| 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 2 I | 8 2 4 | 9 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| HL_15942.4_Instance_1 HL_15942.4_HL_5J7L_157_U826_G831 | U | U | U | A | G | G | ||||||||
| HL_15942.4_Sequence_1 HL_15942.4_HL_5J7L_157_U826_G831 | U | U | U | A | G | G | true | 100 | 0 | 0 | 0.00 | |||
| HL_15942.4_Instance_2 HL_15942.4_HL_4WF9_025_U871_G876 | U | U | U | A | G | G | ||||||||
| HL_15942.4_Sequence_2 HL_15942.4_HL_4WF9_025_U871_G876 | U | U | U | A | G | G | true | 100 | 0 | 0 | 0.00 | |||
| HL_15942.4_Instance_3 HL_15942.4_HL_4Y4O_127_U826_G831 | U | U | U | A | G | G | ||||||||
| HL_15942.4_Sequence_3 HL_15942.4_HL_4Y4O_127_U826_G831 | U | U | U | A | G | G | true | 100 | 0 | 0 | 0.00 | |||
| HL_15942.4_Instance_4 HL_15942.4_HL_5TBW_022_C958_G963 | C | C | U | C | A | G | ||||||||
| HL_15942.4_Sequence_4 HL_15942.4_HL_5TBW_022_C958_G963 | C | C | U | C | A | G | true | 59 | 0 | 0 | 3.89 | |||
| HL_15942.4_Instance_5 HL_15942.4_HL_4V9F_026_U919_G924 | U | C | G | A | A | G | ||||||||
| HL_15942.4_Sequence_5 HL_15942.4_HL_4V9F_026_U919_G924 | U | C | G | A | A | G | true | 81 | 0 | 0 | 1.76 | |||
| HL_15942.4_Instance_6 HL_15942.4_HL_7A0S_024_U839_G844 | U | U | G | A | G | G | ||||||||
| HL_15942.4_Sequence_6 HL_15942.4_HL_7A0S_024_U839_G844 | U | U | G | A | G | G | true | 94 | 0 | 0 | 0.59 |
1 2 perp 1 4 cWW 2 3 s35JAR3D SCFG/MRF model for HL_15942.4:
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 [4] // Initial node U826 - G831 from junction BasepairNode | Deletion Probability [0.0000000006195971] | Pair Probability [[0.010547588,0.013956235,0.013207310,0.061771316,0.000000000],[0.245853224,0.023971034,0.076912099,0.015069266,0.000000000],[0.013477701,0.062338547,0.002986305,0.015528739,0.000000000],[0.101411502,0.013901952,0.316578930,0.012488251,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.008193363,0.983203605,0.008193363,0.000409668] | Left Letter Distribution [0.062500000,0.312500000,0.062500000,0.562500000,0.000000000] | Right Length Distribution [0.008193363,0.983203605,0.008193363,0.000409668] | Right Letter Distribution [0.312500000,0.062500000,0.562500000,0.062500000,0.000000000] | Left Index [1] | Right Index [4] // Basepair U826 - G831 cWW HairpinNode | Num Bases [2] | Left Index [2] | Right Index [3] | Norm Constant [1.000000000000000] // Hairpin node U828:A829 Interaction | Interacting Bases [1,1] | Pair Probability [[0.062500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.062500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.312500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.562500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U828 Interaction | Interacting Bases [2,2] | Pair Probability [[0.687500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.187500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.062500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.062500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A829Sequences of instances from HL_15942.4:
> HL_15942.4 HL_5J7L_157 U 826 G 831 UUUAGG > HL_15942.4 HL_4WF9_025 U 871 G 876 UUUAGG > HL_15942.4 HL_4Y4O_127 U 826 G 831 UUUAGG > HL_15942.4 HL_5TBW_022 C 958 G 963 CCUCAG > HL_15942.4 HL_4V9F_026 U 919 G 924 UCGAAG > HL_15942.4 HL_7A0S_024 U 839 G 844 UUGAGG