my $k = 15;
my %repo = (
    "readA" => "AAACATGAAAAGAAATGATGAAACAGA",
    "readB" => "AAATCATGAAACAGAGCCTCATCTCCC ",
);
my @order = (  "readB_1","readA_2");

##</code><code>##

AAACATGAAAAGGAGCCTCATCTCCC GCCTCATCTCCC

##</code><code>##

AAACATGAAAAGAAAT(G,C)ATGAAACAGAGCCTCATCTCCC

##</code><code>##

readA      AAACATGAAAAGAAATGATGAAACAGA
readB                  AAATCATGAAACAGAGCCTCATCTCCC