Alignment of IL_82563.1 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
6
I

6
7


7
6
I

8
5

3
9
5
I

10
5

4
11
5
I

12
5

5
13
5
I

14
5

6
15
5
I

16
5

7
17
5
I

18
5

8
19
4
I

20
3

9
21
2
I

22
2

10
23
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
IL_82563.1_Instance_1 IL_82563.1_IL_2GDI_006_U20_A45UGCUGAGAAA
IL_82563.1_Sequence_1 IL_82563.1_IL_2GDI_006_U20_A45UG*CUGAGAAAtrue100000.00
IL_82563.1_Instance_2 IL_82563.1_IL_2GDI_002_U20_A45UGCUGAGAAA
IL_82563.1_Sequence_2 IL_82563.1_IL_2GDI_002_U20_A45UG*CUGAGAAAtrue100000.00
IL_82563.1_Instance_3 IL_82563.1_IL_2HOJ_002_U20_A45UGCUGAGAAA
IL_82563.1_Sequence_3 IL_82563.1_IL_2HOJ_002_U20_A45UG*CUGAGAAAtrue100000.00

Conserved interactions between motif group positions in IL_82563.1:
1 9 s35 
1 10 cWW 
2 3 cWW 
2 4 s55 
2 8 s53 
3 4 s35 
4 5 s35 
4 8 tWH 
5 7 s33 
5 8 s55 
6 7 s35 
9 10 s55 
5 8 6BPh
JAR3D SCFG/MRF model for IL_82563.1:
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 [10] // Initial node U20 - A45 from junction 
BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.009027553,0.019940410,0.009723686,0.205285714,0.000000000],[0.024262390,0.009440542,0.191977271,0.010276342,0.000000000],[0.009740283,0.190868689,0.002132868,0.023419534,0.000000000],[0.242412981,0.010204177,0.027588121,0.013699440,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [10] // Basepair U20 - A45 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.700000000,0.100000000,0.100000000,0.100000000,0.000000000] | Position [2] | Left Index [2] | Right Index [9] // 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 [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [8] // New Initial node after Fixed node
ClusterNode  | Deletion Probability [0.000000000000000078125000000000012000000000000000000000000000] | Num Left Bases [1] | Num Right Bases [6] | Left Index [2] | Right Index [8] | Norm Constant [1.000000000000000] // Cluster node G21:G21 and C38:A43
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.010096111,0.020567805,0.011689796,0.191596493,0.000000000],[0.017034996,0.008324961,0.206359029,0.013134669,0.000000000],[0.011542646,0.241989936,0.002128637,0.027303363,0.000000000],[0.190490110,0.013787581,0.023552083,0.010401784,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G21 - C38 cWW 
Interaction  | Interacting Bases [3,7] | Pair Probability [[0.025719646,0.005394014,0.026458819,0.005394014,0.000000000],[0.053578574,0.044783309,0.035804622,0.005394014,0.000000000],[0.005394014,0.005394014,0.063126898,0.025161497,0.000000000],[0.568527570,0.005394014,0.066543467,0.057931515,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U39 - A43 tWH 
Interaction  | Interacting Bases [4,4] | Pair Probability [[0.021739130,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.021739130,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.934782609,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.021739130,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion G40
Interaction  | Interacting Bases [5,5] | Pair Probability [[0.700000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.100000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.100000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion A41
Interaction  | Interacting Bases [6,6] | Pair Probability [[0.100000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.700000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.100000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion G42
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 [3] | Right Index [2] // New Initial node after Cluster
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_82563.1:
> IL_82563.1 IL_2GDI_006 U   20 A   45
UG*CUGAGAAA
> IL_82563.1 IL_2GDI_002 U   20 A   45
UG*CUGAGAAA
> IL_82563.1 IL_2HOJ_002 U   20 A   45
UG*CUGAGAAA