Alignment of IL_10484.1 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

4
9
5
I

10
6


11
5
I

12
5

5
13
4
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_10484.1_Instance_1 IL_10484.1,IL_6E7L_002,U10_G13UUCGUUCG
IL_10484.1_Sequence_1 IL_10484.16E7L_U10_G13UUCG*UUCGtrue100000.00
IL_10484.1_Instance_2 IL_10484.1,IL_3PDR_003,U28_G157UGAGUAAAG
IL_10484.1_Sequence_2 IL_10484.13PDR_U28_G157UGAG*UAAAGtrue96000.49

Conserved interactions between motif group positions in IL_10484.1:
1 2 s35 
1 8 cWW 
2 6 s33 
2 7 tSH 
2 8 s55 
3 4 s35 
3 6 tHS 
3 7 s55 
4 5 cWW 
4 6 s55 
5 6 s35 
7 8 s35 
6 2 6BR
2 6 6BR
JAR3D SCFG/MRF model for IL_10484.1:
Character Definition | A,C,G,U,* // Identity and order of characters in matrices
InitialNode  | Left Length Distribution [0.999900000,0.000100000] | Left Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Right Length Distribution [0.999900000,0.000100000] | Right Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Left Index [1] | Right Index [8] // Initial node
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.011246147,0.013983971,0.014277598,0.037274594,0.000000000],[0.302538153,0.027950744,0.042354115,0.016034133,0.000000000],[0.014590167,0.037125289,0.003306148,0.014672010,0.000000000],[0.086192816,0.014679149,0.350222612,0.013552354,0.000000000],[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 [1] | Right Index [8] // Basepair U10 - G13 cWW 
BasepairNode | Deletion Probability [0.0000015195492620] | Pair Probability [[0.057931739,0.051027289,0.000668749,0.003159858,0.000000000],[0.058657208,0.058062256,0.000668749,0.000668749,0.000000000],[0.204265319,0.001986984,0.009815751,0.153395607,0.000000000],[0.187402695,0.208238033,0.002025508,0.002025508,0.000000000],[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 [0.493381468,0.493381468,0.012635379,0.000601685] | Right Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000] | Left Index [2] | Right Index [7] // Basepair U11 - C12 tSH 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.278416766,0.077180422,0.069356742,0.199643724,0.000000000],[0.049755361,0.047983592,0.000815459,0.222194696,0.000000000],[0.002720534,0.000815459,0.005897439,0.002172218,0.000000000],[0.016127954,0.000815459,0.023931959,0.002172218,0.000000000],[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 [3] | Right Index [6] // Basepair C12 - U11 tHS 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.015839826,0.296886961,0.014317634,0.084582798,0.000000000],[0.013722760,0.012789399,0.036431816,0.014404953,0.000000000],[0.014010903,0.041562971,0.003244391,0.344046970,0.000000000],[0.036578332,0.015734627,0.014397948,0.041447713,0.000000000],[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 [4] | Right Index [5] // Basepair G13 - U10 cWW 
HairpinNode  | Num Bases [1] | Left Index [5] | Right Index [5] | 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_10484.1:
> IL_10484.1  6E7L U   10 G   13
UUCG*UUCG
> IL_10484.1  3PDR U   28 G  157
UGAG*UAAAG