| 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 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_23481.4_Instance_1 HL_23481.4_HL_4Y4O_108_G194_C201 | G | A | A | A | C | A | U | C | ||||||||||||
| HL_23481.4_Sequence_1 HL_23481.4_HL_4Y4O_108_G194_C201 | G | A | A | A | C | A | U | C | true | 100 | 0 | 0 | 0.00 | |||||||
| HL_23481.4_Instance_2 HL_23481.4_HL_5J7L_139_G194_C201 | G | A | A | A | C | A | U | C | ||||||||||||
| HL_23481.4_Sequence_2 HL_23481.4_HL_5J7L_139_G194_C201 | G | A | A | A | C | A | U | C | true | 100 | 0 | 0 | 0.00 | |||||||
| HL_23481.4_Instance_3 HL_23481.4_HL_7A0S_006_G171_C178 | G | A | A | A | C | A | U | C | ||||||||||||
| HL_23481.4_Sequence_3 HL_23481.4_HL_7A0S_006_G171_C178 | G | A | A | A | C | A | U | C | true | 100 | 0 | 0 | 0.00 | |||||||
| HL_23481.4_Instance_4 HL_23481.4_HL_4WF9_006_G197_C204 | G | A | A | A | C | A | U | C | ||||||||||||
| HL_23481.4_Sequence_4 HL_23481.4_HL_4WF9_006_G197_C204 | G | A | A | A | C | A | U | C | true | 100 | 0 | 0 | 0.00 | |||||||
| HL_23481.4_Instance_5 HL_23481.4_HL_4V9F_006_G164_C171 | G | A | A | A | C | A | U | C | ||||||||||||
| HL_23481.4_Sequence_5 HL_23481.4_HL_4V9F_006_G164_C171 | G | A | A | A | C | A | U | C | true | 100 | 0 | 0 | 0.00 | |||||||
| HL_23481.4_Instance_6 HL_23481.4_HL_5TBW_001_U38_A45 | U | A | A | G | C | A | U | A | ||||||||||||
| HL_23481.4_Sequence_6 HL_23481.4_HL_5TBW_001_U38_A45 | U | A | A | G | C | A | U | A | true | 76 | 0 | 0 | 3.16 | |||||||
| HL_23481.4_Instance_7 HL_23481.4_HL_3DIL_003_G124_C130 | G | G | A | A | U | A | C | |||||||||||||
| HL_23481.4_Sequence_7 HL_23481.4_HL_3DIL_003_G124_C130 | G | G | A | A | U | A | C | true | 45 | 0 | 0 | 7.28 |
1 2 s35 1 7 cWW 2 4 s33 2 6 tSH 3 4 s35 4 5 perp 6 7 s35 4 3 7BPh 2 4 7BPh 2 5 6BPh 7 6 7BPhJAR3D SCFG/MRF model for HL_23481.4:
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 G194 - C201 from junction BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.004354767,0.047939157,0.004907494,0.091358094,0.000000000],[0.008490175,0.022785803,0.091995623,0.005768198,0.000000000],[0.004870614,0.552009327,0.000949036,0.011730113,0.000000000],[0.100980433,0.032392788,0.014788539,0.004679839,0.000000000],[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 [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [7] // Basepair G194 - C201 cWW BasepairNode | Deletion Probability [0.0000002600501426] | Pair Probability [[0.048876728,0.035529728,0.007110834,0.760351247,0.000000000],[0.006709565,0.006883088,0.000215097,0.000215097,0.000000000],[0.060028161,0.000643714,0.015410861,0.043314483,0.000000000],[0.007349450,0.006931752,0.000215097,0.000215097,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.146977400,0.846630090,0.006090502,0.000302008] | Left Letter Distribution [0.812500000,0.062500000,0.062500000,0.062500000,0.000000000] | 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 [6] // Basepair A195 - U200 tSH HairpinNode | Num Bases [3] | Left Index [3] | Right Index [5] | Norm Constant [1.000000000000000] // Hairpin node A197:A199 Interaction | Interacting Bases [1,1] | Pair Probability [[0.722222222,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.055555556,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.166666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.055555556,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A197 Interaction | Interacting Bases [2,2] | Pair Probability [[0.147058824,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.833333333,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.009803922,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.009803922,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C198 Interaction | Interacting Bases [3,3] | Pair Probability [[0.722222222,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.055555556,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.055555556,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.166666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A199Sequences of instances from HL_23481.4:
> HL_23481.4 HL_4Y4O_108 G 194 C 201 GAAACAUC > HL_23481.4 HL_5J7L_139 G 194 C 201 GAAACAUC > HL_23481.4 HL_7A0S_006 G 171 C 178 GAAACAUC > HL_23481.4 HL_4WF9_006 G 197 C 204 GAAACAUC > HL_23481.4 HL_4V9F_006 G 164 C 171 GAAACAUC > HL_23481.4 HL_5TBW_001 U 38 A 45 UAAGCAUA > HL_23481.4 HL_3DIL_003 G 124 C 130 GGAAUAC