Your problem is with the for loop:

for ($i =0;$i<length($dna);$i++){

    if ($i == $position){

print " mutation at  base position ". ($position+1) . "\n";
    do {
    $nucleotide = randombase();

     } until ($nucleotide ne substr($dna,$position,1));
    substr($dna, $position, 1, $nucleotide);

    print "$dna\n";
    }
$i++;
}
[download]

You increment $i at the top of the loop and at the bottom of the loop so sometimes $i will never be equal to $position.

Better to write the loop as:

for my $i ( 0 .. length( $dna ) - 1 ) {
[download]

Also, you don't need a do block for your until statement modifier:

    $nucleotide = randombase() until $nucleotide ne substr $dna, $posi
+tion, 1;
[download]

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