| 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 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_32512.6_Instance_1 HL_32512.6_HL_4AOB_001_G23_C29 | G | A | C | U | G | G | C | |||||||||||||
| HL_32512.6_Sequence_1 HL_32512.6_HL_4AOB_001_G23_C29 | G | A | C | U | G | G | C | true | 100 | 0 | 0 | 0.00 | ||||||||
| HL_32512.6_Instance_2 HL_32512.6_HL_4AOB_004_G23_C29 | G | A | C | U | G | G | C | |||||||||||||
| HL_32512.6_Sequence_2 HL_32512.6_HL_4AOB_004_G23_C29 | G | A | C | U | G | G | C | true | 100 | 0 | 0 | 0.00 | ||||||||
| HL_32512.6_Instance_3 HL_32512.6_HL_5FJC_001_G23_C29 | G | A | C | U | G | G | C | |||||||||||||
| HL_32512.6_Sequence_3 HL_32512.6_HL_5FJC_001_G23_C29 | G | A | C | U | G | G | C | true | 100 | 0 | 0 | 0.00 | ||||||||
| HL_32512.6_Instance_4 HL_32512.6_HL_4KQY_004_G23_C29 | G | A | C | U | G | G | C | |||||||||||||
| HL_32512.6_Sequence_4 HL_32512.6_HL_4KQY_004_G23_C29 | G | A | C | U | G | G | C | true | 100 | 0 | 0 | 0.00 | ||||||||
| HL_32512.6_Instance_5 HL_32512.6_HL_4KQY_001_G23_C29 | G | A | C | U | G | G | C | |||||||||||||
| HL_32512.6_Sequence_5 HL_32512.6_HL_4KQY_001_G23_C29 | G | A | C | U | G | G | C | true | 100 | 0 | 0 | 0.00 | ||||||||
| HL_32512.6_Instance_6 HL_32512.6_HL_3V7E_001_G23_C29 | G | A | C | U | G | G | C | |||||||||||||
| HL_32512.6_Sequence_6 HL_32512.6_HL_3V7E_001_G23_C29 | G | A | C | U | G | G | C | true | 100 | 0 | 0 | 0.00 | ||||||||
| HL_32512.6_Instance_7 HL_32512.6_HL_6MWN_004_G650_C656 | G | C | U | G | G | A | C | |||||||||||||
| HL_32512.6_Sequence_7 HL_32512.6_HL_6MWN_004_G650_C656 | G | C | U | G | G | A | C | true | 51 | 0 | 0 | 5.25 | ||||||||
| HL_32512.6_Instance_8 HL_32512.6_HL_3HHN_009_G75_C82 | G | U | G | G | C | A | G | C | ||||||||||||
| HL_32512.6_Sequence_8 HL_32512.6_HL_3HHN_009_G75_C82 | G | U | G | G | C | A | G | C | true | 63 | 0 | 0 | 3.89 | |||||||
| HL_32512.6_Instance_9 HL_32512.6_HL_3IVK_004_G75_C82 | G | U | G | G | C | A | G | C | ||||||||||||
| HL_32512.6_Sequence_9 HL_32512.6_HL_3IVK_004_G75_C82 | G | U | G | G | C | A | G | C | true | 63 | 0 | 0 | 3.89 | |||||||
| HL_32512.6_Instance_10 HL_32512.6_HL_5U30_002_U43_G49 | U | U | U | C | C | A | G | |||||||||||||
| HL_32512.6_Sequence_10 HL_32512.6_HL_5U30_002_U43_G49 | U | U | U | C | C | A | G | true | 34 | 0 | 0 | 7.01 | ||||||||
| HL_32512.6_Instance_11 HL_32512.6_HL_6VMY_003_G268_C274 | G | U | C | C | C | G | C | |||||||||||||
| HL_32512.6_Sequence_11 HL_32512.6_HL_6VMY_003_G268_C274 | G | U | C | C | C | G | C | true | 79 | 0 | 0 | 2.27 | ||||||||
| HL_32512.6_Instance_12 HL_32512.6_HL_4WF9_014_G456_C463 | G | G | A | C | C | A | U | C | ||||||||||||
| HL_32512.6_Sequence_12 HL_32512.6_HL_4WF9_014_G456_C463 | G | G | A | C | C | A | U | C | true | 81 | 0 | 0 | 2.01 | |||||||
| HL_32512.6_Instance_13 HL_32512.6_HL_4Y4O_116_G410_C417 | G | G | A | C | C | A | C | C | ||||||||||||
| HL_32512.6_Sequence_13 HL_32512.6_HL_4Y4O_116_G410_C417 | G | G | A | C | C | A | C | C | true | 84 | 0 | 0 | 1.67 | |||||||
| HL_32512.6_Instance_14 HL_32512.6_HL_5J7L_146_G410_C417 | G | G | A | C | C | A | U | C | ||||||||||||
| HL_32512.6_Sequence_14 HL_32512.6_HL_5J7L_146_G410_C417 | G | G | A | C | C | A | U | C | true | 81 | 0 | 0 | 2.01 | |||||||
| HL_32512.6_Instance_15 HL_32512.6_HL_4OQU_002_G32_C40 | G | A | C | G | G | A | C | A | C | |||||||||||
| HL_32512.6_Sequence_15 HL_32512.6_HL_4OQU_002_G32_C40 | G | A | C | G | G | A | C | A | C | true | 6 | 0 | 0 | 9.98 | ||||||
| HL_32512.6_Instance_16 HL_32512.6_HL_7A0S_014_G423_C430 | G | G | A | C | C | A | C | C | ||||||||||||
| HL_32512.6_Sequence_16 HL_32512.6_HL_7A0S_014_G423_C430 | G | G | A | C | C | A | C | C | true | 84 | 0 | 0 | 1.67 |
1 7 cWW 2 3 s35 3 4 s35 4 5 s35 5 6 s35 6 7 s35JAR3D SCFG/MRF model for HL_32512.6:
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 G23 - C29 from junction BasepairNode | Deletion Probability [0.0000017102807318] | Pair Probability [[0.008642056,0.017479640,0.009921850,0.168007953,0.000000000],[0.030720937,0.009404426,0.169693359,0.011831898,0.000000000],[0.009837554,0.303581170,0.001904001,0.022870291,0.000000000],[0.168572384,0.012172502,0.046130308,0.009229670,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.561258214,0.437225398,0.001448346,0.000068043] | Left Letter Distribution [0.166666667,0.055555556,0.500000000,0.277777778,0.000000000] | Right Length Distribution [0.934446650,0.065203005,0.000340613,0.000009732] | Right Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000] | Left Index [1] | Right Index [7] // Basepair G23 - C29 cWW HairpinNode | Num Bases [5] | Left Index [2] | Right Index [6] | Norm Constant [1.000000000000000] // Hairpin node A24:G28 Interaction | Interacting Bases [1,1] | Pair Probability [[0.583333333,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.138888889,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.138888889,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.138888889,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A24 Interaction | Interacting Bases [2,2] | Pair Probability [[0.027777778,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.638888889,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.194444444,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.138888889,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C25 Interaction | Interacting Bases [3,3] | Pair Probability [[0.027777778,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.472222222,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.138888889,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.361111111,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U26 Interaction | Interacting Bases [4,4] | Pair Probability [[0.416666667,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.138888889,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.416666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.027777778,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G27 Interaction | Interacting Bases [5,5] | Pair Probability [[0.138888889,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.194444444,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.527777778,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.138888889,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G28Sequences of instances from HL_32512.6:
> HL_32512.6 HL_4AOB_001 G 23 C 29 GACUGGC > HL_32512.6 HL_4AOB_004 G 23 C 29 GACUGGC > HL_32512.6 HL_5FJC_001 G 23 C 29 GACUGGC > HL_32512.6 HL_4KQY_004 G 23 C 29 GACUGGC > HL_32512.6 HL_4KQY_001 G 23 C 29 GACUGGC > HL_32512.6 HL_3V7E_001 G 23 C 29 GACUGGC > HL_32512.6 HL_6MWN_004 G 650 C 656 GCUGGAC > HL_32512.6 HL_3HHN_009 G 75 C 82 GUGGCAGC > HL_32512.6 HL_3IVK_004 G 75 C 82 GUGGCAGC > HL_32512.6 HL_5U30_002 U 43 G 49 UUUCCAG > HL_32512.6 HL_6VMY_003 G 268 C 274 GUCCCGC > HL_32512.6 HL_4WF9_014 G 456 C 463 GGACCAUC > HL_32512.6 HL_4Y4O_116 G 410 C 417 GGACCACC > HL_32512.6 HL_5J7L_146 G 410 C 417 GGACCAUC > HL_32512.6 HL_4OQU_002 G 32 C 40 GACGGACAC > HL_32512.6 HL_7A0S_014 G 423 C 430 GGACCACC