| Column number: Node in JAR3D model: Insertion positions indicated by I: Position in motif group: | 1 1 I | 2 2 1 | 3 2 I | 4 3 2 | 5 3 I | 6 3 3 | 7 3 I | 8 3 4 | 9 4 I | 10 7 5 | 11 7 I | 12 8 6 | 13 8 I | 14 8 7 | 15 8 I | 16 8 8 | 17 8 I | 18 8 9 | 19 8 I | 20 8 10 | 21 8 I | 22 8 11 | 23 8 I | 24 8 12 | 25 7 I | 26 7 13 | 27 6 I | 28 5 14 | 29 4 I | 30 3 15 | 31 3 I | 32 3 16 | 33 2 I | 34 2 17 | 35 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| HL_10456.1_Instance_1 HL_10456.1,HL_3D0U_005,C35_G52 | C | A | U | C | A | G | G | G | G | A | G | G | A | A | U | C | G | G | ||||||||||||||||||||||
| HL_10456.1_Sequence_1 HL_10456.13D0U_C35_G52 | C | A | U | C | A | G | G | G | G | A | G | G | A | A | U | C | G | G | true | 100 | 0 | 0 | 0.00 | |||||||||||||||||
| HL_10456.1_Instance_2 HL_10456.1,HL_3DIL_005,C38_G55 | C | A | U | C | A | G | G | G | G | A | G | G | A | A | U | C | G | G | ||||||||||||||||||||||
| HL_10456.1_Sequence_2 HL_10456.13DIL_C38_G55 | C | A | U | C | A | G | G | G | G | A | G | G | A | A | U | C | G | G | true | 100 | 0 | 0 | 0.00 |
1 2 s35 1 17 cWW 2 3 cSH 2 4 cSH 3 4 s53 3 15 tWW 4 16 cWW 4 17 s55 5 13 tHW 6 7 perp 6 9 perp 7 8 s35 8 9 s35 9 10 s35 10 11 s35 11 12 s35 12 13 s35 13 14 s35 14 16 perp 15 16 s55 16 17 s35 3 2 7BR 4 2 7BR 14 17 2BRJAR3D SCFG/MRF model for HL_10456.1:
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 [17] // Initial node BasepairNode | Deletion Probability [0.0000229437914523] | 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]] | 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 [1] | Right Index [17] // Basepair C35 - G52 cWW ClusterNode | Deletion Probability [0.000000000000015429359482326747228196069233951473250875292831] | Num Left Bases [3] | Num Right Bases [2] | Left Index [2] | Right Index [16] | Norm Constant [0.038195331392119] // Cluster node 3D0U|1|A|A|36:3D0U|1|A|C|38 and 3D0U|1|A|U|49:3D0U|1|A|G|51 Interaction | Interacting Bases [2,4] | Pair Probability [[0.006681812,0.008114022,0.001433010,0.009758613,0.000000000],[0.012596057,0.008176970,0.005081026,0.007315571,0.000000000],[0.001433010,0.004845919,0.006864957,0.010428524,0.000000000],[0.062376330,0.038987277,0.079794189,0.736112713,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 3D0U|1|A|U|37 - 3D0U|1|A|U|49 tWW Interaction | Interacting Bases [3,5] | Pair Probability [[0.004694951,0.008419175,0.005397424,0.097865947,0.000000000],[0.049911347,0.023908359,0.534011162,0.033946338,0.000000000],[0.005458039,0.099974695,0.001028807,0.011552643,0.000000000],[0.099134681,0.006541329,0.013179748,0.004975356,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 3D0U|1|A|C|38 - 3D0U|1|A|G|51 cWW Interaction | Interacting Bases [1,2] | Pair Probability [[0.012882168,0.043056077,0.009630348,0.221342956,0.000000000],[0.034946749,0.095347950,0.001126086,0.093809522,0.000000000],[0.098420880,0.001126086,0.093255681,0.090396795,0.000000000],[0.014634711,0.096563920,0.001126086,0.092333986,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 3D0U|1|A|A|36 - 3D0U|1|A|U|37 cSH Interaction | Interacting Bases [1,3] | Pair Probability [[0.103145582,0.133194674,0.005565984,0.043430123,0.000000000],[0.099556957,0.098312651,0.001135868,0.009226384,0.000000000],[0.009906224,0.001135868,0.103159102,0.093301337,0.000000000],[0.103522381,0.102278412,0.001135868,0.091992584,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 3D0U|1|A|A|36 - 3D0U|1|A|C|38 cSH Insertion | Location [4] | Length Distribution [0.023781213,0.951248514,0.023781213,0.001189061] | Letter Distribution [0.125000000,0.625000000,0.125000000,0.125000000,0.000000000]// Insertion after nucleotide 15, position 4 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 [5] | Right Index [14] // Initial node 3D0U|1|A|A|39 - 3D0U|1|A|A|48 from node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.875000000,0.041666667,0.041666667,0.041666667,0.000000000] | Position [2] | Left Index [5] | Right Index [14] // Fixed node on right for 3D0U|1|A|A|48 InitialNode | Left Length Distribution [1.000000000] | 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 [5] | Right Index [13] // New Initial node after Fixed node BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.381184813,0.030948835,0.003615770,0.016338652,0.000000000],[0.003615770,0.015344049,0.008956754,0.003615770,0.000000000],[0.318975856,0.003615770,0.132906372,0.017330382,0.000000000],[0.003615770,0.003615770,0.038702064,0.017617604,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | 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 [5] | Right Index [13] // Basepair A39 - A47 tHW HairpinNode | Num Bases [7] | Left Index [6] | Right Index [12] | Norm Constant [1.000000000000000] // Hairpin node G40:G46 Interaction | Interacting Bases [1,1] | Pair Probability [[0.125000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.125000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.625000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.125000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G40 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],[0.000000000,0.000000000,0.625000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.125000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G41 Interaction | Interacting Bases [3,3] | Pair Probability [[0.125000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.125000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.625000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.125000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G42 Interaction | Interacting Bases [4,4] | Pair Probability [[0.125000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.125000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.625000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.125000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G43 Interaction | Interacting Bases [5,5] | 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]] // Hairpin conserved non-basepairing position A44 Interaction | Interacting Bases [6,6] | Pair Probability [[0.125000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.125000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.625000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.125000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G45 Interaction | Interacting Bases [7,7] | Pair Probability [[0.125000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.125000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.625000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.125000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G46Sequences of instances from HL_10456.1:
> HL_10456.1 3D0U C 35 G 52 CAUCAGGGGAGGAAUCGG > HL_10456.1 3DIL C 38 G 55 CAUCAGGGGAGGAAUCGG