Alignment of HL_76094.1 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
3
I

4
4

2
5
4
I

6
4

3
7
3
I

8
2

4
9
2
I

10
2

5
11
1
I


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HL_76094.1_Instance_1 HL_76094.1,HL_9E7E_001,C20_G24CAAUG
HL_76094.1_Sequence_1 HL_76094.19E7E_C20_G24CAAUGtrue100000.00

Conserved interactions between motif group positions in HL_76094.1:
1 2 s35 
1 5 cWW 
2 3 s35 
2 5 s55 
4 5 cWS
JAR3D SCFG/MRF model for HL_76094.1:
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
ClusterNode  | Deletion Probability [0.0000001250000000] | Num Left Bases [1] | Num Right Bases [2] | Left Index [1] | Right Index [5] | Norm Constant [0.250517660965201] // Cluster node 9E7E|1|C|C|20:9E7E|1|C|C|20 and 9E7E|1|C|U|23:9E7E|1|C|G|24
Interaction  | Interacting Bases [1,3] | Pair Probability [[0.009631000,0.017270697,0.011072020,0.200757565,0.000000000],[0.020477154,0.009808895,0.220945507,0.013927182,0.000000000],[0.011196362,0.205083350,0.002110445,0.023698544,0.000000000],[0.203360186,0.013418572,0.027036311,0.010206209,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 9E7E|1|C|C|20 - 9E7E|1|C|G|24 cWW 
Interaction  | Interacting Bases [2,3] | Pair Probability [[0.007621108,0.007878219,0.007225892,0.008042656,0.000000000],[0.011893482,0.011962372,0.002557227,0.012112360,0.000000000],[0.009982001,0.002557227,0.009162302,0.007119248,0.000000000],[0.212206128,0.210847785,0.265623667,0.213208328,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 9E7E|1|C|U|23 - 9E7E|1|C|G|24 cWS 
InitialNode  | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [3] // New Initial node after Cluster
HairpinNode  | Num Bases [2] | Left Index [2] | Right Index [3] | Norm Constant [1.000000000000000] // Hairpin node A21:A22
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.500000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.166666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.166666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.166666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A21
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.500000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.166666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.166666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.166666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A22
Sequences of instances from HL_76094.1:
> HL_76094.1  9E7E C   20 G   24
CAAUG