Alignment of HL_99223.1 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
3

3
7
2
I

8
2

4
9
1
I


In
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region


Cutoff
score

Full
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distance

Interior
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Alignment
score
deficit
HL_99223.1_Instance_1 HL_99223.1_HL_6FQL_001_U5_A9UUUAA
HL_99223.1_Sequence_1 HL_99223.1_HL_6FQL_001_U5_A9UUUAAtrue100000.00
HL_99223.1_Instance_2 HL_99223.1_HL_6FQ3_001_U5_A9UCCAA
HL_99223.1_Sequence_2 HL_99223.1_HL_6FQ3_001_U5_A9UCCAAtrue95000.51
HL_99223.1_Instance_3 HL_99223.1_HL_5TBW_045_G2110_C2114GGUAC
HL_99223.1_Sequence_3 HL_99223.1_HL_5TBW_045_G_2110_C_2114GGUACtrue99000.06

Conserved interactions between motif group positions in HL_99223.1:
1 3 s33 
1 4 cWW 
2 3 s55 
3 4 s35 
3 1 2BR
JAR3D SCFG/MRF model for HL_99223.1:
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 [4] // Initial node U5 - A9 from junction 
BasepairNode | Deletion Probability [0.0000001200211660] | Pair Probability [[0.009177479,0.018274610,0.010201403,0.196065482,0.000000000],[0.020197122,0.009641546,0.197064662,0.011676789,0.000000000],[0.010173530,0.207057088,0.002039267,0.024050960,0.000000000],[0.219982557,0.011400443,0.042929120,0.010067941,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.016116035,0.966962127,0.016116035,0.000805802] | Left Letter Distribution [0.100000000,0.300000000,0.300000000,0.300000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [4] // Basepair U5 - A9 cWW 
HairpinNode  | Num Bases [2] | Left Index [2] | Right Index [3] | Norm Constant [1.000000000000000] // Hairpin node U7:A8
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.100000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.300000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.100000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.500000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U7
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.911764706,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.029411765,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.029411765,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.029411765,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A8
Sequences of instances from HL_99223.1:
> HL_99223.1 HL_6FQL_001 U    5 A    9
UUUAA
> HL_99223.1 HL_6FQ3_001 U    5 A    9
UCCAA
> HL_99223.1 HL_5TBW_045 G 2110 C 2114
GGUAC