Alignment of HL_93383.1 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
3
I

4
4

2
5
4
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
2

7
15
2
I

16
2

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_93383.1_Instance_1 HL_93383.1,HL_5K7D_002,G33_C41GCCCUAAGC
HL_93383.1_Sequence_1 HL_93383.15K7D_G33_C41GCCCUAAGCtrue100000.00
HL_93383.1_Instance_2 HL_93383.1,HL_6UFJ_004,G33_C41GCUCAAAGC
HL_93383.1_Sequence_2 HL_93383.16UFJ_G33_C41GCUCAAAGCtrue100000.00

Conserved interactions between motif group positions in HL_93383.1:
1 7 wat 
1 8 tHS 
1 9 cWW 
2 3 s35 
3 4 s35 
4 5 s35 
5 6 s35 
6 7 s35 
7 8 s35 
7 9 s35 
8 9 cSH 
9 8 7BR
JAR3D SCFG/MRF model for HL_93383.1:
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 [9] // Initial node
ClusterNode  | Deletion Probability [0.0000000006250000] | Num Left Bases [1] | Num Right Bases [3] | Left Index [1] | Right Index [9] | Norm Constant [0.017343279517751] // Cluster node 5K7D|1|A|G|33:5K7D|1|A|G|33 and 5K7D|1|A|A|39:5K7D|1|A|C|41
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.008525149,0.008525149,0.008525149,0.008525149,0.000000000],[0.008525149,0.008525149,0.008525149,0.008525149,0.000000000],[0.872122762,0.008525149,0.008525149,0.008525149,0.000000000],[0.008525149,0.008525149,0.008525149,0.008525149,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5K7D|1|A|G|33 - 5K7D|1|A|A|39 wat 
Interaction  | Interacting Bases [1,3] | Pair Probability [[0.034904092,0.027881299,0.019643132,0.024833736,0.000000000],[0.017270646,0.017645157,0.004018083,0.020851658,0.000000000],[0.004018083,0.004018083,0.421416153,0.004018083,0.000000000],[0.362655466,0.004018083,0.028790164,0.004018083,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5K7D|1|A|G|33 - 5K7D|1|A|G|40 tHS 
Interaction  | Interacting Bases [1,4] | 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]] // Cluster Interaction 5K7D|1|A|G|33 - 5K7D|1|A|C|41 cWW 
Interaction  | Interacting Bases [3,4] | Pair Probability [[0.061274510,0.061274510,0.061274510,0.061274510,0.000000000],[0.061274510,0.061274510,0.061274510,0.061274510,0.000000000],[0.061274510,0.080882353,0.061274510,0.061274510,0.000000000],[0.061274510,0.061274510,0.061274510,0.061274510,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5K7D|1|A|G|40 - 5K7D|1|A|C|41 cSH 
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 [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [6] // New Initial node after Cluster
HairpinNode  | Num Bases [5] | Left Index [2] | Right Index [6] | Norm Constant [1.000000000000000] // Hairpin node C34:A38
Interaction  | Interacting Bases [1,1] | Pair Probability [[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],[0.000000000,0.000000000,0.000000000,0.125000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C34
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.125000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.375000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.125000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.375000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C35
Interaction  | Interacting Bases [3,3] | Pair Probability [[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],[0.000000000,0.000000000,0.000000000,0.125000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C36
Interaction  | Interacting Bases [4,4] | Pair Probability [[0.375000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.125000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.125000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.375000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U37
Interaction  | Interacting Bases [5,5] | Pair Probability [[0.625000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.125000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.125000000,0.000000000,0.000000000],[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 A38
Sequences of instances from HL_93383.1:
> HL_93383.1  5K7D G   33 C   41
GCCCUAAGC
> HL_93383.1  6UFJ G   33 C   41
GCUCAAAGC