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 [6] // Initial node A144 - U122 from junction 
BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.009264210,0.022192915,0.010074369,0.234029155,0.000000000],[0.019865957,0.008943928,0.203731184,0.010973984,0.000000000],[0.010098514,0.193326205,0.002107237,0.026270642,0.000000000],[0.199529587,0.010865754,0.024111426,0.014614932,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [6] // Basepair A144 - U122 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.583333333,0.083333333,0.250000000,0.083333333,0.000000000] | Position [1] | Left Index [2] | Right Index [5] // Fixed node on left
InitialNode  | Left Length Distribution [0.000000000,0.012187690,0.975015235,0.012187690,0.000609385] | Left Letter Distribution [0.150000000,0.050000000,0.250000000,0.550000000,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [5] // New Initial node after Fixed node
ClusterNode  | Deletion Probability [0.0000001250000000] | Num Left Bases [2] | Num Right Bases [1] | Left Index [3] | Right Index [5] | Norm Constant [0.259243905872397] // Cluster node G148:U149 and A121:A121
Interaction  | Interacting Bases [2,3] | Pair Probability [[0.008973807,0.020802927,0.009627934,0.214768857,0.000000000],[0.022945963,0.009293412,0.189732133,0.010152995,0.000000000],[0.009636163,0.189182448,0.002110966,0.024208445,0.000000000],[0.237966914,0.010117212,0.026275422,0.014204402,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U149 - A121 cWW 
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.076779974,0.079320859,0.012294084,0.010181688,0.000000000],[0.074799046,0.092378832,0.002581015,0.088429265,0.000000000],[0.192506263,0.010059924,0.020642474,0.156176861,0.000000000],[0.013567760,0.076991426,0.002581015,0.090709515,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G148 - U149 cSH 
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 [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
