while ($content =~ /^[\w]+?([VMFWLCA]{8,})[\w]+?$/mg) {
    my $sequence = $1;
    print $header, "contains $sequence at position ", pos($content) - 
+length($sequence), "\n";
}
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What did you want "pos($content) - length($sequence)" to give you?    The whole pattern starts at 371 and ends at 428 while the contents of $1 start at 416 and end at 424 so 420 is somewhere in the middle of $1.    Have a look at the @- and @+ arrays for the start and end positions of matches.