| 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 5 I | 8 6 4 | 9 6 I | 10 7 5 | 11 7 I | 12 8 6 | 13 8 I | 14 9 | 15 8 I | 16 8 7 | 17 7 I | 18 7 8 | 19 6 I | 20 6 9 | 21 3 I | 22 3 10 | 23 2 I | 24 2 11 | 25 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| IL_30840.2_Instance_1 IL_30840.2_IL_4BPP_010_U113_A290 | U | U | A | U | U | U | A | U | C | U | A | |||||||||||||||||||
| IL_30840.2_Sequence_1 IL_30840.2_IL_4BPP_010_U113_A290 | U | U | A | U | U | U | * | A | U | C | U | A | true | 100 | 0 | 0 | 0.00 | |||||||||||||
| IL_30840.2_Instance_2 IL_30840.2_IL_3U5F_010_U117_A299 | U | U | A | U | U | U | A | U | U | C | A | |||||||||||||||||||
| IL_30840.2_Sequence_2 IL_30840.2_IL_3U5F_010_U117_A299 | U | U | A | U | U | U | * | A | U | U | C | A | true | 95 | 0 | 0 | 0.85 | |||||||||||||
| IL_30840.2_Instance_3 IL_30840.2_IL_4A1B_014_G430_C650 | G | A | G | C | A | A | U | A | U | G | G | C | ||||||||||||||||||
| IL_30840.2_Sequence_3 IL_30840.2_IL_4A1B_014_G430_C650 | G | A | G | C | A | A | U | * | A | U | G | G | C | true | 75 | 0 | 0 | 4.42 |
1 2 s35 1 11 cWW 2 10 cWW 2 11 s55 3 4 s35 4 9 cWW 5 6 s35 5 8 cWW 5 9 s55 6 7 cWW 7 8 s35 8 9 s35 9 10 s35 10 11 s35JAR3D SCFG/MRF model for IL_30840.2:
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 U113 - A290 from junction BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.009383739,0.020149542,0.010379056,0.200722640,0.000000000],[0.021853259,0.009068682,0.196771190,0.011229117,0.000000000],[0.010341071,0.207909105,0.002131458,0.024714144,0.000000000],[0.225105357,0.011398645,0.026242775,0.012600221,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [11] // Basepair U113 - A290 cWW BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.099583908,0.086557364,0.158164716,0.024220246,0.000000000],[0.015062866,0.011799751,0.018800670,0.024418272,0.000000000],[0.142777257,0.019104895,0.003734971,0.030026250,0.000000000],[0.021360132,0.082092454,0.015680755,0.246615493,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [10] // Basepair U114 - U289 cWW FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.500000000,0.100000000,0.300000000,0.100000000,0.000000000] | Position [1] | Left Index [3] | Right Index [9] // Fixed node on left InitialNode | Left Length Distribution [0.657073038,0.336682053,0.005973391,0.000271518] | Left Letter Distribution [0.166666667,0.500000000,0.166666667,0.166666667,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [9] // New Initial node after Fixed node BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.025453598,0.088611510,0.084813384,0.026213276,0.000000000],[0.016484420,0.013468173,0.021954124,0.153449855,0.000000000],[0.027442117,0.022697844,0.004075038,0.032332908,0.000000000],[0.023304903,0.193624328,0.017284210,0.248790312,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [9] // Basepair U116 - C288 cWW BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.013792873,0.121236027,0.013575643,0.105505658,0.000000000],[0.019894961,0.016573698,0.079066334,0.014789670,0.000000000],[0.013369986,0.079724271,0.003963030,0.042304006,0.000000000],[0.089148150,0.015787988,0.021031523,0.350236181,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [8] // Basepair U117 - U287 cWW BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009027553,0.019940410,0.009723686,0.205285714,0.000000000],[0.024262390,0.009440542,0.191977271,0.010276342,0.000000000],[0.009740283,0.190868689,0.002132868,0.023419534,0.000000000],[0.242412981,0.010204177,0.027588121,0.013699440,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | 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 [6] | Right Index [7] // Basepair U118 - A286 cWW HairpinNode | Num Bases [1] | Left Index [7] | Right Index [7] | Norm Constant [1.000000000000000] // Hairpin node type * Interaction | Interacting Bases [1,1] | Pair Probability [[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,1.000000000]] // Hairpin for truncationSequences of instances from IL_30840.2:
> IL_30840.2 IL_4BPP_010 U 113 A 290 UUAUUU*AUCUA > IL_30840.2 IL_3U5F_010 U 117 A 299 UUAUUU*AUUCA > IL_30840.2 IL_4A1B_014 G 430 C 650 GAGCAAU*AUGGC