tr/A/A/ and tr/A// are the same actually. The problem with your code is that when you use

while(<FH>){
#The next line is in $_
}
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The next line is automagically assigned to $_, so you don't need $line=<MYFILE> which then grabs the second (..,forth, sixth..) line.. However, if you want to count every char, you should use one of the ways demerphq and jmcnamara showed above, and not tr///..