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 [6] // Initial node
ClusterNode  | Deletion Probability [0.0000000003110069] | Num Left Bases [3] | Num Right Bases [1] | Left Index [1] | Right Index [6] | Norm Constant [0.063001153906314] // Cluster node 3MXH|1|R|A|61:3MXH|1|R|A|63 and 3MXH|1|R|U|77:3MXH|1|R|U|77
Interaction  | Interacting Bases [1,4] | Pair Probability [[0.008874834,0.018163668,0.009886445,0.207536427,0.000000000],[0.018165448,0.009130305,0.208151098,0.011446284,0.000000000],[0.009886458,0.208149880,0.001951325,0.029866332,0.000000000],[0.207539466,0.011446018,0.029877333,0.009928679,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 3MXH|1|R|A|61 - 3MXH|1|R|U|77 cWW 
Interaction  | Interacting Bases [3,4] | Pair Probability [[0.170467240,0.166301040,0.136971357,0.205943433,0.000000000],[0.019820634,0.017474116,0.002085912,0.017096107,0.000000000],[0.072315416,0.002085912,0.148434418,0.009860109,0.000000000],[0.008027459,0.008438658,0.006786122,0.007892067,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 3MXH|1|R|A|63 - 3MXH|1|R|U|77 cWS 
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.119745586,0.094479268,0.004908919,0.020690521,0.000000000],[0.119288416,0.091354616,0.001054420,0.008300314,0.000000000],[0.008518046,0.001054420,0.087230987,0.130059640,0.000000000],[0.137288177,0.089788077,0.001054420,0.085184173,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 3MXH|1|R|A|61 - 3MXH|1|R|A|62 cSH 
Insertion    | Location [1] | Length Distribution [0.869396619,0.129517605,0.001046999,0.000038778] | Letter Distribution [0.166666667,0.500000000,0.166666667,0.166666667,0.000000000]// Insertion after nucleotide 1, 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 [4] | Right Index [5] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.008994017,0.016952215,0.010258508,0.188051808,0.000000000],[0.018608027,0.009147540,0.240841489,0.012580721,0.000000000],[0.010304402,0.210675231,0.001968173,0.022892025,0.000000000],[0.199180633,0.012323190,0.027633566,0.009588455,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | 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 [4] | Right Index [5] // Basepair C64 - G76 cWW 
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
