Alignment of HL_02817.2 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
3

2
5
3
I

6
3

3
7
3
I

8
3

4
9
3
I

10
3

5
11
2
I

12
2

6
13
1
I


In
acceptance
region

Cutoff
score
Full
edit
distance
Interior
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distance
Alignment
score
deficit
HL_02817.2_Instance_1 HL_02817.2,HL_8SYK_002,C32_G39CCAAAUAG
HL_02817.2_Sequence_1 HL_02817.28SYK_C32_G39CCAAAUAGtrue100000.00
HL_02817.2_Instance_2 HL_02817.2,HL_2OEU_002,C25_G32CCAAAUAG
HL_02817.2_Sequence_2 HL_02817.22OEU_C25_G32CCAAAUAGtrue100000.00
HL_02817.2_Instance_3 HL_02817.2,HL_5BTP_003,G28_C35GAAUUAAC
HL_02817.2_Sequence_3 HL_02817.25BTP_G28_C35GAAUUAACtrue81002.25

Conserved interactions between motif group positions in HL_02817.2:
1 2 s35 
1 6 cWW 
2 3 s35 
2 6 s55 
4 5 s35
JAR3D SCFG/MRF model for HL_02817.2:
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 [6] // Initial node
BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.009509057,0.017981890,0.010896842,0.197694967,0.000000000],[0.019030193,0.009563019,0.224400354,0.013489511,0.000000000],[0.010937493,0.212742702,0.002069309,0.024327358,0.000000000],[0.198545855,0.013323228,0.025418591,0.010069631,0.000000000],[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 C32 - G39 cWW 
HairpinNode  | Num Bases [4] | Left Index [2] | Right Index [5] | Norm Constant [1.000000000000000] // Hairpin node C33:A38
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.300000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.500000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.100000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.100000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C33
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.700000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.100000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.100000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A34
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.300000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.100000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.500000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U37
Interaction  | Interacting Bases [4,4] | Pair Probability [[0.700000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.100000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.100000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A38
Insertion    | Location [2] | Length Distribution [0.000000000,0.016116035,0.966962127,0.016116035,0.000805802] | Letter Distribution [0.562500000,0.062500000,0.062500000,0.312500000,0.000000000]// Insertion in Hairpin after nucleotide 3, position 2
Sequences of instances from HL_02817.2:
> HL_02817.2  8SYK C   32 G   39
CCAAAUAG
> HL_02817.2  2OEU C   25 G   32
CCAAAUAG
> HL_02817.2  5BTP G   28 C   35
GAAUUAAC