“One code to find them all”: a perl tool to conveniently parse RepeatMasker output files

Table 1 Copy number per chromosome for each category of TEs in D. melanogaster

Chromatin type	Chromosome	Without --strict option				With --strict option
		DNA	Non-LTR	LTR	Total	DNA	Non-LTR	LTR	Total
Euchromatin	2L	914	263	498	1,675	589	204	278	1,071
	2R	1,018	343	707	2,068	649	246	357	1,252
	3L	892	369	771	2,032	595	289	393	1,277
	3R	549	125	455	1,129	289	91	247	627
	4	626	77	35	738	431	54	21	506
	X	720	187	585	1,492	454	137	332	923
	Total	4,719	1,364	3,051	9,134	3,007	1,021	1,628	5,656
Heterochromatin	2LHet	46	23	88	157	38	21	65	124
	2RHet	462	441	811	1,714	370	372	424	1,166
	3LHet	463	339	708	1,510	366	274	357	997
	3RHet	363	319	683	1,365	282	276	375	933
	XHet	65	54	21	140	43	37	14	94
	YHet	46	45	89	180	37	41	59	137
	Total	1,445	1,221	2,400	5,066	1,136	1,021	1,294	3,451
Unplaced	U	909	1,589	3,365	5,863	777	1,399	2,334	4,510
	Uextra	2,132	8,253	11,827	22,212	1,866	7,668	9,635	19,169
	Total	3,041	9,842	15,192	28,075	2,643	9,067	11,969	23,679
Total		9,205	12,427	20,643	42,275	6,786	11,109	14,891	32,786
Total (without unplaced)		6,164	2,585	5,451	14,200	4,143	2,042	2,922	9,107

ISSN: 1759-8753