Alignment of IL_16166.4 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
5

2
5
5
I

6
6


7
5
I

8
5

3
9
4
I

10
3

4
11
2
I

12
2

5
13
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
IL_16166.4_Instance_1 IL_16166.4_IL_1U6B_010_A150_U162AGUAU
IL_16166.4_Sequence_1 IL_16166.4_IL_1U6B_010_A150_U162AG*UAUtrue100000.00
IL_16166.4_Instance_2 IL_16166.4_IL_4FNJ_004_A11_U27AGUAU
IL_16166.4_Sequence_2 IL_16166.4_IL_4FNJ_004_A11_U27AG*UAUtrue100000.00
IL_16166.4_Instance_3 IL_16166.4_IL_1NTB_001_G114_C7GGCGC
IL_16166.4_Sequence_3 IL_16166.4_IL_1NTB_001_G114_C7GG*CGCtrue85001.44

Conserved interactions between motif group positions in IL_16166.4:
1 2 s35 
1 4 s55 
1 5 cWW 
2 3 cWW 
2 5 s55 
4 5 s53 
JAR3D SCFG/MRF model for IL_16166.4:
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 [5] // Initial node A150 - U162 from junction 
BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.009472747,0.022988174,0.010372983,0.225098889,0.000000000],[0.018936855,0.008916940,0.195696316,0.011163054,0.000000000],[0.010312898,0.208310389,0.002127705,0.027444663,0.000000000],[0.199992661,0.011428674,0.023422512,0.014314540,0.000000000],[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 [5] // Basepair A150 - U162 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.500000000,0.100000000,0.300000000,0.100000000,0.000000000] | Position [2] | Left Index [2] | Right Index [4] // 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 [3] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000249735224443] | 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]] | 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 [2] | Right Index [3] // Basepair G151 - U160 cWW 
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_16166.4:
> IL_16166.4 IL_1U6B_010 A  150 U  162
AG*UAU
> IL_16166.4 IL_4FNJ_004 A   11 U   27
AG*UAU
> IL_16166.4 IL_1NTB_001 G  114 C    7
GG*CGC