Alignment of IL_84251.1 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
4
I

8
5

4
9
5
I

10
6


11
5
I

12
5

5
13
4
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_84251.1_Instance_1 IL_84251.1,IL_7EDT_002,U5_G20UCCGUCCG
IL_84251.1_Sequence_1 IL_84251.17EDT_U5_G20UCCG*UCCGtrue100000.00
IL_84251.1_Instance_2 IL_84251.1,IL_4R4V_002,C637_G623CAAGCGAAG
IL_84251.1_Sequence_2 IL_84251.14R4V_C637_G623CAAG*CGAAGtrue76002.59

Conserved interactions between motif group positions in IL_84251.1:
1 2 s35 
1 8 cWW 
2 6 s33 
2 7 tWH 
2 8 s55 
3 4 s35 
3 6 tHS 
4 5 cWW 
4 6 s55 
5 6 s35 
7 8 s35
JAR3D SCFG/MRF model for IL_84251.1:
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 [0.0000015195492620] | Pair Probability [[0.010391363,0.015542673,0.012620534,0.118031974,0.000000000],[0.161407275,0.018831736,0.135468706,0.014912387,0.000000000],[0.012838381,0.120099009,0.002697951,0.019069108,0.000000000],[0.143779637,0.013983083,0.188496931,0.011829251,0.000000000],[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 [0.493381468,0.493381468,0.012635379,0.000601685] | Right Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000] | Left Index [1] | Right Index [8] // Basepair U5 - G20 cWW 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.115304547,0.003858489,0.017522074,0.003858489,0.000000000],[0.028111585,0.395652859,0.003858489,0.003858489,0.000000000],[0.003858489,0.005619874,0.023675467,0.018172120,0.000000000],[0.310920509,0.003858489,0.016844403,0.045025626,0.000000000],[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 [2] | Right Index [7] // Basepair C6 - C19 tWH 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.089641297,0.115395982,0.151169707,0.134165871,0.000000000],[0.134917876,0.153102782,0.001514306,0.130994855,0.000000000],[0.001514306,0.001514306,0.006986476,0.001514306,0.000000000],[0.006675235,0.001514306,0.067864081,0.001514306,0.000000000],[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 [3] | Right Index [6] // Basepair C7 - C18 tHS 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.012786759,0.158579378,0.012700856,0.142951775,0.000000000],[0.015410127,0.011167131,0.119729226,0.013844477,0.000000000],[0.012485943,0.135049418,0.002666836,0.185406071,0.000000000],[0.117661282,0.014761069,0.018929413,0.025870238,0.000000000],[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 G8 - U17 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_84251.1:
> IL_84251.1  7EDT U    5 G   20
UCCG*UCCG
> IL_84251.1  4R4V C  637 G  623
CAAG*CGAAG