Character Definition | A,C,G,U,* // Identity and order of characters in matrices
InitialNode  | Left Length Distribution [0.999900000,0.000100000] | Left Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Right Length Distribution [0.999900000,0.000100000] | Right Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Left Index [1] | Right Index [10] // Initial node
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.008660927,0.020132690,0.009277219,0.263590965,0.000000000],[0.016863721,0.008991154,0.181989365,0.009764926,0.000000000],[0.009263175,0.183821034,0.001910391,0.046659830,0.000000000],[0.193482797,0.010251972,0.024683320,0.010656514,0.000000000],[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 [10] // Basepair A30 - U40 cWW 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.014436950,0.264791255,0.012889761,0.022512775,0.000000000],[0.015956256,0.017204790,0.019243046,0.014149980,0.000000000],[0.012620538,0.019602827,0.003979087,0.050833588,0.000000000],[0.019666410,0.015324417,0.016310825,0.480477495,0.000000000],[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 [2] | Right Index [9] // Basepair U31 - U39 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.227272727,0.045454545,0.681818182,0.045454545,0.000000000] | Position [1] | Left Index [3] | Right Index [8] // Fixed node on left for 4LX6|1|A|G|32
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 [8] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.045454545,0.045454545,0.863636364,0.045454545,0.000000000] | Position [2] | Left Index [4] | Right Index [8] // Fixed node on right for 4LX6|1|A|G|37
InitialNode  | Left Length Distribution [1.000000000] | 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 [4] | Right Index [7] // New Initial node after Fixed node
ClusterNode  | Deletion Probability [0.0000001250000000] | Num Left Bases [2] | Num Right Bases [1] | Left Index [4] | Right Index [7] | Norm Constant [0.254903752478470] // Cluster node 4LX6|1|A|A|33:4LX6|1|A|U|34 and 4LX6|1|A|G|37:4LX6|1|A|G|37
Interaction  | Interacting Bases [1,3] | Pair Probability [[0.073792229,0.076245171,0.177564044,0.075112783,0.000000000],[0.080050626,0.075296342,0.003143338,0.069039891,0.000000000],[0.071753000,0.003078342,0.006839640,0.071214051,0.000000000],[0.066559058,0.018358256,0.057161984,0.074791246,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4LX6|1|A|A|33 - 4LX6|1|A|G|37 cSS 
Interaction  | Interacting Bases [2,3] | Pair Probability [[0.069829061,0.072864383,0.073175033,0.067175553,0.000000000],[0.079179257,0.070983057,0.003192756,0.062386608,0.000000000],[0.067697012,0.003241272,0.007248810,0.063576568,0.000000000],[0.069848860,0.064138152,0.160061465,0.065402151,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4LX6|1|A|U|34 - 4LX6|1|A|G|37 cSS 
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 [0.005492996,0.988739357,0.005492996,0.000274650] | Right Letter Distribution [0.045454545,0.045454545,0.045454545,0.863636364,0.000000000] | Left Index [6] | Right Index [6] // New Initial node after Cluster
HairpinNode  | Num Bases [1] | Left Index [6] | Right Index [6] | Norm Constant [1.000000000000000] // Hairpin node A35:A35
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.772727273,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.045454545,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.136363636,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.045454545,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A35
