Alignment of HL_20743.2 sequences from 3D to the JAR3D model

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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
4
I

6
7

3
7
7
I

8
8

4
9
8
I

10
8

5
11
7
I

12
7

6
13
6
I

14
5

7
15
2
I

16
2

8
17
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
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distance

Alignment
score
deficit
HL_20743.2_Instance_1 HL_20743.2_HL_5KPY_001_G31_C39GGAUAUGGC
HL_20743.2_Sequence_1 HL_20743.2_HL_5KPY_001_G31_C39GGAUAUGGCtrue100000.00
HL_20743.2_Instance_2 HL_20743.2_HL_1Y27_001_G31_C39GGAUAUGGC
HL_20743.2_Sequence_2 HL_20743.2_HL_1Y27_001_G31_C39GGAUAUGGCtrue100000.00
HL_20743.2_Instance_3 HL_20743.2_HL_6P2H_001_A31_U39AAAUAUGGU
HL_20743.2_Sequence_3 HL_20743.2_HL_6P2H_001_A31_U39AAAUAUGGUtrue97000.40
HL_20743.2_Instance_4 HL_20743.2_HL_3RKF_007_G31_C39GGAUAUAGC
HL_20743.2_Sequence_4 HL_20743.2_HL_3RKF_007_G31_C39GGAUAUAGCtrue98000.32
HL_20743.2_Instance_5 HL_20743.2_HL_4FEN_001_G31_C39GGAUAUGGC
HL_20743.2_Sequence_5 HL_20743.2_HL_4FEN_001_G31_C39GGAUAUGGCtrue100000.00
HL_20743.2_Instance_6 HL_20743.2_HL_3SKL_004_C38_G46CAUAAUGGG
HL_20743.2_Sequence_6 HL_20743.2_HL_3SKL_004_C38_G46CAUAAUGGGtrue92001.22
HL_20743.2_Instance_7 HL_20743.2_HL_3SKI_001_C39_G47CAUAAUGGG
HL_20743.2_Sequence_7 HL_20743.2_HL_3SKI_001_C39_G47CAUAAUGGGtrue92001.22

Conserved interactions between motif group positions in HL_20743.2:
1 2 s35 
1 8 cWW 
2 3 s35 
2 8 s55 
3 4 s35 
3 6 cSS 
5 6 s55 
6 7 s35 
JAR3D SCFG/MRF model for HL_20743.2:
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 G31 - C39 from junction 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.009163774,0.018697796,0.010373988,0.200950124,0.000000000],[0.017221651,0.009149382,0.212644579,0.012402890,0.000000000],[0.010337841,0.233285914,0.001985225,0.028217760,0.000000000],[0.189800820,0.012631146,0.023205154,0.009931957,0.000000000],[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 G31 - C39 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.388888889,0.055555556,0.500000000,0.055555556,0.000000000] | Position [1] | Left Index [2] | Right Index [7] // Fixed node on left
InitialNode  | 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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [7] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.055555556,0.055555556,0.833333333,0.055555556,0.000000000] | Position [2] | Left Index [3] | Right Index [7] // Fixed node on right
InitialNode  | Left Length Distribution [1.000000000] | 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 [3] | Right Index [6] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000001232089072] | Pair Probability [[0.085442255,0.077767185,0.117184383,0.075950894,0.000000000],[0.070630775,0.076690491,0.003189304,0.070257479,0.000000000],[0.072441527,0.003122949,0.006832457,0.071535525,0.000000000],[0.067174129,0.018021842,0.107403135,0.076355670,0.000000000],[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 [0.007039775,0.985568462,0.007039775,0.000351989] | Right Letter Distribution [0.055555556,0.055555556,0.055555556,0.833333333,0.000000000] | Left Index [3] | Right Index [6] // Basepair A33 - G37 cSS 
HairpinNode  | Num Bases [2] | Left Index [4] | Right Index [5] | Norm Constant [1.000000000000000] // Hairpin node U34:A35
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.277777778,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.055555556,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.055555556,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.611111111,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U34
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.833333333,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.055555556,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.055555556,0.000000000,0.000000000],[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 A35
Sequences of instances from HL_20743.2:
> HL_20743.2 HL_5KPY_001 G   31 C   39
GGAUAUGGC
> HL_20743.2 HL_1Y27_001 G   31 C   39
GGAUAUGGC
> HL_20743.2 HL_6P2H_001 A   31 U   39
AAAUAUGGU
> HL_20743.2 HL_3RKF_007 G   31 C   39
GGAUAUAGC
> HL_20743.2 HL_4FEN_001 G   31 C   39
GGAUAUGGC
> HL_20743.2 HL_3SKL_004 C   38 G   46
CAUAAUGGG
> HL_20743.2 HL_3SKI_001 C   39 G   47
CAUAAUGGG