Alignment of IL_11399.2 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 3 2	6 4 3	8 6 4	10 10 5	12 11	14 10 6	16 8 7	18 3 8	20 2 9	In acceptance region	Cutoff score	Full edit distance	Interior edit distance	Alignment score deficit
IL_11399.2_Instance_1 IL_11399.2,IL_9J6P_001,A16_U9	A	G	G	A	C		G	G	G	U
IL_11399.2_Sequence_1 IL_11399.29J6P_A16_U9	A	G	G	A	C	*	G	G	G	U	true	100	0	0	0.00
IL_11399.2_Instance_2 IL_11399.2,IL_9J6P_002,A16_U9	A	G	G	A	C		G	G	G	U
IL_11399.2_Sequence_2 IL_11399.29J6P_A16_U9	A	G	G	A	C	*	G	G	G	U	true	100	0	0	0.00
IL_11399.2_Instance_3 IL_11399.2,IL_8CRE_469,A1740_U1634	A	A	A	A	G		C	G	C	U
IL_11399.2_Sequence_3 IL_11399.28CRE_A_1740_U_1634	A	A	A	A	G	*	C	G	C	U	true	76	0	0	3.14

Conserved interactions between motif group positions in IL_11399.2:

1 2 s33 
1 9 cWW 
2 8 cHW 
3 4 s35 
5 6 cWW 
5 7 s55 
6 7 s35 
7 8 s35 
8 9 s35 
2 2 2BPh

JAR3D SCFG/MRF model for IL_11399.2:

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
BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.009192800,0.021796849,0.009818110,0.231259682,0.000000000],[0.017348091,0.009487247,0.192280868,0.010258268,0.000000000],[0.009798999,0.194773596,0.002021335,0.052697140,0.000000000],[0.194120479,0.010921091,0.022789191,0.011436255,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [9] // Basepair A16 - U9 cWW 
BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.001043809,0.056984632,0.043401437,0.003607637,0.000000000],[0.001043809,0.011063945,0.001043809,0.001043809,0.000000000],[0.075145025,0.007306661,0.750083616,0.022856920,0.000000000],[0.008842979,0.003764637,0.001043809,0.011723468,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [8] // Basepair G17 - G8 cHW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.300000000,0.100000000,0.500000000,0.100000000,0.000000000] | Position [1] | Left Index [3] | Right Index [7] // Fixed node on left for 9J6P|1|A|G|8
InitialNode  | Left Length Distribution [0.993970181,0.005999820,0.000029999] | 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 [7] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.700000000,0.100000000,0.100000000,0.100000000,0.000000000] | Position [1] | Left Index [4] | Right Index [7] // Fixed node on left for 9J6P|1|A|U|9
InitialNode  | Left Length Distribution [0.993970181,0.005999820,0.000029999] | 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 [5] | Right Index [7] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.100000000,0.100000000,0.700000000,0.100000000,0.000000000] | Position [2] | Left Index [5] | Right Index [7] // Fixed node on right for 9J6P|1|B|G|18
InitialNode  | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [6] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009509057,0.017981890,0.010896842,0.197694967,0.000000000],[0.019030193,0.009563019,0.224400354,0.013489511,0.000000000],[0.010937493,0.212742702,0.002069309,0.024327358,0.000000000],[0.198545855,0.013323228,0.025418591,0.010069631,0.000000000],[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 [5] | Right Index [6] // Basepair C20 - G6 cWW 
HairpinNode  | Num Bases [1] | Left Index [6] | Right Index [6] | 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_11399.2:> IL_11399.2 9J6P A 16 U 9 AGGAC*GGGU > IL_11399.2 9J6P A 16 U 9 AGGAC*GGGU > IL_11399.2 8CRE A 1740 U 1634 AAAAG*CGCU