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 [5] // Initial node A20 - U41 from junction 
BasepairNode | Deletion Probability [0.0000015195492620] | Pair Probability [[0.012875655,0.167362170,0.012690460,0.139544678,0.000000000],[0.017278970,0.010426425,0.115221913,0.012854497,0.000000000],[0.012509796,0.118823330,0.002800872,0.196378937,0.000000000],[0.122336675,0.013723253,0.019374350,0.025798019,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.991950402,0.007999600,0.000049998] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.493381468,0.493381468,0.012635379,0.000601685] | Right Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000] | Left Index [1] | Right Index [5] // Basepair A20 - U41 cWW 
ClusterNode  | Deletion Probability [0.0000000006171744] | Num Left Bases [1] | Num Right Bases [2] | Left Index [2] | Right Index [4] | Norm Constant [0.316951872077325] // Cluster node G21:G21 and U38:A40
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.016500430,0.310288742,0.015571103,0.044672112,0.000000000],[0.014475176,0.011549597,0.038212544,0.015431970,0.000000000],[0.015226490,0.044298882,0.003453650,0.364972803,0.000000000],[0.037922120,0.017096803,0.015161977,0.035165601,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G21 - U38 cWW 
Interaction  | Interacting Bases [1,3] | Pair Probability [[0.073244666,0.074626455,0.002664993,0.188942478,0.000000000],[0.070262839,0.067908836,0.002664993,0.002664993,0.000000000],[0.086862504,0.002664993,0.212156020,0.069245779,0.000000000],[0.072228285,0.068532177,0.002664993,0.002664993,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G21 - A40 tSH 
Insertion    | Location [2] | Length Distribution [0.023781213,0.951248514,0.023781213,0.001189061] | Letter Distribution [0.375000000,0.125000000,0.125000000,0.375000000,0.000000000]// Insertion after nucleotide 3, 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 [3] | Right Index [2] // New Initial node after Cluster
HairpinNode  | Num Bases [1] | Left Index [3] | Right Index [3] | 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
