Alignment of IL_47875.1 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


7
3
I

8
3

3
9
2
I

10
2

4
11
1
I


In
acceptance
region


Cutoff
score

Full
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distance

Interior
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Alignment
score
deficit
IL_47875.1_Instance_1 IL_47875.1_IL_2AW7_029_C569_G881CGUAAAGCG
IL_47875.1_Sequence_1 IL_47875.1_IL_2AW7_029_C569_G881CGUAAAG*CGtrue71002.74
IL_47875.1_Instance_2 IL_47875.1_IL_1FJG_022_C569_G881CGUAAAGCG
IL_47875.1_Sequence_2 IL_47875.1_IL_1FJG_022_C569_G881CGUAAAG*CGtrue71002.74
IL_47875.1_Instance_3 IL_47875.1_IL_3U5F_086_U1656_A1744UUGUA
IL_47875.1_Sequence_3 IL_47875.1_IL_3U5F_086_U_1656_A_1744UUG*UAtrue100000.00

Conserved interactions between motif group positions in IL_47875.1:
1 4 cWW 
2 3 cWW 
2 4 s55 
3 4 s35 
JAR3D SCFG/MRF model for IL_47875.1:
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 [4] // Initial node C569 - G881 from junction 
BasepairNode | Deletion Probability [0.0000000000000877] | Pair Probability [[0.009631464,0.018005765,0.010937883,0.195447676,0.000000000],[0.021802108,0.008803023,0.225347764,0.012619028,0.000000000],[0.011041535,0.201223421,0.002130335,0.023511078,0.000000000],[0.208561169,0.012159610,0.027401966,0.011376175,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.005372012,0.322320709,0.005372012,0.000268601,0.010744024,0.644641418,0.010744024,0.000537201] | Left Letter Distribution [0.500000000,0.038461538,0.192307692,0.269230769,0.000000000] | 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 [4] // Basepair C569 - G881 cWW 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.012177484,0.116137280,0.012933173,0.142477129,0.000000000],[0.016134877,0.009362462,0.150186535,0.013850494,0.000000000],[0.012721318,0.175949556,0.002559131,0.141914947,0.000000000],[0.139511388,0.014835325,0.020706313,0.018542585,0.000000000],[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 [2] | Right Index [3] // Basepair G575 - C880 cWW 
HairpinNode  | Num Bases [1] | Left Index [3] | Right Index [3] | 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_47875.1:
> IL_47875.1 IL_2AW7_029 C  569 G  881
CGUAAAG*CG
> IL_47875.1 IL_1FJG_022 C  569 G  881
CGUAAAG*CG
> IL_47875.1 IL_3U5F_086 U 1656 A 1744
UUG*UA