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use strict;
use warnings;
...
    my $GCcount = $seq =~ tr/GC//;
    printf "%s, %.2f%%\n", ">$id", ( $GCcount / length $seq ) * 100;
}

>gi|5524211|gb|AAD44166.1| cytochrome b [Elephas maximus maximus]
LCLYTHIGRNIYYGSYLYSETWNTGIMLLLITMATAFMGYVLPWGQMSFWGATVITNLFSAIPYIGTNLV
...
LLILILLLLLLALLSPDMLGDPDNHMPADPLNTPLHIKPEWYFLFAYAILRSVPNKLGGVLALFLSIVIL
GLMPFLHTSKHRSMMLRPLSQALFWTLTMDLLTLTWIGSQPVEYPYTIIGQMASILYFSIILAFLPIAGX
IENY

>gi|5524211|gb|AAD44166.1| cytochrome b [Elephas maximus maximus], 7.3
+9%