use strict;
use warnings;

my $ref       = 'agctagctagctagacatgctagctagctgatcgatgctagctagctgactga
+cgacgacat';
my @fragments = qw(agc tagcg agca atgctagctagc acga gcatgc acat tagctg
+atcgatgct);
my @out;
my @nomatch;

# what it does *not*: 
# a) show each occurence of a fragment, e.g. 'acat' 
# b) separate adjacent fragment, e.g. agc and tagcg will be 
#    seen as agctagcg 
# c) optimising (minimum number of lines)
# d) check that a fragment is a fragment of another fragment 
#    (e.g. "agc" is part of serveral other fragments)
 
outer:
foreach my $fragm (@fragments) {
    my $pos = index($ref,$fragm);
    push (@nomatch, $fragm), next if ($pos<0); # no match

    my $len = length($fragm);
    foreach  (@out) {
      if (substr($_,$pos,$len) =~ /^\s+$/) {  # found first empty slot
           substr($_,$pos,$len) = $fragm;
           next outer;                        # done, try next fragm.
       }
    }

    # could not fit fragment -> add it as a new line
    push @out, ' ' x length($ref); 
    substr($out[-1],$pos,$len) = $fragm;  
}

# and out
print "ref: $ref\n";  
print "out: ", join("\nout: ", @out), "\n";
print "no match: ", join(", ", @nomatch),"\n";
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