Alignment of IL_93568.2 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
6

5
11
7
I

12
10

6
13
10
I

14
11


15
10
I

16
10

7
17
9
I

18
8

8
19
5
I

20
5

9
21
4
I

22
4

10
23
3
I

24
3

11
25
2
I

26
2

12
27
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
IL_93568.2_Instance_1 IL_93568.2_IL_4GMA_004_C97_G143CGAAGCGUGGAG
IL_93568.2_Sequence_1 IL_93568.2_IL_4GMA_004_C97_G143CGAAGC*GUGGAGtrue100000.05
IL_93568.2_Instance_2 IL_93568.2_IL_4IOA_017_U716_G741UGAAACGCGGAG
IL_93568.2_Sequence_2 IL_93568.2_IL_4IOA_017_U716_G741UGAAAC*GCGGAGtrue98000.22
IL_93568.2_Instance_3 IL_93568.2_IL_4A1B_033_C794_G786CGAAGGCUUGAG
IL_93568.2_Sequence_3 IL_93568.2_IL_4A1B_033_C794_G786CGAAGG*CUUGAGtrue100000.00
IL_93568.2_Instance_4 IL_93568.2_IL_1FJG_026_U605_G633UGAAAGACGGGGAG
IL_93568.2_Sequence_4 IL_93568.2_IL_1FJG_026_U605_G633UGAAAGAC*GGGGAGtrue78003.12

Conserved interactions between motif group positions in IL_93568.2:
1 2 s35 
1 12 cWW 
2 10 s33 
2 11 tSH 
2 12 s55 
3 4 s35 
3 10 tHS 
3 11 s55 
4 5 s35 
4 9 tHS 
5 6 s35 
6 7 cWW 
6 8 s55 
7 8 s35 
8 9 s35 
9 10 s35 
11 12 s35 
4 9 6BR
JAR3D SCFG/MRF model for IL_93568.2:
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 [12] // Initial node C97 - G143 from junction 
BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.011302835,0.015688748,0.013344805,0.113345681,0.000000000],[0.165628431,0.012077874,0.146852417,0.015393651,0.000000000],[0.013590323,0.121350928,0.002784428,0.019260671,0.000000000],[0.117275121,0.014236258,0.205766953,0.012100875,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [12] // Basepair C97 - G143 cWW 
BasepairNode | Deletion Probability [0.0000015977316803] | Pair Probability [[0.109749162,0.127926698,0.001322337,0.006296802,0.000000000],[0.110725601,0.116056577,0.001322337,0.001322337,0.000000000],[0.170695282,0.001322337,0.006406447,0.109991924,0.000000000],[0.119293454,0.114924027,0.001322337,0.001322337,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.738007380,0.012300123,0.246463715,0.003075031,0.000153752] | Left Letter Distribution [0.625000000,0.125000000,0.125000000,0.125000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [11] // Basepair G98 - A142 tSH 
BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.106208866,0.107153807,0.197447047,0.115445278,0.000000000],[0.123800031,0.112312816,0.001279681,0.111216801,0.000000000],[0.001279681,0.001279681,0.006199787,0.001279681,0.000000000],[0.006093680,0.001279681,0.106443797,0.001279681,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [10] // Basepair A99 - G141 tHS 
BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.099771965,0.100659637,0.139443264,0.161770273,0.000000000],[0.116296998,0.105505979,0.001202125,0.104476389,0.000000000],[0.001202125,0.001202125,0.059145721,0.001202125,0.000000000],[0.005724366,0.001202125,0.099992658,0.001202125,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [9] // Basepair A100 - G140 tHS 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.416666667,0.083333333,0.416666667,0.083333333,0.000000000] | Position [1] | Left Index [5] | Right Index [8] // Fixed node on left
InitialNode  | Left Length Distribution [0.995990040,0.003999960,0.000010000] | 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 [6] | Right Index [8] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.083333333,0.250000000,0.250000000,0.416666667,0.000000000] | Position [2] | Left Index [6] | Right Index [8] // 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 [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [6] | Right Index [7] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009878188,0.017748468,0.011469828,0.188961043,0.000000000],[0.019498419,0.008363241,0.238084568,0.013495422,0.000000000],[0.011542717,0.215631747,0.002108490,0.024257963,0.000000000],[0.189509081,0.013172006,0.026116132,0.010162687,0.000000000],[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 [6] | Right Index [7] // Basepair C102 - G138 cWW 
HairpinNode  | Num Bases [1] | Left Index [7] | Right Index [7] | 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_93568.2:
> IL_93568.2 IL_4GMA_004 C   97 G  143
CGAAGC*GUGGAG
> IL_93568.2 IL_4IOA_017 U  716 G  741
UGAAAC*GCGGAG
> IL_93568.2 IL_4A1B_033 C  794 G  786
CGAAGG*CUUGAG
> IL_93568.2 IL_1FJG_026 U  605 G  633
UGAAAGAC*GGGGAG