Alignment of IL_43858.1 sequences from 3D to the JAR3D model

Previous group | Next group | List of all groups | Motif atlas entry for IL_43858.1
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
4

4
9
4
I

10
4

5
11
4
I

12
4

6
13
5
I

14
6

7
15
6
I

16
7

8
17
7
I

18
8


19
7
I

20
7

9
21
6
I

22
6

10
23
5
I

24
4

11
25
4
I

26
4

12
27
4
I

28
4

13
29
3
I

30
3

14
31
2
I

32
2

15
33
1
I


In
acceptance
region

Cutoff
score
Full
edit
distance
Interior
edit
distance
Alignment
score
deficit
IL_43858.1_Instance_1 IL_43858.1,IL_8P9A_248,U553_G538UAUUAUAGCGAAUGUAG
IL_43858.1_Sequence_1 IL_43858.18P9A_U553_G538UAUUAUAGC*GAAUGUAGtrue98000.37
IL_43858.1_Instance_2 IL_43858.1,IL_8CRE_022,U551_G534UGUUAUAGCGAAUGUGG
IL_43858.1_Sequence_2 IL_43858.18CRE_U551_G534UGUUAUAGC*GAAUGUGGtrue100000.00

Conserved interactions between motif group positions in IL_43858.1:
1 2 s35 
1 15 cWW 
2 12 s33 
2 14 tSH 
2 15 s55 
3 4 cSH 
3 10 s33 
3 11 tWH 
3 12 s55 
4 5 s55 
4 6 cWH 
4 7 s35 
4 13 s55 
5 13 cHW 
5 14 s35 
6 7 s35 
6 11 cWW 
6 13 s55 
7 8 s35 
7 10 cWW 
8 9 cWW 
9 10 s35 
10 11 s35 
11 12 s35 
12 13 cSH 
13 14 s35 
14 15 s35 
2 12 6BR
JAR3D SCFG/MRF model for IL_43858.1:
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 [15] // Initial node
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.011246147,0.013983971,0.014277598,0.037274594,0.000000000],[0.302538153,0.027950744,0.042354115,0.016034133,0.000000000],[0.014590167,0.037125289,0.003306148,0.014672010,0.000000000],[0.086192816,0.014679149,0.350222612,0.013552354,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.991950402,0.007999600,0.000049998] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [15] // Basepair U553 - G538 cWW 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.254054619,0.030817459,0.003085436,0.078069718,0.000000000],[0.051066155,0.022009051,0.001180361,0.001180361,0.000000000],[0.056885153,0.003996729,0.365987125,0.035619494,0.000000000],[0.047237901,0.046449718,0.001180361,0.001180361,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.991950402,0.007999600,0.000049998] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [14] // Basepair A554 - A537 tSH 
ClusterNode  | Deletion Probability [0.000000000000000000001904521072278912302090434780238574181827] | Num Left Bases [4] | Num Right Bases [3] | Left Index [3] | Right Index [13] | Norm Constant [0.004275561412192] // Cluster node 8P9A|1|AR|U|555:8P9A|1|AR|A|559 and 8P9A|1|AR|A|533:8P9A|1|AR|U|536
Interaction  | Interacting Bases [1,5] | Pair Probability [[0.018775607,0.004155072,0.019501541,0.004155072,0.000000000],[0.041784723,0.334819390,0.004155072,0.004155072,0.000000000],[0.004155072,0.009959982,0.031598971,0.018480329,0.000000000],[0.435115030,0.004155072,0.024107229,0.040926768,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8P9A|1|AR|U|555 - 8P9A|1|AR|A|533 tWH 
Interaction  | Interacting Bases [4,5] | Pair Probability [[0.615264647,0.027680686,0.049320315,0.027089794,0.000000000],[0.018530781,0.010338068,0.027182752,0.026285801,0.000000000],[0.037714972,0.027750896,0.005956568,0.029081265,0.000000000],[0.026324389,0.029605623,0.020261781,0.021611660,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8P9A|1|AR|A|559 - 8P9A|1|AR|A|533 cWW 
Interaction  | Interacting Bases [3,7] | Pair Probability [[0.003068279,0.003068279,0.011304130,0.326435762,0.000000000],[0.003068279,0.014755072,0.003068279,0.003068279,0.000000000],[0.013222312,0.003068279,0.010604660,0.283904858,0.000000000],[0.013284346,0.290617672,0.003068279,0.014393233,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8P9A|1|AR|A|557 - 8P9A|1|AR|U|536 cHW 
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.076635853,0.076984536,0.004307628,0.077941519,0.000000000],[0.076263771,0.087816675,0.000950558,0.078833738,0.000000000],[0.077619343,0.000950558,0.079946321,0.090505528,0.000000000],[0.078194836,0.077434927,0.000950558,0.114663652,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8P9A|1|AR|U|555 - 8P9A|1|AR|U|556 cSH 
Interaction  | Interacting Bases [2,4] | Pair Probability [[0.003068279,0.003068279,0.013222312,0.013284346,0.000000000],[0.003068279,0.014755072,0.003068279,0.290617672,0.000000000],[0.011304130,0.003068279,0.010604660,0.003068279,0.000000000],[0.326435762,0.003068279,0.283904858,0.014393233,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8P9A|1|AR|U|556 - 8P9A|1|AR|A|559 cWH 
Interaction  | Interacting Bases [6,7] | Pair Probability [[0.079296878,0.080799881,0.004442628,0.078964610,0.000000000],[0.059200300,0.089215891,0.000983673,0.079130149,0.000000000],[0.069281848,0.000983673,0.084512044,0.117975163,0.000000000],[0.080527243,0.080043827,0.000983673,0.093658519,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8P9A|1|AR|G|535 - 8P9A|1|AR|U|536 cSH 
Insertion    | Location [3] | Length Distribution [0.023781213,0.951248514,0.023781213,0.001189061] | Letter Distribution [0.125000000,0.125000000,0.125000000,0.625000000,0.000000000]// Insertion after nucleotide 5, position 3 in cluster node
Insertion    | Location [5] | Length Distribution [0.023781213,0.951248514,0.023781213,0.001189061] | Letter Distribution [0.125000000,0.125000000,0.125000000,0.625000000,0.000000000]// Insertion after nucleotide 11, position 5 in cluster node
InitialNode  | Left Length Distribution [0.991950402,0.007999600,0.000049998] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [7] | Right Index [10] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.022937090,0.014347847,0.348044880,0.017561601,0.000000000],[0.014692845,0.010155161,0.019218678,0.045122890,0.000000000],[0.381868061,0.019005244,0.003622602,0.015644206,0.000000000],[0.017595852,0.042706478,0.015986694,0.011489870,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.991950402,0.007999600,0.000049998] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [7] | Right Index [10] // Basepair G560 - A532 cWW 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009536579,0.017101376,0.010963471,0.198789353,0.000000000],[0.020276398,0.009712729,0.228583296,0.013790641,0.000000000],[0.011086594,0.203072729,0.002089755,0.023466206,0.000000000],[0.201366458,0.013287017,0.026771249,0.010106148,0.000000000],[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 [8] | Right Index [9] // Basepair C561 - G531 cWW 
HairpinNode  | Num Bases [1] | Left Index [9] | Right Index [9] | 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_43858.1:
> IL_43858.1  8P9A U  553 G  538
UAUUAUAGC*GAAUGUAG
> IL_43858.1  8CRE U  551 G  534
UGUUAUAGC*GAAUGUGG