Alignment of HL_57052.2 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
2
I

6
2

3
7
1
I


In
acceptance
region


Cutoff
score

Full
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distance

Interior
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distance

Alignment
score
deficit
HL_57052.2_Instance_1 HL_57052.2_HL_6MSF_001_G6_C10GUCAC
HL_57052.2_Sequence_1 HL_57052.2_HL_6MSF_001_G6_C10GUCACtrue100000.00
HL_57052.2_Instance_2 HL_57052.2_HL_6MSF_005_G6_C10GUCAC
HL_57052.2_Sequence_2 HL_57052.2_HL_6MSF_005_G6_C10GUCACtrue100000.00
HL_57052.2_Instance_3 HL_57052.2_HL_6MSF_006_G6_C10GUCAC
HL_57052.2_Sequence_3 HL_57052.2_HL_6MSF_006_G6_C10GUCACtrue100000.00
HL_57052.2_Instance_4 HL_57052.2_HL_6MSF_002_G6_C10GUCAC
HL_57052.2_Sequence_4 HL_57052.2_HL_6MSF_002_G6_C10GUCACtrue100000.00
HL_57052.2_Instance_5 HL_57052.2_HL_4LFB_005_C201_G216CUUUG
HL_57052.2_Sequence_5 HL_57052.2_HL_4LFB_005_C201_G216CUUUGtrue78002.13
HL_57052.2_Instance_6 HL_57052.2_HL_4YAZ_004_C56_G60CCCUG
HL_57052.2_Sequence_6 HL_57052.2_HL_4YAZ_004_C56_G60CCCUGtrue76002.30
HL_57052.2_Instance_7 HL_57052.2_HL_4L8H_001_C9_G13CUAAG
HL_57052.2_Sequence_7 HL_57052.2_HL_4L8H_001_C9_G13CUAAGtrue86001.34

Conserved interactions between motif group positions in HL_57052.2:
1 2 s35 
1 3 cWW 
JAR3D SCFG/MRF model for HL_57052.2:
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 [3] // Initial node G6 - C10 from junction 
BasepairNode | Deletion Probability [0.0000000006203550] | Pair Probability [[0.009198317,0.018029257,0.010516857,0.190879051,0.000000000],[0.017597271,0.009167422,0.224007152,0.012870238,0.000000000],[0.010500105,0.234156059,0.001991844,0.024166688,0.000000000],[0.190528416,0.012938760,0.023717011,0.009735553,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.007039775,0.985568462,0.007039775,0.000351989] | Left Letter Distribution [0.055555556,0.166666667,0.055555556,0.722222222,0.000000000] | Right Length Distribution [0.007039775,0.985568462,0.007039775,0.000351989] | Right Letter Distribution [0.611111111,0.055555556,0.055555556,0.277777778,0.000000000] | Left Index [1] | Right Index [3] // Basepair G6 - C10 cWW 
HairpinNode  | Num Bases [1] | Left Index [2] | Right Index [2] | Norm Constant [1.000000000000000] // Hairpin node C8:C8
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.166666667,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.611111111,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.055555556,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.166666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C8
Sequences of instances from HL_57052.2:
> HL_57052.2 HL_6MSF_001 G    6 C   10
GUCAC
> HL_57052.2 HL_6MSF_005 G    6 C   10
GUCAC
> HL_57052.2 HL_6MSF_006 G    6 C   10
GUCAC
> HL_57052.2 HL_6MSF_002 G    6 C   10
GUCAC
> HL_57052.2 HL_4LFB_005 C  201 G  216
CUUUG
> HL_57052.2 HL_4YAZ_004 C   56 G   60
CCCUG
> HL_57052.2 HL_4L8H_001 C    9 G   13
CUAAG