| 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 4 3 | 7 3 I | 8 3 4 | 9 2 I | 10 2 5 | 11 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| HL_55511.1_Instance_1 HL_55511.1_HL_3AL0_001_U13_G22 | U | A | A | CGGU | A | G | ||||||||||
| HL_55511.1_Sequence_1 HL_55511.1_HL_3AL0_001_U13_G22 | U | A | A | CGGU | A | G | true | 100 | 0 | 0 | 0.00 | |||||
| HL_55511.1_Instance_2 HL_55511.1_HL_6UFM_001_C13_G23 | C | A | G | GCGGUU | A | G | ||||||||||
| HL_55511.1_Sequence_2 HL_55511.1_HL_6UFM_001_C13_G23 | C | A | G | GCGGUU | A | G | true | 84 | 0 | 0 | 2.34 |
1 5 cWW 2 3 s35 2 4 cWS 2 5 s55 3 4 s53JAR3D SCFG/MRF model for HL_55511.1:
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 [5] // Initial node U13 - G22 from junction BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.010391363,0.015542673,0.012620534,0.118031974,0.000000000],[0.161407275,0.018831736,0.135468706,0.014912387,0.000000000],[0.012838381,0.120099009,0.002697951,0.019069108,0.000000000],[0.143779637,0.013983083,0.188496931,0.011829251,0.000000000],[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 [5] // Basepair U13 - G22 cWW BasepairNode | Deletion Probability [0.0000000000000001] | Pair Probability [[0.308644650,0.183882729,0.194324745,0.187834025,0.000000000],[0.014692188,0.011983187,0.001999102,0.012161323,0.000000000],[0.019866299,0.001999102,0.025462132,0.009509275,0.000000000],[0.007136885,0.007528516,0.005957773,0.007018068,0.000000000],[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 [0.000000000,0.000000000,0.000000000,0.011890606,0.475624257,0.023781213,0.476218787,0.011890606,0.000594530] | Right Letter Distribution [0.041666667,0.208333333,0.458333333,0.291666667,0.000000000] | Left Index [2] | Right Index [4] // Basepair A14 - A21 cWS HairpinNode | Num Bases [1] | Left Index [3] | Right Index [3] | Norm Constant [1.000000000000000] // Hairpin node A15:A15 Interaction | Interacting Bases [1,1] | Pair Probability [[0.375000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.125000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.375000000,0.000000000,0.000000000],[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 A15Sequences of instances from HL_55511.1:
> HL_55511.1 HL_3AL0_001 U 13 G 22 UAACGGUAG > HL_55511.1 HL_6UFM_001 C 13 G 23 CAGGCGGUUAG