Alignment of HL_82678.2 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_82678.2_Instance_1 HL_82678.2_HL_6D12_001_C309_G315CAUGUGG
HL_82678.2_Sequence_1 HL_82678.2_HL_6D12_001_C309_G315CAUGUGGtrue88001.15
HL_82678.2_Instance_2 HL_82678.2_HL_6D12_002_C328_G334CAUGUGG
HL_82678.2_Sequence_2 HL_82678.2_HL_6D12_002_C328_G334CAUGUGGtrue88001.15
HL_82678.2_Instance_3 HL_82678.2_HL_2Y9H_007_C11_G16CGCGUG
HL_82678.2_Sequence_3 HL_82678.2_HL_2Y9H_007_C11_G16CGCGUGtrue86001.30
HL_82678.2_Instance_4 HL_82678.2_HL_4V88_216_C1359_G1364CAUUUG
HL_82678.2_Sequence_4 HL_82678.2_HL_4V88_216_C_1359_G_1364CAUUUGtrue100000.00
HL_82678.2_Instance_5 HL_82678.2_HL_2QUS_003_C42_G47CGUGAG
HL_82678.2_Sequence_5 HL_82678.2_HL_2QUS_003_C42_G47CGUGAGtrue100000.00
HL_82678.2_Instance_6 HL_82678.2_HL_2QUW_003_C42_G47CGUGAG
HL_82678.2_Sequence_6 HL_82678.2_HL_2QUW_003_C42_G47CGUGAGtrue100000.00

Conserved interactions between motif group positions in HL_82678.2:
1 2 s35 
1 6 cWW 
2 3 s35 
2 6 s55 
JAR3D SCFG/MRF model for HL_82678.2:
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 [6] // Initial node C309 - G315 from junction 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.009176708,0.016456041,0.010549755,0.191287868,0.000000000],[0.019511251,0.009346211,0.257693361,0.013270239,0.000000000],[0.010668232,0.195409608,0.002010896,0.022580688,0.000000000],[0.193767724,0.012785620,0.025761014,0.009724784,0.000000000],[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 [6] // Basepair C309 - G315 cWW 
HairpinNode  | Num Bases [4] | Left Index [2] | Right Index [5] | Norm Constant [1.000000000000000] // Hairpin node A310:G314
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.437500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.062500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.437500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.062500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A310
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.062500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.187500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.062500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.687500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U311
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.062500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.062500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.437500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.437500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U313
Interaction  | Interacting Bases [4,4] | Pair Probability [[0.312500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.062500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.312500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.312500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G314
Insertion    | Location [2] | Length Distribution [0.661815186,0.335026775,0.003020733,0.000137306] | Letter Distribution [0.125000000,0.125000000,0.625000000,0.125000000,0.000000000]// Insertion in Hairpin after nucleotide 3, position 2
Sequences of instances from HL_82678.2:
> HL_82678.2 HL_6D12_001 C  309 G  315
CAUGUGG
> HL_82678.2 HL_6D12_002 C  328 G  334
CAUGUGG
> HL_82678.2 HL_2Y9H_007 C   11 G   16
CGCGUG
> HL_82678.2 HL_4V88_216 C 1359 G 1364
CAUUUG
> HL_82678.2 HL_2QUS_003 C   42 G   47
CGUGAG
> HL_82678.2 HL_2QUW_003 C   42 G   47
CGUGAG