Alignment of HL_93535.1 sequences from 3D to the JAR3D model

Previous group | Next group | List of all groups | Motif atlas entry for HL_93535.1
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
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_93535.1_Instance_1 HL_93535.1,HL_8CRE_205,C567_G572CAGCCG
HL_93535.1_Sequence_1 HL_93535.18CRE_C567_G572CAGCCGtrue98000.16
HL_93535.1_Instance_2 HL_93535.1,HL_8P9A_204,C569_G574CAGCCG
HL_93535.1_Sequence_2 HL_93535.18P9A_C569_G574CAGCCGtrue98000.16
HL_93535.1_Instance_3 HL_93535.1,HL_5J7L_026,U1165_A1171UGAUAAA
HL_93535.1_Sequence_3 HL_93535.15J7L_U_1165_A_1171UGAUAAAtrue84001.54
HL_93535.1_Instance_4 HL_93535.1,HL_7A0S_046,C1797_G1803CGAACAG
HL_93535.1_Sequence_4 HL_93535.17A0S_C_1797_G_1803CGAACAGtrue85001.42
HL_93535.1_Instance_5 HL_93535.1,HL_7A0S_004,C133_G138CGUAAG
HL_93535.1_Sequence_5 HL_93535.17A0S_C133_G138CGUAAGtrue100000.00
HL_93535.1_Instance_6 HL_93535.1,HL_8P9A_198,U368_G373UAAGGG
HL_93535.1_Sequence_6 HL_93535.18P9A_U368_G373UAAGGGtrue82001.72

Conserved interactions between motif group positions in HL_93535.1:
1 2 s35 
1 6 cWW 
4 5 s35 
5 6 s35
JAR3D SCFG/MRF model for HL_93535.1:
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 [6] // Initial node
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.009370335,0.016027189,0.010912327,0.164988716,0.000000000],[0.065063121,0.012290252,0.210179617,0.013189690,0.000000000],[0.011044540,0.167414220,0.002198680,0.021103155,0.000000000],[0.185220961,0.012541795,0.088178334,0.010277067,0.000000000],[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 [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [6] // Basepair C567 - G572 cWW 
HairpinNode  | Num Bases [4] | Left Index [2] | Right Index [5] | Norm Constant [1.000000000000000] // Hairpin node A568:C571
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.437500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.062500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.437500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.062500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A568
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.437500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.062500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.312500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.187500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G569
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.437500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.312500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.187500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.062500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C570
Interaction  | Interacting Bases [4,4] | Pair Probability [[0.437500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.312500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.187500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.062500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C571
Insertion    | Location [2] | Length Distribution [0.826344012,0.171868555,0.001718686,0.000068747] | Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000]// Insertion in Hairpin after nucleotide 3, position 2
Insertion    | Location [3] | Length Distribution [0.826344012,0.171868555,0.001718686,0.000068747] | Letter Distribution [0.166666667,0.500000000,0.166666667,0.166666667,0.000000000]// Insertion in Hairpin after nucleotide 4, position 3
Sequences of instances from HL_93535.1:
> HL_93535.1  8CRE C  567 G  572
CAGCCG
> HL_93535.1  8P9A C  569 G  574
CAGCCG
> HL_93535.1  5J7L U 1165 A 1171
UGAUAAA
> HL_93535.1  7A0S C 1797 G 1803
CGAACAG
> HL_93535.1  7A0S C  133 G  138
CGUAAG
> HL_93535.1  8P9A U  368 G  373
UAAGGG