Alignment of IL_29357.1 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
5
I

8
6

4
9
6
I

10
6

5
11
6
I

12
6

6
13
6
I

14
6

7
15
6
I

16
6

8
17
7
I

18
8

9
19
8
I

20
9

10
21
9
I

22
10


23
9
I

24
9

11
25
8
I

26
8

12
27
7
I

28
6

13
29
6
I

30
6

14
31
6
I

32
6

15
33
6
I

34
6

16
35
3
I

36
3

17
37
2
I

38
2

18
39
1
I


In
acceptance
region

Cutoff
score
Full
edit
distance
Interior
edit
distance
Alignment
score
deficit
IL_29357.1_Instance_1 IL_29357.1,IL_8DK7_004,C21_G11CCCUUGGCAGCGAUACCAG
IL_29357.1_Sequence_1 IL_29357.18DK7_C21_G11CCCUUGGCAGC*GAUACCAGtrue100000.00

Conserved interactions between motif group positions in IL_29357.1:
1 2 s35 
1 18 cWW 
2 14 s33 
2 17 bif 
2 18 s55 
3 13 s33 
3 14 s55 
4 8 cWH 
4 13 tHW 
5 7 s33 
6 7 s35 
6 14 cWW 
6 16 cWW 
6 17 s55 
7 15 cWW 
7 16 s55 
8 9 s35 
8 13 tHS 
9 10 s35 
9 12 cWW 
10 11 cWW 
11 12 s35 
12 13 s35 
14 15 cSH 
15 16 s35 
16 17 s35 
17 18 s35 
15 14 7BR
JAR3D SCFG/MRF model for IL_29357.1:
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 [18] // 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 [18] // Basepair C21 - G11 cWW 
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.028776211,0.032326394,0.007021393,0.007021393,0.000000000],[0.712040258,0.082230039,0.007021393,0.007021393,0.000000000],[0.007021393,0.007021393,0.029462996,0.044950176,0.000000000],[0.007021393,0.007021393,0.007021393,0.007021393,0.000000000],[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 [17] // Basepair C22 - A10 bif 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.166666667,0.500000000,0.166666667,0.166666667,0.000000000] | Position [1] | Left Index [3] | Right Index [16] // Fixed node on left for 8DK7|1|C|U|6
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 [4] | Right Index [16] // New Initial node after Fixed node
ClusterNode  | Deletion Probability [0.000000000000000000000009533766986221214533025748902239021246] | Num Left Bases [5] | Num Right Bases [4] | Left Index [4] | Right Index [16] | Norm Constant [0.000378449897444] // Cluster node 8DK7|1|C|U|24:8DK7|1|C|A|29 and 8DK7|1|C|U|6:8DK7|1|C|C|9
Interaction  | Interacting Bases [1,6] | Pair Probability [[0.019248377,0.341640756,0.003950463,0.038911407,0.000000000],[0.003950463,0.046098892,0.012361189,0.003950463,0.000000000],[0.034274119,0.003950463,0.025404521,0.016144783,0.000000000],[0.003950463,0.003950463,0.037265855,0.404947322,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8DK7|1|C|U|24 - 8DK7|1|C|U|6 tHW 
Interaction  | Interacting Bases [5,6] | Pair Probability [[0.121583738,0.122053423,0.125556588,0.144924515,0.000000000],[0.111055049,0.114840499,0.001350235,0.124802948,0.000000000],[0.001350235,0.001350235,0.008345120,0.001350235,0.000000000],[0.006642085,0.001350235,0.112094623,0.001350235,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8DK7|1|C|A|29 - 8DK7|1|C|U|6 tHS 
Interaction  | Interacting Bases [3,7] | Pair Probability [[0.023164190,0.014489905,0.351490869,0.017735478,0.000000000],[0.014838319,0.010255708,0.019408962,0.045569652,0.000000000],[0.375747942,0.019193415,0.003658470,0.015799099,0.000000000],[0.017770069,0.043129315,0.016144978,0.011603631,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8DK7|1|C|G|26 - 8DK7|1|C|A|7 cWW 
Interaction  | Interacting Bases [4,8] | Pair Probability [[0.004841606,0.050416664,0.005513298,0.100138349,0.000000000],[0.008504413,0.023738407,0.100986868,0.006607555,0.000000000],[0.005452069,0.529512277,0.001039223,0.013313184,0.000000000],[0.098856770,0.034290020,0.011669605,0.005119692,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8DK7|1|C|G|27 - 8DK7|1|C|C|8 cWW 
Interaction  | Interacting Bases [3,9] | 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]] // Cluster Interaction 8DK7|1|C|G|26 - 8DK7|1|C|C|9 cWW 
Interaction  | Interacting Bases [1,5] | Pair Probability [[0.003098658,0.003098658,0.013353226,0.013415874,0.000000000],[0.003098658,0.014901162,0.003098658,0.293495075,0.000000000],[0.011416052,0.003098658,0.010709656,0.003098658,0.000000000],[0.319766810,0.003098658,0.286715797,0.014535741,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8DK7|1|C|U|24 - 8DK7|1|C|A|29 cWH 
Interaction  | Interacting Bases [7,8] | Pair Probability [[0.104166825,0.124612443,0.005621093,0.043860124,0.000000000],[0.100542670,0.099286043,0.001147115,0.009317734,0.000000000],[0.010004306,0.001147115,0.104180479,0.094225112,0.000000000],[0.104547355,0.103291070,0.001147115,0.092903402,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8DK7|1|C|A|7 - 8DK7|1|C|C|8 cSH 
Interaction  | Interacting Bases [2,2] | Pair Probability [[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],[0.000000000,0.000000000,0.000000000,0.500000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 8DK7|1|C|U|25
Insertion    | Location [4] | Length Distribution [0.045351474,0.907029478,0.045351474,0.002267574] | Letter Distribution [0.166666667,0.500000000,0.166666667,0.166666667,0.000000000]// Insertion after nucleotide 7, 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 [9] | Right Index [12] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.023164190,0.014489905,0.351490869,0.017735478,0.000000000],[0.014838319,0.010255708,0.019408962,0.045569652,0.000000000],[0.375747942,0.019193415,0.003658470,0.015799099,0.000000000],[0.017770069,0.043129315,0.016144978,0.011603631,0.000000000],[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 [9] | Right Index [12] // Basepair G30 - A5 cWW 
BasepairNode | Deletion Probability [0.0000249735224443] | 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 [0.999900000,0.000100000] | 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 [10] | Right Index [11] // Basepair C31 - G4 cWW 
HairpinNode  | Num Bases [1] | Left Index [11] | Right Index [11] | 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_29357.1:
> IL_29357.1  8DK7 C   21 G   11
CCCUUGGCAGC*GAUACCAG