Table 1.

Summary of tRNA gene predictions in the cow genome.

Amino acid/Pseudo genes	Numbers of tRNAscan-SE predictions		Numbers of RepMask3 tRNAs		RepMask % of removed tRNAs		Numbers of tRNAs without RE4		Numbers of tRNAs with 95% similarity
	Chr1-X1	ChrUn2	Chr 1-X	ChrUn	Chr 1-X	ChrUn	Chr 1-X	ChrUn	Chr 1-X	ChrUn
Ala	293	41	216	30	73.7	73.2	77	11	18	2
Arg	811	120	755	109	93.1	90.8	56	11	18	5
Asn	57	24	25	4	43.9	16.7	32	20	20	11
Asp	316	44	238	29	75.3	65.9	78	15	12	5
Cys	12062	2061	12033	2059	99.8	99.9	29	2	25	0
Gln	142	30	79	15	55.6	50.0	63	15	14	9
Glu	2163	330	817	113	37.8	34.2	1346	217	14	10
Gly	7449	927	7141	881	95.9	95.0	308	46	22	10
His	193	44	178	36	92.2	81.8	15	8	10	8
Ile	59	9	29	5	49.2	55.6	30	4	17	3
Leu	144	30	92	11	63.9	36.7	52	19	12	4
Lys	300	57	93	20	31.0	35.1	207	37	14	7
Met	39	7	10	2	25.6	28.6	29	5	12	2
Phe	352	61	324	58	92.1	95.1	28	3	11	3
Pro	27	10	8	1	29.6	10.0	19	9	15	9
Ser	539	98	491	88	91.1	89.8	48	10	14	2
Thr	48	7	14	5	29.2	71.4	34	2	8	0
Trp	1558	191	1519	191	97.5	100.0	39	0	5	0
Tyr	822	145	799	144	97.2	99.3	23	1	15	0
Val	209	49	148	20	70.8	40.8	61	29	22	17
Pseudogenes	163490	25693	158551	25038	97.0	97.5	-	-
Total	191073	29978	183560	28859	96.1	96.3	2574	464	298	107

¹Chr1-X refers to assembled cow chromosomes

²ChrUn refers to the unordered cow contigs

³RepMask refers to the RepeatMasker program

⁴RE refers to repetitive elements.