Alignment of HL_04642.1 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
4
I

8
4

4
9
4
I

10
4

5
11
3
I

12
3

6
13
2
I

14
2

7
15
1
I


In
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Alignment
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HL_04642.1_Instance_1 HL_04642.1,HL_6UFM_001,C13_G23CAGGCGGUUAG
HL_04642.1_Sequence_1 HL_04642.16UFM_C13_G23CAGGCGGUUAGtrue100000.00
HL_04642.1_Instance_2 HL_04642.1,HL_8VU0_001,C13_G23CAGGUGGUUAG
HL_04642.1_Sequence_2 HL_04642.18VU0_C13_G23CAGGUGGUUAGtrue97000.51
HL_04642.1_Instance_3 HL_04642.1,HL_7OSM_115,C13_G22CAGUCGGUAG
HL_04642.1_Sequence_3 HL_04642.17OSM_C13_G22CAGUCGGUAGtrue94001.09

Conserved interactions between motif group positions in HL_04642.1:
1 7 cWW 
2 3 s35 
2 6 cWS 
2 7 s55
JAR3D SCFG/MRF model for HL_04642.1:
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 [7] // Initial node
BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.009443990,0.016935343,0.010857030,0.196859360,0.000000000],[0.020079540,0.009618431,0.236072779,0.013656751,0.000000000],[0.010978957,0.201101150,0.002069466,0.023238378,0.000000000],[0.199411444,0.013158017,0.026511334,0.010008030,0.000000000],[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 [7] // Basepair C13 - G23 cWW 
BasepairNode | Deletion Probability [0.0000001200211660] | Pair Probability [[0.282754783,0.190768767,0.201601816,0.194868032,0.000000000],[0.015242381,0.012431933,0.002073965,0.012616740,0.000000000],[0.020610252,0.002073965,0.026415638,0.009865379,0.000000000],[0.007404147,0.007810443,0.006180879,0.007280880,0.000000000],[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 [0.016116035,0.966962127,0.016116035,0.000805802] | Right Letter Distribution [0.100000000,0.100000000,0.100000000,0.700000000,0.000000000] | Left Index [2] | Right Index [6] // Basepair A14 - A22 cWS 
HairpinNode  | Num Bases [3] | Left Index [3] | Right Index [5] | Norm Constant [1.000000000000000] // Hairpin node G15:U20
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],[0.000000000,0.000000000,0.700000000,0.000000000,0.000000000],[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 G15
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.100000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.500000000,0.000000000,0.000000000],[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 G16
Interaction  | Interacting Bases [3,3] | 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 U20
Insertion    | Location [2] | Length Distribution [0.000000000,0.005372012,0.333064733,0.650013430,0.011012624,0.000537201] | Letter Distribution [0.050000000,0.250000000,0.550000000,0.150000000,0.000000000]// Insertion in Hairpin after nucleotide 4, position 2
Sequences of instances from HL_04642.1:
> HL_04642.1  6UFM C   13 G   23
CAGGCGGUUAG
> HL_04642.1  8VU0 C   13 G   23
CAGGUGGUUAG
> HL_04642.1  7OSM C   13 G   22
CAGUCGGUAG