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
ClusterNode  | Deletion Probability [0.0000000000031250] | Num Left Bases [4] | Num Right Bases [1] | Left Index [1] | Right Index [14] | Norm Constant [0.254438718607324] // Cluster node 4V9F|1|9|U|33:4V9F|1|9|C|36 and 4V9F|1|9|A|47:4V9F|1|9|A|47
Interaction  | Interacting Bases [1,5] | Pair Probability [[0.008813022,0.019031325,0.009538180,0.220964650,0.000000000],[0.019034606,0.009339704,0.188193685,0.010298025,0.000000000],[0.009538194,0.188191846,0.001965618,0.036691769,0.000000000],[0.220970559,0.010297537,0.036713825,0.010417454,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4V9F|1|9|U|33 - 4V9F|1|9|A|47 cWW 
Interaction  | Interacting Bases [4,5] | Pair Probability [[0.016928915,0.021002337,0.015034330,0.020479771,0.000000000],[0.274597519,0.240082617,0.002522161,0.274677841,0.000000000],[0.025717256,0.002522161,0.026883247,0.010505346,0.000000000],[0.016529218,0.025475028,0.011839067,0.015203186,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4V9F|1|9|C|36 - 4V9F|1|9|A|47 cWS 
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.187500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.437500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.062500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.312500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 4V9F|1|9|A|34
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.062500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.812500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.062500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.062500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 4V9F|1|9|C|35
InitialNode  | 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 [5] | Right Index [13] // Initial node 4V9F|1|9|C|37 - 4V9F|1|9|C|46 from node 
ClusterNode  | Deletion Probability [0.000000000000000078125000000000012233710187403301545271878291] | Num Left Bases [3] | Num Right Bases [4] | Left Index [5] | Right Index [13] | Norm Constant [0.518576767782631] // Cluster node 4V9F|1|9|C|37:4V9F|1|9|U|39 and 4V9F|1|9|G|43:4V9F|1|9|C|46
Interaction  | Interacting Bases [1,4] | Pair Probability [[0.003603143,0.006461301,0.004142256,0.075107278,0.000000000],[0.053626290,0.025687878,0.609294550,0.036472991,0.000000000],[0.004188775,0.076725638,0.000789558,0.008866083,0.000000000],[0.076080968,0.005020146,0.010114806,0.003818340,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4V9F|1|9|C|37 - 4V9F|1|9|G|43 cWW 
Interaction  | Interacting Bases [3,5] | Pair Probability [[0.044713444,0.040841430,0.000496560,0.002442683,0.000000000],[0.044886175,0.042233561,0.000496560,0.000496560,0.000000000],[0.046174493,0.000496560,0.003068988,0.041223742,0.000000000],[0.404196047,0.321281350,0.003475923,0.003475923,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4V9F|1|9|U|39 - 4V9F|1|9|A|44 tSH 
Interaction  | Interacting Bases [2,6] | Pair Probability [[0.637247869,0.008534762,0.011540428,0.004145851,0.000000000],[0.106818357,0.001392218,0.000232258,0.000874670,0.000000000],[0.112884174,0.000232258,0.002958215,0.000692180,0.000000000],[0.109113684,0.001412914,0.001104797,0.000815366,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4V9F|1|9|A|38 - 4V9F|1|9|A|45 cSW 
Interaction  | Interacting Bases [4,7] | Pair Probability [[0.007129110,0.007129110,0.007129110,0.007129110,0.000000000],[0.007129110,0.007129110,0.130677665,0.007129110,0.000000000],[0.007129110,0.769514793,0.007129110,0.007129110,0.000000000],[0.007129110,0.007129110,0.007129110,0.007129110,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4V9F|1|9|G|43 - 4V9F|1|9|C|46 tSW 
InitialNode  | Left Length Distribution [0.008193363,0.983203605,0.008193363,0.000409668] | Left Letter Distribution [0.062500000,0.187500000,0.562500000,0.187500000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [8] | Right Index [9] // New Initial node after Cluster
HairpinNode  | Num Bases [2] | Left Index [8] | Right Index [9] | Norm Constant [1.000000000000000] // Hairpin node C41:C42
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.062500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.812500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.062500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.062500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C41
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.015625000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.953125000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.015625000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.015625000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C42
