| 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 5 4 | 9 5 I | 10 6 5 | 11 6 I | 12 6 6 | 13 6 I | 14 6 7 | 15 5 I | 16 5 8 | 17 4 I | 18 4 9 | 19 3 I | 20 3 10 | 21 2 I | 22 2 11 | 23 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| HL_91939.2_Instance_1 HL_91939.2,HL_4WF9_050,C2291_G2303 | C | U | A | A | A | A | G | G | U | A | A | C | G | |||||||||||||||
| HL_91939.2_Sequence_1 HL_91939.24WF9_C_2291_G_2303 | C | U | A | A | A | A | G | G | U | A | A | C | G | true | 100 | 0 | 0 | 0.00 | ||||||||||
| HL_91939.2_Instance_2 HL_91939.2,HL_5J7L_187,C2264_G2276 | C | U | A | A | A | G | A | G | U | A | A | C | G | |||||||||||||||
| HL_91939.2_Sequence_2 HL_91939.25J7L_C_2264_G_2276 | C | U | A | A | A | G | A | G | U | A | A | C | G | true | 90 | 0 | 0 | 1.89 | ||||||||||
| HL_91939.2_Instance_3 HL_91939.2,HL_9DFE_052,C2264_G2276 | C | U | A | A | A | A | G | G | U | A | A | C | G | |||||||||||||||
| HL_91939.2_Sequence_3 HL_91939.29DFE_C_2264_G_2276 | C | U | A | A | A | A | G | G | U | A | A | C | G | true | 100 | 0 | 0 | 0.00 | ||||||||||
| HL_91939.2_Instance_4 HL_91939.2,HL_4V9F_056,C2298_G2310 | C | G | A | A | A | A | G | A | U | A | U | C | G | |||||||||||||||
| HL_91939.2_Sequence_4 HL_91939.24V9F_C_2298_G_2310 | C | G | A | A | A | A | G | A | U | A | U | C | G | true | 98 | 0 | 0 | 0.48 | ||||||||||
| HL_91939.2_Instance_5 HL_91939.2,HL_8P9A_166,U2633_G2645 | U | U | A | A | A | C | G | A | U | A | A | C | G | |||||||||||||||
| HL_91939.2_Sequence_5 HL_91939.28P9A_U_2633_G_2645 | U | U | A | A | A | C | G | A | U | A | A | C | G | true | 98 | 0 | 0 | 0.39 | ||||||||||
| HL_91939.2_Instance_6 HL_91939.2,HL_8CRE_054,U2605_G2617 | U | U | A | A | A | C | G | A | U | A | A | C | G | |||||||||||||||
| HL_91939.2_Sequence_6 HL_91939.28CRE_U_2605_G_2617 | U | U | A | A | A | C | G | A | U | A | A | C | G | true | 98 | 0 | 0 | 0.39 | ||||||||||
| HL_91939.2_Instance_7 HL_91939.2,HL_7A0S_053,C2243_G2255 | C | C | A | A | A | A | U | G | U | A | A | C | G | |||||||||||||||
| HL_91939.2_Sequence_7 HL_91939.27A0S_C_2243_G_2255 | C | C | A | A | A | A | U | G | U | A | A | C | G | true | 91 | 0 | 0 | 1.78 | ||||||||||
| HL_91939.2_Instance_8 HL_91939.2,HL_4V9F_059,U2389_G2399 | U | U | C | C | C | A | A | C | G | A | G | |||||||||||||||||
| HL_91939.2_Sequence_8 HL_91939.24V9F_U_2389_G_2399 | U | U | C | C | C | A | A | C | G | A | G | true | 60 | 0 | 0 | 7.77 |
1 2 s35 1 11 cWW 2 3 s33 2 10 tSH 2 11 s55 3 8 s53 3 9 tHH 4 8 tWW 5 6 s35 6 7 s35 7 8 s35 9 10 s35 10 11 s35 3 9 6BPhJAR3D SCFG/MRF model for HL_91939.2:
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 [11] // Initial node BasepairNode | Deletion Probability [0.0000002372133371] | Pair Probability [[0.009612241,0.015047219,0.011528143,0.130542356,0.000000000],[0.119117636,0.015632430,0.184650278,0.013819064,0.000000000],[0.011711521,0.133017859,0.002404463,0.019047917,0.000000000],[0.149388768,0.013041896,0.160672982,0.010765227,0.000000000],[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 [0.128917709,0.865369770,0.005442334,0.000270187] | Right Letter Distribution [0.055555556,0.833333333,0.055555556,0.055555556,0.000000000] | Left Index [1] | Right Index [11] // Basepair C2291 - G2303 cWW BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.111060251,0.088358762,0.001436312,0.007407855,0.000000000],[0.118617396,0.098201096,0.001436312,0.001436312,0.000000000],[0.129399722,0.001436312,0.009313408,0.119251266,0.000000000],[0.192360827,0.117411548,0.001436312,0.001436312,0.000000000],[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 [2] | Right Index [10] // Basepair U2292 - A2301 tSH BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.384933761,0.258062085,0.015362931,0.015689024,0.000000000],[0.097214135,0.001133009,0.113152516,0.009943605,0.000000000],[0.003487446,0.060347814,0.001779186,0.000708579,0.000000000],[0.004663108,0.032105642,0.000708579,0.000708579,0.000000000],[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 [3] | Right Index [9] // Basepair A2293 - A2300 tHH BasepairNode | Deletion Probability [0.0000002372133371] | Pair Probability [[0.016021688,0.039591410,0.003351574,0.399972264,0.000000000],[0.015733335,0.058405784,0.013957679,0.038710035,0.000000000],[0.003351574,0.016613309,0.016041319,0.268476754,0.000000000],[0.038286769,0.032140264,0.016522447,0.022823794,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.128917709,0.865369770,0.005442334,0.000270187] | Left Letter Distribution [0.833333333,0.055555556,0.055555556,0.055555556,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [8] // Basepair A2294 - U2299 tWW HairpinNode | Num Bases [3] | Left Index [5] | Right Index [7] | Norm Constant [1.000000000000000] // Hairpin node A2296:G2298 Interaction | Interacting Bases [1,1] | Pair Probability [[0.450000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.350000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.150000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.050000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A2296 Interaction | Interacting Bases [2,2] | Pair Probability [[0.250000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.050000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.550000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.150000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G2297 Interaction | Interacting Bases [3,3] | Pair Probability [[0.450000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.050000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.450000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.050000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G2298Sequences of instances from HL_91939.2:
> HL_91939.2 4WF9 C 2291 G 2303 CUAAAAGGUAACG > HL_91939.2 5J7L C 2264 G 2276 CUAAAGAGUAACG > HL_91939.2 9DFE C 2264 G 2276 CUAAAAGGUAACG > HL_91939.2 4V9F C 2298 G 2310 CGAAAAGAUAUCG > HL_91939.2 8P9A U 2633 G 2645 UUAAACGAUAACG > HL_91939.2 8CRE U 2605 G 2617 UUAAACGAUAACG > HL_91939.2 7A0S C 2243 G 2255 CCAAAAUGUAACG > HL_91939.2 4V9F U 2389 G 2399 UUCCCAACGAG