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$seq=UUUUUUUUIIIIIIIIIIIIIIIMMMMMMMMMMMMMMMMMMMMMMMMOOOOO

if($seq=~/^(U+)([I|O|P|B|M])/) 
{
...
 $char1=$2;
 substr($top, 0, $len1, ($char1 x $len1));             
 }

$seq=IIIIIIIIIIIIIIIMMMMMMMMMMMMMMMMMMMMMMMMOOOOOUUUUUUUU

if($seq=~/.*?([I|O])(U+)$/) 
{ 
...
  $len2=length($part_to_change2);
  substr($top, -$len2, $len2, ($char2 x $len2));             
}

* $seq=IIIIIIIIIIIIIIIMMMMMMMMMMMUUUUUUUUMMMMMMMMMMMMMOOOO
* $seq=IIIIIIIUUUUUIIIIIIIIMMMMMMMMMMMMMMMMMMMMMMMMOOUUUUUUUOO
* $seq=IIIIIIIIIIIIIIIMMMMMMMMMMMMMMMMMMMMMMMMOOUUOO