Alignment of IL_09530.1 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
8

4
9
8
I

10
9


11
8
I

12
8

5
13
7
I

14
6

6
15
3
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_09530.1_Instance_1 IL_09530.1_IL_2GDI_008_U59_A80UGAUCGCGUA
IL_09530.1_Sequence_1 IL_09530.1_IL_2GDI_008_U59_A80UGAUC*GCGUAtrue100000.00
IL_09530.1_Instance_2 IL_09530.1_IL_2GDI_004_U59_A80UGAUCGCGUA
IL_09530.1_Sequence_2 IL_09530.1_IL_2GDI_004_U59_A80UGAUC*GCGUAtrue100000.00
IL_09530.1_Instance_3 IL_09530.1_IL_3D2V_003_U47_A68UGAACGCGCA
IL_09530.1_Sequence_3 IL_09530.1_IL_3D2V_003_U47_A68UGAAC*GCGCAtrue96000.51
IL_09530.1_Instance_4 IL_09530.1_IL_4LCK_005_A36_U72AUGAUUAGCGACGGAU
IL_09530.1_Sequence_4 IL_09530.1_IL_4LCK_005_A36_U72AUGAUUAGCGAC*GGAUtrue-70015.07

Conserved interactions between motif group positions in IL_09530.1:
1 2 s35 
1 8 cWW 
2 3 s33 
2 7 cWH 
2 8 s55 
3 4 s55 
4 5 cWW 
5 6 s35 
6 7 s33 
7 8 s55 
JAR3D SCFG/MRF model for IL_09530.1:
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 U59 - A80 from junction 
BasepairNode | Deletion Probability [0.0000004444241139] | Pair Probability [[0.008973807,0.020802927,0.009627934,0.214768857,0.000000000],[0.022945963,0.009293412,0.189732133,0.010152995,0.000000000],[0.009636163,0.189182448,0.002110966,0.024208445,0.000000000],[0.237966914,0.010117212,0.026275422,0.014204402,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.253667482,0.736552567,0.009321516,0.000458435] | Right Letter Distribution [0.100000000,0.300000000,0.100000000,0.500000000,0.000000000] | Left Index [1] | Right Index [8] // Basepair U59 - A80 cWW 
BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.004508284,0.004508284,0.045685474,0.026411789,0.000000000],[0.004508284,0.042422116,0.209928331,0.023825784,0.000000000],[0.034825799,0.004508284,0.479674580,0.004508284,0.000000000],[0.058674243,0.004508284,0.013869760,0.037632420,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [7] // Basepair G60 - G78 cWH 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.583333333,0.083333333,0.250000000,0.083333333,0.000000000] | Position [1] | Left Index [3] | Right Index [6] // Fixed node on left
InitialNode  | Left Length Distribution [0.009140559,0.731244716,0.009140559,0.000457028,0.000007617,0.000007617,0.000007617,0.003046853,0.243748239,0.003046853,0.000152343] | Left Letter Distribution [0.346153846,0.115384615,0.192307692,0.346153846,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [6] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.083333333,0.583333333,0.250000000,0.083333333,0.000000000] | Position [2] | Left Index [4] | 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 [0.995990040,0.003999960,0.000010000] | 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 [[0.009837906,0.016874612,0.011433973,0.188696651,0.000000000],[0.020374159,0.008402684,0.249321155,0.013657771,0.000000000],[0.011579737,0.204416164,0.002108596,0.023330341,0.000000000],[0.189792617,0.013011006,0.027046303,0.010116326,0.000000000],[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 C63 - G76 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_09530.1:
> IL_09530.1 IL_2GDI_008 U   59 A   80
UGAUC*GCGUA
> IL_09530.1 IL_2GDI_004 U   59 A   80
UGAUC*GCGUA
> IL_09530.1 IL_3D2V_003 U   47 A   68
UGAAC*GCGCA
> IL_09530.1 IL_4LCK_005 A   36 U   72
AUGAUUAGCGAC*GGAU