Alignment of HL_04725.1 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
2

2
5
2
I

6
2

3
7
2
I

8
2

4
9
2
I

10
2

5
11
2
I

12
2

6
13
2
I

14
2

7
15
2
I

16
2

8
17
1
I


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Alignment
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HL_04725.1_Instance_1 HL_04725.1,HL_4M4O_002,G28_C39GUUACUUAGUUC
HL_04725.1_Sequence_1 HL_04725.14M4O_G28_C39GUUACUUAGUUCtrue100000.00
HL_04725.1_Instance_2 HL_04725.1,HL_4M6D_010,G28_C39GUUACUUAGUUC
HL_04725.1_Sequence_2 HL_04725.14M6D_G28_C39GUUACUUAGUUCtrue100000.00

Conserved interactions between motif group positions in HL_04725.1:
1 8 cWW 
2 3 perp 
2 6 cWW 
3 4 s35 
3 8 cWS 
4 5 s35 
4 7 cWW 
5 6 cWS 
6 7 s35 
7 8 s35 
8 7 7BR
JAR3D SCFG/MRF model for HL_04725.1:
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 [8] // Initial node
HairpinNode  | Num Bases [8] | Left Index [1] | Right Index [8] | Norm Constant [0.112416937282600] // Hairpin node G28:C39
Interaction  | Interacting Bases [2,6] | Pair Probability [[0.009034335,0.017544761,0.009910087,0.196321162,0.000000000],[0.022043953,0.009831675,0.196981684,0.011044900,0.000000000],[0.009929415,0.194460696,0.002044250,0.023047545,0.000000000],[0.224032836,0.010374563,0.053294552,0.010103588,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin Interaction U30 - A35 cWW 
Interaction  | Interacting Bases [5,6] | Pair Probability [[0.008335090,0.008456775,0.008103673,0.008758894,0.000000000],[0.015122597,0.014345643,0.003255280,0.015476731,0.000000000],[0.010786459,0.002334730,0.009842452,0.008380535,0.000000000],[0.253080851,0.210591316,0.193742704,0.229386269,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin Interaction U33 - A35 cWS 
Interaction  | Interacting Bases [4,7] | 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]] // Hairpin Interaction C32 - G36 cWW 
Interaction  | Interacting Bases [1,8] | Pair Probability [[0.004794140,0.049922383,0.005459246,0.099156600,0.000000000],[0.008421037,0.023505677,0.099996800,0.006542775,0.000000000],[0.005398618,0.534124901,0.001029034,0.013182663,0.000000000],[0.097887586,0.033953843,0.011555197,0.005069499,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin Interaction G28 - C39 cWW 
Interaction  | Interacting Bases [3,8] | Pair Probability [[0.099820651,0.562213751,0.099700937,0.097788684,0.000000000],[0.009694335,0.043025138,0.001085212,0.008387967,0.000000000],[0.009062072,0.005426059,0.026872012,0.004801924,0.000000000],[0.003930815,0.020984238,0.003343284,0.003862922,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin Interaction A31 - C39 cWS 
Insertion    | Location [1] | Length Distribution [0.023781213,0.951248514,0.023781213,0.001189061] | Letter Distribution [0.125000000,0.125000000,0.125000000,0.625000000,0.000000000]// Insertion in Hairpin after nucleotide 1, position 1
Insertion    | Location [5] | Length Distribution [0.023781213,0.951248514,0.023781213,0.001189061] | Letter Distribution [0.125000000,0.125000000,0.125000000,0.625000000,0.000000000]// Insertion in Hairpin after nucleotide 5, position 5
Insertion    | Location [7] | Length Distribution [0.000000000,0.023781213,0.951248514,0.023781213,0.001189061] | Letter Distribution [0.083333333,0.083333333,0.083333333,0.750000000,0.000000000]// Insertion in Hairpin after nucleotide 7, position 7
Sequences of instances from HL_04725.1:
> HL_04725.1  4M4O G   28 C   39
GUUACUUAGUUC
> HL_04725.1  4M6D G   28 C   39
GUUACUUAGUUC