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 [9] // Initial node G1401 - C1501 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 [9] // Basepair G1401 - C1501 cWW 
BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.011872772,0.014708582,0.014301144,0.033757857,0.000000000],[0.399542582,0.017945751,0.034889197,0.016036878,0.000000000],[0.014645019,0.028896488,0.003610810,0.015133880,0.000000000],[0.041074697,0.014455142,0.324408656,0.014720545,0.000000000],[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 [8] // Basepair C1402 - A1500 cWW 
ClusterNode  | Deletion Probability [0.0000001250000000] | Num Left Bases [1] | Num Right Bases [2] | Left Index [3] | Right Index [7] | Norm Constant [0.326407563543262] // Cluster node C1403:C1403 and U1498:A1499
Interaction  | Interacting Bases [1,3] | Pair Probability [[0.177419266,0.022538031,0.009786791,0.007644646,0.000000000],[0.238046717,0.018024818,0.009854628,0.008394557,0.000000000],[0.172050331,0.019796743,0.093017756,0.006569858,0.000000000],[0.180923828,0.019886693,0.009052772,0.006992564,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction C1403 - A1499 cSW 
Interaction  | Interacting Bases [2,3] | Pair Probability [[0.021745117,0.127570845,0.025990805,0.016040998,0.000000000],[0.031117562,0.014978621,0.002550147,0.017709157,0.000000000],[0.011100813,0.205739968,0.053341346,0.018363188,0.000000000],[0.293476277,0.144133058,0.002550147,0.013591951,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U1498 - A1499 cSH 
InitialNode  | 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 [4] | Right Index [5] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009837906,0.016874612,0.011433973,0.188696651,0.000000000],[0.020374159,0.008402684,0.249321155,0.013657771,0.000000000],[0.011579737,0.204416164,0.002108596,0.023330341,0.000000000],[0.189792617,0.013011006,0.027046303,0.010116326,0.000000000],[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 C1404 - G1497 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
