# 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

begin {trans BG; }
BG { trans BG:0.995 E1:0.00048828125 ER1:3.0517578125e-05 ER15:0.000457763671875 endst:0.0025; label x; emit A:0.288 C:0.212 G:0.212 T:0.288; }
E1 { trans E2; label E;  emit A:0.288 C:0.212 G:0.212 T:0.288; }
E2 { trans E3; emit A:0.288 C:0.212 G:0.212 T:0.288; }
E3 { trans E4; emit A:0.288 C:0.212 G:0.212 T:0.288; }
E4 { trans E5; emit A:0.288 C:0.212 G:0.212 T:0.288; }
E5 { trans E6; emit A:0.288 C:0.212 G:0.212 T:0.288; }
E6 { trans E7; emit A:0.288 C:0.212 G:0.212 T:0.288; }
E7 { trans E8; emit A:0.15 C:0.15 G:0.3 T:0.4; }
E8 { trans E9; emit A:0.017857 C:0.946429 G:0.017857 T:0.017857; }
E9 { trans E10; emit A:0.946429 C:0.017857 G:0.017857 T:0.017857; }
E10 { trans E11; emit A:0.017857 C:0.946429 G:0.017857 T:0.017857; }
E11 { trans E12; emit A:0.017857 C:0.017857 G:0.946429 T:0.017857; }
E12 { trans E13; emit A:0.017857 C:0.017857 G:0.017857 T:0.946429; }
E13 { trans E14; emit A:0.017857 C:0.017857 G:0.946429 T:0.017857; }
E14 { trans E15; emit A:0.288 C:0.212 G:0.212 T:0.288; }
E15 { trans E16; emit A:0.288 C:0.212 G:0.212 T:0.288; }
E16 { trans E17:0.03125 BG0:0.03125 BG:0.9375; emit A:0.288 C:0.212 G:0.212 T:0.288; }
BG0 { trans E17; label y1; tied BG; }
E17 { trans E18; label F; emit A:0.288 C:0.212 G:0.212 T:0.288; }
E18 { trans E19; emit A:0.288 C:0.212 G:0.212 T:0.288; }
E19 { trans E20; emit A:0.288 C:0.212 G:0.212 T:0.288; }
E20 { trans E21; emit A:0.288 C:0.212 G:0.212 T:0.288; }
E21 { trans E22; emit A:0.288 C:0.212 G:0.212 T:0.288; }
E22 { trans E23; emit A:0.288 C:0.212 G:0.212 T:0.288; }
E23 { trans E24; emit A:0.288 C:0.212 G:0.212 T:0.288; }
E24 { trans E25; emit A:0.288 C:0.212 G:0.212 T:0.288; }
E25 { trans E26; emit A:0.288 C:0.212 G:0.212 T:0.288; }
E26 { trans E27; emit A:0.288 C:0.212 G:0.212 T:0.288; }
E27 { trans E28; emit A:0.288 C:0.212 G:0.212 T:0.288; }
E28 { trans E29; emit A:0.288 C:0.212 G:0.212 T:0.288; }
E29 { trans E30; emit A:0.288 C:0.212 G:0.212 T:0.288; }
E30 { trans BG; emit A:0.288 C:0.212 G:0.212 T:0.288; }
#
ER1 { trans ER2; label f; tied E30:C; }
ER2 { trans ER3; tied E29:C; }
ER3 { trans ER4; tied E28:C; }
ER4 { trans ER5; tied E27:C; }
ER5 { trans ER6; tied E26:C; }
ER6 { trans ER7; tied E25:C; }
ER7 { trans ER8; tied E24:C; }
ER8 { trans ER9; tied E23:C; }
ER9 { trans ER10; tied E22:C; }
ER10 { trans ER11; tied E21:C; }
ER11 { trans ER12; tied E20:C; }
ER12 { trans ER13; tied E19:C; }
ER13 { trans ER14; tied E18:C; }
ER14 { trans BGR0:0.5 ER15:0.5; tied E17:C; }
BGR0 { trans ER15; label z1; tied BG:C; }
ER15 { trans ER16; label e; tied E16:C; }
ER16 { trans ER17; tied E15:C; }
ER17 { trans ER18; tied E14:C; }
ER18 { trans ER19; tied E13:C; }
ER19 { trans ER20; tied E12:C; }
ER20 { trans ER21; tied E11:C; }
ER21 { trans ER22; tied E10:C; }
ER22 { trans ER23; tied E9:C; }
ER23 { trans ER24; tied E8:C; }
ER24 { trans ER25; tied E7:C; }
ER25 { trans ER26; tied E6:C; }
ER26 { trans ER27; tied E5:C; }
ER27 { trans ER28; tied E4:C; }
ER28 { trans ER29; tied E3:C; }
ER29 { trans ER30; tied E2:C; }
ER30 { trans BG; tied E1:C; }
endst {letter NULL; end 1; }