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 [13] // Initial node
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.009090944,0.016302246,0.010451159,0.189500131,0.000000000],[0.019328903,0.009258863,0.264630806,0.013146218,0.000000000],[0.010568529,0.193583350,0.001992102,0.022369654,0.000000000],[0.191956811,0.012666128,0.025520256,0.009633898,0.000000000],[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 [13] // Basepair C2745 - G2759 cWW 
ClusterNode  | Deletion Probability [0.0000000000031250] | Num Left Bases [2] | Num Right Bases [3] | Left Index [2] | Right Index [12] | Norm Constant [0.033373703837395] // Cluster node 5J7L|1|DA|U|2746:5J7L|1|DA|G|2747 and 5J7L|1|DA|U|2756:5J7L|1|DA|A|2758
Interaction  | Interacting Bases [1,3] | Pair Probability [[0.018169029,0.003728942,0.032352206,0.003728942,0.000000000],[0.322483331,0.043513907,0.003728942,0.003728942,0.000000000],[0.003728942,0.011668038,0.023979968,0.035176181,0.000000000],[0.036729459,0.003728942,0.015239468,0.438314762,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DA|U|2746 - 5J7L|1|DA|U|2756 tWH 
Interaction  | Interacting Bases [2,4] | Pair Probability [[0.041656033,0.044098525,0.000500053,0.002356751,0.000000000],[0.041965507,0.043996411,0.000500053,0.000500053,0.000000000],[0.415457595,0.003500370,0.017112199,0.297098200,0.000000000],[0.046499257,0.043758888,0.000500053,0.000500053,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DA|G|2747 - 5J7L|1|DA|A|2757 tSH 
Interaction  | Interacting Bases [1,5] | Pair Probability [[0.114765959,0.104827663,0.001274521,0.006269632,0.000000000],[0.115209306,0.108400844,0.001274521,0.001274521,0.000000000],[0.118516031,0.001274521,0.007877169,0.105808943,0.000000000],[0.192872673,0.117804652,0.001274521,0.001274521,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DA|U|2746 - 5J7L|1|DA|A|2758 tSH 
Interaction  | Interacting Bases [3,5] | Pair Probability [[0.002924902,0.002924902,0.012604447,0.012663582,0.000000000],[0.002924902,0.014065583,0.002924902,0.277037407,0.000000000],[0.010775899,0.002924902,0.010109115,0.002924902,0.000000000],[0.357910727,0.002924902,0.270638276,0.013720652,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DA|U|2756 - 5J7L|1|DA|A|2758 cWH 
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 [0.007039775,0.985568462,0.007039775,0.000351989] | Right Letter Distribution [0.055555556,0.833333333,0.055555556,0.055555556,0.000000000] | Left Index [4] | Right Index [9] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.017898242,0.039832166,0.003960910,0.461511524,0.000000000],[0.003960910,0.319173624,0.009494562,0.003960910,0.000000000],[0.018590254,0.003960910,0.030122383,0.022980723,0.000000000],[0.003960910,0.003960910,0.017616762,0.039014302,0.000000000],[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 [4] | Right Index [9] // Basepair A2748 - U2754 tHW 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.301295842,0.137508415,0.003439441,0.020954516,0.000000000],[0.003439441,0.017569130,0.009511229,0.003439441,0.000000000],[0.245154562,0.003439441,0.099286633,0.016194963,0.000000000],[0.003439441,0.003439441,0.035362340,0.096525722,0.000000000],[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 [5] | Right Index [8] // Basepair A2749 - A2753 tHW 
HairpinNode  | Num Bases [2] | Left Index [6] | Right Index [7] | Norm Constant [1.000000000000000] // Hairpin node A2750:C2752
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.024202650,0.234114099,0.003212502,0.015890427,0.000000000],[0.145480432,0.201142827,0.003212502,0.016802123,0.000000000],[0.144998478,0.003212502,0.003212502,0.011460402,0.000000000],[0.023352794,0.134602537,0.017843833,0.017259392,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin Interaction A2750 - C2752 tSW 
Insertion    | Location [1] | Length Distribution [0.007039775,0.985568462,0.007039775,0.000351989] | Letter Distribution [0.055555556,0.055555556,0.833333333,0.055555556,0.000000000]// Insertion in Hairpin after nucleotide 6, position 1
