my $k =25;
my %readrepo =(
 "readA" => "GCTGAGGCAGGAGAATTGCTTGAACCTGGGAGGCA",
 "readB" => "TACTCAGGAGGCTGAGGCAGGAGAATTGCTTGAAC",
 "readC" => "GCTGAGGCAGGAGAATTGCTTGAACTTAGGGGATG",
 "readD" => "TACTCGGGAGGCTGAGGCAGGAGAATTGCTTGAAC",
);


# This array is already ordered
# It says the first(_1) 25 bases of readA overlap with second(_2)part of readB, etc.
my @readstoconcate = (
        "readA_1",
        "readB_2",
        "readC_1",
       "readD_2");


##</code><code>##

 readA                 GCTGAGGCAGGAGAATTGCTTGAACCTGGGAGGCA
 readB       TACTCAGGAGGCTGAGGCAGGAGAATTGCTTGAAC
 readC                 GCTGAGGCAGGAGAATTGCTTGAACTTAGGGGATG
 readD       TACTCGGGAGGCTGAGGCAGGAGAATTGCTTGAAC


##</code><code>##

TACTC(A,G)GGAGGAGAATTGCTTGAACCTGGGAGGCA(T,C)T(A,G)GG(A,G)G(A,G)(T,C)(A,G)