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#!/usr/bin/perl

...
my $seqs = join '|', map tr/ACGT//cdr, <$patterns>;
my $match = qr/^\w*($seqs)/;
/$match/ and print "$1\t$_" while <$fh>;

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ATCCCACCGCTGCCACCA      AACCCCATCCCACCGCTGCCACCA        1
ATCCCACCGCTGCCACCA      AACTGGATTCTCTGAAATCCCACCGCTGCCACCA      1