Alignment of IL_41344.1 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
5
I

8
6

4
9
6
I

10
7


11
6
I

12
6

5
13
3
I

14
3

6
15
2
I

16
2

7
17
1
I


In
acceptance
region

Cutoff
score
Full
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distance
Interior
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Alignment
score
deficit
IL_41344.1_Instance_1 IL_41344.1,IL_4PDQ_003,G16_C32GAAGCAC
IL_41344.1_Sequence_1 IL_41344.14PDQ_G16_C32GAAG*CACtrue100000.00
IL_41344.1_Instance_2 IL_41344.1,IL_3PDR_002,U159_G26UCUAUUAG
IL_41344.1_Sequence_2 IL_41344.13PDR_U159_G26UCUA*UUAGtrue96000.35

Conserved interactions between motif group positions in IL_41344.1:
1 2 s35 
1 7 cWW 
2 3 s35 
2 5 s33 
2 6 tSH 
2 7 s55 
3 4 s35 
3 6 s55 
4 5 cWW 
6 7 s35
JAR3D SCFG/MRF model for IL_41344.1:
Character Definition | A,C,G,U,* // Identity and order of characters in matrices
InitialNode  | Left Length Distribution [0.999900000,0.000100000] | Left Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Right Length Distribution [0.999900000,0.000100000] | Right Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Left Index [1] | Right Index [7] // Initial node
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.010489920,0.017127883,0.012680838,0.119297674,0.000000000],[0.159817824,0.018747803,0.122690376,0.014659067,0.000000000],[0.012775575,0.132830577,0.002697714,0.020718591,0.000000000],[0.142468525,0.014233330,0.186841746,0.011922559,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.991950402,0.007999600,0.000049998] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [7] // Basepair G16 - C32 cWW 
BasepairNode | Deletion Probability [0.0000015195492620] | Pair Probability [[0.180812125,0.021011724,0.001735938,0.009628288,0.000000000],[0.180711351,0.094703270,0.001735938,0.001735938,0.000000000],[0.145136160,0.001735938,0.013591626,0.030084499,0.000000000],[0.156610988,0.157294343,0.001735938,0.001735938,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.991950402,0.007999600,0.000049998] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.493381468,0.493381468,0.012635379,0.000601685] | Right Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000] | Left Index [2] | Right Index [6] // Basepair A17 - A31 tSH 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.375000000,0.125000000,0.125000000,0.375000000,0.000000000] | Position [1] | Left Index [3] | Right Index [5] // Fixed node on left for 4PDQ|1|A|A|18
InitialNode  | Left Length Distribution [0.991950402,0.007999600,0.000049998] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [5] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009508309,0.021141169,0.010499222,0.212521883,0.000000000],[0.017307832,0.009562561,0.198596306,0.011821420,0.000000000],[0.010428025,0.212609503,0.002065216,0.039989476,0.000000000],[0.197383927,0.012407836,0.023236747,0.010920569,0.000000000],[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 [4] | Right Index [5] // Basepair G19 - C30 cWW 
HairpinNode  | Num Bases [1] | Left Index [5] | Right Index [5] | 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_41344.1:
> IL_41344.1  4PDQ G   16 C   32
GAAG*CAC
> IL_41344.1  3PDR U  159 G   26
UCUA*UUAG