| 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_69774.3_Instance_1 HL_69774.3_HL_6DB9_001_G23_C29 | G | A | A | A | C | A | C | |||||||||||
| HL_69774.3_Sequence_1 HL_69774.3_HL_6DB9_001_G23_C29 | G | A | A | A | C | A | C | true | 100 | 0 | 0 | 0.00 | ||||||
| HL_69774.3_Instance_2 HL_69774.3_HL_4KZD_001_G37_C43 | G | A | A | A | C | A | C | |||||||||||
| HL_69774.3_Sequence_2 HL_69774.3_HL_4KZD_001_G37_C43 | G | A | A | A | C | A | C | true | 100 | 0 | 0 | 0.00 | ||||||
| HL_69774.3_Instance_3 HL_69774.3_HL_3IVK_003_G59_C65 | G | A | A | A | C | A | C | |||||||||||
| HL_69774.3_Sequence_3 HL_69774.3_HL_3IVK_003_G59_C65 | G | A | A | A | C | A | C | true | 100 | 0 | 0 | 0.00 | ||||||
| HL_69774.3_Instance_4 HL_69774.3_HL_3IGI_009_C368_G373 | C | G | A | A | C | G | ||||||||||||
| HL_69774.3_Sequence_4 HL_69774.3_HL_3IGI_009_C368_G373 | C | G | A | A | C | G | true | 72 | 0 | 0 | 2.62 | |||||||
| HL_69774.3_Instance_5 HL_69774.3_HL_6OL3_001_G64_C70 | G | A | A | C | C | C | C | |||||||||||
| HL_69774.3_Sequence_5 HL_69774.3_HL_6OL3_001_G64_C70 | G | A | A | C | C | C | C | true | 73 | 0 | 0 | 2.57 |
1 2 s33 1 6 cWW 2 5 tSW 3 4 s35 4 5 s35 5 6 s35 4 3 7BPhJAR3D SCFG/MRF model for HL_69774.3:
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 G23 - C29 from junction BasepairNode | Deletion Probability [0.0000003483978778] | Pair Probability [[0.009417290,0.019076634,0.010743958,0.195076917,0.000000000],[0.017226610,0.009304766,0.207905455,0.013002891,0.000000000],[0.010672216,0.239916288,0.002029679,0.025359511,0.000000000],[0.193575287,0.013296343,0.023433726,0.009962428,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.204221895,0.787432499,0.007952872,0.000392734] | Left Letter Distribution [0.750000000,0.083333333,0.083333333,0.083333333,0.000000000] | 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 G23 - C29 cWW BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.203107741,0.046494307,0.003483177,0.010868727,0.000000000],[0.145237611,0.015974221,0.033903959,0.009508809,0.000000000],[0.140766888,0.186788362,0.003483177,0.007980206,0.000000000],[0.155220156,0.012097436,0.013661963,0.011423258,0.000000000],[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 [2] | Right Index [5] // Basepair A25 - A28 tSW HairpinNode | Num Bases [2] | Left Index [3] | Right Index [4] | Norm Constant [1.000000000000000] // Hairpin node A26:C27 Interaction | Interacting Bases [1,1] | Pair Probability [[0.642857143,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.214285714,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.071428571,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.071428571,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A26 Interaction | Interacting Bases [2,2] | Pair Probability [[0.202702703,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.770270270,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.013513514,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.013513514,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C27Sequences of instances from HL_69774.3:
> HL_69774.3 HL_6DB9_001 G 23 C 29 GAAACAC > HL_69774.3 HL_4KZD_001 G 37 C 43 GAAACAC > HL_69774.3 HL_3IVK_003 G 59 C 65 GAAACAC > HL_69774.3 HL_3IGI_009 C 368 G 373 CGAACG > HL_69774.3 HL_6OL3_001 G 64 C 70 GAACCCC