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              for my$i(0..($replication_rounds-1))
...
                }
            }

for my $i ( 0 .. ( $replication_rounds - 1 ) ) {
    for my $j ( 0 .. ( @{ $allgen{$i} } ) ) {
# the counter divided by 30 will give a decimal,
...
} ## end for my $i ( 0 .. ( $replication_rounds...))
###################

for my $i ( 0 .. ( $replication_rounds - 1 ) ) {
...
        print "\>RandomHA $date \n" . $allgen{$i}[ $j - 1 ] ."\n";
    }
}

for my $i ( 0 .. ( $replication_rounds - 1 ) ) {
    for my $j ( 0 .. $#{ $allgen{$i} }  ) {
...
        print "\>RandomHA $date \n" . $allgen{$i}[ $j ] ."\n";
    }
}

foreach my $nucleotide (@nucleotide_array) {
    chomp $nucleotide;
...
   my( $nucleotide, $score ) = @_;
   ...
   $$nucleotide =~ s/A/T/g;

my $maxNumberOfThreads = 5;
my $threadCount = 0;
for ( $i = 1 ; $i < $replication_rounds ; $i++ ) {
...
        }
    }
}