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 [15] // Initial node
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.010489920,0.017127883,0.012680838,0.119297674,0.000000000],[0.159817824,0.018747803,0.122690376,0.014659067,0.000000000],[0.012775575,0.132830577,0.002697714,0.020718591,0.000000000],[0.142468525,0.014233330,0.186841746,0.011922559,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | 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 [1] | Right Index [15] // Basepair G409 - C433 cWW 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.043697995,0.046260217,0.000524565,0.002472278,0.000000000],[0.044022640,0.046153098,0.000524565,0.000524565,0.000000000],[0.386803555,0.003671957,0.017951032,0.311661837,0.000000000],[0.048778633,0.045903932,0.000524565,0.000524565,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | 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 [2] | Right Index [14] // Basepair G410 - A432 tSH 
ClusterNode  | Deletion Probability [0.000000000000000000001953125000000000515889489244815448855715] | Num Left Bases [5] | Num Right Bases [4] | Left Index [3] | Right Index [13] | Norm Constant [0.280868878847896] // Cluster node 4LFB|1|A|A|411:4LFB|1|A|A|415 and 4LFB|1|A|G|428:4LFB|1|A|A|431
Interaction  | Interacting Bases [3,6] | Pair Probability [[0.001221525,0.001022446,0.008175813,0.000734405,0.000000000],[0.000143014,0.000143014,0.088049063,0.000143014,0.000000000],[0.097318616,0.001001098,0.720376451,0.080241401,0.000000000],[0.000143014,0.000143014,0.001001098,0.000143014,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4LFB|1|A|G|413 - 4LFB|1|A|G|428 tSS 
Interaction  | Interacting Bases [5,6] | Pair Probability [[0.005347053,0.006149377,0.800291450,0.094216747,0.000000000],[0.005088969,0.001115262,0.033568158,0.011931507,0.000000000],[0.009171003,0.004845667,0.007806836,0.001115262,0.000000000],[0.005355260,0.005075351,0.007806836,0.001115262,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4LFB|1|A|A|415 - 4LFB|1|A|G|428 tHH 
Interaction  | Interacting Bases [1,8] | Pair Probability [[0.381184813,0.003615770,0.318975856,0.003615770,0.000000000],[0.030948835,0.015344049,0.003615770,0.003615770,0.000000000],[0.003615770,0.008956754,0.132906372,0.038702064,0.000000000],[0.016338652,0.003615770,0.017330382,0.017617604,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4LFB|1|A|A|411 - 4LFB|1|A|A|430 tWH 
Interaction  | Interacting Bases [4,8] | Pair Probability [[0.381184813,0.030948835,0.003615770,0.016338652,0.000000000],[0.003615770,0.015344049,0.008956754,0.003615770,0.000000000],[0.318975856,0.003615770,0.132906372,0.017330382,0.000000000],[0.003615770,0.003615770,0.038702064,0.017617604,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4LFB|1|A|A|414 - 4LFB|1|A|A|430 tHW 
Interaction  | Interacting Bases [7,9] | Pair Probability [[0.003068279,0.003068279,0.013222312,0.013284346,0.000000000],[0.003068279,0.014755072,0.003068279,0.290617672,0.000000000],[0.011304130,0.003068279,0.010604660,0.003068279,0.000000000],[0.326435762,0.003068279,0.283904858,0.014393233,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4LFB|1|A|U|429 - 4LFB|1|A|A|431 cWH 
Interaction  | Interacting Bases [2,2] | Pair Probability [[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],[0.000000000,0.000000000,0.000000000,0.125000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 4LFB|1|A|A|412
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
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.015839826,0.296886961,0.014317634,0.084582798,0.000000000],[0.013722760,0.012789399,0.036431816,0.014404953,0.000000000],[0.014010903,0.041562971,0.003244391,0.344046970,0.000000000],[0.036578332,0.015734627,0.014397948,0.041447713,0.000000000],[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 [8] | Right Index [9] // Basepair G416 - U427 cWW 
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
