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 [6] // Initial node
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.007705814,0.014839876,0.008790270,0.155389627,0.000000000],[0.023809383,0.008301058,0.229841017,0.010553458,0.000000000],[0.008791465,0.253458850,0.001707631,0.019700595,0.000000000],[0.197190366,0.010458354,0.041176743,0.008285493,0.000000000],[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 [6] // Basepair U751 - A655 cWW 
ClusterNode  | Deletion Probability [0.0000000006250000] | Num Left Bases [3] | Num Right Bases [1] | Left Index [2] | Right Index [5] | Norm Constant [0.269834917482945] // Cluster node 4LFB|1|A|G|752:4LFB|1|A|C|754 and 4LFB|1|A|G|654:4LFB|1|A|G|654
Interaction  | Interacting Bases [1,4] | Pair Probability [[0.049969097,0.033434352,0.026086782,0.137906964,0.000000000],[0.032069949,0.023767963,0.002385199,0.002385199,0.000000000],[0.144696098,0.002385199,0.224189228,0.158804201,0.000000000],[0.094603355,0.050695225,0.014235990,0.002385199,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4LFB|1|A|G|752 - 4LFB|1|A|G|654 tSH 
Interaction  | Interacting Bases [3,4] | Pair Probability [[0.007536218,0.016378002,0.008226958,0.226355717,0.000000000],[0.022037854,0.010650771,0.320218524,0.014309867,0.000000000],[0.004712413,0.090038483,0.000933994,0.015002766,0.000000000],[0.214217315,0.008820279,0.032391549,0.008169291,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4LFB|1|A|C|754 - 4LFB|1|A|G|654 cWW 
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.500000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.017241379,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.017241379,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.465517241,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 4LFB|1|A|A|753
InitialNode  | Left Length Distribution [0.998007243,0.001900449,0.000092308] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.998007243,0.001900449,0.000092308] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [4] // New Initial node after Cluster
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
