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 [9] // Initial node
ClusterNode  | Deletion Probability [0.000000000000000000000000000000075522783116710514280331600352] | Num Left Bases [5] | Num Right Bases [4] | Left Index [1] | Right Index [9] | Norm Constant [0.004618463055059] // Cluster node 8CRE|1|CM|G|1474:8CRE|1|CM|C|1481 and 8CRE|1|CM|G|1500:8CRE|1|CM|C|1505
Interaction  | Interacting Bases [1,6] | Pair Probability [[0.020814325,0.017422103,0.019901827,0.012513985,0.000000000],[0.002436905,0.002436905,0.214331865,0.002436905,0.000000000],[0.236896108,0.002436905,0.263298345,0.195326202,0.000000000],[0.002436905,0.002436905,0.002436905,0.002436905,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8CRE|1|CM|G|1474 - 8CRE|1|CM|G|1500 tSS 
Interaction  | Interacting Bases [5,6] | 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]] // Cluster Interaction 8CRE|1|CM|C|1481 - 8CRE|1|CM|G|1500 cWW 
Interaction  | Interacting Bases [1,9] | Pair Probability [[0.009733692,0.020271796,0.011084078,0.201320753,0.000000000],[0.017097495,0.009544863,0.203026637,0.013284001,0.000000000],[0.010960983,0.228535864,0.002089280,0.026765173,0.000000000],[0.198744233,0.013787510,0.023460879,0.010292763,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8CRE|1|CM|G|1474 - 8CRE|1|CM|C|1505 cWW 
Interaction  | Interacting Bases [4,5] | Pair Probability [[0.082210046,0.097234592,0.033420247,0.052352316,0.000000000],[0.080415734,0.079793580,0.031205189,0.035250447,0.000000000],[0.035590367,0.041009111,0.082216806,0.077287923,0.000000000],[0.082398445,0.081776461,0.031205189,0.076633547,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8CRE|1|CM|G|1480 - 8CRE|1|CM|C|1481 cSH 
Interaction  | Interacting Bases [6,8] | Pair Probability [[0.186693611,0.024987054,0.025580639,0.023621300,0.000000000],[0.193995912,0.027238031,0.001093673,0.003725525,0.000000000],[0.221428767,0.001117795,0.002478354,0.019882187,0.000000000],[0.190424981,0.025084591,0.025283684,0.027363897,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8CRE|1|CM|G|1500 - 8CRE|1|CM|A|1502 cSS 
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.125000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.125000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.125000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.625000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 8CRE|1|CM|U|1475
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.625000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.125000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.125000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.125000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 8CRE|1|CM|A|1478
Interaction  | Interacting Bases [7,7] | Pair Probability [[0.375000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.125000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.125000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.375000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion 8CRE|1|CM|A|1501
Insertion    | Location [2] | Length Distribution [0.000000000,0.023781213,0.951248514,0.023781213,0.001189061] | Letter Distribution [0.250000000,0.250000000,0.083333333,0.416666667,0.000000000]// Insertion after nucleotide 2, position 2 in cluster node
Insertion    | Location [3] | Length Distribution [0.493381468,0.493381468,0.012635379,0.000601685] | Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000]// Insertion after nucleotide 3, position 3 in cluster node
Insertion    | Location [8] | Length Distribution [0.000000000,0.023781213,0.951248514,0.023781213,0.001189061] | Letter Distribution [0.416666667,0.083333333,0.083333333,0.416666667,0.000000000]// Insertion after nucleotide 8, position 8 in cluster node
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 [0.991950402,0.007999600,0.000049998] | 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
