| 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 4 I | 12 4 6 | 13 3 I | 14 3 7 | 15 2 I | 16 2 8 | 17 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| HL_05018.4_Instance_1 HL_05018.4_HL_7A0S_067_G2794_C2802 | G | A | A | G | A | C | C | A | C | |||||||||||||
| HL_05018.4_Sequence_1 HL_05018.4_HL_7A0S_067_G_2794_C_2802 | G | A | A | G | A | C | C | A | C | true | 96 | 0 | 0 | 0.59 | ||||||||
| HL_05018.4_Instance_2 HL_05018.4_HL_4WF9_064_A2839_U2847 | A | A | A | G | A | U | G | A | U | |||||||||||||
| HL_05018.4_Sequence_2 HL_05018.4_HL_4WF9_064_A_2839_U_2847 | A | A | A | G | A | U | G | A | U | true | 92 | 0 | 0 | 1.29 | ||||||||
| HL_05018.4_Instance_3 HL_05018.4_HL_4Y4O_171_G2819_C2827 | G | A | A | G | A | C | C | A | C | |||||||||||||
| HL_05018.4_Sequence_3 HL_05018.4_HL_4Y4O_171_G_2819_C_2827 | G | A | A | G | A | C | C | A | C | true | 96 | 0 | 0 | 0.59 | ||||||||
| HL_05018.4_Instance_4 HL_05018.4_HL_5J7L_201_G2819_C2827 | G | A | A | G | A | C | G | A | C | |||||||||||||
| HL_05018.4_Sequence_4 HL_05018.4_HL_5J7L_201_G_2819_C_2827 | G | A | A | G | A | C | G | A | C | true | 100 | 0 | 0 | 0.00 | ||||||||
| HL_05018.4_Instance_5 HL_05018.4_HL_4V9F_069_G2836_C2844 | G | U | A | C | A | A | G | A | C | |||||||||||||
| HL_05018.4_Sequence_5 HL_05018.4_HL_4V9F_069_G_2836_C_2844 | G | U | A | C | A | A | G | A | C | true | 81 | 0 | 0 | 3.02 | ||||||||
| HL_05018.4_Instance_6 HL_05018.4_HL_5TBW_070_G3303_C3311 | G | U | A | U | A | C | G | A | C | |||||||||||||
| HL_05018.4_Sequence_6 HL_05018.4_HL_5TBW_070_G_3303_C_3311 | G | U | A | U | A | C | G | A | C | true | 88 | 0 | 0 | 1.92 |
1 2 s35 1 8 cWW 2 3 s35 2 7 cSW 4 5 s35 5 6 s35 6 7 s35 7 8 s35 3 5 2BPhJAR3D SCFG/MRF model for HL_05018.4:
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 [8] // Initial node G2794 - C2802 from junction BasepairNode | Deletion Probability [0.0000001231336240] | Pair Probability [[0.009294090,0.019785678,0.010478215,0.203605867,0.000000000],[0.016519773,0.009190356,0.193944205,0.012313588,0.000000000],[0.010376412,0.246249955,0.002002721,0.029996924,0.000000000],[0.190808126,0.012824690,0.022503671,0.010105729,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.008193363,0.983203605,0.008193363,0.000409668] | Left Letter Distribution [0.562500000,0.062500000,0.062500000,0.312500000,0.000000000] | 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 [8] // Basepair G2794 - C2802 cWW BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.268206884,0.015551543,0.021028290,0.007554325,0.000000000],[0.194638134,0.012684090,0.002116031,0.007968863,0.000000000],[0.205690910,0.002116031,0.026951427,0.006306246,0.000000000],[0.198820544,0.012872646,0.010065478,0.007428559,0.000000000],[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 [7] // Basepair A2796 - A2801 cSW HairpinNode | Num Bases [4] | Left Index [3] | Right Index [6] | Norm Constant [1.000000000000000] // Hairpin node G2797:C2800 Interaction | Interacting Bases [1,1] | Pair Probability [[0.011363636,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.170454545,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.647727273,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.170454545,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G2797 Interaction | Interacting Bases [2,2] | Pair Probability [[0.812500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.062500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.062500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.062500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A2798 Interaction | Interacting Bases [3,3] | Pair Probability [[0.187500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.562500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.062500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.187500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C2799 Interaction | Interacting Bases [4,4] | Pair Probability [[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],[0.000000000,0.000000000,0.000000000,0.062500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C2800Sequences of instances from HL_05018.4:
> HL_05018.4 HL_7A0S_067 G 2794 C 2802 GAAGACCAC > HL_05018.4 HL_4WF9_064 A 2839 U 2847 AAAGAUGAU > HL_05018.4 HL_4Y4O_171 G 2819 C 2827 GAAGACCAC > HL_05018.4 HL_5J7L_201 G 2819 C 2827 GAAGACGAC > HL_05018.4 HL_4V9F_069 G 2836 C 2844 GUACAAGAC > HL_05018.4 HL_5TBW_070 G 3303 C 3311 GUAUACGAC