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

AAACATGAAAAGGAGCCTCATCTCCC GCCTCATCTCCC

AAACATGAAAAGAAAT(G,C)ATGAAACAGAGCCTCATCTCCC

readA      AAACATGAAAAGAAATGATGAAACAGA
readB                  AAATCATGAAACAGAGCCTCATCTCCC