Alignment of HL_10751.2 sequences from 3D to the JAR3D model

Previous group | Next group | List of all groups | Motif atlas entry for HL_10751.2
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
4

3
7
4
I

8
4

4
9
4
I

10
4

5
11
4
I

12
4

6
13
3
I

14
3

7
15
2
I

16
2

8
17
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
HL_10751.2_Instance_1 HL_10751.2_HL_1J1U_004_C513_G523CAGCCUGGUAG
HL_10751.2_Sequence_1 HL_10751.2_HL_1J1U_004_C513_G523CAGCCUGGUAGtrue100000.00
HL_10751.2_Instance_2 HL_10751.2_HL_1J1U_001_C513_G523CAGCCUGGUAG
HL_10751.2_Sequence_2 HL_10751.2_HL_1J1U_001_C513_G523CAGCCUGGUAGtrue100000.00
HL_10751.2_Instance_3 HL_10751.2_HL_1H4S_001_C13_G22CAGCCCGGUAG
HL_10751.2_Sequence_3 HL_10751.2_HL_1H4S_001_C13_G22CAGCCCGGUAGtrue94001.30
HL_10751.2_Instance_4 HL_10751.2_HL_6CFJ_106_C13_G22CAGCCUGGUAG
HL_10751.2_Sequence_4 HL_10751.2_HL_6CFJ_106_C13_G22CAGCCUGGUAGtrue100000.00
HL_10751.2_Instance_5 HL_10751.2_HL_4V9Q_213_C13_G22CAGCCUGGUAG
HL_10751.2_Sequence_5 HL_10751.2_HL_4V9Q_213_C13_G22CAGCCUGGUAGtrue100000.00
HL_10751.2_Instance_6 HL_10751.2_HL_2ZUE_001_U913_G922UAGCCAGGACAG
HL_10751.2_Sequence_6 HL_10751.2_HL_2ZUE_001_U913_G922UAGCCAGGACAGtrue58008.40
HL_10751.2_Instance_7 HL_10751.2_HL_4WT8_215_C13_G23CAGCCUGGUAG
HL_10751.2_Sequence_7 HL_10751.2_HL_4WT8_215_C13_G23CAGCCUGGUAGtrue100000.00

Conserved interactions between motif group positions in HL_10751.2:
1 8 cWW 
2 3 s35 
2 7 cWS 
2 8 s55 
5 6 s33 
4 3 7BPh
5 4 7BPh
JAR3D SCFG/MRF model for HL_10751.2:
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 [8] // Initial node C513 - G523 from junction 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.009323756,0.015877713,0.010902482,0.167504797,0.000000000],[0.057767753,0.011742545,0.232594255,0.013451740,0.000000000],[0.011045651,0.170984366,0.002157753,0.021172046,0.000000000],[0.176272283,0.012855711,0.076243940,0.010103208,0.000000000],[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 [8] // Basepair C513 - G523 cWW 
BasepairNode | Deletion Probability [0.0000000000014450] | Pair Probability [[0.275046072,0.192819086,0.203768565,0.196962408,0.000000000],[0.015406201,0.012565548,0.002096255,0.012752341,0.000000000],[0.020831764,0.002096255,0.026699544,0.009971408,0.000000000],[0.007483724,0.007894387,0.006247309,0.007359133,0.000000000],[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 [0.000000000,0.000000000,0.006034093,0.845778649,0.146829587,0.001307387,0.000050284] | Right Letter Distribution [0.062500000,0.062500000,0.604166667,0.270833333,0.000000000] | Left Index [2] | Right Index [7] // Basepair A514 - A522 cWS 
HairpinNode  | Num Bases [4] | Left Index [3] | Right Index [6] | Norm Constant [1.000000000000000] // Hairpin node G515:U518
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.055555556,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.055555556,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.833333333,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.055555556,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G515
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.009803922,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.970588235,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.009803922,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.009803922,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C516
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.009803922,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.970588235,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.009803922,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.009803922,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C517
Interaction  | Interacting Bases [4,4] | Pair Probability [[0.166666667,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.166666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.055555556,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.611111111,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U518
Sequences of instances from HL_10751.2:
> HL_10751.2 HL_1J1U_004 C  513 G  523
CAGCCUGGUAG
> HL_10751.2 HL_1J1U_001 C  513 G  523
CAGCCUGGUAG
> HL_10751.2 HL_1H4S_001 C   13 G   22
CAGCCCGGUAG
> HL_10751.2 HL_6CFJ_106 C   13 G   22
CAGCCUGGUAG
> HL_10751.2 HL_4V9Q_213 C   13 G   22
CAGCCUGGUAG
> HL_10751.2 HL_2ZUE_001 U  913 G  922
UAGCCAGGACAG
> HL_10751.2 HL_4WT8_215 C   13 G   23
CAGCCUGGUAG