| 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_67216.4_Instance_1 HL_67216.4_HL_4Y4O_110_C246_G252 | C | G | G | C | G | A | G | |||||||||||||
| HL_67216.4_Sequence_1 HL_67216.4_HL_4Y4O_110_C246_G252 | C | G | G | C | G | A | G | true | 100 | 0 | 0 | 0.00 | ||||||||
| HL_67216.4_Instance_2 HL_67216.4_HL_7A0S_008_C223_G229 | C | G | G | C | G | A | G | |||||||||||||
| HL_67216.4_Sequence_2 HL_67216.4_HL_7A0S_008_C223_G229 | C | G | G | C | G | A | G | true | 100 | 0 | 0 | 0.00 | ||||||||
| HL_67216.4_Instance_3 HL_67216.4_HL_5J7L_141_C246_G252 | C | G | G | C | G | A | G | |||||||||||||
| HL_67216.4_Sequence_3 HL_67216.4_HL_5J7L_141_C246_G252 | C | G | G | C | G | A | G | true | 100 | 0 | 0 | 0.00 | ||||||||
| HL_67216.4_Instance_4 HL_67216.4_HL_5TBW_003_C90_G96 | C | G | G | C | G | A | G | |||||||||||||
| HL_67216.4_Sequence_4 HL_67216.4_HL_5TBW_003_C90_G96 | C | G | G | C | G | A | G | true | 100 | 0 | 0 | 0.00 | ||||||||
| HL_67216.4_Instance_5 HL_67216.4_HL_4WF9_008_C249_G255 | C | G | G | C | G | A | G | |||||||||||||
| HL_67216.4_Sequence_5 HL_67216.4_HL_4WF9_008_C249_G255 | C | G | G | C | G | A | G | true | 100 | 0 | 0 | 0.00 | ||||||||
| HL_67216.4_Instance_6 HL_67216.4_HL_4V9F_008_C217_G223 | C | C | G | C | G | A | G | |||||||||||||
| HL_67216.4_Sequence_6 HL_67216.4_HL_4V9F_008_C217_G223 | C | C | G | C | G | A | G | true | 90 | 0 | 0 | 1.44 | ||||||||
| HL_67216.4_Instance_7 HL_67216.4_HL_4V88_217_U1396_G1402 | U | U | U | C | A | A | G | |||||||||||||
| HL_67216.4_Sequence_7 HL_67216.4_HL_4V88_217_U_1396_G_1402 | U | U | U | C | A | A | G | true | 61 | 0 | 0 | 5.45 |
1 2 s35 1 7 cWW 2 4 s35 2 6 tSH 2 7 s55 3 5 s55 5 6 s35 6 7 s35 4 1 6BPh 4 2 7BPh 2 6 6BPhJAR3D SCFG/MRF model for HL_67216.4:
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 C246 - G252 from junction BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.009323756,0.015877713,0.010902482,0.167504797,0.000000000],[0.057767753,0.011742545,0.232594255,0.013451740,0.000000000],[0.011045651,0.170984366,0.002157753,0.021172046,0.000000000],[0.176272283,0.012855711,0.076243940,0.010103208,0.000000000],[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 C246 - G252 cWW BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.068633616,0.049385507,0.000771139,0.003732319,0.000000000],[0.078968013,0.063136280,0.000771139,0.000771139,0.000000000],[0.333146473,0.002914223,0.014957341,0.230264202,0.000000000],[0.081727946,0.069278386,0.000771139,0.000771139,0.000000000],[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 [6] // Basepair G247 - A251 tSH HairpinNode | Num Bases [3] | Left Index [3] | Right Index [5] | Norm Constant [1.000000000000000] // Hairpin node G248:G250 Interaction | Interacting Bases [1,1] | Pair Probability [[0.055555556,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.055555556,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.722222222,0.000000000,0.000000000],[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 G248 Interaction | Interacting Bases [2,2] | Pair Probability [[0.001449275,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.995652174,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.001449275,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.001449275,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C249 Interaction | Interacting Bases [3,3] | Pair Probability [[0.166666667,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.055555556,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.722222222,0.000000000,0.000000000],[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 G250Sequences of instances from HL_67216.4:
> HL_67216.4 HL_4Y4O_110 C 246 G 252 CGGCGAG > HL_67216.4 HL_7A0S_008 C 223 G 229 CGGCGAG > HL_67216.4 HL_5J7L_141 C 246 G 252 CGGCGAG > HL_67216.4 HL_5TBW_003 C 90 G 96 CGGCGAG > HL_67216.4 HL_4WF9_008 C 249 G 255 CGGCGAG > HL_67216.4 HL_4V9F_008 C 217 G 223 CCGCGAG > HL_67216.4 HL_4V88_217 U 1396 G 1402 UUUCAAG