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 [7] // Initial node
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.008897843,0.016739593,0.010199678,0.185036135,0.000000000],[0.017917438,0.008959651,0.255758750,0.012646747,0.000000000],[0.010245353,0.217205367,0.001937640,0.022677285,0.000000000],[0.185992170,0.012459917,0.023903365,0.009423069,0.000000000],[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 [7] // Basepair C44 - G58 cWW 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.046967002,0.014536140,0.105980053,0.395526003,0.000000000],[0.017410647,0.014569211,0.003500715,0.003500715,0.000000000],[0.016498878,0.003500715,0.315959935,0.021245930,0.000000000],[0.017220735,0.016581893,0.003500715,0.003500715,0.000000000],[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 [2] | Right Index [6] // Basepair A45 - U57 tSH 
ClusterNode  | Deletion Probability [0.0000000419957704] | Num Left Bases [2] | Num Right Bases [1] | Left Index [3] | Right Index [5] | Norm Constant [0.251944856311106] // Cluster node 5FJC|1|A|A|46:5FJC|1|A|C|47 and 5FJC|1|A|G|56:5FJC|1|A|G|56
Interaction  | Interacting Bases [2,3] | Pair Probability [[0.009941414,0.069110789,0.010496330,0.191906093,0.000000000],[0.016819060,0.009540080,0.203113054,0.011946947,0.000000000],[0.010491161,0.156573618,0.002138385,0.104033421,0.000000000],[0.154674638,0.012146236,0.021483980,0.015584793,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5FJC|1|A|C|47 - 5FJC|1|A|G|56 cWW 
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.098653659,0.156748817,0.004663545,0.031576760,0.000000000],[0.085523153,0.083479635,0.000966041,0.007634808,0.000000000],[0.008097881,0.000966041,0.086188950,0.079045931,0.000000000],[0.140302093,0.085781856,0.052205711,0.078165119,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5FJC|1|A|A|46 - 5FJC|1|A|C|47 cSH 
Insertion    | Location [1] | Length Distribution [0.894854586,0.004971414,0.099652001,0.000497141,0.000024857] | Letter Distribution [0.375000000,0.375000000,0.125000000,0.125000000,0.000000000]// Insertion after nucleotide 3, 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 [5] | Right Index [4] // New Initial node after Cluster
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
