Alignment of IL_13874.1 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
3
I

10
3

5
11
4
I

12
5

6
13
5
I

14
6

7
15
6
I

16
7


17
6
I

18
6

8
19
5
I

20
5

9
21
4
I

22
3

10
23
3
I

24
3

11
25
2
I

26
2

12
27
1
I


In
acceptance
region

Cutoff
score
Full
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distance
Interior
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distance
Alignment
score
deficit
IL_13874.1_Instance_1 IL_13874.1,IL_7OAX_013,U8_G45UGGAGGGGCGGUCG
IL_13874.1_Sequence_1 IL_13874.17OAX_U8_G45UGGAGGGG*CGGUCGtrue100000.00

Conserved interactions between motif group positions in IL_13874.1:
1 12 cWW 
2 3 s53 
2 5 cWH 
2 6 s33 
3 4 cSH 
3 11 cWW 
3 12 s55 
4 5 s35 
4 11 tHS 
5 6 s33 
5 9 s33 
5 10 cWH 
6 7 s55 
6 9 cHW 
7 8 cWW 
7 9 s55 
8 9 s35 
9 10 s33 
10 11 s55 
11 12 s35 
4 11 6BR
JAR3D SCFG/MRF model for IL_13874.1:
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 [12] // Initial node
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.011357495,0.014122426,0.014418960,0.037643649,0.000000000],[0.305533580,0.028227484,0.042773463,0.016192886,0.000000000],[0.014734624,0.037492866,0.003338882,0.014817277,0.000000000],[0.087046211,0.014824487,0.343789173,0.013686536,0.000000000],[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 [12] // Basepair U8 - G45 cWW 
ClusterNode  | Deletion Probability [0.000000000000000076270135889769347254524013854470196433658662] | Num Left Bases [4] | Num Right Bases [2] | Left Index [2] | Right Index [11] | Norm Constant [0.012695853013397] // Cluster node 7OAX|1|A|G|9:7OAX|1|A|G|12 and 7OAX|1|A|G|42:7OAX|1|A|C|44
Interaction  | Interacting Bases [4,5] | Pair Probability [[0.004966430,0.004966430,0.051077026,0.042074794,0.000000000],[0.004966430,0.052642128,0.004966430,0.017912101,0.000000000],[0.206503547,0.004966430,0.506544030,0.004966430,0.000000000],[0.017165095,0.004966430,0.015536138,0.055780127,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 7OAX|1|A|G|12 - 7OAX|1|A|G|42 cWH 
Interaction  | Interacting Bases [2,6] | 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 7OAX|1|A|G|10 - 7OAX|1|A|C|44 cWW 
Interaction  | Interacting Bases [3,6] | Pair Probability [[0.166739042,0.181862370,0.144313661,0.155443097,0.000000000],[0.021588854,0.120317856,0.001719614,0.157162461,0.000000000],[0.001719614,0.001719614,0.011932323,0.001719614,0.000000000],[0.008552422,0.001719614,0.021770231,0.001719614,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 7OAX|1|A|A|11 - 7OAX|1|A|C|44 tHS 
Interaction  | Interacting Bases [2,3] | Pair Probability [[0.032737334,0.008059162,0.004482243,0.080765445,0.000000000],[0.040867917,0.068020615,0.000924080,0.087159768,0.000000000],[0.471941158,0.000924080,0.011539641,0.065084617,0.000000000],[0.039437551,0.011675048,0.000924080,0.075457260,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 7OAX|1|A|G|10 - 7OAX|1|A|A|11 cSH 
Interaction  | Interacting Bases [1,4] | Pair Probability [[0.004966430,0.004966430,0.051077026,0.042074794,0.000000000],[0.004966430,0.052642128,0.004966430,0.017912101,0.000000000],[0.206503547,0.004966430,0.506544030,0.004966430,0.000000000],[0.017165095,0.004966430,0.015536138,0.055780127,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 7OAX|1|A|G|9 - 7OAX|1|A|G|12 cWH 
Insertion    | Location [5] | 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 10, position 5 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 [6] | Right Index [9] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000001156129129] | Pair Probability [[0.004966430,0.004966430,0.206503547,0.017165095,0.000000000],[0.004966430,0.052642128,0.004966430,0.004966430,0.000000000],[0.051077026,0.004966430,0.506544030,0.015536138,0.000000000],[0.042074794,0.017912101,0.004966430,0.055780127,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.045351474,0.907029478,0.045351474,0.002267574] | Left Letter Distribution [0.166666667,0.166666667,0.500000000,0.166666667,0.000000000] | 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 G13 - G41 cHW 
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 [7] | Right Index [8] // Basepair G15 - C40 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_13874.1:
> IL_13874.1  7OAX U    8 G   45
UGGAGGGG*CGGUCG