Alignment of IL_25271.2 sequences from 3D to the JAR3D model

Previous group | Next group | List of all groups | Motif atlas entry for IL_25271.2
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

7
15
8
I

16
9


17
8
I

18
8

8
19
7
I

20
7

9
21
6
I

22
6

10
23
5
I

24
5

11
25
4
I

26
4

12
27
3
I

28
3

13
29
2
I

30
2

14
31
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
IL_25271.2_Instance_1 IL_25271.2_IL_3U5F_011_G143_C172GUAUAACGCUAAUAC
IL_25271.2_Sequence_1 IL_25271.2_IL_3U5F_011_G143_C172GUAUAAC*GCUAAUACtrue95001.03
IL_25271.2_Instance_2 IL_25271.2_IL_4BPP_011_G137_C166GGAUAACGCUAAUAC
IL_25271.2_Sequence_2 IL_25271.2_IL_4BPP_011_G137_C166GGAUAAC*GCUAAUACtrue100000.00
IL_25271.2_Instance_3 IL_25271.2_IL_2AW7_012_G147_C175GGAUAACGCUAAUAC
IL_25271.2_Sequence_3 IL_25271.2_IL_2AW7_012_G147_C175GGAUAAC*GCUAAUACtrue100000.00

Conserved interactions between motif group positions in IL_25271.2:
1 2 s35 
1 14 cWW 
2 3 s35 
2 13 cWW 
3 4 s35 
3 12 tWH 
3 13 s55 
4 10 s33 
4 11 tWH 
5 6 s35 
5 10 tHW 
5 11 s55 
6 7 s35 
6 9 tHW 
6 10 s55 
7 8 cWW 
8 9 s35 
9 10 s35 
11 12 s35 
12 13 s35 
13 14 s35 
9 5 7BPh
7 6 7BPh
14 13 7BPh
JAR3D SCFG/MRF model for IL_25271.2:
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 [14] // Initial node G143 - C172 from junction 
BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.003914340,0.055820081,0.004532224,0.074283445,0.000000000],[0.006604600,0.022593563,0.080006995,0.005092413,0.000000000],[0.004475173,0.606828618,0.000825289,0.010585725,0.000000000],[0.073854492,0.037418864,0.009131325,0.004032852,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [14] // Basepair G143 - C172 cWW 
BasepairNode | Deletion Probability [0.0000001200211660] | Pair Probability [[0.033086515,0.015955142,0.229039548,0.079143101,0.000000000],[0.017619624,0.006968133,0.076899009,0.032271219,0.000000000],[0.257684928,0.076367016,0.003061163,0.018168131,0.000000000],[0.091537145,0.030518877,0.019792168,0.011888281,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.016116035,0.966962127,0.016116035,0.000805802] | Right Letter Distribution [0.100000000,0.100000000,0.100000000,0.700000000,0.000000000] | Left Index [2] | Right Index [13] // Basepair U144 - A171 cWW 
BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.423793690,0.003946675,0.338433368,0.003946675,0.000000000],[0.031158431,0.014498516,0.022591591,0.003946675,0.000000000],[0.003946675,0.003946675,0.048887368,0.035214972,0.000000000],[0.018818469,0.003946675,0.023364549,0.019558996,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [12] // Basepair A145 - A169 tWH 
BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.025719646,0.005394014,0.026458819,0.005394014,0.000000000],[0.053578574,0.044783309,0.035804622,0.005394014,0.000000000],[0.005394014,0.005394014,0.063126898,0.025161497,0.000000000],[0.568527570,0.005394014,0.066543467,0.057931515,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [11] // Basepair U146 - A168 tWH 
BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.025719646,0.053578574,0.005394014,0.568527570,0.000000000],[0.005394014,0.044783309,0.005394014,0.005394014,0.000000000],[0.026458819,0.035804622,0.063126898,0.066543467,0.000000000],[0.005394014,0.005394014,0.025161497,0.057931515,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [10] // Basepair A147 - U167 tHW 
BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.004849642,0.459121292,0.000614279,0.006101612,0.000000000],[0.000614279,0.020347277,0.000614279,0.000614279,0.000000000],[0.034415907,0.398668342,0.004195929,0.002940416,0.000000000],[0.000614279,0.004299951,0.006344208,0.055644030,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [6] | Right Index [9] // Basepair A148 - C166 tHW 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.003849333,0.006602625,0.004473835,0.073832405,0.000000000],[0.055803388,0.023014360,0.606655854,0.037407674,0.000000000],[0.004530869,0.079983068,0.000825042,0.009128594,0.000000000],[0.074261230,0.005090890,0.010582560,0.003958272,0.000000000],[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 C149 - G165 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_25271.2:
> IL_25271.2 IL_3U5F_011 G  143 C  172
GUAUAAC*GCUAAUAC
> IL_25271.2 IL_4BPP_011 G  137 C  166
GGAUAAC*GCUAAUAC
> IL_25271.2 IL_2AW7_012 G  147 C  175
GGAUAAC*GCUAAUAC