Character Definition | A,C,G,U,* // Define characters here
InitialNode  | 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 [1] | Right Index [12] // Initial node C242 - G284 from junction 
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.010130121,0.017375838,0.011773595,0.194301502,0.000000000],[0.020979332,0.008652269,0.227023763,0.014063448,0.000000000],[0.011923689,0.210487931,0.002171228,0.024023321,0.000000000],[0.195430021,0.013397471,0.027849658,0.010416811,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [12] // Basepair C242 - G284 cWW 
ClusterNode  | Deletion Probability [0.000000000000000000000000000232685345145757480000000000000000] | Num Left Bases [4] | Num Right Bases [6] | Left Index [2] | Right Index [11] | Norm Constant [0.028977363705361] // Cluster node A243:G247 and C277:C283
Interaction  | Interacting Bases [4,5] | Pair Probability [[0.010296034,0.020975088,0.011921277,0.195390483,0.000000000],[0.017372323,0.008489812,0.210445347,0.013394761,0.000000000],[0.011771213,0.226979836,0.002170788,0.027844024,0.000000000],[0.194262192,0.014060602,0.024018461,0.010607760,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G247 - C277 cWW 
Interaction  | Interacting Bases [3,8] | Pair Probability [[0.190666382,0.192362741,0.239629664,0.207247608,0.000000000],[0.044449215,0.040324841,0.000459457,0.039931327,0.000000000],[0.000459457,0.000459457,0.002225974,0.000459457,0.000000000],[0.002187877,0.000459457,0.038217626,0.000459457,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A246 - G281 tHS 
Interaction  | Interacting Bases [1,9] | Pair Probability [[0.821017114,0.001622232,0.139108884,0.001622232,0.000000000],[0.012807291,0.001191887,0.001857199,0.000324446,0.000000000],[0.001622232,0.000324446,0.004018911,0.002894936,0.000000000],[0.007735101,0.000324446,0.001920742,0.001607897,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A243 - A282 tWH 
Interaction  | Interacting Bases [4,9] | Pair Probability [[0.027712781,0.006212429,0.007326944,0.006291967,0.000000000],[0.006675544,0.001335109,0.001335109,0.001335109,0.000000000],[0.677455366,0.118763300,0.120038767,0.014836705,0.000000000],[0.006675544,0.001335109,0.001335109,0.001335109,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G247 - A282 tSS 
Interaction  | Interacting Bases [2,10] | Pair Probability [[0.001230782,0.029830503,0.001880084,0.005330434,0.000000000],[0.006116993,0.871448255,0.004904624,0.003243165,0.000000000],[0.002001172,0.033694550,0.001230782,0.004115946,0.000000000],[0.005447712,0.018814483,0.005603215,0.005107300,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction C245 - C283 cWW 
Interaction  | Interacting Bases [5,9] | Pair Probability [[0.152585019,0.031075256,0.030154202,0.030666816,0.000000000],[0.184000410,0.031248979,0.003826899,0.028728496,0.000000000],[0.162621226,0.033023087,0.029991440,0.033218374,0.000000000],[0.157692540,0.030743306,0.029504872,0.030919078,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction C277 - A282 cSS 
Interaction  | Interacting Bases [6,6] | Pair Probability [[0.166666667,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.166666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.500000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.166666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion G278
Interaction  | Interacting Bases [7,7] | Pair Probability [[0.500000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.166666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.166666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.166666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion A279
Insertion    | Location [1] | Length Distribution [0.045351474,0.907029478,0.045351474,0.002267574] | Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000]// Insertion after nucleotide 2, position 1 in cluster node
Insertion    | Location [7] | Length Distribution [0.045351474,0.907029478,0.045351474,0.002267574] | Letter Distribution [0.166666667,0.500000000,0.166666667,0.166666667,0.000000000]// Insertion after nucleotide 8, position 7 in cluster node
InitialNode  | 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 [5] // New Initial node after Cluster
HairpinNode  | Num Bases [1] | Left Index [6] | Right Index [6] | 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
