Alignment of HL_98557.4 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
2
I

6
2

3
7
1
I


In
acceptance
region


Cutoff
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Full
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distance

Interior
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Alignment
score
deficit
HL_98557.4_Instance_1 HL_98557.4_HL_4Y4O_113_C319_G323CAGAG
HL_98557.4_Sequence_1 HL_98557.4_HL_4Y4O_113_C319_G323CAGAGtrue88001.10
HL_98557.4_Instance_2 HL_98557.4_HL_5TBW_006_C208_G212CAUAG
HL_98557.4_Sequence_2 HL_98557.4_HL_5TBW_006_C208_G212CAUAGtrue95000.51
HL_98557.4_Instance_3 HL_98557.4_HL_4WF9_011_C362_G366CAAAG
HL_98557.4_Sequence_3 HL_98557.4_HL_4WF9_011_C362_G366CAAAGtrue100000.00
HL_98557.4_Instance_4 HL_98557.4_HL_7A0S_011_C330_G334CUCAG
HL_98557.4_Sequence_4 HL_98557.4_HL_7A0S_011_C330_G334CUCAGtrue75002.40
HL_98557.4_Instance_5 HL_98557.4_HL_4V9F_011_G326_C330GAUAC
HL_98557.4_Sequence_5 HL_98557.4_HL_4V9F_011_G326_C330GAUACtrue93000.64
HL_98557.4_Instance_6 HL_98557.4_HL_2Y9H_003_C11_G16CGCGUG
HL_98557.4_Sequence_6 HL_98557.4_HL_2Y9H_003_C11_G16CGCGUGtrue31006.58
HL_98557.4_Instance_7 HL_98557.4_HL_5J7L_143_G319_C323GAUAC
HL_98557.4_Sequence_7 HL_98557.4_HL_5J7L_143_G319_C323GAUACtrue93000.64

Conserved interactions between motif group positions in HL_98557.4:
1 2 s35 
1 3 cWW 
2 3 s55 
JAR3D SCFG/MRF model for HL_98557.4:
Character Definition | A,C,G,U,* // Define characters here
InitialNode  | Left Length Distribution [0.999900000,0.000100000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.999900000,0.000100000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [3] // Initial node C319 - G323 from junction 
BasepairNode | Deletion Probability [0.0000000002889971] | Pair Probability [[0.009144630,0.017165752,0.010484008,0.190189591,0.000000000],[0.018463087,0.009213143,0.244318979,0.013008228,0.000000000],[0.010534317,0.213869704,0.001991973,0.023268171,0.000000000],[0.191242613,0.012802444,0.024618634,0.009684725,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.000000000,0.006034093,0.845778649,0.146829587,0.001307387,0.000050284] | Right Letter Distribution [0.441176471,0.147058824,0.147058824,0.264705882,0.000000000] | Left Index [1] | Right Index [3] // Basepair C319 - G323 cWW 
HairpinNode  | Num Bases [1] | Left Index [2] | Right Index [2] | Norm Constant [1.000000000000000] // Hairpin node A320:A320
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.611111111,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.055555556,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.166666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.166666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A320
Sequences of instances from HL_98557.4:
> HL_98557.4 HL_4Y4O_113 C  319 G  323
CAGAG
> HL_98557.4 HL_5TBW_006 C  208 G  212
CAUAG
> HL_98557.4 HL_4WF9_011 C  362 G  366
CAAAG
> HL_98557.4 HL_7A0S_011 C  330 G  334
CUCAG
> HL_98557.4 HL_4V9F_011 G  326 C  330
GAUAC
> HL_98557.4 HL_2Y9H_003 C   11 G   16
CGCGUG
> HL_98557.4 HL_5J7L_143 G  319 C  323
GAUAC