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 [10] // Initial node
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.005850100,0.027393284,0.006655921,0.215812969,0.000000000],[0.011528573,0.013404573,0.161453244,0.011933967,0.000000000],[0.006669430,0.334471092,0.001272985,0.036564873,0.000000000],[0.122069314,0.018941238,0.015404638,0.010573800,0.000000000],[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 [10] // Basepair A885 - U894 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.346153846,0.269230769,0.346153846,0.038461538,0.000000000] | Position [1] | Left Index [2] | Right Index [9] // Fixed node on left for 8CRE|1|CM|G|886
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 [9] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.115384615,0.346153846,0.192307692,0.346153846,0.000000000] | Position [2] | Left Index [3] | Right Index [9] // Fixed node on right for 8CRE|1|CM|U|893
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 [8] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000035196243062] | Pair Probability [[0.106056673,0.104321352,0.001223907,0.005893693,0.000000000],[0.106649285,0.105900781,0.019152727,0.001223907,0.000000000],[0.163171360,0.001223907,0.006768990,0.102750762,0.000000000],[0.163118923,0.110095920,0.001223907,0.001223907,0.000000000],[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 [0.633943052,0.364188787,0.001786044,0.000082117] | Right Letter Distribution [0.083333333,0.083333333,0.083333333,0.750000000,0.000000000] | Left Index [3] | Right Index [8] // Basepair G887 - A892 tSH 
HairpinNode  | Num Bases [4] | Left Index [4] | Right Index [7] | Norm Constant [0.999999999999999] // Hairpin node U888:A891
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.094936709,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.183544304,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.006329114,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.715189873,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U888
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.500000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.038461538,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.423076923,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.038461538,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G889
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.423076923,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.038461538,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.423076923,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.115384615,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A890
Interaction  | Interacting Bases [4,4] | Pair Probability [[0.730769231,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.038461538,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.038461538,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.192307692,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A891
