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 [12] // Initial node
ClusterNode  | Deletion Probability [0.000000000000000000001948010068092961341050756773210484931265] | Num Left Bases [5] | Num Right Bases [3] | Left Index [1] | Right Index [12] | Norm Constant [0.033621768617430] // Cluster node 6UFM|1|B|C|3:6UFM|1|B|A|8 and 6UFM|1|B|G|25:6UFM|1|B|G|27
Interaction  | Interacting Bases [5,6] | Pair Probability [[0.039531668,0.039825360,0.425090578,0.064305282,0.000000000],[0.041849598,0.041752691,0.003321859,0.041527282,0.000000000],[0.000474551,0.000474551,0.016239515,0.000474551,0.000000000],[0.002236562,0.000474551,0.281946850,0.000474551,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 6UFM|1|B|A|8 - 6UFM|1|B|G|25 tHS 
Interaction  | Interacting Bases [2,7] | Pair Probability [[0.111101318,0.052400834,0.054200741,0.049388083,0.000000000],[0.028255171,0.019164262,0.118559039,0.019164262,0.000000000],[0.206476690,0.019164262,0.129550183,0.106827196,0.000000000],[0.028255171,0.019164262,0.019164262,0.019164262,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 6UFM|1|B|G|4 - 6UFM|1|B|A|26 tSS 
Interaction  | Interacting Bases [4,7] | Pair Probability [[0.067003226,0.070931945,0.000804329,0.003790805,0.000000000],[0.067501012,0.070767696,0.000804329,0.000804329,0.000000000],[0.342472894,0.002515638,0.012298155,0.213517844,0.000000000],[0.074793495,0.070385643,0.000804329,0.000804329,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 6UFM|1|B|G|7 - 6UFM|1|B|A|26 tSH 
Interaction  | Interacting Bases [1,8] | Pair Probability [[0.008843009,0.015857640,0.010166128,0.184331946,0.000000000],[0.018801751,0.009006349,0.284686329,0.012787685,0.000000000],[0.010280296,0.188303804,0.001937772,0.021759572,0.000000000],[0.186721625,0.012320688,0.024824249,0.009371156,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 6UFM|1|B|C|3 - 6UFM|1|B|G|27 cWW 
Interaction  | Interacting Bases [5,8] | Pair Probability [[0.168972788,0.168568456,0.301674653,0.159859182,0.000000000],[0.001734057,0.001734057,0.017968699,0.001734057,0.000000000],[0.013596605,0.001734057,0.014161773,0.141325392,0.000000000],[0.001734057,0.001734057,0.001734057,0.001734057,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 6UFM|1|B|A|8 - 6UFM|1|B|G|27 tSS 
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.375000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.041666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.125000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.458333333,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 6UFM|1|B|A|5
Insertion    | Location [3] | Length Distribution [0.004949270,0.989853997,0.004949270,0.000247463] | Letter Distribution [0.291666667,0.291666667,0.208333333,0.208333333,0.000000000]// Insertion after nucleotide 3, position 3 in cluster node
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 [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [6] | Right Index [9] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.015178830,0.010913304,0.316584574,0.042859977,0.000000000],[0.036613397,0.010759673,0.004270706,0.023132666,0.000000000],[0.000610101,0.000610101,0.109226680,0.000610101,0.000000000],[0.012748860,0.000610101,0.414660830,0.000610101,0.000000000],[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 [6] | Right Index [9] // Basepair U9 - G24 tHS 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.005096422,0.010158915,0.005769065,0.116017074,0.000000000],[0.040968590,0.019986131,0.492108108,0.028026816,0.000000000],[0.005775826,0.126921291,0.001109330,0.015878667,0.000000000],[0.106354829,0.006965885,0.013307720,0.005555333,0.000000000],[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 [7] | Right Index [8] // Basepair C10 - G23 cWW 
HairpinNode  | Num Bases [1] | Left Index [8] | Right Index [8] | 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
