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 [9] // Initial node
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.009733692,0.020271796,0.011084078,0.201320753,0.000000000],[0.017097495,0.009544863,0.203026637,0.013284001,0.000000000],[0.010960983,0.228535864,0.002089280,0.026765173,0.000000000],[0.198744233,0.013787510,0.023460879,0.010292763,0.000000000],[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 [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [9] // Basepair G4 - C30 cWW 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.029784876,0.014589866,0.379329069,0.017472527,0.000000000],[0.014247286,0.009703380,0.018872041,0.042407159,0.000000000],[0.345605520,0.019083979,0.003597212,0.015874647,0.000000000],[0.017438516,0.044806635,0.015534560,0.011652725,0.000000000],[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 [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [8] // Basepair A5 - G29 cWW 
BasepairNode | Deletion Probability [0.0000001182498160] | Pair Probability [[0.120391741,0.109966274,0.001336998,0.006576967,0.000000000],[0.120856821,0.113714611,0.001336998,0.001336998,0.000000000],[0.124325641,0.001336998,0.008263305,0.110995656,0.000000000],[0.153307608,0.123579390,0.001336998,0.001336998,0.000000000],[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 [0.023781213,0.951248514,0.023781213,0.001189061] | Right Letter Distribution [0.125000000,0.625000000,0.125000000,0.125000000,0.000000000] | Left Index [3] | Right Index [7] // Basepair U6 - A28 tSH 
ClusterNode  | Deletion Probability [0.0000001250000000] | Num Left Bases [2] | Num Right Bases [1] | Left Index [4] | Right Index [6] | Norm Constant [0.294300469160113] // Cluster node 8D28|1|B|A|7:8D28|1|B|C|8 and 8D28|1|B|G|26:8D28|1|B|G|26
Interaction  | Interacting Bases [2,3] | Pair Probability [[0.004694951,0.008419175,0.005397424,0.097865947,0.000000000],[0.049911347,0.023908359,0.534011162,0.033946338,0.000000000],[0.005458039,0.099974695,0.001028807,0.011552643,0.000000000],[0.099134681,0.006541329,0.013179748,0.004975356,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8D28|1|B|C|8 - 8D28|1|B|G|26 cWW 
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.103145582,0.133194674,0.005565984,0.043430123,0.000000000],[0.099556957,0.098312651,0.001135868,0.009226384,0.000000000],[0.009906224,0.001135868,0.103159102,0.093301337,0.000000000],[0.103522381,0.102278412,0.001135868,0.091992584,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8D28|1|B|A|7 - 8D28|1|B|C|8 cSH 
InitialNode  | 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 [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [6] | Right Index [5] // New Initial node after Cluster
HairpinNode  | Num Bases [1] | Left Index [6] | Right Index [6] | 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
