| 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_05123.1_Instance_1 HL_05123.1_HL_3SUX_001_A38_U47 | A | C | G | G | G | G | A | G | U | U | ||||||||||||||
| HL_05123.1_Sequence_1 HL_05123.1_HL_3SUX_001_A38_U47 | A | C | G | G | G | G | A | G | U | U | true | 94 | 0 | 0 | 0.91 | |||||||||
| HL_05123.1_Instance_2 HL_05123.1_HL_3SUX_003_A38_U47 | A | C | G | G | G | G | A | G | U | U | ||||||||||||||
| HL_05123.1_Sequence_2 HL_05123.1_HL_3SUX_003_A38_U47 | A | C | G | G | G | G | A | G | U | U | true | 94 | 0 | 0 | 0.91 | |||||||||
| HL_05123.1_Instance_3 HL_05123.1_HL_3D0U_002_U90_G98 | U | U | C | C | U | C | C | C | G | |||||||||||||||
| HL_05123.1_Sequence_3 HL_05123.1_HL_3D0U_002_U90_G98 | U | U | C | C | U | C | C | C | G | true | 100 | 0 | 0 | 0.00 | ||||||||||
| HL_05123.1_Instance_4 HL_05123.1_HL_3DIL_002_U93_G101 | U | U | C | C | U | C | C | C | G | |||||||||||||||
| HL_05123.1_Sequence_4 HL_05123.1_HL_3DIL_002_U93_G101 | U | U | C | C | U | C | C | C | G | true | 100 | 0 | 0 | 0.00 |
1 2 s35 1 9 cWW 2 3 perp 2 4 perp 2 8 cWW 3 4 s35 4 5 s35 5 6 s35 6 7 s35 7 8 s35 8 9 s35JAR3D SCFG/MRF model for HL_05123.1:
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 [9] // Initial node A38 - U47 from junction BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.010067142,0.017651156,0.011863367,0.137604595,0.000000000],[0.156950697,0.018404626,0.115985813,0.012942707,0.000000000],[0.012007182,0.114656057,0.002622233,0.033290147,0.000000000],[0.138394599,0.012606469,0.192644198,0.012309012,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [9] // Basepair A38 - U47 cWW BasepairNode | Deletion Probability [0.0000016375373120] | Pair Probability [[0.014682862,0.013410453,0.039224619,0.016885792,0.000000000],[0.014715495,0.011531794,0.021957090,0.351955909,0.000000000],[0.041444021,0.021155234,0.003327251,0.014772849,0.000000000],[0.017976843,0.388991313,0.016136481,0.011831996,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.496627836,0.496627836,0.006437768,0.000306560] | Left Letter Distribution [0.125000000,0.125000000,0.625000000,0.125000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [8] // Basepair C39 - U46 cWW HairpinNode | Num Bases [5] | Left Index [3] | Right Index [7] | Norm Constant [1.000000000000000] // Hairpin node G41:G45 Interaction | Interacting Bases [1,1] | Pair Probability [[0.083333333,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.416666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.416666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.083333333,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G41 Interaction | Interacting Bases [2,2] | Pair Probability [[0.083333333,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.416666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.416666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.083333333,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G42 Interaction | Interacting Bases [3,3] | Pair Probability [[0.083333333,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.083333333,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.416666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.416666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G43 Interaction | Interacting Bases [4,4] | Pair Probability [[0.416666667,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.416666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.083333333,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.083333333,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A44 Interaction | Interacting Bases [5,5] | Pair Probability [[0.083333333,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.416666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.416666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.083333333,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G45Sequences of instances from HL_05123.1:
> HL_05123.1 HL_3SUX_001 A 38 U 47 ACGGGGAGUU > HL_05123.1 HL_3SUX_003 A 38 U 47 ACGGGGAGUU > HL_05123.1 HL_3D0U_002 U 90 G 98 UUCCUCCCG > HL_05123.1 HL_3DIL_002 U 93 G 101 UUCCUCCCG