#! perl -slw use strict; use Data::Dump qw[ pp ]; sub maxMatches { my $s = shift; my @matches; my $vec = ''; for my $o ( 0 .. length( $s ) - 10 ) { my( $match ) = $s =~ m[.{$o}([ACGT].{0,8}[ACGT])] or next; my $mask = ''; vec( $mask , $_, 1 ) = 1 for $-[1] .. $+[1]-1; next if ( $vec | $mask ) eq $vec; $vec |= $mask; push @matches, $match; } return @matches; } while( ) { chomp; printf "$_ : [ %s ]\n", join ', ', maxMatches( $_ ); } __DATA__ AGRTGAXWXX ACRMGAHKMAHGTXX AXXAXXAXXXXXXXXXXXXXXAXXA