Alignment of IL_43644.1 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_43644.1_Instance_1 IL_43644.1,IL_5J7L_327,A2183_U2106AAUGCCUU
IL_43644.1_Sequence_1 IL_43644.15J7L_A_2183_U_2106AAUG*CCUUtrue100000.00
IL_43644.1_Instance_2 IL_43644.1,IL_5EW4_001,C8_G17CCCGCCCG
IL_43644.1_Sequence_2 IL_43644.15EW4_C8_G17CCCG*CCCGtrue93000.80

Conserved interactions between motif group positions in IL_43644.1:
1 2 s35 
1 8 cWW 
2 3 s35 
2 7 tSH 
3 4 perp 
3 6 cWW 
3 7 s55 
4 5 cWW 
4 6 s55 
5 6 s35 
6 7 s35 
7 8 s35
JAR3D SCFG/MRF model for IL_43644.1:
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 [[0.009409752,0.019555960,0.010438919,0.211256183,0.000000000],[0.018897284,0.009646494,0.211374635,0.012074740,0.000000000],[0.010490831,0.199877935,0.002065453,0.038339992,0.000000000],[0.198695040,0.012157589,0.024891932,0.010827262,0.000000000],[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 A2183 - U2106 cWW 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.023021455,0.015676229,0.003775280,0.387331964,0.000000000],[0.018776188,0.114642375,0.003775280,0.003775280,0.000000000],[0.017792908,0.003775280,0.340741106,0.022912277,0.000000000],[0.018571381,0.017882434,0.003775280,0.003775280,0.000000000],[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 [7] // Basepair A2184 - U2105 tSH 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.014388070,0.019784648,0.031169817,0.023945648,0.000000000],[0.041286450,0.311661147,0.025588574,0.168232395,0.000000000],[0.030241091,0.025802615,0.004820457,0.020692235,0.000000000],[0.023678038,0.205465918,0.033279936,0.019962963,0.000000000],[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 U2185 - C2104 cWW 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009733692,0.020271796,0.011084078,0.201320753,0.000000000],[0.017097495,0.009544863,0.203026637,0.013284001,0.000000000],[0.010960983,0.228535864,0.002089280,0.026765173,0.000000000],[0.198744233,0.013787510,0.023460879,0.010292763,0.000000000],[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 G2186 - C2103 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_43644.1:
> IL_43644.1  5J7L A 2183 U 2106
AAUG*CCUU
> IL_43644.1  5EW4 C    8 G   17
CCCG*CCCG