| 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 4 I | 10 4 5 | 11 4 I | 12 4 6 | 13 4 I | 14 4 7 | 15 3 I | 16 3 8 | 17 2 I | 18 2 9 | 19 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| HL_53454.2_Instance_1 HL_53454.2,HL_7A0S_058,C2383_G2392 | C | G | U | G | U | G | G | A | A | G | ||||||||||||||
| HL_53454.2_Sequence_1 HL_53454.27A0S_C_2383_G_2392 | C | G | U | G | U | G | G | A | A | G | true | 100 | 0 | 0 | 0.00 | |||||||||
| HL_53454.2_Instance_2 HL_53454.2,HL_4WF9_055,C2431_G2440 | C | G | C | A | U | G | G | A | A | G | ||||||||||||||
| HL_53454.2_Sequence_2 HL_53454.24WF9_C_2431_G_2440 | C | G | C | A | U | G | G | A | A | G | true | 94 | 0 | 0 | 0.84 | |||||||||
| HL_53454.2_Instance_3 HL_53454.2,HL_9DFE_057,C2404_G2413 | C | G | U | G | U | G | G | A | A | G | ||||||||||||||
| HL_53454.2_Sequence_3 HL_53454.29DFE_C_2404_G_2413 | C | G | U | G | U | G | G | A | A | G | true | 100 | 0 | 0 | 0.00 | |||||||||
| HL_53454.2_Instance_4 HL_53454.2,HL_5J7L_192,U2404_G2413 | U | G | A | A | U | G | G | A | A | G | ||||||||||||||
| HL_53454.2_Sequence_4 HL_53454.25J7L_U_2404_G_2413 | U | G | A | A | U | G | G | A | A | G | true | 91 | 0 | 0 | 1.39 | |||||||||
| HL_53454.2_Instance_5 HL_53454.2,HL_7KGA_004,U53_G64 | U | A | UC | G | G | U | U | A | G | A | G | |||||||||||||
| HL_53454.2_Sequence_5 HL_53454.27KGA_U53_G64 | U | A | UC | G | G | U | U | A | G | A | G | true | 55 | 0 | 0 | 6.71 | ||||||||
| HL_53454.2_Instance_6 HL_53454.2,HL_7KGA_002,U53_G64 | U | A | UC | G | G | U | U | A | G | A | G | |||||||||||||
| HL_53454.2_Sequence_6 HL_53454.27KGA_U53_G64 | U | A | UC | G | G | U | U | A | G | A | G | true | 55 | 0 | 0 | 6.71 |
1 2 s35 1 9 cWW 2 7 s33 2 8 tSH 2 9 s55 3 4 s35 4 5 s35 5 6 s35 6 7 s35 7 8 s35 8 9 s35 8 2 6BRJAR3D SCFG/MRF model for HL_53454.2:
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 [9] // Initial node BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.009999236,0.014956157,0.012144288,0.113577937,0.000000000],[0.155316435,0.018121105,0.149224604,0.014349655,0.000000000],[0.012353913,0.115566971,0.002596142,0.018349519,0.000000000],[0.138353991,0.013455419,0.200251764,0.011382864,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [9] // Basepair C2383 - G2392 cWW BasepairNode | Deletion Probability [0.0000000210555535] | Pair Probability [[0.147940785,0.083190769,0.001435697,0.007552335,0.000000000],[0.127886887,0.098929966,0.001435697,0.001435697,0.000000000],[0.171830914,0.001435697,0.009173896,0.086078246,0.000000000],[0.131833920,0.126968101,0.001435697,0.001435697,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.005462242,0.658200191,0.333196777,0.003004233,0.000136556] | Left Letter Distribution [0.150000000,0.350000000,0.050000000,0.450000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [8] // Basepair G2384 - A2391 tSH HairpinNode | Num Bases [5] | Left Index [3] | Right Index [7] | Norm Constant [1.000000000000000] // Hairpin node G2386:A2390 Interaction | Interacting Bases [1,1] | Pair Probability [[0.312500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.062500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.562500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.062500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G2386 Interaction | Interacting Bases [2,2] | Pair Probability [[0.062500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.062500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.312500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.562500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U2387 Interaction | Interacting Bases [3,3] | Pair Probability [[0.062500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.062500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.562500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.312500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G2388 Interaction | Interacting Bases [4,4] | Pair Probability [[0.187500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.062500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.562500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.187500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G2389 Interaction | Interacting Bases [5,5] | Pair Probability [[0.562500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.062500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.312500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.062500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A2390 Insertion | Location [3] | Length Distribution [0.826344012,0.171868555,0.001718686,0.000068747] | Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000]// Insertion in Hairpin after nucleotide 5, position 3 Insertion | Location [4] | Length Distribution [0.826344012,0.171868555,0.001718686,0.000068747] | Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000]// Insertion in Hairpin after nucleotide 6, position 4Sequences of instances from HL_53454.2:
> HL_53454.2 7A0S C 2383 G 2392 CGUGUGGAAG > HL_53454.2 4WF9 C 2431 G 2440 CGCAUGGAAG > HL_53454.2 9DFE C 2404 G 2413 CGUGUGGAAG > HL_53454.2 5J7L U 2404 G 2413 UGAAUGGAAG > HL_53454.2 7KGA U 53 G 64 UAUCGGUUAGAG > HL_53454.2 7KGA U 53 G 64 UAUCGGUUAGAG