Alignment of HL_09452.1 sequences from 3D to the JAR3D model

Previous group | Next group | List of all groups | Motif atlas entry for HL_09452.1
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
3
I

8
3

4
9
2
I

10
2

5
11
1
I


In
acceptance
region

Cutoff
score
Full
edit
distance
Interior
edit
distance
Alignment
score
deficit
HL_09452.1_Instance_1 HL_09452.1,HL_2ZZN_004,U13_A22UAGGGGCUA
HL_09452.1_Sequence_1 HL_09452.12ZZN_U13_A22UAGGGGCUAtrue100000.00
HL_09452.1_Instance_2 HL_09452.1,HL_5X6B_005,U13_A21UAGGGGCUA
HL_09452.1_Sequence_2 HL_09452.15X6B_U13_A21UAGGGGCUAtrue100000.00
HL_09452.1_Instance_3 HL_09452.1,HL_5J7L_149,G543_C550GCUUAGGC
HL_09452.1_Sequence_3 HL_09452.15J7L_G543_C550GCUUAGGCtrue90001.12

Conserved interactions between motif group positions in HL_09452.1:
1 2 s35 
1 5 cWW 
2 3 s35 
2 5 s55
JAR3D SCFG/MRF model for HL_09452.1:
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 [0.0000000000000877] | 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 [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.000000000,0.000000000,0.005372012,0.333064733,0.650013430,0.011012624,0.000537201] | Right Letter Distribution [0.115384615,0.192307692,0.500000000,0.192307692,0.000000000] | Left Index [1] | Right Index [5] // Basepair U13 - A22 cWW 
HairpinNode  | Num Bases [3] | Left Index [2] | Right Index [4] | Norm Constant [1.000000000000000] // Hairpin node A14:G16
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.500000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.300000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.100000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.100000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A14
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.100000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.500000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.300000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G15
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.100000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.500000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.300000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G16
Sequences of instances from HL_09452.1:
> HL_09452.1  2ZZN U   13 A   22
UAGGGGCUA
> HL_09452.1  5X6B U   13 A   21
UAGGGGCUA
> HL_09452.1  5J7L G  543 C  550
GCUUAGGC