Alignment of IL_49493.4 sequences from 3D to the JAR3D model

Previous group | Next group | List of all groups | Motif atlas entry for IL_49493.4
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
5

5
11
6
I

12
7

6
13
7
I

14
8

7
15
8
I

16
9


17
8
I

18
8

8
19
7
I

20
7

9
21
6
I

22
5

10
23
4
I

24
4

11
25
3
I

26
3

12
27
2
I

28
2

13
29
1
I


In
acceptance
region

Cutoff
score
Full
edit
distance
Interior
edit
distance
Alignment
score
deficit
IL_49493.4_Instance_1 IL_49493.4_IL_2QBG_012_C239_G258CCAGUAGCGAACG
IL_49493.4_Sequence_1 IL_49493.4_IL_2QBG_012_C239_G258CCAGUAG*CGAACG
IL_49493.4_Instance_2 IL_49493.4_IL_1S72_007_U210_G229UUAGUAAUGAACG
IL_49493.4_Sequence_2 IL_49493.4_IL_1S72_007_U210_G229UUAGUAA*UGAACG
IL_49493.4_Instance_3 IL_49493.4_IL_3V2F_007_U239_G258UGAGUAGCGAAAG
IL_49493.4_Sequence_3 IL_49493.4_IL_3V2F_007_U239_G258UGAGUAG*CGAAAG
IL_49493.4_Instance_4 IL_49493.4_IL_1S72_103_G75_C106GGAGUACGGAAAC
IL_49493.4_Sequence_4 IL_49493.4_IL_1S72_103_G75_C106GGAGUAC*GGAAAC
IL_49493.4_Instance_5 IL_49493.4_IL_1S72_049_A1367_U2057AUAGUAGUGAACU
IL_49493.4_Sequence_5 IL_49493.4_IL_1S72_049_A_1367_U_2057AUAGUAG*UGAACU
IL_49493.4_Instance_6 IL_49493.4_IL_1S72_090_A2689_U2705AUAGUACGGAACU
IL_49493.4_Sequence_6 IL_49493.4_IL_1S72_090_A_2689_U_2705AUAGUAC*GGAACU
IL_49493.4_Instance_7 IL_49493.4_IL_1NBS_007_U165_A143UGAGUAUAAAAAA
IL_49493.4_Sequence_7 IL_49493.4_IL_1NBS_007_U165_A143UGAGUAU*AAAAAA
IL_49493.4_Instance_8 IL_49493.4_IL_3U5H_066_G1444_C2359GUAGUAGCGAAAC
IL_49493.4_Sequence_8 IL_49493.4_IL_3U5H_066_G_1444_C_2359GUAGUAG*CGAAAC
IL_49493.4_Instance_9 IL_49493.4_IL_4A1B_064_G1470_C2354GUAGUAGCGAACC
IL_49493.4_Sequence_9 IL_49493.4_IL_4A1B_064_G_1470_C_2354GUAGUAG*CGAACC
IL_49493.4_Instance_10 IL_49493.4_IL_1S72_020_C585_G572CCAGUAAUGACCG
IL_49493.4_Sequence_10 IL_49493.4_IL_1S72_020_C585_G572CCAGUAA*UGACCG
IL_49493.4_Instance_11 IL_49493.4_IL_3DVZ_001_C2652_G2668CUAGUACGGACCG
IL_49493.4_Sequence_11 IL_49493.4_IL_3DVZ_001_C_2652_G_2668CUAGUAC*GGACCG
IL_49493.4_Instance_12 IL_49493.4_IL_4IOA_096_C2631_G2647CUAGUACGGACCG
IL_49493.4_Sequence_12 IL_49493.4_IL_4IOA_096_C_2631_G_2647CUAGUAC*GGACCG
IL_49493.4_Instance_13 IL_49493.4_IL_3V2F_099_C2652_G2668CUAGUACGGACCG
IL_49493.4_Sequence_13 IL_49493.4_IL_3V2F_099_C_2652_G_2668CUAGUAC*GGACCG

Conserved interactions between motif group positions in IL_49493.4:
1 2 s35 
1 13 cWW 
2 3 s33 
2 12 tSH 
3 5 s55 
3 10 s53 
3 11 tHH 
4 5 cSH 
4 9 s33 
5 6 s35 
5 9 s33 
5 10 tWH 
6 7 s35 
6 9 tHS 
6 10 s55 
7 8 cWW 
7 9 s55 
8 9 s35 
10 11 s35 
11 12 s35 
12 13 s35 
9 5 6BPh
4 10 6BPh
3 11 6BPh
9 4 6BR
6 9 6BR
JAR3D SCFG/MRF model for IL_49493.4:
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 [13] // Initial node C239 - G258 from junction 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.009331601,0.017144707,0.010710502,0.174400287,0.000000000],[0.059304213,0.008909929,0.208735593,0.012170573,0.000000000],[0.010778878,0.189337741,0.002131960,0.021653241,0.000000000],[0.166105499,0.011847821,0.086431832,0.011005623,0.000000000],[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 [1] | Right Index [13] // Basepair C239 - G258 cWW 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.104529735,0.113299638,0.001277766,0.006118877,0.000000000],[0.110346799,0.139011852,0.001277766,0.001277766,0.000000000],[0.142769417,0.001277766,0.006329975,0.044930558,0.000000000],[0.125686650,0.199309903,0.001277766,0.001277766,0.000000000],[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 [12] // Basepair C240 - C257 tSH 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.452436966,0.270694434,0.023721799,0.023598430,0.000000000],[0.027506654,0.000722793,0.061292121,0.035597978,0.000000000],[0.004033740,0.051298036,0.001989661,0.000722793,0.000000000],[0.003962864,0.040976145,0.000722793,0.000722793,0.000000000],[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 [11] // Basepair A241 - A256 tHH 
ClusterNode  | Deletion Probability [0.0000001250000000] | Num Left Bases [2] | Num Right Bases [1] | Left Index [4] | Right Index [10] | Norm Constant [0.502422063208130] // Cluster node G242:U243 and A255:A255
Interaction  | Interacting Bases [2,3] | Pair Probability [[0.023443571,0.004916667,0.024117331,0.004916667,0.000000000],[0.048837108,0.040820184,0.032636071,0.004916667,0.000000000],[0.004916667,0.004916667,0.057540447,0.022934816,0.000000000],[0.606710971,0.004916667,0.060654664,0.052804832,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U243 - A255 tWH 
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.049766715,0.051268642,0.002796023,0.002313363,0.000000000],[0.048139606,0.055918343,0.000594689,0.056354723,0.000000000],[0.034035869,0.018612615,0.038046497,0.531326889,0.000000000],[0.004282260,0.049868653,0.000594689,0.056080422,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G242 - U243 cSH 
InitialNode  | 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 [6] | Right Index [9] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.070082871,0.041560238,0.417526916,0.044166373,0.000000000],[0.062344794,0.040489348,0.003121759,0.042544838,0.000000000],[0.000686958,0.000488494,0.015314889,0.000488494,0.000000000],[0.004053340,0.000488494,0.256153702,0.000488494,0.000000000],[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 [6] | Right Index [9] // Basepair A244 - G254 tHS 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009377379,0.038078223,0.010451230,0.185556239,0.000000000],[0.017484928,0.008065063,0.219573479,0.011737618,0.000000000],[0.010436472,0.210767302,0.002031067,0.054246668,0.000000000],[0.175757611,0.011812423,0.022442019,0.012182279,0.000000000],[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 [7] | Right Index [8] // Basepair G245 - C253 cWW 
HairpinNode  | Num Bases [1] | Left Index [8] | Right Index [8] | 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_49493.4:
> IL_49493.4 IL_2QBG_012 C  239 G  258
CCAGUAG*CGAACG
> IL_49493.4 IL_1S72_007 U  210 G  229
UUAGUAA*UGAACG
> IL_49493.4 IL_3V2F_007 U  239 G  258
UGAGUAG*CGAAAG
> IL_49493.4 IL_1S72_103 G   75 C  106
GGAGUAC*GGAAAC
> IL_49493.4 IL_1S72_049 A 1367 U 2057
AUAGUAG*UGAACU
> IL_49493.4 IL_1S72_090 A 2689 U 2705
AUAGUAC*GGAACU
> IL_49493.4 IL_1NBS_007 U  165 A  143
UGAGUAU*AAAAAA
> IL_49493.4 IL_3U5H_066 G 1444 C 2359
GUAGUAG*CGAAAC
> IL_49493.4 IL_4A1B_064 G 1470 C 2354
GUAGUAG*CGAACC
> IL_49493.4 IL_1S72_020 C  585 G  572
CCAGUAA*UGACCG
> IL_49493.4 IL_3DVZ_001 C 2652 G 2668
CUAGUAC*GGACCG
> IL_49493.4 IL_4IOA_096 C 2631 G 2647
CUAGUAC*GGACCG
> IL_49493.4 IL_3V2F_099 C 2652 G 2668
CUAGUAC*GGACCG