Alignment of HL_05018.4 sequences from 3D to the JAR3D model

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The correspondence between sequences from 3D structures and the motif group is shown in blue and the JAR3D alignment of the sequences to the motif group is shown in black. Occasionally the two disagree, in which case the JAR3D alignment is shown in red.
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_C2802GAAGACCAC
HL_05018.4_Sequence_1 HL_05018.4_HL_7A0S_067_G_2794_C_2802GAAGACCACtrue96000.59
HL_05018.4_Instance_2 HL_05018.4_HL_4WF9_064_A2839_U2847AAAGAUGAU
HL_05018.4_Sequence_2 HL_05018.4_HL_4WF9_064_A_2839_U_2847AAAGAUGAUtrue92001.29
HL_05018.4_Instance_3 HL_05018.4_HL_4Y4O_171_G2819_C2827GAAGACCAC
HL_05018.4_Sequence_3 HL_05018.4_HL_4Y4O_171_G_2819_C_2827GAAGACCACtrue96000.59
HL_05018.4_Instance_4 HL_05018.4_HL_5J7L_201_G2819_C2827GAAGACGAC
HL_05018.4_Sequence_4 HL_05018.4_HL_5J7L_201_G_2819_C_2827GAAGACGACtrue100000.00
HL_05018.4_Instance_5 HL_05018.4_HL_4V9F_069_G2836_C2844GUACAAGAC
HL_05018.4_Sequence_5 HL_05018.4_HL_4V9F_069_G_2836_C_2844GUACAAGACtrue81003.02
HL_05018.4_Instance_6 HL_05018.4_HL_5TBW_070_G3303_C3311GUAUACGAC
HL_05018.4_Sequence_6 HL_05018.4_HL_5TBW_070_G_3303_C_3311GUAUACGACtrue88001.92

Conserved interactions between motif group positions in HL_05018.4:
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 2BPh
JAR3D 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 C2800
Sequences 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