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 [15] // Initial node
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.004553963,0.008166350,0.026176706,0.094927059,0.000000000],[0.009682505,0.004638079,0.555559699,0.006585388,0.000000000],[0.005294135,0.096972482,0.004989559,0.011205720,0.000000000],[0.096157693,0.006344894,0.063919821,0.004825947,0.000000000],[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 [15] // Basepair C2285 - G2383 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.437500000,0.062500000,0.187500000,0.312500000,0.000000000] | Position [1] | Left Index [2] | Right Index [14] // Fixed node on left for 4Y4O|1|2A|A|2286
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 [3] | Right Index [14] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.062500000,0.062500000,0.562500000,0.312500000,0.000000000] | Position [2] | Left Index [3] | Right Index [14] // Fixed node on right for 4Y4O|1|2A|C|2381
InitialNode  | Left Length Distribution [1.000000000] | 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 [13] // New Initial node after Fixed node
JunctionNode | Branches [2]  | Left Index [3] | Right Index [13] // Junction node A2287 - C2381 ID J6323
InitialNode  | Left Length Distribution [1.000000000] | Left Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | 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 [6] // Initial node
BasepairNode | Deletion Probability [0.0000001231336240] | Pair Probability [[0.015768747,0.038966363,0.003298662,0.431393572,0.000000000],[0.015484946,0.035535304,0.013737323,0.038098902,0.000000000],[0.003298662,0.016351027,0.015788067,0.264238191,0.000000000],[0.037682318,0.031632851,0.016261599,0.022463465,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.008193363,0.983203605,0.008193363,0.000409668] | Left Letter Distribution [0.687500000,0.062500000,0.062500000,0.187500000,0.000000000] | 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 [6] // Basepair A2287 - U2344 tWW 
BasepairNode | Deletion Probability [0.0000224863733088] | Pair Probability [[0.004415529,0.072449384,0.004136539,0.033074219,0.000000000],[0.004376309,0.003672370,0.021641442,0.004297347,0.000000000],[0.028386345,0.172159827,0.006373413,0.603433192,0.000000000],[0.021404270,0.004648070,0.004942750,0.010588996,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.990049834,0.009900498,0.000049502,0.000000165] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.990049834,0.009900498,0.000049502,0.000000165] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [5] // Basepair G2289 - C2343 cWW 
HairpinNode  | Num Bases [1] | Left Index [5] | Right Index [5] | 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
InitialNode  | Left Length Distribution [1.000000000] | 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 [7] | Right Index [13] // Initial node 4Y4O|1|2A|G|2345 - 4Y4O|1|2A|C|2381 from node 
JunctionNode | Branches [2]  | Left Index [7] | Right Index [13] // Junction node G2345 - C2381 ID J975
InitialNode  | Left Length Distribution [1.000000000] | Left Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | 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 [11] // Initial node
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.005428049,0.005428049,0.046000828,0.007552856,0.000000000],[0.005428049,0.013114330,0.005428049,0.005428049,0.000000000],[0.210874063,0.047430306,0.539876129,0.051111671,0.000000000],[0.025251681,0.007664253,0.005428049,0.018555587,0.000000000],[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 [11] // Basepair G2345 - G2371 cHW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.812500000,0.062500000,0.062500000,0.062500000,0.000000000] | Position [1] | Left Index [8] | Right Index [10] // Fixed node on left for 4Y4O|1|2A|G|2345
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 [9] | Right Index [10] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000224863733088] | Pair Probability [[0.009096159,0.016527150,0.010380816,0.190892026,0.000000000],[0.019794727,0.009365287,0.246335869,0.012829884,0.000000000],[0.010482647,0.194028432,0.002003598,0.022513545,0.000000000],[0.203692206,0.012318528,0.030014751,0.009724374,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.990049834,0.009900498,0.000049502,0.000000165] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.990049834,0.009900498,0.000049502,0.000000165] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [9] | Right Index [10] // Basepair C2347 - G2370 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
InitialNode  | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Left Index [12] | Right Index [13] // Initial node
BasepairNode | Deletion Probability [0.0000224863733088] | Pair Probability [[0.009190997,0.018052541,0.010438844,0.192109964,0.000000000],[0.018265254,0.009284521,0.215171816,0.012586124,0.000000000],[0.010422211,0.225147488,0.002003370,0.024100784,0.000000000],[0.202430569,0.012559332,0.028422025,0.009814160,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.990049834,0.009900498,0.000049502,0.000000165] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.990049834,0.009900498,0.000049502,0.000000165] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [12] | Right Index [13] // Basepair G2372 - C2381 cWW 
HairpinNode  | Num Bases [1] | Left Index [13] | Right Index [13] | 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
