| 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 2 I | 12 2 6 | 13 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| HL_28567.3_Instance_1 HL_28567.3_HL_6U8D_001_G161_C166 | G | A | G | U | A | C | ||||||||||||
| HL_28567.3_Sequence_1 HL_28567.3_HL_6U8D_001_G161_C166 | G | A | G | U | A | C | true | 90 | 0 | 0 | 0.92 | |||||||
| HL_28567.3_Instance_2 HL_28567.3_HL_4XWF_001_G24_C29 | G | G | A | A | A | C | ||||||||||||
| HL_28567.3_Sequence_2 HL_28567.3_HL_4XWF_001_G24_C29 | G | G | A | A | A | C | true | 100 | 0 | 0 | 0.00 | |||||||
| HL_28567.3_Instance_3 HL_28567.3_HL_3ADD_003_C47D_G47I | C | G | A | G | U | G | ||||||||||||
| HL_28567.3_Sequence_3 HL_28567.3_HL_3ADD_003_C47D_G47I | C | G | A | G | U | G | true | 88 | 0 | 0 | 1.10 | |||||||
| HL_28567.3_Instance_4 HL_28567.3_HL_4RUM_001_C27_G33 | C | A | G | A | G | C | G | |||||||||||
| HL_28567.3_Sequence_4 HL_28567.3_HL_4RUM_001_C27_G33 | C | A | G | A | G | C | G | true | 61 | 0 | 0 | 3.73 | ||||||
| HL_28567.3_Instance_5 HL_28567.3_HL_4KR9_002_G19_C24 | G | G | A | A | A | C | ||||||||||||
| HL_28567.3_Sequence_5 HL_28567.3_HL_4KR9_002_G19_C24 | G | G | A | A | A | C | true | 100 | 0 | 0 | 0.00 | |||||||
| HL_28567.3_Instance_6 HL_28567.3_HL_2OEU_002_C25_G32 | C | C | A | AA | U | A | G | |||||||||||
| HL_28567.3_Sequence_6 HL_28567.3_HL_2OEU_002_C25_G32 | C | C | A | AA | U | A | G | true | 69 | 0 | 0 | 2.94 |
1 2 s35 1 6 cWW 2 3 s35 2 6 s55 4 5 s35JAR3D SCFG/MRF model for HL_28567.3:
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 G161 - C166 from junction BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.009271545,0.017981432,0.010607783,0.192505806,0.000000000],[0.017981779,0.009265445,0.226529308,0.013026479,0.000000000],[0.010607796,0.226528663,0.002010668,0.024167927,0.000000000],[0.192506087,0.013026424,0.024168288,0.009814571,0.000000000],[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 [6] // Basepair G161 - C166 cWW HairpinNode | Num Bases [4] | Left Index [2] | Right Index [5] | Norm Constant [1.000000000000000] // Hairpin node A162:A165 Interaction | Interacting Bases [1,1] | Pair Probability [[0.312500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.187500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.437500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.062500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A162 Interaction | Interacting Bases [2,2] | Pair Probability [[0.562500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.062500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.312500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.062500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G163 Interaction | Interacting Bases [3,3] | Pair Probability [[0.312500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.062500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.312500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.312500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U164 Interaction | Interacting Bases [4,4] | Pair Probability [[0.562500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.187500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.062500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.187500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A165 Insertion | Location [2] | Length Distribution [0.660442125,0.171632569,0.166414939,0.001441714,0.000068653] | Letter Distribution [0.700000000,0.100000000,0.100000000,0.100000000,0.000000000]// Insertion in Hairpin after nucleotide 3, position 2Sequences of instances from HL_28567.3:
> HL_28567.3 HL_6U8D_001 G 161 C 166 GAGUAC > HL_28567.3 HL_4XWF_001 G 24 C 29 GGAAAC > HL_28567.3 HL_3ADD_003 C 47D G 47I CGAGUG > HL_28567.3 HL_4RUM_001 C 27 G 33 CAGAGCG > HL_28567.3 HL_4KR9_002 G 19 C 24 GGAAAC > HL_28567.3 HL_2OEU_002 C 25 G 32 CCAAAUAG