| 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 3 3 | 7 3 I | 8 3 4 | 9 3 I | 10 3 5 | 11 3 I | 12 3 6 | 13 2 I | 14 2 7 | 15 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| HL_46771.1_Instance_1 HL_46771.1_HL_3FOZ_005_A31_U39 | A | U | U | G | A | A | A | A | U | |||||||||||
| HL_46771.1_Sequence_1 HL_46771.1_HL_3FOZ_005_A31_U39 | A | U | U | G | A | A | A | A | U | true | 100 | 0 | 0 | 0.00 |
1 2 s35 1 7 cWW 2 5 tSS 2 6 cSW 3 4 cSS 5 6 s55 6 7 s35 5 3 6BPhJAR3D SCFG/MRF model for HL_46771.1:
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 [7] // Initial node A31 - U39 from junction BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.009374836,0.022228469,0.010012528,0.216037101,0.000000000],[0.017691617,0.009675113,0.196088410,0.010461402,0.000000000],[0.009993038,0.198630499,0.002061361,0.053740648,0.000000000],[0.197964449,0.011137350,0.023240462,0.011662716,0.000000000],[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 [7] // Basepair A31 - U39 cWW HairpinNode | Num Bases [5] | Left Index [2] | Right Index [6] | Norm Constant [0.249828046770445] // Hairpin node U32:A38 Interaction | Interacting Bases [2,3] | Pair Probability [[0.075546420,0.080149405,0.080218061,0.073628336,0.000000000],[0.075234216,0.076775930,0.003502316,0.071936579,0.000000000],[0.072824620,0.003553643,0.007936721,0.070454160,0.000000000],[0.075679016,0.069367749,0.092944564,0.070248265,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin Interaction U33 - G34 cSS Interaction | Interacting Bases [1,4] | Pair Probability [[0.173267327,0.024752475,0.024752475,0.024752475,0.000000000],[0.173267327,0.024752475,0.024752475,0.024752475,0.000000000],[0.173267327,0.024752475,0.024752475,0.024752475,0.000000000],[0.183168317,0.024752475,0.024752475,0.024752475,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin Interaction U32 - A36 tSS Interaction | Interacting Bases [1,5] | Pair Probability [[0.180519376,0.017157494,0.024883181,0.007207709,0.000000000],[0.173124567,0.013878938,0.001921253,0.007559536,0.000000000],[0.178058238,0.001921253,0.155093256,0.006042475,0.000000000],[0.202026315,0.014064519,0.009451832,0.007090057,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin Interaction U32 - A38 cSW Insertion | Location [3] | Length Distribution [0.045351474,0.907029478,0.045351474,0.002267574] | Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000]// Insertion in Hairpin after nucleotide 4, position 3 Insertion | Location [4] | Length Distribution [0.045351474,0.907029478,0.045351474,0.002267574] | Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000]// Insertion in Hairpin after nucleotide 5, position 4Sequences of instances from HL_46771.1:
> HL_46771.1 HL_3FOZ_005 A 31 U 39 AUUGAAAAU