Alignment of HL_34964.1 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
4
I

12
4

6
13
4
I

14
4

7
15
3
I

16
3

8
17
2
I

18
2

9
19
1
I


In
acceptance
region

Cutoff
score
Full
edit
distance
Interior
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distance
Alignment
score
deficit
HL_34964.1_Instance_1 HL_34964.1,HL_2DU3_001,A912_U922AGAGGGGCUUU
HL_34964.1_Sequence_1 HL_34964.12DU3_A912_U922AGAGGGGCUUUtrue91001.43
HL_34964.1_Instance_2 HL_34964.1,HL_4YYE_002,G30_C40GUUUUGUAAUC
HL_34964.1_Sequence_2 HL_34964.14YYE_G30_C40GUUUUGUAAUCtrue100000.00

Conserved interactions between motif group positions in HL_34964.1:
1 2 s35 
1 9 cWW 
2 3 s35 
2 8 cWW 
3 4 s35 
3 5 perp 
3 8 s55 
4 5 s35 
6 7 cSH 
8 9 s35
JAR3D SCFG/MRF model for HL_34964.1:
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 [9] // Initial node
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.009508309,0.021141169,0.010499222,0.212521883,0.000000000],[0.017307832,0.009562561,0.198596306,0.011821420,0.000000000],[0.010428025,0.212609503,0.002065216,0.039989476,0.000000000],[0.197383927,0.012407836,0.023236747,0.010920569,0.000000000],[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 [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [9] // Basepair A912 - U922 cWW 
BasepairNode | Deletion Probability [0.0000000005912491] | Pair Probability [[0.014025201,0.257239276,0.012522138,0.021870700,0.000000000],[0.015501176,0.016714101,0.018694225,0.013746415,0.000000000],[0.012260594,0.019043745,0.003865601,0.148314270,0.000000000],[0.019105514,0.014887357,0.015845632,0.396364055,0.000000000],[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 [0.416666667,0.250000000,0.083333333,0.250000000,0.000000000] | Left Index [2] | Right Index [8] // Basepair G913 - U921 cWW 
HairpinNode  | Num Bases [5] | Left Index [3] | Right Index [7] | Norm Constant [1.000000000000000] // Hairpin node A914:G918
Interaction  | Interacting Bases [4,5] | Pair Probability [[0.072088071,0.073454437,0.004038753,0.071786009,0.000000000],[0.053818455,0.081105356,0.000894248,0.071936499,0.000000000],[0.062983498,0.000894248,0.175759612,0.099228758,0.000000000],[0.073206585,0.072767115,0.000894248,0.085144108,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin Interaction G917 - G918 cSH 
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.375000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.125000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.125000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.375000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A914
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.125000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.125000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.375000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.375000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G915
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.125000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.125000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.375000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.375000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G916
Sequences of instances from HL_34964.1:
> HL_34964.1  2DU3 A  912 U  922
AGAGGGGCUUU
> HL_34964.1  4YYE G   30 C   40
GUUUUGUAAUC