Alignment of IL_24293.1 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
7

2
5
7
I

6
8

3
7
8
I

8
9


9
8
I

10
8

4
11
7
I

12
7

5
13
6
I

14
5

6
15
4
I

16
3

7
17
2
I

18
2

8
19
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
IL_24293.1_Instance_1 IL_24293.1_IL_3E5C_001_G12_C32GAUAGAUGC
IL_24293.1_Sequence_1 IL_24293.1_IL_3E5C_001_G12_C32GAU*AGAUGCtrue94000.69
IL_24293.1_Instance_2 IL_24293.1_IL_3V2F_085_C2297_G2321CAGCGGAG
IL_24293.1_Sequence_2 IL_24293.1_IL_3V2F_085_C_2297_G_2321CAG*CGGAGtrue100000.00

Conserved interactions between motif group positions in IL_24293.1:
1 2 s35 
1 7 perp 
1 8 cWW 
2 3 s35 
2 5 cWW 
2 8 s55 
3 4 cWW 
3 5 perp 
4 5 perp 
5 8 s35 
6 7 s33 
7 8 perp 
JAR3D SCFG/MRF model for IL_24293.1:
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 [8] // Initial node G12 - C32 from junction 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.010112949,0.018987468,0.011731285,0.192935737,0.000000000],[0.018987829,0.008487010,0.221492059,0.013594505,0.000000000],[0.011731300,0.221491395,0.002149724,0.025679421,0.000000000],[0.192935850,0.013594439,0.025679804,0.010409224,0.000000000],[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 [8] // Basepair G12 - C32 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.375000000,0.125000000,0.375000000,0.125000000,0.000000000] | Position [2] | Left Index [2] | Right Index [7] // Fixed node on right
InitialNode  | Left Length Distribution [1.000000000] | 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] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.375000000,0.125000000,0.375000000,0.125000000,0.000000000] | Position [2] | Left Index [2] | Right Index [6] // Fixed node on right
InitialNode  | Left Length Distribution [1.000000000] | 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 [2] | Right Index [5] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.177190689,0.011030368,0.380694223,0.012419737,0.000000000],[0.010771367,0.004154329,0.014747163,0.031379647,0.000000000],[0.261287932,0.014935165,0.002719598,0.012261563,0.000000000],[0.012398575,0.033379576,0.011990196,0.008639871,0.000000000],[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 [2] | Right Index [5] // Basepair A13 - G28 cWW 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009655575,0.020452677,0.010811709,0.200386604,0.000000000],[0.020851131,0.008969837,0.201120779,0.011820265,0.000000000],[0.010745793,0.213649208,0.002151642,0.025610090,0.000000000],[0.213671659,0.012113485,0.025820790,0.012168755,0.000000000],[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 [3] | Right Index [4] // Basepair U14 - A27 cWW 
HairpinNode  | Num Bases [1] | Left Index [4] | Right Index [4] | 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_24293.1:
> IL_24293.1 IL_3E5C_001 G   12 C   32
GAU*AGAUGC
> IL_24293.1 IL_3V2F_085 C 2297 G 2321
CAG*CGGAG