Alignment of IL_85599.2 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 5	10 4 4	12 3 5	13 2 I	14 2 6	In acceptance region	Cutoff score	Full edit distance	Interior edit distance	Alignment score deficit
IL_85599.2_Instance_1 IL_85599.2,IL_5J7L_325,U2081_G2239	U	A	G		U	G	G	G
IL_85599.2_Sequence_1 IL_85599.25J7L_U_2081_G_2239	U	A	G	*	U	G	G	G	true	100	0	0	0.00
IL_85599.2_Instance_2 IL_85599.2,IL_8CRE_100,U2401_G2579	U	A	G		U	G	G	G
IL_85599.2_Sequence_2 IL_85599.28CRE_U_2401_G_2579	U	A	G	*	U	G	G	G	true	100	0	0	0.00
IL_85599.2_Instance_3 IL_85599.2,IL_7A0S_077,U2064_G2218	U	A	G		C	G	G	G
IL_85599.2_Sequence_3 IL_85599.27A0S_U_2064_G_2218	U	A	G	*	C	G	G	G	true	99	0	0	0.14
IL_85599.2_Instance_4 IL_85599.2,IL_8P9A_323,U2423_G2607	U	A	G		U	G	G	G
IL_85599.2_Sequence_4 IL_85599.28P9A_U_2423_G_2607	U	A	G	*	U	G	G	G	true	100	0	0	0.00
IL_85599.2_Instance_5 IL_85599.2,IL_4WF9_082,U2108_G2266	U	A	G		C	G	G	G
IL_85599.2_Sequence_5 IL_85599.24WF9_U_2108_G_2266	U	A	G	*	C	G	G	G	true	99	0	0	0.14
IL_85599.2_Instance_6 IL_85599.2,IL_9DFE_010,C288_G353	C	A	G		U	G	G	G
IL_85599.2_Sequence_6 IL_85599.29DFE_C288_G353	C	A	G	*	U	G	G	G	true	91	0	0	0.82
IL_85599.2_Instance_7 IL_85599.2,IL_9DFE_082,C2081_G2239	C	A	G		C	G	G	G
IL_85599.2_Sequence_7 IL_85599.29DFE_C_2081_G_2239	C	A	G	*	C	G	G	G	true	90	0	0	0.96
IL_85599.2_Instance_8 IL_85599.2,IL_4V9F_076,C2122_G2272	C	A	G		C	G	G	G
IL_85599.2_Sequence_8 IL_85599.24V9F_C_2122_G_2272	C	A	G	*	C	G	G	G	true	90	0	0	0.96
IL_85599.2_Instance_9 IL_85599.2,IL_1L9A_004,U132_G165	U	A	U		A	G		G
IL_85599.2_Sequence_9 IL_85599.21L9A_U132_G165	U	A	U	*	A	G		G	true	76	0	0	2.24

Conserved interactions between motif group positions in IL_85599.2:

1 5 s33 
1 6 cWW 
2 3 s35 
2 5 tHS 
2 6 s55 
3 4 cWW 
3 5 s55 
4 5 s35 
2 5 6BR

JAR3D SCFG/MRF model for IL_85599.2:

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 [6] // Initial node
BasepairNode | Deletion Probability [0.0000002208070251] | Pair Probability [[0.009990658,0.014058319,0.012326924,0.085261563,0.000000000],[0.195064146,0.020466820,0.119130690,0.014304613,0.000000000],[0.012560326,0.086504518,0.002714401,0.016472914,0.000000000],[0.116583221,0.013302208,0.269651622,0.011607056,0.000000000],[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 [0.114812666,0.880026871,0.004916181,0.000244282] | Right Letter Distribution [0.050000000,0.050000000,0.850000000,0.050000000,0.000000000] | Left Index [1] | Right Index [6] // Basepair U2081 - G2239 cWW 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.105505226,0.106289054,0.209220798,0.117772008,0.000000000],[0.111691501,0.111432869,0.001266520,0.110831278,0.000000000],[0.001266520,0.001266520,0.006191614,0.001266520,0.000000000],[0.005969112,0.001266520,0.107497421,0.001266520,0.000000000],[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 [2] | Right Index [5] // Basepair A2082 - G2237 tHS 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.011575431,0.133731232,0.011595033,0.139320497,0.000000000],[0.015110242,0.010311121,0.120072559,0.012664295,0.000000000],[0.011418277,0.161096143,0.002430837,0.185160248,0.000000000],[0.128300668,0.013357021,0.021286897,0.022569501,0.000000000],[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 [3] | Right Index [4] // Basepair G2083 - U2236 cWW 
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_85599.2:> IL_85599.2 5J7L U 2081 G 2239 UAG*UGGG > IL_85599.2 8CRE U 2401 G 2579 UAG*UGGG > IL_85599.2 7A0S U 2064 G 2218 UAG*CGGG > IL_85599.2 8P9A U 2423 G 2607 UAG*UGGG > IL_85599.2 4WF9 U 2108 G 2266 UAG*CGGG > IL_85599.2 9DFE C 288 G 353 CAG*UGGG > IL_85599.2 9DFE C 2081 G 2239 CAG*CGGG > IL_85599.2 4V9F C 2122 G 2272 CAG*CGGG > IL_85599.2 1L9A U 132 G 165 UAU*AGG