| 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_35894.3_Instance_1 HL_35894.3_HL_5M3H_001_U3_A8 | U | A | G | U | A | A | ||||||||||||
| HL_35894.3_Sequence_1 HL_35894.3_HL_5M3H_001_U3_A8 | U | A | G | U | A | A | true | 100 | 0 | 0 | 0.00 | |||||||
| HL_35894.3_Instance_2 HL_35894.3_HL_4WSB_001_U3_A8 | U | A | G | U | A | A | ||||||||||||
| HL_35894.3_Sequence_2 HL_35894.3_HL_4WSB_001_U3_A8 | U | A | G | U | A | A | true | 100 | 0 | 0 | 0.00 | |||||||
| HL_35894.3_Instance_3 HL_35894.3_HL_4WRT_001_U3_A8 | U | A | G | U | A | A | ||||||||||||
| HL_35894.3_Sequence_3 HL_35894.3_HL_4WRT_001_U3_A8 | U | A | G | U | A | A | true | 100 | 0 | 0 | 0.00 | |||||||
| HL_35894.3_Instance_4 HL_35894.3_HL_5FMZ_001_U3_A8 | U | A | G | U | A | A | ||||||||||||
| HL_35894.3_Sequence_4 HL_35894.3_HL_5FMZ_001_U3_A8 | U | A | G | U | A | A | true | 100 | 0 | 0 | 0.00 | |||||||
| HL_35894.3_Instance_5 HL_35894.3_HL_4KJI_001_G5_C12 | G | A | A | G | G | A | U | C | ||||||||||
| HL_35894.3_Sequence_5 HL_35894.3_HL_4KJI_001_G5_C12 | G | A | A | G | G | A | U | C | true | 42 | 0 | 0 | 5.78 | |||||
| HL_35894.3_Instance_6 HL_35894.3_HL_5J7L_140_C225_G230 | C | A | A | C | C | G | ||||||||||||
| HL_35894.3_Sequence_6 HL_35894.3_HL_5J7L_140_C225_G230 | C | A | A | C | C | G | true | 54 | 0 | 0 | 4.54 |
1 2 s35 1 6 cWW 2 3 s33 2 5 cSW 5 6 s35 3 3 2BPhJAR3D SCFG/MRF model for HL_35894.3:
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 U3 - A8 from junction BasepairNode | Deletion Probability [0.0000097596267952] | Pair Probability [[0.008886126,0.017248940,0.009893342,0.190110480,0.000000000],[0.020135330,0.009395594,0.201875378,0.011427567,0.000000000],[0.009905745,0.200257925,0.001981628,0.022841193,0.000000000],[0.233045106,0.010997521,0.042245054,0.009753071,0.000000000],[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 [0.826344012,0.171868555,0.001718686,0.000068747] | Right Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000] | Left Index [1] | Right Index [6] // Basepair U3 - A8 cWW BasepairNode | Deletion Probability [0.0000097596267952] | Pair Probability [[0.296711805,0.052159493,0.019116627,0.006867568,0.000000000],[0.176943758,0.011530991,0.001923665,0.007244421,0.000000000],[0.186991736,0.001923665,0.024501297,0.005732951,0.000000000],[0.180745949,0.011702405,0.009150435,0.006753235,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.826344012,0.171868555,0.001718686,0.000068747] | Left Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000] | 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 [5] // Basepair A4 - A7 cSW HairpinNode | Num Bases [2] | Left Index [3] | Right Index [4] | Norm Constant [1.000000000000000] // Hairpin node G5:U6 Interaction | Interacting Bases [1,1] | Pair Probability [[0.170454545,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.011363636,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.806818182,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.011363636,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G5 Interaction | Interacting Bases [2,2] | Pair Probability [[0.062500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.187500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.187500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.562500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U6Sequences of instances from HL_35894.3:
> HL_35894.3 HL_5M3H_001 U 3 A 8 UAGUAA > HL_35894.3 HL_4WSB_001 U 3 A 8 UAGUAA > HL_35894.3 HL_4WRT_001 U 3 A 8 UAGUAA > HL_35894.3 HL_5FMZ_001 U 3 A 8 UAGUAA > HL_35894.3 HL_4KJI_001 G 5 C 12 GAAGGAUC > HL_35894.3 HL_5J7L_140 C 225 G 230 CAACCG