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 [7] // Initial node
ClusterNode  | Deletion Probability [0.0000000622013889] | Num Left Bases [2] | Num Right Bases [1] | Left Index [1] | Right Index [7] | Norm Constant [0.250699937715072] // Cluster node 2QEK|1|B|G|7:2QEK|1|B|A|8 and 2QEK|1|A|C|17:2QEK|1|A|C|17
Interaction  | Interacting Bases [1,3] | Pair Probability [[0.008951320,0.018332685,0.010038774,0.198246118,0.000000000],[0.017740498,0.009106308,0.199235598,0.011731804,0.000000000],[0.009997466,0.228805224,0.001956951,0.027133389,0.000000000],[0.207551081,0.011830860,0.029539446,0.009802478,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 2QEK|1|B|G|7 - 2QEK|1|A|C|17 cWW 
Interaction  | Interacting Bases [2,3] | Pair Probability [[0.098902659,0.229281229,0.078616169,0.095024619,0.000000000],[0.075619268,0.054407566,0.001922404,0.081869324,0.000000000],[0.001922404,0.001922404,0.124060402,0.001922404,0.000000000],[0.102545196,0.001922404,0.048139149,0.001922404,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 2QEK|1|B|A|8 - 2QEK|1|A|C|17 tHS 
Insertion    | Location [1] | Length Distribution [0.869396619,0.129517605,0.001046999,0.000038778] | Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000]// Insertion after nucleotide 1, position 1 in cluster node
InitialNode  | Left Length Distribution [0.869396619,0.129517605,0.001046999,0.000038778] | Left Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000] | 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 [6] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.089384739,0.097324691,0.203498886,0.053822351,0.000000000],[0.011078492,0.008491859,0.016846217,0.026853964,0.000000000],[0.203449339,0.018065177,0.002750772,0.081946322,0.000000000],[0.052056042,0.027164183,0.047614634,0.059652332,0.000000000],[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 [6] // Basepair A9 - A16 cWW 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.008984793,0.017610738,0.010272725,0.186448108,0.000000000],[0.017188779,0.008954615,0.219198431,0.012571477,0.000000000],[0.010256362,0.251542629,0.001945607,0.023605698,0.000000000],[0.186105612,0.012638408,0.023166459,0.009509558,0.000000000],[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 G10 - C15 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
