Alignment of IL_05723.1 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
5

2
5
5
I

6
5

3
7
6
I

8
7

4
9
7
I

10
8

5
11
8
I

12
9


13
8
I

14
8

6
15
7
I

16
7

7
17
6
I

18
5

8
19
4
I

20
3

9
21
2
I

22
2

10
23
1
I


In
acceptance
region

Cutoff
score
Full
edit
distance
Interior
edit
distance
Alignment
score
deficit
IL_05723.1_Instance_1 IL_05723.1_IL_1S72_034_G952_C1015GGUAGCAAAC
IL_05723.1_Sequence_1 IL_05723.1_IL_1S72_034_G952_C_1015GGUAG*CAAAC
IL_05723.1_Instance_2 IL_05723.1_IL_2QBG_031_G858_U919GGUAGCGAAU
IL_05723.1_Sequence_2 IL_05723.1_IL_2QBG_031_G858_U919GGUAG*CGAAU
IL_05723.1_Instance_3 IL_05723.1_IL_3V2F_027_U858_G919UGUAGCGAAG
IL_05723.1_Sequence_3 IL_05723.1_IL_3V2F_027_U858_G919UGUAG*CGAAG

Conserved interactions between motif group positions in IL_05723.1:
1 10 cWW 
2 3 cSH 
2 7 s33 
3 4 s35 
3 7 s33 
3 8 tWH 
4 5 s35 
4 7 tHS 
4 8 s55 
5 6 cWW 
5 7 s55 
6 7 s35 
8 9 s35 
9 10 s35 
7 3 6BPh
2 8 6BPh
4 7 6BR
JAR3D SCFG/MRF model for IL_05723.1:
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 [10] // Initial node G952 - C1015 from junction 
BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.013109355,0.114162575,0.014171158,0.091399496,0.000000000],[0.115090206,0.011889478,0.096338389,0.015237550,0.000000000],[0.014124560,0.108172043,0.003014204,0.137926655,0.000000000],[0.091078740,0.015443339,0.139026204,0.019816049,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | 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 [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [10] // Basepair G952 - C1015 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.700000000,0.100000000,0.100000000,0.100000000,0.000000000] | Position [2] | Left Index [2] | Right Index [9] // 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 [2] | Right Index [8] // New Initial node after Fixed node
ClusterNode  | Deletion Probability [0.0000001250000000] | Num Left Bases [2] | Num Right Bases [1] | Left Index [2] | Right Index [8] | Norm Constant [0.468094416354501] // Cluster node G953:U954 and A1013:A1013
Interaction  | Interacting Bases [2,3] | Pair Probability [[0.025719646,0.005394014,0.026458819,0.005394014,0.000000000],[0.053578574,0.044783309,0.035804622,0.005394014,0.000000000],[0.005394014,0.005394014,0.063126898,0.025161497,0.000000000],[0.568527570,0.005394014,0.066543467,0.057931515,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U954 - A1013 tWH 
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.054598435,0.056246180,0.003067482,0.002537961,0.000000000],[0.052813354,0.061347309,0.000652426,0.061826055,0.000000000],[0.037340322,0.020419665,0.041740332,0.485824646,0.000000000],[0.004698014,0.054710269,0.000652426,0.061525124,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G953 - U954 cSH 
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 [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [7] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.091132140,0.080083906,0.306460603,0.079821059,0.000000000],[0.075776061,0.051397235,0.002959806,0.076856845,0.000000000],[0.000873363,0.000873363,0.016359060,0.000873363,0.000000000],[0.005815985,0.000873363,0.208970488,0.000873363,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | 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 [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [7] // Basepair A955 - A1012 tHS 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.010096111,0.020567805,0.011689796,0.191596493,0.000000000],[0.017034996,0.008324961,0.206359029,0.013134669,0.000000000],[0.011542646,0.241989936,0.002128637,0.027303363,0.000000000],[0.190490110,0.013787581,0.023552083,0.010401784,0.000000000],[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 [5] | Right Index [6] // Basepair G956 - C1011 cWW 
HairpinNode  | Num Bases [1] | Left Index [6] | Right Index [6] | 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_05723.1:
> IL_05723.1 IL_1S72_034 G  952 C 1015
GGUAG*CAAAC
> IL_05723.1 IL_2QBG_031 G  858 U  919
GGUAG*CGAAU
> IL_05723.1 IL_3V2F_027 U  858 G  919
UGUAG*CGAAG