while(my $line=<FILE>) {
    my $linecopy=$line;
    while ($line=~m/(ct[ag]a[ct])/g) {
        my $match=$1;
        my ($rest)=$linecopy=~m/(?:$match)(.*)$/;
        print "$match\t".length($rest)."\t";
    }
    print "\n";
}

##</code><code>##

sub matchit {
    my $data=shift;
    if ($data =~ m/(ct[ag]a[ct])(.*)$/) {
        print "$1\t".length($2)."\t";
        matchit($2);
    } else {
        print "\n";
    }
}
matchit($_) while(<FILE>);