Alignment of HL_26055.5 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
3
I

12
3

6
13
2
I

14
2

7
15
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
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distance

Alignment
score
deficit
HL_26055.5_Instance_1 HL_26055.5_HL_4FEN_002_G46_C53GUUUCUAC
HL_26055.5_Sequence_1 HL_26055.5_HL_4FEN_002_G46_C53GUUUCUACtrue100000.00
HL_26055.5_Instance_2 HL_26055.5_HL_1Y27_002_G46_C53GUUUCUAC
HL_26055.5_Sequence_2 HL_26055.5_HL_1Y27_002_G46_C53GUUUCUACtrue100000.00
HL_26055.5_Instance_3 HL_26055.5_HL_1Y26_002_G46_C53GUUUCUAC
HL_26055.5_Sequence_3 HL_26055.5_HL_1Y26_002_G46_C53GUUUCUACtrue100000.00
HL_26055.5_Instance_4 HL_26055.5_HL_4XNR_002_G46_C53GUUUCUAC
HL_26055.5_Sequence_4 HL_26055.5_HL_4XNR_002_G46_C53GUUUCUACtrue100000.00
HL_26055.5_Instance_5 HL_26055.5_HL_4LX6_002_G46_C53GCUUCCAC
HL_26055.5_Sequence_5 HL_26055.5_HL_4LX6_002_G46_C53GCUUCCACtrue84001.60
HL_26055.5_Instance_6 HL_26055.5_HL_3LA5_002_G46_C53GCUUCCAC
HL_26055.5_Sequence_6 HL_26055.5_HL_3LA5_002_G46_C53GCUUCCACtrue84001.60
HL_26055.5_Instance_7 HL_26055.5_HL_3AL0_002_A31_U39ACUCUGGAU
HL_26055.5_Sequence_7 HL_26055.5_HL_3AL0_002_A31_U39ACUCUGGAUtrue24007.85
HL_26055.5_Instance_8 HL_26055.5_HL_4LFB_002_G80_C89GUUUUAC
HL_26055.5_Sequence_8 HL_26055.5_HL_4LFB_002_G80_C89GUUUUACtrue97000.33
HL_26055.5_Instance_9 HL_26055.5_HL_2GDI_001_C27_G33CUGCGUG
HL_26055.5_Sequence_9 HL_26055.5_HL_2GDI_001_C27_G33CUGCGUGtrue61004.06
HL_26055.5_Instance_10 HL_26055.5_HL_4LFB_014_G617_C623GCUCAAC
HL_26055.5_Sequence_10 HL_26055.5_HL_4LFB_014_G617_C623GCUCAACtrue91000.95
HL_26055.5_Instance_11 HL_26055.5_HL_6CZR_085_G601_C607GCUCAAC
HL_26055.5_Sequence_11 HL_26055.5_HL_6CZR_085_G601_C607GCUCAACtrue91000.95
HL_26055.5_Instance_12 HL_26055.5_HL_5J7L_014_G617_C623GCUCAAC
HL_26055.5_Sequence_12 HL_26055.5_HL_5J7L_014_G617_C623GCUCAACtrue91000.95
HL_26055.5_Instance_13 HL_26055.5_HL_7A0S_061_C2530_G2536CUGUUCG
HL_26055.5_Sequence_13 HL_26055.5_HL_7A0S_061_C_2530_G_2536CUGUUCGtrue74002.64
HL_26055.5_Instance_14 HL_26055.5_HL_4WF9_058_C2578_G2584CUGUUCG
HL_26055.5_Sequence_14 HL_26055.5_HL_4WF9_058_C_2578_G_2584CUGUUCGtrue74002.64
HL_26055.5_Instance_15 HL_26055.5_HL_5TBW_063_U2920_A2926UUGUUCA
HL_26055.5_Sequence_15 HL_26055.5_HL_5TBW_063_U_2920_A_2926UUGUUCAtrue73002.74

Conserved interactions between motif group positions in HL_26055.5:
1 2 s35 
1 7 cWW 
3 4 s35 
4 5 s35 
5 6 s35 
6 7 s35 
JAR3D SCFG/MRF model for HL_26055.5:
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 [7] // Initial node G46 - C53 from junction 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.008530388,0.017359359,0.009671116,0.186678966,0.000000000],[0.016046005,0.008514709,0.206336649,0.011566840,0.000000000],[0.009620172,0.269648411,0.001847676,0.024498429,0.000000000],[0.185613341,0.011775168,0.023133583,0.009159189,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [7] // Basepair G46 - C53 cWW 
HairpinNode  | Num Bases [5] | Left Index [2] | Right Index [6] | Norm Constant [1.000000000000000] // Hairpin node U47:A52
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.029411765,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.382352941,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.029411765,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.558823529,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U47
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.029411765,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.088235294,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.264705882,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.617647059,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U49
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.029411765,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.617647059,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.029411765,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.323529412,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C50
Interaction  | Interacting Bases [4,4] | Pair Probability [[0.205882353,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.147058824,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.147058824,0.000000000,0.000000000],[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 U51
Interaction  | Interacting Bases [5,5] | Pair Probability [[0.676470588,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.205882353,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.029411765,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.088235294,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A52
Insertion    | Location [1] | Length Distribution [0.532198331,0.466088110,0.001636173,0.000077387] | Letter Distribution [0.055555556,0.055555556,0.055555556,0.833333333,0.000000000]// Insertion in Hairpin after nucleotide 2, position 1
Insertion    | Location [4] | Length Distribution [0.930093541,0.069519013,0.000376377,0.000011070] | Letter Distribution [0.166666667,0.166666667,0.500000000,0.166666667,0.000000000]// Insertion in Hairpin after nucleotide 5, position 4
Sequences of instances from HL_26055.5:
> HL_26055.5 HL_4FEN_002 G   46 C   53
GUUUCUAC
> HL_26055.5 HL_1Y27_002 G   46 C   53
GUUUCUAC
> HL_26055.5 HL_1Y26_002 G   46 C   53
GUUUCUAC
> HL_26055.5 HL_4XNR_002 G   46 C   53
GUUUCUAC
> HL_26055.5 HL_4LX6_002 G   46 C   53
GCUUCCAC
> HL_26055.5 HL_3LA5_002 G   46 C   53
GCUUCCAC
> HL_26055.5 HL_3AL0_002 A   31 U   39
ACUCUGGAU
> HL_26055.5 HL_4LFB_002 G   80 C   89
GUUUUAC
> HL_26055.5 HL_2GDI_001 C   27 G   33
CUGCGUG
> HL_26055.5 HL_4LFB_014 G  617 C  623
GCUCAAC
> HL_26055.5 HL_6CZR_085 G  601 C  607
GCUCAAC
> HL_26055.5 HL_5J7L_014 G  617 C  623
GCUCAAC
> HL_26055.5 HL_7A0S_061 C 2530 G 2536
CUGUUCG
> HL_26055.5 HL_4WF9_058 C 2578 G 2584
CUGUUCG
> HL_26055.5 HL_5TBW_063 U 2920 A 2926
UUGUUCA