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 [10] // Initial node U33 - A47 from junction 
ClusterNode  | Deletion Probability [0.0000000000031250] | Num Left Bases [4] | Num Right Bases [1] | Left Index [1] | Right Index [10] | Norm Constant [0.251650942015211] // Cluster node U33:C36 and A47:A47
Interaction  | Interacting Bases [1,5] | Pair Probability [[0.008836923,0.021444779,0.009444062,0.231391450,0.000000000],[0.021450321,0.009062771,0.185760612,0.009937356,0.000000000],[0.009444083,0.185759190,0.002069769,0.024746647,0.000000000],[0.231401709,0.009937264,0.024751992,0.014561070,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U33 - A47 cWW 
Interaction  | Interacting Bases [4,5] | Pair Probability [[0.011432356,0.021811391,0.011494353,0.016673006,0.000000000],[0.228765464,0.193675299,0.188597845,0.228798602,0.000000000],[0.014037200,0.009841650,0.018209719,0.008628830,0.000000000],[0.013451764,0.014992714,0.009651048,0.009938760,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction C36 - A47 cWS 
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.171875000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.328125000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.015625000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.484375000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion A34
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.062500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.812500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.062500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.062500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion C35
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 [9] // New Initial node after Cluster
ClusterNode  | Deletion Probability [0.0000000000031250] | Num Left Bases [1] | Num Right Bases [4] | Left Index [5] | Right Index [9] | Norm Constant [0.257704817211151] // Cluster node C37:C37 and G43:C46
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.009652285,0.016556223,0.011218237,0.185136336,0.000000000],[0.019989741,0.008244143,0.263484907,0.013400077,0.000000000],[0.011361251,0.200559255,0.002068811,0.022890146,0.000000000],[0.186211624,0.012765515,0.026535995,0.009925452,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction C37 - G43 cWW 
Interaction  | Interacting Bases [2,5] | Pair Probability [[0.193309940,0.027745336,0.002379316,0.076728268,0.000000000],[0.055696564,0.025093188,0.025457850,0.017196014,0.000000000],[0.064841819,0.294535384,0.002379316,0.010117074,0.000000000],[0.022532745,0.014381501,0.157640183,0.009965502,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G43 - C46 tSW 
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.812500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.062500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.062500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.062500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion A44
Interaction  | Interacting Bases [4,4] | Pair Probability [[0.796875000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.015625000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.015625000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.171875000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion A45
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 [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
