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 G894 - C915 from junction 
BasepairNode | Deletion Probability [0.0000135111498549] | Pair Probability [[0.008932872,0.016290939,0.010331188,0.153396411,0.000000000],[0.045391698,0.008156512,0.215817026,0.011782149,0.000000000],[0.010352346,0.232691981,0.001990992,0.021205394,0.000000000],[0.171676602,0.011675089,0.070593401,0.009715400,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.886338815,0.113215093,0.000430710,0.000015382] | Left Letter Distribution [0.375000000,0.125000000,0.125000000,0.375000000,0.000000000] | 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 [7] // Basepair G894 - C915 cWW 
ClusterNode  | Deletion Probability [0.0000000117080752] | Num Left Bases [2] | Num Right Bases [1] | Left Index [2] | Right Index [6] | Norm Constant [0.334293237869045] // Cluster node A895:U896 and U914:U914
Interaction  | Interacting Bases [2,3] | Pair Probability [[0.058992769,0.156320290,0.012890526,0.031035873,0.000000000],[0.031742405,0.016837534,0.019466934,0.029412503,0.000000000],[0.012640957,0.019827790,0.004057590,0.041315015,0.000000000],[0.026061957,0.015427032,0.016516928,0.507453895,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U896 - U914 cWW 
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.101544766,0.094028770,0.005043888,0.018571486,0.000000000],[0.103752614,0.100300448,0.001088231,0.101311333,0.000000000],[0.036651732,0.005055117,0.008908682,0.162632283,0.000000000],[0.014736849,0.109801903,0.001088231,0.135483665,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A895 - U896 cSH 
Insertion    | Location [1] | Length Distribution [0.554488312,0.444143909,0.001306306,0.000061473] | Letter Distribution [0.350000000,0.150000000,0.150000000,0.350000000,0.000000000]// Insertion after nucleotide 2, position 1 in cluster node
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 [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [5] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009030986,0.016350867,0.010422527,0.155516523,0.000000000],[0.059754563,0.008559478,0.198415479,0.011808726,0.000000000],[0.010459788,0.215045531,0.002057107,0.020817135,0.000000000],[0.165266294,0.011623489,0.094677147,0.010194359,0.000000000],[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 [4] | Right Index [5] // Basepair A897 - U913 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
