Alignment of HL_05123.1 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_05123.1_Instance_1 HL_05123.1_HL_3SUX_001_A38_U47ACGGGGAGUU
HL_05123.1_Sequence_1 HL_05123.1_HL_3SUX_001_A38_U47ACGGGGAGUUtrue94000.91
HL_05123.1_Instance_2 HL_05123.1_HL_3SUX_003_A38_U47ACGGGGAGUU
HL_05123.1_Sequence_2 HL_05123.1_HL_3SUX_003_A38_U47ACGGGGAGUUtrue94000.91
HL_05123.1_Instance_3 HL_05123.1_HL_3D0U_002_U90_G98UUCCUCCCG
HL_05123.1_Sequence_3 HL_05123.1_HL_3D0U_002_U90_G98UUCCUCCCGtrue100000.00
HL_05123.1_Instance_4 HL_05123.1_HL_3DIL_002_U93_G101UUCCUCCCG
HL_05123.1_Sequence_4 HL_05123.1_HL_3DIL_002_U93_G101UUCCUCCCGtrue100000.00

Conserved interactions between motif group positions in HL_05123.1:
1 2 s35 
1 9 cWW 
2 3 perp 
2 4 perp 
2 8 cWW 
3 4 s35 
4 5 s35 
5 6 s35 
6 7 s35 
7 8 s35 
8 9 s35 
JAR3D SCFG/MRF model for HL_05123.1:
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 A38 - U47 from junction 
BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.010067142,0.017651156,0.011863367,0.137604595,0.000000000],[0.156950697,0.018404626,0.115985813,0.012942707,0.000000000],[0.012007182,0.114656057,0.002622233,0.033290147,0.000000000],[0.138394599,0.012606469,0.192644198,0.012309012,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [9] // Basepair A38 - U47 cWW 
BasepairNode | Deletion Probability [0.0000016375373120] | Pair Probability [[0.014682862,0.013410453,0.039224619,0.016885792,0.000000000],[0.014715495,0.011531794,0.021957090,0.351955909,0.000000000],[0.041444021,0.021155234,0.003327251,0.014772849,0.000000000],[0.017976843,0.388991313,0.016136481,0.011831996,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.496627836,0.496627836,0.006437768,0.000306560] | Left Letter Distribution [0.125000000,0.125000000,0.625000000,0.125000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [8] // Basepair C39 - U46 cWW 
HairpinNode  | Num Bases [5] | Left Index [3] | Right Index [7] | Norm Constant [1.000000000000000] // Hairpin node G41:G45
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.083333333,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.416666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.416666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.083333333,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G41
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.083333333,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.416666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.416666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.083333333,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G42
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.083333333,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.083333333,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.416666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.416666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G43
Interaction  | Interacting Bases [4,4] | Pair Probability [[0.416666667,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.416666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.083333333,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.083333333,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A44
Interaction  | Interacting Bases [5,5] | Pair Probability [[0.083333333,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.416666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.416666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.083333333,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G45
Sequences of instances from HL_05123.1:
> HL_05123.1 HL_3SUX_001 A   38 U   47
ACGGGGAGUU
> HL_05123.1 HL_3SUX_003 A   38 U   47
ACGGGGAGUU
> HL_05123.1 HL_3D0U_002 U   90 G   98
UUCCUCCCG
> HL_05123.1 HL_3DIL_002 U   93 G  101
UUCCUCCCG