Alignment of IL_12147.1 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


9
4
I

10
4

4
11
3
I

12
3

5
13
2
I

14
2

6
15
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
IL_12147.1_Instance_1 IL_12147.1_IL_4BPP_063_A1206_U1223ACAUUU
IL_12147.1_Sequence_1 IL_12147.1_IL_4BPP_063_A_1206_U_1223ACA*UUUtrue99000.09
IL_12147.1_Instance_2 IL_12147.1_IL_1LNG_001_U175_G154UAACGAG
IL_12147.1_Sequence_2 IL_12147.1_IL_1LNG_001_U175_G154UAAC*GAGtrue100000.00

Conserved interactions between motif group positions in IL_12147.1:
1 6 cWW 
2 3 s35 
2 5 tHS 
3 4 cWW 
3 5 s55 
4 5 s35 
5 6 s35 
JAR3D SCFG/MRF model for IL_12147.1:
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 [6] // Initial node A1206 - U1223 from junction 
BasepairNode | Deletion Probability [0.0000015195492620] | Pair Probability [[0.011134496,0.019611426,0.012682293,0.136578475,0.000000000],[0.168530603,0.012682600,0.118742615,0.013871213,0.000000000],[0.012849956,0.116192085,0.002838101,0.021636967,0.000000000],[0.126193227,0.013057190,0.198002729,0.015396023,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.493381468,0.493381468,0.012635379,0.000601685] | Left Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000] | 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 [6] // Basepair A1206 - U1223 cWW 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.219224696,0.122253927,0.117835681,0.124855324,0.000000000],[0.114760798,0.117297984,0.001355839,0.145387869,0.000000000],[0.001355839,0.001355839,0.006771811,0.001355839,0.000000000],[0.006593576,0.001355839,0.016883297,0.001355839,0.000000000],[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 [5] // Basepair C1207 - U1222 tHS 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009640843,0.020820542,0.010733993,0.213406915,0.000000000],[0.020428208,0.008935347,0.213416622,0.012101297,0.000000000],[0.010799946,0.200886051,0.002149018,0.025786435,0.000000000],[0.200132635,0.011807914,0.025581673,0.013372561,0.000000000],[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 [3] | Right Index [4] // Basepair A1208 - U1221 cWW 
HairpinNode  | Num Bases [1] | Left Index [4] | Right Index [4] | 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_12147.1:
> IL_12147.1 IL_4BPP_063 A 1206 U 1223
ACA*UUU
> IL_12147.1 IL_1LNG_001 U  175 G  154
UAAC*GAG