open(DNA,"<$filename") or croak("Cannot open $filename:$!\n");
FASTAKEY:  for my $g (@fastarray){
 print "\$g is: $g\n";
 if (@{$sets{$g}}){
   print "This \$g, $g, has a set.\n";
  $buffer = '';
  my $skip = 0;
  my $i = 0;
  $position = 0;
  $num = (@{$sets{$g}});
  LINE: while ($newline = <DNA> ) {
    
    if ($skip == 1) {  
      unless ($newline =~ /^>/) {
        next LINE;
        }
      if ($newline =~ /^>/) {
        $skip = 0;
        goto NOSKIP;
        }
      }
      
      else {
      # If new fasta header, 
        NOSKIP: if($newline =~ /^>/) { 
          print "....We've hit a newline, which is: $newline";
          if ($buffer eq '') { 
            chomp $newline;
            print "We are in the 'if buffer eq' loop.\n";
            print "..\$g is: $g, and \$newline is $newline\n";
            if ($newline ne $g) {
              $skip = 1;
              next LINE;
              }
            if ($newline eq $g) {
              $header = $newline;
              $g = $header;
              $skip = 0;
              print "Gathering sequence data from sequence $g\n";
              next LINE;
              }
              
            # closes if buffer eq ''
            }
            
          else { # ($buffer ne '')
            FINISH: print "......At FINISH, \$num is: $num, and \$i is: $i\n"; 
            if ($i == $num) {
              print "in FINISH, \$i is: $i, and \$num is $num.  They should be equal\n";
              $position = 0;
              $skip = 1;
              seek(DNA,(0-length($buffer)),1);
              $len = 0;
              $buffer = '';
              next FASTAKEY;
              }    
              else {
                print "in FINISH, \$i is: $i, and \$num is $num.  They should not be equal\n";
                print "\$i is: $i, \$HoA{$g}[$i][0] is: $HoA{$g}[$i][0], \$HoA{$g}[$i][1] is: $HoA{$g}[$i][1], \$position is: $position and length(\$buffer) is: ".length($buffer)."\n";
                if ($HoA{$g}[$i][0] >= ($position + length($buffer))) {print "The position of \$lowest is past the end of the buffer!  How did that happen?!\n";}
                if ($HoA{$g}[$i][1] < $position) {print "The position of \$highest is below that of \$position!  How did this happen?!\n";}
                
                if ($HoA{$g}[$i][1] >= ($position + length($buffer))) {
                  $match{$g}[$i] = uc(substr($buffer, ($HoA{$g}[$i][0] - $position)));
                  }
                  else {  
                    $match{$g}[$i] = uc(substr($buffer, ($HoA{$g}[$i][0] - $position), $HoA{$g}[$i][2]));  
                    }
                
                $i++; 
                goto FINISH;
                # close uncommented else
                }
                
              #closes else  ($buffer ne ''  )
              }
            # closes if newline    
            }
            
          # closes else statement  
          }

        
    chomp $newline;
    $buffer .= $newline;
    $len = length($newline);
    
    if (($position + $span) < $HoA{$g}[$i][0] && length($buffer) > $span) {
    # Reset the position counter
    # (will be accurate after you reset the buffer, next)
      $position += $span;
     
    # Reset the buffer
    # Discard the first $max worth of data in the buffer
      $buffer = substr($buffer, $span);
      }
    
    unless (length($buffer) >= $HoA{$g}[$i][2] && $position <= $HoA{$g}[$i][0] && (length($buffer) + $position) >= $HoA{$g}[$i][1]) {
      next LINE;
      }
    
    if ($i < $num) {  
      $match{$g}[$i] = uc(substr($buffer, ($HoA{$g}[$i][0] - $position), $HoA{$g}[$i][2]));  
      $i++;
      }
    if ($i == $num) {
      seek(DNA,(0-length($buffer)),1);
      $buffer = '';
      $position = 0;
      $skip = 1;
      $len = 0;
      next FASTAKEY;
      }
      else {
        if ($position + $len < $HoA{$g}[$i][0]) {
          # Reset the position counter
          # (will be accurate after you reset the buffer, next)
          $position += $len;
     
          # Reset the buffer
          # Discard the first $max worth of data in the buffer
          $buffer = substr($buffer, $len); 
          }
        $len = 0;
        next LINE;   
        }
    # closes LINE
    }
   }
  # closes FASTAKEY
  }   
close(DNA) or croak("Cannot close $filename:$!\n");    
    
print "Finished gathering all the sequences, now moving on.\n";

##</code><code>##

$g is: >LG_I
This $g, >LG_I, has a set.
....We've hit a newline, which is: >LG_I
We are in the 'if buffer eq' loop.
..$g is: >LG_I, and $newline is >LG_I
Gathering sequence data from sequence >LG_I
....We've hit a newline, which is: >LG_II
......At FINISH, $num is: 73, and $i is: 68
in FINISH, $i is: 68, and $num is 73.  They should not be equal
$i is: 68, $HoA{>LG_I}[68][0] is: 22325699, $HoA{>LG_I}[68][1] is: 22326343, $position is: 33722650 and length($buffer) is: 1848919
The position of $highest is below that of $position!  How did this happen?!
substr outside of string at Test3 line 1483, <DNA> line 508168.
......At FINISH, $num is: 73, and $i is: 69
in FINISH, $i is: 69, and $num is 73.  They should not be equal
$i is: 69, $HoA{>LG_I}[69][0] is: 27156174, $HoA{>LG_I}[69][1] is: 27156931, $position is: 33722650 and length($buffer) is: 1848919
The position of $highest is below that of $position!  How did this happen?!
substr outside of string at Test3 line 1483, <DNA> line 508168.
......At FINISH, $num is: 73, and $i is: 70
in FINISH, $i is: 70, and $num is 73.  They should not be equal
$i is: 70, $HoA{>LG_I}[70][0] is: 10031764, $HoA{>LG_I}[70][1] is: 10032474, $position is: 33722650 and length($buffer) is: 1848919
The position of $highest is below that of $position!  How did this happen?!
substr outside of string at Test3 line 1483, <DNA> line 508168.
......At FINISH, $num is: 73, and $i is: 71
in FINISH, $i is: 71, and $num is 73.  They should not be equal
$i is: 71, $HoA{>LG_I}[71][0] is: 22783500, $HoA{>LG_I}[71][1] is: 22784101, $position is: 33722650 and length($buffer) is: 1848919
The position of $highest is below that of $position!  How did this happen?!
substr outside of string at Test3 line 1483, <DNA> line 508168.
......At FINISH, $num is: 73, and $i is: 72
in FINISH, $i is: 72, and $num is 73.  They should not be equal
$i is: 72, $HoA{>LG_I}[72][0] is: 28700514, $HoA{>LG_I}[72][1] is: 28701277, $position is: 33722650 and length($buffer) is: 1848919
The position of $highest is below that of $position!  How did this happen?!
substr outside of string at Test3 line 1483, <DNA> line 508168.
......At FINISH, $num is: 73, and $i is: 73
in FINISH, $i is: 73, and $num is 73.  They should be equal
$g is: >LG_II
This $g, >LG_II, has a set.
....We've hit a newline, which is: >LG_II
......At FINISH, $num is: 61, and $i is: 4
in FINISH, $i is: 4, and $num is 61.  They should not be equal
$i is: 4, $HoA{>LG_II}[4][0] is: 2635020, $HoA{>LG_II}[4][1] is: 2635237, $position is: 1822784 and length($buffer) is: 86
The position of $lowest is past the end of the buffer!  How did that happen?!
substr outside of string at Test3 line 1480, <DNA> line 534211.

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