Alignment of IL_06211.3 sequences from 3D to the JAR3D model

Previous group | Next group | List of all groups | Motif atlas entry for IL_06211.3
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
6
I

8
9

4
9
9
I

10
10


11
9
I

12
9

5
13
8
I

14
7

6
15
2
I

16
2

7
17
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
IL_06211.3_Instance_1 IL_06211.3_IL_2AW7_003_C47_G361CCUAACGGG
IL_06211.3_Sequence_1 IL_06211.3_IL_2AW7_003_C47_G361CCUAAC*GGGtrue98000.29
IL_06211.3_Instance_2 IL_06211.3_IL_1FJG_003_C47_G361CCUAAGUAG
IL_06211.3_Sequence_2 IL_06211.3_IL_1FJG_003_C47_G361CCUAAG*UAGtrue100000.00
IL_06211.3_Instance_3 IL_06211.3_IL_4BPP_004_U41_A425UAUUAACGAA
IL_06211.3_Sequence_3 IL_06211.3_IL_4BPP_004_U41_A425UAUUAAC*GAAtrue74003.44

Conserved interactions between motif group positions in IL_06211.3:
1 2 s53 
1 7 cWW 
2 7 s33 
4 5 cWW 
4 6 s55 
5 6 s35 
6 7 s35 
7 2 2BR
JAR3D SCFG/MRF model for IL_06211.3:
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 [7] // Initial node C47 - G361 from junction 
BasepairNode | Deletion Probability [0.0000000205233307] | Pair Probability [[0.006245839,0.012198524,0.022050021,0.130509465,0.000000000],[0.014790529,0.005911317,0.430272268,0.007918832,0.000000000],[0.007056476,0.130875485,0.004179580,0.015482156,0.000000000],[0.143245792,0.007681992,0.053686990,0.007894735,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.010744024,0.650013430,0.333064733,0.005909213,0.000268601] | Left Letter Distribution [0.250000000,0.416666667,0.083333333,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [7] // Basepair C47 - G361 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.100000000,0.100000000,0.100000000,0.700000000,0.000000000] | Position [1] | Left Index [2] | Right Index [6] // Fixed node on left
InitialNode  | Left Length Distribution [0.993970181,0.005999820,0.000029999] | 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 [6] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.700000000,0.100000000,0.100000000,0.100000000,0.000000000] | Position [1] | Left Index [3] | Right Index [6] // Fixed node on left
InitialNode  | Left Length Distribution [0.016116035,0.966962127,0.016116035,0.000805802] | Left Letter Distribution [0.700000000,0.100000000,0.100000000,0.100000000,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [6] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.500000000,0.100000000,0.300000000,0.100000000,0.000000000] | Position [2] | Left Index [4] | Right Index [6] // Fixed node on right
InitialNode  | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [5] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.012069023,0.113784372,0.012836630,0.141765239,0.000000000],[0.018492858,0.009468664,0.173969190,0.014287629,0.000000000],[0.012820994,0.152223457,0.002559418,0.139417271,0.000000000],[0.140274824,0.014401822,0.023210850,0.018417758,0.000000000],[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 C52 - G359 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_06211.3:
> IL_06211.3 IL_2AW7_003 C   47 G  361
CCUAAC*GGG
> IL_06211.3 IL_1FJG_003 C   47 G  361
CCUAAG*UAG
> IL_06211.3 IL_4BPP_004 U   41 A  425
UAUUAAC*GAA