$re = '/SRR([0-9]+)([\.])([0-9]+)([\s]+)([A-Z]+)/m';
$str = ' sequence_id cdr3_aa
0 SRR11610498.829751 AKDLGPDAGYTVFNDYFDN
1 SRR11610498.853725 AKDLGPDAGYTVFNDYFDN
2 SRR11610498.856922 AKDLGPDAGYTVFNHYFDN
3 SRR11610498.861591 AKDLGPDAGYTVFNDYFDN
4 SRR11610498.909314 AKDLGPDAGYTVFNDYFDN
5 SRR11610498.915768 AKDLGPDAGYTVFNDYFDN
6 SRR11610498.922245 ARGGLVVVDSFDY
7 SRR11610498.1017490 ASDLSYASSWLHYFDV
8 SRR11610498.1022079 ARLRFDNGALYFDY
9 SRR11610498.1037667 ASSAPPSGFNWFDP
10 SRR11610498.1111232 AKGPQIVATTTDNLEV
11 SRR11610498.1183596 AKDLGPDAGYTVFNDYFDN
';
preg_match_all($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