| 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_26055.5_Instance_1 HL_26055.5_HL_4FEN_002_G46_C53 | G | U | U | U | C | U | A | C | ||||||||||||
| HL_26055.5_Sequence_1 HL_26055.5_HL_4FEN_002_G46_C53 | G | U | U | U | C | U | A | C | true | 100 | 0 | 0 | 0.00 | |||||||
| HL_26055.5_Instance_2 HL_26055.5_HL_1Y27_002_G46_C53 | G | U | U | U | C | U | A | C | ||||||||||||
| HL_26055.5_Sequence_2 HL_26055.5_HL_1Y27_002_G46_C53 | G | U | U | U | C | U | A | C | true | 100 | 0 | 0 | 0.00 | |||||||
| HL_26055.5_Instance_3 HL_26055.5_HL_1Y26_002_G46_C53 | G | U | U | U | C | U | A | C | ||||||||||||
| HL_26055.5_Sequence_3 HL_26055.5_HL_1Y26_002_G46_C53 | G | U | U | U | C | U | A | C | true | 100 | 0 | 0 | 0.00 | |||||||
| HL_26055.5_Instance_4 HL_26055.5_HL_4XNR_002_G46_C53 | G | U | U | U | C | U | A | C | ||||||||||||
| HL_26055.5_Sequence_4 HL_26055.5_HL_4XNR_002_G46_C53 | G | U | U | U | C | U | A | C | true | 100 | 0 | 0 | 0.00 | |||||||
| HL_26055.5_Instance_5 HL_26055.5_HL_4LX6_002_G46_C53 | G | C | U | U | C | C | A | C | ||||||||||||
| HL_26055.5_Sequence_5 HL_26055.5_HL_4LX6_002_G46_C53 | G | C | U | U | C | C | A | C | true | 84 | 0 | 0 | 1.60 | |||||||
| HL_26055.5_Instance_6 HL_26055.5_HL_3LA5_002_G46_C53 | G | C | U | U | C | C | A | C | ||||||||||||
| HL_26055.5_Sequence_6 HL_26055.5_HL_3LA5_002_G46_C53 | G | C | U | U | C | C | A | C | true | 84 | 0 | 0 | 1.60 | |||||||
| HL_26055.5_Instance_7 HL_26055.5_HL_3AL0_002_A31_U39 | A | C | U | C | U | G | G | A | U | |||||||||||
| HL_26055.5_Sequence_7 HL_26055.5_HL_3AL0_002_A31_U39 | A | C | U | C | U | G | G | A | U | true | 24 | 0 | 0 | 7.85 | ||||||
| HL_26055.5_Instance_8 HL_26055.5_HL_4LFB_002_G80_C89 | G | U | U | U | U | A | C | |||||||||||||
| HL_26055.5_Sequence_8 HL_26055.5_HL_4LFB_002_G80_C89 | G | U | U | U | U | A | C | true | 97 | 0 | 0 | 0.33 | ||||||||
| HL_26055.5_Instance_9 HL_26055.5_HL_2GDI_001_C27_G33 | C | U | G | C | G | U | G | |||||||||||||
| HL_26055.5_Sequence_9 HL_26055.5_HL_2GDI_001_C27_G33 | C | U | G | C | G | U | G | true | 61 | 0 | 0 | 4.06 | ||||||||
| HL_26055.5_Instance_10 HL_26055.5_HL_4LFB_014_G617_C623 | G | C | U | C | A | A | C | |||||||||||||
| HL_26055.5_Sequence_10 HL_26055.5_HL_4LFB_014_G617_C623 | G | C | U | C | A | A | C | true | 91 | 0 | 0 | 0.95 | ||||||||
| HL_26055.5_Instance_11 HL_26055.5_HL_6CZR_085_G601_C607 | G | C | U | C | A | A | C | |||||||||||||
| HL_26055.5_Sequence_11 HL_26055.5_HL_6CZR_085_G601_C607 | G | C | U | C | A | A | C | true | 91 | 0 | 0 | 0.95 | ||||||||
| HL_26055.5_Instance_12 HL_26055.5_HL_5J7L_014_G617_C623 | G | C | U | C | A | A | C | |||||||||||||
| HL_26055.5_Sequence_12 HL_26055.5_HL_5J7L_014_G617_C623 | G | C | U | C | A | A | C | true | 91 | 0 | 0 | 0.95 | ||||||||
| HL_26055.5_Instance_13 HL_26055.5_HL_7A0S_061_C2530_G2536 | C | U | G | U | U | C | G | |||||||||||||
| HL_26055.5_Sequence_13 HL_26055.5_HL_7A0S_061_C_2530_G_2536 | C | U | G | U | U | C | G | true | 74 | 0 | 0 | 2.64 | ||||||||
| HL_26055.5_Instance_14 HL_26055.5_HL_4WF9_058_C2578_G2584 | C | U | G | U | U | C | G | |||||||||||||
| HL_26055.5_Sequence_14 HL_26055.5_HL_4WF9_058_C_2578_G_2584 | C | U | G | U | U | C | G | true | 74 | 0 | 0 | 2.64 | ||||||||
| HL_26055.5_Instance_15 HL_26055.5_HL_5TBW_063_U2920_A2926 | U | U | G | U | U | C | A | |||||||||||||
| HL_26055.5_Sequence_15 HL_26055.5_HL_5TBW_063_U_2920_A_2926 | U | U | G | U | U | C | A | true | 73 | 0 | 0 | 2.74 |
1 2 s35 1 7 cWW 3 4 s35 4 5 s35 5 6 s35 6 7 s35JAR3D SCFG/MRF model for HL_26055.5:
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 G46 - C53 from junction BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.008530388,0.017359359,0.009671116,0.186678966,0.000000000],[0.016046005,0.008514709,0.206336649,0.011566840,0.000000000],[0.009620172,0.269648411,0.001847676,0.024498429,0.000000000],[0.185613341,0.011775168,0.023133583,0.009159189,0.000000000],[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 G46 - C53 cWW HairpinNode | Num Bases [5] | Left Index [2] | Right Index [6] | Norm Constant [1.000000000000000] // Hairpin node U47:A52 Interaction | Interacting Bases [1,1] | Pair Probability [[0.029411765,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.382352941,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.029411765,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.558823529,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U47 Interaction | Interacting Bases [2,2] | Pair Probability [[0.029411765,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.088235294,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.264705882,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.617647059,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U49 Interaction | Interacting Bases [3,3] | Pair Probability [[0.029411765,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.617647059,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.029411765,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.323529412,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C50 Interaction | Interacting Bases [4,4] | Pair Probability [[0.205882353,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.147058824,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.147058824,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.500000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U51 Interaction | Interacting Bases [5,5] | Pair Probability [[0.676470588,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.205882353,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.029411765,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.088235294,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A52 Insertion | Location [1] | Length Distribution [0.532198331,0.466088110,0.001636173,0.000077387] | Letter Distribution [0.055555556,0.055555556,0.055555556,0.833333333,0.000000000]// Insertion in Hairpin after nucleotide 2, position 1 Insertion | Location [4] | Length Distribution [0.930093541,0.069519013,0.000376377,0.000011070] | Letter Distribution [0.166666667,0.166666667,0.500000000,0.166666667,0.000000000]// Insertion in Hairpin after nucleotide 5, position 4Sequences of instances from HL_26055.5:
> HL_26055.5 HL_4FEN_002 G 46 C 53 GUUUCUAC > HL_26055.5 HL_1Y27_002 G 46 C 53 GUUUCUAC > HL_26055.5 HL_1Y26_002 G 46 C 53 GUUUCUAC > HL_26055.5 HL_4XNR_002 G 46 C 53 GUUUCUAC > HL_26055.5 HL_4LX6_002 G 46 C 53 GCUUCCAC > HL_26055.5 HL_3LA5_002 G 46 C 53 GCUUCCAC > HL_26055.5 HL_3AL0_002 A 31 U 39 ACUCUGGAU > HL_26055.5 HL_4LFB_002 G 80 C 89 GUUUUAC > HL_26055.5 HL_2GDI_001 C 27 G 33 CUGCGUG > HL_26055.5 HL_4LFB_014 G 617 C 623 GCUCAAC > HL_26055.5 HL_6CZR_085 G 601 C 607 GCUCAAC > HL_26055.5 HL_5J7L_014 G 617 C 623 GCUCAAC > HL_26055.5 HL_7A0S_061 C 2530 G 2536 CUGUUCG > HL_26055.5 HL_4WF9_058 C 2578 G 2584 CUGUUCG > HL_26055.5 HL_5TBW_063 U 2920 A 2926 UUGUUCA