Alignment of HL_32527.2 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
4

3
7
3
I

8
3

4
9
2
I

10
2

5
11
1
I


In
acceptance
region


Cutoff
score

Full
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distance

Interior
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distance

Alignment
score
deficit
HL_32527.2_Instance_1 HL_32527.2_HL_3OXE_002_G49_C54GGAAAC
HL_32527.2_Sequence_1 HL_32527.2_HL_3OXE_002_G49_C54GGAAACtrue100000.00
HL_32527.2_Instance_2 HL_32527.2_HL_5J7L_179_C1806_G1811CGAAAG
HL_32527.2_Sequence_2 HL_32527.2_HL_5J7L_179_C_1806_G_1811CGAAAGtrue99000.05
HL_32527.2_Instance_3 HL_32527.2_HL_3IGI_004_G135_C141GGAACAC
HL_32527.2_Sequence_3 HL_32527.2_HL_3IGI_004_G135_C141GGAACACtrue83001.60

Conserved interactions between motif group positions in HL_32527.2:
1 2 s35 
1 5 cWW 
2 4 tSH 
2 5 s55 
3 4 s35 
4 5 s35 
2 4 6BPh
3 2 7BR
JAR3D SCFG/MRF model for HL_32527.2:
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 [5] // Initial node G49 - C54 from junction 
BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.009574124,0.019028436,0.010936653,0.198530575,0.000000000],[0.017980846,0.009507606,0.212727929,0.013322270,0.000000000],[0.010896029,0.224384255,0.002069153,0.025416337,0.000000000],[0.197680266,0.013488440,0.024325847,0.010131233,0.000000000],[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 [5] // Basepair G49 - C54 cWW 
BasepairNode | Deletion Probability [0.0000000205233307] | Pair Probability [[0.043273743,0.045811089,0.000519472,0.002448275,0.000000000],[0.043595236,0.045705009,0.000519472,0.000519472,0.000000000],[0.392756919,0.003636307,0.017776750,0.308635994,0.000000000],[0.048305054,0.045458262,0.000519472,0.000519472,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.010744024,0.650013430,0.333064733,0.005909213,0.000268601] | Left Letter Distribution [0.750000000,0.083333333,0.083333333,0.083333333,0.000000000] | 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 G50 - A53 tSH 
HairpinNode  | Num Bases [1] | Left Index [3] | Right Index [3] | Norm Constant [1.000000000000000] // Hairpin node A52:A52
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.617647059,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.323529412,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.029411765,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.029411765,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A52
Sequences of instances from HL_32527.2:
> HL_32527.2 HL_3OXE_002 G   49 C   54
GGAAAC
> HL_32527.2 HL_5J7L_179 C 1806 G 1811
CGAAAG
> HL_32527.2 HL_3IGI_004 G  135 C  141
GGAACAC