Alignment of IL_58454.1 sequences from 3D to the JAR3D model

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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
10

4
9
10
I

10
11


11
10
I

12
10

5
13
9
I

14
8

6
15
7
I

16
6

7
17
3
I

18
3

8
19
2
I

20
2

9
21
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
IL_58454.1_Instance_1 IL_58454.1_IL_3V2F_101_U2687_G2722UUUCCGGUAG
IL_58454.1_Sequence_1 IL_58454.1_IL_3V2F_101_U_2687_G_2722UUUCC*GGUAGtrue100000.00

Conserved interactions between motif group positions in IL_58454.1:
1 2 s35 
1 9 cWW 
2 6 s33 
2 8 tSH 
4 5 cWW 
4 6 s55 
5 6 s35 
7 8 s35 
8 9 s35 
2 7 6BPh
4 3 7BR
JAR3D SCFG/MRF model for IL_58454.1:
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 [9] // Initial node U2687 - G2722 from junction 
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.013147005,0.014933664,0.015708775,0.039123268,0.000000000],[0.320116843,0.016220977,0.045702007,0.017638328,0.000000000],[0.016064303,0.039422890,0.003563041,0.015642218,0.000000000],[0.046087059,0.015920763,0.366205057,0.014503803,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [9] // Basepair U2687 - G2722 cWW 
BasepairNode | Deletion Probability [0.0000001156129129] | Pair Probability [[0.048873198,0.046365433,0.000530214,0.002697542,0.000000000],[0.049515142,0.044757460,0.000530214,0.000530214,0.000000000],[0.047832737,0.000530214,0.003039291,0.024543938,0.000000000],[0.381050549,0.341780864,0.003711496,0.003711496,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.045351474,0.907029478,0.045351474,0.002267574] | Left Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [8] // Basepair U2688 - A2721 tSH 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.166666667,0.500000000,0.166666667,0.166666667,0.000000000] | Position [1] | Left Index [3] | Right Index [7] // Fixed node on left
InitialNode  | Left Length Distribution [0.989901010,0.009999000,0.000099990] | 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 [7] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000] | Position [2] | Left Index [4] | Right Index [7] // 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 [0.989901010,0.009999000,0.000099990] | 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 [0.166666667,0.166666667,0.500000000,0.166666667,0.000000000] | 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 [0.989901010,0.009999000,0.000099990] | 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 [[0.004932610,0.008460731,0.005732859,0.094610276,0.000000000],[0.051076816,0.021065034,0.538513617,0.034239227,0.000000000],[0.005805943,0.102491854,0.001057225,0.011697558,0.000000000],[0.095159780,0.006523565,0.013560697,0.005072207,0.000000000],[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 C2691 - G2718 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_58454.1:
> IL_58454.1 IL_3V2F_101 U 2687 G 2722
UUUCC*GGUAG