Alignment of HL_68493.4 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
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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Alignment
score
deficit
HL_68493.4_Instance_1 HL_68493.4_HL_5DH6_002_C27_G34CUGGGAUG
HL_68493.4_Sequence_1 HL_68493.4_HL_5DH6_002_C27_G34CUGGGAUGtrue92000.89
HL_68493.4_Instance_2 HL_68493.4_HL_5J7L_142_C305_G312CUGGAAAG
HL_68493.4_Sequence_2 HL_68493.4_HL_5J7L_142_C305_G312CUGGAAAGtrue100000.00
HL_68493.4_Instance_3 HL_68493.4_HL_4V9F_010_U312_A319UUGGAAUA
HL_68493.4_Sequence_3 HL_68493.4_HL_4V9F_010_U312_A319UUGGAAUAtrue99000.17
HL_68493.4_Instance_4 HL_68493.4_HL_7A0S_010_C316_G323CUGGAAAG
HL_68493.4_Sequence_4 HL_68493.4_HL_7A0S_010_C316_G323CUGGAAAGtrue100000.00
HL_68493.4_Instance_5 HL_68493.4_HL_5TBW_005_U194_A201UUGGAACA
HL_68493.4_Sequence_5 HL_68493.4_HL_5TBW_005_U194_A201UUGGAACAtrue89001.27
HL_68493.4_Instance_6 HL_68493.4_HL_4Y4O_112_U305_G312UUGGGAAG
HL_68493.4_Sequence_6 HL_68493.4_HL_4Y4O_112_U305_G312UUGGGAAGtrue81002.18
HL_68493.4_Instance_7 HL_68493.4_HL_2A64_002_C69_G76CUGAGAUG
HL_68493.4_Sequence_7 HL_68493.4_HL_2A64_002_C69_G76CUGAGAUGtrue85001.77
HL_68493.4_Instance_8 HL_68493.4_HL_4V88_191_G243_C250GAUGAUUC
HL_68493.4_Sequence_8 HL_68493.4_HL_4V88_191_G243_C250GAUGAUUCtrue70003.47
HL_68493.4_Instance_9 HL_68493.4_HL_2GDI_002_G66_C73GAUAAUGC
HL_68493.4_Sequence_9 HL_68493.4_HL_2GDI_002_G66_C73GAUAAUGCtrue53005.45
HL_68493.4_Instance_10 HL_68493.4_HL_4WF9_010_C348_G355CUGGAAAG
HL_68493.4_Sequence_10 HL_68493.4_HL_4WF9_010_C348_G355CUGGAAAGtrue100000.00
HL_68493.4_Instance_11 HL_68493.4_HL_4V9F_039_C1594_G1600CGUAAUG
HL_68493.4_Sequence_11 HL_68493.4_HL_4V9F_039_C_1594_G_1600CGUAAUGtrue52005.63

Conserved interactions between motif group positions in HL_68493.4:
1 2 s35 
1 7 cWW 
2 3 s35 
2 6 tWH 
2 7 s55 
3 6 s55 
4 5 s35 
6 7 s35 
3 6 6BPh
JAR3D SCFG/MRF model for HL_68493.4:
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 C27 - G34 from junction 
BasepairNode | Deletion Probability [0.0000001988889326] | Pair Probability [[0.008855177,0.016058137,0.010195552,0.169189225,0.000000000],[0.041976169,0.010440606,0.229168546,0.012316502,0.000000000],[0.010266039,0.190301874,0.002014248,0.021310121,0.000000000],[0.193508978,0.011923006,0.062870450,0.009605372,0.000000000],[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 [0.094202453,0.901476521,0.004116238,0.000204788] | Right Letter Distribution [0.375000000,0.125000000,0.125000000,0.375000000,0.000000000] | Left Index [1] | Right Index [7] // Basepair C27 - G34 cWW 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.016629649,0.003680168,0.017272612,0.043406641,0.000000000],[0.037008937,0.296551202,0.003680168,0.003680168,0.000000000],[0.003680168,0.008821605,0.027987366,0.036231356,0.000000000],[0.440088858,0.003680168,0.021351893,0.036249042,0.000000000],[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 [2] | Right Index [6] // Basepair U28 - A32 tWH 
HairpinNode  | Num Bases [3] | Left Index [3] | Right Index [5] | Norm Constant [1.000000000000000] // Hairpin node G29:G31
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.006329114,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.006329114,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.715189873,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.272151899,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G29
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.269230769,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.038461538,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.653846154,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.038461538,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G30
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.653846154,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.038461538,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.269230769,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.038461538,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G31
Sequences of instances from HL_68493.4:
> HL_68493.4 HL_5DH6_002 C   27 G   34
CUGGGAUG
> HL_68493.4 HL_5J7L_142 C  305 G  312
CUGGAAAG
> HL_68493.4 HL_4V9F_010 U  312 A  319
UUGGAAUA
> HL_68493.4 HL_7A0S_010 C  316 G  323
CUGGAAAG
> HL_68493.4 HL_5TBW_005 U  194 A  201
UUGGAACA
> HL_68493.4 HL_4Y4O_112 U  305 G  312
UUGGGAAG
> HL_68493.4 HL_2A64_002 C   69 G   76
CUGAGAUG
> HL_68493.4 HL_4V88_191 G  243 C  250
GAUGAUUC
> HL_68493.4 HL_2GDI_002 G   66 C   73
GAUAAUGC
> HL_68493.4 HL_4WF9_010 C  348 G  355
CUGGAAAG
> HL_68493.4 HL_4V9F_039 C 1594 G 1600
CGUAAUG