Alignment of IL_19048.1 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
3
I

6
4

3
7
4
I

8
4

4
9
4
I

10
4

5
11
4
I

12
4

6
13
5
I

14
6

7
15
6
I

16
7


17
6
I

18
6

8
19
5
I

20
4

9
21
4
I

22
4

10
23
4
I

24
4

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_19048.1_Instance_1 IL_19048.1,IL_4WF9_113,A20_U59AGGUCACAUUAAGGU
IL_19048.1_Sequence_1 IL_19048.14WF9_A20_U59AGGUCACA*UUAAGGUtrue100000.00

Conserved interactions between motif group positions in IL_19048.1:
1 2 s35 
1 14 cWW 
2 3 s35 
2 13 bif 
2 14 s55 
3 9 s33 
3 12 bif 
3 13 s55 
4 5 s35 
5 6 s35 
6 7 s35 
6 9 cWW 
6 12 cSW 
7 8 cWW 
9 11 cSH 
10 11 s35 
11 12 s35 
12 13 s35 
13 14 s35 
9 3 7BR
JAR3D SCFG/MRF model for IL_19048.1:
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 [14] // Initial node
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.009374836,0.022228469,0.010012528,0.216037101,0.000000000],[0.017691617,0.009675113,0.196088410,0.010461402,0.000000000],[0.009993038,0.198630499,0.002061361,0.053740648,0.000000000],[0.197964449,0.011137350,0.023240462,0.011662716,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [14] // Basepair A20 - U59 cWW 
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.286859111,0.207254157,0.003021830,0.003021830,0.000000000],[0.012680128,0.008875223,0.003021830,0.003021830,0.000000000],[0.003021830,0.003021830,0.312083968,0.142029115,0.000000000],[0.003021830,0.003021830,0.003021830,0.003021830,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [13] // Basepair G21 - G58 bif 
ClusterNode  | Deletion Probability [0.000000000000000000001906753397244242883095262764002054089856] | Num Left Bases [4] | Num Right Bases [4] | Left Index [3] | Right Index [12] | Norm Constant [0.139964537215204] // Cluster node 4WF9|1|Y|G|22:4WF9|1|Y|C|26 and 4WF9|1|Y|U|54:4WF9|1|Y|G|57
Interaction  | Interacting Bases [4,5] | Pair Probability [[0.006110784,0.005581227,0.016324689,0.035138048,0.000000000],[0.006124365,0.004799357,0.009138207,0.702276689,0.000000000],[0.017248371,0.008804486,0.001384751,0.030741174,0.000000000],[0.007481688,0.117508923,0.006715758,0.024621483,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4WF9|1|Y|C|26 - 4WF9|1|Y|U|54 cWW 
Interaction  | Interacting Bases [1,8] | Pair Probability [[0.286859111,0.207254157,0.003021830,0.003021830,0.000000000],[0.012680128,0.008875223,0.003021830,0.003021830,0.000000000],[0.003021830,0.003021830,0.312083968,0.142029115,0.000000000],[0.003021830,0.003021830,0.003021830,0.003021830,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4WF9|1|Y|G|22 - 4WF9|1|Y|G|57 bif 
Interaction  | Interacting Bases [4,8] | Pair Probability [[0.008445076,0.008445076,0.008445076,0.008445076,0.000000000],[0.008445076,0.008445076,0.854408615,0.008445076,0.000000000],[0.008445076,0.027360318,0.008445076,0.008445076,0.000000000],[0.008445076,0.008445076,0.008445076,0.008445076,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4WF9|1|Y|C|26 - 4WF9|1|Y|G|57 cSW 
Interaction  | Interacting Bases [5,7] | Pair Probability [[0.049690992,0.047063074,0.002405339,0.006710993,0.000000000],[0.048534439,0.045419489,0.000516385,0.004323811,0.000000000],[0.004407621,0.000516385,0.043501911,0.042273287,0.000000000],[0.268093732,0.221566027,0.002581927,0.212394587,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4WF9|1|Y|U|54 - 4WF9|1|Y|A|56 cSH 
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.166666667,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.500000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.166666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.166666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 4WF9|1|Y|C|24
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.500000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.166666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.166666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.166666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 4WF9|1|Y|A|25
Interaction  | Interacting Bases [6,6] | Pair Probability [[0.500000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.166666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.166666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.166666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion 4WF9|1|Y|A|55
Insertion    | Location [1] | Length Distribution [0.045351474,0.907029478,0.045351474,0.002267574] | Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000]// Insertion after nucleotide 3, position 1 in cluster node
InitialNode  | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [7] | Right Index [8] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009374836,0.022228469,0.010012528,0.216037101,0.000000000],[0.017691617,0.009675113,0.196088410,0.010461402,0.000000000],[0.009993038,0.198630499,0.002061361,0.053740648,0.000000000],[0.197964449,0.011137350,0.023240462,0.011662716,0.000000000],[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 A27 - U53 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_19048.1:
> IL_19048.1  4WF9 A   20 U   59
AGGUCACA*UUAAGGU