Alignment of HL_21372.1 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
3
I

8
3

4
9
2
I

10
2

5
11
1
I


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HL_21372.1_Instance_1 HL_21372.1,HL_1KOG_007,U82_G90UUUCGUGUG
HL_21372.1_Sequence_1 HL_21372.11KOG_U82_G90UUUCGUGUGtrue95000.66
HL_21372.1_Instance_2 HL_21372.1,HL_1QF6_002,A31_U39AUUCGUAAU
HL_21372.1_Sequence_2 HL_21372.11QF6_A31_U39AUUCGUAAUtrue100000.00

Conserved interactions between motif group positions in HL_21372.1:
1 2 s35 
1 5 cWW 
3 4 cSH
JAR3D SCFG/MRF model for HL_21372.1:
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 [0.0000000005912491] | Pair Probability [[0.010264537,0.017997257,0.012095982,0.130498803,0.000000000],[0.160028161,0.018765501,0.118260045,0.013196486,0.000000000],[0.012242617,0.116904215,0.002673650,0.033942895,0.000000000],[0.141108219,0.012853655,0.186617613,0.012550365,0.000000000],[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 [0.000000000,0.023781213,0.951248514,0.023781213,0.001189061] | Right Letter Distribution [0.416666667,0.083333333,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [5] // Basepair U82 - G90 cWW 
HairpinNode  | Num Bases [3] | Left Index [2] | Right Index [4] | Norm Constant [1.000000000000000] // Hairpin node U83:U87
Interaction  | Interacting Bases [2,3] | Pair Probability [[0.079296878,0.080799881,0.004442628,0.078964610,0.000000000],[0.059200300,0.089215891,0.000983673,0.079130149,0.000000000],[0.069281848,0.000983673,0.084512044,0.117975163,0.000000000],[0.080527243,0.080043827,0.000983673,0.093658519,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin Interaction G86 - U87 cSH 
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],[0.000000000,0.000000000,0.125000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.625000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U83
Insertion    | Location [1] | Length Distribution [0.000000000,0.023781213,0.951248514,0.023781213,0.001189061] | Letter Distribution [0.083333333,0.416666667,0.083333333,0.416666667,0.000000000]// Insertion in Hairpin after nucleotide 2, position 1
Sequences of instances from HL_21372.1:
> HL_21372.1  1KOG U   82 G   90
UUUCGUGUG
> HL_21372.1  1QF6 A   31 U   39
AUUCGUAAU