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 [8] // Initial node
ClusterNode  | Deletion Probability [0.0000000006250000] | Num Left Bases [3] | Num Right Bases [1] | Left Index [1] | Right Index [8] | Norm Constant [0.150830715907617] // Cluster node 4YAZ|1|R|G|77:4YAZ|1|R|A|79 and 4YAZ|1|R|C|7:4YAZ|1|R|C|7
Interaction  | Interacting Bases [1,4] | Pair Probability [[0.003823887,0.055746509,0.004354386,0.079088977,0.000000000],[0.006716761,0.026247934,0.079759134,0.005218628,0.000000000],[0.004306029,0.594150318,0.000820775,0.010514714,0.000000000],[0.078076789,0.037915021,0.009216620,0.004043518,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4YAZ|1|R|G|77 - 4YAZ|1|R|C|7 cWW 
Interaction  | Interacting Bases [3,4] | Pair Probability [[0.072613517,0.661332808,0.072526432,0.071135383,0.000000000],[0.007052045,0.043817479,0.000789426,0.006101741,0.000000000],[0.006592112,0.005525984,0.019547772,0.003493111,0.000000000],[0.002859431,0.021370678,0.002432038,0.002810043,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4YAZ|1|R|A|79 - 4YAZ|1|R|C|7 cWS 
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.051095468,0.056684490,0.007186864,0.119586646,0.000000000],[0.051807891,0.110499726,0.001396703,0.086880833,0.000000000],[0.102035962,0.001396703,0.074683770,0.106765195,0.000000000],[0.052960781,0.060245256,0.001396703,0.115377010,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4YAZ|1|R|G|77 - 4YAZ|1|R|A|78 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 [4] | Right Index [7] // Initial node 4YAZ|1|R|A|80 - 4YAZ|1|R|A|6 from node 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.375000000,0.375000000,0.125000000,0.125000000,0.000000000] | Position [1] | Left Index [4] | Right Index [7] // Fixed node on left for 4YAZ|1|R|C|7
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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [7] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.375000000,0.125000000,0.375000000,0.125000000,0.000000000] | Position [2] | Left Index [5] | Right Index [7] // Fixed node on right for 4YAZ|1|R|A|79
InitialNode  | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.493381468,0.493381468,0.012635379,0.000601685] | Right Letter Distribution [0.166666667,0.500000000,0.166666667,0.166666667,0.000000000] | Left Index [5] | Right Index [6] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009285457,0.017323068,0.010436779,0.197555258,0.000000000],[0.021160175,0.009772202,0.212782490,0.012417770,0.000000000],[0.010508004,0.198766713,0.002067002,0.023256875,0.000000000],[0.212699647,0.011830790,0.040032900,0.010104868,0.000000000],[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 [5] | Right Index [6] // Basepair U81 - A4 cWW 
HairpinNode  | Num Bases [1] | Left Index [6] | Right Index [6] | 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
