Alignment of HL_46501.1 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
4

3
7
3
I

8
3

4
9
2
I

10
2

5
11
1
I


In
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Alignment
score
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HL_46501.1_Instance_1 HL_46501.1,HL_3DD2_001,C11_G16CUGAAG
HL_46501.1_Sequence_1 HL_46501.13DD2_C11_G16CUGAAGtrue93000.69
HL_46501.1_Instance_2 HL_46501.1,HL_4M4O_001,C32_G36CUUAG
HL_46501.1_Sequence_2 HL_46501.14M4O_C32_G36CUUAGtrue100000.00

Conserved interactions between motif group positions in HL_46501.1:
1 2 s35 
1 5 cWW 
2 3 s33 
2 4 cWS 
2 5 s55 
4 5 s35
JAR3D SCFG/MRF model for HL_46501.1:
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 [5] // Initial node
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.009536579,0.017101376,0.010963471,0.198789353,0.000000000],[0.020276398,0.009712729,0.228583296,0.013790641,0.000000000],[0.011086594,0.203072729,0.002089755,0.023466206,0.000000000],[0.201366458,0.013287017,0.026771249,0.010106148,0.000000000],[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 C11 - G16 cWW 
BasepairNode | Deletion Probability [0.0000015195492620] | Pair Probability [[0.007577355,0.007687977,0.007366975,0.007962631,0.000000000],[0.013747816,0.013041493,0.002959345,0.014069756,0.000000000],[0.009805871,0.002122482,0.008947684,0.007618668,0.000000000],[0.320982592,0.191446651,0.176129731,0.208532972,0.000000000],[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 [0.493381468,0.493381468,0.012635379,0.000601685] | Right Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000] | Left Index [2] | Right Index [4] // Basepair U12 - A15 cWS 
HairpinNode  | Num Bases [1] | Left Index [3] | Right Index [3] | Norm Constant [1.000000000000000] // Hairpin node G13:G13
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.125000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.125000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.375000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.375000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G13
Sequences of instances from HL_46501.1:
> HL_46501.1  3DD2 C   11 G   16
CUGAAG
> HL_46501.1  4M4O C   32 G   36
CUUAG