Alignment of IL_79846.1 sequences from 3D to the JAR3D model

Previous group | Next group | List of all groups | Motif atlas entry for IL_79846.1
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
3

3
7
3
I

8
3

4
9
3
I

10
3

5
11
3
I

12
3

6
13
3
I

14
3

7
15
3
I

16
3

8
17
3
I

18
3

9
19
3
I

20
3

10
21
3
I

22
3

11
23
3
I

24
3

12
25
3
I

26
3

13
27
3
I

28
3

14
29
3
I

30
3

15
31
4
I

32
5

16
33
5
I

34
6


35
5
I

36
5

17
37
4
I

38
3

18
39
2
I

40
2

19
41
1
I


In
acceptance
region

Cutoff
score
Full
edit
distance
Interior
edit
distance
Alignment
score
deficit
IL_79846.1_Instance_1 IL_79846.1,IL_3Q3Z_005,U60_A14UAGUAGUGCAACCGACGAA
IL_79846.1_Sequence_1 IL_79846.13Q3Z_U60_A14UAGUAGUGCAACCGAC*GAAtrue100000.00

Conserved interactions between motif group positions in IL_79846.1:
1 19 cWW 
2 3 s35 
2 9 bif 
3 7 s33 
3 8 tWH 
5 6 s35 
6 7 s35 
8 9 s35 
9 10 s33 
10 12 s55 
11 12 cSH 
12 13 s35 
13 14 s35 
14 15 s35 
15 16 s35 
15 18 cWW 
16 17 cWW 
17 18 s35 
4 7 6BPh
2 8 7BPh
12 11 7BR
JAR3D SCFG/MRF model for IL_79846.1:
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 [19] // Initial node
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.009123784,0.017718471,0.010008206,0.198264936,0.000000000],[0.022262210,0.009929018,0.198931998,0.011154256,0.000000000],[0.010027726,0.196386049,0.002064490,0.023275738,0.000000000],[0.216349992,0.010477281,0.053822220,0.010203624,0.000000000],[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 [19] // Basepair U60 - A14 cWW 
ClusterNode  | Deletion Probability [0.000000000000000000000000000000000030517578125000007888755147] | Num Left Bases [14] | Num Right Bases [1] | Left Index [2] | Right Index [18] | Norm Constant [0.999999999999999] // Cluster node 3Q3Z|1|V|A|61:3Q3Z|1|V|A|74 and 3Q3Z|1|V|A|13:3Q3Z|1|V|A|13
Interaction  | Interacting Bases [14,15] | Pair Probability [[0.611455387,0.027954752,0.049808635,0.027358010,0.000000000],[0.018714254,0.010440425,0.027451888,0.026546056,0.000000000],[0.038088387,0.028025658,0.006015544,0.029369199,0.000000000],[0.026585026,0.029898748,0.020462393,0.021825637,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 3Q3Z|1|V|A|74 - 3Q3Z|1|V|A|13 cWW 
Interaction  | Interacting Bases [2,7] | Pair Probability [[0.172874286,0.004703112,0.090279950,0.004703112,0.000000000],[0.042292986,0.028858025,0.004703112,0.004703112,0.000000000],[0.004703112,0.007289268,0.480212228,0.047363501,0.000000000],[0.035766773,0.004703112,0.036599675,0.030244634,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 3Q3Z|1|V|G|62 - 3Q3Z|1|V|G|67 tWH 
Interaction  | Interacting Bases [1,8] | Pair Probability [[0.363832236,0.507916817,0.004980158,0.004980158,0.000000000],[0.003275511,0.002345856,0.000711451,0.000711451,0.000000000],[0.000711451,0.000711451,0.048795341,0.058182313,0.000000000],[0.000711451,0.000711451,0.000711451,0.000711451,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 3Q3Z|1|V|A|61 - 3Q3Z|1|V|C|68 bif 
Interaction  | Interacting Bases [10,11] | Pair Probability [[0.104166825,0.124612443,0.005621093,0.043860124,0.000000000],[0.100542670,0.099286043,0.001147115,0.009317734,0.000000000],[0.010004306,0.001147115,0.104180479,0.094225112,0.000000000],[0.104547355,0.103291070,0.001147115,0.092903402,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 3Q3Z|1|V|A|70 - 3Q3Z|1|V|C|71 cSH 
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.055555556,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.055555556,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.055555556,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.833333333,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 3Q3Z|1|V|U|63
Interaction  | Interacting Bases [4,4] | Pair Probability [[0.500000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.166666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.166666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.166666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 3Q3Z|1|V|A|64
Interaction  | Interacting Bases [5,5] | Pair Probability [[0.166666667,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.166666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.500000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.166666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 3Q3Z|1|V|G|65
Interaction  | Interacting Bases [6,6] | Pair Probability [[0.166666667,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.166666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.166666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.500000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 3Q3Z|1|V|U|66
Interaction  | Interacting Bases [9,9] | Pair Probability [[0.500000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.166666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.166666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.166666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 3Q3Z|1|V|A|69
Interaction  | Interacting Bases [12,12] | Pair Probability [[0.166666667,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.500000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.166666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.166666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 3Q3Z|1|V|C|72
Interaction  | Interacting Bases [13,13] | Pair Probability [[0.166666667,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.166666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.500000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.166666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 3Q3Z|1|V|G|73
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 [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [16] | Right Index [17] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009631000,0.017270697,0.011072020,0.200757565,0.000000000],[0.020477154,0.009808895,0.220945507,0.013927182,0.000000000],[0.011196362,0.205083350,0.002110445,0.023698544,0.000000000],[0.203360186,0.013418572,0.027036311,0.010206209,0.000000000],[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 [16] | Right Index [17] // Basepair C75 - G12 cWW 
HairpinNode  | Num Bases [1] | Left Index [17] | Right Index [17] | 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_79846.1:
> IL_79846.1  3Q3Z U   60 A   14
UAGUAGUGCAACCGAC*GAA