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#! perl
use strict;
...
    my $matches = () = $string =~ /$seq/g;
    printf "%s: %d\n", $seq, $matches;
}

17:30 >perl 914_SoPW.pl
0a0a: 3
...
2e2e: 2

17:30 >

0a0axxx0a0a0yyyy
^^^^   ^^^^