Alignment of HL_28567.3 sequences from 3D to the JAR3D model

Previous group | Next group | List of all groups | Motif atlas entry for HL_28567.3
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
2
I

12
2

6
13
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
HL_28567.3_Instance_1 HL_28567.3_HL_6U8D_001_G161_C166GAGUAC
HL_28567.3_Sequence_1 HL_28567.3_HL_6U8D_001_G161_C166GAGUACtrue90000.92
HL_28567.3_Instance_2 HL_28567.3_HL_4XWF_001_G24_C29GGAAAC
HL_28567.3_Sequence_2 HL_28567.3_HL_4XWF_001_G24_C29GGAAACtrue100000.00
HL_28567.3_Instance_3 HL_28567.3_HL_3ADD_003_C47D_G47ICGAGUG
HL_28567.3_Sequence_3 HL_28567.3_HL_3ADD_003_C47D_G47ICGAGUGtrue88001.10
HL_28567.3_Instance_4 HL_28567.3_HL_4RUM_001_C27_G33CAGAGCG
HL_28567.3_Sequence_4 HL_28567.3_HL_4RUM_001_C27_G33CAGAGCGtrue61003.73
HL_28567.3_Instance_5 HL_28567.3_HL_4KR9_002_G19_C24GGAAAC
HL_28567.3_Sequence_5 HL_28567.3_HL_4KR9_002_G19_C24GGAAACtrue100000.00
HL_28567.3_Instance_6 HL_28567.3_HL_2OEU_002_C25_G32CCAAAUAG
HL_28567.3_Sequence_6 HL_28567.3_HL_2OEU_002_C25_G32CCAAAUAGtrue69002.94

Conserved interactions between motif group positions in HL_28567.3:
1 2 s35 
1 6 cWW 
2 3 s35 
2 6 s55 
4 5 s35 
JAR3D SCFG/MRF model for HL_28567.3:
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 G161 - C166 from junction 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.009271545,0.017981432,0.010607783,0.192505806,0.000000000],[0.017981779,0.009265445,0.226529308,0.013026479,0.000000000],[0.010607796,0.226528663,0.002010668,0.024167927,0.000000000],[0.192506087,0.013026424,0.024168288,0.009814571,0.000000000],[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 G161 - C166 cWW 
HairpinNode  | Num Bases [4] | Left Index [2] | Right Index [5] | Norm Constant [1.000000000000000] // Hairpin node A162:A165
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.312500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.187500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.437500000,0.000000000,0.000000000],[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 A162
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.562500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.062500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.312500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.062500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G163
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.312500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.062500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.312500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.312500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U164
Interaction  | Interacting Bases [4,4] | Pair Probability [[0.562500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.187500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.062500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.187500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A165
Insertion    | Location [2] | Length Distribution [0.660442125,0.171632569,0.166414939,0.001441714,0.000068653] | Letter Distribution [0.700000000,0.100000000,0.100000000,0.100000000,0.000000000]// Insertion in Hairpin after nucleotide 3, position 2
Sequences of instances from HL_28567.3:
> HL_28567.3 HL_6U8D_001 G  161 C  166
GAGUAC
> HL_28567.3 HL_4XWF_001 G   24 C   29
GGAAAC
> HL_28567.3 HL_3ADD_003 C  47D G  47I
CGAGUG
> HL_28567.3 HL_4RUM_001 C   27 G   33
CAGAGCG
> HL_28567.3 HL_4KR9_002 G   19 C   24
GGAAAC
> HL_28567.3 HL_2OEU_002 C   25 G   32
CCAAAUAG