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 [11] // Initial node G81 - C105 from junction 
BasepairNode | Deletion Probability [0.0000224390099112] | 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]] | 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 [11] // Basepair G81 - C105 cWW 
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.129850760,0.123187903,0.001408720,0.007167075,0.000000000],[0.131556337,0.118915693,0.001408720,0.001408720,0.000000000],[0.127086369,0.001408720,0.008075066,0.065210568,0.000000000],[0.150772980,0.129724929,0.001408720,0.001408720,0.000000000],[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 [2] | Right Index [10] // Basepair U82 - A104 tSH 
ClusterNode  | Deletion Probability [0.000000000000000000000009533766986221214500000000000000000000] | Num Left Bases [3] | Num Right Bases [4] | Left Index [3] | Right Index [9] | Norm Constant [0.006232170137623] // Cluster node A83:G85 and C97:A103
Interaction  | Interacting Bases [3,4] | 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 G85 - C97 cWW 
Interaction  | Interacting Bases [2,5] | Pair Probability [[0.174118473,0.194070639,0.222296295,0.186214291,0.000000000],[0.002123953,0.002123953,0.002123953,0.002123953,0.000000000],[0.011656043,0.013453433,0.020740876,0.160458324,0.000000000],[0.002123953,0.002123953,0.002123953,0.002123953,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A84 - G98 tSS 
Interaction  | Interacting Bases [1,7] | Pair Probability [[0.170710115,0.128906975,0.001608091,0.012727400,0.000000000],[0.155925473,0.063872294,0.001608091,0.001608091,0.000000000],[0.133465681,0.001608091,0.013969090,0.019871564,0.000000000],[0.148228098,0.142674762,0.001608091,0.001608091,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A83 - A103 tSH 
Interaction  | Interacting Bases [3,7] | Pair Probability [[0.012966971,0.014534159,0.017141599,0.014720238,0.000000000],[0.003123526,0.003123526,0.003123526,0.003123526,0.000000000],[0.322253558,0.277850187,0.280834180,0.034710902,0.000000000],[0.003123526,0.003123526,0.003123526,0.003123526,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G85 - A103 tSS 
Interaction  | Interacting Bases [4,7] | Pair Probability [[0.063946723,0.065116510,0.063186491,0.064260646,0.000000000],[0.082864165,0.065480538,0.008019060,0.060199002,0.000000000],[0.068152788,0.069198085,0.062845432,0.069607299,0.000000000],[0.066087230,0.064420927,0.061825857,0.064789247,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction C97 - A103 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],[0.000000000,0.000000000,0.166666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.500000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion U99
Insertion    | Location [6] | Length Distribution [0.000000000,0.000000000,0.045351474,0.907029478,0.045351474,0.002267574] | Letter Distribution [0.300000000,0.100000000,0.100000000,0.500000000,0.000000000]// Insertion after nucleotide 8, position 6 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
