Alignment of IL_56455.6 sequences from 3D to the JAR3D model

Previous group | Next group | List of all groups | Motif atlas entry for IL_56455.6
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
5

4
9
5
I

10
6

5
11
6
I

12
7

6
13
7
I

14
8

7
15
8
I

16
9

8
17
9
I

18
10

9
19
10
I

20
11


21
10
I

22
10

10
23
9
I

24
9

11
25
8
I

26
8

12
27
7
I

28
7

13
29
6
I

30
6

14
31
5
I

32
5

15
33
4
I

34
4

16
35
3
I

36
3

17
37
2
I

38
2

18
39
1
I


In
acceptance
region

Cutoff
score
Full
edit
distance
Interior
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Alignment
score
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IL_56455.6_Instance_1 IL_56455.6,IL_1DFU_001,C97_G79CGAGAGUAGCGAUGGUAG
IL_56455.6_Sequence_1 IL_56455.61DFU_C97_G79CGAGAGUAG*CGAUGGUAGtrue100000.00
IL_56455.6_Instance_2 IL_56455.6,IL_354D_001,C97_G79CGAGAGUAGCGAUGGUAG
IL_56455.6_Sequence_2 IL_56455.6354D_C97_G79CGAGAGUAG*CGAUGGUAGtrue100000.00
IL_56455.6_Instance_3 IL_56455.6,IL_5J7L_359,C97_G79CGAGAGUAGCGAUGGUAG
IL_56455.6_Sequence_3 IL_56455.65J7L_C97_G79CGAGAGUAG*CGAUGGUAGtrue100000.00
IL_56455.6_Instance_4 IL_56455.6,IL_1FEU_001,C97_G79CGAGAGUAGCGAUGGUAG
IL_56455.6_Sequence_4 IL_56455.61FEU_C97_G79CGAGAGUAG*CGAUGGUAGtrue100000.00
IL_56455.6_Instance_5 IL_56455.6,IL_9DFE_114,G98_C79GGAGAGUAGCGAUGGUAC
IL_56455.6_Sequence_5 IL_56455.69DFE_G98_C79GGAGAGUAG*CGAUGGUACtrue99000.13
IL_56455.6_Instance_6 IL_56455.6,IL_7A0S_106,G100_C81GAAAAGUCGCAAUGAUAC
IL_56455.6_Sequence_6 IL_56455.67A0S_G100_C81GAAAAGUCG*CAAUGAUACtrue95001.06
IL_56455.6_Instance_7 IL_56455.6,IL_364D_003,C97_G79CGAGAGUAGCGAUGGUAG
IL_56455.6_Sequence_7 IL_56455.6364D_C97_G79CGAGAGUAG*CGAUGGUAGtrue100000.00

Conserved interactions between motif group positions in IL_56455.6:
1 2 s35 
1 18 cWW 
2 16 s33 
2 17 tSH 
2 18 s55 
3 4 s35 
3 16 tHW 
3 17 s55 
4 5 s35 
4 15 bif 
5 6 s35 
5 14 wat 
6 7 s35 
6 13 bif 
6 14 s55 
7 8 s35 
7 11 s33 
7 12 tWH 
8 9 s35 
8 11 tHS 
8 12 s55 
9 10 cWW 
9 11 s55 
10 11 s35 
12 13 s35 
13 14 s35 
14 15 s35 
15 16 s35 
16 17 s35 
17 18 s35 
17 2 6BR
8 11 6BR
JAR3D SCFG/MRF model for IL_56455.6:
Character Definition | A,C,G,U,* // Identity and order of characters in matrices
InitialNode  | Left Length Distribution [0.999900000,0.000100000] | Left Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Right Length Distribution [0.999900000,0.000100000] | Right Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Left Index [1] | Right Index [18] // Initial node
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.009144630,0.017165752,0.010484008,0.190189591,0.000000000],[0.018463087,0.009213143,0.244318979,0.013008228,0.000000000],[0.010534317,0.213869704,0.001991973,0.023268171,0.000000000],[0.191242613,0.012802444,0.024618634,0.009684725,0.000000000],[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 [18] // Basepair C97 - G79 cWW 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.125561346,0.100336661,0.001346801,0.006681142,0.000000000],[0.116168301,0.106868438,0.001346801,0.001346801,0.000000000],[0.186732308,0.001346801,0.007499122,0.099121172,0.000000000],[0.124528414,0.118422287,0.001346801,0.001346801,0.000000000],[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 [17] // Basepair G98 - A78 tSH 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.017898242,0.039832166,0.003960910,0.461511524,0.000000000],[0.003960910,0.319173624,0.009494562,0.003960910,0.000000000],[0.018590254,0.003960910,0.030122383,0.022980723,0.000000000],[0.003960910,0.003960910,0.017616762,0.039014302,0.000000000],[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 [16] // Basepair A99 - U77 tHW 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.286333919,0.012099244,0.002893863,0.002893863,0.000000000],[0.200484693,0.008433586,0.002893863,0.002893863,0.000000000],[0.002893863,0.002893863,0.343184380,0.002893863,0.000000000],[0.002893863,0.002893863,0.120525543,0.002893863,0.000000000],[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 [15] // Basepair G100 - G76 bif 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.008126778,0.008126778,0.878098334,0.008126778,0.000000000],[0.008126778,0.008126778,0.008126778,0.008126778,0.000000000],[0.008126778,0.008126778,0.008126778,0.008126778,0.000000000],[0.008126778,0.008126778,0.008126778,0.008126778,0.000000000],[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 [14] // Basepair A101 - G75 wat 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.043944313,0.287462646,0.003515083,0.003515083,0.000000000],[0.022503169,0.013476736,0.003515083,0.003515083,0.000000000],[0.003515083,0.003515083,0.165212509,0.432249801,0.000000000],[0.003515083,0.003515083,0.003515083,0.003515083,0.000000000],[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 [13] // Basepair G102 - U74 bif 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.017898242,0.003960910,0.018590254,0.003960910,0.000000000],[0.039832166,0.319173624,0.003960910,0.003960910,0.000000000],[0.003960910,0.009494562,0.030122383,0.017616762,0.000000000],[0.461511524,0.003960910,0.022980723,0.039014302,0.000000000],[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 [7] | Right Index [12] // Basepair U103 - A73 tWH 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.095295147,0.096219847,0.190630355,0.125187794,0.000000000],[0.134048753,0.121712839,0.001377659,0.114372990,0.000000000],[0.001377659,0.001377659,0.006574466,0.001377659,0.000000000],[0.006340534,0.001377659,0.101351318,0.001377659,0.000000000],[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 [8] | Right Index [11] // Basepair A104 - G72 tHS 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009126734,0.019007720,0.010392915,0.188767123,0.000000000],[0.016031357,0.008949680,0.190366634,0.012455659,0.000000000],[0.010277496,0.276641564,0.001959000,0.025096194,0.000000000],[0.186351265,0.012927771,0.021997944,0.009650944,0.000000000],[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 [9] | Right Index [10] // Basepair G105 - C71 cWW 
HairpinNode  | Num Bases [1] | Left Index [10] | Right Index [10] | 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_56455.6:
> IL_56455.6  1DFU C   97 G   79
CGAGAGUAG*CGAUGGUAG
> IL_56455.6  354D C   97 G   79
CGAGAGUAG*CGAUGGUAG
> IL_56455.6  5J7L C   97 G   79
CGAGAGUAG*CGAUGGUAG
> IL_56455.6  1FEU C   97 G   79
CGAGAGUAG*CGAUGGUAG
> IL_56455.6  9DFE G   98 C   79
GGAGAGUAG*CGAUGGUAC
> IL_56455.6  7A0S G  100 C   81
GAAAAGUCG*CAAUGAUAC
> IL_56455.6  364D C   97 G   79
CGAGAGUAG*CGAUGGUAG