Do yourself a big favor and use warnings and strict in your code at the beginning of each and every script:
    use warnings;
    use strict;

Using warnings and, in particular, strictures would have alerted you to the misuse of  @$DNAsequence1 and  $base1->[0] et al.

In reply to Re: nested foreach loop, match DNA sequences and calculate score by AnomalousMonk
in thread nested foreach loop, match DNA sequences and calculate score by NadjaPadjala

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