Sorry I thought it would be easier to answer and didn't want to burden you with code. But here comes now the important part of the code.. I hope there is all you need and I did't forget anything.
open(FILE, "<", $multiz);
my @content = <FILE>;
close FILE;
s/^\w\w\t(.+)(?:\n)?/$1/ for(@content); 
my $len = length($content[0]) - 5;
my $allseq = join("", @content);
my @branchPoints;
while($allseq =~ /(ct(?:a|g)a(?:c|t))(?:.{$len})(ct(?:a|g)a(?:c|t))(?:
+.{$len})(ct(?:a|g)a(?:c|t))(?:.{$len})(ct(?:a|g)a(?:c|t))(?:.{$len})(
+ct(?:a|g)a(?:c|t))(?:.{$len})(ct(?:a|g)a(?:c|t))(.*)/ig)
{
my $dist = length($7);
push(@branchPoints, "\nBranchpoint:\t$1\t$dist\n\t\t$2\t$dist\n\t\t$3\
+t$dist\n\t\t$4\t$dist\n\t\t$5\t$dist\n\t\t$6\t$dist\n\n");
}
print REPORT @branchPoints;

[download]
File $multiz comes here: 
aa ctgacaaaaaaaaaaactgataaaaaaaaaaaaactaac
aa ctgacaaaaaaaaaaactgataaaaaaaaaaaaactaac
aa ctgacaaaaaaaaaaactgataaaaaaaaaaaaactaac
aa ctgacaaaaaaaaaaactgataaaaaaaaaaaaactaac
aa ctgacaaaaaaaaaaactgataaaaaaaaaaaaactaac
aa ctgacaaaaaaaaaaactgataaaaaaaaaaaaactaac

[download]

20051115 Janitored by Corion: Fixed code tags

In reply to Re^4: Regex /g and interpolated lengths by Anonymous Monk
in thread Regex /g and interpolated lengths by Anonymous Monk

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