     1.0
#           -----  3' UTR initial exon  -----
# 3' UTR intron single base
31 32    1.0
# 3' UTR intron variable length
31 33    1.0
#           -----  3' UTR intron  single base -----
# 3' UTR intron single base
32 32    .995
# 3' UTR internal exon
32 34    .001
# 3' UTR terminal exon
32 35    .004
#           -----  3' UTR intron variable length -----
# 3' UTR internal exon
33 34    .2
# 3' UTR terminal exon
33 35    .8
#           -----  3' UTR internal exon  -----
# 3' UTR intron single base
34 32    1.0
# 3' UTR intron variable length
34 33    1.0
#           -----  3' UTR terminal exon  -----
# intergenic region
35 0     1.0
#
# ------------------------ reverse strand --------------------------
#
#           -----  reverse Single Exon  -----
# reverse 5' UTR single exon
36 59	 .95
# reverse 5' UTR terminal exon
36 64    .05
#           -----  reverse Initial Exon   -----
# reverse 5' UTR single exon
37 59	 .9
# reverse 5' UTR terminal exon
37 64    .1
#           -----  reverse Internal Exon 0  -----
# reverse longass0
38 48	   1.0
#           -----  reverse Internal Exon 1  -----
# reverse longass1
39 53	   1.0
#           -----  reverse Internal Exon 2  -----
# reverse longass2
40 58	   1.0
#           -----  reverse Terminal Exon  0  -----
# reverse longass0 
41 48	   1.0
#           -----  reverse Terminal Exon  1 -----
# reverse longass1
42 53	   1.0
#           -----  reverse Terminal Exon  2  -----
# reverse longass2 
43 58	   1.0
#           -----  reverse lessD0 Intron 0  -----
# longdss0
44 45	   1.0
#           -----  reverse longdss0 Intron 0    -----
# reverse internal exon 0, 45% of all internal exons 
45 38	   .25
# reverse internal exon 1, 33% of all internal exons 
45 39	   .25
# reverse internal exon 2, 22% of all internal exons 
45 40	   .25
# reverse initial exon
45 37	   .25
#           -----  reverse equalD0 Intron 0    -----
# reverse geometric0
46 47	1.0
#           -----  reverse geometric0 Intron 0  -----
# reverse geometric0 intron
47 47	     .9997447
# reverse longdss0
47 45	     .0002553
#           -----  reverse longass0 Intron 0     -----
# reverse intron equalD0
48 46	   .5
# reverse intron lessD0
48 44	   .5
#           -----  reverse lessD1 Intron 1  -----
# longdss1
49 50	   1.0
#           -----  reverse longdss1 Intron 1    -----
# reverse internal exon 0, 45% of all internal exons 
50 38	   .25
# reverse internal exon 1, 33% of all internal exons 
50 39	   .25
# reverse internal exon 2, 22% of all internal exons 
50 40	   .25
# reverse initial exon
50 37	   .25
#           -----  reverse equalD1 Intron 1    -----
# reverse geometric1
51 52	1.0
#           -----  reverse geometric1 Intron 1  -----
# reverse geometric1 intron
52 52	     .9997447
# reverse longdss1
52 50	     .0002553
#           -----  reverse longass1 Intron 1     -----
# reverse intron equalD1
53 51	   .5
# reverse intron lessD1
53 49 	   .5
#           -----  reverse lessD2 Intron 2  -----
# longdss2
54 55	   1.0
#           -----  reverse longdss2 Intron 2    -----
# reverse internal exon 0, 45% of all internal exons 
55 38	   .25
# reverse internal exon 1, 33% of all internal exons 
55 39	   .25
# reverse internal exon 2, 22% of all internal exons 
55 40	   .25
# reverse initial exon
55 37	   .25
#           -----  reverse equalD2 Intron 2    -----
# reverse geometric2
56 57	1.0
#           -----  reverse geometric2 Intron 2  -----
# reverse geometric2 intron
57 57      .9997447
# reverse longdss2
57 55	   .0002553
#           -----  reverse longass2 Intron 2     -----
# reverse intron equalD2
58 56	   .5
# reverse intron lessD2
58 54	   .5
#           -----  reverse 5' UTR single exon  -----
59 0      1.0
#           -----  reverse 5' UTR initial exon  -----
60 0      1.0
#           -----  reverse 5' UTR intron single base -----
# reverse 5' UTR intron
61 61     .995
# reverse 5' UTR internal exon
61 63     .001
# reverse 5' UTR initial exon
61 60     .004
#           -----  reverse 5' UTR intron variable length -----
# reverse 5' UTR internal exon
62 63     .2
# reverse 5' UTR initial exon
62 60     .8
#           -----  reverse 5' UTR internal exon  -----
# revserse 5' UTR intron single base
63 61     1.0
# revserse 5' UTR intron variable length
63 62     1.0
#           -----  reverse 5' UTR terminal exon  -----
# revserse 5' UTR intron single base
64 61      1.0
# revserse 5' UTR intron variable length
64 62      1.0
#           -----  reverse 3' UTR single exon  -----
# reverse single exon
65 36	  .18
# reverse terminal exon 0
65 41     .28
# reverse terminal exon 1
65 42     .28
# reverse terminal exon 2
65 43     .26
#           -----  reverse 3' UTR initial exon  -----
# reverse single exon
66 36	  .18
# reverse terminal exon 0
66 41     .28
# reverse terminal exon 1
66 42     .28
# reverse terminal exon 2
66 43     .26
#           -----  reverse 3' UTR intron single base -----
# reverse 3' UTR intron
67 67     .995
# reverse 3' UTR internal exon
67 69     .001
# reverse 3' UTR initial exon
67 66     .004
#           -----  reverse 3' UTR intron variable length -----
# reverse 3' UTR internal exon
68 69     .2
# reverse 3' UTR initial exon
68 66     .8
#           -----  reverse 3' UTR internal exon  -----
# reverse 3' intron single base
69 67     1.0
# reverse 3' intron variable length
69 68     1.0
#           -----  reverse 3' UTR terminal exon  -----
# reverse 3' intron single base
70 67     1.0
# reverse 3' intron variable length
70 68     1.0
