Alignment of IL_33711.1 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:	2 2 1	4 2 2	6 4 3	8 6 4	9 7 I	10 8 5	12 10 6	14 12 7	16 13	18 12 8	20 2 9	In acceptance region	Cutoff score	Full edit distance	Interior edit distance	Alignment score deficit
IL_33711.1_Instance_1 IL_33711.1,IL_6N2V_002,A45_U65	A	A	C	A	UA	C	U	C		G	U
IL_33711.1_Sequence_1 IL_33711.16N2V_A45_U65	A	A	C	A	UA	C	U	C	*	G	U	true	100	0	0	0.00
IL_33711.1_Instance_2 IL_33711.1,IL_6CB3_004,G38_C60	G	U	C	A	AU	U	C	G		C	C
IL_33711.1_Sequence_2 IL_33711.16CB3_G38_C60	G	U	C	A	AU	U	C	G	*	C	C	true	100	0	0	0.02

Conserved interactions between motif group positions in IL_33711.1:

1 2 cSH 
1 7 s35 
1 9 cWW 
2 3 s35 
3 4 s35 
4 6 s53 
5 6 s35 
7 8 cWW 
7 9 s55 
8 9 s35 
3 2 7BPh
6 5 7BPh
3 1 7BR
3 7 6BR

JAR3D SCFG/MRF model for IL_33711.1:

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 [9] // Initial node
ClusterNode  | Deletion Probability [0.0000001250000000] | Num Left Bases [2] | Num Right Bases [1] | Left Index [1] | Right Index [9] | Norm Constant [0.249963258463274] // Cluster node 6N2V|1|A|A|45:6N2V|1|A|A|46 and 6N2V|1|A|U|65:6N2V|1|A|U|65
Interaction  | Interacting Bases [1,3] | 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 6N2V|1|A|A|45 - 6N2V|1|A|U|65 cWW 
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.108776215,0.094270565,0.004919958,0.046268822,0.000000000],[0.084121076,0.095557053,0.001085075,0.043754752,0.000000000],[0.038844248,0.001085075,0.091547205,0.106810339,0.000000000],[0.097350067,0.089867163,0.001085075,0.094657312,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 6N2V|1|A|A|45 - 6N2V|1|A|A|46 cSH 
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 [3] | Right Index [8] // Initial node 6N2V|1|A|C|47 - 6N2V|1|A|G|64 from node 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.006944444,0.979166667,0.006944444,0.006944444,0.000000000] | Position [1] | Left Index [3] | Right Index [8] // Fixed node on left for 6N2V|1|A|C|47
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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [8] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.625000000,0.125000000,0.125000000,0.125000000,0.000000000] | Position [1] | Left Index [4] | Right Index [8] // Fixed node on left for 6N2V|1|A|A|48
InitialNode  | Left Length Distribution [0.000000000,0.023781213,0.951248514,0.023781213,0.001189061] | Left Letter Distribution [0.416666667,0.083333333,0.083333333,0.416666667,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [8] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.125000000,0.375000000,0.125000000,0.375000000,0.000000000] | Position [1] | Left Index [5] | Right Index [8] // Fixed node on left for 6N2V|1|A|U|49
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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [6] | Right Index [8] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.031250000,0.468750000,0.031250000,0.468750000,0.000000000] | Position [1] | Left Index [6] | Right Index [8] // Fixed node on left for 6N2V|1|A|A|50
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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [7] | Right Index [8] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009635135,0.018686586,0.011023774,0.200055053,0.000000000],[0.018686946,0.009628796,0.215804967,0.013537321,0.000000000],[0.011023788,0.215804297,0.002089517,0.025115689,0.000000000],[0.200055346,0.013537264,0.025116064,0.010199456,0.000000000],[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 C53 - G64 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_33711.1:> IL_33711.1 6N2V A 45 U 65 AACAUACUC*GU > IL_33711.1 6CB3 G 38 C 60 GUCAAUUCG*CC