| 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 2 2 | 5 2 I | 6 2 3 | 7 2 I | 8 2 4 | 9 2 I | 10 2 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_27747.3_Instance_1 HL_27747.3_HL_4WF9_024_A824_U830 | A | G | A | A | A | U | U | |||||||||||
| HL_27747.3_Sequence_1 HL_27747.3_HL_4WF9_024_A824_U830 | A | G | A | A | A | U | U | true | 81 | 0 | 0 | 1.82 | ||||||
| HL_27747.3_Instance_2 HL_27747.3_HL_4Y4O_126_U779_G785 | U | G | A | A | A | A | G | |||||||||||
| HL_27747.3_Sequence_2 HL_27747.3_HL_4Y4O_126_U779_G785 | U | G | A | A | A | A | G | true | 100 | 0 | 0 | 0.00 |
1 2 s35 1 6 cWW 2 3 s35 2 4 tSW 2 6 s55 3 4 s53 4 6 s55 5 6 cSHJAR3D SCFG/MRF model for HL_27747.3:
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 A824 - U830 from junction HairpinNode | Num Bases [6] | Left Index [1] | Right Index [6] | Norm Constant [0.261695661959888] // Hairpin node A824:U830 Interaction | Interacting Bases [2,4] | Pair Probability [[0.164953708,0.164163419,0.002050251,0.009913829,0.000000000],[0.191858170,0.009040203,0.002050251,0.008196877,0.000000000],[0.224632991,0.002050251,0.002050251,0.006723465,0.000000000],[0.177428395,0.008910309,0.016132178,0.009845451,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin Interaction G825 - A828 tSW Interaction | Interacting Bases [1,6] | Pair Probability [[0.010264537,0.017997257,0.012095982,0.130498803,0.000000000],[0.160028161,0.018765501,0.118260045,0.013196486,0.000000000],[0.012242617,0.116904215,0.002673650,0.033942895,0.000000000],[0.141108219,0.012853655,0.186617613,0.012550365,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin Interaction A824 - U830 cWW Interaction | Interacting Bases [5,6] | Pair Probability [[0.051659617,0.052863984,0.305245965,0.064052936,0.000000000],[0.052094350,0.057926514,0.003408161,0.052910508,0.000000000],[0.053035589,0.003408161,0.056429117,0.058498733,0.000000000],[0.052758870,0.061676615,0.003408161,0.070622718,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin Interaction U829 - U830 cSH 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]] // Hairpin conserved non-basepairing position A827 Insertion | Location [2] | Length Distribution [0.023781213,0.951248514,0.023781213,0.001189061] | Letter Distribution [0.625000000,0.125000000,0.125000000,0.125000000,0.000000000]// Insertion in Hairpin after nucleotide 2, position 2Sequences of instances from HL_27747.3:
> HL_27747.3 HL_4WF9_024 A 824 U 830 AGAAAUU > HL_27747.3 HL_4Y4O_126 U 779 G 785 UGAAAAG