Alignment of J3_91491.2 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	5 4 I	6 5 3	8 6 4	10 10 5	12 11	14 10 6	16 13 7	18 15 8	20 16	22 15 9	24 5 10	26 2 11	In acceptance region	Cutoff score	Full edit distance	Interior edit distance	Alignment score deficit
J3_91491.2_Instance_1 J3_91491.2,J3_4WF9_008,C2359_G2350	C	A	U	A	A	G		C	U	C		G	A	G
J3_91491.2_Sequence_1 J3_91491.24WF9_C_2359_G_2350	C	A	U	A	A	G	*	C	U	C	*	G	A	G	true	100	0	0	0.00
J3_91491.2_Instance_2 J3_91491.2,J3_4V9F_008,C2366_G2357	C	A	A	A	A	G		C	U	C		G	A	G
J3_91491.2_Sequence_2 J3_91491.24V9F_C_2366_G_2357	C	A	A	A	A	G	*	C	U	C	*	G	A	G	true	100	0	0	0.00
J3_91491.2_Instance_3 J3_91491.2,J3_4Y4O_025,U2332_G2323	U	A	G	A	A	G		C	U	C		G	A	G
J3_91491.2_Sequence_3 J3_91491.24Y4O_U_2332_G_2323	U	A	G	A	A	G	*	C	U	C	*	G	A	G	true	99	0	0	0.21
J3_91491.2_Instance_4 J3_91491.2,J3_7A0S_010,U2311_G2302	U	A	G	A	A	G		C	U	C		G	A	G
J3_91491.2_Sequence_4 J3_91491.27A0S_U_2311_G_2302	U	A	G	A	A	G	*	C	U	C	*	G	A	G	true	99	0	0	0.21
J3_91491.2_Instance_5 J3_91491.2,J3_5TBW_013,U2701_A2692	U	A	A	A	A	G		C	U	C		G	A	A
J3_91491.2_Sequence_5 J3_91491.25TBW_U_2701_A_2692	U	A	A	A	A	G	*	C	U	C	*	G	A	A	true	96	0	0	0.76
J3_91491.2_Instance_6 J3_91491.2,J3_5J7L_045,C2332_G2323	C	A	U	A	A	G		C	U	A		U	A	G
J3_91491.2_Sequence_6 J3_91491.25J7L_C_2332_G_2323	C	A	U	A	A	G	*	C	U	A	*	U	A	G	true	92	0	0	1.40

Conserved interactions between motif group positions in J3_91491.2:

1 11 cWW 
2 3 s55 
2 8 perp 
2 10 s55 
3 5 s35 
3 7 tHW 
3 10 tWW 
5 6 cWW 
5 7 s55 
6 7 s35 
8 9 cWW 
8 10 perp 
9 10 perp 
10 11 s35 
11 5 2BR
2 7 2BR
9 10 2BR

JAR3D SCFG/MRF model for J3_91491.2:

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 [11] // Initial node
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.007287674,0.007218623,0.022711650,0.067805592,0.000000000],[0.051091079,0.006563798,0.319756252,0.006160844,0.000000000],[0.008429976,0.068660751,0.004703091,0.009264364,0.000000000],[0.150079944,0.005819298,0.259548313,0.004898750,0.000000000],[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 [11] // Basepair C2359 - G2350 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.953125000,0.015625000,0.015625000,0.015625000,0.000000000] | Position [1] | Left Index [2] | Right Index [10] // Fixed node on left for 4WF9|1|X|U|2323
InitialNode  | Left Length Distribution [0.008193363,0.983203605,0.008193363,0.000409668] | Left Letter Distribution [0.312500000,0.062500000,0.312500000,0.312500000,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [10] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.442172116,0.028311602,0.003670704,0.017547237,0.000000000],[0.027577755,0.013381271,0.010932050,0.013390996,0.000000000],[0.003670704,0.010947776,0.339440300,0.020687729,0.000000000],[0.017526310,0.013387729,0.020240030,0.017115692,0.000000000],[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 [3] | Right Index [10] // Basepair A2362 - A2349 tWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.812500000,0.062500000,0.062500000,0.062500000,0.000000000] | Position [1] | Left Index [4] | Right Index [9] // Fixed node on left for 4WF9|1|X|G|2348
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 [9] // New Initial node after Fixed node
JunctionNode | Branches [2]  | Left Index [5] | Right Index [9] // Junction node G2364 - G2348 ID J3499
InitialNode  | Left Length Distribution [1.000000000] | Left Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | 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 [6] // Initial node
BasepairNode | Deletion Probability [0.0000224863733088] | Pair Probability [[0.009366383,0.019506822,0.010665810,0.193723744,0.000000000],[0.016452306,0.009184679,0.195365254,0.012782718,0.000000000],[0.010547361,0.257647718,0.002010439,0.025755166,0.000000000],[0.191244451,0.013267227,0.022575563,0.009904357,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.990049834,0.009900498,0.000049502,0.000000165] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.990049834,0.009900498,0.000049502,0.000000165] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [6] // Basepair G2364 - C2322 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
InitialNode  | Left Length Distribution [1.000000000] | 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 [7] | Right Index [9] // Initial node 4WF9|1|X|U|2323 - 4WF9|1|X|G|2348 from node 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.062500000,0.062500000,0.062500000,0.812500000,0.000000000] | Position [1] | Left Index [7] | Right Index [9] // Fixed node on left for 4WF9|1|X|C|2359
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 [8] | Right Index [9] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000224863733088] | Pair Probability [[0.005283740,0.010335284,0.023403961,0.121275296,0.000000000],[0.010878272,0.005401523,0.494106242,0.007149146,0.000000000],[0.005998724,0.112353924,0.004485321,0.017872385,0.000000000],[0.111569161,0.007056079,0.056957219,0.005873721,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.990049834,0.009900498,0.000049502,0.000000165] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.990049834,0.009900498,0.000049502,0.000000165] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [8] | Right Index [9] // Basepair C2324 - G2348 cWW 
HairpinNode  | Num Bases [1] | Left Index [9] | Right Index [9] | 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 J3_91491.2:> J3_91491.2 4WF9 C 2359 G 2350 CAUAAG*CUC*GAG > J3_91491.2 4V9F C 2366 G 2357 CAAAAG*CUC*GAG > J3_91491.2 4Y4O U 2332 G 2323 UAGAAG*CUC*GAG > J3_91491.2 7A0S U 2311 G 2302 UAGAAG*CUC*GAG > J3_91491.2 5TBW U 2701 A 2692 UAAAAG*CUC*GAA > J3_91491.2 5J7L C 2332 G 2323 CAUAAG*CUA*UAG