Alignment of IL_68243.1 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
3

3
7
3
I

8
3

4
9
4
I

10
5

5
11
6
I

12
9

6
13
9
I

14
10

7
15
10
I

16
11


17
10
I

18
10

8
19
9
I

20
9

9
21
8
I

22
7

10
23
4
I

24
3

11
25
3
I

26
3

12
27
2
I

28
2

13
29
1
I


In
acceptance
region

Cutoff
score
Full
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distance
Interior
edit
distance
Alignment
score
deficit
IL_68243.1_Instance_1 IL_68243.1,IL_9DFE_024,C844_G934CGCUGACGGUGGAG
IL_68243.1_Sequence_1 IL_68243.19DFE_C844_G934CGCUGAC*GGUGGAGtrue100000.00

Conserved interactions between motif group positions in IL_68243.1:
1 2 s33 
1 13 cWW 
2 12 cHW 
3 4 s53 
3 10 s35 
3 11 cWW 
4 12 cWW 
4 13 s55 
5 6 s35 
5 9 s33 
5 11 perp 
5 12 perp 
6 7 s35 
6 9 tHS 
7 8 cWW 
7 9 s55 
8 9 s35 
10 11 s55 
11 12 s35 
12 13 s35 
2 2 2BPh
9 5 6BPh
7 6 7BPh
3 2 7BR
4 2 7BR
6 9 6BR
JAR3D SCFG/MRF model for IL_68243.1:
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 [0.0000224390099112] | 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 [13] // Basepair C844 - G934 cWW 
ClusterNode  | Deletion Probability [0.000000000000015254027177953870338373321144532320374926368314] | Num Left Bases [3] | Num Right Bases [2] | Left Index [2] | Right Index [12] | Norm Constant [0.434514801692339] // Cluster node 9DFE|1|1A|G|845:9DFE|1|1A|U|847 and 9DFE|1|1A|G|931:9DFE|1|1A|A|933
Interaction  | Interacting Bases [2,4] | Pair Probability [[0.004741436,0.008502533,0.005450864,0.098834917,0.000000000],[0.050405519,0.024145075,0.529397411,0.034282440,0.000000000],[0.005512079,0.100964543,0.001038993,0.011667026,0.000000000],[0.100116212,0.006606094,0.013310241,0.005024617,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 9DFE|1|1A|C|846 - 9DFE|1|1A|G|931 cWW 
Interaction  | Interacting Bases [1,5] | Pair Probability [[0.000947917,0.000947917,0.082044077,0.004084912,0.000000000],[0.000947917,0.009900096,0.000947917,0.000947917,0.000000000],[0.673442726,0.006635417,0.068241646,0.026881602,0.000000000],[0.081999547,0.004176819,0.000947917,0.036905658,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 9DFE|1|1A|G|845 - 9DFE|1|1A|A|933 cHW 
Interaction  | Interacting Bases [3,5] | Pair Probability [[0.004273342,0.008298869,0.004687582,0.092862112,0.000000000],[0.010427037,0.004650493,0.093174546,0.005224362,0.000000000],[0.004696725,0.091982091,0.000966953,0.010901747,0.000000000],[0.493377563,0.024536423,0.126044604,0.023895553,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 9DFE|1|1A|U|847 - 9DFE|1|1A|A|933 cWW 
Insertion    | Location [4] | Length Distribution [0.045351474,0.907029478,0.045351474,0.002267574] | Letter Distribution [0.166666667,0.166666667,0.500000000,0.166666667,0.000000000]// Insertion after nucleotide 11, position 4 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 [5] | Right Index [10] // Initial node 9DFE|1|1A|G|848 - 9DFE|1|1A|U|930 from node 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.166666667,0.166666667,0.500000000,0.166666667,0.000000000] | Position [1] | Left Index [5] | Right Index [10] // Fixed node on left for 9DFE|1|1A|G|848
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 [6] | Right Index [10] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000] | Position [2] | Left Index [6] | Right Index [10] // Fixed node on right for 9DFE|1|1A|U|930
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 [6] | Right Index [9] // New Initial node after Fixed node
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 [9] // Basepair A849 - G928 tHS 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.003781516,0.006781167,0.004347319,0.078825460,0.000000000],[0.056281056,0.026959555,0.589952696,0.038278585,0.000000000],[0.004396140,0.080523937,0.000828645,0.009304998,0.000000000],[0.079847353,0.005268669,0.010615539,0.004007366,0.000000000],[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 C850 - G927 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_68243.1:
> IL_68243.1  9DFE C  844 G  934
CGCUGAC*GGUGGAG