Alignment of HL_97917.2 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
3
I

8
3

4
9
3
I

10
3

5
11
2
I

12
2

6
13
1
I


In
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Full
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Alignment
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HL_97917.2_Instance_1 HL_97917.2,HL_3OIN_001,C4_G11CUUCAACG
HL_97917.2_Sequence_1 HL_97917.23OIN_C4_G11CUUCAACGtrue99000.13
HL_97917.2_Instance_2 HL_97917.2,HL_4PQV_003,G57_C63GGAGGAC
HL_97917.2_Sequence_2 HL_97917.24PQV_G57_C63GGAGGACtrue88001.18
HL_97917.2_Instance_3 HL_97917.2,HL_8P9A_212,U1055_G1064UUUUUUAAUG
HL_97917.2_Sequence_3 HL_97917.28P9A_U_1055_G_1064UUUUUUAAUGtrue100000.00

Conserved interactions between motif group positions in HL_97917.2:
1 2 s35 
1 6 cWW 
2 6 s55 
5 6 s35
JAR3D SCFG/MRF model for HL_97917.2:
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 [6] // Initial node
BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.010073381,0.016952843,0.011990825,0.144379416,0.000000000],[0.112203976,0.015583334,0.159690398,0.014230081,0.000000000],[0.012094013,0.157963935,0.002470837,0.021424419,0.000000000],[0.160527372,0.013782767,0.135425190,0.011207214,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [6] // Basepair C4 - G11 cWW 
HairpinNode  | Num Bases [4] | Left Index [2] | Right Index [5] | Norm Constant [1.000000000000000] // Hairpin node U5:C10
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.100000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.300000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.500000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U5
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.500000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.300000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.100000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A8
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.500000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.300000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.100000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A9
Interaction  | Interacting Bases [4,4] | Pair Probability [[0.300000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.300000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.100000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.300000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C10
Insertion    | Location [1] | Length Distribution [0.005372012,0.327692721,0.327692721,0.011012624,0.322589310,0.005372012,0.000268601] | Letter Distribution [0.166666667,0.166666667,0.055555556,0.611111111,0.000000000]// Insertion in Hairpin after nucleotide 2, position 1
Sequences of instances from HL_97917.2:
> HL_97917.2  3OIN C    4 G   11
CUUCAACG
> HL_97917.2  4PQV G   57 C   63
GGAGGAC
> HL_97917.2  8P9A U 1055 G 1064
UUUUUUAAUG