Because $qbase is a letter, $query_sequence[$qbase] is not valid. To fix it change to this

foreach $qbase ($q_start .. $q_end)
# qbase is now a number
{
  if ( ($query_sequence[$qbase] =~ /[nN]/) && ($subj_sequence[$qbase] 
+!~ /[nN]/) )
  {
    ++$ncount;    
  }
}
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poj