# # transition probabilities and initial probabilities for the overall HMM # number of states 71 # # Transition probabilities of the Generalised Hidden-Markov Model # Date: 14.10.2006 # 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 .001 # 3' UTR single exon 31 .001 # 3' UTR initial exon 32 .02 # 3' UTR intron single base 33 .0 # 3' UTR intron variable length 34 .001 # 3' UTR internal exon 35 .001 # 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 .001 # reverse 3' UTR single exon 66 .001 # reverse 3' UTR initial exon 67 .02 # 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 # Terminal probabilities (a priori probs for a state ending at # the last position. # only non-zero probabilities neccessary [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 .01 # 3' UTR single exon 31 .005 # 3' UTR initial exon 32 .02 # 3' UTR intron single base 33 .0 # 3' UTR intron variable length 34 .003 # 3' UTR internal exon 35 .004 # 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 .9999 # 5' UTR single exon 0 24 .00003 # 5' UTR initial exon 0 25 .00002 # reverse 3' UTR single exon 0 65 .00004 # reverse 3' UTR terminal exon 0 70 .00001 # ----- Single Exon ----- # intergenic region #1 0 1.0 # 3' UTR single exon 1 30 0.8 # 3' UTR initial exon 1 31 0.2 # ----- 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 0.8 # 3' UTR initial exon 8 31 0.2 # ----- 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 .3 # internal exon 1, 33% of all internal exons 13 6 .3 # internal exon 2, 22% of all internal exons 13 7 .3 # terminal exon 13 8 .1 # ----- 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 .3 # internal exon 1, 33% of all internal exons 18 6 .3 # internal exon 2, 22% of all internal exons 18 7 .3 # terminal exon 18 8 .1 # ----- 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 .3 # internal exon 1, 33% of all internal exons 23 6 .3 # internal exon 2, 22% of all internal exons 23 7 .3 # terminal exon 23 8 .1 # ----- 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 .9995 # 5' UTR internal exon 26 28 .00005 # 5' UTR terminal exon 26 29 .00045 # ----- 5' UTR intron variable length ---- # 5' UTR internal exon 27 28 .1 # 5' UTR terminal exon 27 29 .9 # ----- 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 .9995 # 3' UTR internal exon 32 34 .00005 # 3' UTR terminal exon 32 35 .00045 # ----- 3' UTR intron variable length ----- # 3' UTR internal exon 33 34 .1 # 3' UTR terminal exon 33 35 .9 # ----- 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 .6 # reverse 5' UTR terminal exon 36 64 .4 # ----- reverse Initial Exon ----- # reverse 5' UTR single exon 37 59 .6 # reverse 5' UTR terminal exon 37 64 .4 # ----- 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 .3 # reverse internal exon 1, 33% of all internal exons 45 39 .3 # reverse internal exon 2, 22% of all internal exons 45 40 .3 # reverse initial exon 45 37 .1 # ----- 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 .3 # reverse internal exon 1, 33% of all internal exons 50 39 .3 # reverse internal exon 2, 22% of all internal exons 50 40 .3 # reverse initial exon 50 37 .1 # ----- 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 .3 # reverse internal exon 1, 33% of all internal exons 55 39 .3 # reverse internal exon 2, 22% of all internal exons 55 40 .3 # reverse initial exon 55 37 .1 # ----- 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 .9995 # reverse 5' UTR internal exon 61 63 .00005 # reverse 5' UTR initial exon 61 60 .00045 # ----- reverse 5' UTR intron variable length ----- # reverse 5' UTR internal exon 62 63 .1 # reverse 5' UTR initial exon 62 60 .9 # ----- 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 .9995 # reverse 3' UTR internal exon 67 69 .00005 # reverse 3' UTR initial exon 67 66 .00045 # ----- reverse 3' UTR intron variable length ----- # reverse 3' UTR internal exon 68 69 .1 # reverse 3' UTR initial exon 68 66 .9 # ----- 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