Alignment of HL_73266.9 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 7 3	8 8 4	10 8 5	12 8 6	14 7 7	16 5 8	18 2 9	In acceptance region	Cutoff score	Full edit distance	Interior edit distance	Alignment score deficit
HL_73266.9_Instance_1 HL_73266.9,HL_5SWD_006,G59_C67	G	C	C	U	U	A	A	A	C
HL_73266.9_Sequence_1 HL_73266.95SWD_G59_C67	G	C	C	U	U	A	A	A	C	true	100	0	0	0.00
HL_73266.9_Instance_2 HL_73266.9,HL_3LA5_003,G59_C67	G	C	C	U	U	A	A	A	C
HL_73266.9_Sequence_2 HL_73266.93LA5_G59_C67	G	C	C	U	U	A	A	A	C	true	100	0	0	0.00
HL_73266.9_Instance_3 HL_73266.9,HL_4FEN_003,A59_U67	A	C	C	G	U	A	A	A	U
HL_73266.9_Sequence_3 HL_73266.94FEN_A59_U67	A	C	C	G	U	A	A	A	U	true	98	0	0	0.26
HL_73266.9_Instance_4 HL_73266.9,HL_4LX6_003,G59_C67	G	C	C	U	U	A	A	A	C
HL_73266.9_Sequence_4 HL_73266.94LX6_G59_C67	G	C	C	U	U	A	A	A	C	true	100	0	0	0.00
HL_73266.9_Instance_5 HL_73266.9,HL_1Y27_003,A59_U67	A	C	C	G	U	A	A	A	U
HL_73266.9_Sequence_5 HL_73266.91Y27_A59_U67	A	C	C	G	U	A	A	A	U	true	98	0	0	0.26
HL_73266.9_Instance_6 HL_73266.9,HL_4XNR_003,G59_C67	G	C	C	U	U	A	A	A	C
HL_73266.9_Sequence_6 HL_73266.94XNR_G59_C67	G	C	C	U	U	A	A	A	C	true	100	0	0	0.00
HL_73266.9_Instance_7 HL_73266.9,HL_1Y26_003,G59_C67	G	C	C	U	U	A	A	A	C
HL_73266.9_Sequence_7 HL_73266.91Y26_G59_C67	G	C	C	U	U	A	A	A	C	true	100	0	0	0.00
HL_73266.9_Instance_8 HL_73266.9,HL_7KVT_002,G55_C63	G	C	C	U	U	A	A	A	C
HL_73266.9_Sequence_8 HL_73266.97KVT_G55_C63	G	C	C	U	U	A	A	A	C	true	100	0	0	0.00
HL_73266.9_Instance_9 HL_73266.9,HL_5KPY_002,A59_U67	A	C	C	G	U	A	A	A	U
HL_73266.9_Sequence_9 HL_73266.95KPY_A59_U67	A	C	C	G	U	A	A	A	U	true	98	0	0	0.26
HL_73266.9_Instance_10 HL_73266.9,HL_3RKF_009,A59_U67	A	C	U	G	U	A	A	A	U
HL_73266.9_Sequence_10 HL_73266.93RKF_A59_U67	A	C	U	G	U	A	A	A	U	true	96	0	0	0.65
HL_73266.9_Instance_11 HL_73266.9,HL_8KEB_003,A47_U55	A	C	C	A	C	A	A	A	U
HL_73266.9_Sequence_11 HL_73266.98KEB_A47_U55	A	C	C	A	C	A	A	A	U	true	96	0	0	0.64
HL_73266.9_Instance_12 HL_73266.9,HL_9IWF_006,A46_U54	A	C	C	C	U	A	A	A	U
HL_73266.9_Sequence_12 HL_73266.99IWF_A46_U54	A	C	C	C	U	A	A	A	U	true	96	0	0	0.64
HL_73266.9_Instance_13 HL_73266.9,HL_6MJ0_006,U12_A20	U	C	U	U	U	A	A	A	A
HL_73266.9_Sequence_13 HL_73266.96MJ0_U12_A20	U	C	U	U	U	A	A	A	A	true	96	0	0	0.62

Conserved interactions between motif group positions in HL_73266.9:

1 2 s35 
1 9 cWW 
2 3 s35 
3 7 cSW 
4 5 cSH 
5 6 s55 
6 7 s35 
7 8 s35 
8 9 s35 
6 4 2BPh
5 4 7BR

JAR3D SCFG/MRF model for HL_73266.9:

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 [9] // Initial node
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.008549811,0.018833463,0.009436267,0.235637538,0.000000000],[0.015951852,0.008650378,0.179151811,0.010616745,0.000000000],[0.009378286,0.235581363,0.001862721,0.034920332,0.000000000],[0.187508016,0.011058813,0.023061826,0.009800778,0.000000000],[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 [9] // Basepair G59 - C67 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.033333333,0.900000000,0.033333333,0.033333333,0.000000000] | Position [1] | Left Index [2] | Right Index [8] // Fixed node on left for 5SWD|1|B|C|60
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 [3] | Right Index [8] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.900000000,0.033333333,0.033333333,0.033333333,0.000000000] | Position [2] | Left Index [3] | Right Index [8] // Fixed node on right for 5SWD|1|B|A|66
InitialNode  | Left Length Distribution [1.000000000] | 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 [7] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.175120870,0.016977452,0.016576027,0.006903952,0.000000000],[0.293785413,0.014961987,0.001900552,0.007360351,0.000000000],[0.174731717,0.001900552,0.055641936,0.005865017,0.000000000],[0.198376040,0.014627322,0.008485558,0.006785253,0.000000000],[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 [7] // Basepair C61 - A65 cSW 
HairpinNode  | Num Bases [3] | Left Index [4] | Right Index [6] | Norm Constant [1.000000000000000] // Hairpin node U62:A64
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.070934828,0.081279033,0.003963804,0.066646368,0.000000000],[0.063987010,0.079149636,0.000868314,0.081125505,0.000000000],[0.060667246,0.000868314,0.074217992,0.118394426,0.000000000],[0.072115706,0.071492142,0.000868314,0.153421361,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin Interaction U62 - U63 cSH 
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.983870968,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.005376344,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.005376344,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.005376344,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A64

Sequences of instances from HL_73266.9:> HL_73266.9 5SWD G 59 C 67 GCCUUAAAC > HL_73266.9 3LA5 G 59 C 67 GCCUUAAAC > HL_73266.9 4FEN A 59 U 67 ACCGUAAAU > HL_73266.9 4LX6 G 59 C 67 GCCUUAAAC > HL_73266.9 1Y27 A 59 U 67 ACCGUAAAU > HL_73266.9 4XNR G 59 C 67 GCCUUAAAC > HL_73266.9 1Y26 G 59 C 67 GCCUUAAAC > HL_73266.9 7KVT G 55 C 63 GCCUUAAAC > HL_73266.9 5KPY A 59 U 67 ACCGUAAAU > HL_73266.9 3RKF A 59 U 67 ACUGUAAAU > HL_73266.9 8KEB A 47 U 55 ACCACAAAU > HL_73266.9 9IWF A 46 U 54 ACCCUAAAU > HL_73266.9 6MJ0 U 12 A 20 UCUUUAAAA