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 [0.0000239574126029] | Pair Probability [[0.012540860,0.155529775,0.012456608,0.140202703,0.000000000],[0.015113779,0.010952378,0.117426741,0.013578237,0.000000000],[0.012245828,0.142067698,0.002615550,0.191455955,0.000000000],[0.115398566,0.014477202,0.018565386,0.025372734,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [14] // Basepair G991 - U1058 cWW 
BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.324258723,0.020669487,0.207340113,0.021874517,0.000000000],[0.016183108,0.009938791,0.022669555,0.034351847,0.000000000],[0.201673460,0.022947797,0.004691252,0.021989185,0.000000000],[0.021499233,0.035975684,0.017664835,0.016272412,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [13] // Basepair A992 - A1057 cWW 
BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.045965469,0.300684085,0.003676754,0.003676754,0.000000000],[0.023538170,0.014096579,0.003676754,0.003676754,0.000000000],[0.003676754,0.003676754,0.172811225,0.406136932,0.000000000],[0.003676754,0.003676754,0.003676754,0.003676754,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [12] // Basepair G993 - U1056 bif 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.750000000,0.083333333,0.083333333,0.083333333,0.000000000] | Position [2] | Left Index [4] | Right Index [11] // Fixed node on right for 8P9A|1|AR|A|1055
InitialNode  | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [10] // New Initial node after Fixed node
ClusterNode  | Deletion Probability [0.0000001250000000] | Num Left Bases [2] | Num Right Bases [1] | Left Index [4] | Right Index [10] | Norm Constant [0.269832767432214] // Cluster node 8P9A|1|AR|G|994:8P9A|1|AR|U|995 and 8P9A|1|AR|A|1054:8P9A|1|AR|A|1054
Interaction  | Interacting Bases [2,3] | Pair Probability [[0.018414538,0.004075167,0.019126511,0.004075167,0.000000000],[0.040981170,0.328380556,0.004075167,0.004075167,0.000000000],[0.004075167,0.009768444,0.030991298,0.018124938,0.000000000],[0.445978203,0.004075167,0.023643628,0.040139714,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8P9A|1|AR|U|995 - 8P9A|1|AR|A|1054 tWH 
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.030507812,0.031086061,0.001709208,0.030379978,0.000000000],[0.022776075,0.034323944,0.000378448,0.030443666,0.000000000],[0.186583170,0.002649134,0.227599663,0.303374889,0.000000000],[0.030981169,0.030795185,0.000378448,0.036033152,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8P9A|1|AR|G|994 - 8P9A|1|AR|U|995 cSH 
InitialNode  | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [6] | Right Index [9] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.279711057,0.072417813,0.219753102,0.072117434,0.000000000],[0.055760800,0.046991416,0.002083215,0.070257469,0.000000000],[0.002658770,0.000790331,0.011958295,0.000790331,0.000000000],[0.015765394,0.000790331,0.147363911,0.000790331,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [6] | Right Index [9] // Basepair A996 - A1053 tHS 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009325457,0.020734609,0.010297314,0.218050308,0.000000000],[0.016974989,0.009378665,0.194777146,0.011594085,0.000000000],[0.010227486,0.218136243,0.002025500,0.039220448,0.000000000],[0.193588082,0.012169223,0.022789886,0.010710558,0.000000000],[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 [7] | Right Index [8] // Basepair A997 - U1052 cWW 
HairpinNode  | Num Bases [1] | Left Index [8] | Right Index [8] | 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
