Alignment of IL_31754.1 sequences from 3D to the JAR3D model

Previous group | Next group | List of all groups | Motif atlas entry for IL_31754.1
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
4
I

8
5

4
9
5
I

10
5

5
11
6
I

12
7

6
13
7
I

14
8

7
15
8
I

16
9


17
8
I

18
8

8
19
7
I

20
7

9
21
6
I

22
5

10
23
4
I

24
4

11
25
3
I

26
3

12
27
2
I

28
2

13
29
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
IL_31754.1_Instance_1 IL_31754.1_IL_2QBG_101_C2652_G2668CUAGUACGGACCG
IL_31754.1_Sequence_1 IL_31754.1_IL_2QBG_101_C_2652_G_2668CUAGUAC*GGACCGtrue100000.00

Conserved interactions between motif group positions in IL_31754.1:
1 2 s35 
1 13 cWW 
2 3 s33 
2 12 cSW 
3 5 s55 
3 10 s53 
3 11 tHW 
4 5 cSH 
4 9 s33 
5 6 s35 
5 9 s33 
5 10 tWH 
6 7 s35 
6 9 tHS 
6 10 s55 
7 8 cWW 
7 9 s55 
8 9 s35 
10 11 s33 
11 12 s55 
12 13 s35 
9 5 6BPh
7 6 7BPh
4 10 6BPh
3 11 6BPh
12 11 7BPh
5 4 7BR
9 4 6BR
6 9 6BR
JAR3D SCFG/MRF model for IL_31754.1:
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 [13] // Initial node C2652 - G2668 from junction 
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.010130121,0.017375838,0.011773595,0.194301502,0.000000000],[0.020979332,0.008652269,0.227023763,0.014063448,0.000000000],[0.011923689,0.210487931,0.002171228,0.024023321,0.000000000],[0.195430021,0.013397471,0.027849658,0.010416811,0.000000000],[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 [13] // Basepair C2652 - G2668 cWW 
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.001791371,0.239209592,0.002204493,0.002376080,0.000000000],[0.003571518,0.240441448,0.001689592,0.002453572,0.000000000],[0.001915832,0.233023057,0.002967661,0.001700970,0.000000000],[0.002623970,0.260810191,0.001476768,0.001743884,0.000000000],[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 [12] // Basepair U2653 - C2667 cSW 
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.049616382,0.638365634,0.006284646,0.062425204,0.000000000],[0.000897807,0.004248402,0.000897807,0.000897807,0.000000000],[0.050300996,0.083239809,0.006132612,0.004297602,0.000000000],[0.000897807,0.000897807,0.009272457,0.081327223,0.000000000],[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 [3] | Right Index [11] // Basepair A2654 - C2666 tHW 
ClusterNode  | Deletion Probability [0.0000001250000000] | Num Left Bases [2] | Num Right Bases [1] | Left Index [4] | Right Index [10] | Norm Constant [0.565894006694928] // Cluster node G2655:U2656 and A2665:A2665
Interaction  | Interacting Bases [2,3] | Pair Probability [[0.006980622,0.001464000,0.007181242,0.001464000,0.000000000],[0.014541871,0.012154730,0.009717806,0.001464000,0.000000000],[0.001464000,0.001464000,0.017133401,0.006829134,0.000000000],[0.741901139,0.007320001,0.090303495,0.078616557,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U2656 - A2665 tWH 
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.055679592,0.057359966,0.003128224,0.002588218,0.000000000],[0.053859163,0.062562107,0.000665346,0.063050334,0.000000000],[0.038079735,0.020824015,0.042566873,0.475642955,0.000000000],[0.004791044,0.055793641,0.000665346,0.062743443,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G2655 - U2656 cSH 
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 [6] | Right Index [9] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.044149057,0.044541851,0.382258874,0.047988462,0.000000000],[0.051461378,0.046686356,0.003723579,0.046230763,0.000000000],[0.000531940,0.000531940,0.018039957,0.000531940,0.000000000],[0.002533030,0.000531940,0.309726994,0.000531940,0.000000000],[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 [9] // Basepair A2657 - G2664 tHS 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.003925557,0.006733370,0.004562426,0.075294433,0.000000000],[0.056908405,0.023470090,0.598866861,0.038148420,0.000000000],[0.004620589,0.081566892,0.000841380,0.009309359,0.000000000],[0.075731750,0.005191700,0.010792115,0.004036654,0.000000000],[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 C2658 - G2663 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_31754.1:
> IL_31754.1 IL_2QBG_101 C 2652 G 2668
CUAGUAC*GGACCG