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 [19] // Initial node
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.009096159,0.016527150,0.010380816,0.190892026,0.000000000],[0.019794727,0.009365287,0.246335869,0.012829884,0.000000000],[0.010482647,0.194028432,0.002003598,0.022513545,0.000000000],[0.203692206,0.012318528,0.030014751,0.009724374,0.000000000],[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 [19] // Basepair C245 - G437 cWW 
JunctionNode | Branches [2]  | Left Index [2] | Right Index [18] // Junction node C246 - A436 ID J6550
InitialNode  | Left Length Distribution [1.000000000] | Left Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [3] // Initial node
BasepairNode | Deletion Probability [0.0000224863733088] | Pair Probability [[0.009450884,0.015956080,0.011081266,0.165384558,0.000000000],[0.064779646,0.012271176,0.221537108,0.013630044,0.000000000],[0.011230126,0.168795395,0.002205978,0.021170298,0.000000000],[0.175296480,0.013008887,0.083924597,0.010277478,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.990049834,0.009900498,0.000049502,0.000000165] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.990049834,0.009900498,0.000049502,0.000000165] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [3] // Basepair C246 - G383 cWW 
HairpinNode  | Num Bases [1] | Left Index [3] | Right Index [3] | 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
InitialNode  | Left Length Distribution [1.000000000] | 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 [4] | Right Index [18] // Initial node 7A0S|1|X|A|384 - 7A0S|1|X|A|436 from node 
JunctionNode | Branches [2]  | Left Index [4] | Right Index [18] // Junction node A384 - A436 ID J1626
InitialNode  | Left Length Distribution [1.000000000] | Left Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [12] // Initial node
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.417171827,0.289668157,0.017287202,0.017637068,0.000000000],[0.067920990,0.000772046,0.065817481,0.007336049,0.000000000],[0.003849208,0.064976341,0.001927026,0.000772046,0.000000000],[0.005243791,0.038076678,0.000772046,0.000772046,0.000000000],[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 [4] | Right Index [12] // Basepair A384 - A415 tHH 
ClusterNode  | Deletion Probability [0.0000001250000000] | Num Left Bases [2] | Num Right Bases [1] | Left Index [5] | Right Index [11] | Norm Constant [0.283040840551315] // Cluster node 7A0S|1|X|G|385:7A0S|1|X|U|386 and 7A0S|1|X|A|414:7A0S|1|X|A|414
Interaction  | Interacting Bases [2,3] | Pair Probability [[0.018067094,0.003998277,0.018765634,0.003998277,0.000000000],[0.040207941,0.322184696,0.003998277,0.003998277,0.000000000],[0.003998277,0.009584133,0.030406557,0.017782958,0.000000000],[0.456431444,0.003998277,0.023197522,0.039382361,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 7A0S|1|X|U|386 - 7A0S|1|X|A|414 tWH 
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.037660918,0.038374747,0.002109963,0.037503112,0.000000000],[0.028116336,0.042371811,0.000467182,0.037581732,0.000000000],[0.163663517,0.002323717,0.199641593,0.288975486,0.000000000],[0.038245262,0.038015670,0.000467182,0.044481773,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 7A0S|1|X|G|385 - 7A0S|1|X|U|386 cSH 
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 [7] | Right Index [10] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.056207763,0.056830275,0.362233015,0.060888198,0.000000000],[0.052349381,0.057195926,0.003180057,0.069800068,0.000000000],[0.000656205,0.000656205,0.015617141,0.000656205,0.000000000],[0.003098284,0.000656205,0.259318862,0.000656205,0.000000000],[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 [7] | Right Index [10] // Basepair A387 - G413 tHS 
BasepairNode | Deletion Probability [0.0000224863733088] | Pair Probability [[0.011261729,0.107215514,0.011664304,0.155467535,0.000000000],[0.016389492,0.010279223,0.162705215,0.013304776,0.000000000],[0.011565927,0.164350628,0.002381099,0.139045256,0.000000000],[0.140070064,0.013731238,0.020730402,0.019837597,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.990049834,0.009900498,0.000049502,0.000000165] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.990049834,0.009900498,0.000049502,0.000000165] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [8] | Right Index [9] // Basepair G388 - U412 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
InitialNode  | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.400000000,0.200000000,0.200000000,0.200000000,0.000000000] | Left Index [13] | Right Index [18] // Initial node 7A0S|1|X|U|416 - 7A0S|1|X|A|436 from node 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.062500000,0.062500000,0.187500000,0.687500000,0.000000000] | Position [1] | Left Index [13] | Right Index [18] // Fixed node on left for 7A0S|1|X|U|416
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 [14] | Right Index [18] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.312500000,0.437500000,0.062500000,0.187500000,0.000000000] | Position [1] | Left Index [14] | Right Index [18] // Fixed node on left for 7A0S|1|X|C|417
InitialNode  | Left Length Distribution [0.170928484,0.821824149,0.006905511,0.000341857] | Left Letter Distribution [0.214285714,0.214285714,0.071428571,0.500000000,0.000000000] | 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 [0.965909091,0.011363636,0.011363636,0.011363636,0.000000000] | Position [2] | Left Index [15] | Right Index [18] // Fixed node on right for 7A0S|1|X|A|435
InitialNode  | Left Length Distribution [1.000000000] | 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 [15] | Right Index [17] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.953125000,0.015625000,0.015625000,0.015625000,0.000000000] | Position [2] | Left Index [15] | Right Index [17] // Fixed node on right for 7A0S|1|X|C|434
InitialNode  | Left Length Distribution [1.000000000] | 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 [15] | Right Index [16] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000224863733088] | Pair Probability [[0.012272627,0.152086787,0.012202235,0.137151389,0.000000000],[0.015338437,0.010772651,0.125599160,0.013403298,0.000000000],[0.012034920,0.138448119,0.002566276,0.196748461,0.000000000],[0.113641780,0.014123779,0.018746004,0.024864074,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.990049834,0.009900498,0.000049502,0.000000165] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.990049834,0.009900498,0.000049502,0.000000165] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [15] | Right Index [16] // Basepair G419 - C434 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
