Alignment of HL_35894.3 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
3
I

10
3

5
11
2
I

12
2

6
13
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
HL_35894.3_Instance_1 HL_35894.3_HL_5M3H_001_U3_A8UAGUAA
HL_35894.3_Sequence_1 HL_35894.3_HL_5M3H_001_U3_A8UAGUAAtrue100000.00
HL_35894.3_Instance_2 HL_35894.3_HL_4WSB_001_U3_A8UAGUAA
HL_35894.3_Sequence_2 HL_35894.3_HL_4WSB_001_U3_A8UAGUAAtrue100000.00
HL_35894.3_Instance_3 HL_35894.3_HL_4WRT_001_U3_A8UAGUAA
HL_35894.3_Sequence_3 HL_35894.3_HL_4WRT_001_U3_A8UAGUAAtrue100000.00
HL_35894.3_Instance_4 HL_35894.3_HL_5FMZ_001_U3_A8UAGUAA
HL_35894.3_Sequence_4 HL_35894.3_HL_5FMZ_001_U3_A8UAGUAAtrue100000.00
HL_35894.3_Instance_5 HL_35894.3_HL_4KJI_001_G5_C12GAAGGAUC
HL_35894.3_Sequence_5 HL_35894.3_HL_4KJI_001_G5_C12GAAGGAUCtrue42005.78
HL_35894.3_Instance_6 HL_35894.3_HL_5J7L_140_C225_G230CAACCG
HL_35894.3_Sequence_6 HL_35894.3_HL_5J7L_140_C225_G230CAACCGtrue54004.54

Conserved interactions between motif group positions in HL_35894.3:
1 2 s35 
1 6 cWW 
2 3 s33 
2 5 cSW 
5 6 s35 
3 3 2BPh
JAR3D SCFG/MRF model for HL_35894.3:
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 [6] // Initial node U3 - A8 from junction 
BasepairNode | Deletion Probability [0.0000097596267952] | Pair Probability [[0.008886126,0.017248940,0.009893342,0.190110480,0.000000000],[0.020135330,0.009395594,0.201875378,0.011427567,0.000000000],[0.009905745,0.200257925,0.001981628,0.022841193,0.000000000],[0.233045106,0.010997521,0.042245054,0.009753071,0.000000000],[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 [0.826344012,0.171868555,0.001718686,0.000068747] | Right Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000] | Left Index [1] | Right Index [6] // Basepair U3 - A8 cWW 
BasepairNode | Deletion Probability [0.0000097596267952] | Pair Probability [[0.296711805,0.052159493,0.019116627,0.006867568,0.000000000],[0.176943758,0.011530991,0.001923665,0.007244421,0.000000000],[0.186991736,0.001923665,0.024501297,0.005732951,0.000000000],[0.180745949,0.011702405,0.009150435,0.006753235,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.826344012,0.171868555,0.001718686,0.000068747] | Left Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [5] // Basepair A4 - A7 cSW 
HairpinNode  | Num Bases [2] | Left Index [3] | Right Index [4] | Norm Constant [1.000000000000000] // Hairpin node G5:U6
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.170454545,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.011363636,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.806818182,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.011363636,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G5
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.062500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.187500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.187500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.562500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U6
Sequences of instances from HL_35894.3:
> HL_35894.3 HL_5M3H_001 U    3 A    8
UAGUAA
> HL_35894.3 HL_4WSB_001 U    3 A    8
UAGUAA
> HL_35894.3 HL_4WRT_001 U    3 A    8
UAGUAA
> HL_35894.3 HL_5FMZ_001 U    3 A    8
UAGUAA
> HL_35894.3 HL_4KJI_001 G    5 C   12
GAAGGAUC
> HL_35894.3 HL_5J7L_140 C  225 G  230
CAACCG