| 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_19870.4_Instance_1 HL_19870.4_HL_4WF9_050_C2291_G2303 | C | U | A | A | A | A | G | G | U | A | A | C | G | |||||||||||||||
| HL_19870.4_Sequence_1 HL_19870.4_HL_4WF9_050_C_2291_G_2303 | C | U | A | A | A | A | G | G | U | A | A | C | G | true | 100 | 0 | 0 | 0.00 | ||||||||||
| HL_19870.4_Instance_2 HL_19870.4_HL_4Y4O_157_C2264_G2276 | C | U | A | A | A | A | G | G | U | A | A | C | G | |||||||||||||||
| HL_19870.4_Sequence_2 HL_19870.4_HL_4Y4O_157_C_2264_G_2276 | C | U | A | A | A | A | G | G | U | A | A | C | G | true | 100 | 0 | 0 | 0.00 | ||||||||||
| HL_19870.4_Instance_3 HL_19870.4_HL_5J7L_187_C2264_G2276 | C | U | A | A | A | G | A | G | U | A | A | C | G | |||||||||||||||
| HL_19870.4_Sequence_3 HL_19870.4_HL_5J7L_187_C_2264_G_2276 | C | U | A | A | A | G | A | G | U | A | A | C | G | true | 89 | 0 | 0 | 2.20 | ||||||||||
| HL_19870.4_Instance_4 HL_19870.4_HL_4V9F_056_C2298_G2310 | C | G | A | A | A | A | G | A | U | A | U | C | G | |||||||||||||||
| HL_19870.4_Sequence_4 HL_19870.4_HL_4V9F_056_C_2298_G_2310 | C | G | A | A | A | A | G | A | U | A | U | C | G | true | 95 | 0 | 0 | 0.97 | ||||||||||
| HL_19870.4_Instance_5 HL_19870.4_HL_7A0S_053_C2243_G2255 | C | C | A | A | A | A | U | G | U | A | A | C | G | |||||||||||||||
| HL_19870.4_Sequence_5 HL_19870.4_HL_7A0S_053_C_2243_G_2255 | C | C | A | A | A | A | U | G | U | A | A | C | G | true | 92 | 0 | 0 | 1.51 | ||||||||||
| HL_19870.4_Instance_6 HL_19870.4_HL_5TBW_055_U2633_G2645 | U | U | A | A | A | C | G | A | U | A | A | C | G | |||||||||||||||
| HL_19870.4_Sequence_6 HL_19870.4_HL_5TBW_055_U_2633_G_2645 | U | U | A | A | A | C | G | A | U | A | A | C | G | true | 87 | 0 | 0 | 2.66 |
1 2 s35 1 11 cWW 2 3 s33 2 10 tSH 2 11 s55 3 4 s53 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_19870.4:
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 [11] // Initial node C2291 - G2303 from junction BasepairNode | Deletion Probability [0.0000001231336240] | Pair Probability [[0.009450884,0.015956080,0.011081266,0.165384558,0.000000000],[0.064779646,0.012271176,0.221537108,0.013630044,0.000000000],[0.011230126,0.168795395,0.002205978,0.021170298,0.000000000],[0.175296480,0.013008887,0.083924597,0.010277478,0.000000000],[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 [0.008193363,0.983203605,0.008193363,0.000409668] | Right Letter Distribution [0.062500000,0.812500000,0.062500000,0.062500000,0.000000000] | Left Index [1] | Right Index [11] // Basepair C2291 - G2303 cWW BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.112258085,0.084762344,0.001522367,0.007953908,0.000000000],[0.119230564,0.096930765,0.001522367,0.001522367,0.000000000],[0.135910265,0.001522367,0.010001683,0.123254686,0.000000000],[0.180699689,0.119863808,0.001522367,0.001522367,0.000000000],[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 [[0.417171827,0.289668157,0.017287202,0.017637068,0.000000000],[0.067920990,0.000772046,0.065817481,0.007336049,0.000000000],[0.003849208,0.064976341,0.001927026,0.000772046,0.000000000],[0.005243791,0.038076678,0.000772046,0.000772046,0.000000000],[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 [0.0000001231336240] | Pair Probability [[0.016557184,0.040914681,0.003463595,0.402963250,0.000000000],[0.016259194,0.037312069,0.014424190,0.040003847,0.000000000],[0.003463595,0.017168579,0.016577471,0.277450101,0.000000000],[0.039566434,0.033214493,0.017074679,0.023586638,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.008193363,0.983203605,0.008193363,0.000409668] | Left Letter Distribution [0.812500000,0.062500000,0.062500000,0.062500000,0.000000000] | 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 [[0.562500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.187500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.187500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.062500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A2296 Interaction | Interacting Bases [2,2] | 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 G2297 Interaction | Interacting Bases [3,3] | 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 G2298Sequences of instances from HL_19870.4:
> HL_19870.4 HL_4WF9_050 C 2291 G 2303 CUAAAAGGUAACG > HL_19870.4 HL_4Y4O_157 C 2264 G 2276 CUAAAAGGUAACG > HL_19870.4 HL_5J7L_187 C 2264 G 2276 CUAAAGAGUAACG > HL_19870.4 HL_4V9F_056 C 2298 G 2310 CGAAAAGAUAUCG > HL_19870.4 HL_7A0S_053 C 2243 G 2255 CCAAAAUGUAACG > HL_19870.4 HL_5TBW_055 U 2633 G 2645 UUAAACGAUAACG