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 [20] // Initial node
ClusterNode  | Deletion Probability [0.0000000006250000] | Num Left Bases [2] | Num Right Bases [2] | Left Index [1] | Right Index [20] | Norm Constant [0.102960781865258] // Cluster node 4N0T|1|B|G|39:4N0T|1|B|A|40 and 4N0T|1|B|A|91:4N0T|1|B|C|92
Interaction  | Interacting Bases [2,3] | Pair Probability [[0.414443196,0.029718936,0.003853170,0.018419488,0.000000000],[0.028948610,0.014046437,0.011475468,0.014056646,0.000000000],[0.003853170,0.011491976,0.356313449,0.021716090,0.000000000],[0.018397520,0.014053216,0.021246137,0.017966491,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4N0T|1|B|A|40 - 4N0T|1|B|A|91 tWW 
Interaction  | Interacting Bases [1,4] | Pair Probability [[0.009639190,0.020074982,0.010976465,0.199366183,0.000000000],[0.016931500,0.009452194,0.201055505,0.013155030,0.000000000],[0.010854565,0.236025807,0.002068996,0.026505317,0.000000000],[0.196814677,0.013653651,0.023233104,0.010192834,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4N0T|1|B|G|39 - 4N0T|1|B|C|92 cWW 
Interaction  | Interacting Bases [2,4] | Pair Probability [[0.027592739,0.433108352,0.003577501,0.042260225,0.000000000],[0.016009541,0.015725019,0.010497055,0.015889125,0.000000000],[0.003577501,0.013947311,0.020907921,0.328397734,0.000000000],[0.016793903,0.015291395,0.016168069,0.020256609,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4N0T|1|B|A|40 - 4N0T|1|B|C|92 tWW 
InitialNode  | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [18] // Initial node 4N0T|1|B|A|41 - 4N0T|1|B|U|90 from node 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.700000000,0.100000000,0.100000000,0.100000000,0.000000000] | Position [1] | Left Index [3] | Right Index [18] // Fixed node on left for 4N0T|1|B|A|41
InitialNode  | Left Length Distribution [0.016116035,0.966962127,0.016116035,0.000805802] | Left Letter Distribution [0.700000000,0.100000000,0.100000000,0.100000000,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [18] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.100000000,0.700000000,0.100000000,0.100000000,0.000000000] | Position [1] | Left Index [4] | Right Index [18] // Fixed node on left for 4N0T|1|B|A|42
InitialNode  | Left Length Distribution [0.993970181,0.005999820,0.000029999] | 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 [5] | Right Index [18] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.700000000,0.100000000,0.100000000,0.100000000,0.000000000] | Position [1] | Left Index [5] | Right Index [18] // Fixed node on left for 4N0T|1|B|C|43
InitialNode  | Left Length Distribution [0.993970181,0.005999820,0.000029999] | 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 [18] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.700000000,0.100000000,0.100000000,0.100000000,0.000000000] | Position [1] | Left Index [6] | Right Index [18] // Fixed node on left for 4N0T|1|B|A|44
InitialNode  | Left Length Distribution [0.993970181,0.005999820,0.000029999] | 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 [18] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.100000000,0.100000000,0.100000000,0.700000000,0.000000000] | Position [1] | Left Index [7] | Right Index [18] // Fixed node on left for 4N0T|1|B|A|45
InitialNode  | Left Length Distribution [0.993970181,0.005999820,0.000029999] | 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 [18] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.700000000,0.100000000,0.100000000,0.100000000,0.000000000] | Position [1] | Left Index [8] | Right Index [18] // Fixed node on left for 4N0T|1|B|U|46
InitialNode  | Left Length Distribution [0.993970181,0.005999820,0.000029999] | 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 [18] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.021739130,0.934782609,0.021739130,0.021739130,0.000000000] | Position [1] | Left Index [9] | Right Index [18] // Fixed node on left for 4N0T|1|B|A|47
InitialNode  | Left Length Distribution [0.016116035,0.966962127,0.016116035,0.000805802] | Left Letter Distribution [0.700000000,0.100000000,0.100000000,0.100000000,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [10] | Right Index [18] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.100000000,0.100000000,0.700000000,0.100000000,0.000000000] | Position [1] | Left Index [10] | Right Index [18] // Fixed node on left for 4N0T|1|B|C|48
InitialNode  | Left Length Distribution [0.993970181,0.005999820,0.000029999] | 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 [11] | Right Index [18] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.700000000,0.100000000,0.100000000,0.100000000,0.000000000] | Position [1] | Left Index [11] | Right Index [18] // Fixed node on left for 4N0T|1|B|A|49
InitialNode  | Left Length Distribution [0.993970181,0.005999820,0.000029999] | 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 [12] | Right Index [18] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.100000000,0.100000000,0.700000000,0.100000000,0.000000000] | Position [1] | Left Index [12] | Right Index [18] // Fixed node on left for 4N0T|1|B|G|50
InitialNode  | Left Length Distribution [0.993970181,0.005999820,0.000029999] | 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 [13] | Right Index [18] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.700000000,0.100000000,0.100000000,0.100000000,0.000000000] | Position [1] | Left Index [13] | Right Index [18] // Fixed node on left for 4N0T|1|B|A|51
InitialNode  | Left Length Distribution [0.000000000,0.016116035,0.966962127,0.016116035,0.000805802] | Left Letter Distribution [0.062500000,0.062500000,0.437500000,0.437500000,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [14] | Right Index [18] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.700000000,0.100000000,0.100000000,0.100000000,0.000000000] | Position [1] | Left Index [14] | Right Index [18] // Fixed node on left for 4N0T|1|B|G|52
InitialNode  | Left Length Distribution [0.000000000,0.016116035,0.966962127,0.016116035,0.000805802] | Left Letter Distribution [0.062500000,0.437500000,0.062500000,0.437500000,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [15] | Right Index [18] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.100000000,0.100000000,0.100000000,0.700000000,0.000000000] | Position [2] | Left Index [15] | Right Index [18] // Fixed node on right for 4N0T|1|B|A|56
InitialNode  | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [15] | Right Index [17] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.100000000,0.100000000,0.100000000,0.700000000,0.000000000] | Position [2] | Left Index [15] | Right Index [17] // Fixed node on right for 4N0T|1|B|G|55
InitialNode  | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [15] | Right Index [16] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009192800,0.021796849,0.009818110,0.231259682,0.000000000],[0.017348091,0.009487247,0.192280868,0.010258268,0.000000000],[0.009798999,0.194773596,0.002021335,0.052697140,0.000000000],[0.194120479,0.010921091,0.022789191,0.011436255,0.000000000],[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 [15] | Right Index [16] // Basepair A59 - U88 cWW 
HairpinNode  | Num Bases [1] | Left Index [16] | Right Index [16] | 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
