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$2\t$d
+ist\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 formatting, code tags

In reply to Re^2: Regex /g and interpolated lengths by Anonymous Monk
in thread Regex /g and interpolated lengths by Anonymous Monk

Title:
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and:  <code> code here </code>
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