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 [21] // Initial node
BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.009401513,0.017549866,0.010782207,0.195587161,0.000000000],[0.019107025,0.009484786,0.232344244,0.013401212,0.000000000],[0.010842591,0.210218542,0.002049451,0.023823814,0.000000000],[0.196851077,0.013154215,0.025444740,0.009957556,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [21] // Basepair C1168 - G1074 cWW 
BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.042857649,0.045370598,0.000514478,0.002424734,0.000000000],[0.043176051,0.045265538,0.000514478,0.000514478,0.000000000],[0.398595795,0.003601343,0.017605820,0.305668340,0.000000000],[0.047840582,0.045021164,0.000514478,0.000514478,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [20] // Basepair G1169 - A1073 tSH 
BasepairNode | Deletion Probability [0.0000001215781528] | Pair Probability [[0.767445428,0.083662994,0.004992951,0.005094001,0.000000000],[0.091617979,0.000148772,0.012682939,0.001413647,0.000000000],[0.005192160,0.012520853,0.000371335,0.000148772,0.000000000],[0.007073299,0.007337324,0.000148772,0.000148772,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.012187690,0.975015235,0.012187690,0.000609385] | Left Letter Distribution [0.750000000,0.083333333,0.083333333,0.083333333,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [19] // Basepair A1170 - A1072 tHH 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.583333333,0.083333333,0.250000000,0.083333333,0.000000000] | Position [1] | Left Index [4] | Right Index [18] // Fixed node on left for 4WF9|1|X|A|1071
InitialNode  | Left Length Distribution [0.995990040,0.003999960,0.000010000] | 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 [18] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.750000000,0.083333333,0.083333333,0.083333333,0.000000000] | Position [1] | Left Index [5] | Right Index [18] // Fixed node on left for 4WF9|1|X|A|1072
InitialNode  | Left Length Distribution [0.496627836,0.496627836,0.006437768,0.000306560] | Left Letter Distribution [0.125000000,0.125000000,0.125000000,0.625000000,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [6] | Right Index [18] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.583333333,0.083333333,0.083333333,0.250000000,0.000000000] | Position [2] | Left Index [6] | Right Index [18] // Fixed node on right for 4WF9|1|X|C|1178
InitialNode  | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [6] | Right Index [17] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.250000000,0.083333333,0.250000000,0.416666667,0.000000000] | Position [2] | Left Index [6] | Right Index [17] // Fixed node on right for 4WF9|1|X|A|1177
InitialNode  | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [6] | Right Index [16] // New Initial node after Fixed node
ClusterNode  | Deletion Probability [0.000000000000000000000008744450558789937820511531234700380977] | Num Left Bases [8] | Num Right Bases [1] | Left Index [6] | Right Index [16] | Norm Constant [1.000000000000000] // Cluster node 4WF9|1|X|G|1175:4WF9|1|X|G|1183 and 4WF9|1|X|G|1069:4WF9|1|X|G|1069
Interaction  | Interacting Bases [8,9] | Pair Probability [[0.344802048,0.021791490,0.003728686,0.017846250,0.000000000],[0.043205333,0.014077990,0.012049275,0.014040701,0.000000000],[0.003728686,0.011140973,0.411330104,0.018428277,0.000000000],[0.019015698,0.014180515,0.032771384,0.017862592,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4WF9|1|X|G|1183 - 4WF9|1|X|G|1069 tWW 
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.070701762,0.072041852,0.003961084,0.070405509,0.000000000],[0.052783485,0.079545637,0.000877051,0.070553105,0.000000000],[0.061772277,0.000877051,0.075351648,0.106935897,0.000000000],[0.178442123,0.071367748,0.000877051,0.083506721,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4WF9|1|X|G|1175 - 4WF9|1|X|U|1176 cSH 
Interaction  | Interacting Bases [4,7] | Pair Probability [[0.024038462,0.024038462,0.024038462,0.024038462,0.000000000],[0.168269231,0.168269231,0.206730769,0.168269231,0.000000000],[0.024038462,0.024038462,0.024038462,0.024038462,0.000000000],[0.024038462,0.024038462,0.024038462,0.024038462,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4WF9|1|X|C|1179 - 4WF9|1|X|G|1182 tWH 
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.416666667,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.083333333,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.083333333,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.416666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 4WF9|1|X|A|1177
Interaction  | Interacting Bases [5,5] | Pair Probability [[0.083333333,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.083333333,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.750000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.083333333,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 4WF9|1|X|G|1180
Interaction  | Interacting Bases [6,6] | Pair Probability [[0.083333333,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.083333333,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.750000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.083333333,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 4WF9|1|X|G|1181
Insertion    | Location [1] | Length Distribution [0.496627836,0.496627836,0.006437768,0.000306560] | Letter Distribution [0.125000000,0.125000000,0.625000000,0.125000000,0.000000000]// Insertion after nucleotide 6, position 1 in cluster node
Insertion    | Location [3] | Length Distribution [0.496627836,0.496627836,0.006437768,0.000306560] | Letter Distribution [0.375000000,0.375000000,0.125000000,0.125000000,0.000000000]// Insertion after nucleotide 8, position 3 in cluster node
InitialNode  | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [14] | Right Index [15] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009353183,0.016772504,0.010752635,0.194966481,0.000000000],[0.019886467,0.009525946,0.243418233,0.013525436,0.000000000],[0.010873390,0.199167485,0.002049567,0.023014932,0.000000000],[0.197494026,0.013031497,0.026256418,0.009911799,0.000000000],[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 [14] | Right Index [15] // Basepair C1184 - G1068 cWW 
HairpinNode  | Num Bases [1] | Left Index [15] | Right Index [15] | 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
