When you strip off the header the line endings remain. Try deleting "\n" characters. If on windows also delete "\r" characters. 
# Remove fasta header line
if ( $para =~ s/^>(.*)//m ){
    $name = $1;
};
# Remove comment line(s)
$para =~ s/^\s*#.*//mg;

$para =~ tr/\r\n//d;

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In reply to Re^3: Count the sequence length of each entry in the file by wazat
in thread Count the sequence length of each entry in the file by davi54

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