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 U247 - G227 from junction 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.012182087,0.013837615,0.014555837,0.036251835,0.000000000],[0.296622029,0.015030447,0.042347731,0.016343772,0.000000000],[0.014885271,0.036529467,0.003301533,0.014494165,0.000000000],[0.042704523,0.014752267,0.412722117,0.013439304,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | 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 [1] | Right Index [9] // Basepair U247 - G227 cWW 
ClusterNode  | Deletion Probability [0.0000000006250000] | Num Left Bases [1] | Num Right Bases [3] | Left Index [2] | Right Index [8] | Norm Constant [1.000000000000000] // Cluster node A248:A248 and U224:A226
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.024303886,0.050629295,0.005097095,0.592278346,0.000000000],[0.005097095,0.042318173,0.005097095,0.005097095,0.000000000],[0.025002371,0.033833725,0.059652023,0.062880524,0.000000000],[0.005097095,0.005097095,0.023776461,0.054742624,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A248 - U224 tHW 
Interaction  | Interacting Bases [3,4] | Pair Probability [[0.410544386,0.302233525,0.014876145,0.012827737,0.000000000],[0.042406868,0.039953161,0.000472966,0.041617784,0.000000000],[0.002226097,0.002186075,0.002779584,0.039725290,0.000000000],[0.006415640,0.041366531,0.000472966,0.039895244,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A225 - A226 cSH 
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 [3] | Right Index [5] // Initial node U249 - C223 from junction 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.045454545,0.045454545,0.045454545,0.863636364,0.000000000] | Position [1] | Left Index [3] | Right Index [5] // Fixed node on left
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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [5] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009540362,0.019435632,0.011046321,0.181049897,0.000000000],[0.016097290,0.007866706,0.194999817,0.012411659,0.000000000],[0.010907271,0.283715261,0.002011465,0.025800426,0.000000000],[0.180004416,0.013028632,0.022255638,0.009829209,0.000000000],[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 G250 - C223 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
