Alignment of HL_27483.1 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
3

3
7
2
I

8
2

4
9
1
I


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HL_27483.1_Instance_1 HL_27483.1,HL_8CRE_012,G539_C546GCUUCUGC
HL_27483.1_Sequence_1 HL_27483.18CRE_G539_C546GCUUCUGCtrue59003.91
HL_27483.1_Instance_2 HL_27483.1,HL_1KH6_003,C42_G45CGUG
HL_27483.1_Sequence_2 HL_27483.11KH6_C42_G45CGUGtrue100000.00

Conserved interactions between motif group positions in HL_27483.1:
1 2 s35 
1 4 cWW 
2 3 cWW 
2 4 s55
JAR3D SCFG/MRF model for HL_27483.1:
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 [4] // Initial node
BasepairNode | Deletion Probability [0.0000001040770180] | 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 [0.481347774,0.024067389,0.481949458,0.012033694,0.000601685] | Right Letter Distribution [0.125000000,0.125000000,0.375000000,0.375000000,0.000000000] | Left Index [1] | Right Index [4] // Basepair G539 - C546 cWW 
HairpinNode  | Num Bases [2] | Left Index [2] | Right Index [3] | Norm Constant [1.000000000000000] // Hairpin node C540:C543
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.014399842,0.269897237,0.013016031,0.076893452,0.000000000],[0.012475237,0.110557207,0.033119833,0.013095412,0.000000000],[0.012737184,0.037784519,0.002949447,0.304748582,0.000000000],[0.033253029,0.014304206,0.013089043,0.037679739,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin Interaction C540 - C543 cWW 
Insertion    | Location [1] | Length Distribution [0.481347774,0.024067389,0.481949458,0.012033694,0.000601685] | Letter Distribution [0.125000000,0.125000000,0.125000000,0.625000000,0.000000000]// Insertion in Hairpin after nucleotide 2, position 1
Sequences of instances from HL_27483.1:
> HL_27483.1  8CRE G  539 C  546
GCUUCUGC
> HL_27483.1  1KH6 C   42 G   45
CGUG