Alignment of HL_22584.6 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 4 3	8 3 4	10 2 5	In acceptance region	Cutoff score	Full edit distance	Interior edit distance	Alignment score deficit
HL_22584.6_Instance_1 HL_22584.6,HL_8VM9_006,G57_C63	G	A	A	A	C	A	C
HL_22584.6_Sequence_1 HL_22584.68VM9_G57_C63	G	A	A	A	C	A	C	true	100	0	0	0.00
HL_22584.6_Instance_2 HL_22584.6,HL_8D29_002,G13_C19	G	A	A	A	C	A	C
HL_22584.6_Sequence_2 HL_22584.68D29_G13_C19	G	A	A	A	C	A	C	true	100	0	0	0.00
HL_22584.6_Instance_3 HL_22584.6,HL_8D29_003,G13_C19	G	A	A	A	C	A	C
HL_22584.6_Sequence_3 HL_22584.68D29_G13_C19	G	A	A	A	C	A	C	true	100	0	0	0.00
HL_22584.6_Instance_4 HL_22584.6,HL_6DB9_001,G23_C29	G	A	A	A	C	A	C
HL_22584.6_Sequence_4 HL_22584.66DB9_G23_C29	G	A	A	A	C	A	C	true	100	0	0	0.00
HL_22584.6_Instance_5 HL_22584.6,HL_8VM8_003,G63_C69	G	A	A	A	C	A	C
HL_22584.6_Sequence_5 HL_22584.68VM8_G63_C69	G	A	A	A	C	A	C	true	100	0	0	0.00
HL_22584.6_Instance_6 HL_22584.6,HL_8DK7_001,G13_C19	G	A	A	A	C	A	C
HL_22584.6_Sequence_6 HL_22584.68DK7_G13_C19	G	A	A	A	C	A	C	true	100	0	0	0.00
HL_22584.6_Instance_7 HL_22584.6,HL_4KZD_001,G37_C43	G	A	A	A	C	A	C
HL_22584.6_Sequence_7 HL_22584.64KZD_G37_C43	G	A	A	A	C	A	C	true	100	0	0	0.00
HL_22584.6_Instance_8 HL_22584.6,HL_9C2K_002,G49_C55	G	A	A	A	C	A	C
HL_22584.6_Sequence_8 HL_22584.69C2K_G49_C55	G	A	A	A	C	A	C	true	100	0	0	0.00
HL_22584.6_Instance_9 HL_22584.6,HL_9AUS_002,G5_C11	G	A	A	A	C	A	C
HL_22584.6_Sequence_9 HL_22584.69AUS_G5_C11	G	A	A	A	C	A	C	true	100	0	0	0.00
HL_22584.6_Instance_10 HL_22584.6,HL_9E7E_002,G49_C55	G	A	A	A	C	A	C
HL_22584.6_Sequence_10 HL_22584.69E7E_G49_C55	G	A	A	A	C	A	C	true	100	0	0	0.00
HL_22584.6_Instance_11 HL_22584.6,HL_9DN4_002,G8_C14	G	A	A	A	C	A	C
HL_22584.6_Sequence_11 HL_22584.69DN4_G8_C14	G	A	A	A	C	A	C	true	100	0	0	0.00
HL_22584.6_Instance_12 HL_22584.6,HL_9C2K_004,G49_C55	G	A	A	A	C	A	C
HL_22584.6_Sequence_12 HL_22584.69C2K_G49_C55	G	A	A	A	C	A	C	true	100	0	0	0.00
HL_22584.6_Instance_13 HL_22584.6,HL_8D29_001,G13_C19	G	A	A	A	C	A	C
HL_22584.6_Sequence_13 HL_22584.68D29_G13_C19	G	A	A	A	C	A	C	true	100	0	0	0.00
HL_22584.6_Instance_14 HL_22584.6,HL_3IVK_003,G59_C65	G	A	A	A	C	A	C
HL_22584.6_Sequence_14 HL_22584.63IVK_G59_C65	G	A	A	A	C	A	C	true	100	0	0	0.00
HL_22584.6_Instance_15 HL_22584.6,HL_9C75_002,G49_C55	G	A	A	A	C	A	C
HL_22584.6_Sequence_15 HL_22584.69C75_G49_C55	G	A	A	A	C	A	C	true	100	0	0	0.00
HL_22584.6_Instance_16 HL_22584.6,HL_8T29_001,G35_C41	G	A	A	A	C	A	C
HL_22584.6_Sequence_16 HL_22584.68T29_G35_C41	G	A	A	A	C	A	C	true	100	0	0	0.00
HL_22584.6_Instance_17 HL_22584.6,HL_8DP3_001,G20_C26	G	A	A	A	C	A	C
HL_22584.6_Sequence_17 HL_22584.68DP3_G20_C26	G	A	A	A	C	A	C	true	100	0	0	0.00
HL_22584.6_Instance_18 HL_22584.6,HL_8VMB_001,G18_C24	G	A	A	A	C	A	C
HL_22584.6_Sequence_18 HL_22584.68VMB_G18_C24	G	A	A	A	C	A	C	true	100	0	0	0.00
HL_22584.6_Instance_19 HL_22584.6,HL_8UIW_001,G29_C35	G	A	A	A	C	A	C
HL_22584.6_Sequence_19 HL_22584.68UIW_G29_C35	G	A	A	A	C	A	C	true	100	0	0	0.00
HL_22584.6_Instance_20 HL_22584.6,HL_6X5M_002,G14_C20	G	A	A	A	C	A	C
HL_22584.6_Sequence_20 HL_22584.66X5M_G14_C20	G	A	A	A	C	A	C	true	100	0	0	0.00
HL_22584.6_Instance_21 HL_22584.6,HL_7MLX_002,G40_C46	G	A	A	A	C	A	C
HL_22584.6_Sequence_21 HL_22584.67MLX_G40_C46	G	A	A	A	C	A	C	true	100	0	0	0.00
HL_22584.6_Instance_22 HL_22584.6,HL_7SZU_001,G35_C41	G	A	A	A	C	A	C
HL_22584.6_Sequence_22 HL_22584.67SZU_G35_C41	G	A	A	A	C	A	C	true	100	0	0	0.00
HL_22584.6_Instance_23 HL_22584.6,HL_8VMA_003,G60_C66	G	A	A	A	C	A	C
HL_22584.6_Sequence_23 HL_22584.68VMA_G60_C66	G	A	A	A	C	A	C	true	100	0	0	0.00
HL_22584.6_Instance_24 HL_22584.6,HL_6OL3_001,G64_C70	G	A	A	C	C	C	C
HL_22584.6_Sequence_24 HL_22584.66OL3_G64_C70	G	A	A	C	C	C	C	true	56	0	0	5.00
HL_22584.6_Instance_25 HL_22584.6,HL_3IGI_009,C368_G373	C		G	A	A	C	G
HL_22584.6_Sequence_25 HL_22584.63IGI_C368_G373	C		G	A	A	C	G	true	27	0	0	8.29
HL_22584.6_Instance_26 HL_22584.6,HL_9DFE_063,C2701_G2706	C		U	C	C	A	G
HL_22584.6_Sequence_26 HL_22584.69DFE_C_2701_G_2706	C		U	C	C	A	G	true	46	0	0	6.11

Conserved interactions between motif group positions in HL_22584.6:

1 2 s33 
1 5 cWW 
2 4 tSW 
3 4 s35 
4 5 s35

JAR3D SCFG/MRF model for HL_22584.6:

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 [5] // Initial node
BasepairNode | Deletion Probability [0.0000001854263003] | Pair Probability [[0.007867381,0.016213076,0.008965314,0.162816310,0.000000000],[0.014038783,0.007737247,0.180598352,0.010785264,0.000000000],[0.008880998,0.359243783,0.001691352,0.021461615,0.000000000],[0.161051477,0.011130152,0.019198281,0.008320616,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.078400743,0.919735029,0.001775806,0.000088422] | Left Letter Distribution [0.942307692,0.019230769,0.019230769,0.019230769,0.000000000] | 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 [5] // Basepair G57 - C63 cWW 
BasepairNode | Deletion Probability [0.0000001235438727] | Pair Probability [[0.369808211,0.024438067,0.002118038,0.010112269,0.000000000],[0.155555172,0.015638532,0.006412983,0.008640273,0.000000000],[0.150715994,0.034589795,0.002118038,0.006985689,0.000000000],[0.177576486,0.011442242,0.013135709,0.010712501,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.001915525,0.996073173,0.001915525,0.000095776] | Left Letter Distribution [0.875000000,0.089285714,0.017857143,0.017857143,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [4] // Basepair A59 - A62 tSW 
HairpinNode  | Num Bases [1] | Left Index [3] | Right Index [3] | Norm Constant [1.000000000000000] // Hairpin node C61:C61
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.053571429,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.910714286,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.017857143,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.017857143,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C61

Sequences of instances from HL_22584.6:> HL_22584.6 8VM9 G 57 C 63 GAAACAC > HL_22584.6 8D29 G 13 C 19 GAAACAC > HL_22584.6 8D29 G 13 C 19 GAAACAC > HL_22584.6 6DB9 G 23 C 29 GAAACAC > HL_22584.6 8VM8 G 63 C 69 GAAACAC > HL_22584.6 8DK7 G 13 C 19 GAAACAC > HL_22584.6 4KZD G 37 C 43 GAAACAC > HL_22584.6 9C2K G 49 C 55 GAAACAC > HL_22584.6 9AUS G 5 C 11 GAAACAC > HL_22584.6 9E7E G 49 C 55 GAAACAC > HL_22584.6 9DN4 G 8 C 14 GAAACAC > HL_22584.6 9C2K G 49 C 55 GAAACAC > HL_22584.6 8D29 G 13 C 19 GAAACAC > HL_22584.6 3IVK G 59 C 65 GAAACAC > HL_22584.6 9C75 G 49 C 55 GAAACAC > HL_22584.6 8T29 G 35 C 41 GAAACAC > HL_22584.6 8DP3 G 20 C 26 GAAACAC > HL_22584.6 8VMB G 18 C 24 GAAACAC > HL_22584.6 8UIW G 29 C 35 GAAACAC > HL_22584.6 6X5M G 14 C 20 GAAACAC > HL_22584.6 7MLX G 40 C 46 GAAACAC > HL_22584.6 7SZU G 35 C 41 GAAACAC > HL_22584.6 8VMA G 60 C 66 GAAACAC > HL_22584.6 6OL3 G 64 C 70 GAACCCC > HL_22584.6 3IGI C 368 G 373 CGAACG > HL_22584.6 9DFE C 2701 G 2706 CUCCAG