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 [15] // Initial node C6 - G24 from junction 
BasepairNode | Deletion Probability [0.0000174430812709] | Pair Probability [[0.008675828,0.017305933,0.009868939,0.208763802,0.000000000],[0.017525751,0.007668670,0.260538742,0.011333681,0.000000000],[0.009914276,0.206893488,0.001889988,0.022419314,0.000000000],[0.172878144,0.011132189,0.022745860,0.010445394,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.934446650,0.065203005,0.000340613,0.000009732] | Left Letter Distribution [0.166666667,0.500000000,0.166666667,0.166666667,0.000000000] | 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 [15] // Basepair C6 - G24 cWW 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.012043709,0.122205117,0.011969405,0.029253075,0.000000000],[0.035781168,0.089520195,0.019193391,0.013829750,0.000000000],[0.011822882,0.019450683,0.004113380,0.037329396,0.000000000],[0.061924409,0.088229224,0.017064970,0.426269247,0.000000000],[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 [2] | Right Index [14] // Basepair U7 - C23 cWW 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.094201538,0.129338943,0.001354713,0.006427133,0.000000000],[0.106675245,0.182885554,0.001354713,0.001354713,0.000000000],[0.147691304,0.001354713,0.006637998,0.038275031,0.000000000],[0.118683445,0.146725775,0.015684468,0.001354713,0.000000000],[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 [3] | Right Index [13] // Basepair C8 - C22 tSH 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.617640543,0.095681848,0.023662502,0.023698462,0.000000000],[0.008744982,0.000677143,0.058212869,0.048098828,0.000000000],[0.004230257,0.056186787,0.001658919,0.000677143,0.000000000],[0.004161052,0.055314377,0.000677143,0.000677143,0.000000000],[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 [12] // Basepair A9 - A21 tHH 
ClusterNode  | Deletion Probability [0.0000001250000000] | Num Left Bases [2] | Num Right Bases [1] | Left Index [5] | Right Index [11] | Norm Constant [0.511983607588030] // Cluster node G10:U11 and A20:A20
Interaction  | Interacting Bases [2,3] | Pair Probability [[0.022837272,0.004789512,0.023493607,0.004789512,0.000000000],[0.047574079,0.039764490,0.031792035,0.004789512,0.000000000],[0.004789512,0.004789512,0.056052332,0.022341674,0.000000000],[0.616882239,0.004789512,0.059086009,0.051439190,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U11 - A20 tWH 
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.048479644,0.049942729,0.002723713,0.002253535,0.000000000],[0.046894616,0.054472179,0.000579310,0.054897273,0.000000000],[0.033155631,0.018131255,0.037062536,0.543447746,0.000000000],[0.004171512,0.048578946,0.000579310,0.054630067,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G10 - U11 cSH 
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 [7] | Right Index [10] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.038440127,0.038782129,0.462139192,0.041783058,0.000000000],[0.044806889,0.040649327,0.003242082,0.040252647,0.000000000],[0.000463155,0.000463155,0.015707204,0.000463155,0.000000000],[0.002205483,0.000463155,0.269676090,0.000463155,0.000000000],[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 [7] | Right Index [10] // Basepair A12 - G19 tHS 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.008515984,0.017593209,0.009557680,0.211161401,0.000000000],[0.018336446,0.007836719,0.240176240,0.010785029,0.000000000],[0.009597611,0.195328240,0.001890644,0.022188538,0.000000000],[0.202408459,0.010607771,0.023000835,0.011015193,0.000000000],[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 [8] | Right Index [9] // Basepair U13 - A18 cWW 
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
