Alignment of IL_63519.1 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
4
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
4

7
17
3
I

18
3

8
19
2
I

20
2

9
21
1
I


In
acceptance
region

Cutoff
score
Full
edit
distance
Interior
edit
distance
Alignment
score
deficit
IL_63519.1_Instance_1 IL_63519.1,IL_8D28_003,G4_C30GAUACGCAGC
IL_63519.1_Sequence_1 IL_63519.18D28_G4_C30GAUAC*GCAGCtrue100000.00
IL_63519.1_Instance_2 IL_63519.1,IL_8DK7_001,G4_C31GAUACGCAGC
IL_63519.1_Sequence_2 IL_63519.18DK7_G4_C31GAUAC*GCAGCtrue100000.00

Conserved interactions between motif group positions in IL_63519.1:
1 2 s35 
1 9 cWW 
2 3 s35 
2 8 cWW 
3 7 tSH 
4 5 cSH 
5 6 cWW 
7 8 s35 
8 9 s35 
5 4 7BR
JAR3D SCFG/MRF model for IL_63519.1:
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 [9] // Initial node
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.009733692,0.020271796,0.011084078,0.201320753,0.000000000],[0.017097495,0.009544863,0.203026637,0.013284001,0.000000000],[0.010960983,0.228535864,0.002089280,0.026765173,0.000000000],[0.198744233,0.013787510,0.023460879,0.010292763,0.000000000],[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 [9] // Basepair G4 - C30 cWW 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.029784876,0.014589866,0.379329069,0.017472527,0.000000000],[0.014247286,0.009703380,0.018872041,0.042407159,0.000000000],[0.345605520,0.019083979,0.003597212,0.015874647,0.000000000],[0.017438516,0.044806635,0.015534560,0.011652725,0.000000000],[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 [8] // Basepair A5 - G29 cWW 
BasepairNode | Deletion Probability [0.0000001182498160] | Pair Probability [[0.120391741,0.109966274,0.001336998,0.006576967,0.000000000],[0.120856821,0.113714611,0.001336998,0.001336998,0.000000000],[0.124325641,0.001336998,0.008263305,0.110995656,0.000000000],[0.153307608,0.123579390,0.001336998,0.001336998,0.000000000],[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 [0.023781213,0.951248514,0.023781213,0.001189061] | Right Letter Distribution [0.125000000,0.625000000,0.125000000,0.125000000,0.000000000] | Left Index [3] | Right Index [7] // Basepair U6 - A28 tSH 
ClusterNode  | Deletion Probability [0.0000001250000000] | Num Left Bases [2] | Num Right Bases [1] | Left Index [4] | Right Index [6] | Norm Constant [0.294300469160113] // Cluster node 8D28|1|B|A|7:8D28|1|B|C|8 and 8D28|1|B|G|26:8D28|1|B|G|26
Interaction  | Interacting Bases [2,3] | Pair Probability [[0.004694951,0.008419175,0.005397424,0.097865947,0.000000000],[0.049911347,0.023908359,0.534011162,0.033946338,0.000000000],[0.005458039,0.099974695,0.001028807,0.011552643,0.000000000],[0.099134681,0.006541329,0.013179748,0.004975356,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8D28|1|B|C|8 - 8D28|1|B|G|26 cWW 
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.103145582,0.133194674,0.005565984,0.043430123,0.000000000],[0.099556957,0.098312651,0.001135868,0.009226384,0.000000000],[0.009906224,0.001135868,0.103159102,0.093301337,0.000000000],[0.103522381,0.102278412,0.001135868,0.091992584,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8D28|1|B|A|7 - 8D28|1|B|C|8 cSH 
InitialNode  | 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 [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_63519.1:
> IL_63519.1  8D28 G    4 C   30
GAUAC*GCAGC
> IL_63519.1  8DK7 G    4 C   31
GAUAC*GCAGC