| 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_48376.3_Instance_1 HL_48376.3_HL_4Y4O_162_C2404_G2413 | C | G | U | G | U | G | G | A | A | G | ||||||||||||||
| HL_48376.3_Sequence_1 HL_48376.3_HL_4Y4O_162_C_2404_G_2413 | C | G | U | G | U | G | G | A | A | G | true | 100 | 0 | 0 | 0.00 | |||||||||
| HL_48376.3_Instance_2 HL_48376.3_HL_4WF9_055_C2431_G2440 | C | G | C | A | U | G | G | A | A | G | ||||||||||||||
| HL_48376.3_Sequence_2 HL_48376.3_HL_4WF9_055_C_2431_G_2440 | C | G | C | A | U | G | G | A | A | G | true | 95 | 0 | 0 | 0.67 | |||||||||
| HL_48376.3_Instance_3 HL_48376.3_HL_5J7L_192_U2404_G2413 | U | G | A | A | U | G | G | A | A | G | ||||||||||||||
| HL_48376.3_Sequence_3 HL_48376.3_HL_5J7L_192_U_2404_G_2413 | U | G | A | A | U | G | G | A | A | G | true | 92 | 0 | 0 | 1.21 | |||||||||
| HL_48376.3_Instance_4 HL_48376.3_HL_7A0S_058_C2383_G2392 | C | G | U | G | U | G | G | A | A | G | ||||||||||||||
| HL_48376.3_Sequence_4 HL_48376.3_HL_7A0S_058_C_2383_G_2392 | C | G | U | G | U | G | G | A | A | G | true | 100 | 0 | 0 | 0.00 | |||||||||
| HL_48376.3_Instance_5 HL_48376.3_HL_7KGA_002_U53_G64 | U | A | UC | G | G | U | U | A | G | A | G | |||||||||||||
| HL_48376.3_Sequence_5 HL_48376.3_HL_7KGA_002_U53_G64 | U | A | UC | G | G | U | U | A | G | A | G | true | 37 | 0 | 0 | 9.24 |
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_48376.3:
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 [9] // Initial node C2404 - G2413 from junction BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.009928394,0.015401431,0.011938004,0.130349637,0.000000000],[0.129375926,0.016521994,0.166831863,0.014268379,0.000000000],[0.012131223,0.132788217,0.002502703,0.019378569,0.000000000],[0.150859944,0.013448331,0.163118886,0.011156498,0.000000000],[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 C2404 - G2413 cWW BasepairNode | Deletion Probability [0.0000000426384269] | Pair Probability [[0.131514874,0.096768403,0.001395529,0.007053160,0.000000000],[0.121598179,0.106194466,0.001395529,0.001395529,0.000000000],[0.171909266,0.001395529,0.008127753,0.096775848,0.000000000],[0.128757113,0.122927761,0.001395529,0.001395529,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.007839294,0.785889270,0.203821656,0.002351788,0.000097991] | Left Letter Distribution [0.187500000,0.312500000,0.062500000,0.437500000,0.000000000] | 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 G2405 - A2412 tSH HairpinNode | Num Bases [5] | Left Index [3] | Right Index [7] | Norm Constant [1.000000000000000] // Hairpin node G2407:A2411 Interaction | Interacting Bases [1,1] | Pair Probability [[0.357142857,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.071428571,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.500000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.071428571,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G2407 Interaction | Interacting Bases [2,2] | Pair Probability [[0.071428571,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.071428571,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.214285714,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.642857143,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U2408 Interaction | Interacting Bases [3,3] | Pair Probability [[0.071428571,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.071428571,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.642857143,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.214285714,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G2409 Interaction | Interacting Bases [4,4] | Pair Probability [[0.214285714,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.071428571,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.642857143,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.071428571,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G2410 Interaction | Interacting Bases [5,5] | Pair Probability [[0.642857143,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.071428571,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.214285714,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.071428571,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A2411 Insertion | Location [3] | Length Distribution [0.792098765,0.205432099,0.002370370,0.000098765] | Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000]// Insertion in Hairpin after nucleotide 5, position 3Sequences of instances from HL_48376.3:
> HL_48376.3 HL_4Y4O_162 C 2404 G 2413 CGUGUGGAAG > HL_48376.3 HL_4WF9_055 C 2431 G 2440 CGCAUGGAAG > HL_48376.3 HL_5J7L_192 U 2404 G 2413 UGAAUGGAAG > HL_48376.3 HL_7A0S_058 C 2383 G 2392 CGUGUGGAAG > HL_48376.3 HL_7KGA_002 U 53 G 64 UAUCGGUUAGAG