Alignment of IL_00998.1 sequences from 3D to the JAR3D model

Previous group | Next group | List of all groups | Motif atlas entry for IL_00998.1
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
4
I

6
5

3
7
5
I

8
6


9
5
I

10
5

4
11
4
I

12
3

5
13
3
I

14
3

6
15
3
I

16
3

7
17
2
I

18
2

8
19
1
I


In
acceptance
region

Cutoff
score
Full
edit
distance
Interior
edit
distance
Alignment
score
deficit
IL_00998.1_Instance_1 IL_00998.1_IL_2QBG_015_U293_A347UAGCAAAA
IL_00998.1_Sequence_1 IL_00998.1_IL_2QBG_015_U293_A347UAG*CAAAA
IL_00998.1_Instance_2 IL_00998.1_IL_3V2F_013_U293_A347UAGCGAAA
IL_00998.1_Sequence_2 IL_00998.1_IL_3V2F_013_U293_A347UAG*CGAAA

Conserved interactions between motif group positions in IL_00998.1:
1 6 s33 
1 8 cWW 
2 5 tHS 
2 6 s55 
2 7 s53 
3 4 cWW 
3 5 s55 
4 5 s35 
6 7 cSH 
6 8 s35 
7 8 s35 
2 6 6BR
8 6 7BR
JAR3D SCFG/MRF model for IL_00998.1:
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 [8] // Initial node U293 - A347 from junction 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.022169121,0.009793604,0.004775726,0.100824755,0.000000000],[0.059581583,0.004636662,0.094288399,0.005047159,0.000000000],[0.023919386,0.093743926,0.001047544,0.011502353,0.000000000],[0.543379946,0.005011716,0.013549728,0.006728391,0.000000000],[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 [8] // Basepair U293 - A347 cWW 
ClusterNode  | Deletion Probability [0.0000000006250000] | Num Left Bases [1] | Num Right Bases [3] | Left Index [2] | Right Index [7] | Norm Constant [1.000000000000000] // Cluster node A294:A294 and A344:A346
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.220680561,0.208179152,0.220214683,0.209973218,0.000000000],[0.040680831,0.029217611,0.000460433,0.040438504,0.000000000],[0.000460433,0.000460433,0.003125708,0.000460433,0.000000000],[0.002926969,0.000460433,0.021800166,0.000460433,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A294 - A344 tHS 
Interaction  | Interacting Bases [3,4] | Pair Probability [[0.229647066,0.105109998,0.005315249,0.004606709,0.000000000],[0.108444679,0.102278578,0.001209127,0.106627582,0.000000000],[0.005651620,0.005459270,0.006110837,0.101186016,0.000000000],[0.010310227,0.104576192,0.001209127,0.102257723,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A345 - A346 cSH 
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 [3] | Right Index [4] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.010195092,0.020769450,0.011804402,0.193474890,0.000000000],[0.017202006,0.008406578,0.208382157,0.013263440,0.000000000],[0.011655809,0.234558465,0.002149506,0.027571043,0.000000000],[0.192357660,0.013922753,0.023782986,0.010503762,0.000000000],[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 [3] | Right Index [4] // Basepair G295 - C343 cWW 
HairpinNode  | Num Bases [1] | Left Index [4] | Right Index [4] | 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_00998.1:
> IL_00998.1 IL_2QBG_015 U  293 A  347
UAG*CAAAA
> IL_00998.1 IL_3V2F_013 U  293 A  347
UAG*CGAAA