Character Definition | A,C,G,U,* // Define characters here
InitialNode  | 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 [1] | Right Index [7] // Initial node G516 - C536 from junction 
BasepairNode | Deletion Probability [0.0000040507541457] | Pair Probability [[0.009286488,0.019798872,0.010378792,0.203290480,0.000000000],[0.019928641,0.008620290,0.203764573,0.011464360,0.000000000],[0.010357661,0.214071747,0.002069606,0.024700235,0.000000000],[0.213844488,0.011558359,0.024769722,0.012095683,0.000000000],[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 [0.661815186,0.335026775,0.003020733,0.000137306] | Right Letter Distribution [0.125000000,0.125000000,0.625000000,0.125000000,0.000000000] | Left Index [1] | Right Index [7] // Basepair G516 - C536 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.062500000,0.312500000,0.437500000,0.187500000,0.000000000] | Position [1] | Left Index [2] | Right Index [6] // Fixed node on left
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 [6] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.437500000,0.187500000,0.062500000,0.312500000,0.000000000] | Position [2] | Left Index [3] | Right Index [6] // Fixed node on right
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 [5] // New Initial node after Fixed node
ClusterNode  | Deletion Probability [0.0000000034668202] | Num Left Bases [1] | Num Right Bases [2] | Left Index [3] | Right Index [5] | Norm Constant [0.271490520016192] // Cluster node A518:A518 and U533:A534
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.011482008,0.112765157,0.011905390,0.153344322,0.000000000],[0.017883524,0.009447760,0.151510989,0.012622831,0.000000000],[0.011794866,0.153462523,0.002487231,0.146131042,0.000000000],[0.151182686,0.013156782,0.021350858,0.019472030,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A518 - U533 cWW 
Interaction  | Interacting Bases [1,3] | Pair Probability [[0.083316030,0.057750357,0.002817434,0.213979904,0.000000000],[0.097281044,0.044047618,0.002817434,0.002817434,0.000000000],[0.059598005,0.002817434,0.257800837,0.030806940,0.000000000],[0.076365633,0.062149028,0.002817434,0.002817434,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A518 - A534 tSH 
Insertion    | Location [2] | Length Distribution [0.659069065,0.008238363,0.329809145,0.002746121,0.000137306] | Letter Distribution [0.083333333,0.416666667,0.083333333,0.416666667,0.000000000]// Insertion after nucleotide 4, position 2 in cluster node
InitialNode  | 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 [4] | Right Index [3] // New Initial node after Cluster
HairpinNode  | Num Bases [1] | Left Index [4] | Right Index [4] | 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
