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 [14] // Initial node
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.003861747,0.056298454,0.004397499,0.079872036,0.000000000],[0.006783263,0.026507815,0.080548829,0.005270297,0.000000000],[0.004348662,0.590132004,0.000828901,0.010618820,0.000000000],[0.078849827,0.038290418,0.009307874,0.004083553,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [14] // Basepair G21 - C59 cWW 
ClusterNode  | Deletion Probability [0.000000000000015625000000000002841172490091166211760239940914] | Num Left Bases [5] | Num Right Bases [1] | Left Index [2] | Right Index [13] | Norm Constant [0.378910815823155] // Cluster node 4V9F|1|9|G|22:4V9F|1|9|C|26 and 4V9F|1|9|G|58:4V9F|1|9|G|58
Interaction  | Interacting Bases [1,6] | Pair Probability [[0.286859111,0.207254157,0.003021830,0.003021830,0.000000000],[0.012680128,0.008875223,0.003021830,0.003021830,0.000000000],[0.003021830,0.003021830,0.312083968,0.142029115,0.000000000],[0.003021830,0.003021830,0.003021830,0.003021830,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4V9F|1|9|G|22 - 4V9F|1|9|G|58 bif 
Interaction  | Interacting Bases [1,5] | Pair Probability [[0.007482036,0.007482036,0.007482036,0.007482036,0.000000000],[0.007482036,0.007482036,0.137146856,0.007482036,0.000000000],[0.007482036,0.758104634,0.007482036,0.007482036,0.000000000],[0.007482036,0.007482036,0.007482036,0.007482036,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4V9F|1|9|G|22 - 4V9F|1|9|C|26 tSW 
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.166666667,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.166666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.166666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.500000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 4V9F|1|9|U|23
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.166666667,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.166666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.166666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.500000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 4V9F|1|9|U|24
Interaction  | Interacting Bases [4,4] | Pair Probability [[0.166666667,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.166666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.500000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.166666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 4V9F|1|9|G|25
InitialNode  | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [7] | Right Index [12] // Initial node 4V9F|1|9|C|27 - 4V9F|1|9|A|57 from node 
ClusterNode  | Deletion Probability [0.000000000000015625000000000002841172490091166211760239940914] | Num Left Bases [2] | Num Right Bases [4] | Left Index [7] | Right Index [12] | Norm Constant [0.022107374884817] // Cluster node 4V9F|1|9|C|27:4V9F|1|9|U|28 and 4V9F|1|9|A|54:4V9F|1|9|A|57
Interaction  | Interacting Bases [2,3] | Pair Probability [[0.009123784,0.017718471,0.010008206,0.198264936,0.000000000],[0.022262210,0.009929018,0.198931998,0.011154256,0.000000000],[0.010027726,0.196386049,0.002064490,0.023275738,0.000000000],[0.216349992,0.010477281,0.053822220,0.010203624,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4V9F|1|9|U|28 - 4V9F|1|9|A|54 cWW 
Interaction  | Interacting Bases [1,4] | Pair Probability [[0.016630886,0.015189662,0.044428677,0.019126085,0.000000000],[0.016667847,0.013061754,0.024870209,0.386769861,0.000000000],[0.046942534,0.023961968,0.003768689,0.016732811,0.000000000],[0.020361889,0.319807982,0.018277361,0.013401785,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4V9F|1|9|C|27 - 4V9F|1|9|U|55 cWW 
Interaction  | Interacting Bases [2,6] | Pair Probability [[0.180519376,0.017157494,0.024883181,0.007207709,0.000000000],[0.173124567,0.013878938,0.001921253,0.007559536,0.000000000],[0.178058238,0.001921253,0.155093256,0.006042475,0.000000000],[0.202026315,0.014064519,0.009451832,0.007090057,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4V9F|1|9|U|28 - 4V9F|1|9|A|57 cSW 
Interaction  | Interacting Bases [4,6] | Pair Probability [[0.113280636,0.107289768,0.005483455,0.015299062,0.000000000],[0.110644042,0.103542883,0.001177205,0.009856998,0.000000000],[0.010048060,0.001177205,0.099171378,0.096370483,0.000000000],[0.127621474,0.101020887,0.001177205,0.096839258,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4V9F|1|9|U|55 - 4V9F|1|9|A|57 cSH 
Interaction  | Interacting Bases [5,5] | Pair Probability [[0.500000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.166666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.166666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.166666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion 4V9F|1|9|A|56
InitialNode  | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [9] | Right Index [8] // New Initial node after Cluster
HairpinNode  | Num Bases [1] | Left Index [9] | Right Index [9] | 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
