Alignment of HL_50622.6 sequences from 3D to the JAR3D model

Previous group | Next group | List of all groups | Motif atlas entry for HL_50622.6
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
3
I

14
3

7
15
3
I

16
3

8
17
3
I

18
3

9
19
3
I

20
3

10
21
2
I

22
2

11
23
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
HL_50622.6_Instance_1 HL_50622.6_HL_4WSM_225_C31_G41CCUUGAGGUGG
HL_50622.6_Sequence_1 HL_50622.6_HL_4WSM_225_C31_G41CCUUGAGGUGGtrue97000.51
HL_50622.6_Instance_2 HL_50622.6_HL_6GSK_218_C30_G40CCUUGGUAAGG
HL_50622.6_Sequence_2 HL_50622.6_HL_6GSK_218_C30_G40CCUUGGUAAGGtrue100000.00
HL_50622.6_Instance_3 HL_50622.6_HL_4UYK_001_G21_C31GGUUCGGCGUC
HL_50622.6_Sequence_3 HL_50622.6_HL_4UYK_001_G21_C31GGUUCGGCGUCtrue92001.31
HL_50622.6_Instance_4 HL_50622.6_HL_4V7M_039_G29_C39GAUUGUGAUUC
HL_50622.6_Sequence_4 HL_50622.6_HL_4V7M_039_G29_C39GAUUGUGAUUCtrue98000.29
HL_50622.6_Instance_5 HL_50622.6_HL_6CZR_101_G1338_C1349GAUCAGCCAUGC
HL_50622.6_Sequence_5 HL_50622.6_HL_6CZR_101_G_1338_C_1349GAUCAGCCAUGCtrue77003.94

Conserved interactions between motif group positions in HL_50622.6:
1 2 s35 
1 11 cWW 
2 3 s35 
3 4 s35 
5 6 s35 
6 7 s35 
7 8 s35 
8 9 s35 
9 10 s35 
10 11 s35 
JAR3D SCFG/MRF model for HL_50622.6:
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 [11] // Initial node C31 - G41 from junction 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.009378994,0.018460667,0.010720525,0.194585102,0.000000000],[0.017844226,0.009337380,0.218585035,0.013101324,0.000000000],[0.010696621,0.229254879,0.002029771,0.024718569,0.000000000],[0.194084748,0.013199104,0.024076884,0.009926171,0.000000000],[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 [11] // Basepair C31 - G41 cWW 
HairpinNode  | Num Bases [9] | Left Index [2] | Right Index [10] | Norm Constant [1.000000000000000] // Hairpin node C32:G40
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.357142857,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.357142857,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.214285714,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.071428571,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C32
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.071428571,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.071428571,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.071428571,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.785714286,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U33
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.071428571,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.214285714,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.071428571,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.642857143,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U34
Interaction  | Interacting Bases [4,4] | Pair Probability [[0.214285714,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.214285714,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.500000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.071428571,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G35
Interaction  | Interacting Bases [5,5] | Pair Probability [[0.214285714,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.071428571,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.500000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.214285714,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A36
Interaction  | Interacting Bases [6,6] | Pair Probability [[0.071428571,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.214285714,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.500000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.214285714,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G37
Interaction  | Interacting Bases [7,7] | Pair Probability [[0.357142857,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.357142857,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.214285714,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.071428571,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G38
Interaction  | Interacting Bases [8,8] | Pair Probability [[0.357142857,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.071428571,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.214285714,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.357142857,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U39
Interaction  | Interacting Bases [9,9] | Pair Probability [[0.071428571,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.071428571,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.500000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.357142857,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G40
Insertion    | Location [8] | Length Distribution [0.792098765,0.205432099,0.002370370,0.000098765] | Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000]// Insertion in Hairpin after nucleotide 9, position 8
Sequences of instances from HL_50622.6:
> HL_50622.6 HL_4WSM_225 C   31 G   41
CCUUGAGGUGG
> HL_50622.6 HL_6GSK_218 C   30 G   40
CCUUGGUAAGG
> HL_50622.6 HL_4UYK_001 G   21 C   31
GGUUCGGCGUC
> HL_50622.6 HL_4V7M_039 G   29 C   39
GAUUGUGAUUC
> HL_50622.6 HL_6CZR_101 G 1338 C 1349
GAUCAGCCAUGC