Alignment of IL_92321.4 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
6
I

12
7

6
13
7
I

14
8


15
7
I

16
7

7
17
6
I

18
6

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_92321.4_Instance_1 IL_92321.4_IL_1FJG_053_A1329_U1308AUGAAGCGGAUU
IL_92321.4_Sequence_1 IL_92321.4_IL_1FJG_053_A_1329_U_1308AUGAAG*CGGAUUtrue100000.00
IL_92321.4_Instance_2 IL_92321.4_IL_2AW7_059_A1329_U1308AUGAAGCGGAUU
IL_92321.4_Sequence_2 IL_92321.4_IL_2AW7_059_A_1329_U_1308AUGAAG*CGGAUUtrue100000.00
IL_92321.4_Instance_3 IL_92321.4_IL_4BPP_078_U1538_A1517UUGAACGGGAUA
IL_92321.4_Sequence_3 IL_92321.4_IL_4BPP_078_U_1538_A_1517UUGAAC*GGGAUAtrue99000.10
IL_92321.4_Instance_4 IL_92321.4_IL_3U5F_079_U1566_A1545UUCAACGGGAUA
IL_92321.4_Sequence_4 IL_92321.4_IL_3U5F_079_U_1566_A_1545UUCAAC*GGGAUAtrue97000.51
IL_92321.4_Instance_5 IL_92321.4_IL_4A1B_037_G858_C886GUGAAGUGGAAGC
IL_92321.4_Sequence_5 IL_92321.4_IL_4A1B_037_G858_C886GUGAAG*UGGAAGCtrue65005.66
IL_92321.4_Instance_6 IL_92321.4_IL_3U5H_027_C758_G773CUGAUGCGGAUG
IL_92321.4_Sequence_6 IL_92321.4_IL_3U5H_027_C758_G773CUGAUG*CGGAUGtrue98000.30
IL_92321.4_Instance_7 IL_92321.4_IL_4A1B_017_G457_C521GGGAAGCAGAAC
IL_92321.4_Sequence_7 IL_92321.4_IL_4A1B_017_G457_C521GGGAAG*CAGAACtrue74004.25

Conserved interactions between motif group positions in IL_92321.4:
1 2 s35 
1 12 cWW 
2 3 s35 
2 11 cWW 
2 12 s55 
3 9 s33 
3 10 tSH 
4 5 s35 
4 9 tHS 
4 10 s55 
5 6 s35 
5 8 tHS 
6 7 cWW 
6 8 s55 
7 8 s35 
8 9 s35 
10 11 s35 
11 12 s35 
8 4 6BPh
9 4 6BPh
5 8 6BR
JAR3D SCFG/MRF model for IL_92321.4:
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 A1329 - U1308 from junction 
BasepairNode | Deletion Probability [0.0000111424121612] | Pair Probability [[0.009145256,0.020139538,0.010148883,0.212554478,0.000000000],[0.019656953,0.008586697,0.200536528,0.011134298,0.000000000],[0.010128663,0.210775841,0.002049900,0.024757579,0.000000000],[0.212408170,0.011224014,0.024244846,0.012508357,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.850913138,0.147720949,0.001315324,0.000050589] | Right Letter Distribution [0.166666667,0.166666667,0.500000000,0.166666667,0.000000000] | Left Index [1] | Right Index [12] // Basepair A1329 - U1308 cWW 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.014910173,0.157123927,0.014352410,0.034555578,0.000000000],[0.018417960,0.018747039,0.021674633,0.015823830,0.000000000],[0.041393014,0.022076413,0.004517751,0.046000453,0.000000000],[0.056336058,0.017176575,0.018390073,0.498504113,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [11] // Basepair U1330 - U1307 cWW 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.111467105,0.123315345,0.001308267,0.006561247,0.000000000],[0.122253852,0.111144321,0.001308267,0.001308267,0.000000000],[0.183540869,0.001308267,0.006770963,0.094042494,0.000000000],[0.118679724,0.114374477,0.001308267,0.001308267,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [10] // Basepair G1331 - A1306 tSH 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.051645759,0.052105251,0.389908136,0.056137112,0.000000000],[0.060199743,0.054613902,0.003091666,0.054080947,0.000000000],[0.000622266,0.000622266,0.014978472,0.000622266,0.000000000],[0.002963149,0.000622266,0.257164535,0.000622266,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [9] // Basepair A1332 - G1305 tHS 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.063824391,0.039175388,0.368475929,0.055855887,0.000000000],[0.073443977,0.040643600,0.003285515,0.040806707,0.000000000],[0.000816114,0.000816114,0.016634154,0.000816114,0.000000000],[0.004334704,0.000816114,0.289439177,0.000816114,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [8] // Basepair A1333 - G1304 tHS 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.010532611,0.058255416,0.011725921,0.163876120,0.000000000],[0.016999615,0.008485582,0.195963150,0.013119307,0.000000000],[0.011638528,0.217272232,0.002226781,0.077875731,0.000000000],[0.162652665,0.013525563,0.022530856,0.013319923,0.000000000],[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 G1334 - C1303 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_92321.4:
> IL_92321.4 IL_1FJG_053 A 1329 U 1308
AUGAAG*CGGAUU
> IL_92321.4 IL_2AW7_059 A 1329 U 1308
AUGAAG*CGGAUU
> IL_92321.4 IL_4BPP_078 U 1538 A 1517
UUGAAC*GGGAUA
> IL_92321.4 IL_3U5F_079 U 1566 A 1545
UUCAAC*GGGAUA
> IL_92321.4 IL_4A1B_037 G  858 C  886
GUGAAG*UGGAAGC
> IL_92321.4 IL_3U5H_027 C  758 G  773
CUGAUG*CGGAUG
> IL_92321.4 IL_4A1B_017 G  457 C  521
GGGAAG*CAGAAC