Alignment of IL_77278.1 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	6 4 3	8 6 4	9 6 I	10 7 5	12 9 6	14 10	16 9 7	18 6 8	19 3 I	20 3 9	21 2 I	22 2 10	In acceptance region	Cutoff score	Full edit distance	Interior edit distance	Alignment score deficit
IL_77278.1_Instance_1 IL_77278.1,IL_8CRE_054,C1183_G1315	C	U	C	A	UC	A	G		C	U	C	A	A	G
IL_77278.1_Sequence_1 IL_77278.18CRE_C_1183_G_1315	C	U	C	A	UC	A	G	*	C	U	C	A	A	G	true	100	0	0	0.00
IL_77278.1_Instance_2 IL_77278.1,IL_8P9A_279,C1187_G1319	C	U	C	A	UC	A	G		C	U	C	A	A	G
IL_77278.1_Sequence_2 IL_77278.18P9A_C_1187_G_1319	C	U	C	A	UC	A	G	*	C	U	C	A	A	G	true	100	0	0	0.00

Conserved interactions between motif group positions in IL_77278.1:

1 2 s35 
1 10 cWW 
2 3 perp 
2 9 tWW 
2 10 s55 
3 4 s53 
4 5 s55 
4 8 tWW 
5 6 s35 
5 8 s55 
6 7 cWW 
9 10 s55 
3 8 6BR
6 10 2BR

JAR3D SCFG/MRF model for IL_77278.1:

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 [10] // Initial node
BasepairNode | Deletion Probability [0.0000001182498160] | Pair Probability [[0.009536579,0.017101376,0.010963471,0.198789353,0.000000000],[0.020276398,0.009712729,0.228583296,0.013790641,0.000000000],[0.011086594,0.203072729,0.002089755,0.023466206,0.000000000],[0.201366458,0.013287017,0.026771249,0.010106148,0.000000000],[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 [0.023781213,0.951248514,0.023781213,0.001189061] | Right Letter Distribution [0.625000000,0.125000000,0.125000000,0.125000000,0.000000000] | Left Index [1] | Right Index [10] // Basepair C1183 - G1315 cWW 
BasepairNode | Deletion Probability [0.0000001182498160] | 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 [0.023781213,0.951248514,0.023781213,0.001189061] | Right Letter Distribution [0.125000000,0.625000000,0.125000000,0.125000000,0.000000000] | Left Index [2] | Right Index [9] // Basepair U1184 - A1313 tWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.041666667,0.875000000,0.041666667,0.041666667,0.000000000] | Position [1] | Left Index [3] | Right Index [8] // Fixed node on left for 8CRE|1|1|C|1185
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
BasepairNode | Deletion Probability [0.0000000005912491] | Pair Probability [[0.017206486,0.042519179,0.003599422,0.379550045,0.000000000],[0.016896809,0.038775287,0.014989844,0.041572626,0.000000000],[0.003599422,0.017841856,0.017227568,0.288330497,0.000000000],[0.041118059,0.034517023,0.017744275,0.024511604,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.000000000,0.023781213,0.951248514,0.023781213,0.001189061] | Left Letter Distribution [0.083333333,0.416666667,0.083333333,0.416666667,0.000000000] | 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 A1186 - U1311 tWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.625000000,0.125000000,0.125000000,0.125000000,0.000000000] | Position [1] | Left Index [5] | Right Index [7] // Fixed node on left for 8CRE|1|1|U|1187
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 [7] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.004830920,0.010061077,0.005501129,0.099917326,0.000000000],[0.008485643,0.004737202,0.100763972,0.006592971,0.000000000],[0.027200179,0.538072256,0.005184644,0.066418997,0.000000000],[0.098638576,0.006842867,0.011643848,0.005108392,0.000000000],[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 G1190 - C1310 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_77278.1:> IL_77278.1 8CRE C 1183 G 1315 CUCAUCAG*CUCAAG > IL_77278.1 8P9A C 1187 G 1319 CUCAUCAG*CUCAAG