Alignment of HL_13189.1 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	3 2 I	4 3 2	5 3 I	6 3 3	8 2 4	In acceptance region	Cutoff score	Full edit distance	Interior edit distance	Alignment score deficit
HL_13189.1_Instance_1 HL_13189.1,HL_8P9A_231,C543_G548	C		C	UC	G	G
HL_13189.1_Sequence_1 HL_13189.18P9A_C543_G548	C		C	UC	G	G	true	85	0	0	1.41
HL_13189.1_Instance_2 HL_13189.1,HL_5D0B_001,U33_A37	U	G	U		A	A
HL_13189.1_Sequence_2 HL_13189.15D0B_U33_A37	U	G	U		A	A	true	100	0	0	0.00

Conserved interactions between motif group positions in HL_13189.1:

1 2 s35 
1 4 cWW 
2 3 cSH 
3 4 s35

JAR3D SCFG/MRF model for HL_13189.1:

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 [4] // Initial node
BasepairNode | Deletion Probability [0.0000015195492620] | Pair Probability [[0.009285457,0.017323068,0.010436779,0.197555258,0.000000000],[0.021160175,0.009772202,0.212782490,0.012417770,0.000000000],[0.010508004,0.198766713,0.002067002,0.023256875,0.000000000],[0.212699647,0.011830790,0.040032900,0.010104868,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.493381468,0.493381468,0.012635379,0.000601685] | Left Letter Distribution [0.166666667,0.166666667,0.500000000,0.166666667,0.000000000] | 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 [4] // Basepair C543 - G548 cWW 
HairpinNode  | Num Bases [2] | Left Index [2] | Right Index [3] | Norm Constant [1.000000000000000] // Hairpin node C544:G547
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.101972765,0.096579916,0.004936087,0.013771883,0.000000000],[0.099599360,0.093207052,0.099990175,0.008873056,0.000000000],[0.009045046,0.001059694,0.089271918,0.086750613,0.000000000],[0.115773341,0.090936806,0.001059694,0.087172594,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin Interaction C544 - G547 cSH 
Insertion    | Location [1] | Length Distribution [0.481347774,0.024067389,0.481949458,0.012033694,0.000601685] | Letter Distribution [0.125000000,0.375000000,0.125000000,0.375000000,0.000000000]// Insertion in Hairpin after nucleotide 2, position 1

Sequences of instances from HL_13189.1:> HL_13189.1 8P9A C 543 G 548 CCUCGG > HL_13189.1 5D0B U 33 A 37 UGUAA