It would be better if @seq1 was an array of words, not an array with just a single element.

You can use an old trick: XOR the two strings and count the number of non-null characters:

#!/usr/bin/perl
use strict;
use warnings;

my @seq1 = qw(ATGC TGCT GCTA CTAA TAAC);
my $seq2 = 'GTCA';

for my $seq (@seq1) {
    my $count = ($seq ^ $seq2) =~ tr/\0//c;
    print "$seq $count\n";
}
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