Alignment of IL_39355.1 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
5

2
5
5
I

6
5

3
7
5
I

8
5

4
9
5
I

10
5

5
11
6
I

12
7


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_39355.1_Instance_1 IL_39355.1_IL_4A1B_119_U3036_A3083UAAUUACCA
IL_39355.1_Sequence_1 IL_39355.1_IL_4A1B_119_U_3036_A_3083UAAUU*ACCAtrue100000.00
IL_39355.1_Instance_2 IL_39355.1_IL_3U5H_123_U3047_A3094UAAUUACCA
IL_39355.1_Sequence_2 IL_39355.1_IL_3U5H_123_U_3047_A_3094UAAUU*ACCAtrue100000.00

Conserved interactions between motif group positions in IL_39355.1:
1 2 s35 
1 8 cWW 
2 6 tHH 
2 8 s35 
3 4 s35 
4 5 s35 
5 6 cWW 
6 7 perp 
6 8 s35 
2 6 6BPh
4 8 6BR
JAR3D SCFG/MRF model for IL_39355.1:
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 U3036 - A3083 from junction 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.009116058,0.020135905,0.009819016,0.207298319,0.000000000],[0.024500257,0.009533097,0.193859401,0.010377090,0.000000000],[0.009835776,0.192739951,0.002153778,0.023649137,0.000000000],[0.234985657,0.010304218,0.027858593,0.013833748,0.000000000],[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 U3036 - A3083 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.125000000,0.625000000,0.125000000,0.125000000,0.000000000] | 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 [0.023781213,0.951248514,0.023781213,0.001189061] | Right Letter Distribution [0.125000000,0.625000000,0.125000000,0.125000000,0.000000000] | Left Index [2] | Right Index [6] // New Initial node after Fixed node
ClusterNode  | Deletion Probability [0.0000000000031250] | Num Left Bases [4] | Num Right Bases [1] | Left Index [2] | Right Index [6] | Norm Constant [0.262851887903713] // Cluster node A3037:U3040 and A3080:A3080
Interaction  | Interacting Bases [1,5] | Pair Probability [[0.602055362,0.099581892,0.024626999,0.024664424,0.000000000],[0.009101432,0.000704744,0.060585658,0.050059363,0.000000000],[0.004402684,0.058476991,0.001726538,0.000704744,0.000000000],[0.004330659,0.057569022,0.000704744,0.000704744,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A3037 - A3080 tHH 
Interaction  | Interacting Bases [4,5] | Pair Probability [[0.009116058,0.020135905,0.009819016,0.207298319,0.000000000],[0.024500257,0.009533097,0.193859401,0.010377090,0.000000000],[0.009835776,0.192739951,0.002153778,0.023649137,0.000000000],[0.234985657,0.010304218,0.027858593,0.013833748,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U3040 - A3080 cWW 
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.625000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.125000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.125000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.125000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion A3038
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.041666667,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.041666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.041666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.875000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion U3039
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 [6] | Right Index [5] // New Initial node after Cluster
HairpinNode  | Num Bases [1] | Left Index [6] | Right Index [6] | 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_39355.1:
> IL_39355.1 IL_4A1B_119 U 3036 A 3083
UAAUU*ACCA
> IL_39355.1 IL_3U5H_123 U 3047 A 3094
UAAUU*ACCA