$re = '/^chr(1?[0-9]|2[0-2]|X|Y)/m';
$str = 'chr1 3009844 3009908 DXX 42 -
chr2 3000386 3000450 DXX 15 -
chr3 3000386 3000450 DXX 15 -
chr4 3000386 3000450 DXX 15 -
chr5 3000386 3000450 DXX 15 -
chr6 3000386 3000450 DXX 15 -
chr7 3000386 3000450 DXX 15 -
chr8 3000386 3000450 DXX 15 -
chr9 3000386 3000450 DXX 15 -
chr10 3000386 3000450 DXX 15 -
chr11 3000386 3000450 DXX 15 -
chr12 3000386 3000450 DXX 15 -
chr13 3000386 3000450 DXX 15 -
chr14 3000386 3000450 DXX 15 -
chr15 3000386 3000450 DXX 15 -
chr16 3000386 3000450 DXX 15 -
chr17 3000386 3000450 DXX 15 -
chr18 3000386 3000450 DXX 15 -
chr19 3000386 3000450 DXX 15 -
chrX 3000386 3000450 DXX 15 -
chrY 3000386 3000450 DXX 15 -
chr1_GL456210_random 3000386 3000450 DXX 15 -
chr1_GL456211_random 3000386 3000450 DXX 15 -
chr1_GL456212_random 3000386 3000450 DXX 15 -
chr1_GL456221_random 3000386 3000450 DXX 15 -
chr4_GL456216_random 3000386 3000450 DXX 15 -
chr4_JH584292_random 3000386 3000450 DXX 15 -
chr4_JH584295_random 3000386 3000450 DXX 15 -
chr5_GL456354_random 3000386 3000450 DXX 15 -
chr5_JH584296_random 3000386 3000450 DXX 15 -
chr5_JH584297_random 3000386 3000450 DXX 15 -
chr5_JH584299_random 3000386 3000450 DXX 15 -
chrX_GL456233_random 3000386 3000450 DXX 15 -';
preg_match_all($re, $str, $matches, PREG_SET_ORDER, 0);
// Print the entire match result
var_dump($matches);
Please keep in mind that these code samples are automatically generated and are not guaranteed to work. If you find any syntax errors, feel free to submit a bug report. For a full regex reference for PHP, please visit: http://php.net/manual/en/ref.pcre.php