Alignment of HL_07951.3 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_07951.3_Instance_1 HL_07951.3,HL_1GAX_004,C913_G921CAGCGGAAG
HL_07951.3_Sequence_1 HL_07951.31GAX_C913_G921CAGCGGAAGtrue97000.31
HL_07951.3_Instance_2 HL_07951.3,HL_3WQY_001,C1613_G1622CAGCGGGAG
HL_07951.3_Sequence_2 HL_07951.33WQY_C_1613_G_1622CAGCGGGAGtrue100000.00
HL_07951.3_Instance_3 HL_07951.3,HL_4RDX_001,C13_G22CAGCUGGUUAG
HL_07951.3_Sequence_3 HL_07951.34RDX_C13_G22CAGCUGGUUAGtrue67004.02
HL_07951.3_Instance_4 HL_07951.3,HL_9IMB_001,U8_A17UCAUCUCCAA
HL_07951.3_Sequence_4 HL_07951.39IMB_U8_A17UCAUCUCCAAtrue63004.57

Conserved interactions between motif group positions in HL_07951.3:
1 4 cWW 
2 3 s35 
2 4 s55
JAR3D SCFG/MRF model for HL_07951.3:
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 [0.0000000000000000] | Pair Probability [[0.009230036,0.016881218,0.010494353,0.194361300,0.000000000],[0.020319858,0.009555111,0.230862069,0.012852202,0.000000000],[0.010589659,0.197055880,0.002038410,0.022912280,0.000000000],[0.207859340,0.012317386,0.032759727,0.009911172,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.006093845,0.490554540,0.252894576,0.247105424,0.003199269,0.000152346] | Right Letter Distribution [0.220000000,0.260000000,0.300000000,0.220000000,0.000000000] | Left Index [1] | Right Index [4] // Basepair C913 - G921 cWW 
HairpinNode  | Num Bases [2] | Left Index [2] | Right Index [3] | Norm Constant [1.000000000000000] // Hairpin node A914:G915
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.583333333,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.250000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.083333333,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.083333333,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A914
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.250000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.083333333,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.583333333,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.083333333,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G915
Sequences of instances from HL_07951.3:
> HL_07951.3  1GAX C  913 G  921
CAGCGGAAG
> HL_07951.3  3WQY C 1613 G 1622
CAGCGGGAG
> HL_07951.3  4RDX C   13 G   22
CAGCUGGUUAG
> HL_07951.3  9IMB U    8 A   17
UCAUCUCCAA