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 [14] // Initial node
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 [14] // Basepair C26 - G13 cWW 
ClusterNode  | Deletion Probability [0.000000000000000000000000000001191720873277651707035468314865] | Num Left Bases [9] | Num Right Bases [3] | Left Index [2] | Right Index [13] | Norm Constant [0.101806870731090] // Cluster node 3D2V|1|A|U|27:3D2V|1|A|C|36 and 3D2V|1|A|G|10:3D2V|1|A|U|12
Interaction  | Interacting Bases [9,10] | 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]] // Cluster Interaction 3D2V|1|A|C|36 - 3D2V|1|A|G|10 cWW 
Interaction  | Interacting Bases [4,11] | Pair Probability [[0.021020407,0.017594599,0.020098875,0.012637885,0.000000000],[0.002461033,0.002461033,0.216453963,0.002461033,0.000000000],[0.239241614,0.002461033,0.256004269,0.197260125,0.000000000],[0.002461033,0.002461033,0.002461033,0.002461033,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 3D2V|1|A|G|30 - 3D2V|1|A|G|11 tSS 
Interaction  | Interacting Bases [8,11] | 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 3D2V|1|A|G|34 - 3D2V|1|A|G|11 cHW 
Interaction  | Interacting Bases [7,12] | Pair Probability [[0.003098658,0.003098658,0.011416052,0.319766810,0.000000000],[0.003098658,0.014901162,0.003098658,0.003098658,0.000000000],[0.013353226,0.003098658,0.010709656,0.286715797,0.000000000],[0.013415874,0.293495075,0.003098658,0.014535741,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 3D2V|1|A|A|33 - 3D2V|1|A|U|12 cHW 
Interaction  | Interacting Bases [1,5] | Pair Probability [[0.018961504,0.004196211,0.019694625,0.004196211,0.000000000],[0.042198433,0.338134433,0.004196211,0.004196211,0.000000000],[0.004196211,0.010058595,0.031911832,0.018663303,0.000000000],[0.429522110,0.004196211,0.024345914,0.041331983,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 3D2V|1|A|U|27 - 3D2V|1|A|A|31 tWH 
Interaction  | Interacting Bases [3,9] | Pair Probability [[0.081591666,0.095215600,0.082006787,0.080836575,0.000000000],[0.075904306,0.083072861,0.003458357,0.075094816,0.000000000],[0.078139289,0.003393533,0.007809038,0.077291685,0.000000000],[0.071822400,0.041801731,0.062580800,0.079980554,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 3D2V|1|A|A|29 - 3D2V|1|A|C|36 cSS 
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.055555556,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.055555556,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.833333333,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.055555556,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 3D2V|1|A|G|28
Interaction  | Interacting Bases [6,6] | Pair Probability [[0.833333333,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.055555556,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.055555556,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.055555556,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 3D2V|1|A|A|32
Insertion    | Location [8] | 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 8 in cluster node
InitialNode  | Left Length Distribution [0.952380952,0.047619048] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.952380952,0.047619048] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [11] | Right Index [10] // New Initial node after Cluster
HairpinNode  | Num Bases [1] | Left Index [11] | Right Index [11] | 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
