See also this thread for a very similar, though not identical, problem. Also, Hello! to your perl teacher.

#! /usr/bin/perl

sub ano1 {
    my ($str1, $str2) = @_;

    my ($last) = $str2 =~ /.*(\w)/;

    tr/\0-/-=/, s/=(?=\W*(\w?))/ $1 || $last /ge
      for my $answer = $str1 =~ tr/A-Z/\0/r ^ $str2;

    $answer;
}

sub ano2 {
    my ($x, $y) = @_;
    $y &= ($y =~ tr/-\0-\377/\0\377/r) | ($x =~ tr/-\0-\377/\377\0/r);
    $y =~ s/(\0+)(.)/$2 x (1 + length $1)/eg;
    $y =~ s/(.)(\0+)$/$1 x (1 + length $2)/er;
}

chomp (our ($str1, $str2) = <DATA>);

use Benchmark 'cmpthese';
cmpthese -5, {
    ano1 => q( ano1 $str1, $str2 ),
    ano2 => q( ano2 $str1, $str2 ),
};

__DATA__
MCCAALAPPMAATVGPESIWLWIGTIGMTLGTLYFVGRGRGVRDRKMQEFYIITIFITTIAAAMYFAMAT
+GFGVT-------------EVMVG----DE---ALTIYWARYADWLFTTPLLLLDLSLLAGANRN----T
+IATLIG-LDVFMIG---T---GAIAALSST-PGTRIAWWAIST--GALL--ALLYVLVGTLSENARNRA
+PEVA--SLFGRLRNLVIALWFLYPVVWILGT---EGTFGILP--LYWETAAFMVLDLSAKVGFGVILLQ
+SRSVLERVATPTAAPT
--OOOOOOOOOOOOOOOOMMMMMMMMMMMMMMMMMMMMMIIIIIIIIIIMMMMMMMMMMMMMMMMMMMMM
+OOOOO-------------OOOOO----OO---OOOOMMMMMMMMMMMMMMMMMMMMMIIIIIII----M
+MMMMMM-MMMMMMM---M---MMMMMMOOO-OOOOMMMMMMMM--MMMM--MMMMMMMMMMIIIIIIII
+IIII--IIIIMMMMMMMMMMMMMMMMMMMMO---OOO-OOOO--OOOMMMMMMMMMMMMMMMMMMMMMI
+IIIIIIIIIIII----
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