#!usr/bin/perl -w use strict; my @input_files=<*.seq>; my $sequence='ABCD'; my @headings=('Tags', 'Frequency'); my $headings=join("\t",@headings); #"Tags\nFrequency" foreach my $input_file(@input_files) { open(INPUT, '<', $input_file) or die "Cannot open file: $!\n"; my $outfile=$input_file; $outfile =~ s/.seq/.tag.txt/i; #/g makes no sense open (OUTPUT, '>', $outfile") or die "Cannot open file $!\n"; print OUTPUT "\n$headings\n"; while (my $line=) { if ($line=~m/$sequence(.{11})(.{11})$sequence/o) { print OUTPUT "$1\n$2\n"; } } }