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open(DNA,"<$filename") or croak("Cannot open $filename:$!\n");
FASTAKEY:  for my $g (@fastarray){
...
close(DNA) or croak("Cannot close $filename:$!\n");    
    
print "Finished gathering all the sequences, now moving on.\n";

$g is: >LG_I
This $g, >LG_I, has a set.
...
substr outside of string at Test3 line 1480, <DNA> line 534211.

...and so on.  it continues all the way up to $i is 61.