Alignment of HL_10453.3 sequences from 3D to the JAR3D model

Previous group | Next group | List of all groups | Motif atlas entry for HL_10453.3
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
3
I

10
3

5
11
3
I

12
3

6
13
2
I

14
2

7
15
1
I


In
acceptance
region

Cutoff
score
Full
edit
distance
Interior
edit
distance
Alignment
score
deficit
HL_10453.3_Instance_1 HL_10453.3,HL_6MPI_033,G31_C39GCUGCGAAC
HL_10453.3_Sequence_1 HL_10453.36MPI_G31_C39GCUGCGAACtrue80002.21
HL_10453.3_Instance_2 HL_10453.3,HL_6MKN_034,G31_C39GCUGCGAAC
HL_10453.3_Sequence_2 HL_10453.36MKN_G31_C39GCUGCGAACtrue80002.21
HL_10453.3_Instance_3 HL_10453.3,HL_8H0S_002,A31_U39ACUUUGACU
HL_10453.3_Sequence_3 HL_10453.38H0S_A31_U39ACUUUGACUtrue84001.80
HL_10453.3_Instance_4 HL_10453.3,HL_8H1B_001,A31_U39ACUUUGACU
HL_10453.3_Sequence_4 HL_10453.38H1B_A31_U39ACUUUGACUtrue84001.80
HL_10453.3_Instance_5 HL_10453.3,HL_6UFH_001,G13_C20GCGAUCAC
HL_10453.3_Sequence_5 HL_10453.36UFH_G13_C20GCGAUCACtrue53005.22
HL_10453.3_Instance_6 HL_10453.3,HL_3OXE_001,G17_C24GUUUAAUC
HL_10453.3_Sequence_6 HL_10453.33OXE_G17_C24GUUUAAUCtrue52005.31
HL_10453.3_Instance_7 HL_10453.3,HL_2A43_001,G6_C13GCACCGUC
HL_10453.3_Sequence_7 HL_10453.32A43_G6_C13GCACCGUCtrue47005.92
HL_10453.3_Instance_8 HL_10453.3,HL_5J7L_014,G617_C623GCUCAAC
HL_10453.3_Sequence_8 HL_10453.35J7L_G617_C623GCUCAACtrue100000.00
HL_10453.3_Instance_9 HL_10453.3,HL_4LFB_014,G617_C623GCUCAAC
HL_10453.3_Sequence_9 HL_10453.34LFB_G617_C623GCUCAACtrue100000.00

Conserved interactions between motif group positions in HL_10453.3:
1 2 s35 
1 7 cWW 
3 4 s35 
4 5 s35 
5 6 s35 
6 7 s35
JAR3D SCFG/MRF model for HL_10453.3:
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 [7] // Initial node
BasepairNode | Deletion Probability [0.0000072272017955] | Pair Probability [[0.009014855,0.019331512,0.010129013,0.207321623,0.000000000],[0.016086970,0.008939250,0.188145645,0.011822610,0.000000000],[0.010035408,0.257184473,0.001945098,0.030546325,0.000000000],[0.185415088,0.012328264,0.021861000,0.009892866,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.883805084,0.115305590,0.000858659,0.000030666] | Left Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000] | Right Length Distribution [0.883805084,0.115305590,0.000858659,0.000030666] | Right Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000] | Left Index [1] | Right Index [7] // Basepair G31 - C39 cWW 
HairpinNode  | Num Bases [5] | Left Index [2] | Right Index [6] | Norm Constant [1.000000000000000] // Hairpin node C32:A38
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.045454545,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.772727273,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.045454545,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.136363636,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C32
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.227272727,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.227272727,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.045454545,0.000000000,0.000000000],[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 C35
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.136363636,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.318181818,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.409090909,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.136363636,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G36
Interaction  | Interacting Bases [4,4] | Pair Probability [[0.681818182,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.227272727,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.045454545,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.045454545,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A37
Interaction  | Interacting Bases [5,5] | Pair Probability [[0.500000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.227272727,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.136363636,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.136363636,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A38
Insertion    | Location [1] | Length Distribution [0.441126985,0.115023402,0.441249350,0.002477898,0.000122365] | Letter Distribution [0.045454545,0.045454545,0.318181818,0.590909091,0.000000000]// Insertion in Hairpin after nucleotide 2, position 1
Sequences of instances from HL_10453.3:
> HL_10453.3  6MPI G   31 C   39
GCUGCGAAC
> HL_10453.3  6MKN G   31 C   39
GCUGCGAAC
> HL_10453.3  8H0S A   31 U   39
ACUUUGACU
> HL_10453.3  8H1B A   31 U   39
ACUUUGACU
> HL_10453.3  6UFH G   13 C   20
GCGAUCAC
> HL_10453.3  3OXE G   17 C   24
GUUUAAUC
> HL_10453.3  2A43 G    6 C   13
GCACCGUC
> HL_10453.3  5J7L G  617 C  623
GCUCAAC
> HL_10453.3  4LFB G  617 C  623
GCUCAAC