Alignment of HL_16845.5 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
3
I

8
3

4
9
2
I

10
2

5
11
1
I


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Interior
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Alignment
score
deficit
HL_16845.5_Instance_1 HL_16845.5_HL_4WF9_048_C2236_G2242CUUAUCG
HL_16845.5_Sequence_1 HL_16845.5_HL_4WF9_048_C_2236_G_2242CUUAUCGtrue100000.00
HL_16845.5_Instance_2 HL_16845.5_HL_5J7L_185_G2209_C2215GUAAUCC
HL_16845.5_Sequence_2 HL_16845.5_HL_5J7L_185_G_2209_C_2215GUAAUCCtrue100000.00

Conserved interactions between motif group positions in HL_16845.5:
1 2 s33 
1 5 cWW 
2 3 s53 
2 4 tHH 
3 4 s35 
4 5 s35 
JAR3D SCFG/MRF model for HL_16845.5:
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 [5] // Initial node C2236 - G2242 from junction 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.009635135,0.018686586,0.011023774,0.200055053,0.000000000],[0.018686946,0.009628796,0.215804967,0.013537321,0.000000000],[0.011023788,0.215804297,0.002089517,0.025115689,0.000000000],[0.200055346,0.013537264,0.025116064,0.010199456,0.000000000],[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 [5] // Basepair C2236 - G2242 cWW 
BasepairNode | Deletion Probability [0.0000000006094467] | Pair Probability [[0.130459369,0.015302404,0.012037839,0.011672714,0.000000000],[0.224490191,0.002645205,0.024226344,0.012342007,0.000000000],[0.028299430,0.020741958,0.007941767,0.002645205,0.000000000],[0.217776765,0.284128392,0.002645205,0.002645205,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.023781213,0.951248514,0.023781213,0.001189061] | Left Letter Distribution [0.375000000,0.125000000,0.125000000,0.375000000,0.000000000] | Right Length Distribution [0.023781213,0.951248514,0.023781213,0.001189061] | Right Letter Distribution [0.125000000,0.125000000,0.125000000,0.625000000,0.000000000] | Left Index [2] | Right Index [4] // Basepair U2237 - C2241 tHH 
HairpinNode  | Num Bases [1] | Left Index [3] | Right Index [3] | Norm Constant [1.000000000000000] // Hairpin node A2239:A2239
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.625000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.125000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.125000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.125000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A2239
Sequences of instances from HL_16845.5:
> HL_16845.5 HL_4WF9_048 C 2236 G 2242
CUUAUCG
> HL_16845.5 HL_5J7L_185 G 2209 C 2215
GUAAUCC