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 [9] // Initial node C1466 - G1435 from junction 
BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.010379139,0.018054448,0.011936187,0.166132001,0.000000000],[0.092831895,0.010420694,0.182890129,0.013631115,0.000000000],[0.012091289,0.159186893,0.002446059,0.022275606,0.000000000],[0.156779526,0.012908548,0.115428336,0.012608136,0.000000000],[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 [9] // Basepair C1466 - G1435 cWW 
ClusterNode  | Deletion Probability [0.0000001250000000] | Num Left Bases [1] | Num Right Bases [2] | Left Index [2] | Right Index [8] | Norm Constant [0.287323481329397] // Cluster node G1467:G1467 and A1433:A1434
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.023156674,0.004856498,0.023822189,0.004856498,0.000000000],[0.048239451,0.040320637,0.032236679,0.004856498,0.000000000],[0.111499855,0.004856498,0.056836281,0.022654145,0.000000000],[0.504880592,0.004856498,0.059912387,0.052158619,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G1467 - A1433 tWH 
Interaction  | Interacting Bases [1,3] | Pair Probability [[0.099771965,0.116296998,0.001202125,0.005724366,0.000000000],[0.100659637,0.105505979,0.001202125,0.001202125,0.000000000],[0.139443264,0.001202125,0.005824043,0.099992658,0.000000000],[0.161770273,0.104476389,0.054523803,0.001202125,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G1467 - A1434 tSH 
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 [3] | Right Index [6] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.059593935,0.060124143,0.342732568,0.064776498,0.000000000],[0.069464361,0.063018870,0.003042710,0.062403894,0.000000000],[0.000718031,0.000718031,0.014741292,0.000718031,0.000000000],[0.003419172,0.000718031,0.253092402,0.000718031,0.000000000],[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 [3] | Right Index [6] // Basepair A1468 - G1432 tHS 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.011545053,0.091357941,0.012500960,0.153268922,0.000000000],[0.016202600,0.009015557,0.162650528,0.013540081,0.000000000],[0.012307163,0.197820616,0.002427935,0.114576839,0.000000000],[0.150792068,0.014433261,0.021211816,0.016348660,0.000000000],[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 [4] | Right Index [5] // Basepair G1469 - C1431 cWW 
HairpinNode  | Num Bases [1] | Left Index [5] | Right Index [5] | 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
