Alignment of IL_61341.1 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


9
4
I

10
4

4
11
3
I

12
3

5
13
2
I

14
2

6
15
1
I


In
acceptance
region

Cutoff
score
Full
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distance
Interior
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distance
Alignment
score
deficit
IL_61341.1_Instance_1 IL_61341.1,IL_3OXE_002,C31_G72CGAAGCAG
IL_61341.1_Sequence_1 IL_61341.13OXE_C31_G72CGAAG*CAGtrue94000.60
IL_61341.1_Instance_2 IL_61341.1,IL_8CRE_441,U1036_G1052UUGUACG
IL_61341.1_Sequence_2 IL_61341.18CRE_U_1036_G_1052UUGU*ACGtrue100000.00

Conserved interactions between motif group positions in IL_61341.1:
1 2 s33 
1 6 cWW 
2 3 s55 
2 5 cHW 
2 6 s35 
3 4 cWW 
3 5 s55 
4 5 s35 
5 6 s35
JAR3D SCFG/MRF model for IL_61341.1:
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 [6] // Initial node
BasepairNode | Deletion Probability [0.0000229437914523] | 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 [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [6] // Basepair C31 - G72 cWW 
BasepairNode | Deletion Probability [0.0000000083615247] | Pair Probability [[0.002937728,0.002937728,0.126223793,0.152524149,0.000000000],[0.002937728,0.022212868,0.002937728,0.002937728,0.000000000],[0.155688991,0.002937728,0.019882043,0.143509520,0.000000000],[0.127102272,0.170636211,0.002937728,0.061656056,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.011890606,0.487514863,0.487514863,0.012485137,0.000594530] | Left Letter Distribution [0.500000000,0.100000000,0.300000000,0.100000000,0.000000000] | 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 [5] // Basepair G32 - A71 cHW 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009384013,0.018908278,0.010497082,0.198820958,0.000000000],[0.019570724,0.009688269,0.200004160,0.012164451,0.000000000],[0.010445199,0.211498280,0.002066765,0.024906359,0.000000000],[0.211388534,0.012081037,0.038377715,0.010198176,0.000000000],[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 G35 - C70 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_61341.1:
> IL_61341.1  3OXE C   31 G   72
CGAAG*CAG
> IL_61341.1  8CRE U 1036 G 1052
UUGU*ACG