Alignment of HL_88858.1 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
4
I

8
4

4
9
3
I

10
3

5
11
2
I

12
2

6
13
1
I


In
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region


Cutoff
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Full
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Interior
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Alignment
score
deficit
HL_88858.1_Instance_1 HL_88858.1_HL_1QU2_002_C31_G39CCUGAUAAG
HL_88858.1_Sequence_1 HL_88858.1_HL_1QU2_002_C31_G39CCUGAUAAGtrue100000.00

Conserved interactions between motif group positions in HL_88858.1:
1 2 s35 
1 6 cWW 
2 3 s35 
2 5 bif 
2 6 s55 
3 4 tSW 
4 5 s55 
5 6 s35 
JAR3D SCFG/MRF model for HL_88858.1:
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 [6] // Initial node C31 - G39 from junction 
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.009631000,0.017270697,0.011072020,0.200757565,0.000000000],[0.020477154,0.009808895,0.220945507,0.013927182,0.000000000],[0.011196362,0.205083350,0.002110445,0.023698544,0.000000000],[0.203360186,0.013418572,0.027036311,0.010206209,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [6] // Basepair C31 - G39 cWW 
BasepairNode | Deletion Probability [0.0000001156129129] | Pair Probability [[0.028776211,0.032326394,0.007021393,0.007021393,0.000000000],[0.712040258,0.082230039,0.007021393,0.007021393,0.000000000],[0.007021393,0.007021393,0.029462996,0.044950176,0.000000000],[0.007021393,0.007021393,0.007021393,0.007021393,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.045351474,0.907029478,0.045351474,0.002267574] | Right Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000] | Left Index [2] | Right Index [5] // Basepair C32 - A38 bif 
HairpinNode  | Num Bases [2] | Left Index [3] | Right Index [4] | Norm Constant [1.000000000000000] // Hairpin node U33:U36
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.014980202,0.012933711,0.002677206,0.256666304,0.000000000],[0.013068415,0.016073618,0.002677206,0.215382956,0.000000000],[0.012856130,0.002677206,0.002677206,0.013201594,0.000000000],[0.012480760,0.031277223,0.112748680,0.277621583,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin Interaction U33 - U36 tSW 
Insertion    | Location [1] | Length Distribution [0.000000000,0.045351474,0.907029478,0.045351474,0.002267574] | Letter Distribution [0.375000000,0.125000000,0.375000000,0.125000000,0.000000000]// Insertion in Hairpin after nucleotide 3, position 1
Sequences of instances from HL_88858.1:
> HL_88858.1 HL_1QU2_002 C   31 G   39
CCUGAUAAG