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 [5] // Initial node C2540 - G2523 from junction 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.008928161,0.017727990,0.010179535,0.195813486,0.000000000],[0.017922262,0.007857997,0.240697863,0.011633022,0.000000000],[0.010199025,0.222163351,0.001940544,0.023068404,0.000000000],[0.186561134,0.011546440,0.023304029,0.010456756,0.000000000],[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 [5] // Basepair C2540 - G2523 cWW 
ClusterNode  | Deletion Probability [0.0000000047265970] | Num Left Bases [2] | Num Right Bases [1] | Left Index [2] | Right Index [4] | Norm Constant [0.272916602183047] // Cluster node A2541:G2543 and U2522:U2522
Interaction  | Interacting Bases [1,3] | Pair Probability [[0.047861494,0.037204399,0.025318111,0.379123165,0.000000000],[0.020754977,0.013941450,0.003260258,0.003260258,0.000000000],[0.015524934,0.003260258,0.304157596,0.019139174,0.000000000],[0.016587056,0.059970649,0.003260258,0.047375963,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A2541 - U2522 tSH 
Interaction  | Interacting Bases [2,3] | Pair Probability [[0.011612063,0.139581923,0.011799549,0.134195131,0.000000000],[0.015546252,0.009111562,0.123260216,0.012306578,0.000000000],[0.011634189,0.144484349,0.002483712,0.209875301,0.000000000],[0.121820287,0.013096746,0.018395376,0.020796766,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G2543 - U2522 cWW 
Insertion    | Location [1] | Length Distribution [0.384519277,0.612937839,0.002425294,0.000117590] | Letter Distribution [0.650000000,0.150000000,0.050000000,0.150000000,0.000000000]// Insertion after nucleotide 2, 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 [4] | Right Index [3] // New Initial node after Cluster
HairpinNode  | Num Bases [1] | Left Index [4] | Right Index [4] | 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
