Character Definition | A,C,G,U,* // Define characters here
InitialNode  | 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 [1] | Right Index [19] // Initial node C4 - G28 from junction 
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.009631000,0.017270697,0.011072020,0.200757565,0.000000000],[0.020477154,0.009808895,0.220945507,0.013927182,0.000000000],[0.011196362,0.205083350,0.002110445,0.023698544,0.000000000],[0.203360186,0.013418572,0.027036311,0.010206209,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [19] // Basepair C4 - G28 cWW 
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.044130649,0.046718239,0.000529759,0.002496756,0.000000000],[0.044458508,0.046610059,0.000529759,0.000529759,0.000000000],[0.380732303,0.003708313,0.018128765,0.314747597,0.000000000],[0.049261589,0.046358426,0.000529759,0.000529759,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [18] // Basepair G5 - A27 tSH 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000] | Position [1] | Left Index [3] | Right Index [17] // Fixed node on left
InitialNode  | Left Length Distribution [0.989901010,0.009999000,0.000099990] | 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 [17] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.785714286,0.071428571,0.071428571,0.071428571,0.000000000] | Position [1] | Left Index [4] | Right Index [17] // Fixed node on left
InitialNode  | Left Length Distribution [0.989901010,0.009999000,0.000099990] | 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 [17] // New Initial node after Fixed node
ClusterNode  | Deletion Probability [0.000000000000000000000000000000000000000000016914241669249805] | Num Left Bases [7] | Num Right Bases [6] | Left Index [5] | Right Index [17] | Norm Constant [0.000246975673054] // Cluster node G8:G18 and G19:G26
Interaction  | Interacting Bases [5,8] | Pair Probability [[0.004966430,0.004966430,0.051077026,0.042074794,0.000000000],[0.004966430,0.052642128,0.004966430,0.017912101,0.000000000],[0.206503547,0.004966430,0.506544030,0.004966430,0.000000000],[0.017165095,0.004966430,0.015536138,0.055780127,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G14 - G19 cWH 
Interaction  | Interacting Bases [6,9] | Pair Probability [[0.004966430,0.004966430,0.206503547,0.017165095,0.000000000],[0.004966430,0.052642128,0.004966430,0.004966430,0.000000000],[0.051077026,0.004966430,0.506544030,0.015536138,0.000000000],[0.042074794,0.017912101,0.004966430,0.055780127,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G16 - G21 cHW 
Interaction  | Interacting Bases [7,10] | Pair Probability [[0.113862076,0.120538352,0.001366838,0.006441913,0.000000000],[0.114707989,0.120259235,0.001366838,0.001366838,0.000000000],[0.146584821,0.001366838,0.006682038,0.116012068,0.000000000],[0.127100484,0.119609993,0.001366838,0.001366838,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G18 - A22 tSH 
Interaction  | Interacting Bases [1,11] | Pair Probability [[0.004966430,0.004966430,0.206503547,0.017165095,0.000000000],[0.004966430,0.052642128,0.004966430,0.004966430,0.000000000],[0.051077026,0.004966430,0.506544030,0.015536138,0.000000000],[0.042074794,0.017912101,0.004966430,0.055780127,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G8 - G23 cHW 
Interaction  | Interacting Bases [7,11] | Pair Probability [[0.004966430,0.004966430,0.051077026,0.042074794,0.000000000],[0.004966430,0.052642128,0.004966430,0.017912101,0.000000000],[0.206503547,0.004966430,0.506544030,0.004966430,0.000000000],[0.017165095,0.004966430,0.015536138,0.055780127,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G18 - G23 cWH 
Interaction  | Interacting Bases [2,12] | Pair Probability [[0.004966430,0.004966430,0.206503547,0.017165095,0.000000000],[0.004966430,0.052642128,0.004966430,0.004966430,0.000000000],[0.051077026,0.004966430,0.506544030,0.015536138,0.000000000],[0.042074794,0.017912101,0.004966430,0.055780127,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G9 - G24 cHW 
Interaction  | Interacting Bases [3,13] | Pair Probability [[0.000933318,0.000933318,0.009598669,0.007906921,0.000000000],[0.000933318,0.009892791,0.000933318,0.003366138,0.000000000],[0.271650781,0.006533228,0.663223761,0.006533228,0.000000000],[0.003225757,0.000933318,0.002919634,0.010482501,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G10 - G26 cWH 
Interaction  | Interacting Bases [1,4] | Pair Probability [[0.004966430,0.004966430,0.051077026,0.042074794,0.000000000],[0.004966430,0.052642128,0.004966430,0.017912101,0.000000000],[0.206503547,0.004966430,0.506544030,0.004966430,0.000000000],[0.017165095,0.004966430,0.015536138,0.055780127,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G8 - G13 cWH 
Interaction  | Interacting Bases [2,5] | Pair Probability [[0.004966430,0.004966430,0.051077026,0.042074794,0.000000000],[0.004966430,0.052642128,0.004966430,0.017912101,0.000000000],[0.206503547,0.004966430,0.506544030,0.004966430,0.000000000],[0.017165095,0.004966430,0.015536138,0.055780127,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G9 - G14 cWH 
Interaction  | Interacting Bases [3,6] | Pair Probability [[0.001117702,0.001117702,0.046473914,0.003863029,0.000000000],[0.001117702,0.011847185,0.001117702,0.001117702,0.000000000],[0.080464698,0.007823915,0.792292506,0.024475008,0.000000000],[0.009468992,0.004031144,0.001117702,0.012553396,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G10 - G16 cHW 
Interaction  | Interacting Bases [4,7] | Pair Probability [[0.004966430,0.004966430,0.051077026,0.042074794,0.000000000],[0.004966430,0.052642128,0.004966430,0.017912101,0.000000000],[0.206503547,0.004966430,0.506544030,0.004966430,0.000000000],[0.017165095,0.004966430,0.015536138,0.055780127,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G13 - G18 cWH 
Interaction  | Interacting Bases [8,12] | Pair Probability [[0.004966430,0.004966430,0.051077026,0.042074794,0.000000000],[0.004966430,0.052642128,0.004966430,0.017912101,0.000000000],[0.206503547,0.004966430,0.506544030,0.004966430,0.000000000],[0.017165095,0.004966430,0.015536138,0.055780127,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G19 - G24 cWH 
Interaction  | Interacting Bases [9,13] | Pair Probability [[0.004966430,0.004966430,0.206503547,0.017165095,0.000000000],[0.004966430,0.052642128,0.004966430,0.004966430,0.000000000],[0.051077026,0.004966430,0.506544030,0.015536138,0.000000000],[0.042074794,0.017912101,0.004966430,0.055780127,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G21 - G26 cHW 
Insertion    | Location [3] | Length Distribution [0.000000000,0.045351474,0.907029478,0.045351474,0.002267574] | Letter Distribution [0.375000000,0.375000000,0.125000000,0.125000000,0.000000000]// Insertion after nucleotide 7, position 3 in cluster node
Insertion    | Location [5] | Length Distribution [0.045351474,0.907029478,0.045351474,0.002267574] | Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000]// Insertion after nucleotide 9, position 5 in cluster node
Insertion    | Location [6] | Length Distribution [0.045351474,0.907029478,0.045351474,0.002267574] | Letter Distribution [0.166666667,0.500000000,0.166666667,0.166666667,0.000000000]// Insertion after nucleotide 10, position 6 in cluster node
Insertion    | Location [8] | Length Distribution [0.045351474,0.907029478,0.045351474,0.002267574] | Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000]// Insertion after nucleotide 12, position 8 in cluster node
Insertion    | Location [12] | Length Distribution [0.045351474,0.907029478,0.045351474,0.002267574] | Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000]// Insertion after nucleotide 16, position 12 in cluster node
InitialNode  | 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 [12] | Right Index [11] // New Initial node after Cluster
HairpinNode  | Num Bases [1] | Left Index [11] | Right Index [11] | Norm Constant [1.000000000000000] // Hairpin node G18:G18
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.166666667,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.166666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.500000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.166666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G18
