Alignment of IL_50911.1 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


11
4
I

12
3

5
13
3
I

14
3

6
15
2
I

16
2

7
17
1
I


In
acceptance
region


Cutoff
score

Full
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distance

Interior
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Alignment
score
deficit
IL_50911.1_Instance_1 IL_50911.1_IL_1FJG_041_U1052_G1206UGCAUAUG
IL_50911.1_Sequence_1 IL_50911.1_IL_1FJG_041_U_1052_G_1206UGCAU*AUGtrue100000.00

Conserved interactions between motif group positions in IL_50911.1:
1 7 cWW 
2 4 s53 
2 5 wat 
3 4 s35 
3 6 cWS 
3 7 s55 
4 5 cWW 
5 6 s35 
JAR3D SCFG/MRF model for IL_50911.1:
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 [7] // Initial node U1052 - G1206 from junction 
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.013147005,0.014933664,0.015708775,0.039123268,0.000000000],[0.320116843,0.016220977,0.045702007,0.017638328,0.000000000],[0.016064303,0.039422890,0.003563041,0.015642218,0.000000000],[0.046087059,0.015920763,0.366205057,0.014503803,0.000000000],[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 [7] // Basepair U1052 - G1206 cWW 
ClusterNode  | Deletion Probability [0.000000000000015254027177953870000000000000000000000000000000] | Num Left Bases [3] | Num Right Bases [2] | Left Index [2] | Right Index [6] | Norm Constant [0.268360316384108] // Cluster node G1053:U1056 and A1204:U1205
Interaction  | Interacting Bases [1,4] | Pair Probability [[0.008609557,0.008609557,0.008609557,0.008609557,0.000000000],[0.008609557,0.008609557,0.008609557,0.008609557,0.000000000],[0.870856651,0.008609557,0.008609557,0.008609557,0.000000000],[0.008609557,0.008609557,0.008609557,0.008609557,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G1053 - A1204 wat 
Interaction  | Interacting Bases [3,4] | 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]] // Cluster Interaction U1056 - A1204 cWW 
Interaction  | Interacting Bases [2,5] | Pair Probability [[0.176024722,0.177887855,0.157441102,0.206137050,0.000000000],[0.017524598,0.012464556,0.012725025,0.014365445,0.000000000],[0.011968742,0.015288477,0.159911912,0.009707613,0.000000000],[0.007361925,0.008315159,0.006187823,0.006687996,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A1055 - U1205 cWS 
Insertion    | Location [1] | 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 2, position 1 in cluster node
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 [5] | Right Index [4] // New Initial node after Cluster
HairpinNode  | Num Bases [1] | Left Index [5] | Right Index [5] | 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_50911.1:
> IL_50911.1 IL_1FJG_041 U 1052 G 1206
UGCAU*AUG