Alignment of IL_70411.2 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 8 5	12 9 6	14 10	16 9 7	18 8 8	19 3 I	20 3 9	22 2 10	In acceptance region	Cutoff score	Full edit distance	Interior edit distance	Alignment score deficit
IL_70411.2_Instance_1 IL_70411.2,IL_8CRE_139,U3297_G3336	U	G	U	A	A	G		C	U	G	A	G
IL_70411.2_Sequence_1 IL_70411.28CRE_U_3297_G_3336	U	G	U	A	A	G	*	C	U	G	A	G	true	94	0	0	0.97
IL_70411.2_Instance_2 IL_70411.2,IL_8P9A_360,U3332_G3371	U	G	U	A	A	G		C	U	G	A	G
IL_70411.2_Sequence_2 IL_70411.28P9A_U_3332_G_3371	U	G	U	A	A	G	*	C	U	G	A	G	true	94	0	0	0.97
IL_70411.2_Instance_3 IL_70411.2,IL_7A0S_101,U2822_G2844	U	G	C	A	C	G		U	U	C	A	G
IL_70411.2_Sequence_3 IL_70411.27A0S_U_2822_G_2844	U	G	C	A	C	G	*	U	U	C	A	G	true	82	0	0	2.97
IL_70411.2_Instance_4 IL_70411.2,IL_4V9F_099,U2864_G2892	U	G	U	G	C	G		U	U	A	A	G
IL_70411.2_Sequence_4 IL_70411.24V9F_U_2864_G_2892	U	G	U	G	C	G	*	U	U	A	A	G	true	81	0	0	3.15
IL_70411.2_Instance_5 IL_70411.2,IL_4WF9_108,U2867_G2889	U	G	G	A	A	G		U	G	G	A	G
IL_70411.2_Sequence_5 IL_70411.24WF9_U_2867_G_2889	U	G	G	A	A	G	*	U	G	G	A	G	true	85	0	0	2.57
IL_70411.2_Instance_6 IL_70411.2,IL_5J7L_354,U2847_G2869	U	G	U	A	A	G		U	U	G	A	G
IL_70411.2_Sequence_6 IL_70411.25J7L_U_2847_G_2869	U	G	U	A	A	G	*	U	U	G	A	G	true	100	0	0	0.00
IL_70411.2_Instance_7 IL_70411.2,IL_9DFE_109,U2847_G2869	U	G	U	A	A	G		U	U	G	A	G
IL_70411.2_Sequence_7 IL_70411.29DFE_U_2847_G_2869	U	G	U	A	A	G	*	U	U	G	A	G	true	100	0	0	0.00

Conserved interactions between motif group positions in IL_70411.2:

1 2 s35 
1 10 cWW 
2 3 s35 
2 9 tSH 
3 9 s55 
4 5 s35 
5 6 s35 
5 8 tHH 
6 7 cWW 
7 8 s33 
9 10 s35 
8 4 6BPh
3 2 7BR
9 4 2BR
4 9 7BR

JAR3D SCFG/MRF model for IL_70411.2:

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 [10] // Initial node
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.010720626,0.013330514,0.013610420,0.035532791,0.000000000],[0.288400856,0.026644634,0.040374951,0.015284874,0.000000000],[0.013908384,0.035390462,0.003151655,0.013986402,0.000000000],[0.082165115,0.013993207,0.380586042,0.012919067,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [10] // Basepair U3297 - G3336 cWW 
BasepairNode | Deletion Probability [0.0000001232089072] | Pair Probability [[0.179781315,0.038064550,0.000431631,0.002034278,0.000000000],[0.181116961,0.037976408,0.000431631,0.000431631,0.000000000],[0.281236045,0.000431631,0.002110107,0.036635205,0.000000000],[0.200683960,0.037771386,0.000431631,0.000431631,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.007039775,0.985568462,0.007039775,0.000351989] | Right Letter Distribution [0.166666667,0.166666667,0.611111111,0.055555556,0.000000000] | Left Index [2] | Right Index [9] // Basepair G3298 - A3335 tSH 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.013513514,0.148648649,0.148648649,0.689189189,0.000000000] | Position [1] | Left Index [3] | Right Index [8] // Fixed node on left for 8CRE|1|1|U|3299
InitialNode  | Left Length Distribution [0.997990020,0.001999980,0.000010000] | 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 [0.824324324,0.013513514,0.148648649,0.013513514,0.000000000] | Position [1] | Left Index [4] | Right Index [8] // Fixed node on left for 8CRE|1|1|A|3300
InitialNode  | Left Length Distribution [0.997990020,0.001999980,0.000010000] | 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 [8] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.004335521,0.020477235,0.149411656,0.420632776,0.000000000],[0.003516278,0.000713935,0.007760565,0.367252143,0.000000000],[0.003901095,0.004122716,0.001625204,0.004086278,0.000000000],[0.003234620,0.003218494,0.001625204,0.004086278,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [8] // Basepair A3301 - U3333 tHH 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.013436561,0.207673960,0.012767884,0.112425448,0.000000000],[0.014000663,0.011308071,0.080103685,0.013426519,0.000000000],[0.012525502,0.103896437,0.002778175,0.274931976,0.000000000],[0.079037080,0.014469041,0.016193555,0.031025444,0.000000000],[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 [6] | Right Index [7] // Basepair G3302 - C3332 cWW 
HairpinNode  | Num Bases [1] | Left Index [7] | Right Index [7] | 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_70411.2:> IL_70411.2 8CRE U 3297 G 3336 UGUAAG*CUGAG > IL_70411.2 8P9A U 3332 G 3371 UGUAAG*CUGAG > IL_70411.2 7A0S U 2822 G 2844 UGCACG*UUCAG > IL_70411.2 4V9F U 2864 G 2892 UGUGCG*UUAAG > IL_70411.2 4WF9 U 2867 G 2889 UGGAAG*UGGAG > IL_70411.2 5J7L U 2847 G 2869 UGUAAG*UUGAG > IL_70411.2 9DFE U 2847 G 2869 UGUAAG*UUGAG