| 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 5 5 | 11 4 I | 12 4 6 | 13 3 I | 14 3 7 | 15 2 I | 16 2 8 | 17 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| HL_19958.1_Instance_1 HL_19958.1_HL_4QEI_004_G12_C23 | G | U | A | G | U | GGU | A | U | C | |||||||||||||
| HL_19958.1_Sequence_1 HL_19958.1_HL_4QEI_004_G12_C23 | G | U | A | G | U | GGU | A | U | C | true | 100 | 0 | 0 | 0.00 | ||||||||
| HL_19958.1_Instance_2 HL_19958.1_HL_4QEI_001_G12_C23 | G | U | A | G | U | GGU | A | U | C | |||||||||||||
| HL_19958.1_Sequence_2 HL_19958.1_HL_4QEI_001_G12_C23 | G | U | A | G | U | GGU | A | U | C | true | 100 | 0 | 0 | 0.00 | ||||||||
| HL_19958.1_Instance_3 HL_19958.1_HL_5E6M_001_G12_C23 | G | U | A | G | U | GGU | A | U | C | |||||||||||||
| HL_19958.1_Sequence_3 HL_19958.1_HL_5E6M_001_G12_C23 | G | U | A | G | U | GGU | A | U | C | true | 100 | 0 | 0 | 0.00 | ||||||||
| HL_19958.1_Instance_4 HL_19958.1_HL_2DU3_001_A912_U922 | A | G | A | G | G | GGC | U | U | U | |||||||||||||
| HL_19958.1_Sequence_4 HL_19958.1_HL_2DU3_001_A912_U922 | A | G | A | G | G | GGC | U | U | U | true | 90 | 0 | 0 | 1.75 | ||||||||
| HL_19958.1_Instance_5 HL_19958.1_HL_2DU3_004_A912_U922 | A | G | A | G | G | GGC | U | U | U | |||||||||||||
| HL_19958.1_Sequence_5 HL_19958.1_HL_2DU3_004_A912_U922 | A | G | A | G | G | GGC | U | U | U | true | 90 | 0 | 0 | 1.75 |
1 2 s35 1 8 cWW 2 3 s35 2 7 cWW 3 4 s35 3 6 cWS 3 7 s55 4 5 s35 7 8 s35JAR3D SCFG/MRF model for HL_19958.1:
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 [8] // Initial node G12 - C23 from junction BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.009280432,0.020368229,0.010312873,0.215702181,0.000000000],[0.016772457,0.009285906,0.193782875,0.011767824,0.000000000],[0.010233627,0.226772067,0.002010885,0.036277626,0.000000000],[0.192008674,0.012321377,0.022616385,0.010486579,0.000000000],[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 [8] // Basepair G12 - C23 cWW BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.014050246,0.257698632,0.012544499,0.021909755,0.000000000],[0.015528856,0.016743948,0.018727607,0.013770962,0.000000000],[0.012282488,0.019077752,0.003872504,0.128043403,0.000000000],[0.019139631,0.014913942,0.015873928,0.415821848,0.000000000],[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 [7] // Basepair U13 - U22 cWW BasepairNode | Deletion Probability [0.0000000000030757] | Pair Probability [[0.228838658,0.184211091,0.194671754,0.266740872,0.000000000],[0.014718424,0.012004586,0.002002672,0.012183040,0.000000000],[0.019901775,0.002002672,0.025507600,0.009526256,0.000000000],[0.007149629,0.007541959,0.005968411,0.007030600,0.000000000],[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 [0.000000000,0.000000000,0.009799118,0.979911808,0.009799118,0.000489956] | Right Letter Distribution [0.029411765,0.147058824,0.617647059,0.205882353,0.000000000] | Left Index [3] | Right Index [6] // Basepair A14 - A21 cWS HairpinNode | Num Bases [2] | Left Index [4] | Right Index [5] | Norm Constant [1.000000000000000] // Hairpin node G15:U16 Interaction | Interacting Bases [1,1] | Pair Probability [[0.071428571,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.071428571,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.785714286,0.000000000,0.000000000],[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 G15 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],[0.000000000,0.000000000,0.357142857,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.500000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U16Sequences of instances from HL_19958.1:
> HL_19958.1 HL_4QEI_004 G 12 C 23 GUAGUGGUAUC > HL_19958.1 HL_4QEI_001 G 12 C 23 GUAGUGGUAUC > HL_19958.1 HL_5E6M_001 G 12 C 23 GUAGUGGUAUC > HL_19958.1 HL_2DU3_001 A 912 U 922 AGAGGGGCUUU > HL_19958.1 HL_2DU3_004 A 912 U 922 AGAGGGGCUUU