my @site1 = qw( AATKKM aatkkm ); my @site2 = qw( GGGGGG gggggg ); my %counts; seq_foreach_from_spec( [ \(@site1, @site2) ], sub { seq_foreach( seq_zip( ( map seq(split//), @_ ) ), sub { $counts{"@_"}++ } ) } ); print Dumper(\%counts), "\n";