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 [8] // Initial node
BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.010138447,0.017999390,0.012030637,0.145215023,0.000000000],[0.111154629,0.015527922,0.148017973,0.014062841,0.000000000],[0.012052549,0.169605488,0.002470680,0.022513399,0.000000000],[0.159661783,0.013947978,0.134332446,0.011268815,0.000000000],[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 [8] // Basepair G36 - C23 cWW 
ClusterNode  | Deletion Probability [0.000000000000000431875379607404164121439020408055538594305065] | Num Left Bases [4] | Num Right Bases [2] | Left Index [2] | Right Index [7] | Norm Constant [0.005103161588403] // Cluster node 6DLR|1|A|G|37:6DLR|1|A|G|41 and 6DLR|1|A|C|21:6DLR|1|A|G|22
Interaction  | Interacting Bases [4,5] | 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 6DLR|1|A|G|41 - 6DLR|1|A|C|21 cWW 
Interaction  | Interacting Bases [2,6] | Pair Probability [[0.009443990,0.016935343,0.010857030,0.196859360,0.000000000],[0.020079540,0.009618431,0.236072779,0.013656751,0.000000000],[0.010978957,0.201101150,0.002069466,0.023238378,0.000000000],[0.199411444,0.013158017,0.026511334,0.010008030,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 6DLR|1|A|C|39 - 6DLR|1|A|G|22 cWW 
Interaction  | Interacting Bases [3,6] | Pair Probability [[0.052773480,0.030611226,0.205227064,0.200735390,0.000000000],[0.066622684,0.030100013,0.002417957,0.096500797,0.000000000],[0.002417957,0.002417957,0.017325023,0.002417957,0.000000000],[0.014674646,0.002417957,0.270921933,0.002417957,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 6DLR|1|A|U|40 - 6DLR|1|A|G|22 tHS 
Interaction  | Interacting Bases [2,3] | Pair Probability [[0.011965562,0.013762121,0.007795003,0.141142364,0.000000000],[0.014289258,0.117878865,0.001694267,0.198552910,0.000000000],[0.159804197,0.001694267,0.019602883,0.136292823,0.000000000],[0.014186475,0.019132125,0.001694267,0.140512611,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 6DLR|1|A|C|39 - 6DLR|1|A|U|40 cSH 
Interaction  | Interacting Bases [1,4] | Pair Probability [[0.000915196,0.000915196,0.009412287,0.007753389,0.000000000],[0.000915196,0.009700698,0.000915196,0.003300776,0.000000000],[0.266376008,0.006406369,0.669763106,0.006406369,0.000000000],[0.003163121,0.000915196,0.002862942,0.010278957,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 6DLR|1|A|G|37 - 6DLR|1|A|G|41 cWH 
Insertion    | Location [1] | Length Distribution [0.334863624,0.653524170,0.011072104,0.000540103] | Letter Distribution [0.375000000,0.125000000,0.125000000,0.375000000,0.000000000]// Insertion after nucleotide 2, position 1 in cluster node
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 [6] | Right Index [5] // New Initial node after Cluster
HairpinNode  | Num Bases [1] | Left Index [6] | Right Index [6] | 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
