Alignment of IL_69536.1 sequences from 3D to the JAR3D model

Previous group | Next group | List of all groups | Motif atlas entry for IL_69536.1
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
8

3
7
8
I

8
9


9
8
I

10
8

4
11
7
I

12
6

5
13
5
I

14
4

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_69536.1_Instance_1 IL_69536.1_IL_2QBG_103_U2687_G2722UGUUCGGUAG
IL_69536.1_Sequence_1 IL_69536.1_IL_2QBG_103_U_2687_G_2722UGUUC*GGUAGtrue100000.00
IL_69536.1_Instance_2 IL_69536.1_IL_4IOA_098_U2666_G2702UCUCCGGUAG
IL_69536.1_Sequence_2 IL_69536.1_IL_4IOA_098_U_2666_G_2702UCUCC*GGUAGtrue95000.77

Conserved interactions between motif group positions in IL_69536.1:
1 2 s35 
1 8 cWW 
2 5 s33 
2 6 s33 
2 7 tSH 
3 4 cWW 
3 5 s55 
4 5 s35 
6 7 s35 
7 8 s35 
2 6 6BPh
JAR3D SCFG/MRF model for IL_69536.1:
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 U2687 - G2722 from junction 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.013018113,0.014787255,0.015554767,0.038739706,0.000000000],[0.316978443,0.016061948,0.045253948,0.017465403,0.000000000],[0.015906809,0.039036391,0.003528109,0.015488863,0.000000000],[0.045635225,0.015764677,0.372418733,0.014361609,0.000000000],[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 U2687 - G2722 cWW 
BasepairNode | Deletion Probability [0.0000000005912491] | Pair Probability [[0.050184110,0.049144675,0.000555494,0.003113825,0.000000000],[0.236348772,0.166193375,0.002308285,0.002308285,0.000000000],[0.218619165,0.002135668,0.010958637,0.156748540,0.000000000],[0.051040351,0.049229829,0.000555494,0.000555494,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.000000000,0.023781213,0.951248514,0.023781213,0.001189061] | Left Letter Distribution [0.083333333,0.250000000,0.083333333,0.583333333,0.000000000] | 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 [7] // Basepair G2688 - A2721 tSH 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.125000000,0.125000000,0.125000000,0.625000000,0.000000000] | Position [2] | Left Index [3] | 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 [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [5] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.125000000,0.125000000,0.625000000,0.125000000,0.000000000] | Position [2] | Left Index [3] | Right Index [5] // 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 [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [4] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.010030806,0.017205487,0.011658168,0.192396585,0.000000000],[0.020773653,0.008567443,0.234601962,0.013925571,0.000000000],[0.011806790,0.208424324,0.002149941,0.023787799,0.000000000],[0.193514041,0.013266124,0.027576622,0.010314686,0.000000000],[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 C2691 - G2718 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_69536.1:
> IL_69536.1 IL_2QBG_103 U 2687 G 2722
UGUUC*GGUAG
> IL_69536.1 IL_4IOA_098 U 2666 G 2702
UCUCC*GGUAG