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 [0.247842822744946] // Cluster node 8P9A|1|AS|U|32:8P9A|1|AS|C|35 and 8P9A|1|AS|A|45:8P9A|1|AS|A|45
Interaction  | Interacting Bases [1,5] | Pair Probability [[0.009034335,0.017544761,0.009910087,0.196321162,0.000000000],[0.022043953,0.009831675,0.196981684,0.011044900,0.000000000],[0.009929415,0.194460696,0.002044250,0.023047545,0.000000000],[0.224032836,0.010374563,0.053294552,0.010103588,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8P9A|1|AS|U|32 - 8P9A|1|AS|A|45 cWW 
Interaction  | Interacting Bases [4,5] | Pair Probability [[0.019131699,0.023254427,0.016919571,0.023247238,0.000000000],[0.279924596,0.244907340,0.002603168,0.248178480,0.000000000],[0.029116086,0.002603168,0.029305409,0.011062145,0.000000000],[0.016861330,0.025287480,0.012107149,0.015490714,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8P9A|1|AS|C|35 - 8P9A|1|AS|A|45 cWS 
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.041666667,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.458333333,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.041666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.458333333,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 8P9A|1|AS|U|33
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.125000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.625000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.125000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.125000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 8P9A|1|AS|C|34
InitialNode  | Left Length Distribution [0.991950402,0.007999600,0.000049998] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [13] // Initial node 8P9A|1|AS|C|36 - 8P9A|1|AS|C|44 from node 
ClusterNode  | Deletion Probability [0.000000000000000078125000000000012233710187403301545271878291] | Num Left Bases [3] | Num Right Bases [4] | Left Index [5] | Right Index [13] | Norm Constant [0.262985860300064] // Cluster node 8P9A|1|AS|C|36:8P9A|1|AS|U|38 and 8P9A|1|AS|G|41:8P9A|1|AS|C|44
Interaction  | Interacting Bases [1,4] | Pair Probability [[0.009536579,0.017101376,0.010963471,0.198789353,0.000000000],[0.020276398,0.009712729,0.228583296,0.013790641,0.000000000],[0.011086594,0.203072729,0.002089755,0.023466206,0.000000000],[0.201366458,0.013287017,0.026771249,0.010106148,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8P9A|1|AS|C|36 - 8P9A|1|AS|G|41 cWW 
Interaction  | Interacting Bases [3,5] | Pair Probability [[0.046466913,0.042443055,0.000516033,0.002538474,0.000000000],[0.046646417,0.043889779,0.000516033,0.000516033,0.000000000],[0.047985257,0.000516033,0.003189341,0.042840359,0.000000000],[0.380831186,0.333880619,0.003612233,0.003612233,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8P9A|1|AS|U|38 - 8P9A|1|AS|A|42 tSH 
Interaction  | Interacting Bases [2,6] | Pair Probability [[0.018231098,0.023015437,0.000835306,0.005069496,0.000000000],[0.010574938,0.010398335,0.000835306,0.000835306,0.000000000],[0.354488164,0.004176531,0.029925467,0.437260948,0.000000000],[0.069345941,0.033337114,0.000835306,0.000835306,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8P9A|1|AS|G|37 - 8P9A|1|AS|U|43 tSH 
Interaction  | Interacting Bases [4,7] | Pair Probability [[0.007408683,0.007408683,0.007408683,0.007408683,0.000000000],[0.007408683,0.007408683,0.135802279,0.007408683,0.000000000],[0.007408683,0.760476157,0.007408683,0.007408683,0.000000000],[0.007408683,0.007408683,0.007408683,0.007408683,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8P9A|1|AS|G|41 - 8P9A|1|AS|C|44 tSW 
InitialNode  | Left Length Distribution [0.991950402,0.007999600,0.000049998] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | 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 C39:C40
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.125000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.375000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.125000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.375000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C39
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.125000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.625000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.125000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.125000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C40
