Alignment of HL_50006.2 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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Alignment
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HL_50006.2_Instance_1 HL_50006.2,HL_5HR7_005,C31_G39CCUUUCACG
HL_50006.2_Sequence_1 HL_50006.25HR7_C31_G39CCUUUCACGtrue99000.10
HL_50006.2_Instance_2 HL_50006.2,HL_5HR6_002,C31_G39CCUUUCACG
HL_50006.2_Sequence_2 HL_50006.25HR6_C31_G39CCUUUCACGtrue99000.10
HL_50006.2_Instance_3 HL_50006.2,HL_7D81_001,C26_G31CGAAAG
HL_50006.2_Sequence_3 HL_50006.27D81_C26_G31CGAAAGtrue92000.78
HL_50006.2_Instance_4 HL_50006.2,HL_8CRE_195,C228_G233CUUCGG
HL_50006.2_Sequence_4 HL_50006.28CRE_C228_G233CUUCGGtrue100000.00
HL_50006.2_Instance_5 HL_50006.2,HL_4KJI_001,G5_C12GAAGGAUC
HL_50006.2_Sequence_5 HL_50006.24KJI_G5_C12GAAGGAUCtrue50004.72

Conserved interactions between motif group positions in HL_50006.2:
1 2 s35 
1 4 cWW 
2 3 tSW 
2 4 s55 
3 4 s55
JAR3D SCFG/MRF model for HL_50006.2:
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 [0.0000001180018634] | Pair Probability [[0.009302401,0.017228733,0.010673661,0.193601472,0.000000000],[0.019079457,0.009402609,0.239944194,0.013298189,0.000000000],[0.010745430,0.207932060,0.002029955,0.023436685,0.000000000],[0.195103670,0.013004627,0.025363199,0.009853658,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.395474668,0.204623709,0.395671422,0.004033448,0.000196754] | Right Letter Distribution [0.357142857,0.357142857,0.071428571,0.214285714,0.000000000] | Left Index [1] | Right Index [4] // Basepair C31 - G39 cWW 
HairpinNode  | Num Bases [2] | Left Index [2] | Right Index [3] | Norm Constant [1.000000000000000] // Hairpin node C32:C36
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.067792155,0.017345804,0.003659670,0.068760398,0.000000000],[0.019387209,0.270195397,0.003659670,0.025192021,0.000000000],[0.059585076,0.003659670,0.003659670,0.015824346,0.000000000],[0.017728984,0.216983261,0.141138392,0.065428275,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin Interaction C32 - C36 tSW 
Insertion    | Location [1] | Length Distribution [0.000000000,0.003919647,0.397844194,0.591866732,0.006075453,0.000293974] | Letter Distribution [0.233333333,0.100000000,0.166666667,0.500000000,0.000000000]// Insertion in Hairpin after nucleotide 2, position 1
Sequences of instances from HL_50006.2:
> HL_50006.2  5HR7 C   31 G   39
CCUUUCACG
> HL_50006.2  5HR6 C   31 G   39
CCUUUCACG
> HL_50006.2  7D81 C   26 G   31
CGAAAG
> HL_50006.2  8CRE C  228 G  233
CUUCGG
> HL_50006.2  4KJI G    5 C   12
GAAGGAUC