Alignment of IL_98421.4 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
4
I

6
5

3
7
6
I

8
7

4
9
8
I

10
9

5
11
9
I

12
10


13
9
I

14
9

6
15
2
I

16
2

7
17
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
IL_98421.4_Instance_1 IL_98421.4_IL_1FJG_013_U304_G293UGGCCGG
IL_98421.4_Sequence_1 IL_98421.4_IL_1FJG_013_U304_G293UGGCC*GGtrue95000.51
IL_98421.4_Instance_2 IL_98421.4_IL_2AW7_016_U304_G293UGACCGG
IL_98421.4_Sequence_2 IL_98421.4_IL_2AW7_016_U304_G293UGACC*GGtrue100000.00
IL_98421.4_Instance_3 IL_98421.4_IL_4BPP_023_C435_G453CCAAUAG
IL_98421.4_Sequence_3 IL_98421.4_IL_4BPP_023_C435_G453CCAAU*AGtrue78002.11

Conserved interactions between motif group positions in IL_98421.4:
1 2 s35 
1 7 cWW 
2 7 s55 
3 4 s35 
4 5 s35 
5 6 cWW 
2 6 6BPh
JAR3D SCFG/MRF model for IL_98421.4:
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 [7] // Initial node U304 - G293 from junction 
BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.011905622,0.015441941,0.014117494,0.089085281,0.000000000],[0.216124644,0.013432092,0.110554063,0.016127348,0.000000000],[0.014398970,0.094571860,0.003038926,0.018077940,0.000000000],[0.094006531,0.014786857,0.261444133,0.012886299,0.000000000],[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 [7] // Basepair U304 - G293 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.021739130,0.326086957,0.630434783,0.021739130,0.000000000] | Position [1] | Left Index [2] | Right Index [6] // Fixed node on left
InitialNode  | 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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [6] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.500000000,0.100000000,0.300000000,0.100000000,0.000000000] | Position [1] | Left Index [3] | Right Index [6] // Fixed node on left
InitialNode  | 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 [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 [0.300000000,0.500000000,0.100000000,0.100000000,0.000000000] | Position [1] | Left Index [4] | Right Index [6] // Fixed node on left
InitialNode  | 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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [6] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009631464,0.018005765,0.010937883,0.195447676,0.000000000],[0.021802108,0.008803023,0.225347764,0.012619028,0.000000000],[0.011041535,0.201223421,0.002130335,0.023511078,0.000000000],[0.208561169,0.012159610,0.027401966,0.011376175,0.000000000],[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 [5] | Right Index [6] // Basepair C308 - G292 cWW 
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_98421.4:
> IL_98421.4 IL_1FJG_013 U  304 G  293
UGGCC*GG
> IL_98421.4 IL_2AW7_016 U  304 G  293
UGACC*GG
> IL_98421.4 IL_4BPP_023 C  435 G  453
CCAAU*AG