Alignment of HL_71391.1 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
3
I

8
3

4
9
2
I

10
2

5
11
1
I


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HL_71391.1_Instance_1 HL_71391.1,HL_9DFE_004,G139_C142AGGGAAC
HL_71391.1_Sequence_1 HL_71391.19DFE_G139_C_142AGGGAACtrue90000.97
HL_71391.1_Instance_2 HL_71391.1,HL_3D2V_001,G17_C22GUUCAC
HL_71391.1_Sequence_2 HL_71391.13D2V_G17_C22GUUCACtrue100000.00

Conserved interactions between motif group positions in HL_71391.1:
1 2 s33 
1 5 cWW 
2 3 s53 
2 4 cWH 
2 5 s35 
3 4 s35 
4 5 s35 
5 4 7BPh
JAR3D SCFG/MRF model for HL_71391.1:
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
BasepairNode | Deletion Probability [0.0000001182498160] | Pair Probability [[0.003823887,0.055746509,0.004354386,0.079088977,0.000000000],[0.006716761,0.026247934,0.079759134,0.005218628,0.000000000],[0.004306029,0.594150318,0.000820775,0.010514714,0.000000000],[0.078076789,0.037915021,0.009216620,0.004043518,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.023781213,0.951248514,0.023781213,0.001189061] | Left Letter Distribution [0.125000000,0.125000000,0.375000000,0.375000000,0.000000000] | 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 [5] // Basepair G139 - C142A cWW 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.002789345,0.002789345,0.012020284,0.012076678,0.000000000],[0.002789345,0.013413702,0.002789345,0.264197884,0.000000000],[0.109206963,0.002789345,0.009640600,0.002789345,0.000000000],[0.288738394,0.002789345,0.258095325,0.013084758,0.000000000],[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 [2] | Right Index [4] // Basepair G140 - A142 cWH 
HairpinNode  | Num Bases [1] | Left Index [3] | Right Index [3] | Norm Constant [1.000000000000000] // Hairpin node A141:A141
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.375000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.375000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.125000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.125000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A141
Sequences of instances from HL_71391.1:
> HL_71391.1  9DFE G  139 C 142A
GGGAAC
> HL_71391.1  3D2V G   17 C   22
GUUCAC