Alignment of HL_67216.4 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
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_67216.4_Instance_1 HL_67216.4_HL_4Y4O_110_C246_G252CGGCGAG
HL_67216.4_Sequence_1 HL_67216.4_HL_4Y4O_110_C246_G252CGGCGAGtrue100000.00
HL_67216.4_Instance_2 HL_67216.4_HL_7A0S_008_C223_G229CGGCGAG
HL_67216.4_Sequence_2 HL_67216.4_HL_7A0S_008_C223_G229CGGCGAGtrue100000.00
HL_67216.4_Instance_3 HL_67216.4_HL_5J7L_141_C246_G252CGGCGAG
HL_67216.4_Sequence_3 HL_67216.4_HL_5J7L_141_C246_G252CGGCGAGtrue100000.00
HL_67216.4_Instance_4 HL_67216.4_HL_5TBW_003_C90_G96CGGCGAG
HL_67216.4_Sequence_4 HL_67216.4_HL_5TBW_003_C90_G96CGGCGAGtrue100000.00
HL_67216.4_Instance_5 HL_67216.4_HL_4WF9_008_C249_G255CGGCGAG
HL_67216.4_Sequence_5 HL_67216.4_HL_4WF9_008_C249_G255CGGCGAGtrue100000.00
HL_67216.4_Instance_6 HL_67216.4_HL_4V9F_008_C217_G223CCGCGAG
HL_67216.4_Sequence_6 HL_67216.4_HL_4V9F_008_C217_G223CCGCGAGtrue90001.44
HL_67216.4_Instance_7 HL_67216.4_HL_4V88_217_U1396_G1402UUUCAAG
HL_67216.4_Sequence_7 HL_67216.4_HL_4V88_217_U_1396_G_1402UUUCAAGtrue61005.45

Conserved interactions between motif group positions in HL_67216.4:
1 2 s35 
1 7 cWW 
2 4 s35 
2 6 tSH 
2 7 s55 
3 5 s55 
5 6 s35 
6 7 s35 
4 1 6BPh
4 2 7BPh
2 6 6BPh
JAR3D SCFG/MRF model for HL_67216.4:
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 [7] // Initial node C246 - G252 from junction 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.009323756,0.015877713,0.010902482,0.167504797,0.000000000],[0.057767753,0.011742545,0.232594255,0.013451740,0.000000000],[0.011045651,0.170984366,0.002157753,0.021172046,0.000000000],[0.176272283,0.012855711,0.076243940,0.010103208,0.000000000],[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 C246 - G252 cWW 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.068633616,0.049385507,0.000771139,0.003732319,0.000000000],[0.078968013,0.063136280,0.000771139,0.000771139,0.000000000],[0.333146473,0.002914223,0.014957341,0.230264202,0.000000000],[0.081727946,0.069278386,0.000771139,0.000771139,0.000000000],[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 [6] // Basepair G247 - A251 tSH 
HairpinNode  | Num Bases [3] | Left Index [3] | Right Index [5] | Norm Constant [1.000000000000000] // Hairpin node G248:G250
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.055555556,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.055555556,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.722222222,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.166666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G248
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.001449275,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.995652174,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.001449275,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.001449275,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C249
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.166666667,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.055555556,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.722222222,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.055555556,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G250
Sequences of instances from HL_67216.4:
> HL_67216.4 HL_4Y4O_110 C  246 G  252
CGGCGAG
> HL_67216.4 HL_7A0S_008 C  223 G  229
CGGCGAG
> HL_67216.4 HL_5J7L_141 C  246 G  252
CGGCGAG
> HL_67216.4 HL_5TBW_003 C   90 G   96
CGGCGAG
> HL_67216.4 HL_4WF9_008 C  249 G  255
CGGCGAG
> HL_67216.4 HL_4V9F_008 C  217 G  223
CCGCGAG
> HL_67216.4 HL_4V88_217 U 1396 G 1402
UUUCAAG