| 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 4 I | 8 4 4 | 9 3 I | 10 3 5 | 11 2 I | 12 2 6 | 13 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| HL_60140.1_Instance_1 HL_60140.1_HL_5WT1_002_A31_U39 | A | C | UG | A | A | G | A | U | ||||||||||
| HL_60140.1_Sequence_1 HL_60140.1_HL_5WT1_002_A31_U39 | A | C | UG | A | A | G | A | U | true | 100 | 0 | 0 | 0.00 | |||||
| HL_60140.1_Instance_2 HL_60140.1_HL_7A0S_041_G1646_C1653 | G | U | C | A | A | U | G | C | ||||||||||
| HL_60140.1_Sequence_2 HL_60140.1_HL_7A0S_041_G_1646_C_1653 | G | U | C | A | A | U | G | C | true | 95 | 0 | 0 | 0.60 |
1 2 s35 1 6 cWW 2 5 bif 3 4 s35 4 5 s35 5 6 s35JAR3D SCFG/MRF model for HL_60140.1:
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 [6] // Initial node A31 - U39 from junction BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.009508309,0.021141169,0.010499222,0.212521883,0.000000000],[0.017307832,0.009562561,0.198596306,0.011821420,0.000000000],[0.010428025,0.212609503,0.002065216,0.039989476,0.000000000],[0.197383927,0.012407836,0.023236747,0.010920569,0.000000000],[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 [6] // Basepair A31 - U39 cWW BasepairNode | Deletion Probability [0.0000000000430944] | Pair Probability [[0.025903719,0.029099517,0.006320505,0.006320505,0.000000000],[0.641854421,0.074021693,0.006320505,0.006320505,0.000000000],[0.006320505,0.006320505,0.026521948,0.040463171,0.000000000],[0.006320505,0.006320505,0.105250986,0.006320505,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.011890606,0.487514863,0.487514863,0.012485137,0.000594530] | Left Letter Distribution [0.100000000,0.300000000,0.300000000,0.300000000,0.000000000] | Right Length Distribution [0.023781213,0.951248514,0.023781213,0.001189061] | Right Letter Distribution [0.125000000,0.125000000,0.375000000,0.375000000,0.000000000] | Left Index [2] | Right Index [5] // Basepair C32 - A38 bif HairpinNode | Num Bases [2] | Left Index [3] | Right Index [4] | Norm Constant [1.000000000000000] // Hairpin node A35:A36 Interaction | Interacting Bases [1,1] | 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 A35 Interaction | Interacting Bases [2,2] | 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 A36Sequences of instances from HL_60140.1:
> HL_60140.1 HL_5WT1_002 A 31 U 39 ACUGAAGAU > HL_60140.1 HL_7A0S_041 G 1646 C 1653 GUCAAUGC