Alignment of IL_09587.1 sequences from 3D to the JAR3D model

Previous group | Next group | List of all groups | Motif atlas entry for IL_09587.1
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
2

2
5
3
I

6
4

3
7
5
I

8
12

4
9
12
I

10
13

5
11
13
I

12
14


13
13
I

14
13

6
15
12
I

16
12

7
17
11
I

18
10

8
19
9
I

20
8

9
21
7
I

22
6

10
23
3
I

24
2

11
25
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
IL_09587.1_Instance_1 IL_09587.1_IL_2AW7_053_G1124_C1149GUUGCGAACUC
IL_09587.1_Sequence_1 IL_09587.1_IL_2AW7_053_G_1124_C_1149GUUGC*GAACUCtrue100000.00
IL_09587.1_Instance_2 IL_09587.1_IL_4IOA_107_G46_C40GAACUGCACCCC
IL_09587.1_Sequence_2 IL_09587.1_IL_4IOA_107_G46_C40GAACUG*CACCCCtrue93001.28

Conserved interactions between motif group positions in IL_09587.1:
1 2 cSH 
1 4 s35 
1 7 s33 
1 11 cWW 
2 3 s35 
2 4 s35 
3 4 s35 
4 5 s35 
4 7 cWW 
5 6 cWW 
5 7 s55 
6 7 s35 
7 9 perp 
8 9 s35 
9 10 s35 
10 11 s35 
10 5 6BR
JAR3D SCFG/MRF model for IL_09587.1:
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 [11] // Initial node G1124 - C1149 from junction 
ClusterNode  | Deletion Probability [0.0000000079308950] | Num Left Bases [2] | Num Right Bases [1] | Left Index [1] | Right Index [11] | Norm Constant [0.250704046930271] // Cluster node G1124:U1125 and C1149:C1149
Interaction  | Interacting Bases [1,3] | Pair Probability [[0.010195092,0.020769450,0.011804402,0.193474890,0.000000000],[0.017202006,0.008406578,0.208382157,0.013263440,0.000000000],[0.011655809,0.234558465,0.002149506,0.027571043,0.000000000],[0.192357660,0.013922753,0.023782986,0.010503762,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G1124 - C1149 cWW 
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.098479164,0.101451202,0.005532816,0.004577719,0.000000000],[0.095259415,0.110652104,0.001176781,0.111515620,0.000000000],[0.108552012,0.005261563,0.010755287,0.127482021,0.000000000],[0.008473804,0.098680881,0.001176781,0.110972829,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G1124 - U1125 cSH 
Insertion    | Location [1] | Length Distribution [0.493381468,0.493381468,0.012635379,0.000601685] | Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000]// Insertion after nucleotide 1, position 1 in cluster node
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 [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] // Initial node U1126 - U1148 from junction 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.125000000,0.375000000,0.125000000,0.375000000,0.000000000] | Position [1] | Left Index [3] | Right Index [10] // Fixed node on left
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 [4] | Right Index [10] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.041666667,0.458333333,0.041666667,0.458333333,0.000000000] | Position [2] | Left Index [4] | Right Index [10] // Fixed node on right
InitialNode  | Left Length Distribution [1.000000000] | 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] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.125000000,0.625000000,0.125000000,0.125000000,0.000000000] | Position [2] | Left Index [4] | Right Index [9] // Fixed node on right
InitialNode  | Left Length Distribution [1.000000000] | 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 [8] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.375000000,0.375000000,0.125000000,0.125000000,0.000000000] | Position [2] | Left Index [4] | Right Index [8] // Fixed node on right
InitialNode  | Left Length Distribution [1.000000000] | 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 [7] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.027337184,0.017117650,0.175918530,0.111763840,0.000000000],[0.019469338,0.007660610,0.106704541,0.027034975,0.000000000],[0.192715421,0.106021772,0.002856825,0.019671972,0.000000000],[0.125621360,0.025689616,0.021954305,0.012462061,0.000000000],[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 [7] // Basepair G1127 - A1145 cWW 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.010112949,0.018987468,0.011731285,0.192935737,0.000000000],[0.018987829,0.008487010,0.221492059,0.013594505,0.000000000],[0.011731300,0.221491395,0.002149724,0.025679421,0.000000000],[0.192935850,0.013594439,0.025679804,0.010409224,0.000000000],[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 [5] | Right Index [6] // Basepair C1128 - G1144 cWW 
HairpinNode  | Num Bases [1] | Left Index [6] | Right Index [6] | 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_09587.1:
> IL_09587.1 IL_2AW7_053 G 1124 C 1149
GUUGC*GAACUC
> IL_09587.1 IL_4IOA_107 G   46 C   40
GAACUG*CACCCC