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 [9] // Initial node
ClusterNode  | Deletion Probability [0.0000000006250000] | Num Left Bases [1] | Num Right Bases [3] | Left Index [1] | Right Index [9] | Norm Constant [0.017343279517751] // Cluster node 5K7D|1|A|G|33:5K7D|1|A|G|33 and 5K7D|1|A|A|39:5K7D|1|A|C|41
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.008525149,0.008525149,0.008525149,0.008525149,0.000000000],[0.008525149,0.008525149,0.008525149,0.008525149,0.000000000],[0.872122762,0.008525149,0.008525149,0.008525149,0.000000000],[0.008525149,0.008525149,0.008525149,0.008525149,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5K7D|1|A|G|33 - 5K7D|1|A|A|39 wat 
Interaction  | Interacting Bases [1,3] | Pair Probability [[0.034904092,0.027881299,0.019643132,0.024833736,0.000000000],[0.017270646,0.017645157,0.004018083,0.020851658,0.000000000],[0.004018083,0.004018083,0.421416153,0.004018083,0.000000000],[0.362655466,0.004018083,0.028790164,0.004018083,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5K7D|1|A|G|33 - 5K7D|1|A|G|40 tHS 
Interaction  | Interacting Bases [1,4] | Pair Probability [[0.004794140,0.049922383,0.005459246,0.099156600,0.000000000],[0.008421037,0.023505677,0.099996800,0.006542775,0.000000000],[0.005398618,0.534124901,0.001029034,0.013182663,0.000000000],[0.097887586,0.033953843,0.011555197,0.005069499,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5K7D|1|A|G|33 - 5K7D|1|A|C|41 cWW 
Interaction  | Interacting Bases [3,4] | Pair Probability [[0.061274510,0.061274510,0.061274510,0.061274510,0.000000000],[0.061274510,0.061274510,0.061274510,0.061274510,0.000000000],[0.061274510,0.080882353,0.061274510,0.061274510,0.000000000],[0.061274510,0.061274510,0.061274510,0.061274510,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5K7D|1|A|G|40 - 5K7D|1|A|C|41 cSH 
InitialNode  | Left Length Distribution [0.991950402,0.007999600,0.000049998] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [6] // New Initial node after Cluster
HairpinNode  | Num Bases [5] | Left Index [2] | Right Index [6] | Norm Constant [1.000000000000000] // Hairpin node C34:A38
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.125000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.625000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.125000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.125000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C34
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.125000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.375000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.125000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.375000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C35
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.125000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.625000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.125000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.125000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C36
Interaction  | Interacting Bases [4,4] | Pair Probability [[0.375000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.125000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.125000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.375000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U37
Interaction  | Interacting Bases [5,5] | Pair Probability [[0.625000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.125000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.125000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.125000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A38
