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 [8] // Initial node C44 - G35 from junction 
BasepairNode | Deletion Probability [0.0000006691671388] | Pair Probability [[0.009987650,0.018214897,0.011593253,0.190884602,0.000000000],[0.019392976,0.008431163,0.230141683,0.013571804,0.000000000],[0.011642323,0.218263837,0.002128924,0.024805687,0.000000000],[0.191253546,0.013354078,0.026056620,0.010276957,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.334863624,0.653524170,0.011072104,0.000540103] | Right Letter Distribution [0.125000000,0.125000000,0.125000000,0.625000000,0.000000000] | Left Index [1] | Right Index [8] // Basepair C44 - G35 cWW 
BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.024494901,0.005137156,0.025198876,0.005137156,0.000000000],[0.051027214,0.042650770,0.034099640,0.005137156,0.000000000],[0.005137156,0.061077979,0.060120855,0.023963331,0.000000000],[0.533133053,0.005137156,0.063374730,0.055172872,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [7] // Basepair U45 - A33 tWH 
ClusterNode  | Deletion Probability [0.0000000006250000] | Num Left Bases [3] | Num Right Bases [1] | Left Index [3] | Right Index [6] | Norm Constant [1.000000000000000] // Cluster node A46:G48 and U32:U32
Interaction  | Interacting Bases [3,4] | Pair Probability [[0.014258858,0.211706755,0.014176550,0.093357766,0.000000000],[0.015234759,0.010399964,0.094014042,0.014566320,0.000000000],[0.013899989,0.109909176,0.002989625,0.256526531,0.000000000],[0.088532666,0.015883070,0.017860543,0.026683387,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G48 - U32 cWW 
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.200798898,0.109046156,0.005514295,0.004779221,0.000000000],[0.112505714,0.106108705,0.001254406,0.110620571,0.000000000],[0.005863261,0.005663708,0.006339676,0.104975229,0.000000000],[0.010696325,0.108492360,0.001254406,0.106087070,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A46 - A47 cSH 
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
