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 [13] // Initial node
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.009302401,0.017228733,0.010673661,0.193601472,0.000000000],[0.019079457,0.009402609,0.239944194,0.013298189,0.000000000],[0.010745430,0.207932060,0.002029955,0.023436685,0.000000000],[0.195103670,0.013004627,0.025363199,0.009853658,0.000000000],[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 [13] // Basepair C2774 - G2640 cWW 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.175495676,0.058412380,0.001557052,0.008766466,0.000000000],[0.144118215,0.087227536,0.001557052,0.001557052,0.000000000],[0.157536047,0.001557052,0.011528291,0.067142422,0.000000000],[0.141754217,0.138676440,0.001557052,0.001557052,0.000000000],[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 [12] // Basepair A2775 - A2639 tSH 
ClusterNode  | Deletion Probability [0.000000000000015625000000000002841172490091166211760239940914] | Num Left Bases [4] | Num Right Bases [2] | Left Index [3] | Right Index [11] | Norm Constant [1.000000000000000] // Cluster node 9DFE|1|1A|A|2776:9DFE|1|1A|U|2779 and 9DFE|1|1A|U|2637:9DFE|1|1A|G|2638
Interaction  | Interacting Bases [1,5] | Pair Probability [[0.018239161,0.040590873,0.004036356,0.451254601,0.000000000],[0.004036356,0.325253122,0.009675411,0.004036356,0.000000000],[0.018944354,0.004036356,0.030696143,0.023418451,0.000000000],[0.004036356,0.004036356,0.017952320,0.039757431,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 9DFE|1|1A|A|2776 - 9DFE|1|1A|U|2637 tHW 
Interaction  | Interacting Bases [3,6] | Pair Probability [[0.042449481,0.042764850,0.404323454,0.047384957,0.000000000],[0.044938497,0.044834438,0.003567044,0.044592391,0.000000000],[0.000509578,0.000509578,0.017438145,0.000509578,0.000000000],[0.002401641,0.000509578,0.302757213,0.000509578,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 9DFE|1|1A|A|2778 - 9DFE|1|1A|G|2638 tHS 
Interaction  | Interacting Bases [2,4] | Pair Probability [[0.107905056,0.076576891,0.004210435,0.074837539,0.000000000],[0.056106208,0.084553040,0.000932262,0.074994427,0.000000000],[0.065660845,0.000932262,0.080095038,0.131321409,0.000000000],[0.076318502,0.075860352,0.000932262,0.088763474,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 9DFE|1|1A|G|2777 - 9DFE|1|1A|U|2779 cSH 
InitialNode  | Left Length Distribution [0.009799118,0.979911808,0.009799118,0.000489956] | Left Letter Distribution [0.071428571,0.071428571,0.785714286,0.071428571,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [7] | Right Index [9] // Initial node 9DFE|1|1A|A|2781 - 9DFE|1|1A|U|2636 from node 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.785714286,0.071428571,0.071428571,0.071428571,0.000000000] | Position [1] | Left Index [7] | Right Index [9] // Fixed node on left for 9DFE|1|1A|A|2775
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 [8] | Right Index [9] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.013014590,0.180919726,0.012652091,0.127527180,0.000000000],[0.014642007,0.011163253,0.100124894,0.013557813,0.000000000],[0.012425479,0.124456353,0.002702851,0.228073272,0.000000000],[0.098546273,0.014528472,0.017508174,0.028157569,0.000000000],[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 [8] | Right Index [9] // Basepair G2782 - U2636 cWW 
HairpinNode  | Num Bases [1] | Left Index [9] | Right Index [9] | 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
