Alignment of HL_96776.2 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
5

2
5
5
I

6
6

3
7
5
I

8
5

4
9
4
I

10
3

5
11
2
I

12
2

6
13
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
HL_96776.2_Instance_1 HL_96776.2_HL_4WF9_007_A228_U233AAAAUU
HL_96776.2_Sequence_1 HL_96776.2_HL_4WF9_007_A228_U233AAAAUUtrue100000.00
HL_96776.2_Instance_2 HL_96776.2_HL_5TBW_002_C69_G74CAACCG
HL_96776.2_Sequence_2 HL_96776.2_HL_5TBW_002_C69_G74CAACCGtrue97000.28
HL_96776.2_Instance_3 HL_96776.2_HL_4V88_189_C190_G195CCUUUG
HL_96776.2_Sequence_3 HL_96776.2_HL_4V88_189_C190_G195CCUUUGtrue96000.39

Conserved interactions between motif group positions in HL_96776.2:
1 2 s35 
1 6 cWW 
2 3 s35 
2 4 cSW 
4 6 s35 
JAR3D SCFG/MRF model for HL_96776.2:
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 A228 - U233 from junction 
BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.009360260,0.018555845,0.010510723,0.208326134,0.000000000],[0.019169057,0.009574703,0.221475475,0.012523923,0.000000000],[0.010585638,0.198991965,0.002053422,0.033057966,0.000000000],[0.197647789,0.012412375,0.025270620,0.010484105,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [6] // Basepair A228 - U233 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.100000000,0.300000000,0.100000000,0.500000000,0.000000000] | Position [2] | Left Index [2] | Right Index [5] // Fixed node on right
InitialNode  | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [4] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.091501253,0.108423963,0.020384970,0.077338991,0.000000000],[0.077411456,0.092811797,0.002352171,0.097488279,0.000000000],[0.078964272,0.002352171,0.022281808,0.069399138,0.000000000],[0.078895507,0.094378085,0.009774210,0.076241928,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [4] // Basepair A229 - A231 cSW 
HairpinNode  | Num Bases [1] | Left Index [3] | Right Index [3] | Norm Constant [1.000000000000000] // Hairpin node A230:A230
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.500000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.100000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.300000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A230
Sequences of instances from HL_96776.2:
> HL_96776.2 HL_4WF9_007 A  228 U  233
AAAAUU
> HL_96776.2 HL_5TBW_002 C   69 G   74
CAACCG
> HL_96776.2 HL_4V88_189 C  190 G  195
CCUUUG