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```
@a=@c=@t=@g=@n=@a2=@c2=@t2=@g2=@n2=();
```

(@a, @c, @t, @g, @n, @a2, @c2, @t2, @g2, @n2) = ();

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for (my $k=0;$k<$number_positions; $k++) {
    my (@a,@c,@t,@g,@n,@a2,@c2,@t2,@g2,@n2);

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```
if ($letter1=~ /[aA]/) { ... }
...
```

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if (uc $letter1 eq 'A') { ... }
if (uc $letter1 eq 'C') { ... }
if (uc $letter1 eq 'T') { ... }
if (uc $letter1 eq 'G') { ... }
# ...

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$letter1 = uc $letter1;

...
if ($letter1 eq 'C') { ... }
if ($letter1 eq 'T') { ... }
# ...

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for (my $k=0;$k<$number_positions; $k++) {
    my (%base1, %base2);
...

        push @${$base1{$letter1}}, $letter1;
        push @${$base2{$letter2}}, $letter2;

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for (my $k=0;$k<$number_positions; $k++) {
    my (%base1, %base2);
    # ...
        $base1{uc $letter1}++;
        $base2{uc $letter2}++;

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"$number_a" + "$number_c" + "$number_t" + "$number_g" + "$number_n"

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$number_a + $number_c + $number_t + $number_g + $number_n

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$base1{A} + $base1{C} + $base1{T} + $base1{G} + $base1{N}

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my $total1 = $base1{A} + $base1{C} + $base1{T} + $base1{G} + $base1{N}
+;

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my %percent1 = (
    A => ($base{A} * 100) / $total1,
...
    G => ($base{G} * 100) / $total1,
    N => ($base{N} * 100) / $total1,
);

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my %percent1 = map { $_ => ( $base{$_} * 100) / $total1 } 'A', 'C', 'T
+', 'G', 'N';

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my %percent1 = map { $_ => ( $base1{$_} * 100) / $total1 } qw(A C T G 
+N);

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#!/usr/bin/perl

...
    }
}
close(OUTPUT);