Is that your real program? You never open INFILE, so you never read anything from it, so you never add anything to @newseq. Use use strict; and use warnings;. You would have gotten

Name "main::INFILE" used only once: possible typo at a.pl line 18.
readline() on unopened filehandle INFILE at a.pl line 18.
[download]

instead of having to waste your time waiting for a reply here.

Other problems:

• for (my $i=0;$i<$#bin;$i++)
  ends too soon. You want
  for (my $i=0;$i<@bin;$i++)
  or
  for (my $i=0;$i<=$#bin;$i++)
  Or even better,
  for my $i (0..$#bin)

• $run++ is executed too often. Change
  if ($bin[$i]==1 && $bin[$i+1]==0)
  to
  elsif ($bin[$i]==1 && $bin[$i+1]==0)

• What if the last one isn't followed by a zero?
  elsif ($bin[$i]==1 && $bin[$i+1]==0)
  should be
  elsif ( $bin[$i]==1 && ($i==$#bin || $bin[$i+1]==0) )

• What if you get a sequence of 16 ones?

• You don't need %rules or @arg1.
  $rules{$newseq[$_-1]}
  is a weird way of saying
  $results[$newseq[$_-1]]

• The "1 .." (instead of "0 ..") and the "- 1" look very suspicious in the last loop. Can't say for sure without knowing what you want.

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