What I understand from your question that you want to find string between two primers, now the two primers shown by you is actually having no string in between them, so I changed it little bit in this way AATCGGGTATGAAAAATTTxyzTGCCGGCGTTTGCG now the text you'll get in between these two primers is xyz. Try the following code and it'll work fine. 
$a = 'AATCGGGTATGAAAAATTTxyzTGCCGGCGTTTGCG';
while($a=~/AAAATTT(.*?)TGCCG/g){
print "The variable is $1";
}

[download]
Let me know if your question is different than this.

In reply to Re: Finding patterns by jack123
in thread Finding patterns by MoniqueLT

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