Alignment of IL_09333.1 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
5

4
9
5
I

10
6

5
11
6
I

12
7

6
13
7
I

14
8


15
7
I

16
7

7
17
6
I

18
6

8
19
5
I

20
5

9
21
4
I

22
4

10
23
3
I

24
3

11
25
2
I

26
2

12
27
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
IL_09333.1_Instance_1 IL_09333.1_IL_1FJG_009_G148_C174GACAACGCUAAUC
IL_09333.1_Sequence_1 IL_09333.1_IL_1FJG_009_G148_C174GACAAC*GCUAAUCtrue100000.00

Conserved interactions between motif group positions in IL_09333.1:
1 2 s35 
1 12 cWW 
2 3 s35 
2 11 tWH 
3 4 s35 
3 9 s33 
3 10 tWH 
4 5 s35 
4 9 tHW 
4 10 s55 
5 6 s35 
5 8 tHW 
5 9 s55 
6 7 cWW 
7 8 s35 
8 9 s35 
10 11 s35 
11 12 s35 
6 5 7BPh
JAR3D SCFG/MRF model for IL_09333.1:
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 [12] // Initial node G148 - C174 from junction 
BasepairNode | Deletion Probability [0.0000001156129129] | Pair Probability [[0.010296034,0.020975088,0.011921277,0.195390483,0.000000000],[0.017372323,0.008489812,0.210445347,0.013394761,0.000000000],[0.011771213,0.226979836,0.002170788,0.027844024,0.000000000],[0.194262192,0.014060602,0.024018461,0.010607760,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.045351474,0.907029478,0.045351474,0.002267574] | Right Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000] | Left Index [1] | Right Index [12] // Basepair G148 - C174 cWW 
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.412383664,0.004024827,0.345135019,0.004024827,0.000000000],[0.031775430,0.014785615,0.023038949,0.004024827,0.000000000],[0.004024827,0.004024827,0.049855435,0.035912298,0.000000000],[0.019191112,0.004024827,0.023827214,0.019946303,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [11] // Basepair A149 - A172 tWH 
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.020051501,0.002539818,0.142297221,0.002539818,0.000000000],[0.263882817,0.012018367,0.235478309,0.002539818,0.000000000],[0.002539818,0.002539818,0.017348636,0.026230988,0.000000000],[0.025227938,0.002539818,0.012157548,0.230067766,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [10] // Basepair C150 - A171 tWH 
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.026228946,0.054639536,0.005500826,0.559983562,0.000000000],[0.005500826,0.045670107,0.005500826,0.005500826,0.000000000],[0.026982756,0.036513624,0.064376936,0.067861159,0.000000000],[0.005500826,0.005500826,0.025659745,0.059078674,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [9] // Basepair A151 - U170 tHW 
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.020051501,0.263882817,0.002539818,0.025227938,0.000000000],[0.002539818,0.012018367,0.002539818,0.002539818,0.000000000],[0.142297221,0.235478309,0.017348636,0.012157548,0.000000000],[0.002539818,0.002539818,0.026230988,0.230067766,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [8] // Basepair A152 - C169 tHW 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.003925557,0.006733370,0.004562426,0.075294433,0.000000000],[0.056908405,0.023470090,0.598866861,0.038148420,0.000000000],[0.004620589,0.081566892,0.000841380,0.009309359,0.000000000],[0.075731750,0.005191700,0.010792115,0.004036654,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | 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 [6] | Right Index [7] // Basepair C153 - G168 cWW 
HairpinNode  | Num Bases [1] | Left Index [7] | Right Index [7] | Norm Constant [1.000000000000000] // Hairpin node type *
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,1.000000000]] // Hairpin for truncation
Sequences of instances from IL_09333.1:
> IL_09333.1 IL_1FJG_009 G  148 C  174
GACAAC*GCUAAUC