| 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 3 I | 10 3 5 | 11 2 I | 12 2 6 | 13 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| HL_88858.1_Instance_1 HL_88858.1_HL_1QU2_002_C31_G39 | C | C | U | GA | U | A | A | G | ||||||||||
| HL_88858.1_Sequence_1 HL_88858.1_HL_1QU2_002_C31_G39 | C | C | U | GA | U | A | A | G | true | 100 | 0 | 0 | 0.00 |
1 2 s35 1 6 cWW 2 3 s35 2 5 bif 2 6 s55 3 4 tSW 4 5 s55 5 6 s35JAR3D SCFG/MRF model for HL_88858.1:
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 [6] // Initial node C31 - G39 from junction BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.009631000,0.017270697,0.011072020,0.200757565,0.000000000],[0.020477154,0.009808895,0.220945507,0.013927182,0.000000000],[0.011196362,0.205083350,0.002110445,0.023698544,0.000000000],[0.203360186,0.013418572,0.027036311,0.010206209,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [6] // Basepair C31 - G39 cWW BasepairNode | Deletion Probability [0.0000001156129129] | Pair Probability [[0.028776211,0.032326394,0.007021393,0.007021393,0.000000000],[0.712040258,0.082230039,0.007021393,0.007021393,0.000000000],[0.007021393,0.007021393,0.029462996,0.044950176,0.000000000],[0.007021393,0.007021393,0.007021393,0.007021393,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.045351474,0.907029478,0.045351474,0.002267574] | Right Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000] | Left Index [2] | Right Index [5] // Basepair C32 - A38 bif HairpinNode | Num Bases [2] | Left Index [3] | Right Index [4] | Norm Constant [1.000000000000000] // Hairpin node U33:U36 Interaction | Interacting Bases [1,2] | Pair Probability [[0.014980202,0.012933711,0.002677206,0.256666304,0.000000000],[0.013068415,0.016073618,0.002677206,0.215382956,0.000000000],[0.012856130,0.002677206,0.002677206,0.013201594,0.000000000],[0.012480760,0.031277223,0.112748680,0.277621583,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin Interaction U33 - U36 tSW Insertion | Location [1] | Length Distribution [0.000000000,0.045351474,0.907029478,0.045351474,0.002267574] | Letter Distribution [0.375000000,0.125000000,0.375000000,0.125000000,0.000000000]// Insertion in Hairpin after nucleotide 3, position 1Sequences of instances from HL_88858.1:
> HL_88858.1 HL_1QU2_002 C 31 G 39 CCUGAUAAG