Alignment of HL_24323.1 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
4
I

10
4

5
11
4
I

12
4

6
13
4
I

14
4

7
15
4
I

16
4

8
17
3
I

18
3

9
19
2
I

20
2

10
21
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
HL_24323.1_Instance_1 HL_24323.1_HL_387D_001_G4_C13GAAGUGCAAC
HL_24323.1_Sequence_1 HL_24323.1_HL_387D_001_G4_C13GAAGUGCAACtrue100000.00
HL_24323.1_Instance_2 HL_24323.1_HL_1F27_001_U7_A16UCAGAGGACA
HL_24323.1_Sequence_2 HL_24323.1_HL_1F27_001_U7_A16UCAGAGGACAtrue93001.18

Conserved interactions between motif group positions in HL_24323.1:
1 2 s33 
1 10 cWW 
2 3 s55 
2 9 tWW 
4 5 s35 
5 6 s35 
6 7 s35 
7 8 s35 
8 9 s35 
9 10 s35 
JAR3D SCFG/MRF model for HL_24323.1:
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 [10] // Initial node G4 - C13 from junction 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.009384013,0.018908278,0.010497082,0.198820958,0.000000000],[0.019570724,0.009688269,0.200004160,0.012164451,0.000000000],[0.010445199,0.211498280,0.002066765,0.024906359,0.000000000],[0.211388534,0.012081037,0.038377715,0.010198176,0.000000000],[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 [1] | Right Index [10] // Basepair G4 - C13 cWW 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.363526285,0.027282089,0.003537224,0.016909156,0.000000000],[0.026574928,0.111825161,0.010534521,0.012904051,0.000000000],[0.003537224,0.010549675,0.327097016,0.019935448,0.000000000],[0.016888989,0.012900902,0.019504029,0.016493303,0.000000000],[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 A5 - A12 tWW 
HairpinNode  | Num Bases [6] | Left Index [3] | Right Index [8] | Norm Constant [1.000000000000000] // Hairpin node A6:A11
Interaction  | Interacting Bases [1,1] | 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 A6
Interaction  | Interacting Bases [2,2] | 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 G7
Interaction  | Interacting Bases [3,3] | 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 U8
Interaction  | Interacting Bases [4,4] | 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 G9
Interaction  | Interacting Bases [5,5] | Pair Probability [[0.125000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.375000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.375000000,0.000000000,0.000000000],[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 C10
Interaction  | Interacting Bases [6,6] | 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 A11
Sequences of instances from HL_24323.1:
> HL_24323.1 HL_387D_001 G    4 C   13
GAAGUGCAAC
> HL_24323.1 HL_1F27_001 U    7 A   16
UCAGAGGACA