Alignment of IL_10569.1 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
4
I

8
5


9
4
I

10
3

4
11
2
I

12
2

5
13
1
I


In
acceptance
region

Cutoff
score
Full
edit
distance
Interior
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distance
Alignment
score
deficit
IL_10569.1_Instance_1 IL_10569.1,IL_1HYS_003,A867_U887AAAUU
IL_10569.1_Sequence_1 IL_10569.11HYS_A867_U887AAA*UUtrue97000.28
IL_10569.1_Instance_2 IL_10569.1,IL_4V84_420,C6181_G6195CAGCG
IL_10569.1_Sequence_2 IL_10569.14V84_C_6181_G_6195CAG*CGtrue100000.00

Conserved interactions between motif group positions in IL_10569.1:
1 2 s35 
1 5 cWW 
2 3 s35 
2 4 cWW 
2 5 s55 
3 4 cWW 
3 5 s55 
4 5 s35
JAR3D SCFG/MRF model for IL_10569.1:
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 [5] // Initial node
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.009409752,0.019555960,0.010438919,0.211256183,0.000000000],[0.018897284,0.009646494,0.211374635,0.012074740,0.000000000],[0.010490831,0.199877935,0.002065453,0.038339992,0.000000000],[0.198695040,0.012157589,0.024891932,0.010827262,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.991950402,0.007999600,0.000049998] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [5] // Basepair A867 - U887 cWW 
ClusterNode  | Deletion Probability [0.0000001250000000] | Num Left Bases [2] | Num Right Bases [1] | Left Index [2] | Right Index [4] | Norm Constant [0.257542546037360] // Cluster node 1HYS|1|E|A|868:1HYS|1|E|A|869 and 1HYS|1|F|DT|886:1HYS|1|F|DT|886
Interaction  | Interacting Bases [1,3] | Pair Probability [[0.011552201,0.169520401,0.010988733,0.127897622,0.000000000],[0.014816814,0.010595773,0.109252676,0.011173210,0.000000000],[0.010837459,0.112770670,0.002507688,0.162689177,0.000000000],[0.110774940,0.012091158,0.017796326,0.104735152,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 1HYS|1|E|A|868 - 1HYS|1|F|DT|886 cWW 
Interaction  | Interacting Bases [2,3] | Pair Probability [[0.009508309,0.021141169,0.010499222,0.212521883,0.000000000],[0.017307832,0.009562561,0.198596306,0.011821420,0.000000000],[0.010428025,0.212609503,0.002065216,0.039989476,0.000000000],[0.197383927,0.012407836,0.023236747,0.010920569,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 1HYS|1|E|A|869 - 1HYS|1|F|DT|886 cWW 
InitialNode  | Left Length Distribution [0.991950402,0.007999600,0.000049998] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [3] // New Initial node after Cluster
HairpinNode  | Num Bases [1] | Left Index [4] | Right Index [4] | 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_10569.1:
> IL_10569.1  1HYS A  867 U  887
AAA*UU
> IL_10569.1  4V84 C 6181 G 6195
CAG*CG