Alignment of IL_33964.1 sequences from 3D to the JAR3D model

Previous group | Next group | List of all groups | Motif atlas entry for IL_33964.1
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
3

2
5
3
I

6
4

3
7
5
I

8
6

4
9
7
I

10
8

5
11
8
I

12
9

6
13
9
I

14
10


15
9
I

16
9

7
17
8
I

18
8

8
19
7
I

20
6

9
21
6
I

22
6

10
23
6
I

24
6

11
25
6
I

26
6

12
27
6
I

28
6

13
29
6
I

30
6

14
31
6
I

32
6

15
33
6
I

34
6

16
35
6
I

36
6

17
37
6
I

38
6

18
39
3
I

40
3

19
41
2
I

42
2

20
43
1
I


In
acceptance
region

Cutoff
score
Full
edit
distance
Interior
edit
distance
Alignment
score
deficit
IL_33964.1_Instance_1 IL_33964.1_IL_3V2F_040_G1024_C1140GGUAAAGCGAAAAUGAUCGGGGC
IL_33964.1_Sequence_1 IL_33964.1_IL_3V2F_040_G_1024_C_1140GGUAAAG*CGAAAAUGAUCGGGGC
IL_33964.1_Instance_2 IL_33964.1_IL_4IOA_036_G1035_C1150GGUUAAGCGAAAAUGAUCGGGGC
IL_33964.1_Sequence_2 IL_33964.1_IL_4IOA_036_G_1035_C_1150GGUUAAG*CGAAAAUGAUCGGGGC

Conserved interactions between motif group positions in IL_33964.1:
1 2 s33 
1 20 cWW 
2 15 s55 
2 19 tWW 
3 4 s35 
3 9 s35 
4 5 s35 
4 8 s33 
4 9 tHH 
5 6 s35 
5 8 tHS 
6 7 cWW 
6 8 s55 
7 8 s35 
8 9 s33 
10 11 s35 
12 13 s35 
13 14 s35 
15 17 s33 
15 18 tWH 
15 19 s55 
16 17 s35 
17 18 s35 
18 19 s35 
19 20 s35 
9 4 6BPh
8 5 6BPh
4 9 6BPh
15 18 7BPh
5 8 6BR
JAR3D SCFG/MRF model for IL_33964.1:
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 [20] // Initial node G1024 - C1140 from junction 
BasepairNode | Deletion Probability [0.0000229437914523] | 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]] | 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 [20] // Basepair G1024 - C1140 cWW 
BasepairNode | Deletion Probability [0.0000001182498160] | Pair Probability [[0.350791599,0.040670272,0.003713382,0.018474231,0.000000000],[0.038122680,0.015188207,0.012119555,0.015027400,0.000000000],[0.003713382,0.012224256,0.390946071,0.024547920,0.000000000],[0.018369341,0.015013760,0.022729598,0.018348346,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.023781213,0.951248514,0.023781213,0.001189061] | Left Letter Distribution [0.125000000,0.125000000,0.125000000,0.625000000,0.000000000] | 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 [19] // Basepair G1025 - G1139 tWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.375000000,0.125000000,0.125000000,0.375000000,0.000000000] | Position [1] | Left Index [3] | Right Index [18] // 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 [18] // New Initial node after Fixed node
ClusterNode  | Deletion Probability [0.000000000000000000000000000001190325670174320300000000000000] | Num Left Bases [1] | Num Right Bases [10] | Left Index [4] | Right Index [18] | Norm Constant [1.000000000000000] // Cluster node A1028:A1028 and A1126:G1138
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.874929957,0.024665076,0.006099772,0.006109041,0.000000000],[0.015780104,0.000174556,0.015006241,0.012399021,0.000000000],[0.007633394,0.014483953,0.000427640,0.000174556,0.000000000],[0.007508515,0.014259062,0.000174556,0.000174556,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A1028 - A1126 tHH 
Interaction  | Interacting Bases [8,11] | Pair Probability [[0.003687486,0.000644191,0.008136957,0.000644191,0.000000000],[0.418081731,0.020327964,0.470541785,0.004509339,0.000000000],[0.000644191,0.000644191,0.003127816,0.005098951,0.000000000],[0.004276042,0.000644191,0.002895410,0.056095561,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction C1135 - G1138 tWH 
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.625000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.125000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.125000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.125000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion A1128
Interaction  | Interacting Bases [4,4] | Pair Probability [[0.625000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.125000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.125000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.125000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion A1129
Interaction  | Interacting Bases [5,5] | Pair Probability [[0.125000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.125000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.625000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.125000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion G1131
Interaction  | Interacting Bases [6,6] | Pair Probability [[0.625000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.125000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.125000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.125000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion A1132
Interaction  | Interacting Bases [7,7] | Pair Probability [[0.125000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.125000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.125000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.625000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion U1133
Interaction  | Interacting Bases [9,9] | Pair Probability [[0.125000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.125000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.625000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.125000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion G1136
Interaction  | Interacting Bases [10,10] | Pair Probability [[0.125000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.125000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.625000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.125000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion G1137
Insertion    | Location [2] | Length Distribution [0.023781213,0.951248514,0.023781213,0.001189061] | Letter Distribution [0.625000000,0.125000000,0.125000000,0.125000000,0.000000000]// Insertion after nucleotide 9, position 2 in cluster node
Insertion    | Location [4] | Length Distribution [0.023781213,0.951248514,0.023781213,0.001189061] | Letter Distribution [0.125000000,0.125000000,0.125000000,0.625000000,0.000000000]// Insertion after nucleotide 11, position 4 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 [5] | Right Index [8] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.043716223,0.044105167,0.388315159,0.047517987,0.000000000],[0.050956855,0.046228647,0.003687073,0.045777520,0.000000000],[0.000526725,0.000526725,0.017863095,0.000526725,0.000000000],[0.002508196,0.000526725,0.306690455,0.000526725,0.000000000],[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 [5] | Right Index [8] // Basepair A1029 - G1125 tHS 
BasepairNode | Deletion Probability [0.0000249735224443] | 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]] | 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 G1030 - C1124 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_33964.1:
> IL_33964.1 IL_3V2F_040 G 1024 C 1140
GGUAAAG*CGAAAAUGAUCGGGGC
> IL_33964.1 IL_4IOA_036 G 1035 C 1150
GGUUAAG*CGAAAAUGAUCGGGGC