| 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_27335.1_Instance_1 HL_27335.1_HL_2DU3_002_A930_U938 | A | C | UGC | A | G | A | U | |||||||||||
| HL_27335.1_Sequence_1 HL_27335.1_HL_2DU3_002_A930_U938 | A | C | UGC | A | G | A | U | true | 100 | 0 | 0 | 0.00 | ||||||
| HL_27335.1_Instance_2 HL_27335.1_HL_2DU3_005_A930_U938 | A | C | UGC | A | G | A | U | |||||||||||
| HL_27335.1_Sequence_2 HL_27335.1_HL_2DU3_005_A930_U938 | A | C | UGC | A | G | A | U | true | 100 | 0 | 0 | 0.00 |
1 2 s35 1 6 cWW 2 5 cWW 3 4 s35 5 6 s35JAR3D SCFG/MRF model for HL_27335.1:
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 A930 - U938 from junction BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.009282926,0.022010543,0.009914366,0.223723012,0.000000000],[0.017518170,0.009580259,0.194165974,0.010358839,0.000000000],[0.009895067,0.196683142,0.002041152,0.053213779,0.000000000],[0.196023621,0.011028161,0.023012614,0.011548375,0.000000000],[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 A930 - U938 cWW BasepairNode | Deletion Probability [0.0000000000029562] | Pair Probability [[0.011169172,0.014624785,0.014219668,0.030813201,0.000000000],[0.378631746,0.040992595,0.034835247,0.015878615,0.000000000],[0.014561584,0.029380498,0.003590239,0.015185588,0.000000000],[0.038714962,0.014470422,0.328534713,0.014396965,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.000000000,0.000000000,0.023781213,0.951248514,0.023781213,0.001189061] | Left Letter Distribution [0.062500000,0.312500000,0.312500000,0.312500000,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [5] // Basepair C931 - A937 cWW HairpinNode | Num Bases [2] | Left Index [3] | Right Index [4] | Norm Constant [1.000000000000000] // Hairpin node A935:G936 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 A935 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 G936Sequences of instances from HL_27335.1:
> HL_27335.1 HL_2DU3_002 A 930 U 938 ACUGCAGAU > HL_27335.1 HL_2DU3_005 A 930 U 938 ACUGCAGAU