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 [10] // Initial node
BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.009028682,0.018848565,0.009815285,0.206696649,0.000000000],[0.020335986,0.009653230,0.194139783,0.010711201,0.000000000],[0.009821675,0.193306351,0.002023380,0.032781568,0.000000000],[0.219084491,0.010489590,0.042781149,0.010482415,0.000000000],[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 [10] // Basepair U2909 - A2892 cWW 
ClusterNode  | Deletion Probability [0.000000000000000000390625000000000088131570158437809669143083] | Num Left Bases [5] | Num Right Bases [3] | Left Index [2] | Right Index [9] | Norm Constant [0.013555646888343] // Cluster node 8P9A|1|AR|A|2910:8P9A|1|AR|G|2914 and 8P9A|1|AR|C|2889:8P9A|1|AR|U|2891
Interaction  | Interacting Bases [2,6] | Pair Probability [[0.197909159,0.290316763,0.002708993,0.002708993,0.000000000],[0.012472165,0.008932317,0.002708993,0.002708993,0.000000000],[0.002708993,0.002708993,0.185798035,0.221540810,0.000000000],[0.002708993,0.058649816,0.002708993,0.002708993,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8P9A|1|AR|A|2911 - 8P9A|1|AR|C|2889 bif 
Interaction  | Interacting Bases [5,6] | Pair Probability [[0.009639190,0.020074982,0.010976465,0.199366183,0.000000000],[0.016931500,0.009452194,0.201055505,0.013155030,0.000000000],[0.010854565,0.236025807,0.002068996,0.026505317,0.000000000],[0.196814677,0.013653651,0.023233104,0.010192834,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8P9A|1|AR|G|2914 - 8P9A|1|AR|C|2889 cWW 
Interaction  | Interacting Bases [4,7] | Pair Probability [[0.010534032,0.013793140,0.013411060,0.029060994,0.000000000],[0.358025317,0.038661532,0.088795148,0.014975670,0.000000000],[0.013733533,0.027709762,0.003386078,0.014322053,0.000000000],[0.036513418,0.013647555,0.309852434,0.013578275,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8P9A|1|AR|C|2913 - 8P9A|1|AR|A|2890 cWW 
Interaction  | Interacting Bases [1,8] | Pair Probability [[0.023883562,0.016263272,0.003916657,0.411083184,0.000000000],[0.019479318,0.016300273,0.003916657,0.003916657,0.000000000],[0.018459216,0.003916657,0.353501176,0.079711119,0.000000000],[0.019266842,0.018552095,0.003916657,0.003916657,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8P9A|1|AR|A|2910 - 8P9A|1|AR|U|2891 tSH 
Interaction  | Interacting Bases [3,8] | Pair Probability [[0.015686042,0.294004563,0.014178627,0.083761605,0.000000000],[0.013589530,0.012665230,0.036078109,0.014265099,0.000000000],[0.013874874,0.041159447,0.003212892,0.350415446,0.000000000],[0.036223202,0.015581863,0.014258162,0.041045308,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8P9A|1|AR|G|2912 - 8P9A|1|AR|U|2891 cWW 
Interaction  | Interacting Bases [2,5] | Pair Probability [[0.025166019,0.027108923,0.572637991,0.047311734,0.000000000],[0.026336965,0.026442053,0.005532205,0.025452633,0.000000000],[0.026833908,0.005532205,0.031040363,0.024985461,0.000000000],[0.025769174,0.043307137,0.061473028,0.025070200,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8P9A|1|AR|A|2911 - 8P9A|1|AR|G|2914 cSH 
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 [7] | Right Index [6] // New Initial node after Cluster
HairpinNode  | Num Bases [1] | Left Index [7] | Right Index [7] | 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
