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 [18] // Initial node
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.009144630,0.017165752,0.010484008,0.190189591,0.000000000],[0.018463087,0.009213143,0.244318979,0.013008228,0.000000000],[0.010534317,0.213869704,0.001991973,0.023268171,0.000000000],[0.191242613,0.012802444,0.024618634,0.009684725,0.000000000],[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 [18] // Basepair C97 - G79 cWW 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.125561346,0.100336661,0.001346801,0.006681142,0.000000000],[0.116168301,0.106868438,0.001346801,0.001346801,0.000000000],[0.186732308,0.001346801,0.007499122,0.099121172,0.000000000],[0.124528414,0.118422287,0.001346801,0.001346801,0.000000000],[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 [2] | Right Index [17] // Basepair G98 - A78 tSH 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.017898242,0.039832166,0.003960910,0.461511524,0.000000000],[0.003960910,0.319173624,0.009494562,0.003960910,0.000000000],[0.018590254,0.003960910,0.030122383,0.022980723,0.000000000],[0.003960910,0.003960910,0.017616762,0.039014302,0.000000000],[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 [3] | Right Index [16] // Basepair A99 - U77 tHW 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.286333919,0.012099244,0.002893863,0.002893863,0.000000000],[0.200484693,0.008433586,0.002893863,0.002893863,0.000000000],[0.002893863,0.002893863,0.343184380,0.002893863,0.000000000],[0.002893863,0.002893863,0.120525543,0.002893863,0.000000000],[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 [15] // Basepair G100 - G76 bif 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.008126778,0.008126778,0.878098334,0.008126778,0.000000000],[0.008126778,0.008126778,0.008126778,0.008126778,0.000000000],[0.008126778,0.008126778,0.008126778,0.008126778,0.000000000],[0.008126778,0.008126778,0.008126778,0.008126778,0.000000000],[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 [5] | Right Index [14] // Basepair A101 - G75 wat 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.043944313,0.287462646,0.003515083,0.003515083,0.000000000],[0.022503169,0.013476736,0.003515083,0.003515083,0.000000000],[0.003515083,0.003515083,0.165212509,0.432249801,0.000000000],[0.003515083,0.003515083,0.003515083,0.003515083,0.000000000],[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 [6] | Right Index [13] // Basepair G102 - U74 bif 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.017898242,0.003960910,0.018590254,0.003960910,0.000000000],[0.039832166,0.319173624,0.003960910,0.003960910,0.000000000],[0.003960910,0.009494562,0.030122383,0.017616762,0.000000000],[0.461511524,0.003960910,0.022980723,0.039014302,0.000000000],[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 [7] | Right Index [12] // Basepair U103 - A73 tWH 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.095295147,0.096219847,0.190630355,0.125187794,0.000000000],[0.134048753,0.121712839,0.001377659,0.114372990,0.000000000],[0.001377659,0.001377659,0.006574466,0.001377659,0.000000000],[0.006340534,0.001377659,0.101351318,0.001377659,0.000000000],[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 [8] | Right Index [11] // Basepair A104 - G72 tHS 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009126734,0.019007720,0.010392915,0.188767123,0.000000000],[0.016031357,0.008949680,0.190366634,0.012455659,0.000000000],[0.010277496,0.276641564,0.001959000,0.025096194,0.000000000],[0.186351265,0.012927771,0.021997944,0.009650944,0.000000000],[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 [9] | Right Index [10] // Basepair G105 - C71 cWW 
HairpinNode  | Num Bases [1] | Left Index [10] | Right Index [10] | 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
