# HMM model format
# - each line is one state beginning with the identifier of the state
# - transition probabilities to ther sattes are listed after the 'trans' keyword
# - emission probabilities are listed after the 'emit' keyword
# - emission probabilities that are tied to other states are indicated with the 'tied' keyword, or 'tied:C'
#   when the complementary bases should be used

#double WM model
header { alphabet ACGT; wildcards N; }
begin {trans BG; }
generic {end 0;}
BG { trans BG:0.995 E1:0.000488281 ER1:3.05176e-05 ER14:0.000457764 endst:0.0025; label x; emit A:0.262423 C:0.237577 G:0.237577 T:0.262423; }		#TOT:3206.95
E1 { trans E2:1; label E; emit A:0.181016 C:0.25622 G:0.282951 T:0.279813; }		#TOT:16.8297
E2 { trans E3:1; emit A:0.234673 C:0.115912 G:0.555959 T:0.0934564; }		#TOT:16.8297
E3 { trans E4:1; emit A:0.113601 C:0.358198 G:0.351285 T:0.176916; }		#TOT:16.8297
E4 { trans E5:1; emit A:0.0621879 C:0.033202 G:0.226393 T:0.678218; }		#TOT:16.8297
E5 { trans E6:1; emit A:0.0246762 C:0.925871 G:0.0206482 T:0.0288044; }		#TOT:16.8297
E6 { trans E7:1; emit A:0.938245 C:0.0189767 G:0.020122 T:0.0226561; }		#TOT:16.8297
E7 { trans E8:1; emit A:0.0207328 C:0.916048 G:0.0234886 T:0.0397302; }		#TOT:16.8297
E8 { trans E9:1; emit A:0.15081 C:0.0489418 G:0.770505 T:0.0297427; }		#TOT:16.8297
E9 { trans E10:1; emit A:0.019189 C:0.0202945 G:0.019203 T:0.941313; }		#TOT:16.8297
E10 { trans E11:1; emit A:0.0193307 C:0.0185943 G:0.931763 T:0.0303121; }		#TOT:16.8297
E11 { trans E12:1; emit A:0.0229949 C:0.10378 G:0.228688 T:0.644537; }		#TOT:16.8297
E12 { trans E13:0.03125 BG0:0.03125 BG:0.9375; emit A:0.225677 C:0.175607 G:0.0944391 T:0.504277; }		#TOT:16.8297
BG0 { trans E13:1; label y1; tied BG; }
E13 { trans E14:1; label F; emit A:0.0518623 C:0.192195 G:0.648727 T:0.107215; }		#TOT:6.26535
E14 { trans E15:1; emit A:0.0928867 C:0.557143 G:0.261737 T:0.0882334; }		#TOT:6.26535
E15 { trans E16:1; emit A:0.219281 C:0.0621773 G:0.535652 T:0.182889; }		#TOT:6.26535
E16 { trans E17:1; emit A:0.495476 C:0.275938 G:0.177891 T:0.0506944; }		#TOT:6.26535
E17 { trans E18:1; emit A:0.60643 C:0.184876 G:0.0482255 T:0.160469; }		#TOT:6.26535
E18 { trans E19:1; emit A:0.563477 C:0.0492114 G:0.145333 T:0.241978; }		#TOT:6.26535
E19 { trans E20:1; emit A:0.0486793 C:0.561753 G:0.0554442 T:0.334124; }		#TOT:6.26535
E20 { trans E21:1; emit A:0.0512566 C:0.0511933 G:0.843133 T:0.0544176; }		#TOT:6.26535
E21 { trans E22:1; emit A:0.192067 C:0.0805957 G:0.0482157 T:0.679121; }		#TOT:6.26535
E22 { trans E23:1; emit A:0.0709284 C:0.0530004 G:0.814134 T:0.0619368; }		#TOT:6.26535
E23 { trans E24:1; emit A:0.39925 C:0.32299 G:0.0707173 T:0.207043; }		#TOT:6.26535
E24 { trans E25:1; emit A:0.127843 C:0.358548 G:0.264858 T:0.248751; }		#TOT:6.26535
E25 { trans BG:1; emit A:0.240237 C:0.111923 G:0.451439 T:0.196401; }		#TOT:6.26535
ER1 { trans ER2:1; label f; tied E25:C; }
ER2 { trans ER3:1; tied E24:C; }
ER3 { trans ER4:1; tied E23:C; }
ER4 { trans ER5:1; tied E22:C; }
ER5 { trans ER6:1; tied E21:C; }
ER6 { trans ER7:1; tied E20:C; }
ER7 { trans ER8:1; tied E19:C; }
ER8 { trans ER9:1; tied E18:C; }
ER9 { trans ER10:1; tied E17:C; }
ER10 { trans ER11:1; tied E16:C; }
ER11 { trans ER12:1; tied E15:C; }
ER12 { trans ER13:1; tied E14:C; }
ER13 { trans BGR0:0.5 ER14:0.5; tied E13:C; }
BGR0 { trans ER14:1; label z1; tied BG:C; }
ER14 { trans ER15:1; label e; tied E12:C; }
ER15 { trans ER16:1; tied E11:C; }
ER16 { trans ER17:1; tied E10:C; }
ER17 { trans ER18:1; tied E9:C; }
ER18 { trans ER19:1; tied E8:C; }
ER19 { trans ER20:1; tied E7:C; }
ER20 { trans ER21:1; tied E6:C; }
ER21 { trans ER22:1; tied E5:C; }
ER22 { trans ER23:1; tied E4:C; }
ER23 { trans ER24:1; tied E3:C; }
ER24 { trans ER25:1; tied E2:C; }
ER25 { trans BG:1; tied E1:C; }
endst { letter NULL; end 1; }