Table 1.

Transfer tRNAs in Dermatophagoides farinae and D. pteronyssinus

Ana	Cnb	tRNA	Strc	Lend	Ante	Strf	TRNg	ARWh	BLASTi	Prevj	Cfk	5' overlapl	3' overlapm
1-3	y	Asp/D	+	54	GTC	tv	Y	Y	D		y	-	ATP8 (1)
4-7	y	Gly/G	+	57	TCC	tv	Y	Y	G		y	-	ND3 (1)
8-14	n	Arg/R	+	49	TCG	d	-	y	R	tvn		ND3 (1)	-
15-18	y	Met/M	+	52	CAT	tv	y	-	M			-	-
19-25	y	Ser2/S2	+	52	TGA	d	-	y	S2, W	tvo		-	-
26-28	y	Cys/C	-	53	GCA	d	Y	Y	C	A		-	-
29-32	y	Pro/P	+	57	TGG	tv	Y	y	P			-	-
33-40	n	Tyr/Y	+	55	GTA	d	-	y	Y	Vp		-	K (10)
41-44	y	Lys/K	+	62	TTT	c/tv	y	y	K, W, C, L2	tvq		Y(10)	N(1),-
45-47	y	Asn/N	+	55	GTT	tv	Y	Y	N		y	K(1)	-
48-53	n	Val/Vr	+	52	TAC	d	-	-	V, Y, l-rRNA	l-rRNA		s-rRNA(3,2)	-
54-57	y	Trp/W	+	58	TCA	tv	Y	Y	W, S2, F		y	-	-
58-61	-	-s	+	44	'GGT'	-	-	-	-	Y		-	-
62-67	y	Thr/T	-	55	TGT	tv	Y	y	T			-	ND6 (1)
68-70	y	His/H	+	56	GTG	tv	Y	Y	H		y	-	ND5 (1)
71-77	y	Phe/F	+	55	GAA	tv	Y	Y	F, W		y	-	-
78-80	y	Ser1/S1	-	52	TCT	d	-t	y	S1, S2	du		-, Q (2)v	-
81-83	y	Gln/Q	-	54	TTG	tv	Y	Y	Q, W			-, I (2)v	-, S1(2)v
84-88	y	Ile/I	-	53	GAT	tv	y	-	I			-	-, Q (2)v
89-92	y	Glu/E	-	54	TTC	tv	y	Y	E, W	tvw	y	-	ND2 (1)
93-95	y	Leu1/L1	-	55	TAG	tv	Y	Y	L1	tvx		-	-
96-100	n	Ala/Ay	+	50	TGC	d	-	y	-z	Caa		-	-
101-103	y	Leu2/L2	+	57	TAA	tv	Y	Y	L2			-	COX1(1)

^a refers to IDs from the detailed analyses (Additional file 5)

^b Canonical, can be found confidently either in tRNAscan-SE or ARWEN

^c Strand

^d Length (D. farinae only)

^e Anticodon

^f tRNA secondary structure: tv = TV-replacement loop tRNA, d = D-replacement loop tRNA, c = cloverleaf tRNA

^g tRNAscan-SE analysis: Y = high score or unambiguous tRNA; y = low score or ambiguous tRNA; - = failed to find any tRNAs

^h ARWEN analysis: designations as for tRNAscan-SE

ⁱ BLAST similarity search of tRNA anticodon helix restricted to mitochondrial genomes of arthropods

^j Previously inferred for D. pteronyssinus, if either gene region (bold) or its secondary structure is different from our reconstruction

^k The 5' end of a tRNA is confirmed by EST data (a polyadenylated site immediately upstream of the tRNA 5' end). For others tRNAs these data are not available. Approximated if EST data are missing in one species.

^l in all cases overlaps with the 3' end of a gene. The overlap length (nt) is given in parentheses. tRNAs genes are given using single letter designations. If different in the two species, given as two values separated by a comma, for D. farinae and D. pteronyssinus, respectively.

^m In all cases overlaps with 5' end of a gene; format as in previous column

ⁿ 17 nt overlap with ND3 3' end

^o 12 nt overlap with 3' end tRNA-Met

^p 5' end overlaps with 5' of tRNA-Lys by 7 nt, 3' end overlaps with 3' end of tRNA-Pro by 11 nt

^q 3' part is different from our structure

^r putative; alternatively part of l-rRNA start where it forms stable secondary structure with 6-nt "anticodon", variable loop, and 5-nt stem.

^s not a tRNA, non-coding region between tRNA-Trp and ND1

^t also tRNA-Ser2

^u 3' acceptor and T-stems are separated by 1 nt. These two stems are not separated in our structure (as in the typical tRNA)

^v D. pteronyssinus only

^w 5' acceptor stem and D-stem (3 bp) are separated by 1 nt. These two stems are separated by 2 nt (as in the typical tRNA); D-stem is 4 bp-long in our structure; and the acceptor stem is situated at n-1 position in our structure

^x 3-bp D-stem (4-bp in our structure)

^y alternatively non-coding region between tRNA L1-tRNA L1-L2 structure

^z one hit on Steganacarus magnus may represent tRNA-Ala (originally designated as non-translated intergenic spacer).

^aa cloverleaf, 3' end overlaps with tRNA-Leu1 by 5 nt.