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 [12] // Initial node G10 - C40 from junction 
BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.003914340,0.055820081,0.004532224,0.074283445,0.000000000],[0.006604600,0.022593563,0.080006995,0.005092413,0.000000000],[0.004475173,0.606828618,0.000825289,0.010585725,0.000000000],[0.073854492,0.037418864,0.009131325,0.004032852,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [12] // Basepair G10 - C40 cWW 
ClusterNode  | Deletion Probability [0.000000000000000000000009765625000000002400000000000000000000] | Num Left Bases [3] | Num Right Bases [7] | Left Index [2] | Right Index [11] | Norm Constant [0.023942467794376] // Cluster node G11:G13 and C33:A39
Interaction  | Interacting Bases [3,4] | Pair Probability [[0.010096111,0.020567805,0.011689796,0.191596493,0.000000000],[0.017034996,0.008324961,0.206359029,0.013134669,0.000000000],[0.011542646,0.241989936,0.002128637,0.027303363,0.000000000],[0.190490110,0.013787581,0.023552083,0.010401784,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G13 - C33 cWW 
Interaction  | Interacting Bases [2,5] | Pair Probability [[0.170737532,0.190302277,0.237397338,0.182598480,0.000000000],[0.002082711,0.002082711,0.002082711,0.002082711,0.000000000],[0.011429712,0.013192201,0.020338141,0.157342629,0.000000000],[0.002082711,0.002082711,0.002082711,0.002082711,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A12 - G34 tSS 
Interaction  | Interacting Bases [1,10] | Pair Probability [[0.043291794,0.050462128,0.000521611,0.002483845,0.000000000],[0.043676961,0.045779825,0.000521611,0.000521611,0.000000000],[0.394253847,0.003651276,0.017689667,0.303712878,0.000000000],[0.047056648,0.045333078,0.000521611,0.000521611,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G11 - A39 tSH 
Interaction  | Interacting Bases [3,10] | Pair Probability [[0.027174669,0.006091800,0.007184673,0.006169792,0.000000000],[0.006545922,0.001309184,0.001309184,0.001309184,0.000000000],[0.683718369,0.116457217,0.117707918,0.014548614,0.000000000],[0.006545922,0.001309184,0.001309184,0.001309184,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G13 - A39 tSS 
Interaction  | Interacting Bases [4,10] | Pair Probability [[0.142497337,0.029020812,0.028160651,0.028639375,0.000000000],[0.237947678,0.029183050,0.003573896,0.026829201,0.000000000],[0.151870031,0.030839869,0.028008649,0.031022245,0.000000000],[0.147267189,0.028710808,0.027554250,0.028874959,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction C33 - A39 cSS 
Interaction  | Interacting Bases [6,6] | Pair Probability [[0.500000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.300000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.100000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.100000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion A35
Interaction  | Interacting Bases [7,7] | Pair Probability [[0.100000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.700000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.100000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion G36
Interaction  | Interacting Bases [8,8] | Pair Probability [[0.700000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.100000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.100000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion A37
Interaction  | Interacting Bases [9,9] | Pair Probability [[0.700000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.100000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.100000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion A38
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 [5] | Right Index [4] // New Initial node after Cluster
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
