Alignment of IL_59724.1 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
5

4
9
5
I

10
5

5
11
6
I

12
7

6
13
7
I

14
8

7
15
8
I

16
9

8
17
9
I

18
10


19
9
I

20
9

9
21
8
I

22
8

10
23
7
I

24
7

11
25
6
I

26
5

12
27
4
I

28
4

13
29
3
I

30
3

14
31
2
I

32
2

15
33
1
I


In
acceptance
region

Cutoff
score
Full
edit
distance
Interior
edit
distance
Alignment
score
deficit
IL_59724.1_Instance_1 IL_59724.1,IL_4V9F_012,C355_G296CCAGUACGCCGACCG
IL_59724.1_Sequence_1 IL_59724.14V9F_C355_G296CCAGUACG*CCGACCGtrue100000.00

Conserved interactions between motif group positions in IL_59724.1:
1 2 s35 
1 15 cWW 
2 3 s33 
2 14 bif 
3 5 s55 
3 12 s53 
3 13 tHH 
4 5 cSH 
4 11 s33 
5 6 s35 
5 11 s33 
5 12 tWH 
6 7 s35 
6 11 tHS 
6 12 s55 
7 8 s35 
7 10 bif 
8 9 cWW 
8 10 s55 
9 10 s35 
10 11 s35 
12 13 s35 
13 14 s35 
14 15 s35 
11 5 6BPh
4 12 6BPh
3 13 6BPh
6 11 6BR
JAR3D SCFG/MRF model for IL_59724.1:
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 [15] // Initial node
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.009631000,0.017270697,0.011072020,0.200757565,0.000000000],[0.020477154,0.009808895,0.220945507,0.013927182,0.000000000],[0.011196362,0.205083350,0.002110445,0.023698544,0.000000000],[0.203360186,0.013418572,0.027036311,0.010206209,0.000000000],[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 [15] // Basepair C355 - G296 cWW 
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.020531000,0.024259742,0.007357494,0.007357494,0.000000000],[0.086166243,0.745650406,0.007357494,0.007357494,0.000000000],[0.007357494,0.007357494,0.021609225,0.028208442,0.000000000],[0.007357494,0.007357494,0.007357494,0.007357494,0.000000000],[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 [14] // Basepair C356 - C295 bif 
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.336676802,0.428983641,0.023107542,0.042867175,0.000000000],[0.007325811,0.000598690,0.048529887,0.050808877,0.000000000],[0.002731835,0.049692310,0.000636507,0.000598690,0.000000000],[0.002781463,0.003463394,0.000598690,0.000598690,0.000000000],[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 [3] | Right Index [13] // Basepair A357 - C294 tHH 
ClusterNode  | Deletion Probability [0.0000001250000000] | Num Left Bases [2] | Num Right Bases [1] | Left Index [4] | Right Index [12] | Norm Constant [0.259025769291484] // Cluster node 4V9F|1|0|G|358:4V9F|1|0|U|359 and 4V9F|1|0|A|293:4V9F|1|0|A|293
Interaction  | Interacting Bases [2,3] | Pair Probability [[0.018961504,0.004196211,0.019694625,0.004196211,0.000000000],[0.042198433,0.338134433,0.004196211,0.004196211,0.000000000],[0.004196211,0.010058595,0.031911832,0.018663303,0.000000000],[0.429522110,0.004196211,0.024345914,0.041331983,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4V9F|1|0|U|359 - 4V9F|1|0|A|293 tWH 
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.031413984,0.032009409,0.001759976,0.031282354,0.000000000],[0.023452592,0.035343467,0.000389689,0.031347933,0.000000000],[0.192125245,0.002727821,0.234360049,0.282683054,0.000000000],[0.031901402,0.031709893,0.000389689,0.037103443,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4V9F|1|0|G|358 - 4V9F|1|0|U|359 cSH 
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 [6] | Right Index [11] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.044130649,0.044458508,0.380732303,0.049261589,0.000000000],[0.046718239,0.046610059,0.003708313,0.046358426,0.000000000],[0.000529759,0.000529759,0.018128765,0.000529759,0.000000000],[0.002496756,0.000529759,0.314747597,0.000529759,0.000000000],[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 [6] | Right Index [11] // Basepair A360 - G292 tHS 
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.020531000,0.086166243,0.007357494,0.007357494,0.000000000],[0.024259742,0.745650406,0.007357494,0.007357494,0.000000000],[0.007357494,0.007357494,0.021609225,0.007357494,0.000000000],[0.007357494,0.007357494,0.028208442,0.007357494,0.000000000],[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 [7] | Right Index [10] // Basepair C361 - C291 bif 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009830065,0.020472507,0.011193821,0.203314028,0.000000000],[0.017266777,0.009639366,0.205036802,0.013415526,0.000000000],[0.011069507,0.220897605,0.002109966,0.027030175,0.000000000],[0.200711998,0.013924020,0.023693165,0.010394672,0.000000000],[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 [8] | Right Index [9] // Basepair G362 - C290 cWW 
HairpinNode  | Num Bases [1] | Left Index [9] | Right Index [9] | 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_59724.1:
> IL_59724.1  4V9F C  355 G  296
CCAGUACG*CCGACCG