Alignment of HL_68767.1 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 5 3	8 6 4	9 5 I	10 5 5	12 3 6	14 3 7	16 2 8	In acceptance region	Cutoff score	Full edit distance	Interior edit distance	Alignment score deficit
HL_68767.1_Instance_1 HL_68767.1,HL_3ZGZ_001,G12_C23	G	G	A	A	UCGGU	A	G	A	C
HL_68767.1_Sequence_1 HL_68767.13ZGZ_G12_C23	G	G	A	A	UCGGU	A	G	A	C	true	94	0	0	1.10
HL_68767.1_Instance_2 HL_68767.1,HL_2BTE_001,G12_C23	G	G	A	A	UGGGU	A	G	A	C
HL_68767.1_Sequence_2 HL_68767.12BTE_G12_C23	G	G	A	A	UGGGU	A	G	A	C	true	100	0	0	0.00
HL_68767.1_Instance_3 HL_68767.1,HL_5AH5_005,G12_C23	G	A	A	A	UCGGU	A	A	A	C
HL_68767.1_Sequence_3 HL_68767.15AH5_G12_C23	G	A	A	A	UCGGU	A	A	A	C	true	85	0	0	2.78

Conserved interactions between motif group positions in HL_68767.1:

1 2 s35 
1 8 cWW 
2 3 s35 
2 6 cWS 
2 7 tSH 
2 8 s55 
3 4 s35 
3 5 cWS 
5 6 s35 
7 8 s35 
8 7 7BPh
7 2 6BR
2 6 6BR

JAR3D SCFG/MRF model for HL_68767.1:

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 [8] // Initial node
BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.003786762,0.055205280,0.004312111,0.078321123,0.000000000],[0.006651550,0.025993100,0.078984774,0.005167961,0.000000000],[0.004264222,0.598090606,0.000812806,0.010412629,0.000000000],[0.077318762,0.037546914,0.009127139,0.004004261,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [8] // Basepair G12 - C23 cWW 
ClusterNode  | Deletion Probability [0.0000001250000000] | Num Left Bases [1] | Num Right Bases [2] | Left Index [2] | Right Index [7] | Norm Constant [0.285362311623589] // Cluster node 3ZGZ|1|B|G|13:3ZGZ|1|B|G|13 and 3ZGZ|1|B|G|21:3ZGZ|1|B|A|22
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.104754894,0.110429214,0.092008273,0.210537532,0.000000000],[0.025184133,0.022941046,0.002489079,0.022167953,0.000000000],[0.151236163,0.002489079,0.204982108,0.011956389,0.000000000],[0.010024486,0.010464037,0.008480656,0.009854957,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 3ZGZ|1|B|G|13 - 3ZGZ|1|B|G|21 cWS 
Interaction  | Interacting Bases [1,3] | Pair Probability [[0.104355937,0.045189764,0.001019127,0.005611930,0.000000000],[0.093142996,0.061480989,0.001019127,0.001019127,0.000000000],[0.285637838,0.002759710,0.015709346,0.197413341,0.000000000],[0.093049013,0.090553501,0.001019127,0.001019127,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 3ZGZ|1|B|G|13 - 3ZGZ|1|B|A|22 tSH 
InitialNode  | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [5] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000000000000001] | Pair Probability [[0.246892522,0.200307206,0.211681907,0.204611433,0.000000000],[0.016004500,0.013053530,0.002177663,0.013247577,0.000000000],[0.021640765,0.002177663,0.027736420,0.010358648,0.000000000],[0.007774354,0.008200965,0.006489923,0.007644924,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.016116035,0.966962127,0.016116035,0.000805802] | Right Letter Distribution [0.029411765,0.147058824,0.441176471,0.382352941,0.000000000] | Left Index [3] | Right Index [5] // Basepair A14 - A20A cWS 
HairpinNode  | Num Bases [1] | Left Index [4] | Right Index [4] | Norm Constant [1.000000000000000] // Hairpin node A15:A15
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.700000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.100000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.100000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A15

Sequences of instances from HL_68767.1:> HL_68767.1 3ZGZ G 12 C 23 GGAAUCGGUAGAC > HL_68767.1 2BTE G 12 C 23 GGAAUGGGUAGAC > HL_68767.1 5AH5 G 12 C 23 GAAAUCGGUAAAC