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 G554 - C605 from junction 
ClusterNode  | Deletion Probability [0.000000000000015429359482326747000000000000000000000000000000] | Num Left Bases [2] | Num Right Bases [3] | Left Index [1] | Right Index [5] | Norm Constant [0.004696580370998] // Cluster node G554:U555 and A602:C605
Interaction  | Interacting Bases [2,3] | Pair Probability [[0.009573432,0.018670696,0.010738592,0.199847452,0.000000000],[0.022636955,0.009050270,0.214230681,0.012151330,0.000000000],[0.010821283,0.200582138,0.002151860,0.023718468,0.000000000],[0.214249849,0.011785171,0.027717608,0.012074217,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U555 - A602 cWW 
Interaction  | Interacting Bases [1,5] | Pair Probability [[0.010195092,0.020769450,0.011804402,0.193474890,0.000000000],[0.017202006,0.008406578,0.208382157,0.013263440,0.000000000],[0.011655809,0.234558465,0.002149506,0.027571043,0.000000000],[0.192357660,0.013922753,0.023782986,0.010503762,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G554 - C605 cWW 
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.057311062,0.059127325,0.058376074,0.057761567,0.000000000],[0.062190460,0.060578703,0.008504233,0.053949004,0.000000000],[0.060554353,0.075378184,0.054532050,0.161787815,0.000000000],[0.058781312,0.056539156,0.057004634,0.057624068,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G554 - U555 cSS 
Interaction  | Interacting Bases [3,5] | Pair Probability [[0.057311062,0.158057807,0.058376074,0.057761567,0.000000000],[0.062190460,0.060578703,0.008504233,0.053949004,0.000000000],[0.060554353,0.075378184,0.054532050,0.062857333,0.000000000],[0.058781312,0.056539156,0.057004634,0.057624068,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A602 - C605 cSS 
Interaction  | Interacting Bases [4,4] | Pair Probability [[0.625000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.125000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.125000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.125000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion A603
Insertion    | Location [4] | Length Distribution [0.023781213,0.951248514,0.023781213,0.001189061] | Letter Distribution [0.125000000,0.125000000,0.375000000,0.375000000,0.000000000]// Insertion after nucleotide 4, position 4 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
