This should work: 
my $str1 = "AATAGCAATTGACAAT";
my $str2 = "CAATCGGAACCAGCAT";
($concat = "$str1#$str2") =~ s/(.*?)(.*)#\2(.*)/$1$2$3/;
print $concat, "\n";

[download]
Based on the idea from IO

In reply to Re: How do I Gererate Contigs out of a list of sequences? by busunsl
in thread How do I Gererate Contigs out of a list of sequences? by Anonymous Monk

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