Alignment of HL_74379.3 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
9

5
11
8
I

12
8

6
13
7
I

14
7

7
15
6
I

16
5

8
17
2
I

18
2

9
19
1
I


In
acceptance
region

Cutoff
score
Full
edit
distance
Interior
edit
distance
Alignment
score
deficit
HL_74379.3_Instance_1 HL_74379.3,HL_8JY0_003,G42_C53GCAAGGUUAACC
HL_74379.3_Sequence_1 HL_74379.38JY0_G42_C53GCAAGGUUAACCtrue100000.00
HL_74379.3_Instance_2 HL_74379.3,HL_9DXL_003,G26_C37GCAAGGUUAACC
HL_74379.3_Sequence_2 HL_74379.39DXL_G26_C37GCAAGGUUAACCtrue100000.00

Conserved interactions between motif group positions in HL_74379.3:
1 2 s35 
1 9 cWW 
2 3 s35 
3 4 s35 
3 7 cSS 
4 5 s35 
4 6 cSS 
6 7 s35 
7 8 s35 
8 7 7BPh
JAR3D SCFG/MRF model for HL_74379.3:
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 [9] // Initial node
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.009733692,0.020271796,0.011084078,0.201320753,0.000000000],[0.017097495,0.009544863,0.203026637,0.013284001,0.000000000],[0.010960983,0.228535864,0.002089280,0.026765173,0.000000000],[0.198744233,0.013787510,0.023460879,0.010292763,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.991950402,0.007999600,0.000049998] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [9] // Basepair G42 - C53 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.125000000,0.625000000,0.125000000,0.125000000,0.000000000] | Position [1] | Left Index [2] | Right Index [8] // Fixed node on left for 8JY0|1|B|C|43
InitialNode  | Left Length Distribution [0.991950402,0.007999600,0.000049998] | 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 [8] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.031250000,0.906250000,0.031250000,0.031250000,0.000000000] | Position [2] | Left Index [3] | Right Index [8] // Fixed node on right for 8JY0|1|B|U|49
InitialNode  | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | 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
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.105678172,0.082314407,0.079619001,0.078700115,0.000000000],[0.077024050,0.082309394,0.003607345,0.073784465,0.000000000],[0.079578597,0.003542979,0.006695471,0.078299920,0.000000000],[0.075017401,0.052346388,0.042552099,0.078930195,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.991950402,0.007999600,0.000049998] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [7] // Basepair A44 - A51 cSS 
BasepairNode | Deletion Probability [0.0000000000029562] | Pair Probability [[0.105678172,0.077024050,0.079578597,0.075017401,0.000000000],[0.082314407,0.082309394,0.003542979,0.052346388,0.000000000],[0.079619001,0.003607345,0.006695471,0.042552099,0.000000000],[0.078700115,0.073784465,0.078299920,0.078930195,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.991950402,0.007999600,0.000049998] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.000000000,0.000000000,0.023781213,0.951248514,0.023781213,0.001189061] | Right Letter Distribution [0.062500000,0.062500000,0.312500000,0.562500000,0.000000000] | Left Index [4] | Right Index [6] // Basepair A45 - A50 cSS 
HairpinNode  | Num Bases [1] | Left Index [5] | Right Index [5] | Norm Constant [1.000000000000000] // Hairpin node G46:G46
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.125000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.125000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.625000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.125000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G46
Sequences of instances from HL_74379.3:
> HL_74379.3  8JY0 G   42 C   53
GCAAGGUUAACC
> HL_74379.3  9DXL G   26 C   37
GCAAGGUUAACC