Alignment of IL_44067.4 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
4
I

6
7

3
7
7
I

8
8

4
9
8
I

10
9

5
11
9
I

12
10

6
13
10
I

14
11

7
15
11
I

16
12


17
11
I

18
11

8
19
10
I

20
10

9
21
9
I

22
9

10
23
8
I

24
8

11
25
7
I

26
7

12
27
6
I

28
5

13
29
2
I

30
2

14
31
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
IL_44067.4_Instance_1 IL_44067.4_IL_3V2F_001_G24_C516GUGGAUGCUGAAAC
IL_44067.4_Sequence_1 IL_44067.4_IL_3V2F_001_G24_C516GUGGAUG*CUGAAACtrue100000.00
IL_44067.4_Instance_2 IL_44067.4_IL_4IOA_001_G24_C526GUGGAUGCUGAAAC
IL_44067.4_Sequence_2 IL_44067.4_IL_4IOA_001_G24_C526GUGGAUG*CUGAAACtrue100000.00
IL_44067.4_Instance_3 IL_44067.4_IL_2QBG_006_G24_C516GUGGAUGCUGAAAC
IL_44067.4_Sequence_3 IL_44067.4_IL_2QBG_006_G24_C516GUGGAUG*CUGAAACtrue100000.00
IL_44067.4_Instance_4 IL_44067.4_IL_3U5H_016_A13_U410ACGGAUCGUGAAAU
IL_44067.4_Sequence_4 IL_44067.4_IL_3U5H_016_A13_U410ACGGAUC*GUGAAAUtrue90001.96
IL_44067.4_Instance_5 IL_44067.4_IL_1S72_001_G21_U522GUGGAUUAUGAAAU
IL_44067.4_Sequence_5 IL_44067.4_IL_1S72_001_G21_U522GUGGAUU*AUGAAAUtrue95001.04

Conserved interactions between motif group positions in IL_44067.4:
1 2 s35 
1 14 cWW 
2 3 s35 
3 4 s35 
3 11 s33 
3 12 tSH 
4 5 s35 
4 10 s33 
4 11 tSH 
5 6 s35 
5 10 tHS 
5 11 s55 
6 7 s35 
6 9 cWW 
7 8 cWW 
7 9 s55 
8 9 s35 
9 10 s35 
11 12 s35 
12 13 s35 
13 14 s35 
9 8 7BPh
3 11 6BPh
4 11 6BPh
14 13 7BPh
12 3 6BR
13 3 6BR
10 4 6BR
4 10 6BR
5 10 6BR
JAR3D SCFG/MRF model for IL_44067.4:
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 [14] // Initial node G24 - C516 from junction 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.003849789,0.050954645,0.004205623,0.179999416,0.000000000],[0.006121463,0.014587489,0.063201629,0.013952603,0.000000000],[0.004152707,0.385104148,0.000824854,0.157082684,0.000000000],[0.060630465,0.023681555,0.007901793,0.023749136,0.000000000],[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 [14] // Basepair G24 - C516 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.071428571,0.214285714,0.071428571,0.642857143,0.000000000] | Position [1] | Left Index [2] | Right Index [13] // Fixed node on left
InitialNode  | 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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [13] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.944444444,0.018518519,0.018518519,0.018518519,0.000000000] | Position [2] | Left Index [3] | Right Index [13] // Fixed node on right
InitialNode  | Left Length Distribution [1.000000000] | 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 [3] | Right Index [12] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.042467188,0.049500945,0.000511675,0.002436533,0.000000000],[0.042845019,0.044907828,0.000511675,0.000511675,0.000000000],[0.405791869,0.003581728,0.017352721,0.297927871,0.000000000],[0.046160330,0.044469591,0.000511675,0.000511675,0.000000000],[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 [3] | Right Index [12] // Basepair G26 - A514 tSH 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.042467188,0.049500945,0.000511675,0.002436533,0.000000000],[0.042845019,0.044907828,0.000511675,0.000511675,0.000000000],[0.405791869,0.003581728,0.017352721,0.297927871,0.000000000],[0.046160330,0.044469591,0.000511675,0.000511675,0.000000000],[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 [4] | Right Index [11] // Basepair G27 - A513 tSH 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.064373739,0.064946473,0.330650278,0.069971976,0.000000000],[0.075035834,0.068073375,0.002830312,0.067409074,0.000000000],[0.000775621,0.000775621,0.013712268,0.000775621,0.000000000],[0.003693410,0.000775621,0.235425154,0.000775621,0.000000000],[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 [5] | Right Index [10] // Basepair A28 - G512 tHS 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.003391032,0.035734817,0.003264180,0.055013013,0.000000000],[0.004188811,0.004263654,0.004929479,0.025191782,0.000000000],[0.003200983,0.005020856,0.001027476,0.073233431,0.000000000],[0.006599491,0.003906482,0.004182469,0.766852045,0.000000000],[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 [6] | Right Index [9] // Basepair U29 - U511 cWW 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009662245,0.019360521,0.011052990,0.190423231,0.000000000],[0.018822386,0.008416510,0.210415236,0.012452350,0.000000000],[0.010998513,0.231797422,0.002089006,0.025286298,0.000000000],[0.201082692,0.012694357,0.024632354,0.010813889,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | 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 [7] | Right Index [8] // Basepair G30 - C510 cWW 
HairpinNode  | Num Bases [1] | Left Index [8] | Right Index [8] | Norm Constant [1.000000000000000] // Hairpin node type *
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,1.000000000]] // Hairpin for truncation
Sequences of instances from IL_44067.4:
> IL_44067.4 IL_3V2F_001 G   24 C  516
GUGGAUG*CUGAAAC
> IL_44067.4 IL_4IOA_001 G   24 C  526
GUGGAUG*CUGAAAC
> IL_44067.4 IL_2QBG_006 G   24 C  516
GUGGAUG*CUGAAAC
> IL_44067.4 IL_3U5H_016 A   13 U  410
ACGGAUC*GUGAAAU
> IL_44067.4 IL_1S72_001 G   21 U  522
GUGGAUU*AUGAAAU