Assuming your text is well-formed, the following should work well as a more modular solution:

use strict;
use warnings;

my ($text, %percent);

$text = 'Identities = 1529/1540 (99%), Gaps = 2/1540 (0%)';
$percent{$1} = $2 while $text =~ /(\w+) = \d+\/\d+ \((\d+)%\)/g;

for (sort keys %percent) {
    print "$_ : $percent{$_}\n";
}
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This way you can access any percentage by name.