Alignment of IL_42771.1 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


7
3
I

8
3

3
9
2
I

10
2

4
11
1
I


In
acceptance
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Cutoff
score
Full
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Alignment
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IL_42771.1_Instance_1 IL_42771.1,IL_6JQ5_002,U34_A60UUAUUA
IL_42771.1_Sequence_1 IL_42771.16JQ5_U34_A60UUA*UUAtrue97000.31
IL_42771.1_Instance_2 IL_42771.1,IL_6JQ5_005,U34_A60UUAUUA
IL_42771.1_Sequence_2 IL_42771.16JQ5_U34_A60UUA*UUAtrue97000.31
IL_42771.1_Instance_3 IL_42771.1,IL_6JQ6_005,U34_A60UUAUUA
IL_42771.1_Sequence_3 IL_42771.16JQ6_U34_A60UUA*UUAtrue97000.31
IL_42771.1_Instance_4 IL_42771.1,IL_4PWD_008,A715_U813AAAUU
IL_42771.1_Sequence_4 IL_42771.14PWD_A715_U813AAA*UUtrue99000.06
IL_42771.1_Instance_5 IL_42771.1,IL_4V9F_090,C2636_G2627CAGCG
IL_42771.1_Sequence_5 IL_42771.14V9F_C_2636_G_2627CAG*CGtrue98000.19
IL_42771.1_Instance_6 IL_42771.1,IL_8T29_003,C54_G66CAAUG
IL_42771.1_Sequence_6 IL_42771.18T29_C54_G66CAA*UGtrue100000.00

Conserved interactions between motif group positions in IL_42771.1:
1 2 s35 
1 3 s33 
1 4 cWW 
2 3 cWW 
2 4 s55 
3 4 s35
JAR3D SCFG/MRF model for IL_42771.1:
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 [4] // Initial node
BasepairNode | Deletion Probability [0.0000000084804438] | Pair Probability [[0.008894382,0.017456687,0.009874685,0.200388445,0.000000000],[0.019919321,0.009382195,0.211811819,0.011398792,0.000000000],[0.009920382,0.190241337,0.001981207,0.027150094,0.000000000],[0.222684300,0.011022076,0.037919425,0.009954853,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.008193363,0.983203605,0.008193363,0.000409668] | Left Letter Distribution [0.437500000,0.062500000,0.062500000,0.437500000,0.000000000] | Right Length Distribution [0.497737557,0.497737557,0.004319210,0.000205677] | Right Letter Distribution [0.100000000,0.100000000,0.100000000,0.700000000,0.000000000] | Left Index [1] | Right Index [4] // Basepair U34 - A60 cWW 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009004919,0.020901101,0.009727834,0.243134360,0.000000000],[0.016789640,0.009213063,0.188260006,0.010437069,0.000000000],[0.009692617,0.200658900,0.001971846,0.046963954,0.000000000],[0.189062828,0.011054541,0.022216105,0.010911216,0.000000000],[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 [2] | Right Index [3] // Basepair A36 - U58 cWW 
HairpinNode  | Num Bases [1] | Left Index [3] | Right Index [3] | 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_42771.1:
> IL_42771.1  6JQ5 U   34 A   60
UUA*UUA
> IL_42771.1  6JQ5 U   34 A   60
UUA*UUA
> IL_42771.1  6JQ6 U   34 A   60
UUA*UUA
> IL_42771.1  4PWD A  715 U  813
AAA*UU
> IL_42771.1  4V9F C 2636 G 2627
CAG*CG
> IL_42771.1  8T29 C   54 G   66
CAA*UG