Hmmm,

First:

#...
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
#...
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Second: Why do you print out all elements in "@array"? Ok, this may be test code.

Third: Why do you create %norm_2, %norm_3, %norm_4 (more...) without using them ???

Fourth: Where do you get the data for %counts_1, %total_mono ???

Fifth: What does process_nuc() do????

....

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