#...
if ($i =~ /^>(\S+)/){                # Captured in $1
    unless ($seq1 eq ""){
      $seq1 =~ s/[^ATCG]//g;         #if match The s/// clears $1
      &process_nuc($seq1, $name1);
    }
    $seq1="";
    $name1=$1;                       #hence $name1 may be undef
#...