Alignment of IL_29223.1 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
4
I

6
5

3
7
5
I

8
6

4
9
6
I

10
7

5
11
7
I

12
8

6
13
8
I

14
9


15
8
I

16
8

7
17
7
I

18
7

8
19
6
I

20
6

9
21
5
I

22
5

10
23
2
I

24
2

11
25
1
I


In
acceptance
region

Cutoff
score
Full
edit
distance
Interior
edit
distance
Alignment
score
deficit
IL_29223.1_Instance_1 IL_29223.1,IL_8P9A_382,U117_A299UUAUUUAUUCA
IL_29223.1_Sequence_1 IL_29223.18P9A_U117_A299UUAUUU*AUUCAtrue100000.00
IL_29223.1_Instance_2 IL_29223.1,IL_8CRE_399,U117_A297UUAUUUAUUCA
IL_29223.1_Sequence_2 IL_29223.18CRE_U117_A297UUAUUU*AUUCAtrue100000.00

Conserved interactions between motif group positions in IL_29223.1:
1 2 s35 
1 11 cWW 
2 11 s55 
3 4 s35 
3 10 tHS 
4 5 s35 
4 9 cWW 
5 6 s35 
5 8 cWW 
5 9 s55 
6 7 cWW 
7 8 s35 
8 9 s35 
9 10 s35 
10 11 s35 
4 3 7BPh
JAR3D SCFG/MRF model for IL_29223.1:
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 [11] // Initial node
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.009034335,0.017544761,0.009910087,0.196321162,0.000000000],[0.022043953,0.009831675,0.196981684,0.011044900,0.000000000],[0.009929415,0.194460696,0.002044250,0.023047545,0.000000000],[0.224032836,0.010374563,0.053294552,0.010103588,0.000000000],[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 [11] // Basepair U117 - A299 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.125000000,0.125000000,0.125000000,0.625000000,0.000000000] | Position [1] | Left Index [2] | Right Index [10] // Fixed node on left for 8P9A|1|sR|U|118
InitialNode  | 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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [10] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.165104346,0.189883327,0.142898821,0.153919145,0.000000000],[0.021377199,0.119138269,0.001702755,0.155621653,0.000000000],[0.001702755,0.001702755,0.011815340,0.001702755,0.000000000],[0.008468575,0.001702755,0.021556797,0.001702755,0.000000000],[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 [10] // Basepair A119 - C298 tHS 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.003917817,0.071857546,0.003497950,0.006109389,0.000000000],[0.004330118,0.004668938,0.005222068,0.003839941,0.000000000],[0.003424890,0.005319704,0.001079822,0.013794930,0.000000000],[0.037358709,0.029110573,0.030984372,0.775483232,0.000000000],[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 [4] | Right Index [9] // Basepair U120 - U297 cWW 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.015427721,0.282963204,0.013774352,0.024057770,0.000000000],[0.017051293,0.018385511,0.020563647,0.015121057,0.000000000],[0.013486654,0.020948120,0.004252161,0.054322168,0.000000000],[0.021016065,0.016376093,0.017430195,0.444823990,0.000000000],[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 [5] | Right Index [8] // Basepair U121 - U296 cWW 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009034335,0.017544761,0.009910087,0.196321162,0.000000000],[0.022043953,0.009831675,0.196981684,0.011044900,0.000000000],[0.009929415,0.194460696,0.002044250,0.023047545,0.000000000],[0.224032836,0.010374563,0.053294552,0.010103588,0.000000000],[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 U122 - A295 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_29223.1:
> IL_29223.1  8P9A U  117 A  299
UUAUUU*AUUCA
> IL_29223.1  8CRE U  117 A  297
UUAUUU*AUUCA