use strict;
my $str = '>YBGC_ECOLI
MNTTLFRWPVRVYYEDTDAGGVVYHASYVAFYERARTEMLRHHHFSQQALMAERVAFVVRKMTVEYYAPA
RLDDMLEIQTEITSMRGTSLVFTQRIVNAENTLLNEAEVLVVCVDPLKMKPRALPKSIVAEFKQ
>USHA_ECOLI
MKLLQRGVALALLTTFTLASETALAYEQDKTYKITVLHTNDHHGHFWRNEYGEYGLAAQKTLVDGIRKEV
AAEGGSVLLLSGGDINTGVPESDLQDAEPDFRGMNLVGYDAMAIGNHEFDNPLTVLRQQEKWAKFPLLSA
NIYQKSTGERLFKPWALFKRQDLKIAVIGLTTDDTAKIGNPEYFTDIEFRKPADEAKLVIQELQQTEKPD
IIIAATHMGHYDNGEHGSNAPGDVEMARALPAGSLAMIVGGHSQDPVCMAAENKKQVDYVPGTPCKPDQQ
NGIWIVQAHEWGKYVGRADFEFRNGEMKMVNYQLIPVNLKKKVTWEDGKSERVLYTPEIAENQQMISLLS
PFQNKGKAQLEVKIGETNGRLEGDRDKVRFVQTNMGRLILAAQMDRTGADFAVMSGGGIRDSIEAGDISY
KNVLKVQPFGNVVVYADMTGKEVIDYLTAVAQMKPDSGAYPQFANVSFVAKDGKLNDLKIKGEPVDPAKT
YRMATLNFNATGGDGYPRLDNKPGYVNTGFIDAEVLKAYIQKSSPLDVSVYEPKGEVSWQ
>CN16_ECOLI
MIKFSATLLATLIAASVNAATVDLRIMETTDLHSNMMDFDYYKDTATEKFGLVRTASLINDARNEVKNSV
LVDNGDLIQGSPLADYMSAKGLKAGDIHPVYKALNTLDYTVGTLGNHEFNYGLDYLKNALAGAKFPYVNA
NVIDARTKQPMFTPYLIKDTEVVDKDGKKQTLKIGYIGVVPPQIMGWDKANLSGKVTVNDITETVRKYVP
EMREKGADVVVVLAHSGLSADPYKVMAENSVYYLSEIPGVNAIMFGHAHAVFPGKDFADIEGADIAKGTL
NGVPAVMPGMWGDHLGVVDLQLSNDSGKWQVTQAKAEARPIYDIANKKSLAAEDSKLVETLKADHDATRQ
FVSKPIGKSADNMYSYLALVQDDPTVQVVNNAQKAYVEHYIQGDPDLAKLPVLSAAAPFKVGGRKNDPAS
YVEVEKGQLTFRNAADLYLYPNTLIVVKASGKEVKEWLECSAGQFNQIDPNSTKPQSLINWDGFRTYNFD
VIDGVNYQIDVTQPARYDGECQMINANAERIKNLTFNGKPIDPNAMFLVATNNYRAYGGKFAGTGDSHIA
FASPDENRSVLAAWIADESKRAGEIHPAADNNWRLAPIAGDKKLDIRFETSPSDKAAAFIKEKGQYPMNK
VATDDIGFAIYQVDLSK
>6PGD_ECOLI
MSKQQIGVVGMAVMGRNLALNIESRGYTVSIFNRSREKTEEVIAENPGKKLVPYYTVKEFVESLETPRRI
LLMVKAGAGTDAAIDSLKPYLDKGDIIIDGGNTFFQDTIRRNRELSAEGFNFIGTGVSGGEEGALKGPSI
MPGGQKEAYELVAPILTKIAAVAEDGEPCVTYIGADGAGHYVKMVHNGIEYGDMQLIAEAYSLLKGGLNL
TNEELAQTFTEWNNGELSSYLIDITKDIFTKKDEDGNYLVDVILDEAANKGTGKWTSQSALDLGEPLSLI
TESVFARYISSLKDQRVAASKVLSGPQAQPAGDKAEFIEKVRRALYLGKIVSYAQGFSQLRAASEEYNWD
LNYGEIAKIFRAGCIIRAQFLQKITDAYAENPQIANLLLAPYFKQIADDYQQALRDVVAYAVQNGIPVPT
FSAAVAYYDSYRAAVLPANLIQAQRDYFGAHTYKRIDKEGVFHTEWLD
';
my $regex = qr/([A-Z0-9]*_ECOLI)\n([A-Z\n]*)/p;
if ( $str =~ /$regex/g ) {
print "Whole match is ${^MATCH} and its start/end positions can be obtained via \$-[0] and \$+[0]\n";
# print "Capture Group 1 is $1 and its start/end positions can be obtained via \$-[1] and \$+[1]\n";
# print "Capture Group 2 is $2 ... and so on\n";
}
# ${^POSTMATCH} and ${^PREMATCH} are also available with the use of '/p'
# Named capture groups can be called via $+{name}
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 Perl, please visit: http://perldoc.perl.org/perlre.html