Alignment of HL_20743.5 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
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Full
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Alignment
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HL_20743.5_Instance_1 HL_20743.5,HL_5KPY_001,G31_C39GGAUAUGGC
HL_20743.5_Sequence_1 HL_20743.55KPY_G31_C39GGAUAUGGCtrue100000.00
HL_20743.5_Instance_2 HL_20743.5,HL_1Y27_001,G31_C39GGAUAUGGC
HL_20743.5_Sequence_2 HL_20743.51Y27_G31_C39GGAUAUGGCtrue100000.00
HL_20743.5_Instance_3 HL_20743.5,HL_3RKF_007,G31_C39GGAUAUAGC
HL_20743.5_Sequence_3 HL_20743.53RKF_G31_C39GGAUAUAGCtrue98000.32
HL_20743.5_Instance_4 HL_20743.5,HL_6P2H_001,A31_U39AAAUAUGGU
HL_20743.5_Sequence_4 HL_20743.56P2H_A31_U39AAAUAUGGUtrue97000.40
HL_20743.5_Instance_5 HL_20743.5,HL_4FEN_001,G31_C39GGAUAUGGC
HL_20743.5_Sequence_5 HL_20743.54FEN_G31_C39GGAUAUGGCtrue100000.00
HL_20743.5_Instance_6 HL_20743.5,HL_3SKL_004,C38_G46CAUAAUGGG
HL_20743.5_Sequence_6 HL_20743.53SKL_C38_G46CAUAAUGGGtrue92001.22
HL_20743.5_Instance_7 HL_20743.5,HL_3SKI_001,C39_G47CAUAAUGGG
HL_20743.5_Sequence_7 HL_20743.53SKI_C39_G47CAUAAUGGGtrue92001.22

Conserved interactions between motif group positions in HL_20743.5:
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_20743.5:
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 [8] // Initial node
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 for 5KPY|1|A|G|32
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 for 5KPY|1|A|G|37
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_20743.5:
> HL_20743.5  5KPY G   31 C   39
GGAUAUGGC
> HL_20743.5  1Y27 G   31 C   39
GGAUAUGGC
> HL_20743.5  3RKF G   31 C   39
GGAUAUAGC
> HL_20743.5  6P2H A   31 U   39
AAAUAUGGU
> HL_20743.5  4FEN G   31 C   39
GGAUAUGGC
> HL_20743.5  3SKL C   38 G   46
CAUAAUGGG
> HL_20743.5  3SKI C   39 G   47
CAUAAUGGG