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 [9] // Initial node
ClusterNode  | Deletion Probability [0.000000000000015429359482326747228196069233951473250875292831] | Num Left Bases [4] | Num Right Bases [1] | Left Index [1] | Right Index [9] | Norm Constant [0.005304893250626] // Cluster node 7WIE|1|V|U|17:7WIE|1|V|A|21 and 7WIE|1|V|A|45:7WIE|1|V|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 7WIE|1|V|U|17 - 7WIE|1|V|A|45 cWW 
Interaction  | Interacting Bases [2,5] | Pair Probability [[0.023021455,0.018776188,0.017792908,0.018571381,0.000000000],[0.015676229,0.015711894,0.003775280,0.017882434,0.000000000],[0.003775280,0.003775280,0.340741106,0.003775280,0.000000000],[0.486262445,0.003775280,0.022912277,0.003775280,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 7WIE|1|V|U|18 - 7WIE|1|V|A|45 tHS 
Interaction  | Interacting Bases [4,5] | Pair Probability [[0.308644650,0.183882729,0.194324745,0.187834025,0.000000000],[0.014692188,0.011983187,0.001999102,0.012161323,0.000000000],[0.019866299,0.001999102,0.025462132,0.009509275,0.000000000],[0.007136885,0.007528516,0.005957773,0.007018068,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 7WIE|1|V|A|21 - 7WIE|1|V|A|45 cWS 
Interaction  | Interacting Bases [1,3] | Pair Probability [[0.112170041,0.106237908,0.005429695,0.015149071,0.000000000],[0.109559296,0.102527757,0.001165664,0.009760361,0.000000000],[0.009949550,0.001165664,0.098199110,0.095425674,0.000000000],[0.136174205,0.100030487,0.001165664,0.095889854,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 7WIE|1|V|U|17 - 7WIE|1|V|A|20 cSH 
Interaction  | Interacting Bases [2,4] | Pair Probability [[0.002789345,0.002789345,0.012020284,0.012076678,0.000000000],[0.002789345,0.013413702,0.002789345,0.264197884,0.000000000],[0.010276482,0.002789345,0.009640600,0.002789345,0.000000000],[0.387668875,0.002789345,0.258095325,0.013084758,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 7WIE|1|V|U|18 - 7WIE|1|V|A|21 cWH 
Insertion    | Location [2] | Length Distribution [0.023781213,0.951248514,0.023781213,0.001189061] | Letter Distribution [0.125000000,0.625000000,0.125000000,0.125000000,0.000000000]// Insertion after nucleotide 2, position 2 in cluster node
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 [8] // Initial node 7WIE|1|V|C|22 - 7WIE|1|V|U|44 from node 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.125000000,0.625000000,0.125000000,0.125000000,0.000000000] | Position [1] | Left Index [5] | Right Index [8] // Fixed node on left for 7WIE|1|V|A|21
InitialNode  | Left Length Distribution [0.000000000,0.023781213,0.951248514,0.023781213,0.001189061] | Left Letter Distribution [0.083333333,0.416666667,0.083333333,0.416666667,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [6] | Right Index [8] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.125000000,0.125000000,0.125000000,0.625000000,0.000000000] | Position [2] | Left Index [6] | Right Index [8] // Fixed node on right for 7WIE|1|V|C|24
InitialNode  | Left Length Distribution [1.000000000] | 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 [6] | Right Index [7] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009733692,0.020271796,0.011084078,0.201320753,0.000000000],[0.017097495,0.009544863,0.203026637,0.013284001,0.000000000],[0.010960983,0.228535864,0.002089280,0.026765173,0.000000000],[0.198744233,0.013787510,0.023460879,0.010292763,0.000000000],[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 [6] | Right Index [7] // Basepair G25 - C43 cWW 
HairpinNode  | Num Bases [1] | Left Index [7] | Right Index [7] | 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
