Multiz Alignments of 100 Vertebrates
 

Capitalize exons based on show bases
Place cursor over species for alignment detail. Click on 'B' to link to browser for aligned species, click on 'D' to get DNA for aligned species.
Alignment block 1 of 54 in window, 41507800 - 41507842, 43 bps 
B D                   Human  c-ac--c-----t----------gccccaa-cct--c---gcgatg-----ccaa-g---ccaaca----
B D                   Chimp  c-ac--c-----t----------gccccaa-cct--c---gcgatg-----ccaa-g---ccaaca----
B D                 Gorilla  c-ac--c-----t----------gccccaa-cct--c---gcgatg-----ccaa-g---ccaaca----
B D               Orangutan  c-ac--c-----t----------gccccaa-cgt--c---gcgacg-----ccaa-g---ccaaca----
B D                  Gibbon  c-ac--c-----t----------gccccaa-cct--c---gcgacg-----ccaa-g---ccaaca----
B D                  Rhesus  c-ac--c-----t----------gccccag-cct--c---acgacg-----ccaa-g---ccaaca----
B D     Crab-eating macaque  c-ac--c-----t----------gccccag-cct--c---gcgacg-----ccaa-g---ccaaca----
B D                  Baboon  c-ac--c-----t----------gccccag-cct--c---gcgacg-----ccaa-g---ccaaca----
B D            Green monkey  c-ac--c-----t----------gccccag-cct--c---gcgacg-----ccaa-g---ccaaca----
B D                Marmoset  c-ct--c-----t----------tcc------------------------------a---ccaaca----
B D         Squirrel monkey  c-ct--c-----t----------tcc------------------------------a---ccaaca----
B D                Bushbaby  c-ac--c-----t----------gccccag-tct--t---gtgaca-----ccaaca---ccgtcc----
         Chinese tree shrew  c-ac--t-----t----------gtc-cag-tcg--g---gcgag-----------g---atagca----
B D                Squirrel  c-at--c-----a----------gcc-cac-acg--c---gc--------------aacgccagcg----
     Lesser Egyptian jerboa  c-ac--c-----a----------gcc-cag-ctg--cagggg--------------g---tccgca----
               Prairie vole  c-at--a-----a----------acc-aag-ccg--c---ga--------------a---tctacg----
B D         Chinese hamster  c-at--a-----a----------gcc-aag-ctg--c---ca--------------a---tctatg----
             Golden hamster  c-at--a-----a----------acc-aag-cc---c---ca--------------a---tctttg----
B D                   Mouse  c-ac--a-----a----------gcc-aag-ccgctc---ga--------------a---tctata----
B D                     Rat  c-ac--a-----a----------gcc-aag-ccg--c---ga--------------a---tctacg----
B D          Naked mole-rat  t-gc--c-----a----------gcc-cag-cca--t---gc--------------gatgcccagg----
B D              Guinea pig  a-ag--c-----a----------gcc-cag-cca--t---gc--------------aat-cccag-----
                 Chinchilla  c-ac--c-----a----------acc-cag-cca--t---gc--------------gacgcccagg----
           Brush-tailed rat  c-ac--c-----a----------gcc-cag-ata--c---gc--------------agc-ccaagg----
B D                  Rabbit  c-ac--ctgggga----------tgc-cag-ccg--c---gc--------------g---ccaggg----
B D                     Pig  c-ac--c-----t----------gccccag--cg--a---gcgat-----------g---ccaacg----
B D                 Dolphin  g-ac--c-----t----------gtctcgg-gcg--a---ctgat-----------g---ccaacg----
               Killer whale  g-ac--c-----t----------gtcccgg-gcg--a---ctgat-----------g---ccaacg----
           Tibetan antelope  a-gc--c-----t----------gcaccaa-ccc--a---gtgat-----------g---ccaaca----
B D                     Cow  a-gc--c-----t----------gcaccaa-ccc--a---gtgat-----------g---ccaaaa----
B D                   Sheep  a-gc--c-----t----------gcaccaa-ccc--a---gtgat-----------g---ccaaca----
              Domestic goat  a-gc--c-----t----------gcaccaa-ccc--a---gtgat-----------g---ccaaca----
B D                   Horse  a-aa--c-----t----------tccccat---c--c---agggg-----------g---ccagcg----
B D        White rhinoceros  a-ac--c-----t----------gccccag---t--c---cgggt-----------g---ccaacg----
B D                     Cat  a-at--g-----a----------gccaggg---a--c---gcgga-----------g-------cg----
B D                     Dog  a-gc--g-----a----------gtcccgg-ccg--c---gcgga-----------g---cgatcg----
B D                 Ferret   a-aaagg-----t----------gcccggg-ccg--c---gcgca-----------g---ccaacg----
B D                   Panda  a-aa--g-----a----------gccaggg---a--c---ccgga-----------g----cagcg----
             Pacific walrus  a-ac--g-----t----------gcccggg-ctg--c---gcgaa-----------g---ccaacg----
               Weddell seal  a-ac--g-----t----------gcccggg-ccg--c---gcgaa-----------g---ccatcg----
B D                 Megabat  c-ac--c-----t----------tccccag-ccg--c---gagat-----------g---ccaacg----
              Big brown bat  a-gt--c-----t----------gccccag-ccc--c-----------------------ccagcc----
B D                Elephant  a-ac--c-----g----------gccccag-cag--a---gcgag-----------a---tcaagg----
B D                 Manatee  a-ag--c-----g----------gccccag-cag--a---gcgac-----------a---ttaagg----
           Cape golden mole  a-ac--t-----c----------accccaa-ctg--c---gccat-----------g---tcaaaaggag
B D                  Tenrec  c-ag--c-----g----------gccccag-ctg--c---gcgac-----------g---tcagaa----
                   Aardvark  a-gc--t-----g----------gccccag-cag--c---gcaac-----------g---tctaag----
B D               Armadillo  a-ac--c-----t----------gccccgg-ccg--c---gtggt-----------g---cccaaa--gg
B D         Tasmanian devil  t-ct--c-----c----------gcagcag-cga--c---accatgagggttata-g---acaata----
B D             Zebra finch  ctgc--g-----gccggccca--gac-cag-caa------------------------------------
B D                 Chicken  c-ac--a-----gtcggtgtaacgag-gcg-ctc------------------------------------
B D      American alligator  c-ac--a-----g----------ggg-cag-cct------------------------------------
  D         Green seaturtle  c-ac--a-----g----------ggg-cag----------------------------------------
  D          Painted turtle  c-cc--g-----g----------gcg-cagcccc------------------------------------
B D                    Pika  ======================================================================
            Bactrian camel  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D                Platypus  ======================================================================
          Black flying-fox  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D                Microbat  ======================================================================
      David's myotis (bat)  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D                  Alpaca  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

                      Human  ggggcggcga
                      Chimp  ggggccgcga
                    Gorilla  ggggccgcga
                  Orangutan  ggggcggcca
                     Gibbon  tgggccgcca
                     Rhesus  ggggcggcca
        Crab-eating macaque  ggggcggcca
                     Baboon  ggggcggcca
               Green monkey  ggggcagcca
                   Marmoset  ggggcgccca
            Squirrel monkey  ggggcgccca
                   Bushbaby  gggac----a
         Chinese tree shrew  gaggaggtcg
                   Squirrel  gaggtggctg
     Lesser Egyptian jerboa  aagaagaccc
               Prairie vole  gagtcgacct
            Chinese hamster  gagtccacct
             Golden hamster  gagtccacct
                      Mouse  gagttgatct
                        Rat  gagtcgactt
             Naked mole-rat  gagacagc--
                 Guinea pig  ---gcaat--
                 Chinchilla  gaggcagc--
           Brush-tailed rat  gaagtacc--
                     Rabbit  g---------
                        Pig  gggcag----
                    Dolphin  gggcag----
               Killer whale  gggcag----
           Tibetan antelope  gagcag----
                        Cow  gagcag----
                      Sheep  gagcag----
              Domestic goat  gagcag----
                      Horse  gggcgg----
           White rhinoceros  cggcgg----
                        Cat  acgttc----
                        Dog  tggggc----
                    Ferret   cggtgg----
                      Panda  cggtgg----
             Pacific walrus  cagtgt----
               Weddell seal  cagtgg----
                    Megabat  cggcgg----
              Big brown bat  ccccag----
                   Elephant  gggc-ggccg
                    Manatee  cggc-ggccg
           Cape golden mole  cgac---ccg
                     Tenrec  ----------
                   Aardvark  gggcaggcag
                  Armadillo  gggc-ggccg
            Tasmanian devil  gcggtgg---
                Zebra finch  ----------
                    Chicken  ----------
         American alligator  ----------
            Green seaturtle  ----------
             Painted turtle  ----------
                       Pika  ==========
             Bactrian camel  NNNNNNNNNN
                   Platypus  ==========
           Black flying-fox  NNNNNNNNNN
                   Microbat  ==========
       David's myotis (bat)  NNNNNNNNNN
                     Alpaca  NNNNNNNNNN

Inserts between block 1 and 2 in window
B D                    Pig 5bp
B D                Dolphin 5bp
              Killer whale 5bp
          Tibetan antelope 6bp
B D                    Cow 6bp
B D                  Sheep 6bp
             Domestic goat 6bp
B D                  Horse 4bp
B D       White rhinoceros 5bp
B D                    Cat 2bp
B D                    Dog 6bp
B D                Ferret  6bp
B D                  Panda 6bp
            Pacific walrus 6bp
              Weddell seal 6bp
B D                Megabat 5bp
             Big brown bat 15bp

Alignment block 2 of 54 in window, 41507843 - 41507865, 23 bps 
B D                   Human  ----g-ggctctcg---------gccgtgcg--------------------caaggg
B D                   Chimp  ----g-ggctctcg---------gccgtgcg---------------------aaggg
B D                 Gorilla  ----g-ggctctcg---------gccgtgcg--------------------caaggg
B D               Orangutan  ----g-ggctctcc---------gcagtgcg--------------------caaggg
B D                  Gibbon  ----g-ggttctcg---------gccgtgcg--------------------caaggg
B D                  Rhesus  ----g-ggctctcg---------gcagcacg--------------------caagga
B D     Crab-eating macaque  ----g-ggctctcg---------gccgcacg--------------------caaggg
B D                  Baboon  ----g-ggctctcg---------gccgcacg--------------------caaggg
B D            Green monkey  ----g-ggctctcg---------gccgcacg--------------------caaggg
B D                Marmoset  ----g-gggtgccg---------gccgcgtg--------------------ccagcg
B D         Squirrel monkey  ----g-gggtgctg---------gccgcgtg--------------------ccagag
B D                Bushbaby  ----g-ggttccac---------accgcgcg--------------------ccaagg
         Chinese tree shrew  ----g-gggcccga---------gccttttgg-------------------caaggg
B D                Squirrel  ----g-agttccaa---------cccgtgcg--------------------ccc---
     Lesser Egyptian jerboa  ----g-ggctccac---------gccgcgcg--------------------ccaagg
               Prairie vole  ----g-gggtctc----------------ag--------------------tcacgg
B D         Chinese hamster  ----g-gggtctc--------------------------------------------
             Golden hamster  ----g-ggatctc----------------ag--------------------tcacgg
B D                   Mouse  ----g-ggatctct---------gccgcgcg--------------------tcacgg
B D                     Rat  ----g-ggatctct---------gccgcgcg--------------------acaagg
B D          Naked mole-rat  -----------------------------tg--------------------acacag
B D              Guinea pig  -----------------------------ag--------------------ggacag
                 Chinchilla  -----------------------------cg--------------------ggacag
           Brush-tailed rat  -----------------------------cg--------------------caacag
B D                     Pig  ----g-gcctctga---------ccagcgagc-------------------caaggg
B D                 Dolphin  ----g-gcctctga---------cccgcacgc-------------------caaggc
               Killer whale  ----g-gcctctga---------cccgcgcgc-------------------caaggc
           Tibetan antelope  ----g-gcctctga---------cccccgcgc-------------------caacgc
B D                     Cow  ----g-ggctctga---------ctcccgtgc-------------------caaggc
B D                   Sheep  ----g-gcctctga---------cccccgcgc-------------------caacgc
              Domestic goat  ----g-gcctctga---------cccccgcgc-------------------caacgc
B D                   Horse  ----t-gcctcgga---------acggcgcac-------------------caacgg
B D        White rhinoceros  ----g-gcctcgga---------gcggcgcac-------------------caaggc
B D                     Cat  --------------------------------------------------------g
B D                     Dog  ----g-acctggga---------gctgcgcac-------------------cgaggg
B D                 Ferret   ----g-gcctccga---------acggcgcac-------------------caaggg
B D                   Panda  ----a-g----------------------------------------------aggg
             Pacific walrus  ----a-gcctccga---------gcggcgcac-------------------caaggg
               Weddell seal  ----a-gcctccga---------gcggcgcac-------------------caaggg
B D                 Megabat  ----g-gcctcgga---------gcggcgcgc-------------------caagcg
              Big brown bat  ----g-gtctccaa---------gccgcgcgc-------------------ccctga
B D                Microbat  ----a-ctcttcgc---------gtcg------------------------gtccga
B D                Elephant  ----g-ggggccgc---------gcagctcaggccagagaaaagagaccagtcaagg
B D                 Manatee  ----g-cgggccgc---------tcagctcaggccaaagaatagagaccagtcaagg
           Cape golden mole  ----t-tggcccgc---------gtagctcagaccaaagg--aatgagcagccaagg
B D                  Tenrec  ---------------------------ctcagggcaaagg--cgagaccagccaagg
                   Aardvark  ----g-tggcccgc---------gcagctcacgccaaaggagagagagcagaaaaaa
B D               Armadillo  ----g-tggcccg------------------------------------agcccaga
B D         Tasmanian devil  -----------gac---------cccgtgcg--------------------caacag
B D             Zebra finch  ggtag-agccctgcct-------gcagtgc---------------------------
B D                 Chicken  ggcaa-acccgtgcacactccaagcagcgg---------------------------
B D      American alligator  ggtatcagctgtgcc--------ggagagg---------------------------
  D         Green seaturtle  gggtg-gggagggc---------acagcgg---------------------------
  D          Painted turtle  gggag-gagcaggc---------ccagcgg---------------------------
B D                    Pika  =========================================================
B D                  Rabbit  ---------------------------------------------------------
            Bactrian camel  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D                Platypus  =========================================================
          Black flying-fox  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
      David's myotis (bat)  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D                  Alpaca  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

Inserts between block 2 and 3 in window
B D        Tasmanian devil 72bp

Alignment block 3 of 54 in window, 41507866 - 41507891, 26 bps 
B D                   Human  gtcccaggcg-------cccagc---act--ctc------cca---------------------------
B D                   Chimp  gtcccaggcg-------cccagc---act--ctc------cca---------------------------
B D                 Gorilla  gtcccaggcg-------cccagc---act--ctc------cca---------------------------
B D               Orangutan  gtcccaggag-------cccagc---act--ctc------cca---------------------------
B D                  Gibbon  gtcccaggcg-------cccagc---act--ctc------cca---------------------------
B D                  Rhesus  gtcccaggcg-------cccagc---act--ctc------cca---------------------------
B D     Crab-eating macaque  gtcccaggcg-------cccagc---act--ctc------cca---------------------------
B D                  Baboon  gtcccaggcg-------cccagc---act--ctc------cca---------------------------
B D            Green monkey  gtcccaggcg-------cccagc---act--ctc------cca---------------------------
B D                Marmoset  gtcccaggcc-------cccaga---act--ctc------cca---------------------------
B D         Squirrel monkey  gacccaggct-------cccaga---act--ttc------cca---------------------------
B D                Bushbaby  gtcctcacgg-------tgcagc---ccc--ctt------cag---------------------------
         Chinese tree shrew  gtcccag---------------------------------ccc---------------------------
B D                Squirrel  -accgggggc-------ccgctgt--cgt--cct------gcc---------------------------
     Lesser Egyptian jerboa  ggtc--------------ccag----cct--ctt------tcg---------------------------
               Prairie vole  gatctgggtc--------tcaggt--ctc--ctc------cca---------------------------
B D         Chinese hamster  ------ggtc-------accaggc--ccc--ctc------cta---------------------------
             Golden hamster  gatctgggtc-------accaggca-ccc--ctc------cca---------------------------
B D                   Mouse  aatcggggtc-------gtcgggac-ccc--ttc------cca---------------------------
B D                     Rat  gatcggggtt-------atccgggc-ccg--gtc------cca---------------------------
B D          Naked mole-rat  gctgagtggg-------gtgaggttgggt--ccc------ctg---------------------------
B D              Guinea pig  attgggtggg-------tcggggtggcgt--ccc------ctg---------------------------
                 Chinchilla  gttgggtggg-------gtggagtggggt--ccc------ctg---------------------------
           Brush-tailed rat  gttgggtggg-------gtggagtggagt--ctc------ccg---------------------------
B D                  Rabbit  --------------------------ccc--cgg------gcg---------------------------
B D                     Pig  gtcccaggcg-------cgcgga---atc--ctc------ctg---------------------------
B D                 Dolphin  gtcccaggcg-------cgcgca---gcc--ctc------ctg---------------------------
               Killer whale  gtcccaggcg-------cgcgca---gcc--ctc------ctg---------------------------
           Tibetan antelope  gtcccgggcg-------cgcgga---acc--ctc------ccg---------------------------
B D                     Cow  gtcccaggcg-------ctcgga---aca--ctc------ctg---------------------------
B D                   Sheep  gtcccaggcg-------cgcgga---acc--ctc------ccg---------------------------
              Domestic goat  gtcccgggcg-------cgcgga---acc--ctc------ccg---------------------------
B D                   Horse  gcccctggcg-------cgcgac---acc--ctc------cca---------------------------
B D        White rhinoceros  gtcccaggcg-------cgcggc---acc--ctc------cca---------------------------
B D                     Cat  gccgcgcgaa-------gccggc---ccc--ctc------cgg---------------------------
B D                     Dog  gtcccggggg-------cgccgc---gcc--ctc------cag---------------------------
B D                 Ferret   atcccaggag-------ggtcgc---agc--ctc------cag---------------------------
B D                   Panda  gcgttcggag-------cggcgc---acc--ctc------cag---------------------------
             Pacific walrus  gtcccaggcg-------cgccac---acc--ctc------cag---------------------------
               Weddell seal  gtcccaggcg-------cgccac---acc--ctc------cag---------------------------
B D                 Megabat  gccccaggca-------c-cggc---gcc--ctc------cca---------------------------
              Big brown bat  gtccccggca-------cgtggc---acc--ctc------cca---------------------------
B D                Microbat  ttcacgttca-------ggtgac---aca--ctcgacgggccagaggcgcactagtcgcagcacagtggg
B D                Elephant  gccctgggcg-------cctggc---gtc--ctc------ct----------------------------
B D                 Manatee  gtcccgggcg-------cctggc---gtc--ctc------ct----------------------------
           Cape golden mole  gtccccggca-------cctggc---gtc--ccc------at----------------------------
B D                  Tenrec  gtccggggtg-------cctagc---gcccaccc------cc----------------------------
                   Aardvark  gg-------a-------cctggc---att--ccc------ca----------------------------
B D               Armadillo  gtccgagccg-------ccc-gc---gtcccccc------ac----------------------------
B D             Zebra finch  -ctgcgggca------gtgcc-a---gct--gcc------ag----------------------------
B D                 Chicken  -ctccgagca------------------c--ctc------ag----------------------------
B D      American alligator  -catcgggct------------c---cct--ccc------cc----------------------------
  D         Green seaturtle  -gtctggagc-------tgcagc---cat--gtc------ag----------------------------
  D          Painted turtle  -gcgagaggcccacgtttgccac---ttt--ctc------aa----------------------------
B D                    Pika  ======================================================================
B D         Tasmanian devil  ======================================================================
            Bactrian camel  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D                Platypus  ======================================================================
          Black flying-fox  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
      David's myotis (bat)  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D                  Alpaca  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

                      Human  ----g
                      Chimp  ----g
                    Gorilla  ----g
                  Orangutan  ----g
                     Gibbon  ----g
                     Rhesus  ----g
        Crab-eating macaque  ----g
                     Baboon  ----g
               Green monkey  ----g
                   Marmoset  ----g
            Squirrel monkey  ----g
                   Bushbaby  ----g
         Chinese tree shrew  ----g
                   Squirrel  ----g
     Lesser Egyptian jerboa  ----g
               Prairie vole  ----g
            Chinese hamster  ----g
             Golden hamster  ----g
                      Mouse  ----g
                        Rat  ----g
             Naked mole-rat  ----c
                 Guinea pig  ----a
                 Chinchilla  ----g
           Brush-tailed rat  ----g
                     Rabbit  ----t
                        Pig  ----a
                    Dolphin  ----a
               Killer whale  ----a
           Tibetan antelope  ----a
                        Cow  ----a
                      Sheep  ----a
              Domestic goat  ----a
                      Horse  ----g
           White rhinoceros  ----g
                        Cat  ----c
                        Dog  ----c
                    Ferret   ----c
                      Panda  ----c
             Pacific walrus  ----c
               Weddell seal  ----c
                    Megabat  ----g
              Big brown bat  ----g
                   Microbat  ctagg
                   Elephant  -----
                    Manatee  -----
           Cape golden mole  -----
                     Tenrec  -----
                   Aardvark  -----
                  Armadillo  -----
                Zebra finch  -----
                    Chicken  -----
         American alligator  -----
            Green seaturtle  -----
             Painted turtle  -----
                       Pika  =====
            Tasmanian devil  =====
             Bactrian camel  NNNNN
                   Platypus  =====
           Black flying-fox  NNNNN
       David's myotis (bat)  NNNNN
                     Alpaca  NNNNN

Inserts between block 3 and 4 in window
  D        Green seaturtle 2bp
  D         Painted turtle 23bp

Alignment block 4 of 54 in window, 41507892 - 41507897, 6 bps 
B D                   Human  ca-cccc
B D                   Chimp  ca-cccc
B D                 Gorilla  ca-cccc
B D               Orangutan  caccccc
B D                  Gibbon  ca-cccc
B D                  Rhesus  ca-cccc
B D     Crab-eating macaque  ca-cccc
B D                  Baboon  ca-cccc
B D            Green monkey  ca-ctcc
B D                Marmoset  ca-cccc
B D         Squirrel monkey  ca-cccc
B D                Bushbaby  c--cctt
         Chinese tree shrew  ca----c
B D                Squirrel  cc-cgca
     Lesser Egyptian jerboa  ca-ccc-
               Prairie vole  tc-ccca
B D         Chinese hamster  tc-ccca
             Golden hamster  tc-ccca
B D                   Mouse  tc-ccca
B D                     Rat  tc-ccca
B D          Naked mole-rat  -c-ccca
B D              Guinea pig  cc-ccta
                 Chinchilla  -c-ccca
           Brush-tailed rat  cc-ccca
B D                  Rabbit  cc-cctg
B D                     Pig  cctcgg-
B D                 Dolphin  cctcac-
               Killer whale  cctcac-
           Tibetan antelope  cctcac-
B D                     Cow  cctcac-
B D                   Sheep  cctcac-
              Domestic goat  cctcac-
B D                   Horse  cc-ccc-
B D        White rhinoceros  cc-ccc-
B D                     Cat  cc-----
B D                     Dog  cc-ccc-
B D                 Ferret   cc-cac-
B D                   Panda  cc-cac-
             Pacific walrus  tg-cac-
               Weddell seal  cc-cac-
B D                 Megabat  cc-ccc-
              Big brown bat  cc-ccc-
B D                Microbat  ca-tcc-
B D                    Pika  =======
B D                  Tenrec  -------
B D               Armadillo  -------
                  Aardvark  -------
  D         Green seaturtle  =======
  D          Painted turtle  =======
          Cape golden mole  -------
B D         Tasmanian devil  =======
            Bactrian camel  NNNNNNN
B D                 Manatee  -------
B D                 Chicken  -------
B D                Platypus  =======
B D                Elephant  -------
          Black flying-fox  NNNNNNN
      David's myotis (bat)  NNNNNNN
B D      American alligator  -------
B D             Zebra finch  -------
B D                  Alpaca  NNNNNNN

Inserts between block 4 and 5 in window
B D                  Horse 2bp
B D       White rhinoceros 2bp
B D                    Cat 161bp
B D                Megabat 2bp
             Big brown bat 2bp
B D               Microbat 2bp

Alignment block 5 of 54 in window, 41507898 - 41507917, 20 bps 
B D                   Human  gg------gaggcgccctgcc-cg---------------gct
B D                   Chimp  gg------gaggcgccctgcc-cg---------------gct
B D                 Gorilla  gg------gaggcgccctgcc-cg---------------gct
B D               Orangutan  ag------aaggcgccctgcc-cg---------------gct
B D                  Gibbon  cg------gaggcgccctgcc-cg---------------gct
B D                  Rhesus  cg------gaggcgccctgcc-cg---------------gct
B D     Crab-eating macaque  cg------gaggcgccctgcc-cc---------------gct
B D                  Baboon  cg------gaggcgccctgtc-cg---------------gct
B D            Green monkey  cg------gaggcgtcctgcc-cg---------------gcc
B D                Marmoset  cg------gaggcaccctgcc-ca---------------gct
B D         Squirrel monkey  cg------gaggcaccctggc-cg---------------gct
B D                Bushbaby  gg------agggcgctttgcg-gc---------------tcg
         Chinese tree shrew  gt------aggccgctttgcc-ca------------------
B D                Squirrel  gga-----agggcgctccgcc-gg------------------
               Prairie vole  gaa-----cgtgcgcccggtc-cg------------------
B D         Chinese hamster  gaa-----tgcgcacctagtc-cg------------------
             Golden hamster  gaa-----tgcgcacctagta-ca------------------
B D                   Mouse  gga-----cgtacactcgggc-ga------------------
B D                     Rat  gga-----cgtacacccgggc-cg------------------
B D          Naked mole-rat  gga-----agggcgctctgcc-cg------------------
B D              Guinea pig  gga-----aaggcactctgcc-ca------------------
                 Chinchilla  gg------aaggtgctctacc-tg------------------
           Brush-tailed rat  gg------aaggtgctctatc-tg------------------
B D                  Rabbit  cga-----agggctctcggcc-cg------------------
B D                     Pig  gg------aggtcgctccgcc-cg---------------gct
B D                 Dolphin  gc------aggtcactttgct-cg---------------gct
               Killer whale  gc------aggtcactttgct-tg---------------gct
           Tibetan antelope  gc------aggtcgctttgca-cg---------------gct
B D                     Cow  gc------aggtcgctttgct-cg---------------gct
B D                   Sheep  gc------aggtcgctttgca-cg---------------gct
              Domestic goat  gc------aggtcgctttgca-cg---------------gct
B D                   Horse  gg------aggccactttgcc-tg---------------gct
B D        White rhinoceros  gg------agggcactttgcc-ca---------------gct
B D                     Cat  gg------gggacgcttgggt-tg------------------
B D                     Dog  c-------agggcgctcggcc-cg---------------gcc
B D                 Ferret   cg------agggccctttgcc-cg---------------gcc
B D                   Panda  cg------agggcc----------------------------
             Pacific walrus  cg------agggccctttgcc-cgggggcccttggccctgcc
               Weddell seal  cg------agggccctttgcc-cg---------------gcc
B D                 Megabat  -g------cgggcgcctcgcc-cc---------------gct
              Big brown bat  gg------agagcgcgccgtc-cc---------------gct
B D                Microbat  ag------gcagtctgccgcagcc---------------gca
B D                Elephant  gg------tgggcgcgttgcc-cc---------------gtt
B D                 Manatee  ag------aaggcgcgtggcc-ac---------------gga
           Cape golden mole  gg------agggcacgtggct-cg---------------act
B D                  Tenrec  gg------agggcacgtggcc-cg---------------gcg
                   Aardvark  gg------aaggcgcgtggcc-gt---------------gtc
B D               Armadillo  gg------agggcgccctgcc-cg---------------gcc
B D             Zebra finch  --------ctctgccccagcc-c-------------------
B D                 Chicken  --------cgaggctcccggc-c-------------------
B D      American alligator  --------ctccgccccagct-t-------------------
  D         Green seaturtle  --cgaggggggagtccacacc-c-------------------
B D                    Pika  ==========================================
    Lesser Egyptian jerboa  ------------------------------------------
  D          Painted turtle  ==========================================
B D         Tasmanian devil  ==========================================
            Bactrian camel  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D                Platypus  ==========================================
          Black flying-fox  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
      David's myotis (bat)  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D                  Alpaca  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

Inserts between block 5 and 6 in window
B D            Zebra finch 6bp
B D                Chicken 6bp
B D     American alligator 12bp
  D        Green seaturtle 1bp

Alignment block 6 of 54 in window, 41507918 - 41507949, 32 bps 
B D                   Human  ggcccca--gcgctcgac--cctcgggcgcact--cac--------------------------------
B D                   Chimp  ggcccca--gcgctcgac--cctcgggcgcact--cac--------------------------------
B D                 Gorilla  ggcccca--gcgctcgac--cctcgggcgcact--cac--------------------------------
B D               Orangutan  ggcccca--gcgctcgac--cctcgggcgcact--cac--------------------------------
B D                  Gibbon  ggcccca--gcgctcgac--cttcgggcgcact--cac--------------------------------
B D                  Rhesus  gacccca--gtgctcgac--cctcgggcgcact--cac--------------------------------
B D     Crab-eating macaque  gacccca--gtgctcgac--cgtcgggcgcact--cac--------------------------------
B D                  Baboon  gacccca--gtgctcgac--cctcgggcgcact--cac--------------------------------
B D            Green monkey  gacccca--gtgctcgac--cctcgggcgcact--cac--------------------------------
B D                Marmoset  tgcccca--gcgctcggc--cctcgggcgcact--cac--------------------------------
B D         Squirrel monkey  tgcccca--gcgctcggc--cctcgggcgcact--cac--------------------------------
B D                Bushbaby  gcccaca--gcgctcagc--c--caggaggacg--cac--------------------------------
         Chinese tree shrew  --------------------ccccaagtggacg--cac--------------------------------
B D                Squirrel  -----------cctcagc--cccgagcgctccg--ccc--------------------------------
     Lesser Egyptian jerboa  --------------ccgc-----------------cac--------------------------------
               Prairie vole  ------------ctcagt---cccagaccgtcg--cac--------------------------------
B D         Chinese hamster  ------------ctcagt--ccccagatggtcg--cac--------------------------------
             Golden hamster  ------------ctcaata-ccccagacggtcg--cac--------------------------------
B D                   Mouse  ------------atcagt--c---agacggtcg--cac--------------------------------
B D                     Rat  ------------ctcagt--ctcaagacggtcgcacac--------------------------------
B D          Naked mole-rat  ------------cccaag--cgccaa-----cg--cac--------------------------------
B D              Guinea pig  ------------cca--g--ggccag-----tg--cac--------------------------------
                 Chinchilla  ------------ccc--a--caccag-----tg--cac--------------------------------
           Brush-tailed rat  ------------cct--g--caccag-----cg--caa--------------------------------
B D                  Rabbit  -----------gctcggc--ccgcgggcgaact--cac--------------------------------
B D                     Pig  cagccccgcgcgccccgc--cggcgagaggacg--cac--------------------------------
B D                 Dolphin  cagccccgtgcgtcccgc--gggcgggaggacg--cac--------------------------------
               Killer whale  cagccccgtgcgtcccgc--gggcgggaggacg--cac--------------------------------
           Tibetan antelope  cagcccagtgcgtcccga--cggcgggaggacg--gac--------------------------------
B D                     Cow  cagcccagtgcgtccaga--cggcgggaggacg--gaa--------------------------------
B D                   Sheep  cagcccagtgcgtcccga--cggctggaggacg--gac--------------------------------
              Domestic goat  cagcccagtgcgtcccga--cggctggaggacg--gac--------------------------------
B D                   Horse  cagccccgcgcgtcc----------ggaggacc--cac--------------------------------
B D        White rhinoceros  cagccctgggcggcc----------agaggacg--cac--------------------------------
B D                     Cat  -------------tcccc--tggc----------------------------------------------
B D                     Dog  cggcccggagggtcccgc--cggcgggaagacg--cac--------------------------------
B D                 Ferret   cagcccggagagtcccgc--cggtggaaggacg--cac--------------------------------
B D                   Panda  -------------tccgc--cggcggg-ggacg--cac--------------------------------
             Pacific walrus  cggcccggagcgtcccgc--cggcgggaggact--cac--------------------------------
               Weddell seal  cggcccggagcgtcccgc--cggcggaaggacg--cac--------------------------------
B D                 Megabat  cagccccgcgcgccccg------------------cac--------------------------------
              Big brown bat  caaccccgcgcgtcccg------------------cac--------------------------------
B D                Microbat  cagccgcgtgttaccc---------------------c--------------------------------
B D                Elephant  gagcccagagcacccagtgcccgctagccggct--cac--------------------------------
B D                 Manatee  gtgcccagagcacccagtgcccgcgagccggcg--cac--------------------------------
           Cape golden mole  gagcccagagcatgcagtgctcgcgagcggacg--ctc--------------------------------
B D                  Tenrec  gagtccagagcacccagtgtcagcca--ggacg--cac--------------------------------
                   Aardvark  gcgcccagagcatccagcgcccgcaagcggacg--cac--------------------------------
B D               Armadillo  ccgtcca------------------------cg--cac--------------------------------
B D             Zebra finch  -------------------actctcctctctcg--ccccc---------------------cagatcaac
B D                 Chicken  -------------------acccggcgccgcag--ccc----------------------------cagc
B D      American alligator  -------------------gatttctgctctcg--gccgcaggaaaacaggaagccgaggacaaggcggc
  D         Green seaturtle  -------------------ggctccagggcagg--acc----------------------------ctgg
  D          Painted turtle  -------------------ggccccagctcctg--ccc----------------------------cagg
B D                    Pika  ======================================================================
B D         Tasmanian devil  ======================================================================
            Bactrian camel  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D                Platypus  ======================================================================
          Black flying-fox  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
      David's myotis (bat)  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D                  Alpaca  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

                      Human  -----------------------------------
                      Chimp  -----------------------------------
                    Gorilla  -----------------------------------
                  Orangutan  -----------------------------------
                     Gibbon  -----------------------------------
                     Rhesus  -----------------------------------
        Crab-eating macaque  -----------------------------------
                     Baboon  -----------------------------------
               Green monkey  -----------------------------------
                   Marmoset  -----------------------------------
            Squirrel monkey  -----------------------------------
                   Bushbaby  -----------------------------------
         Chinese tree shrew  -----------------------------------
                   Squirrel  -----------------------------------
     Lesser Egyptian jerboa  -----------------------------------
               Prairie vole  -----------------------------------
            Chinese hamster  -----------------------------------
             Golden hamster  -----------------------------------
                      Mouse  -----------------------------------
                        Rat  -----------------------------------
             Naked mole-rat  -----------------------------------
                 Guinea pig  -----------------------------------
                 Chinchilla  -----------------------------------
           Brush-tailed rat  -----------------------------------
                     Rabbit  -----------------------------------
                        Pig  -----------------------------------
                    Dolphin  -----------------------------------
               Killer whale  -----------------------------------
           Tibetan antelope  -----------------------------------
                        Cow  -----------------------------------
                      Sheep  -----------------------------------
              Domestic goat  -----------------------------------
                      Horse  -----------------------------------
           White rhinoceros  -----------------------------------
                        Cat  -----------------------------------
                        Dog  -----------------------------------
                    Ferret   -----------------------------------
                      Panda  -----------------------------------
             Pacific walrus  -----------------------------------
               Weddell seal  -----------------------------------
                    Megabat  -----------------------------------
              Big brown bat  -----------------------------------
                   Microbat  -----------------------------------
                   Elephant  -----------------------------------
                    Manatee  -----------------------------------
           Cape golden mole  -----------------------------------
                     Tenrec  -----------------------------------
                   Aardvark  -----------------------------------
                  Armadillo  -----------------------------------
                Zebra finch  ag---cgagtaccgggca---gagttcgcccgctg
                    Chicken  cg---tacacacctgcc-----ggccctcccgcag
         American alligator  tggatagcgccacagccaggggggcacggcc-cag
            Green seaturtle  gg---------tcaggaaggaacccaccccttctt
             Painted turtle  gg----------------------ctcgccctctc
                       Pika  ===================================
            Tasmanian devil  ===================================
             Bactrian camel  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
                   Platypus  ===================================
           Black flying-fox  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
       David's myotis (bat)  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
                     Alpaca  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

Alignment block 7 of 54 in window, 41507950 - 41508003, 54 bps 
B D                   Human  ct------gccg-c------gc-cgcg------ctcc---t----ca-----cac-----cc--------
B D                   Chimp  ct------gccg-c------gc-cgcg------ctcc---t----ca-----cac-----cc--------
B D                 Gorilla  ct------gccg-c------gc-cgcg------ctcc---t----ca-----cac-----cc--------
B D               Orangutan  ct------gccg-c------gc-cgcg------ctcc---t----ca-----cac-----cc--------
B D                  Gibbon  ct------gccg-c------gc-cgcg------ctcc---t----ca-----cac-----cc--------
B D                  Rhesus  tt------gccg-c------gc-cgcg------ctcc---t----ca-----cac-----cc--------
B D     Crab-eating macaque  tt------gccg-c------gc-cgcg------ctcc---t----ca-----cac-----cc--------
B D                  Baboon  ct------gccg-c------gc-cgcg------cacc---t----ca-----cac-----cc--------
B D            Green monkey  ct------gccg-c------gc-cgcg------ctcc---t----ca-----cac-----cc--------
B D                Marmoset  ct------gcgg-c------gc-cgcg------ctcc---c----ca-----cag-----cc--------
B D         Squirrel monkey  ct------gccg-c------gc-cgcg------ctcc---c----ca-----cag-----cc--------
B D                Bushbaby  ct------gcag-c------gt-agcg------ctcc---t----tg-----aac-----cg--------
         Chinese tree shrew  ct------gccg-c------gcttgcc------cgcc---t----ca-----cac-----tc--------
B D                Squirrel  gc------gcagacacacctgc-cccg------caca---c----ct-----cgc-ttgcct--------
     Lesser Egyptian jerboa  ct------cccc-ctcccagga-ct--------ccca---c----cc-----ggc-ttcacct-------
               Prairie vole  ct------gtcg-cgccctggc-ctcg------ccta---a----cc-----tac-tgtacc--------
B D         Chinese hamster  ct------gtcg-ctccctggc-ttcg------ccta---a----ct-----cac-tgtacc--------
             Golden hamster  ct------gtag-cgtcctggc-ttcg------ccta---a----ccca---cac-tgtaca--------
B D                   Mouse  ct------gtag-tgccttggc-ctct------ccta---a----ct-----cacttgtacc--------
B D                     Rat  at------gtag-caccttggc-ctca------ccta---a----ct-----cacctgtacc--------
B D          Naked mole-rat  ct------gtgg-c-------c-caca------cctg---a----tt-----cag---------------
B D              Guinea pig  ct------tcag-c-------c-caca------cctg---c----tt-----cag---------------
                 Chinchilla  ct------tcag-c-------c-cacacctgcttctg---c----tt-----cag---------------
           Brush-tailed rat  ct------ttgg-c-------c-caca------tctg---c----tt-----cag---------------
B D                  Rabbit  ct------gccg-cacccccgg-cgct------ccca---c----ct-----ggt-ttcaccgccagcca
B D                     Pig  ct------gtcg-a------gctggag------ccgc---tcgcacg-----cac-----ct--------
B D                 Dolphin  ct------gccg-g------gcaggag------ctgc---t----ca-----cac-----ct--------
               Killer whale  ct------gccg-g------gcaggag------ctgc---t----ca-----cac-----ct--------
           Tibetan antelope  cc------accg-g------gccaaag------ctgc---t----ca-----cac-----ct--------
B D                     Cow  ct------accg-g------gccggag------ctgc---t----ca-----cac-----ct--------
B D                   Sheep  cc------accg-g------gccgaag------ctgc---t----ca-----cac-----ct--------
              Domestic goat  cc------accg-g------gccgaag------ctgc---t----ca-----cac-----ct--------
B D                   Horse  ct------gccg-c------gcttgcg------ctgc---t----ca-----cac-----ct--------
B D        White rhinoceros  ct------gcgg-c------gctcgcg------ctgc---t----ca-----cac-----ct--------
B D                     Cat  -----------------------------------gc---c----ca-----gat-----cc--------
B D                     Dog  ct------gctg-c------gctggcg------ctgc---c----ca-----cac-----ct--------
B D                 Ferret   ct------gccg-c------gctcacg------ccgc---g----ca-----cac-----ct--------
B D                   Panda  ct------gctc-c------gctcgcg------ccgc---t----ca-----cac-----ct--------
             Pacific walrus  ct------gctg-c------gctcgcg------ccgc---t----ca-----cac-----cc--------
               Weddell seal  ct------gctg-c------gctcgcg------ctgc---t----ca-----cgc-----cc--------
B D                 Megabat  ct------gccg-c------gcccgcg------ctgc---g----ca-----cac-----ct--------
              Big brown bat  cg------gcca-c------gctcgcc------ctgc---g----ca-----cac-----ct--------
B D                Microbat  gg------gtct-c---------cgag------ctgc---g----ca-----ccc-----ct--------
B D                Elephant  ct------gctg-c------cc-tggg------tcgc-tcg----cg-----cac-----ct--------
B D                 Manatee  ct------gcag-c------ct-tggg------ttgc-gtg----cg-----cac-----ct--------
           Cape golden mole  ca------gtca-c------ac-cagc------tggc-gcg----cg-----cac-----ct--------
B D                  Tenrec  ct------gctg-c-----ggt-cagc------ttcctgag----aa-----cac-----ct--------
                   Aardvark  tt------ggcg-t------cc-cggc------tctc-gcg----cg-----cac-----ct--------
B D               Armadillo  ctctcggggcca-c------ct-tggc------tcgc---g----cg-----cgc-----cc--------
B D         Tasmanian devil  ------aagcca-c------ga-gacg------cccc---c----ca-----agc-----cc--------
B D             Zebra finch  -----------------------------------------------cctggagc-----cc--------
B D                 Chicken  -----------------------------------------------c----agc-----ac--------
B D      American alligator  -----------------------------------------------cc---agc-----ct--------
  D         Green seaturtle  -----------------------------------------------cca--ggc-----ag--------
  D          Painted turtle  -----------------------------------------------cag--agc-----cg--------
B D                    Pika  ======================================================================
            Bactrian camel  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D                Platypus  ======================================================================
          Black flying-fox  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
      David's myotis (bat)  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D                  Alpaca  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

                      Human  gc-----------------tt--tc---------------------ac--------ct----cc--gggc
                      Chimp  gt-----------------tt--tc---------------------ac--------ct----cc--gggc
                    Gorilla  gc-----------------tt--tc---------------------ac--------ct----cc--gggc
                  Orangutan  gc-----------------tt--tc---------------------ac--------ct----cc--gggc
                     Gibbon  gc-----------------tt--tc---------------------ac--------ct----ct--gggc
                     Rhesus  gc-----------------tt--tc---------------------ac--------ct----cc--gggc
        Crab-eating macaque  gc-----------------tt--tc---------------------ac--------ct----cc--gggc
                     Baboon  gc-----------------tt--tc---------------------ac--------ct----cc--gggc
               Green monkey  gc-----------------tt--tc---------------------ag--------ct----cc--gggc
                   Marmoset  gc-----------------tt--tc---------------------ac--------ct----ct--gggc
            Squirrel monkey  gc-----------------tt--tc---------------------ac--------ct----cc--gggc
                   Bushbaby  gc-----------------tt--ct---------------------cctccagccacc----cc--gacc
         Chinese tree shrew  gg-----------------ctcgtc---------------------ac--------cc---acc--cggc
                   Squirrel  cc-----------------ag--cc---------------------ac--------ccgcaccc--acgc
     Lesser Egyptian jerboa  cc-----------------ag--ac---------------------gc--------cc----ct--cggt
               Prairie vole  cc-----------------ag--ac---------------------gc--------cc-cagcc--gggc
            Chinese hamster  ct-----------------ag--at---------------------ac--------cc-cggcc--cggc
             Golden hamster  ct-----------------ag--ac---------------------ac--------cc-cggcc--aggc
                      Mouse  ct-----------------ag--ac---------------------gc--------cc-aggcc--cggc
                        Rat  tt-----------------ag--ac---------------------tc--------cc-agccc--cggc
             Naked mole-rat  ct-----------------cc--gc---------------------ac--------cc-ccccccaaggt
                 Guinea pig  ct-----------------cc--ac---------------------ac--------cc-ctgcc--aggt
                 Chinchilla  ct-----------------ct--gc---------------------ac--------cc-c-gcc--aggt
           Brush-tailed rat  ct-----------------ct--ac---------------------ac--------cc-ctgcc--agat
                     Rabbit  ac-----------------ac--gc---------------------ac--------cc-agcgc--gagg
                        Pig  ga-----------------cc--tc---------------------ac--------tt----cc--cgtg
                    Dolphin  gg-----------------ct--tc---------------------ac--------ct----cc--cgct
               Killer whale  gg-----------------ct--tc---------------------ac--------ct----cc--cgct
           Tibetan antelope  gg-----------------ct--tc---------------------gc--------at----cc--cgct
                        Cow  gg-----------------ct--tc---------------------ac--------ct----cc--cgct
                      Sheep  gg-----------------ct--tc---------------------ac--------at----cc--cgct
              Domestic goat  gg-----------------ct--tc---------------------ac--------at----cc--cgct
                      Horse  gg-----------------ct--tc---------------------tc--------ct----cc--c---
           White rhinoceros  gg-----------------cc--tc---------------------ac--------ct----cc--tgcc
                        Cat  tt-----------------ct--tt---------------------------------------------
                        Dog  gg-----------------cc--tc---------------------ac----------------------
                    Ferret   gg-----------------cc--tc---------------------cc--------gt----cc--aggc
                      Panda  gg-----------------cc--tc---------------------ac--------gt----cc--agcc
             Pacific walrus  gg-----------------cc--tc---------------------ac--------gt----cc--agcc
               Weddell seal  gg-----------------cc--tc---------------------ac--------gt----cc--agcc
                    Megabat  gg-----------------ct--tc---------------------gc--------ct----gc--cgcc
              Big brown bat  gg-----------------ct--cc---------------------ac--------ct----gc--cgcc
                   Microbat  gggcccccggcacgtggcacc--ct---------------------cc--------ct----gc--cccc
                   Elephant  gg-----------------ct--tc---------------------ag--------cc----tc--cacc
                    Manatee  gg-----------------ct--tc---------------------ac--------cc----tc--cacc
           Cape golden mole  gg-----------------ct--tc---------------------ac--------cc----c-------
                     Tenrec  ga-----------------ct--gc---------------------ac--------cc----cg--cacc
                   Aardvark  ga-----------------ct--tc---------------------ac--------cc----tc--cacc
                  Armadillo  tg-----------------ct--tc---------------------ac--------gc----cc--cacc
            Tasmanian devil  ct-----------------tt--tcggagcaaacggcgcagcagcgat--------tc----gg--gggc
                Zebra finch  ct-----------------cc--tg---------------------at--------gc----tc--agcc
                    Chicken  cg-----------------ag--cc---------------------ga--------gc----gc--agcc
         American alligator  cc-----------------ca--cc---------------------cc--------tt----tc--tgcc
            Green seaturtle  ca-----------------gc--ta---------------------aa--------ct------------
             Painted turtle  tg-----------------gg--ca---------------------gg--------at----tc--cggc
                       Pika  ======================================================================
             Bactrian camel  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
                   Platypus  ======================================================================
           Black flying-fox  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
       David's myotis (bat)  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
                     Alpaca  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

                      Human  -gg------------------g----------gc-a-----ggggg---ca-------------------
                      Chimp  -gg------------------g----------gc-a-----gcggg---ca-------------------
                    Gorilla  -gg------------------g----------gc-a-----ggggg---ca-------------------
                  Orangutan  -gg------------------g----------gc-a-----ggggg---ca-------------------
                     Gibbon  -gg------------------g----------gc-a-----ggggg---ca-------------------
                     Rhesus  -gg------------------g----------gc-a-----ggggg---ca-------------------
        Crab-eating macaque  -gg------------------g----------gc-a-----ggggg---ca-------------------
                     Baboon  -tg------------------g----------gc-a-----ggggg---ca-------------------
               Green monkey  -gg------------------g----------gc-a-----ggggg---ca-------------------
                   Marmoset  -gg------------------g----------gg-c-----ggggg---ca-------------------
            Squirrel monkey  -ag------------------c----------gg-c-----c----------------------------
                   Bushbaby  -cg------------------g----------gc-t-----gg---------------------------
         Chinese tree shrew  -gc------------------g----------ga-g-----gcggg---ag-------------------
                   Squirrel  -ac------------------ccagaactggggc-a-----gggca---at-------------------
     Lesser Egyptian jerboa  -g------------------------------gc-a-----gggtg------------------------
               Prairie vole  -ac------------------c----------gt-c-----gggtg---ga-------------------
            Chinese hamster  -ac------------------c----------gc-g-----gggcg---ga-------------------
             Golden hamster  -ac------------------c----------gc-g-----gggcg---ga-------------------
                      Mouse  -ac------------------c----------gc-c-----ggacg---ga-------------------
                        Rat  -ac------------------c----------gc-g-----gggcg---ga-------------------
             Naked mole-rat  -tg------------------t----------tc-a-----tgggc---gc-------------------
                 Guinea pig  -tg------------------t----------tt-g-----gggga---gc-------------------
                 Chinchilla  -tg------------------t----------tt-g-----gggga---gc-------------------
           Brush-tailed rat  -tg------------------t----------tt-g-----gggca------------------------
                     Rabbit  -ac------------------t---------------------ggg---ga-------------------
                        Pig  -ac------------------t----------cc-c-----gccta---gt-------------------
                    Dolphin  -gc------------------t----------cc-c-----actca---gc-------------------
               Killer whale  -gc------------------t----------cc-c-----accca---gc-------------------
           Tibetan antelope  -ac------------------t----------cc-c-----accca---gt-------------------
                        Cow  -ac------------------t----------ct-c-----accca---gc-------------------
                      Sheep  -ac------------------t----------cc-c-----aacca---gt-------------------
              Domestic goat  -ac------------------t----------cc-c-----accca---gt-------------------
                      Horse  ----------------------------------------------------------------------
           White rhinoceros  -ag------------------c----------cc-c-----agcca---gc-------------------
                        Cat  ----------------------------------------------------------------------
                        Dog  ----------------------------------------------------------------------
                    Ferret   -gc------------------t----------gc-c-----accca---gc-------------------
                      Panda  -gc------------------c----------gc-c-----accca---gc-------------------
             Pacific walrus  -gc------------------c----------gc-c-----accca---ga-------------------
               Weddell seal  -gc------------------c----------ac-c-----accca---gc-------------------
                    Megabat  -ac------------------c----------tc-c-----accca---gc-------------------
              Big brown bat  -ac------------------c----------tc-c-----accgt---gc-------------------
                   Microbat  -acggacagcgctttgccccgc----------tc-a-----acccc---gc-------------------
                   Elephant  cag------------------c----------cc-c-----gggag---g--------------------
                    Manatee  cag------------------c----------gc-c-----gtggg---g--------------------
           Cape golden mole  ---------------------t----------gc-a-----ggtag---g--------------------
                     Tenrec  gag------------------c----------gc-c-----gggagtcag--------------------
                   Aardvark  --------------------------------------------ag---g--------------------
                  Armadillo  cac------------------c----------gc-c-----cccgg------------------------
            Tasmanian devil  -gg------------------a----------gc-g-----agggg---gg-------------------
                Zebra finch  -cc------------------c----------gc-c-----gctcc---gtggtgg-gcagcgctggtg-
                    Chicken  -ac------------------c----------gctt-----tctac---acgaaggcgaagcaccgaga-
         American alligator  -cc------------------c----------ca-----------------------gccaggccatag-
            Green seaturtle  -cc------------------c----------at-tggagatccca---gccgtg--gcagggccggggc
             Painted turtle  -cc------------------c----------at-t-----tccca---gcaggg--gacgcggcgggac
                       Pika  ======================================================================
             Bactrian camel  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
                   Platypus  ======================================================================
           Black flying-fox  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
       David's myotis (bat)  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
                     Alpaca  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

                      Human  -----------
                      Chimp  -----------
                    Gorilla  -----------
                  Orangutan  -----------
                     Gibbon  -----------
                     Rhesus  -----------
        Crab-eating macaque  -----------
                     Baboon  -----------
               Green monkey  -----------
                   Marmoset  -----------
            Squirrel monkey  -----------
                   Bushbaby  -----------
         Chinese tree shrew  -----------
                   Squirrel  -----------
     Lesser Egyptian jerboa  -----------
               Prairie vole  -----------
            Chinese hamster  -----------
             Golden hamster  -----------
                      Mouse  -----------
                        Rat  -----------
             Naked mole-rat  -----------
                 Guinea pig  -----------
                 Chinchilla  -----------
           Brush-tailed rat  -----------
                     Rabbit  -----------
                        Pig  -----------
                    Dolphin  -----------
               Killer whale  -----------
           Tibetan antelope  -----------
                        Cow  -----------
                      Sheep  -----------
              Domestic goat  -----------
                      Horse  -----------
           White rhinoceros  -----------
                        Cat  -----------
                        Dog  -----------
                    Ferret   -----------
                      Panda  -----------
             Pacific walrus  -----------
               Weddell seal  -----------
                    Megabat  -----------
              Big brown bat  -----------
                   Microbat  -----------
                   Elephant  -----------
                    Manatee  -----------
           Cape golden mole  -----------
                     Tenrec  -----------
                   Aardvark  -----------
                  Armadillo  -----------
            Tasmanian devil  -----------
                Zebra finch  --------gca
                    Chicken  --------gcc
         American alligator  --------acc
            Green seaturtle  agagagcggag
             Painted turtle  acaga---gac
                       Pika  ===========
             Bactrian camel  NNNNNNNNNNN
                   Platypus  ===========
           Black flying-fox  NNNNNNNNNNN
       David's myotis (bat)  NNNNNNNNNNN
                     Alpaca  NNNNNNNNNNN

Inserts between block 7 and 8 in window
B D               Marmoset 360bp
        Chinese tree shrew 3bp
B D               Squirrel 2bp
    Lesser Egyptian jerboa 2bp
              Prairie vole 2bp
B D        Chinese hamster 2bp
            Golden hamster 2bp
B D                  Mouse 2bp
B D                    Rat 2bp
B D         Naked mole-rat 2bp
B D             Guinea pig 2bp
                Chinchilla 2bp
          Brush-tailed rat 2bp
B D                 Rabbit 2bp
B D                    Pig 12bp
B D                Dolphin 6bp
              Killer whale 5bp
          Tibetan antelope 2bp
B D                    Cow 2bp
B D                  Sheep 2bp
             Domestic goat 2bp
B D                  Horse 9bp
B D       White rhinoceros 12bp
B D                Ferret  12bp
B D                  Panda 12bp
            Pacific walrus 12bp
              Weddell seal 12bp
B D                Megabat 4bp
             Big brown bat 4bp
B D               Microbat 9bp
B D        Tasmanian devil 4bp

Alignment block 8 of 54 in window, 41508004 - 41508058, 55 bps 
B D                   Human  ---------------------------tcggcgggtcc-ca--g-------g-------cgccca-----
B D                   Chimp  ---------------------------tcggcgggtcc-ca--g-------g-------cgccca-----
B D                 Gorilla  ---------------------------tcggcgggtcc-ca--g-------g-------cgccca-----
B D               Orangutan  ---------------------------tcggcgggtcc-ca--g-------g-------cgccca-----
B D                  Gibbon  ---------------------------tcggccggtcc-ca--g-------g-------cgccca-----
B D                  Rhesus  ---------------------------taggcgggtcc-ca--g-------g-------cgccca-----
B D     Crab-eating macaque  ---------------------------taggcgggtcc-ca--g-------g-------cgccca-----
B D                  Baboon  ---------------------------taggcgggtcc-ca--g-------g-------cgccca-----
B D            Green monkey  ---------------------------taggcgggtcc-ca--g-------g-------cgccca-----
B D                Marmoset  ---------------------------ccggcgggtct-tt--g-------g-------ctcccg-----
B D         Squirrel monkey  ---------------------------ccggcgggtcc-ca--g-------g-------ctccca-----
B D                Bushbaby  -----------------------------ggtagttcc-tg--g-------g-------ccctcc-----
         Chinese tree shrew  ---------------------------tagggagctcc-ta--g-------g-------cgctca-----
B D                Squirrel  ---------------------------ggaggttccca-ga--t----------------gccca-----
     Lesser Egyptian jerboa  ---------------------------cagctcatccc-ca--t-------g-------ctcccg-----
               Prairie vole  ---------------------------cgaatcacccc-ca--t--------------------------
B D         Chinese hamster  ---------------------------aaggtcacccc-ca--t--------------------------
             Golden hamster  ---------------------------catggca-ccc-ca--t--------------------------
B D                   Mouse  ---------------------------caggtc-accc-ca--t--------------------------
B D                     Rat  ---------------------------cgggtcaaccc-ca--t--------------------------
B D          Naked mole-rat  ---------------------------agatccgggtc-ca--g--------------------------
B D              Guinea pig  ---------------------------gtgtccaggtt-ca--g--------------------------
                 Chinchilla  ---------------------------aggtccaggcc-ca--g--------------------------
           Brush-tailed rat  ---------------------------aagtccaggcc-ca--g--------------------------
B D                  Rabbit  ---------------------------cgggtcttccc-cg--ggcgcgggg-------cgcgca-----
B D                     Pig  ---------------------------taggtcgctcc-cc--g-------g-------cgacca-----
B D                 Dolphin  ----------------------------------------g--g-------g-------cgccca-----
               Killer whale  ----------------------------------------g--g-------g-------cgccca-----
           Tibetan antelope  ----------------------------------------g--g-------g-------cgccca-----
B D                     Cow  ----------------------------------------g--g-------g-------cgccca-----
B D                   Sheep  ----------------------------------------g--g-------g-------cgcaca-----
              Domestic goat  ----------------------------------------g--g-------g-------cgccca-----
B D                   Horse  ---------------------------taggtcgttcc-c---g-------g-------cgccca-----
B D        White rhinoceros  ---------------------------taggtcgttcc-tg--g-------g-------cgcccg-----
B D                     Cat  ----------------------------------------------------------------------
B D                     Dog  ----------------------------------------------------------------------
B D                 Ferret   ---------------------------tgactcgtctt-cc--g-------g-------cgccca-----
B D                   Panda  ---------------------------tggggtgtccc-cc--a-------g-------cgccca-----
             Pacific walrus  ---------------------------tgggttgtccc-cc--g-------g-------cgccca-----
               Weddell seal  ---------------------------tgggttgtccc-cc--g-------g-------cgccca-----
B D                 Megabat  -----------------------------ggaa--------------------------cgctga-----
              Big brown bat  -----------------------------ggtcgccct-cg--t-------c-------gaccag-----
B D                Microbat  ---------------------------ccggccgcact-cg--c-------cctgcgcacacccg-----
B D                Elephant  ---------------------------taggtcgtttc-ccaga-------g-------agtcca-----
B D                 Manatee  ---------------------------taggtcgtttt-cc--a-------g-------cgtcca-----
           Cape golden mole  ---------------------------tcg-----tcc-cc--g-------g-------cgtcca-----
B D                  Tenrec  ---------------------------tgg-----tcc-cc--g-------g-------gaacca-----
                   Aardvark  ---------------------------tca----tttc-cc--g-------a-------ggtcca-----
B D               Armadillo  ---------------------------------------ca--g-------g-------cgccca-----
B D         Tasmanian devil  ---------------------------ggagacttccc-cg--g-------gttcggggttctca-----
B D             Zebra finch  tcggtcctggcatcactggca-ccaacatgtgaggtgc-ca--g-------g-------attgcacccaa
B D                 Chicken  acg---cggctctccccagc-----------------c-cg--g-------c-------cctgcccgctc
B D      American alligator  cca---ccgctcccccccttg-tacccaggtgtgtcccgca--a-------g-------cgtgcact---
  D         Green seaturtle  gca---gggat---cccaggg------aaggcagcctg-aa--g-------g-------cggccaca---
  D          Painted turtle  gca---aggacttgcccagggtcccacgggggagccag-ga--g-------c-------cga--gct---
B D                    Pika  ======================================================================
            Bactrian camel  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D                Platypus  ======================================================================
          Black flying-fox  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
      David's myotis (bat)  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D                  Alpaca  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

                      Human  ggt----------tcccc-----------t--cccc-agccc-----g-----------------ga---
                      Chimp  ggt----------tcccc-----------t--cccc-agccc-----c-----------------ga---
                    Gorilla  ggt----------tcccc-----------t--cccc-agccc-----g-----------------ga---
                  Orangutan  ggt----------tcccc-----------t--cccc-agccc-----g-----------------ga---
                     Gibbon  ggt----------tcccc-----------t--cccc-agccc-----g-----------------ga---
                     Rhesus  ggt----------tcccc-----------t--cccc-agccc-----g-----------------ga---
        Crab-eating macaque  ggt----------tcccc-----------t--cccc-agccc-----g-----------------ga---
                     Baboon  ggt----------tcccc-----------t--cccc-agccc-----g-----------------ga---
               Green monkey  gat----------tcccc-----------t--cccc-agccc-----g-----------------ga---
                   Marmoset  ggt----------tcccc-----------t--gccc-agccc-----------------------ga---
            Squirrel monkey  agt----------gcccc-----------t--ttcc-agccc-----------------------ga---
                   Bushbaby  agt------------ctc-----------c--tccc-aaccc-----t-----------------gt---
         Chinese tree shrew  agc----------cggga-----------t--cccg-agcccag---g-----------------aa---
                   Squirrel  ggt----------tcccc-----------t--tcca-agccc-----a-----------------ga---
     Lesser Egyptian jerboa  ggt----------cccct-----------t--tccgtggccg-----g-----------------ga---
               Prairie vole  --t----------tcacc-----------t--ccca-ggcag-----g-----------------ga---
            Chinese hamster  --t----------tcccc-----------t--ccca-ggccc-----g-----------------ga---
             Golden hamster  --t----------tcccc-----------t--ccca-gaccc-----g-----------------ga---
                      Mouse  --t----------tcctt-----------t--tct-----------------------------------
                        Rat  --t----------tcctt-----------t--tct-----------------------------------
             Naked mole-rat  --g----------acccc-----------c-------agcct-----g-----------------ga---
                 Guinea pig  --g----------atccc-----------t-------gacct-----g-----------------ga---
                 Chinchilla  --g----------acccc-----------c-------cgccg-----g-----------------aa---
           Brush-tailed rat  --g----------ccccc-----------c--g----agtct-----a-----------------aa---
                     Rabbit  ggg----------gctcc-----------t--cccg-agccc-----g-----------------ga---
                        Pig  ggt----------cctcc-----------g--cgga-gccca-----g-----------------gc---
                    Dolphin  ggg----------tctct-----------c--tcgc-gctct-----g-----------------ga---
               Killer whale  ggg----------cctcc-----------c--tcgc-gccct-----g-----------------ga---
           Tibetan antelope  ggt----------actcc-----------c--ttgc-tcccg-----c-----------------ga---
                        Cow  ggt----------ccttc-----------c--ttgc-tcccg-----g-----------------ga---
                      Sheep  gga----------actcc-----------c--ttgc-tcccg-----c-----------------gc---
              Domestic goat  ggt----------actcc-----------c--ttgc-tcccg-----c-----------------ga---
                      Horse  ggt----------cctcc-----------ctctcgc-gcccg-----g-----------------ga---
           White rhinoceros  cgt----------cttcc-----------ctctcgc-gcccg-----g-----------------ga---
                        Cat  --------------------------------tcgc-gcctg-----g-----------------ga---
                        Dog  --------------------------------tcac-gt-------------------------------
                    Ferret   ga-----------ccttc-----------cttttgc-gcccg-----g-----------------ga---
                      Panda  gat----------ccttc-----------ctttcgc-gcctg-----g-----------------ga---
             Pacific walrus  gat----------ccttc-----------ctttcgc-gcccg-----c-----------------ga---
               Weddell seal  gat----------ccttc-----------ctttcgc-gcccg-----g-----------------ga---
                    Megabat  ggt-----------cgct-----------cctcggc-gccca-----------------------ggtcc
              Big brown bat  gtt-----------ctcc-----------ctcctgc-gcccg-----g-----------------gatcc
                   Microbat  gctccacctgccgcctcc-----------ccaccgc-gcacg-----ggtcgccctcgcaggccagattc
                   Elephant  ggt----------cccacaaccgggac--c--ctgc-gtccc-----g-----------------ga---
                    Manatee  ggt----------cccacaaccaggat--c--ccgc-gccac-----g-----------------ga---
           Cape golden mole  gga----------cctgcaacccggac--c--cggc-tcccc-----a-----------------ga---
                     Tenrec  ggt----------cccggcacccagactgc--aggg-accctgagcag-----------------ga---
                   Aardvark  ggc----------cctgcaacctgaac--c--cact-gccct-----g-----------------ga---
                  Armadillo  ggg----------accccagcc-ggct--c--cggg-atccc-----g-----------------gg---
            Tasmanian devil  ggt----------ttccg-----------t--cgcc-ggccc-----t-----------------ga---
                Zebra finch  ggc----------a--------------------------------------------------------
                    Chicken  ggg----------a--------------------------------------------------------
         American alligator  ggc----------a--------------------------------------------------------
            Green seaturtle  ggg----------a--------------------------------------------------------
             Painted turtle  ggg----------a--------------------------------------------------------
                       Pika  ======================================================================
             Bactrian camel  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
                   Platypus  ======================================================================
           Black flying-fox  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
       David's myotis (bat)  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
                     Alpaca  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

                      Human  -------------------ccccg-a------------gc---cggga
                      Chimp  -------------------ccccg-a------------gc---cggga
                    Gorilla  -------------------ccccg-a------------gc---cggga
                  Orangutan  -------------------cccca-a------------gc---cggga
                     Gibbon  -------------------ccccg-a------------tc---ccgga
                     Rhesus  -------------------ccccg-a------------gc---cggga
        Crab-eating macaque  -------------------ccccg-a------------gc---cggga
                     Baboon  -------------------ccccg-a------------gc---cggga
               Green monkey  -------------------ccccg-a------------gc---cggga
                   Marmoset  -------------------ccccg-c------------gc---aggga
            Squirrel monkey  -------------------ccccg-c------------gc---aggga
                   Bushbaby  -------------------aagcg-c------------gc---cagga
         Chinese tree shrew  -------------------gcccg-c------------ac---aagaa
                   Squirrel  -------------------cccgg-c------------gc---tcaga
     Lesser Egyptian jerboa  -----a------------ccccgg-c------------gt--------
               Prairie vole  -------------------cccag-t------------gt---ggaga
            Chinese hamster  -------------------cccag-tgcg---------gc---ggaga
             Golden hamster  -------------------cccag-t------------gc---ggaga
                      Mouse  -----------------------g-t------------gc---cggga
                        Rat  -----------------------g-t------------gc---cggga
             Naked mole-rat  -----gccgc--------cctcggag------------ac---ccagg
                 Guinea pig  -----tccg---------actggg-g------------ac---ccagc
                 Chinchilla  -----accac--------cctcgg-g------------ac---ccagc
           Brush-tailed rat  -----actgc--------cctcag-g------------ac---ccagc
                     Rabbit  -----gccacgct-----gcccgg-a------------cc---ccagc
                        Pig  -----cccccggccccagccctgg-c------------ac---cgaac
                    Dolphin  -----tccctagctcccgtcctcg-c-----cctccgacc---agaga
               Killer whale  -----cccccagcccccgcccccg-tccccgcccccgccc---agaga
           Tibetan antelope  -----tctccagc-------------------------ac---agaga
                        Cow  -----tctccagc-------------------------ac---agaga
                      Sheep  -----tctccagc-------------------------ac---agaga
              Domestic goat  -----tctccagc-------------------------ac---agaga
                      Horse  -----ccctcacc-ccggaccccg-c------------ac---agaga
           White rhinoceros  -----cgcgcacc-ctggaccccg-c------------ac---agaga
                        Cat  -----cccgcgcc-ccagactccg-c------------cg---ggaga
                        Dog  ------------------------------------------------
                    Ferret   -----cccgcacg-ccagactc-g-c------------ac---ggaga
                      Panda  -----cccgcacc-ccagactccg-c------------ac---ggaga
             Pacific walrus  -----cccgcacc-gcagactcgg-c------------ac---ggaga
               Weddell seal  -----cccgcacc-ccagactcgg-c------------ac---ggaga
                    Megabat  cccttcttgcgcc-cgggaccccg-c------------gc--------
              Big brown bat  cgcaccccgcacc-ccgcaccccg-c------------ac--------
                   Microbat  tccctcctgcgcc-cgggaccccg-c------------ag--------
                   Elephant  ------------------cctggg-g------------ac---tgaag
                    Manatee  ------------------tctccg-g------------ac---cgaga
           Cape golden mole  ------------------cctgga-g------------ac---agaga
                     Tenrec  ------------------gctggg-g------------accgaggagg
                   Aardvark  ------------------cctggg-g------------at---agaga
                  Armadillo  ------------------cccgag-a------------gc---cgtgg
            Tasmanian devil  -------------------ccccg-t------------gc-tttggga
                Zebra finch  ------------------------------------------------
                    Chicken  ------------------------------------------------
         American alligator  ------------------------------------------------
            Green seaturtle  ------------------------------------------------
             Painted turtle  ------------------------------------------------
                       Pika  ================================================
             Bactrian camel  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
                   Platypus  ================================================
           Black flying-fox  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
       David's myotis (bat)  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
                     Alpaca  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

Inserts between block 8 and 9 in window
B D                 Rabbit 1bp
  D        Green seaturtle 10bp

Alignment block 9 of 54 in window, 41508059 - 41508100, 42 bps 
B D                   Human  ccc------tg------g-----------ta--ccg--------------------------gcgc---c
B D                   Chimp  ccc------tg------g-----------ta--ccg--------------------------gcgc---c
B D                 Gorilla  ccc------tg------g-----------ta--ccg--------------------------gcgc---c
B D               Orangutan  ccc------tg------g-----------ta--ccg--------------------------gcgc---c
B D                  Gibbon  ccc------tg------g-----------ta--ccg--------------------------gcgc---c
B D                  Rhesus  ccc------cg------g-----------ta--cag--------------------------gcgc---c
B D     Crab-eating macaque  ccc------cg------g-----------ta--cag--------------------------gcgc---c
B D                  Baboon  ccc------cg------g-----------ta--cag--------------------------gcgc---c
B D            Green monkey  ccc------gg------g-----------ta--cag--------------------------gcgc---c
B D                Marmoset  ccc------cg------g-----------ca--cac--------------------------acgc---c
B D         Squirrel monkey  ccc------cg------g-----------ca--cgc--------------------------gcgc---c
B D                Bushbaby  ccc------gg------g-----------cc--cggcgag------------caggtcgcgcgcgc---c
         Chinese tree shrew  --c------gg------g-----------tc--ccg-------------------------cgcgc---t
B D                Squirrel  ccc------cgcagagcg----gtgcgt-ct--tga--------------------------g-gc---c
     Lesser Egyptian jerboa  -cc------cg------a----gcgcgt-cctgggc--------------------------gcgc---c
               Prairie vole  cca------cg------a----gcttgt-cc--cgc--------------------------ctgc---t
B D         Chinese hamster  cca------cg------a----gcttct--c--agc--------------------------ctgc---t
             Golden hamster  cca------cg------a----gcttct-cc--cgc--------------------------ctgc---t
B D                   Mouse  -cc------gg------a----gcttgt-ca--ggc--------------------------gcgc---t
B D                     Rat  ccc------cg------a----ccttgt-cc--ggc--------------------------gcgc---t
B D          Naked mole-rat  cag------ag------c----gcaagcttg--cgc--------------------------tggcctgc
B D              Guinea pig  cat------ca------a----gggcac-ca--tgc--------------------------tcacctgt
                 Chinchilla  cag------ag------c----gcacgc-tg--ggc--------------------------tcacctgt
           Brush-tailed rat  cag------ag------c----gcacgc-tg--tgc--------------------------tcacttgt
B D                  Rabbit  ccg------gg------a----gcgggt-cg--cgc--------------------------gcgc---c
B D                     Pig  acc------cg------g-----------cc--cgc--------------------------gcgc---c
B D                 Dolphin  gcc------ca------c-----------cg--cgc--------------------------gcgc---t
               Killer whale  gcc------ca------c-----------cg--cgc--------------------------gcgc---c
           Tibetan antelope  acc------cg------t-----------cg--cgc--------------------------gagc---c
B D                     Cow  acc------cg------t-----------cg--cgc--------------------------gagc---c
B D                   Sheep  acc------cg------t-----------cg--cgc--------------------------gagc---c
              Domestic goat  a-c------cg------t-----------cg--cgc--------------------------gagc---c
B D                   Horse  acc------gg------c-----------cg--c----------------------------gcgc---c
B D        White rhinoceros  acc------gg------c-----------cg--c----------------------------gcgc---c
B D                     Cat  ccc------gg------c-----------cg---gc--------------------------gcgc---c
B D                     Dog  -cc------ag------c-----------cg--cgc--------------------------gcgc---c
B D                 Ferret   acc------gg------c-----------gg--cgc--------------------------gcgc---g
B D                   Panda  acc------gg------c-----------cg--cgc--------------------------gcgc---c
             Pacific walrus  acc------gg------c-----------ag--cga--------------------------gcgc---g
               Weddell seal  acc------gg------c-----------ag--c----------------------------gcgc---g
B D                 Megabat  -cccgggcgcg------c-----------ac--g----------------------------gtgc---c
              Big brown bat  -cc------cg------c-----------ac--a----------------------------ggga---c
B D                Microbat  -cc------cg------c-----------ag--t----------------------------ccgc---a
B D                Elephant  gca------gg------c-----------cg--ctc--------------------------gcgc---c
B D                 Manatee  gcg------ag------c-----------cg--ccc--------------------------gcgt---c
           Cape golden mole  gct------gg------c-----------tg--cca--------------------------gtag---c
B D                  Tenrec  aac------cg------c-----------cg--ccg--------------------------gcgc---c
                   Aardvark  gcg------ag------c-----------ct--cca--------------------------acac---c
B D               Armadillo  ----------------------------------cc--------------------------gcgc---c
B D         Tasmanian devil  tcc------gg------ccttcgcaggc-cc--cgg--------------------------gagg---c
B D             Zebra finch  ------------------------------------catgtgctgttgtgtcc---cctgccacgt---g
B D                 Chicken  ------------------------------------cgcctccaggcgcttctcggcctccctcac---a
B D      American alligator  ------------------------------------cctgcgcgggcacctgccagctgggagcac---g
  D         Green seaturtle  --------------------------------------------------------------ccag---c
  D          Painted turtle  --------------------------------------------------------------acac---g
B D                    Pika  ======================================================================
            Bactrian camel  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D                Platypus  ======================================================================
          Black flying-fox  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
      David's myotis (bat)  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D                  Alpaca  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

                      Human  gctcacc-----------t-------gccgcgc-----------tcca---------gg----------c
                      Chimp  gctcacc-----------t-------gccgcgc-----------tcca---------gg----------c
                    Gorilla  gctcacc-----------t-------gccgcgc-----------tcca---------gg----------c
                  Orangutan  gctcacc-----------t-------gccgcgc-----------tcca---------gg----------c
                     Gibbon  gctcacc-----------t-------gccgcgc-----------tcca---------gg----------c
                     Rhesus  gctcacc-----------t-------gccgagc-----------tccg---------gg----------c
        Crab-eating macaque  gctcacc-----------t-------gccgagc-----------tccg---------gg----------c
                     Baboon  gctcacc-----------t-------gccgagc-----------tccg---------gg----------c
               Green monkey  gctcacc-----------t-------gccgagc-----------tccg---------gg----------c
                   Marmoset  gctcacc-----------t-------gcc-----------------------------------------
            Squirrel monkey  gctcacc-----------t-------gccgcgc-----------tcc----------gg----------c
                   Bushbaby  gctcacc-----------t-------gt--ggc-----------tccc---------gg-----------
         Chinese tree shrew  gcttacc-----------t-------gcctcgc-----------tccc---------gg----------c
                   Squirrel  acttacc-----------t-------gccgcgc-----------tcgg----------------------
     Lesser Egyptian jerboa  gctcacc-----------t-------gcctagc-----------gc------------------------
               Prairie vole  gctcacc-----------t-------gctg----------------------------------------
            Chinese hamster  gctcacc-----------t-------gctg----------------------------------------
             Golden hamster  gctcacc-----------t-------gctg----------------------------------------
                      Mouse  actcacc-----------t-------gttg----------------------------------------
                        Rat  gctcacc-----------t-------gctg----------------------------------------
             Naked mole-rat  gctcgcc-----------tgcgggcacctg----------------------------------------
                 Guinea pig  g-----c-----------tgtggg--actg----------------------------------------
                 Chinchilla  actcacc-----------tgtggc--actg----------------------------------------
           Brush-tailed rat  gctcacc-----------tgcgat--gtga----------------------------------------
                     Rabbit  gcttacc-----------t-------ggcgcgc-----------tcgg---------gg----------c
                        Pig  gcttacc-----------t-------gccgcgc-----------tccg---------gg--------tcc
                    Dolphin  gctcacc-----------t-------gcggtgc-----------tcgg---------gg---gc---tct
               Killer whale  gctcacc-----------t-------gcggtgc-----------tcgg---------gg--------ccc
           Tibetan antelope  acttacc-----------t-------gctgccc-----------tccg---------gg---gcag-ctc
                        Cow  acttacc-----------t-------gctgccc-----------tccg---------gg---gcag-ctc
                      Sheep  acttacc-----------t-------gctgccc-----------tccg---------gg---gcag-ctc
              Domestic goat  acttacc-----------t-------gctgccc-----------tccg---------gg---gcag-ctc
                      Horse  gcttacc-----------t-------gcagcac-----------tccg---------gg---g----cct
           White rhinoceros  gcttacc-----------t-------gcggcgc-----------tccg---------gg---g----tcg
                        Cat  gctcacc-----------t-------gcggggc-----------tccc---------c----g----ccc
                        Dog  gctcacc-----------t-------gcggggc-----------tc----------------g----gcc
                    Ferret   acttacc-----------c-------gaggggc-----------tccc---------gg---g----ccg
                      Panda  gcttacc-----------t-------gc----g-----------tccg---------ga---g----ccc
             Pacific walrus  gcttacc-----------t-------gccgggc-----------tcct---------gg---g----ccc
               Weddell seal  gctcacc-----------t-------gccgggc-----------tccg---------gg---g----ccc
                    Megabat  gctcacc-----------t-------gcgcctc-----------tctg----------g---g----c-c
              Big brown bat  gctcacc-----------t-------gccgcac-----------cctg----------g---g----ctc
                   Microbat  gcccgca-----------c-------cccgcacagggacgctcacctgccgcacgcggg---g----ccc
                   Elephant  gcttacc-----------t-------gtcgccc-----------tccg---------ggtctgtcgccgc
                    Manatee  gcttact-----------t-------gcagcgc-----------tccg---------ggtaggtcgcagt
           Cape golden mole  tcttacc-----------t-------gctgcac-----------tcgg--------------atcgccac
                     Tenrec  gcttacc-----------t-------gccgcgc-----------tcgg--------------gccgccac
                   Aardvark  acttacc-----------t-------gctgcac-----------tctg---------g----gctgccga
                  Armadillo  gcctacc-----------t-------gccgcgc-----------cgcg---------gg---gccgc---
            Tasmanian devil  ctaaaac-----------c-------ccagttc-----------tctc----------------------
                Zebra finch  ----cca-----------c-------gctgca--------------------------------------
                    Chicken  ----cca-----------g-------gctcgg--------------------------------------
         American alligator  gc-ccca-----------g-------actggc--------------------------------------
            Green seaturtle  gt-ccca----------gg-------gcagag--------------------------------------
             Painted turtle  gc-cccatgggcctggcgg-------gcagag--------------------------------------
                       Pika  ======================================================================
             Bactrian camel  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
                   Platypus  ======================================================================
           Black flying-fox  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
       David's myotis (bat)  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
                     Alpaca  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

                      Human  gg-c-g
                      Chimp  gg-c-g
                    Gorilla  gg-c-g
                  Orangutan  gg-c-g
                     Gibbon  gg-c-g
                     Rhesus  gg-c-g
        Crab-eating macaque  gg-c-g
                     Baboon  gg-c-g
               Green monkey  gg-c-g
                   Marmoset  -g-c-g
            Squirrel monkey  gg-c-g
                   Bushbaby  -----g
         Chinese tree shrew  cg-ctg
                   Squirrel  ccgc-g
     Lesser Egyptian jerboa  ---c-g
               Prairie vole  ---c-g
            Chinese hamster  ---c-g
             Golden hamster  ---t-g
                      Mouse  ---c-g
                        Rat  ---t-g
             Naked mole-rat  ---c-a
                 Guinea pig  ---c-g
                 Chinchilla  ---c-g
           Brush-tailed rat  ---c-g
                     Rabbit  cggc-g
                        Pig  cg-c-g
                    Dolphin  gg-c-g
               Killer whale  gg-c-g
           Tibetan antelope  cc-t-t
                        Cow  cc-c-t
                      Sheep  cc-c-t
              Domestic goat  cc-c-t
                      Horse  gg-c-g
           White rhinoceros  ga-c-g
                        Cat  gg-c-g
                        Dog  gg-c-g
                    Ferret   gg-c-g
                      Panda  gg-c-g
             Pacific walrus  gg-c-g
               Weddell seal  gg-c-g
                    Megabat  gg-c-g
              Big brown bat  gg-c-g
                   Microbat  gg-c-g
                   Elephant  gg-c-g
                    Manatee  gg-c-g
           Cape golden mole  gg-c-g
                     Tenrec  gg-c-g
                   Aardvark  gg-t-g
                  Armadillo  -----g
            Tasmanian devil  ------
                Zebra finch  ------
                    Chicken  ------
         American alligator  ------
            Green seaturtle  ------
             Painted turtle  ------
                       Pika  ======
             Bactrian camel  NNNNNN
                   Platypus  ======
           Black flying-fox  NNNNNN
       David's myotis (bat)  NNNNNN
                     Alpaca  NNNNNN

Inserts between block 9 and 10 in window
B D            Zebra finch 3bp
B D                Chicken 3bp
B D     American alligator 3bp
  D        Green seaturtle 80bp
  D         Painted turtle 43bp

Alignment block 10 of 54 in window, 41508101 - 41508115, 15 bps 
B D                   Human  ctccccgc---ccc------------------t-cg---------c----------
B D                   Chimp  ctccccgc---ccc------------------t-cg---------c----------
B D                 Gorilla  ctccccgc---ccc------------------t-cg---------c----------
B D               Orangutan  ctccccgc---ccc------------------t-cg---------c----------
B D                  Gibbon  ctccccgc---ccc------------------t-tg---------c----------
B D                  Rhesus  ctccccgc---ccc------------------t-tg---------c----------
B D     Crab-eating macaque  ctccccgc---ccc------------------t-tg---------c----------
B D                  Baboon  ctccccgc---ccc------------------t-tg---------c----------
B D            Green monkey  ctccccgc---ccc------------------t-tg---------c----------
B D                Marmoset  ctccccgc---ccc------------------t-cg---------c----------
B D         Squirrel monkey  ctccccgc---ccc------------------t-cg---------c----------
B D                Bushbaby  cctcctac---tgc------------------t-ct---------c----------
         Chinese tree shrew  ctcccagc---ccc------------------tccg---------c----------
B D                Squirrel  ctccccgc---ccctccgccttcctccgcgcgt-ct---------t----------
     Lesser Egyptian jerboa  cccctcgccttcct------------------c-ct---------c----------
               Prairie vole  cttcccgc---ccc------------------t-ct---------c----------
B D         Chinese hamster  ctccctggc--ccc------------------t-ct---------c----------
             Golden hamster  ctccccgg---ctc------------------t-ct---------c----------
B D                   Mouse  cttcccgc---ccc------------------t-ct---------c----------
B D                     Rat  ctccccgc---ccc------------------t-ct---------c----------
B D          Naked mole-rat  ctcacctg---cgc------------------t-gc---------t----------
B D              Guinea pig  ctcccagc---cac------------------c-gc---------c----------
                 Chinchilla  ctccccgc---cgc------------------c-ac---------c----------
           Brush-tailed rat  -----tgt---cg-------------------------------------------
B D                  Rabbit  ctccccgc---cccttgcccttcct-------c-ct---------c----------
B D                     Pig  ctccccgc---ccc------------------t-cg---------c----------
B D                 Dolphin  ctctccgc---ccc------------------t-tc---------t----------
               Killer whale  ctccccgc---ccc--------------------tc---------t----------
           Tibetan antelope  cccctcac---ccc------------------t-tc---------t----------
B D                     Cow  cccctcgc---ccc------------------t-tc---------t----------
B D                   Sheep  cccctcac---ccc------------------t-tc---------t----------
              Domestic goat  cccctcag---ccc------------------t-tc---------t----------
B D                   Horse  ctccccgc---tcc------------------t-cg---------c----------
B D        White rhinoceros  cttcccgc---ctc------------------t-cg---------c----------
B D                     Cat  ctctccgc---ccc------------------t-ggctcgtcctcc----------
B D                     Dog  ctccccgc---ccc------------------t-cg---------c----------
B D                 Ferret   ctctccgc---ccc------------------t-tg---------c----------
B D                   Panda  ctctccgc---ccc------------------t-tg---------c----------
             Pacific walrus  ttctccgc---ccc------------------t-tg---------c----------
               Weddell seal  ctctccgc---ccc------------------t-tg---------c----------
B D                 Megabat  c-ccccgt---ccc------------------t-cg---------c----------
              Big brown bat  c-ccccgc---ccc------------------t-cg---------c----------
B D                Microbat  c-ccccgc---ccc------------------t-cg---------c----------
B D                Elephant  ctcaccgc---cgg------------------g-cg---------c----------
B D                 Manatee  ctccgggc---cct------------------g-cg---------c----------
           Cape golden mole  ctctccgc---ccc------------------t-cg---------c----------
B D                  Tenrec  ctcgccgc---ccc------------------g-gg---------t----------
                   Aardvark  ctccctgc---cgc------------------t-cg---------c----------
B D               Armadillo  ctcccgcc---cct------------------c-cg---------c----------
B D             Zebra finch  -------------t------------------c-ct---------c----------
B D                 Chicken  -------------g------------------c-cg---------cgggga-----
B D      American alligator  -------------c------------------t-gc---------cggggaaaacc
  D          Painted turtle  -------------c------------------t-gt---------ccgtgcaaccc
B D                    Pika  ========================================================
  D         Green seaturtle  ========================================================
B D         Tasmanian devil  --------------------------------------------------------
            Bactrian camel  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D                Platypus  ========================================================
          Black flying-fox  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
      David's myotis (bat)  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D                  Alpaca  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

Inserts between block 10 and 11 in window
B D                Dolphin 1bp
              Killer whale 1bp
          Tibetan antelope 1bp
B D                    Cow 1bp
B D                  Sheep 1bp
             Domestic goat 1bp
B D                  Horse 4bp
B D       White rhinoceros 7bp
B D                    Cat 4bp
B D                    Dog 4bp
B D                Ferret  4bp
B D                  Panda 4bp
            Pacific walrus 4bp
              Weddell seal 4bp
B D                Megabat 4bp
             Big brown bat 3bp
B D               Microbat 4bp
B D               Elephant 1bp
B D                Manatee 1bp
          Cape golden mole 1bp
B D                 Tenrec 1bp
                  Aardvark 1bp
B D              Armadillo 1bp

Alignment block 11 of 54 in window, 41508116 - 41508163, 48 bps 
B D                   Human  cctc-cgc--c--tccg-c-----------ct-----c---cgcctcctgcttagctcgc-g-c------
B D                   Chimp  -------c--c--tccg-c-----------ct-----c---cgcctcctgcttagctcgc-g-c------
B D                 Gorilla  -------c--c--tcct-c-----------ct-----c---cgcctccggcttagctcgc-g-c------
B D               Orangutan  -------c--c--tcgt-c-----------ct-----c---cgcctcctgcttggctcgc-g-c------
B D                  Gibbon  -------c--c--tcct-c-----------cg-----c---cgccgcctgcttagctcgc-g-c------
B D                  Rhesus  -------c--c--t-----------------------------cctccgacttagctcgc-g-c------
B D     Crab-eating macaque  -------c--c--tcct-c-----------cg-----c---tgcctccggcttagctcgc-g-c------
B D                  Baboon  -------c--c--tcct-c-----------cg-----c---tgcctcctgcttagctcgc-g-c------
B D            Green monkey  -------c--c--tcct-c-----------cg-----c---tgcctcctgcttagctcgc-g-c------
B D                Marmoset  -------c--t--tcct-c-----------ct-----c---cgcctcctgcttggctcgc-g-c------
B D         Squirrel monkey  -------c--t--tcct-t-----------ct-----c---cgcctcctgcttggctcgc-g-c------
B D                Bushbaby  -------g--c--gtct-c-----------ct-----c---tgca--------ggcaccg-g-a------
         Chinese tree shrew  -------c--t--tcct-c-----------ct-----c---cgcctcctactgagctccc-gtc------
B D                Squirrel  -----cac--c--tccg-c-----------ctcccggg---aggtcgcgccttc-ctctg-c-c------
     Lesser Egyptian jerboa  -----ctc--c--tcct-c-----------ct-----c---ggccccagccggc-gtcgt-c-tggcggc
               Prairie vole  -----cgc--c--tggg-c-----------cc-----a---agctctggatttc-ctcgt-c-c------
B D         Chinese hamster  -----tgc--g--ggtg-c-----------cc-----a---aactccgggcttc-ctcct-c-c------
             Golden hamster  -----cgc--c--ggcg-c-----------cc-----a---agctctgggcttc-ctcct-c-c------
B D                   Mouse  -----cgc--c--tctg-t-----------cc-----g---agctcttggcttc-ctcgt-c-c------
B D                     Rat  -----cgc--c--tccg-c-----------cg-----g---ggctctcggtttc-cttgt-c-c------
B D          Naked mole-rat  -----gga--c--tggg-ctccagtccttacc-----g---cgtcc---------------c-t------
B D              Guinea pig  -----tgt--c--tgaa-c-----------ca-----g---cgtcc---------------c-t------
                 Chinchilla  -----tct--ctctgag-c-----------cc-----c----gtcc---------------c-t------
           Brush-tailed rat  -------------ggag-c-----------cc-----a---ggtac---------------t-t------
B D                  Rabbit  -----cgc--c--tcct-c-----------gg-----g---agctcgcgtcttc-ctcgc-c-c------
B D                     Pig  --tc-ttc--c--ttct-c-----------ct-----c---cgcctcctccgaagctcgc-ggc------
B D                  Alpaca  ---------------cc-t-----------cc-----c---cgcc-------gggttcgc-gtc------
B D                 Dolphin  cctt-tcttct--cctt-c-----------tt-----a---cgcctactt--------------------
               Killer whale  cctt-cct--c--ccct-c-----------tt-----c---cgcctcct---------------------
           Tibetan antelope  cctc-ttt--c--ttct-c-----------ct-----c---tgcctcctctggagttcgc-ttc------
B D                     Cow  cctc-ctc--c--ttct-c-----------ct-----c---cgcctcctctggagttcgc-tgc------
B D                   Sheep  cctc-ctc--c--ttct-c-----------ct-----c---tgcctcctctggagttcgc-ttc------
              Domestic goat  cctc-ctc--c--ttct-c-----------ct-----c---tgcctcctctggagttcgc-ttc------
B D                   Horse  cctc-ttc--c--ttct-c--tttctcctctt-----c---ggcctcttaccgagctcgc-gcc------
B D        White rhinoceros  cctc-ctc--c--tcct-c--tttctcctcct-----c---tgcctcctaccgagctcgc-gtc------
B D                     Cat  cctc-ctc--t--tcct-c-----cgcctcct-----c---ggcctcctgcggaactcgc-gtc------
B D                     Dog  cct--------------------------cct-----c---cgcctcccgcggcgct--c-ggc------
B D                 Ferret   cctc-ctc--c--gccg-c-----cgccgcct-----c---ccccgccccc---gct--c-gtc------
B D                   Panda  cctc-ctc--t--tcct-c-----cgcctcct-----c---ctcctcccgccgagct--c-gtc------
             Pacific walrus  cctc-ctc--t--tcct-c-----cacctcct-----c---cgcctcctgcggagct--c-gtc------
               Weddell seal  cctc-ttc--t--tcct-c-----cacctcct-----c---cgcctcctgcggagct--c-gtc------
B D                 Megabat  cctc-tgc--c--gccgcc-----------------------gcctccttccgagctcgc-gtc------
              Big brown bat  cctc-ctg--c--tcca-c-----------------------gcctcccacggagctcgt-gtc------
B D                Microbat  cctc-ctg--c--tcca-c-----------------------gcctcccacggagctcgt-gcc------
B D                Elephant  ctgc-ctc--c--ttct-c-----------ct-----c---ctcctct-----gctcaat-t-c------
B D                 Manatee  ctgt-ttc--c--tcct-c-----------ct-----c---cgcctttttcaagctcccg-t-c------
           Cape golden mole  tagc-ctc--c--tcct-c-----------ct-----c---cgcttccttccgaggccct-t-c------
B D                  Tenrec  cggc-ctg--c--gcct-c------------------------gtgccctccgagcccct-t-g------
                   Aardvark  ctgc-ctc--c--gcct-c-----------ct-----ccttcgcttccttttgagcttcc-t-t------
B D               Armadillo  ctgcgccg--c--cgcc-c-----------gg-----c---cacctcccgccgagtccccgt-c------
B D         Tasmanian devil  ------------------------------------------catttccccttagctccg-c-c------
B D             Zebra finch  -------------------------------t-----c---agcatctcacca-----tg-c-c------
B D                 Chicken  -------------------------------g-----c---agcgcttcaccgccatccg-c-c------
B D      American alligator  -----------------------------cca-----c---agcgactggctg-----------------
  D          Painted turtle  -----------------------------cct-----c---gataccccccag-gtcctg-c-c------
B D                    Pika  ======================================================================
  D         Green seaturtle  ======================================================================
            Bactrian camel  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D                Platypus  ======================================================================
          Black flying-fox  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
      David's myotis (bat)  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

                      Human  ----ctact-----cgg-c-cc-----------
                      Chimp  ----ctact-----cgg-c-cc-----------
                    Gorilla  ----ctact-----cgg-c-cc-----------
                  Orangutan  ----ctact-----cgg-c-cc-----------
                     Gibbon  ----ctact-----cgg-c-cc-----------
                     Rhesus  ----cttct-----cga-c-cc-----------
        Crab-eating macaque  ----cttct-----cga-c-cc-----------
                     Baboon  ----cttct-----cta-c-cc-----------
               Green monkey  ----cttct-----cga-c-cg-----------
                   Marmoset  ----cttct-----cgg-c-cc-----------
            Squirrel monkey  ----cttcc-----cgg-c-tc-----------
                   Bushbaby  ----gtccc-----caa-c-ct-----------
         Chinese tree shrew  ----ctcct-----agg-c-cg-----------
                   Squirrel  -cggcgctc-----aag-t-cc-----------
     Lesser Egyptian jerboa  cagggcccc-----agt-c-tc-----------
               Prairie vole  ----gtccc-----aag-tccc-----------
            Chinese hamster  ----gcccc-----aag-t-cc-----------
             Golden hamster  ----gcccc-----aag-t-cc-----------
                      Mouse  ----gctcc-----aag-t-ac-----------
                        Rat  ----actcc-----aag-t-ac-----------
             Naked mole-rat  ----gtccc-----agg-c--------------
                 Guinea pig  ----ctccc-----agg-c--------------
                 Chinchilla  ----ctggc-----agg-c--------------
           Brush-tailed rat  ----ctccc-----agg-c--------------
                     Rabbit  ----ggcgccgccgaag-c-tc-----------
                        Pig  ----ttcct-----cgg-c-cc-----------
                     Alpaca  ----ttcct-----ctg-c-cc-----------
                    Dolphin  ---------------------------------
               Killer whale  ---------------------------------
           Tibetan antelope  ----ttcct-----cgg-c-cc-----------
                        Cow  ----ttcct-----cgg-c-cc-----------
                      Sheep  ----ttcct-----cgg-c-cc-----------
              Domestic goat  ----ttcct-----cgg-c-cc-----------
                      Horse  ----ttcct-----cttcc-cc-----------
           White rhinoceros  ----ttcct-----ctg-c-cc-----------
                        Cat  ----ttcct-----ctg-t-cc-----------
                        Dog  ----ttcct-----cgg-c-cc-----------
                    Ferret   ----ttcct-----cgg-c-cc-----------
                      Panda  ----ttcct-----ctg-t-cc-----------
             Pacific walrus  ----ttcct-----ctg-c-cc-----------
               Weddell seal  ----ttccc-----ctg-c-cc-----------
                    Megabat  ----tccct-----ctg-c-cc-----------
              Big brown bat  ----ctccg-----aga-t-cg-----------
                   Microbat  ----ctcct-----cga-t-cc-----------
                   Elephant  ----ttcct-----caa-g-ct-----------
                    Manatee  ----ttcct-----cga-c-cc-----------
           Cape golden mole  ----ttcctc----cag-c-ca-----------
                     Tenrec  ----tccct-----cgg-c-cc-----------
                   Aardvark  ----ctcct-----ccg-c-cc-----------
                  Armadillo  ----ctccg-----ccg-c-cc-----------
            Tasmanian devil  ----cctct-----cac-c-gc-----------
                Zebra finch  ----agcct-----tgg-c-cctgc--------
                    Chicken  ----gaacc-----cgg-c-cccgcgcgggccc
         American alligator  --------c-----tgg-t-gctgg-ggggctg
             Painted turtle  ----cactc-----tgc-a-cctcc-agtgcct
                       Pika  =================================
            Green seaturtle  =================================
             Bactrian camel  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
                   Platypus  =================================
           Black flying-fox  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
       David's myotis (bat)  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

Inserts between block 11 and 12 in window
B D               Marmoset 14bp
B D        Squirrel monkey 14bp
        Chinese tree shrew 15bp
B D               Squirrel 2bp
    Lesser Egyptian jerboa 2bp
              Prairie vole 2bp
B D        Chinese hamster 2bp
            Golden hamster 2bp
B D                  Mouse 2bp
B D                    Rat 2bp
B D         Naked mole-rat 1bp
B D             Guinea pig 1bp
                Chinchilla 1bp
          Brush-tailed rat 1bp
B D                 Rabbit 2bp
B D                    Pig 13bp
B D                 Alpaca 14bp
B D                Dolphin 12bp
              Killer whale 11bp
          Tibetan antelope 14bp
B D                    Cow 14bp
B D                  Sheep 14bp
             Domestic goat 14bp
B D                  Horse 15bp
B D       White rhinoceros 15bp
B D                    Cat 4bp
B D                    Dog 4bp
B D                Ferret  14bp
B D                  Panda 15bp
            Pacific walrus 15bp
              Weddell seal 15bp
B D                Megabat 15bp
             Big brown bat 15bp
B D               Microbat 15bp
B D               Elephant 15bp
B D                Manatee 15bp
          Cape golden mole 14bp
B D                 Tenrec 18bp
                  Aardvark 14bp
B D              Armadillo 15bp
B D        Tasmanian devil 25bp
B D                Chicken 26bp
B D     American alligator 34bp
  D         Painted turtle 1bp

Alignment block 12 of 54 in window, 41508164 - 41508216, 53 bps 
B D                   Human  --ggccc--------g--ccct---gg----ctct-----cgctttaatctc-a---ggaggc-ggtgt-
B D                   Chimp  --ggccc--------g--ccct---gg----ctct-----cgctttaatctc-a---ggaggc-ggtgt-
B D                 Gorilla  --ggccc--------g--ccct---gg----ctct-----cgctttaatctc-a---ggaggc-ggtgt-
B D               Orangutan  --ggccg--------g--ccct---gg----ctct-----cgctttaatctc-a---ggaggc-ggtgt-
B D                  Gibbon  --ggccc--------g--ccct---gg----ctct-----cgctttaacctc-a---ggaggc-ggtgt-
B D                  Rhesus  ---gccg--------g--ccct---gg----ctct-----cactttaatctc-a---ggaggc-ggcgt-
B D     Crab-eating macaque  ---gccg--------g--ccct---gg----ctct-----cactttaatctc-a---ggaggc-ggcgt-
B D                  Baboon  ---gccg--------g--ccct---gg----ctct-----cactttaatctc-a---ggaggc-ggcgt-
B D            Green monkey  ---gccg--------g--ccct---gg----ctct-----cactttaatctc-a---ggaggc-ggcgt-
B D                Marmoset  --gacct--------g--ccct---gg----ctct-----cgcttaaatctc-a---ggaggc-ggcgt-
B D         Squirrel monkey  --gacct--------g--ccca---gg----ctct-----cgcttaaatctc-a---ggaggc-ggcgt-
B D                Bushbaby  ------------------tcct---ga----ctct-----cgcttttatttc-a---ggaggt-ggcgt-
         Chinese tree shrew  --cacct--------t--cccc---ag----ttct-----ctctttaatcaa-a---ggaggc-ggcgt-
B D                Squirrel  --ggcct--------t--cccc---ag----atct-----cgctttaatctc-a---ggaggc-ggtgtc
     Lesser Egyptian jerboa  --taatt--------t--ttct---gg----ctct-----cgctttaatctc-c---ggaggc-ggcgt-
               Prairie vole  --gacct--------c--cccc---ag----ctct-----tgcttaaatctc-c---ggaggc-ggcgt-
B D         Chinese hamster  --gacct--------t--cccc---ag----ctct-----cgcttaaatctc-c---ggaggc-ggcgt-
             Golden hamster  --gacct-------cc--cccc---ag----ctct-----cgcttaaatctc-c---ggaggt-ggcgt-
B D                   Mouse  --gacct--------a--ctcc---ag----ttct-----cgcttaaatctc-c---ggaggc-ggcgt-
B D                     Rat  --gacct--------a--ctcc---ag----ctct-----cgcttaaatctc-c---ggaggc-ggcgt-
B D          Naked mole-rat  --ggcca-----------ggcc---ag----agac-----agctttaacctc-a----ggggc-ggggc-
B D              Guinea pig  --tgctc--------c--agcc---ag----ggcc-----ggctttaacttc-a---gggggc-ggtgc-
                 Chinchilla  --cgctg-----------ggcc---c-----agcc-----ggctttcacttc-a---aggggc-ggtgc-
           Brush-tailed rat  --tgccg--------caaggct---ag----agcc-----ggctttcacctc-c---gggggc-ggtgc-
B D                  Rabbit  --ggcctaacccccac--cccc---cg----ctag-----cgctttaatctc-a---ggaggc-ggcgt-
B D                     Pig  --gatcc--------t--cccc---gg----ctct-----ggctttaatccc-c---ggaggc-ggtgt-
B D                  Alpaca  --gatcc--------t--cccc---gg----ctct-----cgctttaatccc-g---ggaggc-ggtgt-
B D                 Dolphin  --gattc--------t--tcctcg-gg----ctctc----cgccttaatcccga---gaaggctggtgt-
               Killer whale  --gatcc--------t--cccc---gg----ctct-----cgctttaatcc--g---ggaggc-ggtgt-
           Tibetan antelope  --tatcc--------t--cccc---gg----ctct-----tgctttaatcct-g---agaggc-ggtgt-
B D                     Cow  --gatcc--------t--cccc---gg----ctct-----cgctttaatcct-g---ggaggc-ggtgt-
B D                   Sheep  --gatcc--------t--cccc---gg----ctct-----cgctttaatcct-g---ggaggc-ggtgt-
              Domestic goat  --gatcc--------t--cccc---gg----ctct-----cgctttaatcct-g---ggaggc-ggtgt-
B D                   Horse  --gaccc--------t--cccc---tg----ctct-----cgctttaatccc-g---ggaggcgggtgt-
B D        White rhinoceros  --gacac--------t--cccc---tg----ctct-----cgctttaatccc-g---ggaggc-ggttt-
B D                     Cat  ---------------t--ccc-------------------cgctttaatccc-g---ggaggc-ggtgt-
B D                     Dog  ------c--------t--cccc---gg----ctct-----cgctttaatccc-g---ggaggc-ggtgt-
B D                 Ferret   --gacgc--------t--ccct---gg----cgct-----cgcttaaatccc-g---ggaggc-ggtgt-
B D                   Panda  --gacgc--------t--ccct---gg----ctct-----ctctttaatccc-g---ggaggc-ggtat-
             Pacific walrus  --gacac--------t--cccc---gg----ctct-----cgctttaatccc-g---ggaggc-ggtgt-
               Weddell seal  --gacac--------t--cccc---gg----ctct-----cgctttaatccc-g---ggaggc-ggtgt-
B D                 Megabat  --gaccc--------t--ccc----gg----ccct-----cgcttaaatccc-g---ggaggc-ggtgt-
              Big brown bat  --gatcc--------t--cccg---gg----ctct-----cgctttaatccc-g---ggaggc-ggcgt-
B D                Microbat  --ggtcc--------t--cccg---gg----ctcg-----cgctttaatcct-g---ggaggc-ggcgt-
B D                Elephant  --ggccc--------t--ccccccggg----ctct-----cgctttaatatc-c---ggaggc-ggtgt-
B D                 Manatee  --aaccc--------t--cccccc-gg----ctct-----cgctttaacctc-t---ggaggc-ggggt-
           Cape golden mole  --gttcc--------t--ctcct--gg----ctct-----tgctttaatctc-c---agaggc-agcgg-
B D                  Tenrec  --gaccc--------t--ccccg--ggctgcctcg-----ggctttaatccc-c---ggaggc-ggcgt-
                   Aardvark  --gaccc--------t--ccgca--gg----cgct-----agctttaatctc-c---ggaggc-ggtgt-
B D               Armadillo  --gaccc--------t--cctccc-cg----ctct-----cgctttaatctc-g---ggaggc-ggtgt-
B D         Tasmanian devil  --agcct--------t--tcct---gg----cctc-----c-------tctc-a---gctggc-cacgt-
B D             Zebra finch  ---tgct--------g--ccct---tg----agcc-----t------gtcac-c---tcagca-ggggt-
B D                 Chicken  --acccc--------g--cccc---gc----agccctcctt------cccgc-c---ccgccg-ccggt-
B D      American alligator  --gctct--------g--ccct---gg----gttc-----c------cttgg-g---gcagga-ggggg-
  D         Green seaturtle  ga-------------g--ccgc---ct----tggc-----taa----cccag-a---gcaggg-ggtgg-
  D          Painted turtle  gacctct--------g--cccc---cc----agcc-----caacgtccccag-accctcagcg-tccgc-
B D                    Pika  ======================================================================
            Bactrian camel  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D                Platypus  ======================================================================
          Black flying-fox  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
      David's myotis (bat)  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

                      Human  cc--ca----------------------gggt--ccagg
                      Chimp  cc--ca----------------------gggt--ccagg
                    Gorilla  cc--ca----------------------gggt--ccagg
                  Orangutan  cc--ca----------------------gggc--ccagg
                     Gibbon  cc--ca----------------------gggc--ccagg
                     Rhesus  cc--ca----------------------gggc--ccagg
        Crab-eating macaque  cc--ca----------------------gggc--ccagg
                     Baboon  cc--ca----------------------gggc--ccagg
               Green monkey  cc--ca----------------------gggc--ccagg
                   Marmoset  cc--ca----------------------gggc--ccagg
            Squirrel monkey  cc--ca----------------------gggc--ccagg
                   Bushbaby  cc--aa----------------------gtgc--ccagg
         Chinese tree shrew  cc--ta----------------------gagc--ccaag
                   Squirrel  cc--ca----------------------gggc--tcagg
     Lesser Egyptian jerboa  cc--ca----------------------ggac--ccagg
               Prairie vole  cc--ta----------------------g--a--tttag
            Chinese hamster  cc--aa----------------------agag--ccagg
             Golden hamster  cc--ca----------------------ggag--ccagg
                      Mouse  cc--cg----------------------ggag--ccagg
                        Rat  cc--ca----------------------ggag--ccagg
             Naked mole-rat  ca--ca----------------------gggc--ccagg
                 Guinea pig  ca--ca-----------------------gcc--ccggg
                 Chinchilla  ca--ca----------------------gggc--ccagg
           Brush-tailed rat  ca--ca----------------------gggc--ccagg
                     Rabbit  cc--gc----------------------cggc--tctgg
                        Pig  cc--ca----------------------gggc--ccagg
                     Alpaca  cc--ga----------------------gtac--ccagg
                    Dolphin  tccgaa----------------------gtgggcctagg
               Killer whale  cc--ga----------------------gtgg--ccagg
           Tibetan antelope  cc--ga----------------------gcgc--ccagg
                        Cow  cc--ga----------------------gcgc--ccagg
                      Sheep  cc--ga----------------------gcgc--ccagg
              Domestic goat  cc--ga----------------------gcgc--ccagg
                      Horse  cc--ga----------------------gtgc--tcagg
           White rhinoceros  cc--ga----------------------gtgc--tcagg
                        Cat  cg--ga----------------------gcgc--ccagg
                        Dog  cc--aa----------------------gtgc--ccagg
                    Ferret   cc--ga----------------------ctg---ccagg
                      Panda  cc--aa----------------------gtgc--ccagg
             Pacific walrus  cc--ga----------------------gtgc--ccagg
               Weddell seal  cc---a----------------------gtgc--ccagg
                    Megabat  cc--ag----------------------gtgc--ccagg
              Big brown bat  cc--ga----------------------gcgc--ccagg
                   Microbat  cc--ga----------------------gtgc--ccagg
                   Elephant  cc--ca----------------------agaa--ctaga
                    Manatee  cc--ca----------------------ggga--cctga
           Cape golden mole  cc--ca----------------------ggac--ccaag
                     Tenrec  cc--ca----------------------ggtt--ggagg
                   Aardvark  cc--ca----------------------gggc--ccaaa
                  Armadillo  cc--ga----------------------gcgc--cccag
            Tasmanian devil  cc--ca--------------------ctgggt--ctggg
                Zebra finch  ac--ca--------ggacagcacagg-------------
                    Chicken  ac--cgtacccgccgcccgacgcggg-------------
         American alligator  ac--ca---------------------------------
            Green seaturtle  cc--tg---------------------------------
             Painted turtle  tc--ca---------------------------------
                       Pika  =======================================
             Bactrian camel  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
                   Platypus  =======================================
           Black flying-fox  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
       David's myotis (bat)  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

Inserts between block 12 and 13 in window
B D                Dolphin 623bp
B D        Tasmanian devil 7bp

Alignment block 13 of 54 in window, 41508217 - 41508256, 40 bps 
B D                   Human  gcg--------------------acacccc------caa------gcggg-tcgcgggtcaccc-tgggc
B D                   Chimp  gcg--------------------acacccc------caa------gcggg-tcgcgggtcaccc-tgggc
B D                 Gorilla  gcg--------------------acacccc------caa------gcggg-tcgcgggtcaccc-tgggc
B D               Orangutan  gcg--------------------acacccc------caa------gcggg-tcgcgggtcaccc-tgggc
B D                  Gibbon  gcg--------------------acacccc------caa------gcggg-tctccggtcaccc-tgggc
B D                  Rhesus  gca--------------------acacccc------caaat----gcgcg-tcgcaggtcaccc-cgggc
B D     Crab-eating macaque  gca--------------------acacccc------caaat----gcgcg-tcgcgggtcaccc-cgggc
B D                  Baboon  gca--------------------acacccc------caaat----gcgcg-tcgcgggtcaccc-cgggc
B D            Green monkey  gca--------------------acacccc------caaat----gcgcg-tcgcgggtcaccc-cgggc
B D                Marmoset  gcg--------------------acacccc------caagc----gcggg-tcccgggtcaccc-cggga
B D         Squirrel monkey  gcg--------------------acacccc------caaat----gcggg-tcccgggtcaccc-cgggc
B D                Bushbaby  gcg--------------------acacctc------cacgc----gcggg-tcctgggtcacct-ggggc
         Chinese tree shrew  gcg--------------------acacccc------caagc----aaagg-tctccggtcacct-cgagc
B D                Squirrel  gct--------------------acacccc-----ccaaac----gcgaa-tccccgttcaacc-ggggc
     Lesser Egyptian jerboa  gtg--------------------acacccctaaacttaaac----gcagg-tgccaggtcacct-aggcc
               Prairie vole  gca--------------------acacccc------taaac----gcagg-tgccgggtcacct-cggcc
B D         Chinese hamster  gta--------------------acacccc------taaac----gcagg-tgccgggtcacct-cggcc
             Golden hamster  gta--------------------acacccc------taaac----gcagg-tgccgggtcacct-cggcc
B D                   Mouse  gtg--------------------acacccc------taaac----gcagg---------cacct-cggcc
B D                     Rat  gtg--------------------acacccc------taaac----gcagg-tgcccggtcacct-cggcc
B D          Naked mole-rat  acc--------------------acg-ccc------cagac----ac--g-ccccaggtcgc--------
B D              Guinea pig  gct--------------------aca-ccc------cagac----ac--gcccccagggcgc--------
                 Chinchilla  gct--------------------acgcccc------cagat----ac--g-ccccaggtca---------
           Brush-tailed rat  gct--------------------acacccc------cagac----ac--g-ccccgtgtcac--------
B D                  Rabbit  gcg--------------------acacccc------cag-c----acagg-tcccgggccacct-gcgga
B D                     Pig  gtg--------------------acacccc------caagc----g-cgg-tcccaggtcacct-cgggc
B D                  Alpaca  gag--------------------acacccc------caagc----gccgg-tcccgggtcacct-cgggc
B D                 Dolphin  gtg--------------------acacccc------caagc----gccgg-tcccgggtcacct-cgggc
               Killer whale  gtg--------------------acacccc------caagc----gccgg-tcccgggtcacct-cgggc
           Tibetan antelope  gca--------------------acacccc------caagc----gccgg-tcccgggtcacct-ccgac
B D                     Cow  gca--------------------acacccc------caagc----gccgg-tcccgggtcacct-cggac
B D                   Sheep  gca--------------------acacccc------caagc----gccgg-tcccgggtcacct-cggac
              Domestic goat  gca--------------------acacccc------caagc----gccgg-tcccgggtcacct-cgggc
B D                   Horse  gcg--------------------acacccc------caagc----gttag-tcccgggtcacct-cgagg
B D        White rhinoceros  gcg--------------------acacccc------caagc----ctaag-tcccgggtcacct-cgtgt
B D                     Cat  gcg--------------------acacccc------taaac----gc-gg-tcccggggcacct-cgggc
B D                     Dog  gcg--------------------acacccc------taaac----gc-gg-tcccaggtcacct-ctggc
B D                 Ferret   gtg--------------------acacccc------taaac----gc-gg-tccccggtgacct-ccagc
B D                   Panda  gcg--------------------acacccc------taaac----gc-ag-tcccgggtcacct-ccggc
             Pacific walrus  gcg--------------------acacccc------taaac----gc-gg-tcccgggtcacct-ccggc
               Weddell seal  gcg--------------------acacccc------taaac----gc-gg-tcccgggtcacct-ccggc
B D                 Megabat  gcg--------------------acacccc------tgagtgcaagcagg-tccggggtcacct-ggggc
              Big brown bat  gca--------------------acacccc------caggt----gcagg-tcc----ccgtctccgggc
B D                Microbat  gca--------------------acacccc------ca-gt----gcagg-tcc----cagtct-cgggc
B D                Elephant  gag--------------------acacgcc------ctagc----gcagg-tc-taagtcacct-cgggc
B D                 Manatee  gcg--------------------acacgcc------ctagc----gcagg-tc-cgggtcacct-cgggc
           Cape golden mole  gtg----------------------acgcc------cagga----gcagg-tc-caggtcactt-cggac
B D                  Tenrec  gtg--------------------acacgcc------ctaga----gccgg-tc-cgggtcacct-cggac
                   Aardvark  atg--------------------acacgcc------ctaga----gcggg-tc-caggtcacct-cggac
B D               Armadillo  gcg--------------------acacgcc------caggc----gcggg-tcgccggtcacct-cccgc
B D         Tasmanian devil  aca--------------------agaggtc------aacgc----ccacc-ccctgggctgcc-------
B D             Zebra finch  -cacagctgcactgatgaacaacaggcttc------aagtg----acact-t------------------
B D                 Chicken  -cggtgtccgcctaggcagccgctcgctcc------tcccg----gcgca-t------------------
B D      American alligator  ------------aaatgacccccccacctt------tgccc----ccagg-t------------------
  D         Green seaturtle  -----------------------ggccccc------tccca----gcagg-a------------------
  D          Painted turtle  -----------------------gcccccg------gcccg----cccgg-t------------------
B D                    Pika  ======================================================================
            Bactrian camel  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D                Platypus  ======================================================================
          Black flying-fox  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
      David's myotis (bat)  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

                      Human  -------gggc
                      Chimp  -------gggc
                    Gorilla  g-ggcgggggc
                  Orangutan  -------gggc
                     Gibbon  -------gggc
                     Rhesus  -------gggc
        Crab-eating macaque  -------gggc
                     Baboon  -------gggc
               Green monkey  -------gggc
                   Marmoset  -------gggc
            Squirrel monkey  -------aggc
                   Bushbaby  tcggagagggg
         Chinese tree shrew  ----aggggga
                   Squirrel  aggaggagggg
     Lesser Egyptian jerboa  aggaggagggg
               Prairie vole  aggaggagggg
            Chinese hamster  aggaggagggg
             Golden hamster  aggaggagggg
                      Mouse  agaaggaggga
                        Rat  aagaggaggga
             Naked mole-rat  -------cgag
                 Guinea pig  -------agag
                 Chinchilla  -------ggag
           Brush-tailed rat  -------ggag
                     Rabbit  tgggggagggg
                        Pig  -------aggg
                     Alpaca  -------gggg
                    Dolphin  -------aggg
               Killer whale  -------aggg
           Tibetan antelope  -------agag
                        Cow  -------agag
                      Sheep  -------agag
              Domestic goat  -------agag
                      Horse  -------aggg
           White rhinoceros  -------aggg
                        Cat  -------accg
                        Dog  -------agag
                    Ferret   -------aggg
                      Panda  -------aggg
             Pacific walrus  -------aggg
               Weddell seal  -------aggg
                    Megabat  -------aggg
              Big brown bat  -------tggg
                   Microbat  -------tggg
                   Elephant  -------aggg
                    Manatee  -------agga
           Cape golden mole  -------tgga
                     Tenrec  -------aggg
                   Aardvark  -------aggg
                  Armadillo  -------agga
            Tasmanian devil  -----------
                Zebra finch  -----------
                    Chicken  -----------
         American alligator  -----------
            Green seaturtle  -----------
             Painted turtle  -----------
                       Pika  ===========
             Bactrian camel  NNNNNNNNNNN
                   Platypus  ===========
           Black flying-fox  NNNNNNNNNNN
       David's myotis (bat)  NNNNNNNNNNN

Alignment block 14 of 54 in window, 41508257 - 41508261, 5 bps 
B D                   Human  ------ggggg
B D                   Chimp  ------ggggg
B D                 Gorilla  ------ggggg
B D               Orangutan  ------ggggg
B D                  Gibbon  ------ggggg
B D                  Rhesus  ------gaggg
B D     Crab-eating macaque  ------gaggg
B D                  Baboon  ------gaggg
B D            Green monkey  ------gaggg
B D                Marmoset  ------ggggg
B D         Squirrel monkey  -------gggg
B D                Bushbaby  ------acggg
         Chinese tree shrew  ------gggga
B D                Squirrel  ------acaag
     Lesser Egyptian jerboa  ------acgaa
               Prairie vole  ------acgac
B D         Chinese hamster  ------acggc
             Golden hamster  ------acggc
B D                   Mouse  ------acggc
B D                     Rat  ------acagc
B D          Naked mole-rat  ------ccagg
B D              Guinea pig  ------ttggg
                 Chinchilla  ------ccagg
           Brush-tailed rat  ------ccctg
B D                  Rabbit  ------acagc
B D                     Pig  ------gg---
B D                  Alpaca  ------gg---
B D                 Dolphin  ------gg---
               Killer whale  ------gg---
           Tibetan antelope  ------gg---
B D                     Cow  ------gg---
B D                   Sheep  ------gg---
              Domestic goat  ------gg---
B D                   Horse  ------ggagg
B D        White rhinoceros  ------ggagg
B D                     Cat  ------ggagg
B D                     Dog  ------ggagg
B D                 Ferret   ------ggagg
B D                   Panda  ------tgggg
             Pacific walrus  ------ggagg
               Weddell seal  ------ggagg
B D                 Megabat  ------ggagg
              Big brown bat  ------ggcgg
B D                Microbat  ------ggcgg
B D                Elephant  ------ggagg
B D                 Manatee  ------ggagg
           Cape golden mole  ------ggagg
B D                  Tenrec  ------ggagg
                   Aardvark  ------ggagg
B D               Armadillo  ------ggcgg
B D             Zebra finch  c--tggg----
B D                 Chicken  c--ttcg----
B D      American alligator  g--cctg----
  D         Green seaturtle  g--ggcg----
  D          Painted turtle  acctgca----
B D                    Pika  ===========
            Bactrian camel  NNNNNNNNNNN
B D                Platypus  ===========
          Black flying-fox  NNNNNNNNNNN
      David's myotis (bat)  NNNNNNNNNNN

Inserts between block 14 and 15 in window
B D                  Horse 18bp
B D       White rhinoceros 16bp
B D                    Cat 7bp
B D                    Dog 53bp
B D                Ferret  56bp
B D                  Panda 83bp
            Pacific walrus 41bp
              Weddell seal 41bp
B D                Megabat 46bp
             Big brown bat 35bp
B D               Microbat 33bp
B D               Elephant 48bp
B D                Manatee 47bp
          Cape golden mole 25bp
B D                 Tenrec 34bp
                  Aardvark 38bp
B D              Armadillo 7bp
B D            Zebra finch 2bp

Alignment block 15 of 54 in window, 41508262 - 41508270, 9 bps 
B D                   Human  cgg----gggcgg
B D                   Chimp  cgg----gggcgg
B D                 Gorilla  cgg----gggcgg
B D               Orangutan  cgg----gggcgg
B D                  Gibbon  cgg----gggcgg
B D                  Rhesus  cgg----gtgcgg
B D     Crab-eating macaque  cgg----gtgcgg
B D                  Baboon  cgg----gtgcgg
B D            Green monkey  cgg----gtgcgg
B D                Marmoset  cgg----gtgcgg
B D         Squirrel monkey  cgg----gcgcgg
B D                Bushbaby  ccg----gagcgg
         Chinese tree shrew  cggacctgagcgg
B D                Squirrel  ccg----gagcgg
     Lesser Egyptian jerboa  cgg----aggcca
               Prairie vole  cgg----gagcgc
B D         Chinese hamster  ccg----gagcgg
             Golden hamster  cag----gagcgg
B D                   Mouse  cag----gaaagg
B D                     Rat  cag----gaaagg
B D          Naked mole-rat  cag----gggcgg
B D              Guinea pig  ctg----aggctg
                 Chinchilla  cag----gggcgg
           Brush-tailed rat  gag----gggcgg
B D                  Rabbit  ccg----ggg---
B D                     Pig  agg----ggacgg
B D                  Alpaca  agg----ggacgg
B D                 Dolphin  agg----ggacgg
               Killer whale  agg----ggacgg
           Tibetan antelope  agg----ggacgg
B D                     Cow  agg----ggacgg
B D                   Sheep  agg----ggacgg
              Domestic goat  agg----ggacgg
B D                   Horse  cag----gggccg
B D        White rhinoceros  tag----gggcgg
B D                     Cat  gcg----gggcgg
B D                     Dog  cgg----aggcgg
B D                 Ferret   ctc----gggtgg
             Pacific walrus  cgg----gggcgg
               Weddell seal  cag----gggtga
B D                 Megabat  cgg----cggctg
              Big brown bat  cgg----ggaagt
B D                Microbat  cgg----ggaggg
B D                Elephant  cca----ggaagg
B D                 Manatee  ccg----gggagg
           Cape golden mole  cca----gggagg
B D                  Tenrec  cct----gagcgg
                   Aardvark  ccg----ggccag
B D             Zebra finch  gcg----gggtgg
B D                 Chicken  gcc----gcgctg
B D      American alligator  ggg----gagctg
  D         Green seaturtle  gca----tggaag
  D          Painted turtle  gca----gggctg
B D                    Pika  =============
B D               Armadillo  =============
            Bactrian camel  NNNNNNNNNNNNN
B D                Platypus  =============
          Black flying-fox  NNNNNNNNNNNNN
      David's myotis (bat)  NNNNNNNNNNNNN
B D                   Panda  =============

Inserts between block 15 and 16 in window
B D                    Pig 48bp
B D                 Alpaca 50bp
B D                Dolphin 43bp
              Killer whale 43bp
          Tibetan antelope 44bp
B D                    Cow 44bp
B D                  Sheep 18360bp
             Domestic goat 17175bp

Alignment block 16 of 54 in window, 41508271 - 41508297, 27 bps 
B D                   Human  c----------------------gg--------------------------------------g------
B D                   Chimp  c----------------------gg--------------------------------------g------
B D                 Gorilla  c----------------------gg--------------------------------------g------
B D               Orangutan  t----------------------gg--------------------------------------g------
B D                  Gibbon  c----------------------gg--------------------------------------g------
B D                  Rhesus  c----------------------gg--------------------------------------g------
B D     Crab-eating macaque  c----------------------gg--------------------------------------g------
B D                  Baboon  c----------------------gg--------------------------------------g------
B D            Green monkey  c----------------------gg--------------------------------------g------
B D                Marmoset  c----------------------gg--------------------------------------g------
B D         Squirrel monkey  c----------------------gg--------------------------------------g------
B D                Bushbaby  c----------------------tgtccc----------------------------------g------
         Chinese tree shrew  c----------------------tgccccaggcgggcgggtccgggtccctggcgagagctagg------
B D                Squirrel  ccatcc------------------c--------------------------------------g------
     Lesser Egyptian jerboa  ctgtcc------------------c--------------------------------------g------
               Prairie vole  ctgtcc-----------------cg--------------------------------------g------
B D         Chinese hamster  cggtcc-----------------gg--------------------------------------g------
             Golden hamster  ctgtcc-----------------gg--------------------------------------g------
B D                   Mouse  ctgtccaggaggg----------ag--------------------------------------g------
B D                     Rat  ctgtcc-----------------gg--------------------------------------g------
B D          Naked mole-rat  ctccgg-----------------gc--------------------------------------g------
B D              Guinea pig  ctaccg-----------------gc--------------------------------------t------
                 Chinchilla  cgacca-----------------gg--------------------------------------g------
           Brush-tailed rat  ctacca-----------------ag--------------------------------------g------
B D                  Rabbit  ----gc-----------------gg--------------------------------------a------
B D                     Pig  ------------c----------gg--------------------------------------g------
B D                  Alpaca  ------------c----------gg--------------------------------------g------
B D                 Dolphin  ------------c----------ag--------------------------------------g------
               Killer whale  ------------c----------ag--------------------------------------g------
           Tibetan antelope  ------------c----------ga--------------------------------------g------
B D                     Cow  ------------c----------ga--------------------------------------g------
B D                   Horse  ------------c----------gg--------------------------------------g------
B D        White rhinoceros  ------------c----------gg--------------------------------------g------
B D                     Cat  ------------c----------gg--------------------------------------g------
B D                     Dog  -----------------------gg--------------------------------------g------
B D                 Ferret   ------------c----------ag--------------------------------------g------
             Pacific walrus  ------------c----------gg--------------------------------------g------
               Weddell seal  ------------c----------gg--------------------------------------g------
B D                 Megabat  ------------c----------gg--------------------------------------g------
              Big brown bat  ------------g----------gc--------------------------------------g------
B D                Microbat  ------------g----------gc--------------------------------------ggggagg
B D                Elephant  ------------c----------ca--------------------------------------g------
B D                 Manatee  ------------c----------cg--------------------------------------g------
           Cape golden mole  ------------c----------cg--------------------------------------a------
B D                  Tenrec  ------------c----------cg--------------------------------------g------
                   Aardvark  ------------c----------gg--------------------------------------g------
B D               Armadillo  ------------c----------cg--------------------------------------g------
B D             Zebra finch  ------------a----------tg--------------------------------------g------
B D                 Chicken  -----------------------cg--------------------------------------g------
B D      American alligator  ------------------------g--------------------------------------g------
  D         Green seaturtle  ------------ccccaacacaaag--------------------------------------a------
  D          Painted turtle  ------------cctt-------ct--------------------------------------g------
B D                    Pika  ======================================================================
            Bactrian camel  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D                Platypus  ======================================================================
B D                   Sheep  ======================================================================
          Black flying-fox  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
      David's myotis (bat)  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
             Domestic goat  ======================================================================
B D                   Panda  ======================================================================

                      Human  ----a-ggaggcg-------ttt-ccc------------aa--ggg--aagt
                      Chimp  ----a-ggaggcg-------ttt-ccc------------ag--ggg--aagt
                    Gorilla  ----a-ggaggcg-------ttt-ccc------------aa--ggg--aagt
                  Orangutan  ----a-ggaggcg-------ttt-ccc------------aa--ggg--gagc
                     Gibbon  ----a-ggaggcg------tttt-ccc------------aa--ggg--aagc
                     Rhesus  ----a-ggaggcg-------ttt-ccc------------aa--ggg--aagc
        Crab-eating macaque  ----a-ggaggcg-------ttt-ccc------------aa--ggg--aagc
                     Baboon  ----a-ggaggcg-------ttt-ccc------------aa--ggg--aagc
               Green monkey  ----a-ggaggcg-------ttt-ccc------------aa--ggg--aagc
                   Marmoset  ----a-ggaggcg-------ttt-ccc------------gg--ggg--aagc
            Squirrel monkey  ----a-ggagacg-------ttt-cct------------gg--ggg--aagc
                   Bushbaby  ----g-gcgggcg-------gat-cc-------------ag--gga--aggc
         Chinese tree shrew  ----a-ggaggag-------ttt-ccc------------ca--gggaaaagc
                   Squirrel  ----g-actggaggaggagtttc-ccc------------ag--ggg--aagc
     Lesser Egyptian jerboa  ----g-gaaggaggaggagtttc-ccccgaggcggggggcg--gga--aagc
               Prairie vole  ----g-gaaggaggaggagtttc-ccc------------ga--ggg--aagc
            Chinese hamster  ----g-gaaggaggaggagtttc-ccc------------ga--ggg--aaac
             Golden hamster  ----g-aaaggaggaggagtttc-ccc------------ga--ggg--aaac
                      Mouse  ----a-ggaggaggaggagtttc-ccc------------ga--ggg--aagc
                        Rat  ----g-gaaagaggaggagtttc-ccc------------ga--ggg--aagc
             Naked mole-rat  ----g-tg-ggtggagg-----c-tcc------------cg--ggc--aggt
                 Guinea pig  --------------------------c------------aggaggc--gtct
                 Chinchilla  --------------------------c------------cg--ggc--aggt
           Brush-tailed rat  --------------------------c------------cg--ggc--aggt
                     Rabbit  ----g-gtggcaggatccttctt-tcc------------ct--gtt--tgg-
                        Pig  ----g-ggaggag-------tttcccc------------c---ggg--aaaa
                     Alpaca  ----a-ggaggag-------tttcccc------------ca--ggg--aaag
                    Dolphin  ----a-ggagggg-------tttcttc------------ct--ggg--aaag
               Killer whale  ----a-ggagggg-------tttcttc------------ct--ggg--aaag
           Tibetan antelope  ----a-ggaggag-------tttcctc------------ca--ggg--aaag
                        Cow  ----a-ggaggag-------tttcctc------------ca--ggg--aaag
                      Horse  ----a-ggaggag-------ttt-ccc------------ca--ggg--aaag
           White rhinoceros  ----agggaggag-------tct-ccc------------cg--ggg--aaag
                        Cat  ----a-ggaggag-------tttcttc------------cc--ggg--aaag
                        Dog  ----g-ggaggag-------tttgccc------------cg--ggg--actg
                    Ferret   ----a-ggaggag-------tttcccc------------ca--ggg--aaag
             Pacific walrus  ----a-ggaggag-------tttcccc------------ca--ggg--aaag
               Weddell seal  ----a-ggaggag-------tttcccc------------ca--ggg--aaag
                    Megabat  ----g-ggaggag-------tct-ccc------------ag--cgg--a---
              Big brown bat  ----g-ggaggcg-------ttc-ccc------------ga--ggg--aagg
                   Microbat  ggccg-ggaggcg-------gtc-ccg------------gg--ggg--aagg
                   Elephant  ----a-ggtggtg-------ttt-ccc------------gg--agg--aaac
                    Manatee  ----a-ggaggtg-------ttt-ccc------------gg--agg--aaag
           Cape golden mole  ----a-agaggcg-------ttt-cct------------gg--agg--aaag
                     Tenrec  ----a-ggaggtg-------ttt-tcc------------ag--agc--agag
                   Aardvark  ----a-agaggcg-------ttt-ccc------------gg--agg--aaag
                  Armadillo  ----a-ggaggag-------tcc-cca------------ga--ggg--gaag
                Zebra finch  ----c-agagggg-------cgg-gca------------gc--agc--aggg
                    Chicken  ----c-agcgcgc-------cgt-gccgt----------gc--ggc--gggg
         American alligator  ----c-tgggggg-------cgg-ggg------------ga--gga--agcg
            Green seaturtle  ----c-agggccg-------ggc--tg------------gg--ggc--agcg
             Painted turtle  ----c-ggggccg-------aga-gca------------ga--ggc--agag
                       Pika  ====================================================
             Bactrian camel  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
                   Platypus  ====================================================
                      Sheep  ====================================================
           Black flying-fox  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
       David's myotis (bat)  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
              Domestic goat  ====================================================
                      Panda  ====================================================

Inserts between block 16 and 17 in window
B D               Bushbaby 10bp
B D                    Pig 1bp
B D                 Alpaca 1bp
B D                Dolphin 1bp
              Killer whale 1bp
          Tibetan antelope 1bp
B D                    Cow 1bp
B D                  Horse 1bp
B D       White rhinoceros 1bp
B D                    Cat 1bp
B D                    Dog 1bp
B D                Ferret  1bp
            Pacific walrus 1bp
              Weddell seal 1bp
             Big brown bat 1bp
B D               Microbat 1bp
B D               Elephant 1bp
B D                Manatee 1bp
          Cape golden mole 1bp
B D                 Tenrec 1bp
                  Aardvark 1bp
B D              Armadillo 1bp

Alignment block 17 of 54 in window, 41508298 - 41508301, 4 bps 
B D                   Human  ccgg-
B D                   Chimp  ccgg-
B D                 Gorilla  ccgg-
B D               Orangutan  ccgg-
B D                  Gibbon  ccgg-
B D                  Rhesus  ccgg-
B D     Crab-eating macaque  ccgg-
B D                  Baboon  ccgg-
B D            Green monkey  ctgg-
B D                Marmoset  ccgg-
B D         Squirrel monkey  ccgg-
B D                Bushbaby  ctgg-
         Chinese tree shrew  ccgg-
B D                Squirrel  cccg-
     Lesser Egyptian jerboa  ccgg-
               Prairie vole  ccag-
B D         Chinese hamster  ccag-
             Golden hamster  ccag-
B D                   Mouse  ccag-
B D                     Rat  ccag-
B D          Naked mole-rat  cccg-
B D              Guinea pig  ccaa-
                 Chinchilla  ccag-
           Brush-tailed rat  ccag-
B D                     Pig  ccgg-
B D                  Alpaca  ccgg-
B D                 Dolphin  ccgg-
               Killer whale  ccgg-
           Tibetan antelope  ccgg-
B D                     Cow  ccgg-
B D                   Horse  ccgg-
B D        White rhinoceros  ccgg-
B D                     Cat  ccgg-
B D                     Dog  ccgg-
B D                 Ferret   ccgg-
             Pacific walrus  ccga-
               Weddell seal  ccga-
B D                 Megabat  ctgg-
              Big brown bat  ccgg-
       David's myotis (bat)  ccgg-
B D                Microbat  ccgg-
B D                Elephant  ttgg-
B D                 Manatee  ccgg-
           Cape golden mole  ccca-
B D                  Tenrec  cggg-
                   Aardvark  ccgg-
B D               Armadillo  cctg-
B D             Zebra finch  -ctg-
B D                 Chicken  -ccg-
B D      American alligator  -ctg-
  D         Green seaturtle  -ctgg
  D          Painted turtle  -cggt
B D                    Pika  =====
B D                  Rabbit  -----
            Bactrian camel  NNNNN
B D                Platypus  =====
B D                   Sheep  =====
          Black flying-fox  NNNNN
             Domestic goat  =====
B D                   Panda  =====

Alignment block 18 of 54 in window, 41508302 - 41508314, 13 bps 
B D                   Human  ---------gac--gggtt-ccctg
B D                   Chimp  ---------gac--gga-----ctg
B D                 Gorilla  ---------gac--gggtt-ccctg
B D               Orangutan  ---------gac--tggtt-ccctg
B D                  Gibbon  ---------gac--gggtt-ctcag
B D                  Rhesus  ---------gac--gggtt-cccag
B D     Crab-eating macaque  ---------gac--gggtt-cccag
B D                  Baboon  ---------gac--gggtt-cccag
B D            Green monkey  ---------gac--tggtt-cccag
B D                Marmoset  ---------gac--tcgct-ccagg
B D         Squirrel monkey  ---------gac--ttgct-ccagg
B D                Bushbaby  ---------gag--gagtt-tcccg
         Chinese tree shrew  ---------gac--gagct-cctag
B D                Squirrel  ---------gac--gcgcg-cc---
     Lesser Egyptian jerboa  ---------ggc--gcgct-cctcc
               Prairie vole  ---------ggc--gcgct-cctcc
B D         Chinese hamster  ---------gga--gcgct-cctcc
             Golden hamster  ---------ggc--gcgct-cctcc
B D                   Mouse  ---------gga--gcgct-cctcc
B D                     Rat  ---------gga--gcgct-cctcc
B D          Naked mole-rat  ---------gcccaggtcc-ctg--
                 Chinchilla  ---------gac--agacc-ctg--
           Brush-tailed rat  ---------gac--agacg-ctg--
B D                  Rabbit  ---------gat--gggct-cgt--
B D                     Pig  ---------gac--gcgct-ct---
B D                  Alpaca  ---------c-c--gggac-ct---
B D                 Dolphin  ---------gac--gcgct-ct---
               Killer whale  ---------gac--gcgct-ct---
           Tibetan antelope  ---------cac--gcgct-cc---
B D                     Cow  ---------cac--gcgct-cc---
B D                   Horse  ---------cac--gcgca-cctga
B D        White rhinoceros  ---------gac--gcgct-cctga
B D                     Cat  ---------ggc--gctct-cctgg
B D                     Dog  ---------gac--gggct-c--gg
B D                 Ferret   ---------gaa--gcgct-tctgg
             Pacific walrus  ---------gaa--gcgct-cctgg
               Weddell seal  ---------gaa--gcgct-cctga
B D                 Megabat  --------------------ccggt
              Big brown bat  ---------gac--gcgct-ccaga
       David's myotis (bat)  ---------gac--aagct-ccaga
B D                Microbat  ---------gac--gcgct-ccaga
B D                Elephant  ---------gac--ggcta-ctcgc
B D                 Manatee  ---------gac--agctc-cttgt
           Cape golden mole  ---------gac--gcg-----gag
B D                  Tenrec  ---------gac--gcgct-ccccg
                   Aardvark  ---------gaa--gcgcctcttgt
B D               Armadillo  ---------gct--gcgct------
B D             Zebra finch  ------gcagct--g----------
B D                 Chicken  --ccctccagcc--g----------
B D      American alligator  --ccc-acggcc--t----------
  D         Green seaturtle  gacttgttacct--g----------
  D          Painted turtle  ggccaggcattc--g----------
B D                    Pika  =========================
            Bactrian camel  NNNNNNNNNNNNNNNNNNNNNNNNN
B D                Platypus  =========================
B D                   Sheep  =========================
          Black flying-fox  NNNNNNNNNNNNNNNNNNNNNNNNN
             Domestic goat  =========================
B D                   Panda  =========================

Inserts between block 18 and 19 in window
B D         Naked mole-rat 603bp
  D        Green seaturtle 3bp

Alignment block 19 of 54 in window, 41508315 - 41508315, 1 bps 
B D                   Human  -c
B D                   Chimp  -c
B D                 Gorilla  -c
B D               Orangutan  -c
B D                  Gibbon  -c
B D                  Rhesus  -t
B D     Crab-eating macaque  -t
B D                  Baboon  -t
B D            Green monkey  -t
B D                Marmoset  -c
B D         Squirrel monkey  -c
B D                Bushbaby  -a
         Chinese tree shrew  -c
     Lesser Egyptian jerboa  -c
               Prairie vole  -c
B D         Chinese hamster  -c
             Golden hamster  -c
B D                   Mouse  -c
B D                     Rat  -c
                 Chinchilla  -c
           Brush-tailed rat  -t
B D                   Horse  -c
B D        White rhinoceros  -c
B D                     Cat  -t
B D                     Dog  -c
B D                 Ferret   -c
             Pacific walrus  -c
               Weddell seal  -c
B D                 Megabat  -c
              Big brown bat  -c
       David's myotis (bat)  -c
B D                Microbat  -c
B D                Elephant  -a
B D                 Manatee  -c
           Cape golden mole  -c
B D                  Tenrec  -c
                   Aardvark  -c
B D             Zebra finch  g-
B D                 Chicken  g-
B D      American alligator  g-
  D         Green seaturtle  g-
  D          Painted turtle  c-
B D                    Pika  ==
B D                  Rabbit  --
B D          Naked mole-rat  ==
B D               Armadillo  --
B D                 Dolphin  --
B D                     Pig  --
              Killer whale  --
            Bactrian camel  NN
B D                Platypus  ==
B D                   Sheep  ==
B D                     Cow  --
          Tibetan antelope  --
          Black flying-fox  NN
B D                Squirrel  --
             Domestic goat  ==
B D                  Alpaca  --
B D                   Panda  ==

Inserts between block 19 and 20 in window
                Chinchilla 955bp
          Brush-tailed rat 2bp

Alignment block 20 of 54 in window, 41508316 - 41508330, 15 bps 
B D                   Human  ctggctcaa---cccc---gg-------------------------------------
B D                   Chimp  ctggctcaa---cccc---gg-------------------------------------
B D                 Gorilla  ctggctcaa---cccc---gg-------------------------------------
B D               Orangutan  ctggctcaa---cccc---gg-------------------------------------
B D                  Gibbon  ctggctcaa---cccc---gg-------------------------------------
B D                  Rhesus  ctggctcaa---cccc---gg-------------------------------------
B D     Crab-eating macaque  ctggctcaa---cccc---gg-------------------------------------
B D                  Baboon  ctggctcaa---cccc---gg-------------------------------------
B D            Green monkey  ccggctcaa---cccc---gg-------------------------------------
B D                Marmoset  ccggcccaa---accc---ga-------------------------------------
B D         Squirrel monkey  ccggcccaa---cc--------------------------------------------
B D                Bushbaby  gggg---aa-gccccc---gg-------------------------------------
         Chinese tree shrew  cggc--------ccgc---gg-------------------------------------
B D                Squirrel  --------a---gaac---ag-------------------------------------
     Lesser Egyptian jerboa  ------aggtatgcgg---ag-------------------------------------
               Prairie vole  ------cca----cat---gg-------------------------------------
B D         Chinese hamster  ------cca----cat---gg-------------------------------------
             Golden hamster  ------cca----cat---gg-------------------------------------
B D                   Mouse  ------cta---gcac---cg-------------------------------------
B D                     Rat  ------cta---gcag---gg-------------------------------------
B D                  Rabbit  --------------------g-------------------------------------
B D                   Horse  -------------ccc---cg-------------------------------------
B D        White rhinoceros  -------------tcc---cc-------------------------------------
B D                     Cat  -------------ccc---cg-------------------------------------
B D                     Dog  -------------ccc---tg-------------------------------------
B D                 Ferret   -------------ccc---gg-------------------------------------
             Pacific walrus  -------------tca---gg-------------------------------------
               Weddell seal  -------------tca---gg-------------------------------------
B D                 Megabat  -------------cc-------------------------------------------
              Big brown bat  -------------ccg---gc-------------------------------------
       David's myotis (bat)  -------------ctg---gc-------------------------------------
B D                Microbat  -------------ccg---gc-------------------------------------
B D                Elephant  --------------cc---gg-------------------------------------
B D                 Manatee  --------------ct---gg-------------------------------------
           Cape golden mole  --------------ct---gg-------------------------------------
B D                  Tenrec  --------------cc---gg-------------------------------------
                   Aardvark  --------------cc---gg-------------------------------------
B D               Armadillo  -------------------gg-------------------------------------
B D             Zebra finch  ---------------g---ggcctggttaagc---------------ctcactctgtt
B D                 Chicken  ---------------c---cgtc-ggttccgcgggtagcgcggcca-cgcactcctcg
B D      American alligator  ---------------cacaagac-aggggagcatgtgccccgcagaccagacccagct
  D         Green seaturtle  ---------------g---ggtc------------------------tggcctcggtg
  D          Painted turtle  ---------------a---ggcc------------------------tggac-caggg
B D                    Pika  ==========================================================
B D          Naked mole-rat  ==========================================================
                Chinchilla  ==========================================================
          Brush-tailed rat  ==========================================================
B D                 Dolphin  ----------------------------------------------------------
B D                     Pig  ----------------------------------------------------------
              Killer whale  ----------------------------------------------------------
            Bactrian camel  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D                Platypus  ==========================================================
B D                   Sheep  ==========================================================
B D                     Cow  ----------------------------------------------------------
          Tibetan antelope  ----------------------------------------------------------
          Black flying-fox  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
             Domestic goat  ==========================================================
B D                  Alpaca  ----------------------------------------------------------
B D                   Panda  ==========================================================

Inserts between block 20 and 21 in window
B D                  Horse 1bp
B D       White rhinoceros 1bp
B D                    Cat 1bp
B D                    Dog 1bp
B D                Ferret  1bp
            Pacific walrus 1bp
              Weddell seal 1bp
B D               Elephant 7bp
B D                Manatee 7bp
          Cape golden mole 7bp
B D                 Tenrec 7bp
                  Aardvark 7bp
B D              Armadillo 5bp

Alignment block 21 of 54 in window, 41508331 - 41508381, 51 bps 
B D                   Human  ctgcg---------------gagggaccc------------------------------------ataag
B D                   Chimp  ctgcg---------------gagggaccc------------------------------------ataag
B D                 Gorilla  ccgcg---------------gcgggacca------------------------------------ataag
B D               Orangutan  ctgcg---------------gcggaaccc------------------------------------acaag
B D                  Gibbon  ctgcg---------------gcgggaccc------------------------------------aggag
B D                  Rhesus  ctgcg---------------gccggaccc------------------------------------aggag
B D     Crab-eating macaque  ctgcg---------------gccggaccc------------------------------------aggag
B D                  Baboon  ctgcg---------------gccggaccc------------------------------------aggag
B D            Green monkey  ctgcg---------------tcgggaccc------------------------------------aggag
B D                Marmoset  ctgcg---------------gcgggaccc------------------------------------aggtg
B D         Squirrel monkey  --------------------------ccc------------------------------------aggtg
B D                Bushbaby  acgcg---------------gcgggaccc------------------------------------agagg
         Chinese tree shrew  ----------------------ggtaccc------------------------------------tggac
B D                Squirrel  ----------------------ggactcc------------------------------------aggac
     Lesser Egyptian jerboa  ----------------------aggaccc------------------------------------gggag
               Prairie vole  ----------------------cgggacc------------------------------------aaaag
B D         Chinese hamster  ----------------------cgggacc------------------------------------tgaag
             Golden hamster  ----------------------cgggacc------------------------------------tgaag
B D                   Mouse  ----------------------agagatc------------------------------------aaact
B D                     Rat  ----------------------agagacc------------------------------------agacc
           Brush-tailed rat  ----------------------tgaactc------------------------------------aag--
B D                  Rabbit  ----------------------atgtacc------------------------------------g----
B D                     Pig  ---cg---------------gcgggaccc------------------------------------agagg
B D                  Alpaca  ---tg---------------gccggaccc------------------------------------agagg
B D                 Dolphin  ---cg---------------gcgggaccc------------------------------------agagg
               Killer whale  ---cg---------------gcgggaccc------------------------------------agagg
           Tibetan antelope  ---tg---------------gagggaccc------------------------------------agagg
B D                     Cow  ---cg---------------gagggaccc------------------------------------agagg
B D                   Horse  ccacg---------------gtgggaccc------------------------------------ggagg
B D        White rhinoceros  ccgcg---------------gtgagaccc------------------------------------agcgg
B D                     Cat  ccgcg---------------gggtggacc------------------------------------ccttg
B D                     Dog  ccggc---------------gggggaacc------------------------------------ccatg
B D                 Ferret   cggct---------------ggggggatc------------------------------------ccacg
             Pacific walrus  cggctgcggtgggggggaagggggaaacc------------------------------------ccttg
               Weddell seal  cggct---------------agggggacc------------------------------------ccttg
           Black flying-fox  ccgcg---------------gcgggaccc------------------------------------agagg
B D                 Megabat  --gcg---------------gcgggaccc------------------------------------agagg
              Big brown bat  ccggg---------------gcgggaccc------------------------------------agaag
       David's myotis (bat)  ccggg---------------gcggggccc------------------------------------agagg
B D                Microbat  ccggg---------------gcggggccc------------------------------------agagg
B D                Elephant  -agct---------------gggggaccc------------------------------------agagg
B D                 Manatee  -ctct---------------gggggacgc------------------------------------agaag
           Cape golden mole  -agaa---------------ggagagctc------------------------------------ttc--
B D                  Tenrec  -tgcc---------------ggggaaccc------------------------------------ttc--
                   Aardvark  -cgct---------------ggggaac-----------------------------------------ag
B D               Armadillo  -cgcc---------------gggacacg----------------------------------------ag
B D             Zebra finch  ---------------------ccccagcc----------------------------------------c
B D                 Chicken  ---------------------cggcggccgctttcccgcgtagggaaggtgggcggttcacacaaaaggc
B D      American alligator  ---------------------cagcagcc----------------------------------------c
  D         Green seaturtle  ---------------------ccatggca--------------------gagccggtctcagcagcagac
  D          Painted turtle  ---------------------tgggagtg--------------------ggaatggcct-------ggag
B D                    Pika  ======================================================================
B D          Naked mole-rat  ======================================================================
                Chinchilla  ======================================================================
            Bactrian camel  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D                Platypus  ======================================================================
B D                   Sheep  ======================================================================
             Domestic goat  ======================================================================
B D                   Panda  ======================================================================

                      Human  ggactc--tgg-gg--cgcttcccgg---gcccgg--------cc-----aca
                      Chimp  ggactc--tgg-gg--cgcttcccgg---gcccgg--------cc-----cca
                    Gorilla  ggattc--tgg-gg--cgcttcccgg---gcccgg--------cc-----cca
                  Orangutan  ggactc--tgg-gg--cgcttcccgg---gccggg--------cc-----cca
                     Gibbon  ggaccc--tgg-gg--cgcttcccgg---gcccgg--------cc-----cca
                     Rhesus  ggactc--tgg-gg--cacttcccgg---gcccta--------cc-----cca
        Crab-eating macaque  ggactc--tgg-gg--cacttcccgg---gcccta--------cc-----cca
                     Baboon  ggactc--tgg-gg--cactttccgg---gcccta--------cc-----cca
               Green monkey  ggactc--tgg-gg--cacttctcgg---gccctg--------cc-----cca
                   Marmoset  cgactc--tgg-gg--cacttcccgg---gccag----------c-----cca
            Squirrel monkey  cgactc--tgg-gg--cacttcccgg---gccag----------c-----tca
                   Bushbaby  agacgc--ctg-gg--cacttccc-t---gtctgg--------ct-----cta
         Chinese tree shrew  agactc--cgc-ag--cgcttcccgg---gtctg---------cc-----cca
                   Squirrel  -gtcta---gg-gt--caggcacccg---caggcagtcggaggctgagaagag
     Lesser Egyptian jerboa  agaccc---cgcgg--ctctttcctg---gc----------------------
               Prairie vole  agacca---aa-gg--catttccctg---gcagcgacccgcctcc-----gta
            Chinese hamster  ggaccc---aa-gg--catttccctg---gcagcgacaggcctcc-----gga
             Golden hamster  ggaccc---aa-gg--catttccctg---gcagcgactggcctcc-----gga
                      Mouse  ggactc---ta-gg--cattccccta---gcagcgacccgcctcc-----gga
                        Rat  ggactc---ga-gg--catttccctg---gcagcgacccgcctct-----gga
           Brush-tailed rat  -gactc----a-gg--cttttgcc--------gagatgcccgacc-----aga
                     Rabbit  ----ct---aa-ag--gactcctccg---actgccctcgg--tcc-----ata
                        Pig  gagctcc-ggg-gg--cg-----------cttccg-------ttc-----ccg
                     Alpaca  gagttcc-gag-gc--cg-----------cttccg-------tcc-----ccg
                    Dolphin  gagccc--ggg-ga--cg-----------cttccg-------tcc-----cca
               Killer whale  gagccc--agg-ga--cg-----------cttccg-------tcc-----cca
           Tibetan antelope  gagctcg-ggg-ga--cg-----------cttcca-------tcc-----ccg
                        Cow  gagctcg-ggg-ga--cg-----------cttcca-------tcc-----tcg
                      Horse  gaactc--ggg-gc---attccccgg---gcctcg-------tcc-----cct
           White rhinoceros  gagctccgggg-ac---attccccgg---acctcg-------tct-----cct
                        Cat  gagctc--c-g-gctcggt----------ccccgg-------agg-----gtc
                        Dog  gagctc--cgg-gc---------------cccccc-------acc-----gcg
                    Ferret   gag-----tgg-gtttcgttcccc-----caccca-------ccc-----ccg
             Pacific walrus  aagctc--cgg-acttcgttccgcacccaccccca-------ccc-----ccc
               Weddell seal  aagctc--ccg-gcttcgttccccacccacccccc-------acc-----ccc
           Black flying-fox  gagctg--ggg-gt--cgctcccccg---gcctcg-------tcc-----cct
                    Megabat  gagctg--ggg-gt--cgctcccccg---gcctcg-------tcc-----cct
              Big brown bat  gaactt--ggg-ga--cgagccccgg---gccccg-------tct-----ccc
       David's myotis (bat)  gaactt--ggg-ga--cgc-tcccag---gcccag-------tct-----ccc
                   Microbat  gaacct--ggg-ga--cgc-tcccgg---gccc-g-------tct-----ccc
                   Elephant  gagacccgaag-gc--cacttcctgg---gcatag------tcct-----ccc
                    Manatee  gagaccggagg-gc--cgctttcccg---gcttcg------tgtt-----ccc
           Cape golden mole  ------------gc--tgcttcctgg---gtttcg------tcct-----ccc
                     Tenrec  ---------------------ccgga---gcttcg------tcct-----tcc
                   Aardvark  gagatccgaag-gc--cg-------------------------ct-----ccc
                  Armadillo  gaagtgccagg-ac--cg---agcgg---gt------------cc-----ccg
                Zebra finch  ggcccc--tgc-ca--cgctccctgg---agggct--------ct-----gcc
                    Chicken  ggccgc--cgg-cg--cggggcgggc---agggcc-----gcgcc-----gcc
         American alligator  ccccgc--aca-cg--tg-------------------------ct-----gcc
            Green seaturtle  ggaccc--ttg-tg--ctcacccagt---ctgacc--------ct-----gca
             Painted turtle  ggactc----g-gg--ccca--aggc---ctggca---------------gca
                       Pika  =====================================================
             Naked mole-rat  =====================================================
                 Chinchilla  =====================================================
             Bactrian camel  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
                   Platypus  =====================================================
                      Sheep  =====================================================
              Domestic goat  =====================================================
                      Panda  =====================================================

Inserts between block 21 and 22 in window
B D            Zebra finch 36bp
B D                Chicken 33bp
B D     American alligator 133bp
  D        Green seaturtle 11bp
  D         Painted turtle 11bp

Alignment block 22 of 54 in window, 41508382 - 41508388, 7 bps 
B D                   Human  g------------cgg--------------------cca
B D                   Chimp  g------------cgg--------------------cca
B D                 Gorilla  g------------cgg--------------------cta
B D               Orangutan  g------------agg--------------------cca
B D                  Gibbon  g------------cgg--------------------cca
B D                  Rhesus  g------------cgg--------------------cca
B D     Crab-eating macaque  g------------cgg--------------------cca
B D                  Baboon  g------------cgg--------------------cca
B D            Green monkey  g------------cgg--------------------cca
B D                Marmoset  g------------ccg--------------------cca
B D         Squirrel monkey  g------------cgg--------------------cca
B D                Bushbaby  g------------cgg--------------------gca
         Chinese tree shrew  g------------cag--------------------gca
B D                Squirrel  g------------cgc--------------------tgc
     Lesser Egyptian jerboa  -------------ctg--------------------ggt
               Prairie vole  g------------ctg--------------------ggc
B D         Chinese hamster  g------------cag--------------------cgc
             Golden hamster  g------------cag--------------------cgc
B D                   Mouse  c------------cag--------------------cgg
B D                     Rat  g------------cag--------------------ccg
           Brush-tailed rat  g------------ctg-----------------------
B D                  Rabbit  g------------taa--------------------cgg
B D                     Pig  g------------cgg--------------------gca
B D                  Alpaca  g------------cgg--------------------gca
B D                 Dolphin  g------------ccg--------------------gcc
               Killer whale  g------------ccg--------------------gcc
           Tibetan antelope  g------------cgg--------------------gca
B D                     Cow  g------------cgg--------------------gca
B D                   Horse  g------------tgg--------------------gca
B D        White rhinoceros  ggcagtttaggactgg--------------------gga
B D                     Cat  g------------agg--------------------gcg
B D                     Dog  g------------tggccggcagtgcagggctgggagca
B D                 Ferret   g------------cgg--------------------gca
             Pacific walrus  g------------cgg--------------------gca
               Weddell seal  c------------cgg--------------------gca
           Black flying-fox  gg-----------cgg--------------------gca
B D                 Megabat  gg-----------cgg--------------------gca
              Big brown bat  t------------ccg--------------------gca
       David's myotis (bat)  cg-----------ccg--------------------gca
B D                Microbat  cg-----------ccg--------------------gca
B D                Elephant  t------------cgg--------------------gca
B D                 Manatee  g------------cgg--------------------gca
           Cape golden mole  a------------ctg--------------------cta
B D                  Tenrec  g------------tgg--------------------gca
                   Aardvark  a------------tgg--------------------gca
B D               Armadillo  g------------ccg--------------------gca
B D             Zebra finch  ------------ctcg--------------------ccc
B D                 Chicken  ------------ccgg--------------------gcc
  D         Green seaturtle  ------------cctg--------------------aga
  D          Painted turtle  ------------ctgc--------------------tca
B D                    Pika  =======================================
B D          Naked mole-rat  =======================================
                Chinchilla  =======================================
            Bactrian camel  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D                Platypus  =======================================
B D                   Sheep  =======================================
             Domestic goat  =======================================
B D      American alligator  =======================================
B D                   Panda  =======================================

Inserts between block 22 and 23 in window
B D                    Pig 29bp
B D                 Alpaca 19bp
B D                Dolphin 20bp
              Killer whale 20bp
          Tibetan antelope 20bp
B D                    Cow 20bp
B D                  Horse 503bp
B D       White rhinoceros 16bp
          Black flying-fox 20bp
B D                Megabat 20bp
             Big brown bat 20bp
      David's myotis (bat) 20bp
B D               Microbat 24bp

Alignment block 23 of 54 in window, 41508389 - 41508393, 5 bps 
B D                   Human  ----ac-----------------------------------------ctg
B D                   Chimp  ----gc-----------------------------------------ctg
B D                 Gorilla  ----gc-----------------------------------------ctg
B D               Orangutan  ----gc-----------------------------------------ctg
B D                  Gibbon  ----ac-----------------------------------------ctg
B D                  Rhesus  ----gc-----------------------------------------ctg
B D     Crab-eating macaque  ----gc-----------------------------------------ctg
B D                  Baboon  ----gc-----------------------------------------ctg
B D            Green monkey  ----gc-----------------------------------------ctg
B D                Marmoset  ----gc-----------------------------------------cgg
B D         Squirrel monkey  ----gc-----------------------------------------ctg
B D                Bushbaby  ----gtttagggttgcagaggaacacgtctccctccccacgtcc--gctg
         Chinese tree shrew  ----gatgagggctggggaggagcgtgacttgctccctccca-----ctg
B D                Squirrel  ----cc---------------------tctc----cccaagtcc--gcag
     Lesser Egyptian jerboa  ----tc---------------------cctc----cccgtaccc--actg
               Prairie vole  ----ac---------------------cctcgagggccaggccc--atgg
B D         Chinese hamster  ----ac---------------------tctcgaggccccggccc--atgg
             Golden hamster  ----ac---------------------cctcgaggtcccggccc--aagg
B D                   Mouse  ----ac---------------------ccttgaggcccagaccc--atgg
B D                     Rat  ----ac---------------------ccttgaggctcagaccc--aagg
           Brush-tailed rat  --------------------------------------ataccc--a---
B D                  Rabbit  ----ac---------------------tggccgtccccccgccc--ccgg
B D                     Pig  -------------------------------------------------g
B D                  Alpaca  -------------------------------------------------g
B D                 Dolphin  -------------------------------------------------g
               Killer whale  -------------------------------------------------g
           Tibetan antelope  -------------------------------------------------g
B D                     Cow  -------------------------------------------------g
B D                     Cat  -------------------------------------------------g
B D                     Dog  -------------------------------------------------g
B D                 Ferret   -------------------------------------------------a
             Pacific walrus  -------------------------------------------------a
               Weddell seal  -------------------------------------------------g
           Black flying-fox  -------------------------------------------------g
B D                 Megabat  -------------------------------------------------g
              Big brown bat  -------------------------------------------------g
       David's myotis (bat)  -------------------------------------------------g
B D                Microbat  -------------------------------------------------g
B D                Elephant  ----------------------------------gtttaggggtagggag
B D                 Manatee  ----------------------------------gttttgggctagacgg
           Cape golden mole  ----------------------------------gtttagacctagatgg
B D                  Tenrec  ----------------------------------gcggaggact-ggcag
                   Aardvark  ----------------------------------gttaaaggctggagaa
B D               Armadillo  ----------------------------------ggtcagggct-gggtg
B D             Zebra finch  acatg---------------------------------------------
B D                 Chicken  ccgcg---------------------------------------------
  D         Green seaturtle  cc-tg---------------------------------------------
  D          Painted turtle  ccaca---------------------------------------------
B D                    Pika  ==================================================
B D          Naked mole-rat  ==================================================
                Chinchilla  ==================================================
            Bactrian camel  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D                Platypus  ==================================================
B D                   Sheep  ==================================================
             Domestic goat  ==================================================
B D      American alligator  ==================================================
B D                   Panda  ==================================================
B D        White rhinoceros  ==================================================
B D                   Horse  ==================================================

Inserts between block 23 and 24 in window
B D                    Pig 5bp
B D                 Alpaca 5bp
B D                Dolphin 5bp
              Killer whale 5bp
          Tibetan antelope 5bp
B D                    Cow 5bp
B D                    Cat 25bp
B D                    Dog 5bp
B D                Ferret  22bp
            Pacific walrus 24bp
              Weddell seal 24bp
          Black flying-fox 9bp
B D                Megabat 9bp
             Big brown bat 9bp
      David's myotis (bat) 9bp
B D               Microbat 9bp
B D               Elephant 17bp
B D                Manatee 18bp
          Cape golden mole 17bp
B D                 Tenrec 18bp
                  Aardvark 18bp
B D              Armadillo 18bp

Alignment block 24 of 54 in window, 41508394 - 41508410, 17 bps 
B D                   Human  -------------cccctctccggtcc------------gcg
B D                   Chimp  -------------cccctctccggtcc------------gcg
B D                 Gorilla  -------------cccctctccggtcc------------gcg
B D               Orangutan  -------------cccctctccggtcc------------gcg
B D                  Gibbon  -------------cccctctccggtcc------------gtg
B D                  Rhesus  -------------ccccactcgggtcc------------gcg
B D     Crab-eating macaque  -------------ccccactcgggtcc------------gcg
B D                  Baboon  -------------ccccactcgggtcc------------gcg
B D            Green monkey  -------------ccccactcgggtcc------------gcg
B D                Marmoset  -------------ctcctctcaggtcc------------agg
B D         Squirrel monkey  -------------cccctctcgggtct------------agg
B D                Bushbaby  -------------gacctctggggtct------------cca
         Chinese tree shrew  -------------gaccgctccggtct------------ccg
B D                Squirrel  -------------gtcctctccggtc-------------gcg
     Lesser Egyptian jerboa  -------------caccgctcaggt--------------ctc
               Prairie vole  -------------gaccgtcagggta-------------ccg
B D         Chinese hamster  -------------gcccggttgggt--------------ccg
             Golden hamster  -------------gcccgcttgggtc-------------ccg
B D                   Mouse  -------------gaactccagggtc-------------ctg
B D                     Rat  -------------gaacgccagggtc-------------ccg
           Brush-tailed rat  ---------------ccacgcggg---------------ccg
B D                  Rabbit  -------------caccttctg--------------------
B D                     Pig  -------------ccctctcacgtccc------------cg-
B D                  Alpaca  -------------cccgccgtactcct------------cc-
B D                 Dolphin  -------------ccctccccacttcc------------cc-
               Killer whale  -------------ccctccccacttcc------------cc-
           Tibetan antelope  -------------ccctcccgcattccccgggaccgggacc-
B D                     Cow  -------------ccctcccgcattcc------------cc-
B D        White rhinoceros  ------------------cccacatcc------------cc-
B D                     Cat  --------------cctcccctcgtcc------------cc-
B D                     Dog  -------------ccctgcccttgtcc------------tc-
B D                 Ferret   -------------cccctcccccgtct------------cc-
B D                   Panda  -------------ccctcccctcgtcc------------cc-
             Pacific walrus  -------------ccctcctcgcgtcc------------cc-
               Weddell seal  -------------ccctcccctcctcc------------cc-
           Black flying-fox  -----------------ccccacgtcc------------gg-
B D                 Megabat  -----------------ccccacgtcc------------gg-
              Big brown bat  -----------------ccccgagtcc------------gt-
       David's myotis (bat)  -----------------ccc--ggtcc------------gt-
B D                Microbat  -----------------ccc-gggtcc------------gt-
B D                Elephant  -------------atccttcctgaact------------gc-
B D                 Manatee  -------------aacctccctggact------------gc-
           Cape golden mole  -------------agcctccc-tgatt------------gca
B D                  Tenrec  -------------accctctcaaaact------------gcg
                   Aardvark  -------------accctccctggatt------------gcg
B D               Armadillo  -------------accc--ccgaggcg------------acg
B D             Zebra finch  cccgtggtgccgtagcctctttgcccg---------------
B D                 Chicken  cgcgccgccccggcccctcactaacca---------------
  D         Green seaturtle  ccc-----ccagtcaccccgc-----a---------------
  D          Painted turtle  ccc-----tccgtcacctgccaggcaa---------------
B D                    Pika  ==========================================
B D          Naked mole-rat  ==========================================
                Chinchilla  ==========================================
            Bactrian camel  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D                Platypus  ==========================================
B D                   Sheep  ==========================================
             Domestic goat  ==========================================
B D      American alligator  ==========================================
B D                   Horse  ==========================================

Inserts between block 24 and 25 in window
B D                 Alpaca 18bp
B D                Dolphin 19bp
              Killer whale 19bp
          Tibetan antelope 19bp
B D                    Cow 19bp
B D       White rhinoceros 19bp
B D                    Cat 19bp
B D                    Dog 13bp
B D                Ferret  19bp
B D                  Panda 19bp
            Pacific walrus 19bp
              Weddell seal 19bp
          Black flying-fox 18bp
B D                Megabat 18bp
             Big brown bat 19bp
      David's myotis (bat) 19bp
B D               Microbat 19bp
          Cape golden mole 10bp
B D                 Tenrec 10bp
                  Aardvark 10bp
B D              Armadillo 10bp

Alignment block 25 of 54 in window, 41508411 - 41508449, 39 bps 
B D                   Human  gcgca----------gcgctgcccgagggctcgagtttgggttaaggaa
B D                   Chimp  gcgca----------gcgctgcccgagggctcgagtttgggttaaggaa
B D                 Gorilla  gcgca----------gcgctgcccgagggcttgagtttgggttaaggaa
B D               Orangutan  gcgca----------gcgctgcccgagggctcgagtttgggttaaggaa
B D                  Gibbon  gcgcc----------gcgctgcccgagggctcgagtttgggttaagtaa
B D                  Rhesus  gcgca----------gcgctgcccgagggctccagtttgggttaaggag
B D     Crab-eating macaque  gcgca----------gcgctgcccgagggctcgagtttgggttaaggag
B D                  Baboon  gcgca----------gcgctgcccgagggctcgagtttgggttaaggag
B D            Green monkey  gcgca----------gcgctgcccgagggctcgagtttgggttaaggag
B D                Marmoset  gcgca----------gctctgcccgagggctcgagtttgggttaaggag
B D         Squirrel monkey  gcgta----------gctctgcccgagggctcgagtttgggttaaggag
B D                Bushbaby  acaca----------gcactg------------agcttggatgaag---
         Chinese tree shrew  gtgct----------atgggtct---aggctccaatgtggattaagca-
B D                Squirrel  gggcg----------acgcggtctgagggctgc-gtttgaatttaggag
     Lesser Egyptian jerboa  ctacc----------gcgctgcctttgaa------------tgaaggag
               Prairie vole  gcgcg----------acaccgtccttggactgctgtgtgaattaacggg
B D         Chinese hamster  gggcg----------acactgtctttggactgcagtgtggatgaagtgg
             Golden hamster  gcgcg----------acgctgtctttggactgc-----------agtgg
B D                   Mouse  ctgcg----------acg-ggtctttggactgcactattaaagaagtag
B D                     Rat  gtgcg----------acg-gatctctggactgcac-----------gcg
           Brush-tailed rat  tagct----------gcg-------tgga--------------gaaggg
B D                     Pig  ------------------g-gaccgagcaggtcgccggcgcttcaggag
B D                  Alpaca  gcgct----------tcgcggcccgaggagtcgagtttggattcaggag
             Bactrian camel  gcgct----------tcgcggcccgaggagtcgagtttggattcaggag
B D                 Dolphin  gcgct----------tcgc-gcccgaacactcaagtcgggattcaggag
               Killer whale  gcgct----------tcgc-gcccgaaccctcgagtctggattcaggag
           Tibetan antelope  gcgct----------ttgt-gcccgaacgctcaagtttggattcggcaa
B D                     Cow  gcgcc----------ttgt-gcccgaacgctcaagtttgcattcggcaa
B D        White rhinoceros  gtgct-t--------cgca-gcccgaggactcgagtttggattaagcag
B D                     Cat  gcgcttt--------gggg-ccccgaggtctcgagtttgggttaaggag
B D                     Dog  -----------------------------------tttggatggaggag
B D                 Ferret   gcgcc-------------------------tcgaattcggattaaggaa
B D                   Panda  gcgct-------------------------tcgagtttggattaaggaa
             Pacific walrus  gcgct-------------------------tcgaattgggatgaaggaa
               Weddell seal  gcgct-------------------------tcgaattgggattaaggaa
           Black flying-fox  gagct----------ttga-g-ccgaggactcgg-tttggattaaggag
B D                 Megabat  gagct----------ttga-g-ccgaggactcgg-tttggattaaggag
              Big brown bat  gcact----------tgca-gcccgaggactcta-tttgaattaaagag
       David's myotis (bat)  gcgct----------tcca-gcccgaggacgcga-tttgaactaagga-
B D                Microbat  gcgct----------tcca-gcccgaggactcga-tttgaactaaggag
B D                Elephant  -gctc----------aagaggccccgaactccgagtttggattaaggag
B D                 Manatee  -gctc----------aagcagccccgggctctgagtttggattaaggag
           Cape golden mole  ggccc----------aagagacccgaggcttcgaattcggaatgcgaag
B D                  Tenrec  ggccc----------aagcggccagggcaccccaagtttgaatgc---g
                   Aardvark  ggcca----------aagcagccccaggctacgagtttggattaaggag
B D               Armadillo  gcgct----------tcgcggacccgaggatcgagtctggattgaggag
B D             Zebra finch  ------ccact----atttttatcaga-----------atttcagagaa
B D                 Chicken  ------c-------------------------------gcggcagcgga
  D         Green seaturtle  ------acaga----gcgctcaggaaatcagccagtctggctcggggat
  D          Painted turtle  ------acagaggaggagattcggagaggggaggggcgaggctgggggg
B D                    Pika  =================================================
B D                  Rabbit  -------------------------------------------------
B D          Naked mole-rat  =================================================
                Chinchilla  =================================================
B D                Platypus  =================================================
B D                   Sheep  =================================================
             Domestic goat  =================================================
B D      American alligator  =================================================
B D                   Horse  =================================================

Inserts between block 25 and 26 in window
B D                Manatee 728bp

Alignment block 26 of 54 in window, 41508450 - 41508458, 9 bps 
B D                   Human  gggg----att-ct
B D                   Chimp  gggg----att-ct
B D                 Gorilla  gggt----att-ct
B D               Orangutan  gggg----att-ct
B D                  Gibbon  gggg----att-ct
B D                  Rhesus  gggg----att-cc
B D     Crab-eating macaque  gggg----att-cc
B D                  Baboon  gggg----att-cc
B D            Green monkey  gggg----att-cc
B D                Marmoset  gagg----att-cc
B D         Squirrel monkey  gagg----att-cc
         Chinese tree shrew  gggt----att-ct
B D                Squirrel  gggg----att-ct
     Lesser Egyptian jerboa  gacg----tcc-ct
               Prairie vole  gaag----acctta
B D         Chinese hamster  aaag----acc-ta
             Golden hamster  aaag----acc-ta
B D                   Mouse  gaag----ccc-ca
B D                     Rat  gaag----ccc-ca
           Brush-tailed rat  ggtg----act-cc
B D                  Rabbit  ------------ct
B D                     Pig  cggg----att-ct
B D                  Alpaca  gggg----atc-ct
             Bactrian camel  aggg----atc-ct
B D                 Dolphin  ggag----att-ct
               Killer whale  ggaa----att-ct
           Tibetan antelope  cggg----att-ct
B D                     Cow  gggg----att-ct
B D        White rhinoceros  ggag----att-ct
B D                     Cat  ggaa----ctt-ct
B D                     Dog  caga----gtt-ct
B D                 Ferret   ggaa----att-ct
B D                   Panda  ggga----att-ct
             Pacific walrus  ggga----att-ct
               Weddell seal  ggga----att-ct
           Black flying-fox  aggg----gtt-cc
B D                 Megabat  aggg----gtt-cc
              Big brown bat  gggc----att-cc
       David's myotis (bat)  gggg----att-cc
B D                Microbat  gggg----att-cc
B D                Elephant  ggag----att-ct
B D                 Manatee  ggta----att-ct
           Cape golden mole  agtg----att-tt
B D                  Tenrec  ggtg----att-cg
                   Aardvark  ggcg----att-ct
B D               Armadillo  cgtg----att-ct
B D             Zebra finch  gtgctcagcca-tt
B D                 Chicken  gccc----cct-tc
  D         Green seaturtle  ggag----aat-cc
  D          Painted turtle  ggcc----cat-cc
B D                    Pika  ==============
B D          Naked mole-rat  ==============
                Chinchilla  ==============
B D                Platypus  ==============
B D                   Sheep  ==============
             Domestic goat  ==============
B D      American alligator  ==============
B D                   Horse  ==============
B D                Bushbaby  --------------

Inserts between block 26 and 27 in window
B D               Elephant 1183bp

Alignment block 27 of 54 in window, 41508459 - 41508491, 33 bps 
B D                   Human  ------gggga--gcgctcctgga----gtcct--g-ggtgag---ccccc
B D                   Chimp  ------gggga--gcgctcctgga----gtcct--g-ggtgag---cccct
B D                 Gorilla  ------gggga--gcgctcctgga----gtcct--g-ggtgag---ccccc
B D               Orangutan  ------gggga--gcgctcctcga----gtcct--g-ggtgag---ccccc
B D                  Gibbon  ------gggga--gcgctcctcga----gtcct--g-ggtgag---ccccc
B D                  Rhesus  ------gggga--gcgctcctcga----gtcct--g-ggtaag---ccccc
B D     Crab-eating macaque  ------gggga--gcgctcctcga----gtcct--g-gataag---ccccc
B D                  Baboon  ------gggga--gcgctcctcga----gtcct--g-ggtaag---ccccc
B D            Green monkey  ------gagga--gcgctcctcga----gtcct--g-ggtaag---tcccc
B D                Marmoset  ------tggga--gcgctcttcca----gtcct--g-ggtgag---ccccc
B D         Squirrel monkey  ------tggga--gggctcctcga----gtcct--g-ggggag---ccccc
B D                Bushbaby  -------aggg--gcgctaatcca----ggccc----gctgaa---cccct
         Chinese tree shrew  ------gggga--gccctaatcga----gtccccca-agtgag---ccctg
B D                Squirrel  ------cggg--------aatcga----gtctc--cacgtgag----cagg
     Lesser Egyptian jerboa  ------gggga--gcgctaatcga----gtccc--c-tggg----------
               Prairie vole  ------aggga--gcgctaacccg----gcccc--c-tggaag----cccg
B D         Chinese hamster  ------aggga--gtgctaacctg----gcccc--t-tggga---------
             Golden hamster  ------aggga--gcgctaacccg----gtccc--t-aggaag----ccca
B D                   Mouse  ------aggga--gcgctaacctg----gtccc--t-tgaaag----tctg
B D                     Rat  ------aggga--actctaatccg----gtccc--t-tggaag----tctg
           Brush-tailed rat  ------gggaa--gcactcacaca----gtccc--cacaggag----cacc
B D                  Rabbit  ------aggga--at--taaccgg----aaccc--c-cgtgtgcgtccccg
B D                     Pig  ------gggga--gcgctgatcgc----gtctc--g-tatcag---ccggc
B D                  Alpaca  ------gggg---gcgctgatcaa----gtctt--g-tatggg---ccggc
             Bactrian camel  ------gggg---gcgctgatcaa----gtctt--g-tatggg---ccggc
B D                 Dolphin  ------gggca--gtgctgaccga----gtctc--g-cacgac---ccggc
               Killer whale  ------gggca--gtgctgaccga----gtctc--g-tacgac---ccggc
           Tibetan antelope  ------gggga--gcgctgaccga----gtctc--c-tgtaaa---ccggc
B D                     Cow  ------gggga--gcgctgaccga----gtctc--c-tgtgaa---ccggc
B D        White rhinoceros  ------gggga--gcgctgacgga----gtccc--cgtgtgag---cccaa
B D                     Cat  ------ggggggggcagtgattga----gtccc--tgccggag---cccc-
B D                     Dog  ------gggga--gcactgcctga----g-ccc--cgcgggag---cccca
B D                 Ferret   ------gggga--gccctgattga----gtccc--tgggtgag---cccca
B D                   Panda  ------ggaga--gccctgactga----gtccc--c-cgcgag---cccc-
             Pacific walrus  ------gggga--gcgctgattgg----gtccc--cgcgtgag---cccca
               Weddell seal  ------gggga-------gattgg----gtccc--cgcgtgag---cccca
           Black flying-fox  ------gagga--gcgtt---------------------------------
B D                 Megabat  ------gagga--gcact---------------------------------
              Big brown bat  ------cggga--acgccgatggg----gaccc--c-tagtca---ccccc
       David's myotis (bat)  ------cggga--acgccgatcgg----gaccc--c-tggtaa---tcccg
B D                Microbat  ------cggga--acgccgctcgg----gaccc--c-tggtaa---tcccg
B D                 Manatee  ------ggcga--gcgctaatc-a----gtccc--gttgtata---agcct
           Cape golden mole  ------ggcga--gcgcagagcta----gtcat--tttgtgca---cacct
B D                  Tenrec  ------ggaga--acgcgaatcga----gccct--tgaggctt---gccct
                   Aardvark  ------aggaa--gcgttgatcca----gtgtt--cttatgag---ctcct
B D               Armadillo  ------------------gggcca----tccct--ttgcgagg---accca
B D             Zebra finch  cttcaccaggg--at-atatttag----gcctg--t---------------
B D                 Chicken  cgcccccgaga--gc-ctgcccggaaacggccg--c---------------
  D         Green seaturtle  c----ccaggg--gc----tacgg----gtccg--a---------------
  D          Painted turtle  cagagccagga--ga---gggtgg----gccca--a---------------
B D                    Pika  ===================================================
B D          Naked mole-rat  ===================================================
                Chinchilla  ===================================================
B D                Platypus  ===================================================
B D                   Sheep  ===================================================
B D                Elephant  ===================================================
             Domestic goat  ===================================================
B D      American alligator  ===================================================
B D                   Horse  ===================================================

Inserts between block 27 and 28 in window
          Black flying-fox 13bp
B D                Megabat 13bp
B D            Zebra finch 10bp
B D                Chicken 11bp

Alignment block 28 of 54 in window, 41508492 - 41508506, 15 bps 
B D                   Human  -ggagctg------ctacc---t---ca
B D                   Chimp  -ggagctg------ctacc---t---ca
B D                 Gorilla  -ggagctg------ctacc---t---ca
B D               Orangutan  -ggagctg------ctacc---t---ca
B D                  Gibbon  -ggagctg------ctacc---t---ca
B D                  Rhesus  -ggagctg------ctacc---t---ca
B D     Crab-eating macaque  -ggagctg------ctacc---t---ca
B D                  Baboon  -ggagctg------ctacc---t---ca
B D            Green monkey  -ggagctg------ctacc---t---ca
B D                Marmoset  -agagttg------ccact---t---cc
B D         Squirrel monkey  -agagctg------ccact---t---ca
B D                Bushbaby  -ggagcta------ctgct---t---ca
         Chinese tree shrew  -ggag-tg------ctgct---c---ca
B D                Squirrel  -gtagctc------caatt---t---cc
     Lesser Egyptian jerboa  -----ctg------caatt---t---cc
               Prairie vole  -ggagctg------ctg-g---t---tc
B D         Chinese hamster  -----cct------cta-g---t-----
             Golden hamster  -ggagctg------cta-g---t-----
B D                   Mouse  -ggagtgg------ctaca---t---tc
B D                     Rat  -ggagctg------ctata---t---tc
           Brush-tailed rat  -agggagg------ctaca---c---ca
B D                  Rabbit  -g--------------------------
B D                     Pig  -cgggccc------tggca---c---ct
B D                  Alpaca  -ggggtct------tggct---c-----
             Bactrian camel  -ggggtct------tggct---c-----
B D                 Dolphin  -caagccc------tggcg---c---tg
               Killer whale  -caagccc------tggcg---c---tg
           Tibetan antelope  -cgagccc------tggcg---c---aa
B D                     Cow  -cgatccc------tggcg---c---ag
B D        White rhinoceros  -ggagctg------ctgct---a---gc
B D                     Cat  --------------ccacccacc---cc
B D                     Dog  -gaagcag------ctgct---c---cg
B D                 Ferret   -ggatctg------ctgct---c---cc
B D                   Panda  -------g------ctgct---c---cg
             Pacific walrus  -ggagctg------ctgctc-cc---cc
               Weddell seal  -ggagctg------ctgctc-cc---cc
              Big brown bat  -ggagctg------ctgct---t---cg
       David's myotis (bat)  -ggagctg------ctgct---t---cg
B D                Microbat  -ggagctg------ctgct---t---cg
B D                 Manatee  -ggagcag------c-----------tg
           Cape golden mole  -ggagttg------ctgct---a---cg
B D                  Tenrec  -ggagttg------cacca---t---tg
                   Aardvark  -ggagctg------ctgtt---t---ca
B D               Armadillo  -ggagtgg------gaccc---c---tg
B D             Zebra finch  gcagcaca------gggcc---t---g-
B D                 Chicken  gcggcgga------cagcg---c---g-
B D      American alligator  ggggggca------tcccc---c---t-
  D         Green seaturtle  -gggctca------ttgct---cacac-
  D          Painted turtle  -gggggcaaaggggttgtg---c---c-
B D                    Pika  ============================
B D          Naked mole-rat  ============================
                Chinchilla  ============================
B D                 Megabat  ============================
B D                Platypus  ============================
B D                   Sheep  ============================
B D                Elephant  ============================
          Black flying-fox  ============================
             Domestic goat  ============================
B D                   Horse  ============================

Inserts between block 28 and 29 in window
          Brush-tailed rat 596bp
B D                Manatee 9bp
          Cape golden mole 10bp
B D                 Tenrec 9bp
                  Aardvark 10bp
B D              Armadillo 13bp

Alignment block 29 of 54 in window, 41508507 - 41508525, 19 bps 
B D                   Human  cgagctcct----------gtagg---------------------cggcc--------------------
B D                   Chimp  cgagctcct----------gtagg---------------------cggcc--------------------
B D                 Gorilla  cgagctccg----------gtagg---------------------cggcc--------------------
B D               Orangutan  cgagctcct----------gcagg---------------------cggcc--------------------
B D                  Gibbon  cgagctcct----------gcagg---------------------cggcc--------------------
B D                  Rhesus  cgagctcct----------gcagg---------------------cggcc--------------------
B D     Crab-eating macaque  cgagctcct----------gcagg---------------------cggcc--------------------
B D                  Baboon  cgagctcct----------gcagg---------------------cggcc--------------------
B D            Green monkey  cgagctcct----------gcagg---------------------cggcc--------------------
B D                Marmoset  cgagctcct----------gcagg---------------------ctgcc--------------------
B D         Squirrel monkey  cgagctcct----------gcagg---------------------ctgcc--------------------
B D                Bushbaby  tgagcgcac----------atagg---------------------tggcc--------------------
         Chinese tree shrew  cgaactcct----------gtggg---------------------ccgct--------------------
B D                Squirrel  agacttcct----------gtaga-----agtgt------------------------------------
     Lesser Egyptian jerboa  ccaggctca----------gtaggtggcc-----------------------------------------
               Prairie vole  acagtccca----------gcagg----------------------------------------------
B D         Chinese hamster  ----tccca----------gcagg----------------------------------------------
             Golden hamster  ----tccca----------gcagg----------------------------------------------
B D                   Mouse  ccaactccg----------acagg----------------------------------------------
B D                     Rat  ccagccccg----------acagg----------------------------------------------
B D                  Rabbit  -gagccacc----------gtggg----------cg-gcc------------------------------
B D                     Pig  ggga------------------------------------------------------------------
B D                 Dolphin  ggga------------------------------------------------------------------
               Killer whale  ggga------------------------------------------------------------------
           Tibetan antelope  ggga------------------------------------------------------------------
B D                     Cow  ggga------------------------------------------------------------------
B D        White rhinoceros  tgagctcctgtcggcggcc---------------------------------------------------
B D                     Cat  ggagctcct-------------------------------------------------------------
B D                     Dog  agagctcct-------------------------------------------------------------
B D                 Ferret   tgagctcct-------------------------------------------------------------
B D                   Panda  tgaactccc-------------------------------------------------------------
             Pacific walrus  tgagctcct-------------------------------------------------------------
               Weddell seal  tgagctcct-------------------------------------------------------------
              Big brown bat  cgagctgct-------------------------------------------------------------
       David's myotis (bat)  cgagctgct-------------------------------------------------------------
B D                Microbat  cgagctgct-------------------------------------------------------------
B D                 Manatee  taggcatct-------------------------------------------------------------
           Cape golden mole  taagcggcc-------------------------------------------------------------
B D                  Tenrec  taagcgccc-------------------------------------------------------------
                   Aardvark  taggcggcc-------------------------------------------------------------
B D               Armadillo  tctgcgctc-------------------------------------------------------------
B D             Zebra finch  ----------------------------------ccaggccctcccagacagagaggac-----------
B D                 Chicken  ----------------------------------cgcggc------------agcggac-----------
B D      American alligator  ----------------------------------ccagca------------ccggggc-----------
  D         Green seaturtle  ----------------------------------cactgc------------aaatggcccccttcttgc
  D          Painted turtle  ----------------------------------cacagc------------agggag------------
B D                    Pika  ======================================================================
B D          Naked mole-rat  ======================================================================
                Chinchilla  ======================================================================
          Brush-tailed rat  ======================================================================
B D                 Megabat  ======================================================================
            Bactrian camel  ----------------------------------------------------------------------
B D                Platypus  ======================================================================
B D                   Sheep  ======================================================================
B D                Elephant  ======================================================================
          Black flying-fox  ======================================================================
             Domestic goat  ======================================================================
B D                  Alpaca  ----------------------------------------------------------------------
B D                   Horse  ======================================================================

                      Human  ------
                      Chimp  ------
                    Gorilla  ------
                  Orangutan  ------
                     Gibbon  ------
                     Rhesus  ------
        Crab-eating macaque  ------
                     Baboon  ------
               Green monkey  ------
                   Marmoset  ------
            Squirrel monkey  ------
                   Bushbaby  ------
         Chinese tree shrew  ------
                   Squirrel  ------
     Lesser Egyptian jerboa  ------
               Prairie vole  ------
            Chinese hamster  ------
             Golden hamster  ------
                      Mouse  ------
                        Rat  ------
                     Rabbit  ------
                        Pig  ------
                    Dolphin  ------
               Killer whale  ------
           Tibetan antelope  ------
                        Cow  ------
           White rhinoceros  ------
                        Cat  ------
                        Dog  ------
                    Ferret   ------
                      Panda  ------
             Pacific walrus  ------
               Weddell seal  ------
              Big brown bat  ------
       David's myotis (bat)  ------
                   Microbat  ------
                    Manatee  ------
           Cape golden mole  ------
                     Tenrec  ------
                   Aardvark  ------
                  Armadillo  ------
                Zebra finch  --aaac
                    Chicken  --agcc
         American alligator  --agct
            Green seaturtle  caggct
             Painted turtle  --ggct
                       Pika  ======
             Naked mole-rat  ======
                 Chinchilla  ======
           Brush-tailed rat  ======
                    Megabat  ======
             Bactrian camel  ------
                   Platypus  ======
                      Sheep  ======
                   Elephant  ======
           Black flying-fox  ======
              Domestic goat  ======
                     Alpaca  ------
                      Horse  ======

Inserts between block 29 and 30 in window
    Lesser Egyptian jerboa 9513bp
             Big brown bat 42bp
      David's myotis (bat) 522bp
B D               Microbat 89bp
B D                 Tenrec 4bp
                  Aardvark 5bp
B D              Armadillo 1bp
B D            Zebra finch 1bp

Alignment block 30 of 54 in window, 41508526 - 41508529, 4 bps 
B D                   Human  ggcc
B D                   Chimp  ggcc
B D                 Gorilla  ggcc
B D               Orangutan  ggcc
B D                  Gibbon  ggcc
B D                  Rhesus  ggcc
B D     Crab-eating macaque  ggcc
B D                  Baboon  ggcc
B D            Green monkey  ggcc
B D                Marmoset  g---
B D         Squirrel monkey  g---
B D                Bushbaby  tgcg
         Chinese tree shrew  cgcc
B D        White rhinoceros  agcc
B D                 Manatee  agcc
           Cape golden mole  ggcc
B D                  Tenrec  ggct
                   Aardvark  ggcc
B D               Armadillo  ggcc
B D             Zebra finch  ggca
B D                 Chicken  cgcg
B D      American alligator  ggca
  D         Green seaturtle  ggct
  D          Painted turtle  gg--
            Golden hamster  ----
B D                    Pika  ====
B D                  Rabbit  ----
              Prairie vole  ----
B D         Chinese hamster  ----
B D                     Rat  ----
B D          Naked mole-rat  ====
                Chinchilla  ====
B D                   Mouse  ----
          Brush-tailed rat  ====
    Lesser Egyptian jerboa  ====
B D                 Dolphin  ----
B D                 Megabat  ====
B D                     Pig  ----
              Weddell seal  ----
              Killer whale  ----
            Bactrian camel  ----
             Big brown bat  ====
B D                Platypus  ====
B D                   Sheep  ====
B D                     Cow  ----
          Tibetan antelope  ----
B D                Elephant  ====
          Black flying-fox  ====
B D                Squirrel  ----
B D                Microbat  ====
      David's myotis (bat)  ====
B D                     Dog  ----
             Domestic goat  ====
B D                  Alpaca  ----
            Pacific walrus  ----
B D                   Panda  ----
B D                 Ferret   ----
B D                     Cat  ----
B D                   Horse  ====

Alignment block 31 of 54 in window, 41508530 - 41508539, 10 bps 
B D                   Human  ccgtcttggc-
B D                   Chimp  ccgtcttggc-
B D                 Gorilla  ccgtcttggc-
B D               Orangutan  ccgtcttggc-
B D                  Gibbon  ccgtcttggc-
B D                  Rhesus  ccgtcctggc-
B D     Crab-eating macaque  ccgtcctggc-
B D                  Baboon  ccgtcctggc-
B D            Green monkey  ccgtcctggc-
B D                Marmoset  --gtcctggc-
B D         Squirrel monkey  --gtcctggc-
B D                Bushbaby  gggaagtgg--
         Chinese tree shrew  tagctctgga-
B D                Squirrel  --gtcctctg-
               Prairie vole  -----ctctc-
B D                   Mouse  -----ctctg-
B D                     Rat  -----ctctg-
B D                  Rabbit  --ggcc-----
B D                     Pig  -----ctcgc-
B D                  Alpaca  ------ccgc-
             Bactrian camel  ------cggc-
B D                 Dolphin  -----cccgc-
               Killer whale  -----cccgc-
           Tibetan antelope  -----tctgc-
B D                     Cow  -----ttcac-
              Big brown bat  -----cctgc-
B D                Microbat  -----cctgg-
B D                 Manatee  ---------c-
           Cape golden mole  ---------t-
B D                  Tenrec  ---------t-
                   Aardvark  ---------c-
B D               Armadillo  ---------c-
B D             Zebra finch  -----ctgccg
B D                 Chicken  -----tttccg
B D      American alligator  -----ccccca
  D         Green seaturtle  -----acaact
            Golden hamster  -----------
B D                    Pika  ===========
B D         Chinese hamster  -----------
B D          Naked mole-rat  ===========
                Chinchilla  ===========
          Brush-tailed rat  ===========
    Lesser Egyptian jerboa  ===========
B D                 Megabat  ===========
              Weddell seal  -----------
  D          Painted turtle  -----------
B D                Platypus  ===========
B D                   Sheep  ===========
B D                Elephant  ===========
          Black flying-fox  ===========
      David's myotis (bat)  ===========
B D                     Dog  -----------
             Domestic goat  ===========
            Pacific walrus  -----------
B D                   Panda  -----------
B D                 Ferret   -----------
B D                     Cat  -----------
B D        White rhinoceros  -----------
B D                   Horse  ===========

Inserts between block 31 and 32 in window
B D               Squirrel 6bp
B D                  Mouse 8558bp
B D                    Rat 2bp
B D                    Pig 5bp
B D                 Alpaca 5bp
            Bactrian camel 5bp
B D                Dolphin 5bp
              Killer whale 5bp
          Tibetan antelope 5bp
B D                    Cow 5bp
             Big brown bat 4bp
B D               Microbat 2bp
B D                Manatee 1bp
B D                 Tenrec 1bp
                  Aardvark 9bp
B D              Armadillo 9bp

Alignment block 32 of 54 in window, 41508540 - 41508567, 28 bps 
B D                   Human  ct------ccggggaa------------cc--cactg--------------------tagcctc------
B D                   Chimp  ct------ccggggaa------------cc--cactg--------------------tggcctc------
B D                 Gorilla  ct------ccggggaa------------cc--cactg--------------------tggcctc------
B D               Orangutan  ct------ccggggaa------------cc--cactg--------------------tggcttc------
B D                  Gibbon  ct------ccggggaa------------cc--cactg--------------------tggcctc------
B D                  Rhesus  ct------ccggggaa------------cc--cagtg--------------------tggcctc------
B D     Crab-eating macaque  ct------ccggggaa------------cc--cagtg--------------------tggcctc------
B D                  Baboon  ct------ccggggaa------------cc--cagtg--------------------tggcctc------
B D            Green monkey  ct------ccggggaa------------cc--cagtg--------------------tggcctc------
B D                Marmoset  ct------caggggaa-------------c--cactg--------------------tggcctc------
B D         Squirrel monkey  ct------caggggaa-------------c--cactg--------------------tggcctc------
B D                Bushbaby  ----------ggggta------------gcagcaatg--------------------tgacctc------
         Chinese tree shrew  gt------tcgggggg------------ac--caacg--------------------agacctc------
B D                Squirrel  ctctgggctggtggaccgggccaggttggc--ccagg--------------------aggtggc------
               Prairie vole  ------ttctgcggac------------ac--caagg--------------------aggcctc------
B D         Chinese hamster  --------ctagggac------------at--caagg--------------------aggtttc------
             Golden hamster  --------gtgagaac------------at--caagg--------------------aggcctc------
B D                     Rat  --------ttggggac------------gc--caaa----------------------------------
B D                  Rabbit  ---------------------------ggc--cgtgg--------------------cgtctac------
B D                     Pig  ----------------------------------ccc--------------------tgtgccc------
B D                  Alpaca  ----------------------------------ctc--------------------tgtgccc------
             Bactrian camel  ----------------------------------ctc--------------------tgtgccc------
B D                 Dolphin  ----------------------------------ctc--------------------tgtgccc------
               Killer whale  ----------------------------------ctc--------------------tgtgccc------
           Tibetan antelope  ----------------------------------ctc--------------------tgtacct------
B D                     Cow  ----------------------------------ctc--------------------tgtgtcc------
B D        White rhinoceros  ----------------------------------------------------------cagccc------
           Black flying-fox  -----------------------------------tg--------------------tgagccc------
B D                 Megabat  -----------------------------------tg--------------------tgagccc------
              Big brown bat  -----------------------------------cc--------------------tgtgccc------
B D                Microbat  -----------------------------------cc--------------------tgtgtcc------
B D                 Manatee  -----------------------------------------------tgggaa---acgcgcgc------
           Cape golden mole  -----------------------------------------------------------tgccc------
B D                  Tenrec  ---------------------------------------------------------agtgccc------
                   Aardvark  ------------------------------------a--------tgtggaaacctgtgtgact------
B D               Armadillo  ------------------------------------cggaaagtttgcggaga----aaagcct------
B D             Zebra finch  -------------------------------------------------------------ccccatg--
B D                 Chicken  -------------------------------------------------------------ctc------
B D      American alligator  -------------------------------------------------------------ccc------
  D         Green seaturtle  -------------------------------------------------------------cccagccat
  D          Painted turtle  ----------------------------------------------------------------------
B D                    Pika  ======================================================================
B D          Naked mole-rat  ======================================================================
                Chinchilla  ======================================================================
B D                   Mouse  ======================================================================
          Brush-tailed rat  ======================================================================
    Lesser Egyptian jerboa  ======================================================================
              Weddell seal  ----------------------------------------------------------------------
B D                Platypus  ======================================================================
B D                   Sheep  ======================================================================
B D                Elephant  ======================================================================
      David's myotis (bat)  ======================================================================
B D                     Dog  ----------------------------------------------------------------------
             Domestic goat  ======================================================================
            Pacific walrus  ----------------------------------------------------------------------
B D                   Panda  ----------------------------------------------------------------------
B D                 Ferret   ----------------------------------------------------------------------
B D                     Cat  ----------------------------------------------------------------------
B D                   Horse  ======================================================================

                      Human  tgg---------g-----------
                      Chimp  tgg---------g-----------
                    Gorilla  tgg---------g-----------
                  Orangutan  tgt---------g-----------
                     Gibbon  tgt---------g-----------
                     Rhesus  tgt---------g-----------
        Crab-eating macaque  tgt---------g-----------
                     Baboon  tgt---------g-----------
               Green monkey  tgt---------g-----------
                   Marmoset  tgg---------g-----------
            Squirrel monkey  tgg---------g-----------
                   Bushbaby  tgt---------g-----------
         Chinese tree shrew  tgt---------g-----------
                   Squirrel  cct---------------------
               Prairie vole  tgt---------g-----------
            Chinese hamster  tgt---------g-----------
             Golden hamster  tgt---------g-----------
                        Rat  ------------------------
                     Rabbit  ------------------------
                        Pig  acg---------g-----------
                     Alpaca  aag---------g-----------
             Bactrian camel  aag---------g-----------
                    Dolphin  tcg---------g-----------
               Killer whale  tcg---------g-----------
           Tibetan antelope  tag---------g-----------
                        Cow  tag---------g-----------
           White rhinoceros  tcg---------a-----------
           Black flying-fox  gcg---------g-----------
                    Megabat  gcg---------g-----------
              Big brown bat  tcg---------g-----------
                   Microbat  ttg---------g-----------
                    Manatee  acc---------g-----------
           Cape golden mole  ------------------------
                     Tenrec  aca---------g-----------
                   Aardvark  gcagggccgacgg-----------
                  Armadillo  ccc---------c-----------
                Zebra finch  ggg---------accgctcctcgc
                    Chicken  agg---------ggcgccccctgc
         American alligator  tgt---------tcagccccgggg
            Green seaturtle  tgc---------ggcgtgtccg--
             Painted turtle  ggg---------ggcataggag--
                       Pika  ========================
             Naked mole-rat  ========================
                 Chinchilla  ========================
                      Mouse  ========================
           Brush-tailed rat  ========================
     Lesser Egyptian jerboa  ========================
               Weddell seal  ------------------------
                   Platypus  ========================
                      Sheep  ========================
                   Elephant  ========================
       David's myotis (bat)  ========================
                        Dog  ------------------------
              Domestic goat  ========================
             Pacific walrus  ------------------------
                      Panda  ------------------------
                    Ferret   ------------------------
                        Cat  ------------------------
                      Horse  ========================

Inserts between block 32 and 33 in window
          Cape golden mole 11bp
B D            Zebra finch 21bp
  D        Green seaturtle 11bp
  D         Painted turtle 16bp

Alignment block 33 of 54 in window, 41508568 - 41508581, 14 bps 
B D                   Human  caa---------------------------------g--gacccag-------g-gt
B D                   Chimp  caa---------------------------------g--gacccag-------gagt
B D                 Gorilla  caa---------------------------------g--gacccag-------gagt
B D               Orangutan  caa---------------------------------g--gacccag-------gagt
B D                  Gibbon  caa---------------------------------g--gacccag-------gagt
B D                  Rhesus  cag---------------------------------t--gacccag-------gagt
B D     Crab-eating macaque  cag---------------------------------t--gacccag-------gagt
B D                  Baboon  cag---------------------------------t--gacccag-------gagt
B D            Green monkey  cag---------------------------------t--gacccag-------gagt
B D                Marmoset  caa---------------------------------g--gacccag-------gagt
B D         Squirrel monkey  caa---------------------------------g--gacccag-------gagt
B D                Bushbaby  tga---------------------------------g--gacctag-------gagt
         Chinese tree shrew  --a---------------------------------a--gacccag-------t---
B D                Squirrel  --a---------------------------------g--gggaccg-------ctgg
               Prairie vole  caa---------------------------------g--gacccag-------ttgg
B D         Chinese hamster  tca---------------------------------g--gactcag-------ttgg
             Golden hamster  cca---------------------------------g--gatccag-------ttgg
B D                     Rat  --a---------------------------------g--gtcccag-------ttgg
B D                  Rabbit  --a---------------------------------g--gccgcag-------gagg
B D                     Pig  cga---------------------------------g--gacccag-------gcgt
B D                  Alpaca  cga---------------------------------g--gacccag-------gagt
             Bactrian camel  cga---------------------------------g--gacccag-------gagt
B D                 Dolphin  aga---------------------------------g--gacccag-------gagt
               Killer whale  aga---------------------------------g--gacccag-------gagt
           Tibetan antelope  cga---------------------------------g--gacccag-------gaat
B D                     Cow  cga---------------------------------g--gacccag-------gaat
B D        White rhinoceros  ccccggggactcgcgtagcctctgtgcccaaggcgag--gacccag-------gagt
B D                     Cat  ------------------------------------g--gac---a-------gagc
B D                     Dog  ------------------------------------g--gacccgacaagcagaacc
B D                 Ferret   ------------------------------------g--ggcgcga-------ggac
B D                   Panda  ------------------------------------g--gaccaca-------gacc
             Pacific walrus  ------------------------------------g--gacccga-------gagc
               Weddell seal  ------------------------------------g--gacccga-------gagc
           Black flying-fox  cgg---------------------------------g--gacccag-------gagt
B D                 Megabat  cgg---------------------------------g--gacccag-------gagt
              Big brown bat  cga---------------------------------t--g-----------------
B D                Microbat  cga---------------------------------g--g-----------------
B D                 Manatee  tga---------------------------------g--gccccag-------cat-
B D                  Tenrec  tga---------------------------------g--gacccag-------gag-
                   Aardvark  tga---------------------------------g--gatccag-------gag-
B D               Armadillo  cga---------------------------------a--gagccag-------ggt-
B D             Zebra finch  cag---------------------------------ggtggctgag-------ct--
B D      American alligator  cag---------------------------------g--ggctgcg-------ga--
  D          Painted turtle  gga---------------------------------g--ggctggg-------gg--
B D                    Pika  =========================================================
B D          Naked mole-rat  =========================================================
                Chinchilla  =========================================================
B D                   Mouse  =========================================================
          Brush-tailed rat  =========================================================
    Lesser Egyptian jerboa  =========================================================
  D         Green seaturtle  =========================================================
          Cape golden mole  =========================================================
B D                Platypus  =========================================================
B D                   Sheep  =========================================================
B D                Elephant  =========================================================
      David's myotis (bat)  =========================================================
             Domestic goat  =========================================================
B D                   Horse  =========================================================

Inserts between block 33 and 34 in window
B D                Manatee 13bp
B D                 Tenrec 25bp
                  Aardvark 13bp
B D              Armadillo 63bp

Alignment block 34 of 54 in window, 41508582 - 41508635, 54 bps 
B D                   Human  a------gg----------------ccttgggg-a--ctgctggcccaagc-----------------ac
B D                   Chimp  c------gg----------------ccttgggg-a--ctgctggcctaagc-----------------ac
B D                 Gorilla  c------gg----------------ccttgggg-a--ctgctggcccaagc-----------------ac
B D               Orangutan  c------gg----------------ccttggggaa--ccgctggcccaagc-----------------ac
B D                  Gibbon  c------gg----------------ccttggggga--ccgctggcccaagc-----------------ac
B D                  Rhesus  c------ag----------------ccttggggga--ccgctggcccaagc-----------------ac
B D     Crab-eating macaque  c------ag----------------ccttggggga--ccgctggcccaagc-----------------ac
B D                  Baboon  c------ag----------------ccttggggga--ccgctggcccaagc-----------------ac
B D            Green monkey  c------ag----------------ccttggggga--ccactggcccaagc-----------------at
B D                Marmoset  c------gg----------------ccttttggag--ccgctgaccggacc-----------------ac
B D         Squirrel monkey  c------gg----------------ccttttgggg--ccgctgacccgagc-----------------ac
B D                Bushbaby  c------ag----------------cctcagagga--ctactggccccagt-----------------ac
         Chinese tree shrew  --------------------------------------------cccagtc-----------------ac
B D                Squirrel  c--------------------------cc-----a--cgtac---------------------------a
               Prairie vole  c------aa----------------catc-----a--cctct---------------------------a
B D         Chinese hamster  c------aa----------------catc-----a--cctct---------------------------t
             Golden hamster  c------aa----------------catc-----a--cctct---------------------------t
B D                     Rat  g------tg----------------cat----------ccct---------------------------t
B D                  Rabbit  cgcagcgag----------------gacc-----g--ccc------------------------------
B D                     Pig  c------tg----------------ctcccagggc--ccgctggcc-gggc-----------------cc
B D                  Alpaca  c------tg----------------cgcccaggga--ccgctggcccgggc-----------------ag
             Bactrian camel  c------tg----------------cgcccaggga--ccgctggcccgggc-----------------ag
B D                 Dolphin  c------tg----------------ctcccaaggg--ccgctggcccggac-----------------ac
               Killer whale  c------tg----------------ctcccaaggg--ccgctggcccggac-----------------ac
           Tibetan antelope  c------tg----------------cttccggagg--ccgctgacccgggc-----------------gc
B D                     Cow  c------tg----------------gttccagagg--ccgctggcctgggc-----------------gc
B D        White rhinoceros  c------gg-----------------cccccagga--ccgctggcccaggc-----------------ac
B D                     Cat  g------tg--------------------------------tggcctctgt-----------------cc
B D                     Dog  c------ag----------------gcccccagga--cccctggctctggc-----------------gc
B D                 Ferret   c-------------------------ctc--------ccgccggcctagg-------------------c
B D                   Panda  c------ag----------------actccgagga--ctgctggccc-ggc-----------------tc
             Pacific walrus  c------ag----------------cccccgagga--cccctggcccaggc-----------------ac
               Weddell seal  c------ag----------------cccctgagga--cccctggcccaggc-----------------ac
           Black flying-fox  c------ag----------------ccctcggaga--gcgctga-ccaggc-----------------cc
B D                 Megabat  c------ag----------------tccccggaga--gcgctga-ccaggc-----------------cc
              Big brown bat  --------------------------cccctggga--ccgctgacccaggc-----------------ac
B D                Microbat  ---------------------------ccctggga--ccgctgacccaggc-----------------ac
B D                 Manatee  -------atgcagcacgga------gcccagaaga--tc------ctctcc----------------agc
           Cape golden mole  -------aa----------------tcctcgaaga--cctgtggtcgcatc-----------aaaggatt
B D                  Tenrec  -------ag--agcggggagtggcctcctcgaaga--ccttgggcttaaccttttccggtgtggacaaga
                   Aardvark  -------acgcggcacaga------gctgggaa-------------------------------------
B D             Zebra finch  ---------------------------cctggggg--ctgctggccccagc-----------------ac
B D      American alligator  ---------------------------tctgggagacccccctaccccatc-----------------ct
  D         Green seaturtle  ----------------------------ctggaag-----------------------------------
  D          Painted turtle  ---------------------------cctgagag-----------------------------------
B D                    Pika  ======================================================================
B D          Naked mole-rat  ======================================================================
B D               Armadillo  ======================================================================
                Chinchilla  ======================================================================
B D                   Mouse  ======================================================================
          Brush-tailed rat  ======================================================================
    Lesser Egyptian jerboa  ======================================================================
B D                Platypus  ======================================================================
B D                   Sheep  ======================================================================
B D                Elephant  ======================================================================
      David's myotis (bat)  ======================================================================
             Domestic goat  ======================================================================
B D                   Horse  ======================================================================

                      Human  ga---------------gtggcg----gg-------ga-cacagcg-cc----gg-----acg-----
                      Chimp  ga---------------gtggcg----gg-------ga-cacagcg-cc----gg-----acg-----
                    Gorilla  ga---------------gtggcg----gg-------ga-cacagcg-cc----gg-----acg-----
                  Orangutan  ga---------------gtggcg----gg-------ga-cacagcg-cc----gg-----gcg-----
                     Gibbon  ga---------------gtggcg----ag-------ga-cacagcg-cc----gg-----gcg-----
                     Rhesus  ga---------------gtggca----gg-------ga-cacagcg-cc----ag-----gcg-----
        Crab-eating macaque  ga---------------gtggca----gg-------ga-cacagcg-cc----gg-----gcg-----
                     Baboon  ga---------------gtggca----gg-------ga-cacagcg-cc----gg-----gcg-----
               Green monkey  ga---------------gtggca----gg-------ga-cacagcg-cc----gg-----acg-----
                   Marmoset  ga---------------gtggtg----gg-------ga-cgcagcg-cc----gg-----gcg-----
            Squirrel monkey  ga---------------gtggcg----gg-------ga---cagct-gc----gg-----gcg-----
                   Bushbaby  aa---------------g------------------------------c----cg-----gtg-----
         Chinese tree shrew  aa---------------gtgtca----gg-------ga-cgctgcg-cc----tg-----gcg-----
                   Squirrel  aa---------------g-gtcc----gg-------ga-tgcagcg-ccgctggg-----g-g-----
               Prairie vole  aa---------------gcgtag----gt-------gg-ctcagct-cc----ca-----g-g-----
            Chinese hamster  aa---------------gtgtag----tt-------ga-ctcagct-cc----ct-----g-g-----
             Golden hamster  ta---------------gtgtag----gt-------gt-ttcagct-cc----cg-----a-g-----
                        Rat  aa---------------gcatag----gt-------gt-ttcagct-cc----gg-----g-t-----
                     Rabbit  -g---------------gcgcgg----ga-------ga-ccctcccgcc----ga-----g-g-----
                        Pig  tc---------------gagccc----aa-------ga-cgcagcg-ct----tg-----ggg-----
                     Alpaca  ta---------------gagccc----aa-------ggccggagcc-ct----tc-----gcg-----
             Bactrian camel  ta---------------gagccc----aa-------ggacggagcc-ct----tc-----gcg-----
                    Dolphin  ta---------------gagccc----aa-------ga-cgcagcc-ct----ct-----gcg-----
               Killer whale  ta---------------gagccc----aa-------ga-cgcagcc-ct----ct-----gcg-----
           Tibetan antelope  ta---------------gagcct----aa-------gg------------------------------
                        Cow  ta---------------gagtcc----aa-------gg------------------------------
           White rhinoceros  ca---------------gagcca----ga-------ggacgcagcg-cc----gc-----gtg-----
                        Cat  cc---------------acgcaa-----g-------ga----------------------ccg-----
                        Dog  cc--------------------------a-------ggacacagca-cc----gt-----gcg-----
                    Ferret   ca---------------gc-----------------------------------------ttt-----
                      Panda  ca----------------------------------------------------------ccg-----
             Pacific walrus  ca---------------gcgccg-----a-------ggacacaggg-ct----at-----gcg-----
               Weddell seal  ca---------------gcgcca-----a-------ggacacaggg-ct----gt-----gcg-----
           Black flying-fox  ta---------------gggtgg----ga-------ggacccggcg-cc----gt-----gcg-----
                    Megabat  ta---------------gggtgg----ga-------ggacccggcg-cc----gt-----gcg-----
              Big brown bat  ga---------------gcgccc----ga-------gga----------------------cg-----
                   Microbat  ga---------------gcgccc----ga-------gga----------------------cg-----
                    Manatee  ca---------------gcccag----aa---------------------------------------
           Cape golden mole  ca---------------gcaccg----agctcggaa--------------------------------
                     Tenrec  ca---------------gtcccg----gacttgcaa--------------------------------
                   Aardvark  --------------------------------------------------------------------
                Zebra finch  -----------------gggcag----gg-------gg----agca-cg----gc-----gctgcacg
         American alligator  ccatcccattggggagggggcca----gg-------ag----agct-cc----cc-----gcagc---
            Green seaturtle  -----------------gagccccccatg-------ca----ggta-cc----tacagccgggg----
             Painted turtle  -----------------gggcagt---gg-------gg----gggg-cc----ta-----gggg----
                       Pika  ====================================================================
             Naked mole-rat  ====================================================================
                  Armadillo  ====================================================================
                 Chinchilla  ====================================================================
                      Mouse  ====================================================================
           Brush-tailed rat  ====================================================================
     Lesser Egyptian jerboa  ====================================================================
                   Platypus  ====================================================================
                      Sheep  ====================================================================
                   Elephant  ====================================================================
       David's myotis (bat)  ====================================================================
              Domestic goat  ====================================================================
                      Horse  ====================================================================

Inserts between block 34 and 35 in window
B D               Microbat 1bp
B D                 Tenrec 25068bp

Alignment block 35 of 54 in window, 41508636 - 41508640, 5 bps 
B D                   Human  -cccaa
B D                   Chimp  -cccaa
B D                 Gorilla  -cccaa
B D               Orangutan  -ctcaa
B D                  Gibbon  -cccaa
B D                  Rhesus  -cccaa
B D     Crab-eating macaque  -cccaa
B D                  Baboon  -cccaa
B D            Green monkey  -cccaa
B D                Marmoset  -ccaaa
B D         Squirrel monkey  -ccaaa
B D                Bushbaby  -acaag
         Chinese tree shrew  -tctgg
B D                Squirrel  -ccaag
               Prairie vole  -ctaaa
B D         Chinese hamster  -ctaaa
             Golden hamster  -ctgaa
B D                     Rat  -ttaag
B D                  Rabbit  -cccgg
B D                     Pig  -tgggg
B D                  Alpaca  -ccaag
             Bactrian camel  -ccaag
B D                 Dolphin  -ccgag
               Killer whale  -ccgag
B D        White rhinoceros  -ccaac
B D                     Cat  -ccgag
B D                     Dog  -ccaag
B D                 Ferret   -ccctg
B D                   Panda  -ccgag
             Pacific walrus  -ccgag
               Weddell seal  -ccgag
           Black flying-fox  -ccaac
B D                 Megabat  -ccaac
              Big brown bat  -cccag
B D                Microbat  -cccaa
B D      American alligator  tccaa-
  D         Green seaturtle  atcga-
  D          Painted turtle  tggaa-
B D                    Pika  ======
B D                  Tenrec  ======
B D          Naked mole-rat  ======
B D               Armadillo  ======
                Chinchilla  ======
B D                   Mouse  ======
          Brush-tailed rat  ======
    Lesser Egyptian jerboa  ======
                  Aardvark  ------
          Cape golden mole  ------
B D                 Manatee  ------
B D                Platypus  ======
B D                   Sheep  ======
B D                     Cow  ------
          Tibetan antelope  ------
B D                Elephant  ======
      David's myotis (bat)  ======
             Domestic goat  ======
B D                   Horse  ======

Alignment block 36 of 54 in window, 41508641 - 41508644, 4 bps 
B D                   Human  ga---c-----c-
B D                   Chimp  ga---c-----c-
B D                 Gorilla  ga---c-----c-
B D               Orangutan  ga---c-----c-
B D                  Gibbon  ga---c-----c-
B D                  Rhesus  ga---c-----c-
B D     Crab-eating macaque  ga---c-----c-
B D                  Baboon  ga---c-----c-
B D            Green monkey  ga---c-----c-
B D                Marmoset  ga---c-----c-
B D         Squirrel monkey  ga---c-----c-
B D                Bushbaby  ga---c-----c-
         Chinese tree shrew  ga---t-----c-
B D                Squirrel  ga---c-----c-
               Prairie vole  ga---c-----c-
B D         Chinese hamster  ga---c-----c-
             Golden hamster  ga---c-----c-
B D                     Rat  ga---c-----a-
B D                  Rabbit  gc---cggcctc-
B D                     Pig  -a---c-----c-
B D                  Alpaca  ga---c-----c-
             Bactrian camel  ga---c-----c-
B D                 Dolphin  ca---c-----c-
               Killer whale  ca---c-----c-
           Tibetan antelope  -a---c-----c-
B D                     Cow  -a-----------
B D        White rhinoceros  ga-----------
B D                     Cat  ga-----------
B D                     Dog  gc-----------
B D                 Ferret   g------------
B D                   Panda  ga-----------
             Pacific walrus  ga-----------
               Weddell seal  ga-----------
           Black flying-fox  gacccc-----c-
B D                 Megabat  gacccc-----c-
              Big brown bat  ga---c-----c-
B D                Microbat  cacccc-----c-
B D                 Manatee  ga---t-----c-
           Cape golden mole  ga---t-----c-
                   Aardvark  aa---t-----c-
B D      American alligator  ---------cacc
  D         Green seaturtle  ---------ggca
  D          Painted turtle  ---------ggcc
B D                    Pika  =============
B D                  Tenrec  =============
B D          Naked mole-rat  =============
B D               Armadillo  =============
                Chinchilla  =============
B D                   Mouse  =============
          Brush-tailed rat  =============
    Lesser Egyptian jerboa  =============
B D                Platypus  =============
B D                   Sheep  =============
B D                Elephant  =============
      David's myotis (bat)  =============
             Domestic goat  =============
B D                   Horse  =============

Alignment block 37 of 54 in window, 41508645 - 41508654, 10 bps 
B D                   Human  ct--ccc--cagtc
B D                   Chimp  ct--ccc--cagtc
B D                 Gorilla  ct--ccc--cagtc
B D               Orangutan  ct--ccc--cagtc
B D                  Gibbon  ct--ccc--cagtc
B D                  Rhesus  ct--ccc--cagtc
B D     Crab-eating macaque  ct--ccc--cagtc
B D                  Baboon  ct--ccc--cagtc
B D            Green monkey  ct--ccc--cagtc
B D                Marmoset  ct--ccc--gagac
B D         Squirrel monkey  ct--tcc--cagac
B D                Bushbaby  ct--tcc-tcagtg
         Chinese tree shrew  ct--ccc--taggc
B D                Squirrel  ct--tct--cggtt
               Prairie vole  ct--ccc--tagtg
B D         Chinese hamster  ct--ctc--tagtg
             Golden hamster  ct--ccc--tagtg
B D                     Rat  ct--ctc--cggtg
B D                  Rabbit  ct--ccg--tcctg
B D                     Pig  ct--ccc--caatc
B D                  Alpaca  ct--ccg--cagtc
             Bactrian camel  ct--ccg--cagtc
B D                 Dolphin  ct--ccc--cagtc
               Killer whale  ct--ccc--cagtg
           Tibetan antelope  ct--ccc--cagtc
B D                     Cow  ----ccc--cagtc
B D        White rhinoceros  cc--ctcggcagtc
B D                     Cat  ccctctc--cagcc
B D                     Dog  cc--gtc--cagcc
B D                 Ferret   -c--ctg--cagct
B D                   Panda  cc--ctc--cagcc
             Pacific walrus  cc--ctc--cagcc
               Weddell seal  cc--ctc--cagcc
           Black flying-fox  tc--ccc--taagc
B D                 Megabat  tc--ccc--taagc
              Big brown bat  ct--ccc--tggcc
B D                Microbat  cc--ccc--cagtc
B D                 Manatee  ct--ccc--cagcc
           Cape golden mole  ct--ccc--taggc
                   Aardvark  ct--cct--cagcc
B D      American alligator  ----ccc--tcccc
  D         Green seaturtle  --gcccc--aagcc
B D                    Pika  ==============
B D                  Tenrec  ==============
B D          Naked mole-rat  ==============
B D               Armadillo  ==============
                Chinchilla  ==============
B D                   Mouse  ==============
          Brush-tailed rat  ==============
    Lesser Egyptian jerboa  ==============
B D                Platypus  ==============
B D                   Sheep  ==============
B D                Elephant  ==============
      David's myotis (bat)  ==============
             Domestic goat  ==============
B D                   Horse  ==============

Inserts between block 37 and 38 in window
                  Aardvark 26980bp

Alignment block 38 of 54 in window, 41508655 - 41508657, 3 bps 
B D                   Human  cgc
B D                   Chimp  cgc
B D                 Gorilla  cgc
B D               Orangutan  cgc
B D                  Gibbon  cgc
B D                  Rhesus  cgc
B D     Crab-eating macaque  cgc
B D                  Baboon  cgc
B D            Green monkey  cgc
B D                Marmoset  ctc
B D         Squirrel monkey  ctc
B D                Bushbaby  gcc
         Chinese tree shrew  t--
B D                Squirrel  ccc
               Prairie vole  tgc
B D         Chinese hamster  tgc
             Golden hamster  tgc
B D                     Rat  aag
B D                  Rabbit  ggg
B D                     Pig  cgc
B D                  Alpaca  cgc
             Bactrian camel  cgt
B D                 Dolphin  ttc
               Killer whale  ctc
           Tibetan antelope  ctc
B D                     Cow  cta
B D        White rhinoceros  cta
B D                     Cat  ctc
B D                     Dog  cac
B D                 Ferret   ccc
B D                   Panda  tgc
             Pacific walrus  tgc
               Weddell seal  tgc
           Black flying-fox  gcc
B D                 Megabat  tcc
              Big brown bat  ctc
B D                Microbat  ttt
B D                 Manatee  cac
           Cape golden mole  cac
B D      American alligator  tgc
  D         Green seaturtle  tgc
B D                    Pika  ===
B D                  Tenrec  ===
B D          Naked mole-rat  ===
B D               Armadillo  ===
                Chinchilla  ===
B D                   Mouse  ===
          Brush-tailed rat  ===
    Lesser Egyptian jerboa  ===
                  Aardvark  ===
B D                Platypus  ===
B D                   Sheep  ===
B D                Elephant  ===
      David's myotis (bat)  ===
             Domestic goat  ===
B D                   Horse  ===

Alignment block 39 of 54 in window, 41508658 - 41508675, 18 bps 
B D                   Human  -----------ctaggctggcatttcttg
B D                   Chimp  -----------ctaggctggcatttcttg
B D                 Gorilla  -----------ctaggctggcatttcttg
B D               Orangutan  -----------ctaggctggcctttcttg
B D                  Gibbon  -----------ctaggctggcctttcttg
B D                  Rhesus  -----------ctaggctggcctttcttg
B D     Crab-eating macaque  -----------ctaggctggcctttcttg
B D                  Baboon  -----------ctaggctggcctttcttg
B D            Green monkey  -----------ctaggctggcctttcttg
B D                Marmoset  -----------ctagaatgtcctttcttg
B D         Squirrel monkey  -----------ctagactggcctttcttg
B D                Bushbaby  -----------ctcagccagcctttctca
         Chinese tree shrew  ---------------acagtccgatctca
B D                Squirrel  -----------cttggcttttctt-----
               Prairie vole  -----------ccagactttccta-----
B D         Chinese hamster  -----------ccaggctttcctg-----
             Golden hamster  -----------ccagggtttccgg-----
B D                     Rat  -----------ccaggctttccta-----
B D                  Rabbit  -----------ccaaagtcccttg-----
B D                     Pig  -----------tcggg-tggcccttctcg
B D                  Alpaca  -----------tgggg-cggcatctctct
             Bactrian camel  -----------tgggg-cggcatctctct
B D                 Dolphin  -----------ttggg-cggctcttctct
               Killer whale  -----------ttggg-cggctcttctct
           Tibetan antelope  -----------ttggg-gggcctttttct
B D                     Cow  -----------ttggg-gggcctttttct
B D        White rhinoceros  -----------ctgtg-cggcctttccct
B D                     Cat  -----------ctgtgcctgccttttttt
B D                     Dog  -----------cggtgccagcctttcctg
B D                 Ferret   -----------aagttccaa-----gtcc
B D                   Panda  -----------ctgggccagcctttcttt
             Pacific walrus  -----------ctgggccagcctttcttt
               Weddell seal  -----------ctgggccagcctttcttt
           Black flying-fox  -----------ctgtg-cgtcttttctct
B D                 Megabat  -----------ctgtg-cgtcttttctct
              Big brown bat  -----------ctgag-ccgcccgtctc-
B D                Microbat  -----------ctgag-ccccccttctct
B D                 Manatee  -----------ctcagtcggcctttg---
           Cape golden mole  -----------ct-----ggac-------
B D      American alligator  tgcagggcaccccgaa-------------
B D                    Pika  =============================
B D                  Tenrec  =============================
B D          Naked mole-rat  =============================
B D               Armadillo  =============================
                Chinchilla  =============================
B D                   Mouse  =============================
          Brush-tailed rat  =============================
    Lesser Egyptian jerboa  =============================
                  Aardvark  =============================
B D                Platypus  =============================
B D                   Sheep  =============================
B D                Elephant  =============================
      David's myotis (bat)  =============================
             Domestic goat  =============================
B D                   Horse  =============================

Inserts between block 39 and 40 in window
B D               Squirrel 12bp
              Prairie vole 46bp
B D        Chinese hamster 110bp
            Golden hamster 18bp
B D                    Rat 9bp
B D                    Pig 15bp
B D                 Alpaca 15bp
            Bactrian camel 15bp
B D                Dolphin 15bp
              Killer whale 15bp
          Tibetan antelope 15bp
B D                    Cow 15bp
B D       White rhinoceros 13bp
B D                    Cat 15bp
B D                    Dog 15bp
B D                Ferret  15bp
B D                  Panda 15bp
            Pacific walrus 15bp
              Weddell seal 15bp
          Black flying-fox 15bp
B D                Megabat 15bp
B D               Microbat 14bp

Alignment block 40 of 54 in window, 41508676 - 41508779, 104 bps 
B D                   Human  g-----cccc----cac----c---------agc-gtc--------c-gg-tggaaagtg--ctcccccg
B D                   Chimp  g-----cccc----cac----c---------agc-gtc--------c-gg-tggaaatgg--ctcccccg
B D                 Gorilla  g-----cccc----cac----c---------agc-gtc--------c-gg-tggaaaggg--cgccccag
B D               Orangutan  g-----cccc----cac----c---------agc-gtc--------c-tg-tggaaaggg--ctccccag
B D                  Gibbon  g-----ctcc----cac----c---------agc-gta--------c-gg-tggaaaggg--ctccccag
B D                  Rhesus  g-----cccc----cac----c---------agc-gtc--------c-ag-tggaaaggg--ctccccag
B D     Crab-eating macaque  g-----cccc----cac----c---------agc-gtc--------c-ag-tggaaaggg--ctccccag
B D                  Baboon  g-----cccc----cac----c---------agc-gtc--------c-ag-tggaaaggg--ctccccag
B D            Green monkey  g-----cccc----cac----c---------agc-gtc--------c-ag-tggaaaggg--ctccccag
B D                Marmoset  g------tcc----cgc----c---------agc-gtc--------c-ct-tggaaaggg--gtccccag
B D         Squirrel monkey  g-----cccc----cgc----c---------agc-gtt--------c-tg-tggaaaggg--gtccccag
B D                Bushbaby  g------ccc----tgg----a---------aac-gtc--------cttg-aagaagggg--ctcccagg
         Chinese tree shrew  a-----atcc----ctt----c---------agctgtcggagcctgc-ag-tggaaaaga--ctccgcag
B D                Squirrel  g-----cctccagtctc----ccctcctcctaac-gtc--------t-cc-tggacagcg--ttccccag
               Prairie vole  g-----cccccagcacc----c---------aaa-gtc--------c-cc-tgggaagc-----ttccag
             Golden hamster  g-----tccgaagcccc----c---------aaa-gtt--------c-cc-tgggaagc-----ttccag
B D                     Rat  a-----tct