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 [7] // Initial node G2090 - C2654 from junction 
BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.009999033,0.020370037,0.011577394,0.189754219,0.000000000],[0.016871198,0.008244913,0.204374808,0.013008374,0.000000000],[0.011431659,0.249278495,0.002108170,0.027040831,0.000000000],[0.188658474,0.013655008,0.023325621,0.010301767,0.000000000],[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 [7] // Basepair G2090 - C2654 cWW 
BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.073099660,0.013566290,0.254261759,0.019747840,0.000000000],[0.109871186,0.008445315,0.022286642,0.033898979,0.000000000],[0.267935052,0.020718493,0.003381916,0.014787046,0.000000000],[0.021584926,0.032759197,0.092206740,0.011448958,0.000000000],[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 [2] | Right Index [6] // Basepair G2091 - A2653 cWW 
ClusterNode  | Deletion Probability [0.0000000083639467] | Num Left Bases [2] | Num Right Bases [1] | Left Index [3] | Right Index [5] | Norm Constant [0.304182144042249] // Cluster node G2092:G2093 and U2652:U2652
Interaction  | Interacting Bases [2,3] | Pair Probability [[0.012859560,0.163244755,0.012935470,0.131630069,0.000000000],[0.016240342,0.010006059,0.116966177,0.013339541,0.000000000],[0.012725945,0.131450502,0.002747355,0.202165325,0.000000000],[0.116454854,0.014335429,0.019049889,0.023848728,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G2093 - U2652 cWW 
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.015344910,0.030433764,0.296966426,0.058619023,0.000000000],[0.022451578,0.020314918,0.003176647,0.019513038,0.000000000],[0.020835054,0.023314026,0.321313666,0.024246955,0.000000000],[0.095511653,0.026522551,0.003176647,0.018259145,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G2092 - G2093 cSH 
Insertion    | Location [1] | Length Distribution [0.496627836,0.496627836,0.006437768,0.000306560] | Letter Distribution [0.125000000,0.375000000,0.125000000,0.375000000,0.000000000]// Insertion after nucleotide 3, position 1 in cluster node
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
