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 [0.0000244705618206] | Pair Probability [[0.004570114,0.047589562,0.005204141,0.094523114,0.000000000],[0.008027530,0.022407281,0.095324053,0.006237038,0.000000000],[0.005146346,0.555894766,0.000980948,0.012566650,0.000000000],[0.093313400,0.032367215,0.011015235,0.004832607,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | 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 [1] | Right Index [14] // Basepair G1666 - C1994 cWW 
ClusterNode  | Deletion Probability [0.000000000000015625000000000002841172490091166211760239940914] | Num Left Bases [3] | Num Right Bases [3] | Left Index [2] | Right Index [13] | Norm Constant [0.275811635852425] // Cluster node 5J7L|1|DA|G|1667:5J7L|1|DA|A|1669 and 5J7L|1|DA|U|1991:5J7L|1|DA|U|1993
Interaction  | Interacting Bases [2,4] | Pair Probability [[0.017898242,0.039832166,0.003960910,0.461511524,0.000000000],[0.003960910,0.319173624,0.009494562,0.003960910,0.000000000],[0.018590254,0.003960910,0.030122383,0.022980723,0.000000000],[0.003960910,0.003960910,0.017616762,0.039014302,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DA|A|1668 - 5J7L|1|DA|U|1991 tHW 
Interaction  | Interacting Bases [1,6] | Pair Probability [[0.013077402,0.016509270,0.000599176,0.003636415,0.000000000],[0.007585540,0.007458860,0.000599176,0.000599176,0.000000000],[0.355990514,0.004194232,0.030052293,0.484843713,0.000000000],[0.049742739,0.023913142,0.000599176,0.000599176,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DA|G|1667 - 5J7L|1|DA|U|1993 tSH 
Interaction  | Interacting Bases [3,6] | Pair Probability [[0.008849144,0.020982013,0.009451078,0.259997638,0.000000000],[0.016699564,0.009132583,0.185092798,0.009874781,0.000000000],[0.009432681,0.187492341,0.001945771,0.050727154,0.000000000],[0.186863639,0.010512826,0.021937258,0.011008732,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DA|A|1669 - 5J7L|1|DA|U|1993 cWW 
Interaction  | Interacting Bases [5,5] | Pair Probability [[0.055555556,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.055555556,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.833333333,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.055555556,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion 5J7L|1|DA|G|1992
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 [10] // Initial node 5J7L|1|DA|C|1670 - 5J7L|1|DA|C|1990 from node 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.009803922,0.558823529,0.284313725,0.147058824,0.000000000] | Position [1] | Left Index [5] | Right Index [10] // Fixed node on left for 5J7L|1|DA|C|1670
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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [6] | Right Index [10] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.001449275,0.001449275,0.001449275,0.995652174,0.000000000] | Position [1] | Left Index [6] | Right Index [10] // Fixed node on left for 5J7L|1|DA|U|1671
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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [7] | Right Index [10] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.166666667,0.611111111,0.055555556,0.166666667,0.000000000] | Position [1] | Left Index [7] | Right Index [10] // Fixed node on left for 5J7L|1|DA|A|1672
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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [8] | Right Index [10] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.055555556,0.055555556,0.611111111,0.277777778,0.000000000] | Position [1] | Left Index [8] | Right Index [10] // Fixed node on left for 5J7L|1|DA|G|1673
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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [9] | Right Index [10] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009278847,0.019324516,0.010566130,0.191913241,0.000000000],[0.016298546,0.009098841,0.193539411,0.012663253,0.000000000],[0.010448787,0.264585590,0.001991650,0.025514464,0.000000000],[0.189457119,0.013143234,0.022364576,0.009811793,0.000000000],[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 [9] | Right Index [10] // Basepair G1674 - C1990 cWW 
HairpinNode  | Num Bases [1] | Left Index [10] | Right Index [10] | 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
