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 [12] // Initial node
ClusterNode  | Deletion Probability [0.000000000000000000000000000029021405463065428485660525039999] | Num Left Bases [6] | Num Right Bases [4] | Left Index [1] | Right Index [12] | Norm Constant [0.117008820568612] // Cluster node 8CRE|1|CM|U|346:8CRE|1|CM|C|352 and 8CRE|1|CM|A|310:8CRE|1|CM|A|314
Interaction  | Interacting Bases [5,7] | Pair Probability [[0.803231417,0.018844492,0.002201613,0.009948471,0.000000000],[0.001511225,0.001868573,0.001090739,0.000440323,0.000000000],[0.133317176,0.000440323,0.016185120,0.002110466,0.000000000],[0.001511225,0.000440323,0.004713074,0.002145443,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8CRE|1|CM|A|351 - 8CRE|1|CM|A|310 tHW 
Interaction  | Interacting Bases [6,8] | Pair Probability [[0.002258967,0.017330000,0.003007505,0.005237479,0.000000000],[0.069815701,0.643098415,0.029091658,0.021683181,0.000000000],[0.003084620,0.004976126,0.001072788,0.006082084,0.000000000],[0.011408774,0.008425958,0.013315724,0.160111018,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8CRE|1|CM|C|352 - 8CRE|1|CM|C|312 cWW 
Interaction  | Interacting Bases [2,9] | Pair Probability [[0.260468194,0.048672574,0.049381382,0.047608366,0.000000000],[0.094585337,0.018917067,0.021849086,0.018917067,0.000000000],[0.184654794,0.018917067,0.021299188,0.044345720,0.000000000],[0.113632956,0.018917067,0.018917067,0.018917067,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8CRE|1|CM|U|347 - 8CRE|1|CM|A|313 tSS 
Interaction  | Interacting Bases [4,9] | Pair Probability [[0.222551838,0.025457994,0.000451073,0.002385117,0.000000000],[0.201478893,0.030653792,0.000451073,0.000451073,0.000000000],[0.238483019,0.000451073,0.002916006,0.026484733,0.000000000],[0.206969977,0.039912193,0.000451073,0.000451073,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8CRE|1|CM|A|350 - 8CRE|1|CM|A|313 tSH 
Interaction  | Interacting Bases [1,10] | Pair Probability [[0.009068947,0.016785052,0.010240914,0.192150589,0.000000000],[0.020383894,0.009481442,0.226915719,0.012329706,0.000000000],[0.010320187,0.193924261,0.002012365,0.022633063,0.000000000],[0.215849209,0.011775691,0.036312554,0.009816407,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8CRE|1|CM|U|346 - 8CRE|1|CM|A|314 cWW 
Interaction  | Interacting Bases [5,10] | Pair Probability [[0.290766161,0.211686976,0.246332931,0.200749936,0.000000000],[0.000435523,0.000435523,0.004512991,0.000435523,0.000000000],[0.003414902,0.000435523,0.003556849,0.035495069,0.000000000],[0.000435523,0.000435523,0.000435523,0.000435523,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8CRE|1|CM|A|351 - 8CRE|1|CM|A|314 tSS 
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.500000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.071428571,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.071428571,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.357142857,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 8CRE|1|CM|U|348
Insertion    | Location [3] | Length Distribution [0.009799118,0.979911808,0.009799118,0.000489956] | Letter Distribution [0.071428571,0.642857143,0.071428571,0.214285714,0.000000000]// Insertion after nucleotide 3, position 3 in cluster node
Insertion    | Location [7] | Length Distribution [0.007839294,0.783929446,0.009799118,0.196374326,0.001959824,0.000097991] | Letter Distribution [0.277777778,0.055555556,0.166666667,0.500000000,0.000000000]// Insertion after nucleotide 9, position 7 in cluster node
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 [8] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.012976294,0.180303759,0.012628659,0.127035366,0.000000000],[0.015259622,0.011195867,0.110804474,0.013656246,0.000000000],[0.012449884,0.113794944,0.002702943,0.227432330,0.000000000],[0.099055733,0.014431233,0.018151332,0.028121313,0.000000000],[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 [7] | Right Index [8] // Basepair G353 - U309 cWW 
HairpinNode  | Num Bases [1] | Left Index [8] | Right Index [8] | 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
