Alignment of IL_18487.1 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
4
I

6
5

3
7
6
I

8
7

4
9
8
I

10
9

5
11
10
I

12
13

6
13
13
I

14
13

7
15
14
I

16
15


17
14
I

18
13

8
19
13
I

20
13

9
21
13
I

22
13

10
23
13
I

24
13

11
25
12
I

26
11

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_18487.1_Instance_1 IL_18487.1,IL_8P9A_365,G21_C58GAAAGCAUUAAGC
IL_18487.1_Sequence_1 IL_18487.18P9A_G21_C58GAAAGCA*UUAAGCtrue100000.00
IL_18487.1_Instance_2 IL_18487.1,IL_8OI5_135,G21_C58GAAAGCAUUAAGC
IL_18487.1_Sequence_2 IL_18487.18OI5_G21_C58GAAAGCA*UUAAGCtrue100000.00

Conserved interactions between motif group positions in IL_18487.1:
1 13 cWW 
2 3 s35 
3 4 s35 
4 5 s35 
5 6 s35 
6 7 s35 
6 9 cWW 
7 8 cWW 
7 9 s55 
7 11 cSW 
8 9 s35 
9 11 cSH 
10 11 s35 
11 12 s35 
12 13 s35 
13 12 7BPh
JAR3D SCFG/MRF model for IL_18487.1:
Character Definition | A,C,G,U,* // Identity and order of characters in matrices
InitialNode  | Left Length Distribution [0.999900000,0.000100000] | Left Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Right Length Distribution [0.999900000,0.000100000] | Right Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Left Index [1] | Right Index [13] // Initial node
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.003823887,0.055746509,0.004354386,0.079088977,0.000000000],[0.006716761,0.026247934,0.079759134,0.005218628,0.000000000],[0.004306029,0.594150318,0.000820775,0.010514714,0.000000000],[0.078076789,0.037915021,0.009216620,0.004043518,0.000000000],[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 [13] // Basepair G21 - C58 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.625000000,0.125000000,0.125000000,0.125000000,0.000000000] | Position [1] | Left Index [2] | Right Index [12] // Fixed node on left for 8P9A|1|AS|A|22
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 [3] | Right Index [12] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.625000000,0.125000000,0.125000000,0.125000000,0.000000000] | Position [1] | Left Index [3] | Right Index [12] // Fixed node on left for 8P9A|1|AS|A|23
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 [12] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.625000000,0.125000000,0.125000000,0.125000000,0.000000000] | Position [1] | Left Index [4] | Right Index [12] // Fixed node on left for 8P9A|1|AS|A|24
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 [5] | Right Index [12] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.125000000,0.125000000,0.625000000,0.125000000,0.000000000] | Position [1] | Left Index [5] | Right Index [12] // Fixed node on left for 8P9A|1|AS|G|25
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 [6] | Right Index [12] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.125000000,0.125000000,0.625000000,0.125000000,0.000000000] | Position [2] | Left Index [6] | Right Index [12] // Fixed node on right for 8P9A|1|AS|G|57
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 [6] | Right Index [11] // New Initial node after Fixed node
ClusterNode  | Deletion Probability [0.000000000000015625000000000002841172490091166211760239940914] | Num Left Bases [2] | Num Right Bases [4] | Left Index [6] | Right Index [11] | Norm Constant [0.025959859916521] // Cluster node 8P9A|1|AS|C|26:8P9A|1|AS|A|27 and 8P9A|1|AS|U|53:8P9A|1|AS|A|56
Interaction  | Interacting Bases [2,3] | Pair Probability [[0.009282926,0.022010543,0.009914366,0.223723012,0.000000000],[0.017518170,0.009580259,0.194165974,0.010358839,0.000000000],[0.009895067,0.196683142,0.002041152,0.053213779,0.000000000],[0.196023621,0.011028161,0.023012614,0.011548375,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8P9A|1|AS|A|27 - 8P9A|1|AS|U|53 cWW 
Interaction  | Interacting Bases [1,4] | Pair Probability [[0.016467838,0.015040744,0.043993102,0.018938574,0.000000000],[0.016504437,0.012933698,0.024626383,0.392781921,0.000000000],[0.046482313,0.023727047,0.003731741,0.016568763,0.000000000],[0.020162263,0.316672610,0.018098171,0.013270395,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8P9A|1|AS|C|26 - 8P9A|1|AS|U|54 cWW 
Interaction  | Interacting Bases [2,6] | Pair Probability [[0.239509115,0.016161407,0.021852929,0.007850573,0.000000000],[0.202271002,0.013181506,0.002199013,0.008281367,0.000000000],[0.213757220,0.002199013,0.028008345,0.006553550,0.000000000],[0.206617428,0.013377455,0.010460203,0.007719875,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8P9A|1|AS|A|27 - 8P9A|1|AS|A|56 cSW 
Interaction  | Interacting Bases [4,6] | Pair Probability [[0.112170041,0.106237908,0.005429695,0.015149071,0.000000000],[0.109559296,0.102527757,0.001165664,0.009760361,0.000000000],[0.009949550,0.001165664,0.098199110,0.095425674,0.000000000],[0.136174205,0.100030487,0.001165664,0.095889854,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8P9A|1|AS|U|54 - 8P9A|1|AS|A|56 cSH 
Interaction  | Interacting Bases [5,5] | 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 8P9A|1|AS|A|55
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 [8] | Right Index [7] // New Initial node after Cluster
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_18487.1:
> IL_18487.1  8P9A G   21 C   58
GAAAGCA*UUAAGC
> IL_18487.1  8OI5 G   21 C   58
GAAAGCA*UUAAGC