Alignment of IL_95150.6 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
4
I

6
5

3
7
5
I

8
6

4
9
6
I

10
7


11
6
I

12
6

5
13
5
I

14
5

6
15
2
I

16
2

7
17
1
I


In
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Full
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Alignment
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IL_95150.6_Instance_1 IL_95150.6_IL_3OWZ_006_C31_G72CGAAGCAG
IL_95150.6_Sequence_1 IL_95150.6_IL_3OWZ_006_C31_G72CGAAG*CAG
IL_95150.6_Instance_2 IL_95150.6_IL_3OWZ_002_C31_G72CGAAGCAG
IL_95150.6_Sequence_2 IL_95150.6_IL_3OWZ_002_C31_G72CGAAG*CAG
IL_95150.6_Instance_3 IL_95150.6_IL_1FJG_063_C1440_G1461CGGGAGCAG
IL_95150.6_Sequence_3 IL_95150.6_IL_1FJG_063_C_1440_G_1461CGGGAG*CAG

Conserved interactions between motif group positions in IL_95150.6:
1 2 s33 
1 7 cWW 
2 7 s35 
3 4 s35 
3 6 tHS 
4 5 cWW 
4 6 s55 
5 6 s35 
6 7 s35 
2 2 2BPh
3 6 6BR
JAR3D SCFG/MRF model for IL_95150.6:
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 [7] // Initial node C31 - G72 from junction 
BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.009933419,0.017038443,0.011544982,0.190528657,0.000000000],[0.020571967,0.008484264,0.242033011,0.013790371,0.000000000],[0.011692161,0.206400787,0.002129068,0.023556849,0.000000000],[0.191635263,0.013137326,0.027308888,0.010214543,0.000000000],[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 [7] // Basepair C31 - G72 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.021739130,0.021739130,0.934782609,0.021739130,0.000000000] | Position [1] | Left Index [2] | Right Index [6] // Fixed node on left
InitialNode  | Left Length Distribution [0.334863624,0.653524170,0.011072104,0.000540103] | Left Letter Distribution [0.625000000,0.125000000,0.125000000,0.125000000,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [6] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000006376409404] | Pair Probability [[0.169595207,0.145616947,0.124642014,0.138428459,0.000000000],[0.120384692,0.059649576,0.001501777,0.133242265,0.000000000],[0.057442600,0.001501777,0.013045567,0.001501777,0.000000000],[0.011885968,0.001501777,0.018557817,0.001501777,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.651642683,0.016291067,0.326364377,0.005430356,0.000271518] | Left Letter Distribution [0.375000000,0.125000000,0.375000000,0.125000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [6] // Basepair A34 - A71 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 [4] | Right Index [5] // Basepair G35 - C70 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_95150.6:
> IL_95150.6 IL_3OWZ_006 C   31 G   72
CGAAG*CAG
> IL_95150.6 IL_3OWZ_002 C   31 G   72
CGAAG*CAG
> IL_95150.6 IL_1FJG_063 C 1440 G 1461
CGGGAG*CAG