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#!/usr/bin/perl -w
                                                                
...
print OUT "\n\n";
}

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ATGGACTGCACCTGGAGGATCCTCTTCTTGGTGGCAGCAGCTACAGgcaagagaatcctgagttccaggg
+ctgatgaggg
The first occurance of little a is: 48
The first occurance of little c is: 47
The first occurance of little g is: 46
The first occurance of little t is: 49