Alignment of IL_48444.6 sequences from 3D to the JAR3D model

Previous group | Next group | List of all groups | Motif atlas entry for IL_48444.6
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
7

3
7
7
I

8
8

4
9
8
I

10
9


11
8
I

12
8

5
13
7
I

14
7

6
15
6
I

16
5

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_48444.6_Instance_1 IL_48444.6,IL_1L9A_001,U117_A234UAAGCAGUA
IL_48444.6_Sequence_1 IL_48444.61L9A_U117_A234UAAG*CAGUAtrue100000.00
IL_48444.6_Instance_2 IL_48444.6,IL_1MFQ_001,U117_A234UAAGCAGUA
IL_48444.6_Sequence_2 IL_48444.61MFQ_U117_A234UAAG*CAGUAtrue100000.00
IL_48444.6_Instance_3 IL_48444.6,IL_7A0S_058,C1514_G1508CUACGGUCAG
IL_48444.6_Sequence_3 IL_48444.67A0S_C_1514_G_1508CUAC*GGUCAGtrue57004.04
IL_48444.6_Instance_4 IL_48444.6,IL_6XJQ_002,C48_G14CGAUAGAAG
IL_48444.6_Sequence_4 IL_48444.66XJQ_C48_G14CGAU*AGAAGtrue79001.99

Conserved interactions between motif group positions in IL_48444.6:
1 2 s35 
1 8 cWW 
2 3 s35 
2 8 s55 
3 4 s35 
3 6 cWW 
4 5 cWW 
4 6 s55 
5 6 s35 
6 7 s35
JAR3D SCFG/MRF model for IL_48444.6:
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 [8] // Initial node
BasepairNode | Deletion Probability [0.0000001177014991] | Pair Probability [[0.009106890,0.016989933,0.010236072,0.193756118,0.000000000],[0.020753249,0.009584275,0.218305904,0.012178967,0.000000000],[0.010305927,0.194944276,0.002027252,0.022809627,0.000000000],[0.218224654,0.011603275,0.039263037,0.009910544,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.250611247,0.495110024,0.250764059,0.003361858,0.000152812] | Right Letter Distribution [0.250000000,0.250000000,0.083333333,0.416666667,0.000000000] | Left Index [1] | Right Index [8] // Basepair U117 - A234 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.416666667,0.083333333,0.250000000,0.250000000,0.000000000] | Position [1] | Left Index [2] | Right Index [7] // Fixed node on left for 1L9A|1|B|A|118
InitialNode  | Left Length Distribution [0.995990040,0.003999960,0.000010000] | 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 [3] | Right Index [7] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.250000000,0.083333333,0.416666667,0.250000000,0.000000000] | Position [2] | Left Index [3] | Right Index [7] // Fixed node on right for 1L9A|1|B|G|232
InitialNode  | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.741082411,0.255227552,0.003536285,0.000153752] | Right Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000] | Left Index [3] | Right Index [6] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.325937747,0.020728829,0.219818448,0.021852677,0.000000000],[0.016073860,0.009828018,0.022584562,0.033685971,0.000000000],[0.187974472,0.022967102,0.004685027,0.022045688,0.000000000],[0.021460655,0.036490627,0.017553975,0.016312343,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [6] // Basepair A119 - A231 cWW 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009326698,0.018435943,0.010553497,0.195602659,0.000000000],[0.018760973,0.009472791,0.208714091,0.012603753,0.000000000],[0.010528061,0.219157994,0.002038177,0.024530043,0.000000000],[0.206573441,0.012562820,0.031136373,0.010002685,0.000000000],[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 [4] | Right Index [5] // Basepair G120 - C230 cWW 
HairpinNode  | Num Bases [1] | Left Index [5] | Right Index [5] | 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_48444.6:
> IL_48444.6  1L9A U  117 A  234
UAAG*CAGUA
> IL_48444.6  1MFQ U  117 A  234
UAAG*CAGUA
> IL_48444.6  7A0S C 1514 G 1508
CUAC*GGUCAG
> IL_48444.6  6XJQ C   48 G   14
CGAU*AGAAG