Alignment of HL_48376.3 sequences from 3D to the JAR3D model

Previous group | Next group | List of all groups | Motif atlas entry for HL_48376.3
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
4
I

14
4

7
15
3
I

16
3

8
17
2
I

18
2

9
19
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
HL_48376.3_Instance_1 HL_48376.3_HL_4Y4O_162_C2404_G2413CGUGUGGAAG
HL_48376.3_Sequence_1 HL_48376.3_HL_4Y4O_162_C_2404_G_2413CGUGUGGAAGtrue100000.00
HL_48376.3_Instance_2 HL_48376.3_HL_4WF9_055_C2431_G2440CGCAUGGAAG
HL_48376.3_Sequence_2 HL_48376.3_HL_4WF9_055_C_2431_G_2440CGCAUGGAAGtrue95000.67
HL_48376.3_Instance_3 HL_48376.3_HL_5J7L_192_U2404_G2413UGAAUGGAAG
HL_48376.3_Sequence_3 HL_48376.3_HL_5J7L_192_U_2404_G_2413UGAAUGGAAGtrue92001.21
HL_48376.3_Instance_4 HL_48376.3_HL_7A0S_058_C2383_G2392CGUGUGGAAG
HL_48376.3_Sequence_4 HL_48376.3_HL_7A0S_058_C_2383_G_2392CGUGUGGAAGtrue100000.00
HL_48376.3_Instance_5 HL_48376.3_HL_7KGA_002_U53_G64UAUCGGUUAGAG
HL_48376.3_Sequence_5 HL_48376.3_HL_7KGA_002_U53_G64UAUCGGUUAGAGtrue37009.24

Conserved interactions between motif group positions in HL_48376.3:
1 2 s35 
1 9 cWW 
2 7 s33 
2 8 tSH 
2 9 s55 
3 4 s35 
4 5 s35 
5 6 s35 
6 7 s35 
7 8 s35 
8 9 s35 
8 2 6BR
JAR3D SCFG/MRF model for HL_48376.3:
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 [9] // Initial node C2404 - G2413 from junction 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.009928394,0.015401431,0.011938004,0.130349637,0.000000000],[0.129375926,0.016521994,0.166831863,0.014268379,0.000000000],[0.012131223,0.132788217,0.002502703,0.019378569,0.000000000],[0.150859944,0.013448331,0.163118886,0.011156498,0.000000000],[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 [9] // Basepair C2404 - G2413 cWW 
BasepairNode | Deletion Probability [0.0000000426384269] | Pair Probability [[0.131514874,0.096768403,0.001395529,0.007053160,0.000000000],[0.121598179,0.106194466,0.001395529,0.001395529,0.000000000],[0.171909266,0.001395529,0.008127753,0.096775848,0.000000000],[0.128757113,0.122927761,0.001395529,0.001395529,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.007839294,0.785889270,0.203821656,0.002351788,0.000097991] | Left Letter Distribution [0.187500000,0.312500000,0.062500000,0.437500000,0.000000000] | 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 [8] // Basepair G2405 - A2412 tSH 
HairpinNode  | Num Bases [5] | Left Index [3] | Right Index [7] | Norm Constant [1.000000000000000] // Hairpin node G2407:A2411
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.357142857,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.071428571,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.500000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.071428571,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G2407
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.071428571,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.071428571,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.214285714,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.642857143,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U2408
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.071428571,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.071428571,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.642857143,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.214285714,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G2409
Interaction  | Interacting Bases [4,4] | Pair Probability [[0.214285714,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.071428571,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.642857143,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.071428571,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G2410
Interaction  | Interacting Bases [5,5] | Pair Probability [[0.642857143,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.071428571,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.214285714,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.071428571,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A2411
Insertion    | Location [3] | Length Distribution [0.792098765,0.205432099,0.002370370,0.000098765] | Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000]// Insertion in Hairpin after nucleotide 5, position 3
Sequences of instances from HL_48376.3:
> HL_48376.3 HL_4Y4O_162 C 2404 G 2413
CGUGUGGAAG
> HL_48376.3 HL_4WF9_055 C 2431 G 2440
CGCAUGGAAG
> HL_48376.3 HL_5J7L_192 U 2404 G 2413
UGAAUGGAAG
> HL_48376.3 HL_7A0S_058 C 2383 G 2392
CGUGUGGAAG
> HL_48376.3 HL_7KGA_002 U   53 G   64
UAUCGGUUAGAG