| 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 7 2 | 5 7 I | 6 8 3 | 7 8 I | 8 8 4 | 9 8 I | 10 8 5 | 11 8 I | 12 8 6 | 13 7 I | 14 7 7 | 15 6 I | 16 5 8 | 17 4 I | 18 3 9 | 19 2 I | 20 2 10 | 21 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| HL_98864.1_Instance_1 HL_98864.1,HL_4OJI_002,G23_C32 | G | U | C | C | C | A | A | G | C | C | ||||||||||||||||
| HL_98864.1_Sequence_1 HL_98864.14OJI_G23_C32 | G | U | C | C | C | A | A | G | C | C | true | 100 | 0 | 0 | 0.00 | |||||||||||
| HL_98864.1_Instance_2 HL_98864.1,HL_4RGE_003,G29_C38 | G | U | C | C | U | A | A | G | C | C | ||||||||||||||||
| HL_98864.1_Sequence_2 HL_98864.14RGE_G29_C38 | G | U | C | C | U | A | A | G | C | C | true | 97 | 0 | 0 | 0.51 | |||||||||||
| HL_98864.1_Instance_3 HL_98864.1,HL_4QJD_004,G43_C52 | G | U | C | C | C | A | A | G | C | C | ||||||||||||||||
| HL_98864.1_Sequence_3 HL_98864.14QJD_G43_C52 | G | U | C | C | C | A | A | G | C | C | true | 100 | 0 | 0 | 0.00 | |||||||||||
| HL_98864.1_Instance_4 HL_98864.1,HL_8UIW_002,G50_C59 | G | U | A | G | G | U | A | G | U | C | ||||||||||||||||
| HL_98864.1_Sequence_4 HL_98864.18UIW_G50_C59 | G | U | A | G | G | U | A | G | U | C | true | 80 | 0 | 0 | 3.90 |
1 2 s35 1 10 cWW 2 7 tWH 3 4 s35 4 5 s35 5 6 s35 7 10 s35 8 9 s35 10 9 7BPhJAR3D SCFG/MRF model for HL_98864.1:
Character Definition | A,C,G,U,* // Identity and order of characters in matrices InitialNode | Left Length Distribution [0.999900000,0.000100000] | Left Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Right Length Distribution [0.999900000,0.000100000] | Right Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Left Index [1] | Right Index [10] // Initial node BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.003750350,0.054674460,0.004270648,0.077568035,0.000000000],[0.006587592,0.025743166,0.078225305,0.005118269,0.000000000],[0.004223220,0.601955120,0.000804991,0.010312508,0.000000000],[0.076575313,0.037185886,0.009039378,0.003965758,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [10] // Basepair G23 - C32 cWW FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.083333333,0.583333333,0.083333333,0.250000000,0.000000000] | Position [2] | Left Index [2] | Right Index [9] // Fixed node on right for 4OJI|1|A|C|31 InitialNode | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [8] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.083333333,0.083333333,0.750000000,0.083333333,0.000000000] | Position [2] | Left Index [2] | Right Index [8] // Fixed node on right for 4OJI|1|A|G|30 InitialNode | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [7] // New Initial node after Fixed node BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.017820521,0.003943710,0.018509527,0.003943710,0.000000000],[0.039659197,0.317787634,0.003943710,0.003943710,0.000000000],[0.003943710,0.009453333,0.029991579,0.017540263,0.000000000],[0.463849874,0.003943710,0.022880930,0.038844885,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [7] // Basepair U24 - A29 tWH HairpinNode | Num Bases [4] | Left Index [3] | Right Index [6] | Norm Constant [1.000000000000000] // Hairpin node C25:A28 Interaction | Interacting Bases [1,1] | Pair Probability [[0.250000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.583333333,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.083333333,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.083333333,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C25 Interaction | Interacting Bases [2,2] | Pair Probability [[0.083333333,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.583333333,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.250000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.083333333,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C26 Interaction | Interacting Bases [3,3] | Pair Probability [[0.083333333,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.416666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.250000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.250000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C27 Interaction | Interacting Bases [4,4] | Pair Probability [[0.583333333,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.083333333,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.083333333,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.250000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A28Sequences of instances from HL_98864.1:
> HL_98864.1 4OJI G 23 C 32 GUCCCAAGCC > HL_98864.1 4RGE G 29 C 38 GUCCUAAGCC > HL_98864.1 4QJD G 43 C 52 GUCCCAAGCC > HL_98864.1 8UIW G 50 C 59 GUAGGUAGUC