#!/usr/bin/perl

# http://perlmonks.org/?node_id=1123341

use strict;
use warnings;

my $str1='MCCAALAPPMAATVGPESIWLWIGTIGMTLGTLYFVGRGRGVRDRKMQEFYIITIFITTI
+AAAMYFAMATGFGVT-------------EVMVG----DE---ALTIYWARYADWLFTTPLLLLDLSLLA
+GANRN----TIATLIG-LDVFMIG---T---GAIAALSST-PGTRIAWWAIST--GALL--ALLYVLVG
+TLSENARNRAPEVA--SLFGRLRNLVIALWFLYPVVWILGT---EGTFGILP--LYWETAAFMVLDLSA
+KVGFGVILLQSRSVLERVATPTAAPT';

my $str2='--OOOOOOOOOOOOOOOOMMMMMMMMMMMMMMMMMMMMMIIIIIIIIIIMMMMMMMMMMM
+MMMMMMMMMMOOOOO-------------OOOOO----OO---OOOOMMMMMMMMMMMMMMMMMMMMMII
+IIIII----MMMMMMM-MMMMMMM---M---MMMMMMOOO-OOOOMMMMMMMM--MMMM--MMMMMMMM
+MMIIIIIIIIIIII--IIIIMMMMMMMMMMMMMMMMMMMMO---OOO-OOOO--OOOMMMMMMMMMMMM
+MMMMMMMMMIIIIIIIIIIIII----';

my ($last) = $str2 =~ /.*(\w)/; # find letter for ending -'s

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

print "$answer\n";
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Explanation provided on request :)