Alignment of IL_61249.1 sequences from 3D to the JAR3D model

Previous group | Next group | List of all groups | Motif atlas entry for IL_61249.1
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
5
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

8
17
12
I

18
13

9
19
13
I

20
14

10
21
14
I

22
15


23
14
I

24
14

11
25
13
I

26
13

12
27
12
I

28
12

13
29
11
I

30
11

14
31
10
I

32
10

15
33
9
I

34
9

16
35
8
I

36
8

17
37
7
I

38
6

18
39
3
I

40
3

19
41
2
I

42
2

20
43
1
I


In
acceptance
region

Cutoff
score
Full
edit
distance
Interior
edit
distance
Alignment
score
deficit
IL_61249.1_Instance_1 IL_61249.1,IL_5J7L_387,U1851_G1891UUAAUUGAUGUUGAUCGAAG
IL_61249.1_Sequence_1 IL_61249.15J7L_U_1851_G_1891UUAAUUGAUG*UUGAUCGAAGtrue100000.00

Conserved interactions between motif group positions in IL_61249.1:
1 2 s35 
1 20 cWW 
2 19 tSH 
3 4 s35 
3 18 s55 
4 5 s35 
4 17 tHS 
5 6 s35 
5 16 cWW 
5 17 s55 
6 7 s35 
6 15 cWW 
7 13 s33 
7 14 tSH 
8 9 s35 
8 13 tHS 
8 14 s55 
9 10 s35 
9 12 cWW 
10 11 cWW 
10 12 s55 
11 12 s35 
12 13 s35 
14 15 s35 
15 16 s35 
16 17 s35 
18 19 s35 
19 20 s35 
17 4 6BPh
15 14 7BPh
13 7 6BR
14 7 6BR
7 13 6BR
8 13 6BR
4 17 6BR
JAR3D SCFG/MRF model for IL_61249.1:
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 [20] // Initial node
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.011357495,0.014122426,0.014418960,0.037643649,0.000000000],[0.305533580,0.028227484,0.042773463,0.016192886,0.000000000],[0.014734624,0.037492866,0.003338882,0.014817277,0.000000000],[0.087046211,0.014824487,0.343789173,0.013686536,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [20] // Basepair U1851 - G1891 cWW 
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.121583738,0.111055049,0.001350235,0.006642085,0.000000000],[0.122053423,0.114840499,0.001350235,0.001350235,0.000000000],[0.125556588,0.001350235,0.008345120,0.112094623,0.000000000],[0.144924515,0.124802948,0.001350235,0.001350235,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [19] // Basepair U1852 - A1890 tSH 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000] | Position [1] | Left Index [3] | Right Index [18] // Fixed node on left for 5J7L|1|DA|A|1853
InitialNode  | Left Length Distribution [0.989901010,0.009999000,0.000099990] | 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 [4] | Right Index [18] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000] | Position [2] | Left Index [4] | Right Index [18] // Fixed node on right for 5J7L|1|DA|A|1889
InitialNode  | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [17] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.044130649,0.044458508,0.380732303,0.049261589,0.000000000],[0.046718239,0.046610059,0.003708313,0.046358426,0.000000000],[0.000529759,0.000529759,0.018128765,0.000529759,0.000000000],[0.002496756,0.000529759,0.314747597,0.000529759,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [17] // Basepair A1854 - G1888 tHS 
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.018688879,0.016630082,0.046836174,0.020315754,0.000000000],[0.015155246,0.012069984,0.023907676,0.319083377,0.000000000],[0.044328013,0.024813859,0.003760150,0.018235949,0.000000000],[0.019082750,0.385915970,0.016694898,0.014481238,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [16] // Basepair U1855 - C1887 cWW 
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.003732252,0.068454060,0.003332272,0.040740152,0.000000000],[0.004125025,0.004447797,0.004974729,0.025606453,0.000000000],[0.003262672,0.005067740,0.001028677,0.091990797,0.000000000],[0.005084177,0.003961681,0.004216688,0.729974829,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [6] | Right Index [15] // Basepair U1856 - U1886 cWW 
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.055450269,0.058701583,0.000665644,0.003137180,0.000000000],[0.055862225,0.058565654,0.000665644,0.000665644,0.000000000],[0.342722747,0.003328218,0.016270599,0.282486523,0.000000000],[0.061897309,0.058249476,0.000665644,0.000665644,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [7] | Right Index [14] // Basepair G1857 - A1885 tSH 
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.055450269,0.055862225,0.342722747,0.061897309,0.000000000],[0.058701583,0.058565654,0.003328218,0.058249476,0.000000000],[0.000665644,0.000665644,0.016270599,0.000665644,0.000000000],[0.003137180,0.000665644,0.282486523,0.000665644,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [8] | Right Index [13] // Basepair A1858 - G1884 tHS 
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.015580470,0.285764820,0.013910732,0.024295965,0.000000000],[0.017220118,0.018567546,0.020767248,0.015270770,0.000000000],[0.013620185,0.021155527,0.004294262,0.054860011,0.000000000],[0.021224145,0.016538232,0.017602771,0.439327198,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [9] | Right Index [12] // Basepair U1859 - U1883 cWW 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.015996656,0.299826436,0.014459392,0.085420251,0.000000000],[0.013858629,0.012916026,0.036792527,0.014547577,0.000000000],[0.014149624,0.041974486,0.003276514,0.337552385,0.000000000],[0.036940494,0.015890415,0.014540501,0.041858086,0.000000000],[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 [10] | Right Index [11] // Basepair G1860 - U1882 cWW 
HairpinNode  | Num Bases [1] | Left Index [11] | Right Index [11] | 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_61249.1:
> IL_61249.1  5J7L U 1851 G 1891
UUAAUUGAUG*UUGAUCGAAG