use strict;
use warnings;
use feature 'say';

my $txt = q{
    Uninteresting line.
    More boring stuff.
    Here's the AATCCGCTAG string.
    Afterwards, more drivel.
    Footnotes, etc.
};

my @lines = split "\n", $txt;

my $counter = 0;
for my $line ( @lines ) {
    $counter++;
    next unless $line =~ /(\b[ACGT]+\b)/;
    say "Found $1 in line $counter";
}

__END__