Alignment of HL_41543.1 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
3
I

6
4

3
7
5
I

8
10

4
9
10
I

10
11

5
11
10
I

12
10

6
13
9
I

14
8

7
15
7
I

16
6

8
17
3
I

18
3

9
19
2
I

20
2

10
21
1
I


In
acceptance
region

Cutoff
score
Full
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distance
Interior
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distance
Alignment
score
deficit
HL_41543.1_Instance_1 HL_41543.1,HL_7MKY_001,G9_C20GUGCAGCCCGUC
HL_41543.1_Sequence_1 HL_41543.17MKY_G9_C20GUGCAGCCCGUCtrue99000.14
HL_41543.1_Instance_2 HL_41543.1,HL_5X2G_002,G54_C64GUUUGCGGGAC
HL_41543.1_Sequence_2 HL_41543.15X2G_G54_C64GUUUGCGGGACtrue100000.00

Conserved interactions between motif group positions in HL_41543.1:
1 2 s35 
1 9 s33 
1 10 cWW 
2 3 s35 
2 9 bif 
3 4 s33 
4 5 s35 
4 6 cSH 
5 6 s35 
6 7 s35 
7 8 s35 
8 9 s35 
9 10 s35 
10 9 7BR
JAR3D SCFG/MRF model for HL_41543.1:
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 [10] // Initial node
BasepairNode | Deletion Probability [0.0000001182498160] | Pair Probability [[0.004794140,0.049922383,0.005459246,0.099156600,0.000000000],[0.008421037,0.023505677,0.099996800,0.006542775,0.000000000],[0.005398618,0.534124901,0.001029034,0.013182663,0.000000000],[0.097887586,0.033953843,0.011555197,0.005069499,0.000000000],[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 [0.023781213,0.951248514,0.023781213,0.001189061] | Right Letter Distribution [0.375000000,0.125000000,0.125000000,0.375000000,0.000000000] | Left Index [1] | Right Index [10] // Basepair G9 - C20 cWW 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.042606139,0.021817912,0.003408043,0.003408043,0.000000000],[0.278708956,0.013066348,0.003408043,0.003408043,0.000000000],[0.003408043,0.003408043,0.160181528,0.003408043,0.000000000],[0.003408043,0.003408043,0.449538689,0.003408043,0.000000000],[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 [2] | Right Index [9] // Basepair U10 - G18 bif 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.125000000,0.125000000,0.375000000,0.375000000,0.000000000] | Position [1] | Left Index [3] | Right Index [8] // Fixed node on left for 7MKY|1|A|G|11
InitialNode  | Left Length Distribution [0.493381468,0.493381468,0.012635379,0.000601685] | Left Letter Distribution [0.166666667,0.500000000,0.166666667,0.166666667,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [8] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.125000000,0.375000000,0.375000000,0.125000000,0.000000000] | Position [2] | Left Index [4] | Right Index [8] // Fixed node on right for 7MKY|1|A|C|16
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 [4] | Right Index [7] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.125000000,0.375000000,0.375000000,0.125000000,0.000000000] | Position [2] | Left Index [4] | Right Index [7] // Fixed node on right for 7MKY|1|A|C|15
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 [4] | Right Index [6] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.082442164,0.187281378,0.007680972,0.084139219,0.000000000],[0.084342963,0.086292904,0.000981194,0.011079913,0.000000000],[0.012396638,0.000981194,0.089503806,0.079842104,0.000000000],[0.084200391,0.107923341,0.000981194,0.079930624,0.000000000],[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 [4] | Right Index [6] // Basepair A13 - C15 cSH 
HairpinNode  | Num Bases [1] | Left Index [5] | Right Index [5] | Norm Constant [1.000000000000000] // Hairpin node G14:G14
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 G14
Sequences of instances from HL_41543.1:
> HL_41543.1  7MKY G    9 C   20
GUGCAGCCCGUC
> HL_41543.1  5X2G G   54 C   64
GUUUGCGGGAC