#substring(s) to search for:
$substr = "AATGCTCCCCAATGAGGCA";
$substr2 = "TT##CACAAGGAACTTTTTT"; 


#Search for it in this string: 

$str = "CTTGAGTTATTAGCTGTTTGCCCCTGGGCAAGTTGTCTCACCTCTCCGTGTTTGTTTCCTCACCTATTGGACCAGGCCTATGGTTTTCAAACTGTGTTCCCTGGTGCTCTGAGACTTAGGGAAGGGGAACGCCCACACTGGCAAGGCTAACACAAGCCGCCATATACCCACCCCACTTCACCCACAGCACCCCCCTTTCTGTGTCTCATATACTGCGGGCCTATGCGA";

# the second substring  is straightforward
$pos =  index( $string, $substr);