Alignment of IL_28003.1 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
4

4
9
4
I

10
4

5
11
5
I

12
6


13
5
I

14
4

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_28003.1_Instance_1 IL_28003.1_IL_3Q1Q_009_C44_G35CUAAGUAUG
IL_28003.1_Sequence_1 IL_28003.1_IL_3Q1Q_009_C44_G35CUAAG*UAUGtrue100000.00
IL_28003.1_Instance_2 IL_28003.1_IL_4K27_004_C19_G37CUAAGUAUG
IL_28003.1_Sequence_2 IL_28003.1_IL_4K27_004_C19_G37CUAAG*UAUGtrue100000.00
IL_28003.1_Instance_3 IL_28003.1_IL_3V2F_109_G50_C32GGAAGCCC
IL_28003.1_Sequence_3 IL_28003.1_IL_3V2F_109_G50_C32GGAAG*CCCtrue70003.27

Conserved interactions between motif group positions in IL_28003.1:
1 2 s35 
1 8 cWW 
2 3 s35 
2 7 tWH 
2 8 s55 
3 4 cSH 
3 6 s33 
3 7 s55 
4 5 s35 
4 7 s55 
5 6 cWW 
7 8 s35 
JAR3D SCFG/MRF model for IL_28003.1:
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 C44 - G35 from junction 
BasepairNode | Deletion Probability [0.0000006691671388] | Pair Probability [[0.009987650,0.018214897,0.011593253,0.190884602,0.000000000],[0.019392976,0.008431163,0.230141683,0.013571804,0.000000000],[0.011642323,0.218263837,0.002128924,0.024805687,0.000000000],[0.191253546,0.013354078,0.026056620,0.010276957,0.000000000],[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 [0.334863624,0.653524170,0.011072104,0.000540103] | Right Letter Distribution [0.125000000,0.125000000,0.125000000,0.625000000,0.000000000] | Left Index [1] | Right Index [8] // Basepair C44 - G35 cWW 
BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.024494901,0.005137156,0.025198876,0.005137156,0.000000000],[0.051027214,0.042650770,0.034099640,0.005137156,0.000000000],[0.005137156,0.061077979,0.060120855,0.023963331,0.000000000],[0.533133053,0.005137156,0.063374730,0.055172872,0.000000000],[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 [2] | Right Index [7] // Basepair U45 - A33 tWH 
ClusterNode  | Deletion Probability [0.0000000006250000] | Num Left Bases [3] | Num Right Bases [1] | Left Index [3] | Right Index [6] | Norm Constant [1.000000000000000] // Cluster node A46:G48 and U32:U32
Interaction  | Interacting Bases [3,4] | Pair Probability [[0.014258858,0.211706755,0.014176550,0.093357766,0.000000000],[0.015234759,0.010399964,0.094014042,0.014566320,0.000000000],[0.013899989,0.109909176,0.002989625,0.256526531,0.000000000],[0.088532666,0.015883070,0.017860543,0.026683387,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G48 - U32 cWW 
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.200798898,0.109046156,0.005514295,0.004779221,0.000000000],[0.112505714,0.106108705,0.001254406,0.110620571,0.000000000],[0.005863261,0.005663708,0.006339676,0.104975229,0.000000000],[0.010696325,0.108492360,0.001254406,0.106087070,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A46 - A47 cSH 
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_28003.1:
> IL_28003.1 IL_3Q1Q_009 C   44 G   35
CUAAG*UAUG
> IL_28003.1 IL_4K27_004 C   19 G   37
CUAAG*UAUG
> IL_28003.1 IL_3V2F_109 G   50 C   32
GGAAG*CCC