Alignment of IL_17682.1 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
7

3
7
7
I

8
8

4
9
9
I

10
10

5
11
10
I

12
11

6
13
11
I

14
12

7
15
12
I

16
13

8
17
13
I

18
14


19
13
I

20
13

9
21
12
I

22
12

10
23
11
I

24
11

11
25
10
I

26
10

12
27
9
I

28
8

13
29
8
I

30
8

14
31
7
I

32
7

15
33
6
I

34
5

16
35
2
I

36
2

17
37
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
IL_17682.1_Instance_1 IL_17682.1_IL_4A1B_002_C29_G51CUGAACUUAUCAGUAAG
IL_17682.1_Sequence_1 IL_17682.1_IL_4A1B_002_C29_G51CUGAACUU*AUCAGUAAGtrue100000.00

Conserved interactions between motif group positions in IL_17682.1:
1 2 s35 
1 17 cWW 
2 3 s35 
2 17 s55 
3 13 s33 
3 14 s33 
3 15 tSH 
4 5 s35 
4 14 tHW 
4 15 s55 
5 6 s35 
5 12 tHH 
6 7 s35 
6 11 tHS 
7 8 s35 
7 10 cWW 
8 9 cWW 
8 10 s55 
9 10 s35 
10 11 s35 
11 12 s33 
12 14 s55 
13 14 cSH 
15 16 s35 
16 17 s35 
13 4 6BPh
7 6 7BPh
3 14 6BPh
15 3 6BR
14 13 7BR
JAR3D SCFG/MRF model for IL_17682.1:
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 [17] // Initial node C29 - G51 from junction 
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.010130121,0.017375838,0.011773595,0.194301502,0.000000000],[0.020979332,0.008652269,0.227023763,0.014063448,0.000000000],[0.011923689,0.210487931,0.002171228,0.024023321,0.000000000],[0.195430021,0.013397471,0.027849658,0.010416811,0.000000000],[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 [17] // Basepair C29 - G51 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000] | Position [1] | Left Index [2] | Right Index [16] // Fixed node on left
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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [16] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000] | Position [2] | Left Index [3] | Right Index [16] // 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 [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [15] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.044149057,0.051461378,0.000531940,0.002533030,0.000000000],[0.044541851,0.046686356,0.000531940,0.000531940,0.000000000],[0.382258874,0.003723579,0.018039957,0.309726994,0.000000000],[0.047988462,0.046230763,0.000531940,0.000531940,0.000000000],[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 [15] // Basepair G31 - A49 tSH 
ClusterNode  | Deletion Probability [0.0000001250000000] | Num Left Bases [1] | Num Right Bases [2] | Left Index [4] | Right Index [14] | Norm Constant [0.565894006694928] // Cluster node A32:A32 and G47:U48
Interaction  | Interacting Bases [1,3] | Pair Probability [[0.006980622,0.014541871,0.001464000,0.741901139,0.000000000],[0.001464000,0.012154730,0.001464000,0.007320001,0.000000000],[0.007181242,0.009717806,0.017133401,0.090303495,0.000000000],[0.001464000,0.001464000,0.006829134,0.078616557,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A32 - U48 tHW 
Interaction  | Interacting Bases [2,3] | Pair Probability [[0.055679592,0.057359966,0.003128224,0.002588218,0.000000000],[0.053859163,0.062562107,0.000665346,0.063050334,0.000000000],[0.038079735,0.020824015,0.042566873,0.475642955,0.000000000],[0.004791044,0.055793641,0.000665346,0.062743443,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G47 - U48 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 [5] | Right Index [12] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.214636672,0.041327996,0.010220578,0.010236110,0.000000000],[0.026440627,0.002047357,0.176007769,0.145427765,0.000000000],[0.012790266,0.169881869,0.005015775,0.002047357,0.000000000],[0.012581023,0.167244122,0.002047357,0.002047357,0.000000000],[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 [5] | Right Index [12] // Basepair A33 - A46 tHH 
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.067529094,0.118956523,0.149216401,0.143517090,0.000000000],[0.149836953,0.179916717,0.001700157,0.147086012,0.000000000],[0.001700157,0.001700157,0.007466133,0.001700157,0.000000000],[0.007270178,0.001700157,0.019003954,0.001700157,0.000000000],[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 C34 - C45 tHS 
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.003693601,0.038923294,0.003555430,0.008560230,0.000000000],[0.004562562,0.004644083,0.005369317,0.003919935,0.000000000],[0.003486594,0.005468847,0.001119153,0.011395395,0.000000000],[0.050318365,0.029785294,0.031889577,0.793308324,0.000000000],[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 U35 - U44 cWW 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009206316,0.020335270,0.009916234,0.209350778,0.000000000],[0.024742834,0.009627484,0.195778801,0.010479833,0.000000000],[0.009933160,0.194648267,0.002175103,0.023883287,0.000000000],[0.227411257,0.010406240,0.028134421,0.013970716,0.000000000],[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 U36 - A43 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_17682.1:
> IL_17682.1 IL_4A1B_002 C   29 G   51
CUGAACUU*AUCAGUAAG