#! /usr/bin/perl -w
use strict;

my $screen = "ATCGATCGXXXXXATCGATXXXACTGCTACGGTACXXXAATTATXGCGCGXXT";
my @chars = split //, $screen;
my @starts;

foreach ( 0 .. scalar @chars - 1 ) {
    push @starts, $_
        if $chars[$_] ne 'X' &&  ( 0 == $_ || $chars[$_-1] eq 'X' );
}

print "$screen\n@starts\n";