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 [10] // Initial node
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.008469224,0.016757220,0.009371274,0.200342005,0.000000000],[0.019057480,0.008962697,0.210572595,0.010722865,0.000000000],[0.009408594,0.181223228,0.001889386,0.026323806,0.000000000],[0.239733866,0.010372485,0.037266864,0.009526410,0.000000000],[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 [10] // Basepair C1004 - G1151 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.038461538,0.423076923,0.500000000,0.038461538,0.000000000] | Position [1] | Left Index [2] | Right Index [9] // Fixed node on left for 9DFE|1|1A|C|1005
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 [3] | Right Index [9] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.038461538,0.576923077,0.346153846,0.038461538,0.000000000] | Position [1] | Left Index [3] | Right Index [9] // Fixed node on left for 9DFE|1|1A|C|1006
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 [4] | Right Index [9] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.038461538,0.730769231,0.192307692,0.038461538,0.000000000] | Position [1] | Left Index [4] | Right Index [9] // Fixed node on left for 9DFE|1|1A|C|1007
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 [5] | Right Index [9] // New Initial node after Fixed node
ClusterNode  | Deletion Probability [0.0000000000031250] | Num Left Bases [4] | Num Right Bases [1] | Left Index [5] | Right Index [9] | Norm Constant [1.000000000000000] // Cluster node 9DFE|1|1A|C|1008:9DFE|1|1A|G|1011 and 9DFE|1|1A|C|1150:9DFE|1|1A|C|1150
Interaction  | Interacting Bases [4,5] | Pair Probability [[0.008760916,0.018679442,0.009774356,0.221544309,0.000000000],[0.016382900,0.008810829,0.202616130,0.011314118,0.000000000],[0.009737063,0.231963022,0.001903876,0.032881708,0.000000000],[0.182158848,0.011663940,0.021961941,0.009846602,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 9DFE|1|1A|G|1011 - 9DFE|1|1A|C|1150 cWW 
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.118712360,0.094803052,0.004990382,0.024169785,0.000000000],[0.148107514,0.092360640,0.001063811,0.008632871,0.000000000],[0.008920351,0.001063811,0.125394814,0.073914129,0.000000000],[0.119934972,0.090951714,0.001063811,0.085915982,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 9DFE|1|1A|C|1008 - 9DFE|1|1A|A|1009 cSH 
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.884615385,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.038461538,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.038461538,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.038461538,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 9DFE|1|1A|A|1010
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 [9] | Right Index [8] // New Initial node after Cluster
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
