if ($windowSeq =~ /GG$/)
{
  $sequences{$windowSeq}{Count}++; 
  $sequences{$windowSeq}{Position} = $windowStart; 
}

##</code><code>##

if ($windowSeq =~ /GG$/)
{
  $windowStart += $windowSize;
}
else
{
  $windowStart += $stepSize;
}