Alignment of IL_20047.1 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 3 2	5 3 I	6 4 3	8 5 4	10 6 5	11 7 I	12 8 6	14 9	16 8 7	18 5 8	20 4 9	21 3 I	22 3 10	24 2 11	In acceptance region	Cutoff score	Full edit distance	Interior edit distance	Alignment score deficit
IL_20047.1_Instance_1 IL_20047.1,IL_8P9A_311,U2173_G2161	U	G	U	U	G	A	C	G		C	G	A	U	G	G
IL_20047.1_Sequence_1 IL_20047.18P9A_U_2173_G_2161	U	G	U	U	G	A	C	G	*	C	G	A	U	G	G	true	100	0	0	0.00
IL_20047.1_Instance_2 IL_20047.1,IL_8CRE_088,U2151_G2139	U	G	U	U	G	A	C	A		U	G	A	U	G	G
IL_20047.1_Sequence_2 IL_20047.18CRE_U_2151_G_2139	U	G	U	U	G	A	C	A	*	U	G	A	U	G	G	true	100	0	0	0.00

Conserved interactions between motif group positions in IL_20047.1:

1 2 s33 
1 11 cWW 
2 3 s55 
2 9 s55 
2 10 tWW 
3 9 tWW 
4 8 tSS 
4 9 s53 
5 6 s55 
5 7 s53 
5 8 s35 
6 7 cWW 
9 10 s55 
10 11 s35 
8 5 6BPh
5 8 6BPh
8 4 6BR
4 9 6BR

JAR3D SCFG/MRF model for IL_20047.1:

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 [11] // Initial node
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.011246147,0.013983971,0.014277598,0.037274594,0.000000000],[0.302538153,0.027950744,0.042354115,0.016034133,0.000000000],[0.014590167,0.037125289,0.003306148,0.014672010,0.000000000],[0.086192816,0.014679149,0.350222612,0.013552354,0.000000000],[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 [11] // Basepair U2173 - G2161 cWW 
BasepairNode | Deletion Probability [0.0000000006094467] | Pair Probability [[0.351562872,0.022218774,0.003801797,0.018196176,0.000000000],[0.044052496,0.014354029,0.012285535,0.014316008,0.000000000],[0.003801797,0.011359424,0.399787557,0.018789616,0.000000000],[0.019388555,0.014458564,0.033413960,0.018212838,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.023781213,0.951248514,0.023781213,0.001189061] | Left Letter Distribution [0.125000000,0.125000000,0.125000000,0.625000000,0.000000000] | Right Length Distribution [0.023781213,0.951248514,0.023781213,0.001189061] | Right Letter Distribution [0.125000000,0.125000000,0.125000000,0.625000000,0.000000000] | Left Index [2] | Right Index [10] // Basepair G2174 - G2160 tWW 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.017086415,0.016798935,0.003578572,0.040879884,0.000000000],[0.042272887,0.036343475,0.017738508,0.034317084,0.000000000],[0.003578572,0.014903016,0.018250145,0.017641491,0.000000000],[0.377465088,0.041331817,0.286660349,0.031153761,0.000000000],[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 [3] | Right Index [9] // Basepair U2176 - A2158 tWW 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.001642412,0.001374740,0.010992864,0.000987451,0.000000000],[0.000192291,0.000192291,0.118387174,0.000192291,0.000000000],[0.093464740,0.000961454,0.692625592,0.077063793,0.000000000],[0.000192291,0.000192291,0.001346035,0.000192291,0.000000000],[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 [4] | Right Index [8] // Basepair G2177 - G2157 tSS 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.906250000,0.031250000,0.031250000,0.031250000,0.000000000] | Position [1] | Left Index [5] | Right Index [7] // Fixed node on left for 8P9A|1|AR|G|2160
InitialNode  | Left Length Distribution [0.023781213,0.951248514,0.023781213,0.001189061] | Left Letter Distribution [0.125000000,0.625000000,0.125000000,0.125000000,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [6] | Right Index [7] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000249735224443] | 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]] | 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 G2180 - C2156 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_20047.1:> IL_20047.1 8P9A U 2173 G 2161 UGUUGACG*CGAUGG > IL_20047.1 8CRE U 2151 G 2139 UGUUGACA*UGAUGG