Alignment of IL_53581.1 sequences from 3D to the JAR3D model

Previous group | Next group | List of all groups | Motif atlas entry for IL_53581.1
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
6

4
9
6
I

10
7

5
11
7
I

12
7

6
13
7
I

14
7

7
15
7
I

16
7

8
17
7
I

18
7

9
19
7
I

20
7

10
21
7
I

22
7

11
23
7
I

24
7

12
25
8
I

26
9


27
8
I

28
7

13
29
7
I

30
7

14
31
7
I

32
7

15
33
7
I

34
7

16
35
7
I

36
7

17
37
7
I

38
7

18
39
7
I

40
7

19
41
6
I

42
6

20
43
3
I

44
3

21
45
2
I

46
2

22
47
1
I


In
acceptance
region

Cutoff
score
Full
edit
distance
Interior
edit
distance
Alignment
score
deficit
IL_53581.1_Instance_1 IL_53581.1,IL_6SY6_001,G5_C35GAGAAUGUUAUGGCAGAGAAAAC
IL_53581.1_Sequence_1 IL_53581.16SY6_G5_C35GAGAAUGUUAUGG*CAGAGAAAACtrue100000.00
IL_53581.1_Instance_2 IL_53581.1,IL_6SY4_001,G6_C38GAGAAUGUUAUGGCAGAGAAAAC
IL_53581.1_Sequence_2 IL_53581.16SY4_G6_C38GAGAAUGUUAUGG*CAGAGAAAACtrue100000.00

Conserved interactions between motif group positions in IL_53581.1:
1 2 s33 
1 22 cWW 
2 4 s55 
2 21 tWW 
3 17 s55 
4 5 s35 
4 20 tWH 
4 21 s55 
5 6 s35 
5 19 tWH 
5 20 s55 
6 7 s35 
6 18 tWH 
7 15 tSS 
7 16 s35 
7 18 s55 
8 9 s35 
8 16 s53 
10 15 s33 
11 12 s35 
11 14 cWW 
11 15 bif 
12 13 cWW 
12 14 s55 
12 19 tSS 
13 14 s35 
13 19 cSS 
14 18 cSS 
15 18 s55 
18 19 s35 
19 20 s35 
20 21 s35 
21 22 s35 
8 16 6BPh
17 3 2BR
10 8 2BR
16 8 7BR
10 15 6BR
JAR3D SCFG/MRF model for IL_53581.1:
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 [22] // Initial node
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.009733692,0.020271796,0.011084078,0.201320753,0.000000000],[0.017097495,0.009544863,0.203026637,0.013284001,0.000000000],[0.010960983,0.228535864,0.002089280,0.026765173,0.000000000],[0.198744233,0.013787510,0.023460879,0.010292763,0.000000000],[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 [22] // Basepair G5 - C35 cWW 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.408702443,0.030010298,0.003890946,0.018600071,0.000000000],[0.029232420,0.014184148,0.011587973,0.014194456,0.000000000],[0.003890946,0.011604643,0.359806718,0.021928993,0.000000000],[0.018577888,0.014190992,0.021454432,0.018142633,0.000000000],[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 [21] // Basepair A6 - A34 tWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.125000000,0.125000000,0.625000000,0.125000000,0.000000000] | Position [1] | Left Index [3] | Right Index [20] // Fixed node on left for 6SY6|1|D|G|7
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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [20] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.381184813,0.003615770,0.318975856,0.003615770,0.000000000],[0.030948835,0.015344049,0.003615770,0.003615770,0.000000000],[0.003615770,0.008956754,0.132906372,0.038702064,0.000000000],[0.016338652,0.003615770,0.017330382,0.017617604,0.000000000],[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 [4] | Right Index [20] // Basepair A8 - A33 tWH 
ClusterNode  | Deletion Probability [0.000000000000000000000000000000000000150677338694597876100351] | Num Left Bases [8] | Num Right Bases [7] | Left Index [5] | Right Index [19] | Norm Constant [0.000040477505943] // Cluster node 6SY6|1|D|A|9:6SY6|1|D|G|17 and 6SY6|1|D|C|26:6SY6|1|D|A|32
Interaction  | Interacting Bases [8,9] | Pair Probability [[0.009733692,0.020271796,0.011084078,0.201320753,0.000000000],[0.017097495,0.009544863,0.203026637,0.013284001,0.000000000],[0.010960983,0.228535864,0.002089280,0.026765173,0.000000000],[0.198744233,0.013787510,0.023460879,0.010292763,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 6SY6|1|D|G|17 - 6SY6|1|D|C|26 cWW 
Interaction  | Interacting Bases [7,10] | 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]] // Cluster Interaction 6SY6|1|D|G|16 - 6SY6|1|D|A|27 cWW 
Interaction  | Interacting Bases [3,11] | Pair Probability [[0.020814325,0.017422103,0.019901827,0.012513985,0.000000000],[0.002436905,0.002436905,0.214331865,0.002436905,0.000000000],[0.236896108,0.002436905,0.263298345,0.195326202,0.000000000],[0.002436905,0.002436905,0.002436905,0.002436905,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 6SY6|1|D|G|11 - 6SY6|1|D|G|28 tSS 
Interaction  | Interacting Bases [7,11] | Pair Probability [[0.284046767,0.205222254,0.002992204,0.002992204,0.000000000],[0.012555813,0.008788211,0.002992204,0.002992204,0.000000000],[0.002992204,0.002992204,0.318828243,0.140636672,0.000000000],[0.002992204,0.002992204,0.002992204,0.002992204,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 6SY6|1|D|G|16 - 6SY6|1|D|G|28 bif 
Interaction  | Interacting Bases [2,14] | 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 6SY6|1|D|U|10 - 6SY6|1|D|A|31 tWH 
Interaction  | Interacting Bases [1,15] | Pair Probability [[0.381184813,0.003615770,0.318975856,0.003615770,0.000000000],[0.030948835,0.015344049,0.003615770,0.003615770,0.000000000],[0.003615770,0.008956754,0.132906372,0.038702064,0.000000000],[0.016338652,0.003615770,0.017330382,0.017617604,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 6SY6|1|D|A|9 - 6SY6|1|D|A|32 tWH 
Interaction  | Interacting Bases [8,15] | Pair Probability [[0.021432702,0.017618490,0.020295984,0.012884448,0.000000000],[0.002588469,0.002588469,0.225207716,0.002588469,0.000000000],[0.278454716,0.002588469,0.251629900,0.151768294,0.000000000],[0.002588469,0.002588469,0.002588469,0.002588469,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 6SY6|1|D|G|17 - 6SY6|1|D|A|32 tSS 
Interaction  | Interacting Bases [10,14] | Pair Probability [[0.105678172,0.077024050,0.079578597,0.075017401,0.000000000],[0.082314407,0.082309394,0.003542979,0.052346388,0.000000000],[0.079619001,0.003607345,0.006695471,0.042552099,0.000000000],[0.078700115,0.073784465,0.078299920,0.078930195,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 6SY6|1|D|A|27 - 6SY6|1|D|A|31 cSS 
Interaction  | Interacting Bases [9,15] | Pair Probability [[0.074223484,0.073792369,0.071881206,0.074519741,0.000000000],[0.102548686,0.075294337,0.003500217,0.067006249,0.000000000],[0.078701774,0.003446523,0.006762627,0.080050254,0.000000000],[0.074996893,0.072309095,0.071887647,0.069078898,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 6SY6|1|D|C|26 - 6SY6|1|D|A|32 cSS 
Interaction  | Interacting Bases [4,4] | Pair Probability [[0.031250000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.031250000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.031250000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.906250000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 6SY6|1|D|U|12
Interaction  | Interacting Bases [5,5] | Pair Probability [[0.125000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.125000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.125000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.625000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 6SY6|1|D|U|13
Interaction  | Interacting Bases [6,6] | Pair Probability [[0.971153846,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.009615385,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.009615385,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.009615385,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 6SY6|1|D|A|14
Interaction  | Interacting Bases [12,12] | Pair Probability [[0.875000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.041666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.041666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.041666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion 6SY6|1|D|A|29
Interaction  | Interacting Bases [13,13] | Pair Probability [[0.041666667,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.041666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.875000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.041666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion 6SY6|1|D|G|30
Insertion    | Location [6] | 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 10, position 6 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 [13] | Right Index [12] // New Initial node after Cluster
HairpinNode  | Num Bases [1] | Left Index [13] | Right Index [13] | 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_53581.1:
> IL_53581.1  6SY6 G    5 C   35
GAGAAUGUUAUGG*CAGAGAAAAC
> IL_53581.1  6SY4 G    6 C   38
GAGAAUGUUAUGG*CAGAGAAAAC