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 [23] // Initial node
ClusterNode  | Deletion Probability [0.000000000000000000000000000000000000000000000000000011361589] | Num Left Bases [12] | Num Right Bases [9] | Left Index [1] | Right Index [23] | Norm Constant [0.000021674562286] // Cluster node 1NBS|1|B|C|184:1NBS|1|B|G|196 and 1NBS|1|B|G|217:1NBS|1|B|G|226
Interaction  | Interacting Bases [7,13] | Pair Probability [[0.004966430,0.004966430,0.206503547,0.017165095,0.000000000],[0.004966430,0.052642128,0.004966430,0.004966430,0.000000000],[0.051077026,0.004966430,0.506544030,0.015536138,0.000000000],[0.042074794,0.017912101,0.004966430,0.055780127,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 1NBS|1|B|G|190 - 1NBS|1|B|G|217 cHW 
Interaction  | Interacting Bases [4,14] | Pair Probability [[0.182515075,0.189130397,0.188336532,0.209508482,0.000000000],[0.025620151,0.027220148,0.001139121,0.025015907,0.000000000],[0.026251560,0.001114163,0.003092545,0.025986527,0.000000000],[0.023668144,0.021956376,0.023814207,0.025630666,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 1NBS|1|B|A|187 - 1NBS|1|B|U|218 cSS 
Interaction  | Interacting Bases [2,16] | Pair Probability [[0.019674940,0.022627159,0.420271327,0.346678609,0.000000000],[0.018725299,0.004103703,0.017645274,0.043903004,0.000000000],[0.033745492,0.017830048,0.004103703,0.004103703,0.000000000],[0.019705139,0.018675191,0.004103703,0.004103703,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 1NBS|1|B|A|185 - 1NBS|1|B|G|220 tHH 
Interaction  | Interacting Bases [1,17] | Pair Probability [[0.061881188,0.061881188,0.061881188,0.061881188,0.000000000],[0.071782178,0.061881188,0.061881188,0.061881188,0.000000000],[0.061881188,0.061881188,0.061881188,0.061881188,0.000000000],[0.061881188,0.061881188,0.061881188,0.061881188,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 1NBS|1|B|C|184 - 1NBS|1|B|A|221 tSS 
Interaction  | Interacting Bases [5,18] | Pair Probability [[0.071773872,0.071430006,0.000892096,0.004313658,0.000000000],[0.083480414,0.003933530,0.000892096,0.003566586,0.000000000],[0.634367958,0.006244670,0.006244670,0.020478373,0.000000000],[0.077201799,0.003877011,0.007019357,0.004283906,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 1NBS|1|B|G|188 - 1NBS|1|B|A|222 tSW 
Interaction  | Interacting Bases [10,19] | Pair Probability [[0.024752475,0.024752475,0.024752475,0.024752475,0.000000000],[0.024752475,0.024752475,0.024752475,0.024752475,0.000000000],[0.173267327,0.183168317,0.173267327,0.173267327,0.000000000],[0.024752475,0.024752475,0.024752475,0.024752475,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 1NBS|1|B|G|193 - 1NBS|1|B|C|223 cHW 
Interaction  | Interacting Bases [9,20] | Pair Probability [[0.061881188,0.061881188,0.061881188,0.061881188,0.000000000],[0.061881188,0.061881188,0.071782178,0.061881188,0.000000000],[0.061881188,0.061881188,0.061881188,0.061881188,0.000000000],[0.061881188,0.061881188,0.061881188,0.061881188,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 1NBS|1|B|C|192 - 1NBS|1|B|G|224 cWH 
Interaction  | Interacting Bases [1,21] | Pair Probability [[0.009631000,0.017270697,0.011072020,0.200757565,0.000000000],[0.020477154,0.009808895,0.220945507,0.013927182,0.000000000],[0.011196362,0.205083350,0.002110445,0.023698544,0.000000000],[0.203360186,0.013418572,0.027036311,0.010206209,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 1NBS|1|B|C|184 - 1NBS|1|B|G|226 cWW 
Interaction  | Interacting Bases [4,8] | Pair Probability [[0.500586469,0.004906855,0.432872759,0.004906855,0.000000000],[0.005999965,0.002974708,0.000700979,0.000700979,0.000000000],[0.000700979,0.001736421,0.025766190,0.007503062,0.000000000],[0.003167529,0.000700979,0.003359793,0.003415476,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 1NBS|1|B|A|187 - 1NBS|1|B|A|191 tWH 
Interaction  | Interacting Bases [8,9] | Pair Probability [[0.104166825,0.124612443,0.005621093,0.043860124,0.000000000],[0.100542670,0.099286043,0.001147115,0.009317734,0.000000000],[0.010004306,0.001147115,0.104180479,0.094225112,0.000000000],[0.104547355,0.103291070,0.001147115,0.092903402,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 1NBS|1|B|A|191 - 1NBS|1|B|C|192 cSH 
Interaction  | Interacting Bases [7,11] | Pair Probability [[0.083071528,0.077827995,0.079676854,0.073574035,0.000000000],[0.086320773,0.084839186,0.003406498,0.011604013,0.000000000],[0.099703595,0.003481632,0.007719409,0.061927698,0.000000000],[0.084731846,0.078131797,0.078751916,0.085231224,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 1NBS|1|B|G|190 - 1NBS|1|B|A|195 cSS 
Interaction  | Interacting Bases [6,12] | Pair Probability [[0.007621108,0.007878219,0.007225892,0.008042656,0.000000000],[0.011893482,0.011962372,0.002557227,0.012112360,0.000000000],[0.009982001,0.002557227,0.009162302,0.007119248,0.000000000],[0.212206128,0.210847785,0.265623667,0.213208328,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 1NBS|1|B|U|189 - 1NBS|1|B|G|196 cWS 
Interaction  | Interacting Bases [14,18] | Pair Probability [[0.018961504,0.004196211,0.019694625,0.004196211,0.000000000],[0.042198433,0.338134433,0.004196211,0.004196211,0.000000000],[0.004196211,0.010058595,0.031911832,0.018663303,0.000000000],[0.429522110,0.004196211,0.024345914,0.041331983,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 1NBS|1|B|U|218 - 1NBS|1|B|A|222 tWH 
Interaction  | Interacting Bases [18,19] | Pair Probability [[0.104166825,0.124612443,0.005621093,0.043860124,0.000000000],[0.100542670,0.099286043,0.001147115,0.009317734,0.000000000],[0.010004306,0.001147115,0.104180479,0.094225112,0.000000000],[0.104547355,0.103291070,0.001147115,0.092903402,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 1NBS|1|B|A|222 - 1NBS|1|B|C|223 cSH 
Interaction  | Interacting Bases [3,3] | Pair Probability [[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],[0.000000000,0.000000000,0.000000000,0.166666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 1NBS|1|B|C|186
Interaction  | Interacting Bases [15,15] | Pair Probability [[0.055555556,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.055555556,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.833333333,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.055555556,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion 1NBS|1|B|G|219
Insertion    | Location [10] | Length Distribution [0.045351474,0.907029478,0.045351474,0.002267574] | Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000]// Insertion after nucleotide 10, position 10 in cluster node
Insertion    | Location [20] | 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 22, position 20 in cluster node
InitialNode  | 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 [13] | Right Index [14] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009123784,0.017718471,0.010008206,0.198264936,0.000000000],[0.022262210,0.009929018,0.198931998,0.011154256,0.000000000],[0.010027726,0.196386049,0.002064490,0.023275738,0.000000000],[0.216349992,0.010477281,0.053822220,0.010203624,0.000000000],[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 U197 - A216 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
