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 [0.0000229437914523] | Pair Probability [[0.010140241,0.015764366,0.012093842,0.116797878,0.000000000],[0.162291053,0.018891209,0.119667900,0.013539516,0.000000000],[0.012259791,0.115792992,0.002675199,0.018859777,0.000000000],[0.155112826,0.012526856,0.201758582,0.011827971,0.000000000],[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 [7] // Basepair U36 - G23 cWW 
ClusterNode  | Deletion Probability [0.000000000000000978949038075334833545058088525186675539296009] | Num Left Bases [3] | Num Right Bases [2] | Left Index [2] | Right Index [6] | Norm Constant [0.259979854819330] // Cluster node 6CK5|1|A|G|37:6CK5|1|A|G|41 and 6CK5|1|A|C|21:6CK5|1|A|A|22
Interaction  | Interacting Bases [3,4] | 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]] // Cluster Interaction 6CK5|1|A|G|41 - 6CK5|1|A|C|21 cWW 
Interaction  | Interacting Bases [2,5] | Pair Probability [[0.107143513,0.015949783,0.009009170,0.178473784,0.000000000],[0.020039957,0.008937886,0.179074258,0.010040818,0.000000000],[0.009026741,0.176782451,0.001858409,0.020952313,0.000000000],[0.195644824,0.009431421,0.048449592,0.009185080,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 6CK5|1|A|U|39 - 6CK5|1|A|A|22 cWW 
Interaction  | Interacting Bases [1,3] | Pair Probability [[0.001267184,0.001267184,0.013032297,0.010735378,0.000000000],[0.001267184,0.013431632,0.001267184,0.004570270,0.000000000],[0.263446768,0.006335920,0.653199885,0.006335920,0.000000000],[0.004379672,0.001267184,0.003964044,0.014232292,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 6CK5|1|A|G|37 - 6CK5|1|A|G|41 cWH 
Insertion    | Location [1] | Length Distribution [0.023781213,0.951248514,0.023781213,0.001189061] | Letter Distribution [0.125000000,0.375000000,0.125000000,0.375000000,0.000000000]// Insertion after nucleotide 2, position 1 in cluster node
Insertion    | Location [2] | Length Distribution [0.493381468,0.493381468,0.012635379,0.000601685] | Letter Distribution [0.166666667,0.500000000,0.166666667,0.166666667,0.000000000]// Insertion after nucleotide 3, position 2 in cluster node
InitialNode  | Left Length Distribution [0.952380952,0.047619048] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.952380952,0.047619048] | 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
