Character Definition | A,C,G,U,* // Identity and order of characters in matrices
InitialNode  | Left Length Distribution [0.999900000,0.000100000] | Left Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Right Length Distribution [0.999900000,0.000100000] | Right Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Left Index [1] | Right Index [9] // Initial node
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.009395742,0.016407446,0.011144700,0.139212023,0.000000000],[0.111392575,0.014938303,0.141641678,0.012923844,0.000000000],[0.011206404,0.178112619,0.002322517,0.022487942,0.000000000],[0.145012298,0.012695226,0.160469966,0.010636717,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [9] // Basepair G2754 - C2728 cWW 
BasepairNode | Deletion Probability [0.0000013485027022] | Pair Probability [[0.075507066,0.053552974,0.002212523,0.138529665,0.000000000],[0.082854027,0.065729327,0.002212523,0.002212523,0.000000000],[0.123693303,0.044579214,0.180646658,0.077380375,0.000000000],[0.075249967,0.071214808,0.002212523,0.002212523,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.453734282,0.543578593,0.002564050,0.000123074] | Right Letter Distribution [0.062500000,0.187500000,0.062500000,0.687500000,0.000000000] | Left Index [2] | Right Index [8] // Basepair G2755 - A2727 tSH 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.269230769,0.192307692,0.038461538,0.500000000,0.000000000] | Position [1] | Left Index [3] | Right Index [7] // Fixed node on left for 4V9F|1|0|U|2726
InitialNode  | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [7] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.041675690,0.081666289,0.365438636,0.080464028,0.000000000],[0.038965625,0.063318609,0.002854789,0.067060476,0.000000000],[0.000488445,0.000794123,0.014116299,0.000747096,0.000000000],[0.002324203,0.000794123,0.238544473,0.000747096,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [7] // Basepair A2757 - G2725 tHS 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.012465738,0.179588890,0.012046018,0.116098588,0.000000000],[0.014534458,0.010710321,0.117663818,0.012989386,0.000000000],[0.011887226,0.101660012,0.002595468,0.260901100,0.000000000],[0.088457803,0.013682782,0.017088572,0.027629820,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.999900000,0.000100000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.999900000,0.000100000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [6] // Basepair G2758 - U2724 cWW 
HairpinNode  | Num Bases [1] | Left Index [6] | Right Index [6] | Norm Constant [1.000000000000000] // Hairpin node type *
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,1.000000000]] // Hairpin for truncation
