Alignment of HL_31286.3 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
4
I

12
4

6
13
4
I

14
4

7
15
3
I

16
3

8
17
2
I

18
2

9
19
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
HL_31286.3_Instance_1 HL_31286.3_HL_5TPY_011_U28_G38UUUGGGGAAAG
HL_31286.3_Sequence_1 HL_31286.3_HL_5TPY_011_U28_G38UUUGGGGAAAGtrue100000.00
HL_31286.3_Instance_2 HL_31286.3_HL_5TPY_008_U28_G38UUUGGGGAAAG
HL_31286.3_Sequence_2 HL_31286.3_HL_5TPY_008_U28_G38UUUGGGGAAAGtrue100000.00
HL_31286.3_Instance_3 HL_31286.3_HL_5TPY_002_U28_G38UUUGGGGAAAG
HL_31286.3_Sequence_3 HL_31286.3_HL_5TPY_002_U28_G38UUUGGGGAAAGtrue100000.00
HL_31286.3_Instance_4 HL_31286.3_HL_5TPY_005_U28_G38UUUGGGGAAAG
HL_31286.3_Sequence_4 HL_31286.3_HL_5TPY_005_U28_G38UUUGGGGAAAGtrue100000.00
HL_31286.3_Instance_5 HL_31286.3_HL_6VMY_005_U333_A342UCUGCGAGGA
HL_31286.3_Sequence_5 HL_31286.3_HL_6VMY_005_U333_A342UCUGCGAGGAtrue69006.16
HL_31286.3_Instance_6 HL_31286.3_HL_4V83_139_A6160_U6169AUUAAGUGGU
HL_31286.3_Sequence_6 HL_31286.3_HL_4V83_139_A_6160_U_6169AUUAAGUGGUtrue71005.68
HL_31286.3_Instance_7 HL_31286.3_HL_3MJA_001_A6184_U6193AUUAGGUAGU
HL_31286.3_Sequence_7 HL_31286.3_HL_3MJA_001_A_6184_U_6193AUUAGGUAGUtrue82003.60

Conserved interactions between motif group positions in HL_31286.3:
1 2 s35 
1 9 cWW 
2 7 s33 
2 8 tWH 
2 9 s55 
3 4 s35 
4 5 s35 
5 6 s35 
6 7 s35 
7 8 s35 
8 9 s35 
JAR3D SCFG/MRF model for HL_31286.3:
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 [9] // Initial node U28 - G38 from junction 
BasepairNode | Deletion Probability [0.0000011637255024] | Pair Probability [[0.009884709,0.016001571,0.011827262,0.121324816,0.000000000],[0.172573773,0.019173708,0.102780333,0.013059692,0.000000000],[0.011994903,0.100274326,0.002635269,0.025624353,0.000000000],[0.137525817,0.012412607,0.231003262,0.011903598,0.000000000],[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 [0.427699602,0.567912443,0.004186211,0.000201745] | Right Letter Distribution [0.750000000,0.083333333,0.083333333,0.083333333,0.000000000] | Left Index [1] | Right Index [9] // Basepair U28 - G38 cWW 
BasepairNode | Deletion Probability [0.0000001232089072] | Pair Probability [[0.016649528,0.003684567,0.017293259,0.003684567,0.000000000],[0.037053177,0.296905697,0.034764767,0.003684567,0.000000000],[0.003684567,0.008832151,0.028020822,0.016387686,0.000000000],[0.405839888,0.003684567,0.083537816,0.036292374,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.007039775,0.985568462,0.007039775,0.000351989] | Left Letter Distribution [0.055555556,0.055555556,0.055555556,0.833333333,0.000000000] | 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 [8] // Basepair U29 - A36 tWH 
HairpinNode  | Num Bases [5] | Left Index [3] | Right Index [7] | Norm Constant [1.000000000000000] // Hairpin node G31:A35
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.277777778,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.055555556,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.611111111,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.055555556,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G31
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.166666667,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.166666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.611111111,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.055555556,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G32
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.055555556,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.055555556,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.833333333,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.055555556,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G33
Interaction  | Interacting Bases [4,4] | Pair Probability [[0.166666667,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.055555556,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.500000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.277777778,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G34
Interaction  | Interacting Bases [5,5] | Pair Probability [[0.611111111,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.055555556,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.277777778,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.055555556,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A35
Sequences of instances from HL_31286.3:
> HL_31286.3 HL_5TPY_011 U   28 G   38
UUUGGGGAAAG
> HL_31286.3 HL_5TPY_008 U   28 G   38
UUUGGGGAAAG
> HL_31286.3 HL_5TPY_002 U   28 G   38
UUUGGGGAAAG
> HL_31286.3 HL_5TPY_005 U   28 G   38
UUUGGGGAAAG
> HL_31286.3 HL_6VMY_005 U  333 A  342
UCUGCGAGGA
> HL_31286.3 HL_4V83_139 A 6160 U 6169
AUUAAGUGGU
> HL_31286.3 HL_3MJA_001 A 6184 U 6193
AUUAGGUAGU