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 [24] // Initial node
BasepairNode | Deletion Probability [0.0000229437914523] | 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]] | 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 [1] | Right Index [24] // Basepair U1295 - A1201 cWW 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.112745781,0.119356604,0.001353438,0.006378757,0.000000000],[0.113583401,0.119080223,0.001353438,0.001353438,0.000000000],[0.154951637,0.001353438,0.006616528,0.114874695,0.000000000],[0.125854401,0.118437346,0.001353438,0.001353438,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | 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 [2] | Right Index [23] // Basepair G1296 - A1200 tSH 
BasepairNode | Deletion Probability [0.0000001182498160] | Pair Probability [[0.762885534,0.085303445,0.005090852,0.005193883,0.000000000],[0.093414410,0.000151689,0.012931624,0.001441365,0.000000000],[0.005293967,0.012766360,0.000378616,0.000151689,0.000000000],[0.007211991,0.007481193,0.000151689,0.000151689,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.023781213,0.951248514,0.023781213,0.001189061] | Left Letter Distribution [0.625000000,0.125000000,0.125000000,0.125000000,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [22] // Basepair A1297 - A1199 tHH 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.625000000,0.125000000,0.125000000,0.125000000,0.000000000] | Position [1] | Left Index [4] | Right Index [21] // Fixed node on left for 8CRE|1|1|A|1193
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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [21] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.625000000,0.125000000,0.125000000,0.125000000,0.000000000] | Position [1] | Left Index [5] | Right Index [21] // Fixed node on left for 8CRE|1|1|C|1194
InitialNode  | Left Length Distribution [0.000000000,0.023781213,0.951248514,0.023781213,0.001189061] | Left Letter Distribution [0.083333333,0.083333333,0.416666667,0.416666667,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [6] | Right Index [21] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.031250000,0.031250000,0.906250000,0.031250000,0.000000000] | Position [1] | Left Index [6] | Right Index [21] // Fixed node on left for 8CRE|1|1|C|1195
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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [7] | Right Index [21] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.906250000,0.031250000,0.031250000,0.031250000,0.000000000] | Position [1] | Left Index [7] | Right Index [21] // Fixed node on left for 8CRE|1|1|A|1196
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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [8] | Right Index [21] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.125000000,0.125000000,0.125000000,0.625000000,0.000000000] | Position [1] | Left Index [8] | Right Index [21] // Fixed node on left for 8CRE|1|1|C|1197
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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [9] | Right Index [21] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.125000000,0.125000000,0.625000000,0.125000000,0.000000000] | Position [1] | Left Index [9] | Right Index [21] // Fixed node on left for 8CRE|1|1|A|1198
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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [10] | Right Index [21] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.125000000,0.125000000,0.625000000,0.125000000,0.000000000] | Position [1] | Left Index [10] | Right Index [21] // Fixed node on left for 8CRE|1|1|A|1199
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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [11] | Right Index [21] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.125000000,0.625000000,0.125000000,0.125000000,0.000000000] | Position [1] | Left Index [11] | Right Index [21] // Fixed node on left for 8CRE|1|1|A|1200
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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [12] | Right Index [21] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.875000000,0.041666667,0.041666667,0.041666667,0.000000000] | Position [2] | Left Index [12] | Right Index [21] // Fixed node on right for 8CRE|1|1|G|1303
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 [12] | Right Index [20] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.125000000,0.625000000,0.125000000,0.125000000,0.000000000] | Position [2] | Left Index [12] | Right Index [20] // Fixed node on right for 8CRE|1|1|G|1302
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 [12] | Right Index [19] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.625000000,0.125000000,0.125000000,0.125000000,0.000000000] | Position [2] | Left Index [12] | Right Index [19] // Fixed node on right for 8CRE|1|1|U|1301
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 [12] | Right Index [18] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.125000000,0.625000000,0.125000000,0.125000000,0.000000000] | Position [2] | Left Index [12] | Right Index [18] // Fixed node on right for 8CRE|1|1|A|1300
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 [12] | Right Index [17] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.125000000,0.625000000,0.125000000,0.125000000,0.000000000] | Position [2] | Left Index [12] | Right Index [17] // Fixed node on right for 8CRE|1|1|A|1299
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 [12] | Right Index [16] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.625000000,0.125000000,0.125000000,0.125000000,0.000000000] | Position [2] | Left Index [12] | Right Index [16] // Fixed node on right for 8CRE|1|1|A|1298
InitialNode  | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.023781213,0.951248514,0.023781213,0.001189061] | Right Letter Distribution [0.125000000,0.625000000,0.125000000,0.125000000,0.000000000] | Left Index [12] | Right Index [15] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.022937090,0.014347847,0.348044880,0.017561601,0.000000000],[0.014692845,0.010155161,0.019218678,0.045122890,0.000000000],[0.381868061,0.019005244,0.003622602,0.015644206,0.000000000],[0.017595852,0.042706478,0.015986694,0.011489870,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | 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 [12] | Right Index [15] // Basepair G1309 - A1191 cWW 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009536579,0.017101376,0.010963471,0.198789353,0.000000000],[0.020276398,0.009712729,0.228583296,0.013790641,0.000000000],[0.011086594,0.203072729,0.002089755,0.023466206,0.000000000],[0.201366458,0.013287017,0.026771249,0.010106148,0.000000000],[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 [13] | Right Index [14] // Basepair C1310 - G1190 cWW 
HairpinNode  | Num Bases [1] | Left Index [14] | Right Index [14] | 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
