Multiz Alignments of 100 Vertebrates
 

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Alignment block 1 of 1479 in window, 49539157 - 49539194, 38 bps 
B D                     Human  gg----ccgcgg-ggc-----ctggag------cccggg--------------a-------------ttt
B D                     Chimp  gg----ccgcgg-ggc-----ctggag------cccggg--------------a-------------ttt
B D                   Gorilla  gg----ccgcgg-ggc-----ctggag------cccggg--------------a-------------ttt
B D                 Orangutan  gg----ccgcgg-ggc-----ctggag------cccggg--------------a-------------ttc
B D       Crab-eating macaque  gg----ctgcgg-ggc-----ctggag------cccggg--------------a-------------ttt
B D                    Baboon  gg----ctgcgg-ggc-----ctggag------cccggg--------------a-------------ttc
B D              Green monkey  gg----ctgcgg-ggc-----ctggag------cccggg--------------a-------------ttc
B D                  Marmoset  gg----ctgcgg-agc-----ctggag------cccagg--------------a-------------ttc
B D                  Bushbaby  gg----cctcgg-aac-----ctggag------cctggg--------------a-------------ttt
B D                  Squirrel  ag----cttcgg-agc-----ttggag------cccggg--------------a-------------ttc
       Lesser Egyptian jerboa  gg----ccgcgg-ggc-----ctggaa------cccggg--------------a-------------ttc
                 Prairie vole  gg----ctgcgg-ggc-----cggcag------cccgga--------------a-------------tcc
               Golden hamster  gg----ccgcgg-ggc-----ctgcag------cccgga--------------a-------------tcc
B D                     Mouse  gg----ccgcgg-ggc-----ctgcag------cccgga--------------a-------------tcc
B D                       Rat  gg----ccgcgg-ggc-----ctgcag------cccgga--------------a-------------tcc
B D            Naked mole-rat  gg----cttcgg-agc-----ctggaa------ccaggg--------------a-------------ttc
B D                Guinea pig  ag----attcgg-agc-----ctggat------ccaggg--------------a-------------ttt
             Brush-tailed rat  gg----cttcgg-agc-----ctggag------cccgag--------------a-------------ttc
B D                    Rabbit  gg----ccgcgg-ggc-----gcgggg------cccggg--------------c-------------ttc
B D                      Pika  gg----ccgcgg-agc-----ctggag------ccccgg--------------c-------------tt-
B D                       Pig  gg----gcgccg-agc-----ggggag------tccggg--------------a-------------ttc
B D                   Dolphin  gg----gcgcgg-agc-----cgggag------tccggg--------------a-------------atc
                 Killer whale  gg----gcgcgg-agc-----cgggag------tccggg--------------a-------------atc
B D                       Cow  gc----gagcgg-agc-----cgcgag------tccagg--------------a-------------ttc
B D                     Sheep  gc----gagcgg-agc-----cgcgag------tccagg--------------a-------------ttc
B D                     Horse  gg----gcgaag-ggc-----ccgtag------cccggg--------------a-------------ttc
B D          White rhinoceros  gg----gcgaag-ggc-----ccgtag------ctcggg--------------a-------------ttc
B D                       Cat  ga----gcgcgg-agt-----ctggag------cccggc--------------a-------------ttc
B D                       Dog  gg----gcggcg-gg-------cgg----------cggg--------------c-------------ggc
               Pacific walrus  gg----gcgacg-agc-----tcggag------cccggg--------------a-------------ttc
             Black flying-fox  cg----gcgcgg-agc-----cgggag------cccagg--------------a-------------ttc
B D                   Megabat  cg----gcgcgg-agc-----cgggag------cccagg--------------a-------------ttc
                Big brown bat  cg----gcgctg-agc-----ctggag------cccggg--------------a-------------ttc
B D                  Microbat  cg----gcgctgtagt-----ctggag------ccgggg--------------a-------------ttc
B D                  Hedgehog  -g----gcgccg-agc-----cgggcg------gccagg--------------g-------------cag
B D                  Elephant  gg----gcgcgg-agc-----ccggag------ctc----------------------------------
          Cape elephant shrew  gg----gcacag-cac-----ccggag------ctc----------------------------------
B D                   Manatee  cg----gcgcgg-agc-----ccggag------ctc----------------------------------
             Cape golden mole  gg----gcgcgg-cgc-----ccggaa------ctt----------------------------------
                     Aardvark  ga----gcgccg-ctc-----ccggat------ctt----------------------------------
B D                 Armadillo  gg----cctctg-ctg-----gcggag------cgcg---------------------------------
B D                   Opossum  ag----aattga-gcc-----tggagc------cc------------------a----------------
B D           Tasmanian devil  gg----aagagg-gac-----tcgaac------ccgggg--------------a----------------
B D                   Wallaby  gg----aagcgg-gac-----ccgaac------cctagg--------------a----------------
B D                  Platypus  gc----ttgtag-agt-----tggagg------ggaggg--------------agaa-----agagtcca
  D               Rock pigeon  cg----ctgaca-agc-----gggggg------ctcccg--------------g----------------
  D              Saker falcon  tc----ctg------c-----ggggca------cccacc--------------a----------------
  D          Peregrine falcon  tc----ctgtgc-ctc-----gtgccactacagcccaca--------------t----------------
  D       Collared flycatcher  ca----cctcct-ggc-----tcccag------ctcgtc--------------t----------------
  D    White-throated sparrow  gg----ctgacg-agc-----gggggg------ctcccg--------------g----------------
B D               Zebra finch  tc----cccgcg-cgc-----cccggg------cccgcc--------------c----------------
           Tibetan ground jay  tg----ccgagc-ggc-----tcccgg------tgctcc--------------c----------------
B D                Budgerigar  cc----cc---c-ctc-----cctctt------tgctct-------------gt----------------
  D             Scarlet macaw  cc----ccaggc-ttc-----cctcaa------atctcc--------------t----------------
  D              Mallard duck  ag----gatggc-cgcgggctgcgggg------tcgggg--------------t----------------
B D                   Chicken  ag----cggagc-cgc-----gcgcag------ccgagc--------------a----------------
B D                    Turkey  ga----gtgggg-tgc-----acggag------ttgggg--------------t----------------
B D        American alligator  ag----gttgct-tgc-----taaacc------ccggcc--------------g----------------
  D           Green seaturtle  gc----ccagct-gac-----tcgggg------ctggcgagcagtgtagatggt----------------
  D            Painted turtle  gcttctccgctc-gcc-----ccggcg------ctg----------------------------------
  D  Chinese softshell turtle  gc----tcagcc-gcc-----gggagc------cgggcagctggtggaaggggg----------------
B D                    Lizard  ag----gaaagg-cgc-----ccgaag------cagccc--------------a----------------
B D             X. tropicalis  tg----t----g-cgc-----ctatcg------ccgggg--------------c-----------aatga
B D                 Tetraodon  cg----cagcag-acc-----gcagag------t------------------------------------
B D               Stickleback  tg----tggaag-gaa-----gcgg---------------------------------------------
B D              Atlantic cod  tg----cgggcc-gac-----cccgcg------c------------------------------------
     Mexican tetra (cavefish)  -----------g-aag-----ccagcg------c------------------------------------
                  Spotted gar  cg----ggtctg-gcc-----ccggcg------a------------------------------------
B D                   Lamprey  gg----tagcgg-ggc-----ccagag------ctcgct--------------cagagcgcggggctcct
B D                Coelacanth  ======================================================================
B D                     Shrew  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D                    Rhesus  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D                    Gibbon  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D                 Zebrafish  ======================================================================
                  Chinchilla  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
          Chinese tree shrew  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D           Chinese hamster  ----------------------------------------------------------------------
B D                    Tenrec  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D                   Ferret   NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D                     Panda  ======================================================================
               Domestic goat  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
            Tibetan antelope  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
             Star-nosed mole  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
              Bactrian camel  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D                    Alpaca  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
                Weddell seal  ======================================================================
        David's myotis (bat)  ======================================================================
B D           Squirrel monkey  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

                        Human  gtgggcggcga
                        Chimp  gtgggcggcga
                      Gorilla  gtgggcggcga
                    Orangutan  gtgggcggcga
          Crab-eating macaque  gtgggcggcga
                       Baboon  gtgggcggcga
                 Green monkey  gtgggcggcga
                     Marmoset  gtgggccgcga
                     Bushbaby  gtgagcgatca
                     Squirrel  gtgggcggcga
       Lesser Egyptian jerboa  gcaggcagcca
                 Prairie vole  gtgggcggcga
               Golden hamster  gtgggcggcga
                        Mouse  gtgggcggcga
                          Rat  gtgggcggcga
               Naked mole-rat  gtgggtggcga
                   Guinea pig  gtgggtggcga
             Brush-tailed rat  gtgggcggcga
                       Rabbit  gtgggcggcga
                         Pika  -----------
                          Pig  gtgggcggcca
                      Dolphin  gtgggcggcca
                 Killer whale  gtgggcggcca
                          Cow  gtgggctgcca
                        Sheep  gtgggctgcca
                        Horse  gtgggcggcca
             White rhinoceros  gtgggcggcca
                          Cat  gtgggcggcca
                          Dog  gagcggggccg
               Pacific walrus  gtgggcggcca
             Black flying-fox  gtgggcggccg
                      Megabat  gtgggcggccg
                Big brown bat  gggggcggccg
                     Microbat  gtgggcggccg
                     Hedgehog  gtgggccgcga
                     Elephant  gtgggtggtga
          Cape elephant shrew  -tgggtagtta
                      Manatee  gtgggtggtga
             Cape golden mole  gtgggtggtga
                     Aardvark  gtgggtgggga
                    Armadillo  gggggcggcgg
                      Opossum  -----------
              Tasmanian devil  -----------
                      Wallaby  -----------
                     Platypus  gagggcggaga
                  Rock pigeon  -----------
                 Saker falcon  -----------
             Peregrine falcon  -----------
          Collared flycatcher  -----------
       White-throated sparrow  -----------
                  Zebra finch  -----------
           Tibetan ground jay  -----------
                   Budgerigar  -----------
                Scarlet macaw  -----------
                 Mallard duck  -----------
                      Chicken  -----------
                       Turkey  -----------
           American alligator  -----------
              Green seaturtle  -----------
               Painted turtle  -----------
     Chinese softshell turtle  -----------
                       Lizard  -----------
                X. tropicalis  gtgagcgcag-
                    Tetraodon  -----------
                  Stickleback  -----------
                 Atlantic cod  -----------
     Mexican tetra (cavefish)  -----------
                  Spotted gar  -----------
                      Lamprey  gtgcccgggga
                   Coelacanth  ===========
                        Shrew  NNNNNNNNNNN
                       Rhesus  NNNNNNNNNNN
                       Gibbon  NNNNNNNNNNN
                    Zebrafish  ===========
                   Chinchilla  NNNNNNNNNNN
           Chinese tree shrew  NNNNNNNNNNN
              Chinese hamster  -----------
                       Tenrec  NNNNNNNNNNN
                      Ferret   NNNNNNNNNNN
                        Panda  ===========
                Domestic goat  NNNNNNNNNNN
             Tibetan antelope  NNNNNNNNNNN
              Star-nosed mole  NNNNNNNNNNN
               Bactrian camel  NNNNNNNNNNN
                       Alpaca  NNNNNNNNNNN
                 Weddell seal  ===========
         David's myotis (bat)  ===========
              Squirrel monkey  NNNNNNNNNNN

Alignment block 2 of 1479 in window, 49539195 - 49539196, 2 bps 
B D                     Human  gg
B D                     Chimp  gg
B D                   Gorilla  gg
B D                 Orangutan  gg
B D       Crab-eating macaque  gg
B D                    Baboon  gg
B D              Green monkey  gg
B D                  Marmoset  gg
B D                  Bushbaby  gg
B D                  Squirrel  gg
       Lesser Egyptian jerboa  gg
                 Prairie vole  gg
               Golden hamster  gg
B D                     Mouse  gg
B D                       Rat  gg
B D            Naked mole-rat  gg
B D                Guinea pig  gg
             Brush-tailed rat  gg
B D                    Rabbit  gg
B D                       Pig  gg
B D                   Dolphin  gg
                 Killer whale  gg
B D                       Cow  gg
B D                     Sheep  gg
B D                     Horse  gg
B D          White rhinoceros  gg
B D                       Cat  gg
B D                       Dog  gg
               Pacific walrus  gg
             Black flying-fox  ga
B D                   Megabat  ga
                Big brown bat  ga
B D                  Microbat  ga
B D                  Elephant  gg
          Cape elephant shrew  gg
B D                   Manatee  gg
             Cape golden mole  gg
                     Aardvark  gg
B D                 Armadillo  gg
B D                   Opossum  -g
B D           Tasmanian devil  -g
B D                   Wallaby  -g
B D                  Platypus  gg
  D               Rock pigeon  cg
  D              Saker falcon  gc
  D          Peregrine falcon  gg
  D       Collared flycatcher  gg
  D    White-throated sparrow  cg
B D               Zebra finch  cg
           Tibetan ground jay  gg
B D                Budgerigar  gg
  D             Scarlet macaw  gg
  D              Mallard duck  at
B D                   Chicken  gc
B D                    Turkey  gt
B D        American alligator  gg
  D           Green seaturtle  ga
  D            Painted turtle  gg
  D  Chinese softshell turtle  ga
B D                    Lizard  gc
B D             X. tropicalis  ag
B D                 Tetraodon  -a
B D              Atlantic cod  -g
     Mexican tetra (cavefish)  -g
                  Spotted gar  -a
B D                   Lamprey  gg
B D                  Hedgehog  NN
B D                      Pika  --
B D                Coelacanth  ==
B D                     Shrew  NN
B D                    Rhesus  NN
B D                    Gibbon  NN
B D               Stickleback  --
B D                 Zebrafish  ==
                  Chinchilla  NN
          Chinese tree shrew  NN
B D           Chinese hamster  --
B D                    Tenrec  NN
B D                   Ferret   NN
B D                     Panda  ==
               Domestic goat  NN
            Tibetan antelope  NN
             Star-nosed mole  NN
              Bactrian camel  NN
B D                    Alpaca  NN
                Weddell seal  ==
        David's myotis (bat)  ==
B D           Squirrel monkey  NN

Inserts between block 2 and 3 in window
B D                  Opossum 1bp
B D          Tasmanian devil 1bp
B D                  Wallaby 1bp
B D                Tetraodon 1bp
B D             Atlantic cod 1bp
    Mexican tetra (cavefish) 1bp
                 Spotted gar 1bp

Alignment block 3 of 1479 in window, 49539197 - 49539203, 7 bps 
B D                     Human  g----------c--------gcgag------------
B D                     Chimp  g----------c--------gcgag------------
B D                   Gorilla  g----------c--------gcgag------------
B D                 Orangutan  g----------c--------gcgag------------
B D       Crab-eating macaque  g----------t--------gcgag------------
B D                    Baboon  g----------t--------gagag------------
B D              Green monkey  g----------t--------gcgag------------
B D                  Marmoset  g----------c--------gctag------------
B D                  Bushbaby  g----------c--------gcgag------------
B D                  Squirrel  g----------c--------gctag------------
       Lesser Egyptian jerboa  g----------c--------t----------------
                 Prairie vole  g----------g--------tc---------------
B D                     Mouse  g----------g--------tc---------------
B D                       Rat  g----------g--------tc---------------
B D            Naked mole-rat  g----------c--------gcgag------------
B D                Guinea pig  g----------c--------gcgag------------
             Brush-tailed rat  c----------c--------gccag------------
B D                    Rabbit  g----------c--------gcgag------------
B D                      Pika  ---------------------tgag------------
B D                       Pig  g----------c--------gcaag------------
B D                   Dolphin  g----------c--------gcgag------------
                 Killer whale  g----------c--------gcgag------------
B D                       Cow  g----------c--------gcgag------------
B D                     Sheep  g----------c--------gcgag------------
B D                     Horse  g----------c--------gcaag------------
B D          White rhinoceros  g----------c--------gcgag------------
B D                       Cat  a----------c--------gcgag------------
B D                       Dog  gct--------c--------gtggg------------
               Pacific walrus  a----------c--------gcgag------------
             Black flying-fox  g----------a--------gcgag------------
B D                   Megabat  g----------a--------gcgag------------
                Big brown bat  g----------c--------gcgag------------
B D                  Microbat  g----------c--------gcgag------------
B D                  Elephant  g----------c--------gcaag------------
          Cape elephant shrew  g----------c--------gcgtg------------
             Cape golden mole  g----------c--------gcgag------------
                     Aardvark  g----------c--------gggag------------
B D                 Armadillo  g----------c--------gcgag------------
B D                   Opossum  a----------c--------agaga------------
B D           Tasmanian devil  a----------c--------gggag------------
B D                   Wallaby  a----------c--------gggag------------
B D                  Platypus  g----------t--------cttgg------------
  D               Rock pigeon  -c---------c--------ggagg------------
  D              Saker falcon  -ag--------a--------gcttg------------
  D          Peregrine falcon  -ga--------aatgctgctgtttg------------
  D       Collared flycatcher  -at--------c--------aaatg------------
  D    White-throated sparrow  -c---------c--------ggagg------------
B D               Zebra finch  -ct--------c--------ggccg------------
           Tibetan ground jay  -ta--------c--------g---g------------
B D                Budgerigar  -ag--------g--------gggga------------
  D             Scarlet macaw  -ag--------c--------agggg------------
  D              Mallard duck  -ttgtggcagcg--------agggg------------
B D                   Chicken  -tg--------c--------cggtg------------
B D                    Turkey  -ggggagca--c--------ggagg------------
B D        American alligator  -atg-------c--------tggag------------
  D           Green seaturtle  -gg--------c--------aggca------------
  D            Painted turtle  -gg--------c--------ggccc------------
  D  Chinese softshell turtle  -gg--------c---------gccg------------
B D                    Lizard  -agcgagga--t--------ggggg------------
B D             X. tropicalis  --------------------acgca------------
B D                 Tetraodon  ----------gc--------ctggc------------
B D               Stickleback  ----------ga--------ctgaa------------
B D              Atlantic cod  ----------cc--------tgaga------------
     Mexican tetra (cavefish)  ----------cc--------tgtga------------
                  Spotted gar  ----------tt--------gcgag------------
B D                   Lamprey  ----------------------gggcttctccgccgc
B D                  Hedgehog  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D                Coelacanth  =====================================
B D                     Shrew  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
              Golden hamster  -------------------------------------
B D                    Rhesus  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D                    Gibbon  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D                 Zebrafish  =====================================
                  Chinchilla  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
          Chinese tree shrew  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D                   Manatee  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D           Chinese hamster  -------------------------------------
B D                    Tenrec  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D                   Ferret   NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D                     Panda  =====================================
               Domestic goat  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
            Tibetan antelope  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
             Star-nosed mole  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
              Bactrian camel  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D                    Alpaca  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
                Weddell seal  =====================================
        David's myotis (bat)  =====================================
B D           Squirrel monkey  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

Inserts between block 3 and 4 in window
B D                Tetraodon 38bp
B D             Atlantic cod 5bp
    Mexican tetra (cavefish) 17bp

Alignment block 4 of 1479 in window, 49539204 - 49539206, 3 bps 
B D                     Human  ggg--
B D                     Chimp  ggg--
B D                   Gorilla  ggg--
B D                 Orangutan  ggg--
B D       Crab-eating macaque  ggg--
B D                    Baboon  ggg--
B D              Green monkey  ggg--
B D                  Marmoset  ggg--
B D                  Bushbaby  ggg--
B D                  Squirrel  ggg--
                 Prairie vole  -gg--
               Golden hamster  -gg--
B D                     Mouse  -gc--
B D                       Rat  -gc--
B D            Naked mole-rat  ggg--
B D                Guinea pig  ggg--
             Brush-tailed rat  ggg--
B D                    Rabbit  ggg--
B D                      Pika  ggg--
B D                       Pig  gag--
B D                   Dolphin  gag--
                 Killer whale  gag--
B D                       Cow  gag--
B D                     Sheep  gag--
B D                     Horse  ggg--
B D          White rhinoceros  gga--
B D                       Cat  agg--
B D                       Dog  cgg--
               Pacific walrus  agg--
             Black flying-fox  ggg--
B D                   Megabat  ggg--
                Big brown bat  ggg--
B D                  Microbat  ggg--
B D                  Elephant  ggg--
          Cape elephant shrew  ggg--
             Cape golden mole  ggg--
                     Aardvark  ggg--
B D                 Armadillo  ggg--
B D           Tasmanian devil  gaa--
B D                   Wallaby  gag--
B D                  Platypus  ggt--
  D               Rock pigeon  cgg--
  D              Saker falcon  ggg--
  D          Peregrine falcon  tgg--
  D       Collared flycatcher  tgc--
  D    White-throated sparrow  cgg--
B D               Zebra finch  cag--
           Tibetan ground jay  cgg--
B D                Budgerigar  cgg--
  D             Scarlet macaw  tat--
  D              Mallard duck  gct--
B D                   Chicken  ccc--
B D                    Turkey  gct--
B D        American alligator  cgg--
  D           Green seaturtle  ctg--
  D            Painted turtle  ctc--
  D  Chinese softshell turtle  ctc--
B D                    Lizard  ctg--
B D             X. tropicalis  gcg--
B D                 Tetraodon  -gg--
B D              Atlantic cod  --g--
     Mexican tetra (cavefish)  tcg--
                  Spotted gar  -ca--
B D                   Lamprey  --gtc
B D                  Hedgehog  NNNNN
B D                Coelacanth  =====
B D                     Shrew  NNNNN
B D                    Rhesus  NNNNN
B D                    Gibbon  NNNNN
B D               Stickleback  =====
B D                 Zebrafish  =====
B D                   Opossum  -----
                  Chinchilla  NNNNN
      Lesser Egyptian jerboa  -----
          Chinese tree shrew  NNNNN
B D                   Manatee  NNNNN
B D           Chinese hamster  -----
B D                    Tenrec  NNNNN
B D                   Ferret   NNNNN
B D                     Panda  =====
               Domestic goat  NNNNN
            Tibetan antelope  NNNNN
             Star-nosed mole  NNNNN
              Bactrian camel  NNNNN
B D                    Alpaca  NNNNN
                Weddell seal  =====
        David's myotis (bat)  =====
B D           Squirrel monkey  NNNNN

Inserts between block 4 and 5 in window
B D                Tetraodon 1bp
B D             Atlantic cod 3bp
                 Spotted gar 4bp

Alignment block 5 of 1479 in window, 49539207 - 49539210, 4 bps 
B D                     Human  --ccg-------------------------------------c
B D                     Chimp  --ccg-------------------------------------c
B D                   Gorilla  --ccg-------------------------------------c
B D                 Orangutan  --ccg-------------------------------------c
B D       Crab-eating macaque  --tcg-------------------------------------c
B D                    Baboon  --tcg-------------------------------------c
B D              Green monkey  --tcg-------------------------------------c
B D                  Marmoset  --ccg-------------------------------------c
B D                  Bushbaby  --cca-------------------------------------c
B D                  Squirrel  --cct-------------------------------------c
       Lesser Egyptian jerboa  ----g-------------------------------------c
                 Prairie vole  --tcg-------------------------------------c
               Golden hamster  --tcg-------------------------------------c
B D                     Mouse  --gcg-------------------------------------c
B D                       Rat  --gcg-------------------------------------c
B D            Naked mole-rat  --ccg-------------------------------------c
B D                Guinea pig  --ccg-------------------------------------c
             Brush-tailed rat  --ccg-------------------------------------c
B D                    Rabbit  --ccg-------------------------------------c
B D                       Pig  --ccg-------------------------------------c
B D                   Dolphin  --ccg-------------------------------------c
                 Killer whale  --ccg-------------------------------------c
B D                       Cow  --cag-------------------------------------c
B D                     Sheep  --cag-------------------------------------c
B D                     Horse  --ccg-------------------------------------c
B D          White rhinoceros  --ccg-------------------------------------c
B D                       Cat  --ccg-------------------------------------c
B D                       Dog  --ccg-------------------------------------c
               Pacific walrus  --ccg-------------------------------------c
             Black flying-fox  --ccg-------------------------------------c
B D                   Megabat  --ccg-------------------------------------c
                Big brown bat  --ccg-------------------------------------c
B D                  Microbat  --ccg-------------------------------------c
B D                  Elephant  --ccg-------------------------------------c
          Cape elephant shrew  --ctg-------------------------------------c
             Cape golden mole  --tcg-------------------------------------c
                     Aardvark  --c---------------------------------------c
B D                 Armadillo  --ccg-------------------------------------c
B D                   Opossum  ----c-------------------------------------a
B D           Tasmanian devil  --ccc-------------------------------------a
B D                   Wallaby  --ccc-------------------------------------a
B D                  Platypus  --tcc-------------------------------------c
  D               Rock pigeon  --tgc-------------------------------------g
  D              Saker falcon  --cgc----tgg--------------------------ctgtg
  D          Peregrine falcon  --gac----tggtcctgcggggcacccaccagcagagcttggg
  D       Collared flycatcher  --ctcgtgtggg-------------------------cctaag
  D    White-throated sparrow  --cgc-------------------------------------g
B D               Zebra finch  --ccc----cgg-------------------------cagagg
           Tibetan ground jay  --ctc--------------------------------------
B D                Budgerigar  --ctc-------------------------------------c
  D             Scarlet macaw  --c-c-------------------------------------t
  D              Mallard duck  --gag-------ccccnnnnnnnnnnnnnnnnnnnnnnnnnnn
B D                   Chicken  --gcc-------------------------------------g
B D                    Turkey  --cag-------------------------------------g
B D        American alligator  --ggc-------------------------------------t
  D           Green seaturtle  --ctc-------------------------------------a
  D            Painted turtle  --ccc-------------------------------------g
  D  Chinese softshell turtle  --tct-------------------------------------g
B D                    Lizard  --ccc---------------------ctaagcaagagctggac
B D             X. tropicalis  --ggg-------------------------------------g
B D                 Tetraodon  --c----------------------------------------
B D               Stickleback  --c----------------------------------------
B D              Atlantic cod  --c----------------------------------------
     Mexican tetra (cavefish)  --c----------------------------------------
                  Spotted gar  --c----------------------------------------
B D                   Lamprey  ctcc---------------------------------------
B D                  Hedgehog  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D                      Pika  -------------------------------------------
B D                Coelacanth  ===========================================
B D                     Shrew  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D                    Rhesus  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D                    Gibbon  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D                 Zebrafish  ===========================================
                  Chinchilla  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
          Chinese tree shrew  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D                   Manatee  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D           Chinese hamster  -------------------------------------------
B D                    Tenrec  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D                   Ferret   NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D                     Panda  ===========================================
               Domestic goat  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
            Tibetan antelope  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
             Star-nosed mole  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
              Bactrian camel  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D                    Alpaca  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
                Weddell seal  ===========================================
        David's myotis (bat)  ===========================================
B D           Squirrel monkey  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

Inserts between block 5 and 6 in window
  D          Green seaturtle 5bp
  D           Painted turtle 2bp
B D                Tetraodon 3bp
B D              Stickleback 2bp
    Mexican tetra (cavefish) 3bp

Alignment block 6 of 1479 in window, 49539211 - 49539211, 1 bps 
B D                     Human  -g
B D                     Chimp  -g
B D                   Gorilla  -g
B D                 Orangutan  -g
B D       Crab-eating macaque  -g
B D                    Baboon  -g
B D              Green monkey  -g
B D                  Marmoset  -g
B D                  Bushbaby  -g
B D                  Squirrel  -g
       Lesser Egyptian jerboa  -g
                 Prairie vole  -g
               Golden hamster  -g
B D                     Mouse  -g
B D                       Rat  -g
B D            Naked mole-rat  -g
B D                Guinea pig  -g
             Brush-tailed rat  -a
B D                    Rabbit  -g
B D                       Pig  -g
B D                   Dolphin  -g
                 Killer whale  -g
B D                       Cow  -g
B D                     Sheep  -g
B D                     Horse  -g
B D          White rhinoceros  -g
B D                       Cat  -g
B D                       Dog  -g
               Pacific walrus  -g
             Black flying-fox  -g
B D                   Megabat  -g
                Big brown bat  -g
B D                  Microbat  -g
B D                  Elephant  -g
          Cape elephant shrew  -g
             Cape golden mole  -g
                     Aardvark  -g
B D                 Armadillo  -g
B D                   Opossum  -g
B D           Tasmanian devil  -g
B D                   Wallaby  -g
B D                  Platypus  -g
  D               Rock pigeon  -g
  D              Saker falcon  -g
  D          Peregrine falcon  -g
  D       Collared flycatcher  -t
  D    White-throated sparrow  -g
B D               Zebra finch  -g
B D                Budgerigar  -g
  D             Scarlet macaw  -g
  D              Mallard duck  -g
B D                   Chicken  -g
B D                    Turkey  -g
B D        American alligator  -g
  D           Green seaturtle  -g
  D            Painted turtle  -g
  D  Chinese softshell turtle  -g
B D                    Lizard  -g
B D             X. tropicalis  -a
B D                 Tetraodon  -g
           Southern platyfish  -g
B D              Atlantic cod  -g
     Mexican tetra (cavefish)  -g
                  Spotted gar  -g
B D                   Lamprey  c-
B D                  Hedgehog  NN
B D                      Pika  --
B D                Coelacanth  ==
B D                     Shrew  NN
B D                    Rhesus  NN
B D                    Gibbon  NN
B D               Stickleback  ==
          Tibetan ground jay  --
B D                 Zebrafish  ==
                  Chinchilla  NN
          Chinese tree shrew  NN
B D                   Manatee  NN
B D           Chinese hamster  --
B D                    Tenrec  NN
B D                   Ferret   NN
B D                     Panda  ==
               Domestic goat  NN
            Tibetan antelope  NN
             Star-nosed mole  NN
              Bactrian camel  NN
B D                    Alpaca  NN
                Weddell seal  ==
        David's myotis (bat)  ==
B D           Squirrel monkey  NN

Alignment block 7 of 1479 in window, 49539212 - 49539216, 5 bps 
B D                     Human  cgcca
B D                     Chimp  cgcca
B D                   Gorilla  cgcca
B D                 Orangutan  cgcca
B D       Crab-eating macaque  cgcca
B D                    Baboon  cgcca
B D              Green monkey  cgcca
B D                  Marmoset  cgcca
B D                  Bushbaby  cgcca
B D                  Squirrel  cgcca
       Lesser Egyptian jerboa  cgcca
                 Prairie vole  cgcca
               Golden hamster  cgcca
B D                     Mouse  cgcca
B D                       Rat  cg-ca
B D            Naked mole-rat  cgcca
B D                Guinea pig  cgcca
             Brush-tailed rat  cgcca
B D                    Rabbit  cgcca
B D                      Pika  -gcca
B D                       Pig  cgcca
B D                   Dolphin  cgcca
                 Killer whale  cgcca
B D                       Cow  cgcca
B D                     Sheep  cgcca
B D                     Horse  cgcca
B D          White rhinoceros  cgcca
B D                       Cat  cgcca
B D                       Dog  cgcca
               Pacific walrus  cgcca
             Black flying-fox  cgcga
B D                   Megabat  cgcga
                Big brown bat  cgcca
B D                  Microbat  cgcca
B D                  Elephant  cgcca
          Cape elephant shrew  cgcta
             Cape golden mole  cgcca
                     Aardvark  cgcca
B D                 Armadillo  cgcca
B D                   Opossum  cggcg
B D           Tasmanian devil  agaca
B D                   Wallaby  agact
B D                  Platypus  cgagc
  D               Rock pigeon  cggca
  D              Saker falcon  ccata
  D          Peregrine falcon  cgctg
  D       Collared flycatcher  gaaaa
  D    White-throated sparrow  cggca
B D               Zebra finch  aagca
           Tibetan ground jay  caatg
B D                Budgerigar  cacct
  D             Scarlet macaw  cacca
  D              Mallard duck  tgccg
B D                   Chicken  tgccg
B D                    Turkey  ctgcg
B D        American alligator  ggccg
  D           Green seaturtle  cagcg
  D            Painted turtle  cactg
  D  Chinese softshell turtle  cgcta
B D                    Lizard  tggcg
B D             X. tropicalis  cgcga
B D                 Tetraodon  agtca
           Southern platyfish  ctcca
B D               Stickleback  cctct
B D              Atlantic cod  cgcaa
B D                 Zebrafish  cgcca
     Mexican tetra (cavefish)  cgcca
                  Spotted gar  cttct
B D                   Lamprey  ctccc
B D                  Hedgehog  NNNNN
B D                Coelacanth  =====
B D                     Shrew  NNNNN
B D                    Rhesus  NNNNN
B D                    Gibbon  NNNNN
                  Chinchilla  NNNNN
          Chinese tree shrew  NNNNN
B D                   Manatee  NNNNN
B D           Chinese hamster  -----
B D                    Tenrec  NNNNN
B D                   Ferret   NNNNN
B D                     Panda  =====
               Domestic goat  NNNNN
            Tibetan antelope  NNNNN
             Star-nosed mole  NNNNN
              Bactrian camel  NNNNN
B D                    Alpaca  NNNNN
                Weddell seal  =====
        David's myotis (bat)  =====
B D           Squirrel monkey  NNNNN

Inserts between block 7 and 8 in window
          Southern platyfish 1bp
B D              Stickleback 1bp
    Mexican tetra (cavefish) 5bp

Alignment block 8 of 1479 in window, 49539217 - 49539225, 9 bps 
B D                     Human  t------------gctcc-ggg
B D                     Chimp  t------------gctcc-ggg
B D                   Gorilla  t------------gctcc-ggg
B D                 Orangutan  t------------gctcc-ggg
B D       Crab-eating macaque  t------------gctcc-ggg
B D                    Baboon  t------------gctcc-ggg
B D              Green monkey  t------------gctcc-ggg
B D                  Marmoset  t------------gctcc-ggg
B D                  Bushbaby  t------------gcccc-agg
B D                  Squirrel  t------------gctca-cgg
       Lesser Egyptian jerboa  t------------gctcc-ggg
                 Prairie vole  t------------gcgcc-cag
               Golden hamster  t------------gctcc-cag
B D                     Mouse  t------------gcgcc-cag
B D                       Rat  t------------gcgctgcag
B D            Naked mole-rat  t------------gctcc-ggg
B D                Guinea pig  t------------gctcc-ggg
             Brush-tailed rat  t------------gctcc-ggg
B D                    Rabbit  t------------gctca-ggt
B D                      Pika  t------------gcccg-ggg
B D                       Pig  t------------gctcc-cgg
B D                   Dolphin  t------------gctcc-ggg
                 Killer whale  t------------gctcc-ggg
B D                       Cow  t------------gctcc-ggg
B D                     Sheep  t------------gctcc-ggg
B D                     Horse  t------------gctcc-ggg
B D          White rhinoceros  t------------gctcc-cgg
B D                       Cat  t------------gctcc-ggg
B D                       Dog  t------------gctcg-ggg
               Pacific walrus  t------------gctcc-ggg
             Black flying-fox  t------------gctcc-ggg
B D                   Megabat  t------------gctcc-ggg
                Big brown bat  t------------gcccc-ggg
B D                  Microbat  t------------gcccc-ggg
B D                  Elephant  t------------gctct-ggc
          Cape elephant shrew  t------------gctgg-gga
             Cape golden mole  t------------gctcc-gga
                     Aardvark  t------------gctcc-gga
B D                 Armadillo  t------------gcccg-ggg
B D                   Opossum  t------------cgtag-gag
B D           Tasmanian devil  t------------gcttc-tga
B D                   Wallaby  t------------gctac-tga
B D                  Platypus  t------------tcgcc-cgg
  D              Saker falcon  g-------------ctct-agt
  D          Peregrine falcon  g-ctgtggccatagctct-agt
  D       Collared flycatcher  c-----------agtgct-ggg
  D    White-throated sparrow  t-----------c---------
B D               Zebra finch  t-----------cgagcc-gcg
           Tibetan ground jay  c-----------cgagcg-ggt
B D                Budgerigar  g-----------tgcgcg-gct
  D             Scarlet macaw  g----------ctgc-------
  D              Mallard duck  c--------------gcc-ggg
B D                   Chicken  a-------------------ga
B D                    Turkey  c-------------------ag
B D        American alligator  ggctggatgccccagcgc-ggt
  D           Green seaturtle  t---------atcctacg-tgc
  D            Painted turtle  g---------acggggcg-ctg
  D  Chinese softshell turtle  g---------cctgctca-cgg
B D                    Lizard  a-----------aggact-ttc
B D             X. tropicalis  t------------gcctt-agc
B D                 Tetraodon  ------------tgctcc-gac
           Southern platyfish  ------------ctctcc-g--
B D               Stickleback  ------------ccctcc-agc
B D              Atlantic cod  ------------cgcccc-ggg
B D                 Zebrafish  ---------------tct-att
     Mexican tetra (cavefish)  ---------------tcg-agc
                  Spotted gar  --------------cgct-gac
B D                   Lamprey  ------------gcctct-tgg
B D                  Hedgehog  NNNNNNNNNNNNNNNNNNNNNN
B D                Coelacanth  ======================
B D                     Shrew  NNNNNNNNNNNNNNNNNNNNNN
B D                    Rhesus  NNNNNNNNNNNNNNNNNNNNNN
B D                    Gibbon  NNNNNNNNNNNNNNNNNNNNNN
                  Chinchilla  NNNNNNNNNNNNNNNNNNNNNN
  D               Rock pigeon  ----------------------
          Chinese tree shrew  NNNNNNNNNNNNNNNNNNNNNN
B D                   Manatee  NNNNNNNNNNNNNNNNNNNNNN
B D           Chinese hamster  ----------------------
B D                    Tenrec  NNNNNNNNNNNNNNNNNNNNNN
B D                   Ferret   NNNNNNNNNNNNNNNNNNNNNN
B D                     Panda  ======================
               Domestic goat  NNNNNNNNNNNNNNNNNNNNNN
            Tibetan antelope  NNNNNNNNNNNNNNNNNNNNNN
             Star-nosed mole  NNNNNNNNNNNNNNNNNNNNNN
              Bactrian camel  NNNNNNNNNNNNNNNNNNNNNN
B D                    Alpaca  NNNNNNNNNNNNNNNNNNNNNN
                Weddell seal  ======================
        David's myotis (bat)  ======================
B D           Squirrel monkey  NNNNNNNNNNNNNNNNNNNNNN

Inserts between block 8 and 9 in window
B D                Tetraodon 5bp
          Southern platyfish 3bp
B D              Stickleback 1bp
B D             Atlantic cod 2bp
B D                Zebrafish 9bp
    Mexican tetra (cavefish) 6bp
                 Spotted gar 3bp

Alignment block 9 of 1479 in window, 49539226 - 49539233, 8 bps 
B D                     Human  ccccg----acg
B D                     Chimp  ccccg----acg
B D                   Gorilla  ccccg----acg
B D                 Orangutan  ccccg----acg
B D       Crab-eating macaque  tcccg----acg
B D                    Baboon  ccccg----acg
B D              Green monkey  ccccg----acg
B D                  Marmoset  ccccg----acg
B D                  Bushbaby  ccccg----acg
B D                  Squirrel  ccccg----acg
       Lesser Egyptian jerboa  ccccg----acg
                 Prairie vole  ccccg----acg
               Golden hamster  ccccg----acg
B D                     Mouse  ccccg----acg
B D                       Rat  ccccc----gcg
B D            Naked mole-rat  ccccg----acg
B D                Guinea pig  cctcg----acg
             Brush-tailed rat  ccccg----acg
B D                    Rabbit  ccccg----acg
B D                      Pika  ccccg----acg
B D                       Pig  cctcg----acg
B D                   Dolphin  ccccg----acg
                 Killer whale  ccccg----acg
B D                       Cow  ccccg----acg
B D                     Sheep  ccccg----acg
B D                     Horse  ccccg----acg
B D          White rhinoceros  ccccg----acg
B D                       Cat  ccccg----acg
B D                       Dog  ccccg----acg
               Pacific walrus  ccccg----acg
             Black flying-fox  ccccg----acg
B D                   Megabat  ccccg----acg
                Big brown bat  ccccg----acg
B D                  Microbat  ccccg----acg
B D                  Elephant  ccccg----acg
          Cape elephant shrew  ccccg----acg
             Cape golden mole  ccccg----acg
                     Aardvark  ccccg----acg
B D                 Armadillo  ccccg----acg
B D                   Opossum  gagaa----gaa
B D           Tasmanian devil  cccag----aca
B D                   Wallaby  ccccg----acg
B D                  Platypus  ccccg----a--
  D              Saker falcon  ccctt-------
  D          Peregrine falcon  ccctt-------
  D       Collared flycatcher  cttgg-------
  D    White-throated sparrow  cccat-------
B D               Zebra finch  ctccg-------
           Tibetan ground jay  cccgc-------
B D                Budgerigar  ctccg-------
  D              Mallard duck  cgcct-------
B D                   Chicken  cccct-------
B D                    Turkey  ctcct-------
B D        American alligator  ccctt-------
  D           Green seaturtle  ctgaa-------
  D            Painted turtle  gggga-------
  D  Chinese softshell turtle  ccggc-------
B D                    Lizard  ttcgt-------
B D             X. tropicalis  gcctg----tcg
B D                 Tetraodon  cgcag-------
B D                      Fugu  ctcag-------
           Southern platyfish  ctgcg-------
B D               Stickleback  tccag-------
B D              Atlantic cod  caccg-------
B D                 Zebrafish  cg----------
     Mexican tetra (cavefish)  cc----------
                  Spotted gar  -gccggctg---
B D                   Lamprey  actcg----act
B D                  Hedgehog  NNNNNNNNNNNN
B D                Coelacanth  ============
B D                     Shrew  NNNNNNNNNNNN
B D                    Rhesus  NNNNNNNNNNNN
B D                    Gibbon  NNNNNNNNNNNN
  D             Scarlet macaw  ------------
                  Chinchilla  NNNNNNNNNNNN
  D               Rock pigeon  ------------
          Chinese tree shrew  NNNNNNNNNNNN
B D                   Manatee  NNNNNNNNNNNN
B D           Chinese hamster  ------------
B D                    Tenrec  NNNNNNNNNNNN
B D                   Ferret   NNNNNNNNNNNN
B D                     Panda  ============
               Domestic goat  NNNNNNNNNNNN
            Tibetan antelope  NNNNNNNNNNNN
             Star-nosed mole  NNNNNNNNNNNN
              Bactrian camel  NNNNNNNNNNNN
B D                    Alpaca  NNNNNNNNNNNN
                Weddell seal  ============
        David's myotis (bat)  ============
B D           Squirrel monkey  NNNNNNNNNNNN

Inserts between block 9 and 10 in window
B D                Tetraodon 1bp
B D                     Fugu 1bp
B D             Atlantic cod 4bp

Alignment block 10 of 1479 in window, 49539234 - 49539234, 1 bps 
B D                     Human  -g
B D                     Chimp  -g
B D                   Gorilla  -g
B D                 Orangutan  -g
B D       Crab-eating macaque  -g
B D                    Baboon  -g
B D              Green monkey  -g
B D                  Marmoset  -g
B D                  Bushbaby  -g
B D                  Squirrel  -g
       Lesser Egyptian jerboa  -g
                 Prairie vole  -g
               Golden hamster  -g
B D                     Mouse  -g
B D                       Rat  -g
B D            Naked mole-rat  -g
B D                Guinea pig  -g
             Brush-tailed rat  -g
B D                    Rabbit  -g
B D                      Pika  -g
B D                       Pig  -g
B D                   Dolphin  -g
                 Killer whale  -g
B D                       Cow  -g
B D                     Sheep  -g
B D                     Horse  -g
B D          White rhinoceros  -g
B D                       Cat  -g
B D                       Dog  -g
               Pacific walrus  -g
             Black flying-fox  -g
B D                   Megabat  -g
                Big brown bat  -g
B D                  Microbat  -g
B D                  Elephant  -g
          Cape elephant shrew  -g
             Cape golden mole  -g
                     Aardvark  -g
B D                 Armadillo  -g
B D                   Opossum  -g
B D           Tasmanian devil  -g
B D                   Wallaby  -g
B D             X. tropicalis  -c
B D              Nile tilapia  -g
          Princess of Burundi  -g
        Burton's mouthbreeder  -g
                  Zebra mbuna  -g
          Pundamilia nyererei  -g
           Southern platyfish  -a
B D               Stickleback  -g
B D              Atlantic cod  -a
B D                 Zebrafish  -g
     Mexican tetra (cavefish)  -g
                  Spotted gar  -a
B D                   Lamprey  c-
B D                  Hedgehog  NN
B D                Coelacanth  ==
B D                     Shrew  NN
B D                    Rhesus  NN
B D                    Gibbon  NN
B D                      Fugu  ==
B D                 Tetraodon  ==
B D                    Turkey  --
B D                   Chicken  --
  D              Mallard duck  --
          Tibetan ground jay  --
B D               Zebra finch  --
  D    White-throated sparrow  --
  D            Painted turtle  --
  D           Green seaturtle  --
B D        American alligator  --
  D             Scarlet macaw  --
B D                Budgerigar  --
                  Chinchilla  NN
  D               Rock pigeon  --
  D       Collared flycatcher  --
B D                    Lizard  --
  D          Peregrine falcon  --
  D              Saker falcon  --
          Chinese tree shrew  NN
B D                  Platypus  --
B D                   Manatee  NN
B D           Chinese hamster  --
B D                    Tenrec  NN
  D  Chinese softshell turtle  --
B D                   Ferret   NN
B D                     Panda  ==
               Domestic goat  NN
            Tibetan antelope  NN
             Star-nosed mole  NN
              Bactrian camel  NN
B D                    Alpaca  NN
                Weddell seal  ==
        David's myotis (bat)  ==
B D           Squirrel monkey  NN

Inserts between block 10 and 11 in window
B D             Nile tilapia 1bp
         Princess of Burundi 1bp
       Burton's mouthbreeder 1bp
                 Zebra mbuna 1bp
         Pundamilia nyererei 1bp
          Southern platyfish 2bp
B D             Atlantic cod 2bp

Alignment block 11 of 1479 in window, 49539235 - 49539246, 12 bps 
B D                     Human  cgcgg---a-------cgcccc
B D                     Chimp  cgcgg---a-------cgcccc
B D                   Gorilla  cgcgg---a-------cgcccc
B D                 Orangutan  cgcgg---a-------cgcccc
B D       Crab-eating macaque  cgcgg---a-------cgcccc
B D                    Baboon  cgcgg---a-------cgcccc
B D              Green monkey  cgcgg---a-------cgcccc
B D                  Marmoset  cgcgg---a-------cgcccc
B D                  Bushbaby  cgcgg---a-------cgcctc
B D                  Squirrel  cgcgg---a-------cgcccc
       Lesser Egyptian jerboa  cgcgg---a-------cgtccc
                 Prairie vole  cgcgg---a-------cgcccc
               Golden hamster  cgcgg---a-------cgcccc
B D                     Mouse  tgcgg---a-------cgcccc
B D                       Rat  cgcgg---a-------cgcccc
B D            Naked mole-rat  cgcgg---a-------cgcccg
B D                Guinea pig  cgcgg---a-------cgcccg
             Brush-tailed rat  cgcgg---a-------cgcccg
B D                    Rabbit  cgcgc---a-------cggccg
B D                      Pika  cgcgg---a-------cgaccc
B D                       Pig  cgggg---a-------cgcccc
B D                   Dolphin  cgggg---a-------cgcccc
                 Killer whale  cgggg---a-------cgcccc
B D                       Cow  cgggg---a-------cgcccc
B D                     Sheep  cgggg---a-------cgcccc
B D                     Horse  cgggg---a-------cgcccc
B D          White rhinoceros  cgggg---a-------cgcccc
B D                       Cat  cgggg---a-------cgcccc
B D                       Dog  cgggg---a-------cgcccc
               Pacific walrus  cgggg---a-------cgcccc
             Black flying-fox  ccggg---a-------cgcctc
B D                   Megabat  ccggg---a-------cgcctc
                Big brown bat  caggg---a-------cggccc
B D                  Microbat  caggg---a-------cggccc
B D                  Elephant  cgcgg---a-------cgtccc
          Cape elephant shrew  cgcgg---a-------cgcccc
             Cape golden mole  cgcgg---a-------cgcccc
                     Aardvark  cgcgg---a-------cgcccc
B D                 Armadillo  cgcgg---a-------cgcccc
B D                   Opossum  agagg---a-------------
B D           Tasmanian devil  agcgg---a-------tgcccc
B D                   Wallaby  agcgg---a-------ctcccc
B D                  Platypus  -gccc---a-------cccctc
B D             X. tropicalis  t-------a-------cttccc
B D                 Tetraodon  tgtga---t-------cacccg
B D                      Fugu  cgtga---t-------cacccg
B D              Nile tilapia  ccgga---t-------cacctg
          Princess of Burundi  ccgga---t-------cacctg
        Burton's mouthbreeder  ccgga---t-------cacctg
                  Zebra mbuna  ccgga---t-------cacctg
          Pundamilia nyererei  ccgga---t-------cacctg
B D                    Medaka  ggagacgct-------ctctcg
           Southern platyfish  cggga---t-------cacccg
B D               Stickleback  cggga---t-------cacctg
B D              Atlantic cod  cgcgagcct-------cccccg
B D                 Zebrafish  ---aa---c------------a
     Mexican tetra (cavefish)  ---ga---ct-----gcagctg
                  Spotted gar  ctcgg---c-------cggctg
B D                   Lamprey  ---------cgagccgcgctcc
B D                  Hedgehog  NNNNNNNNNNNNNNNNNNNNNN
B D                Coelacanth  ======================
B D                     Shrew  NNNNNNNNNNNNNNNNNNNNNN
B D                    Rhesus  NNNNNNNNNNNNNNNNNNNNNN
B D                    Gibbon  NNNNNNNNNNNNNNNNNNNNNN
B D                    Turkey  ----------------------
B D                   Chicken  ----------------------
  D              Mallard duck  ----------------------
          Tibetan ground jay  ----------------------
B D               Zebra finch  ----------------------
  D    White-throated sparrow  ----------------------
  D            Painted turtle  ----------------------
  D           Green seaturtle  ----------------------
B D        American alligator  ----------------------
  D             Scarlet macaw  ----------------------
B D                Budgerigar  ----------------------
                  Chinchilla  NNNNNNNNNNNNNNNNNNNNNN
  D               Rock pigeon  ----------------------
  D       Collared flycatcher  ----------------------
B D                    Lizard  ----------------------
  D          Peregrine falcon  ----------------------
  D              Saker falcon  ----------------------
          Chinese tree shrew  NNNNNNNNNNNNNNNNNNNNNN
B D                   Manatee  NNNNNNNNNNNNNNNNNNNNNN
B D           Chinese hamster  ----------------------
B D                    Tenrec  NNNNNNNNNNNNNNNNNNNNNN
  D  Chinese softshell turtle  ----------------------
B D                   Ferret   NNNNNNNNNNNNNNNNNNNNNN
B D                     Panda  ======================
               Domestic goat  NNNNNNNNNNNNNNNNNNNNNN
            Tibetan antelope  NNNNNNNNNNNNNNNNNNNNNN
             Star-nosed mole  NNNNNNNNNNNNNNNNNNNNNN
              Bactrian camel  NNNNNNNNNNNNNNNNNNNNNN
B D                    Alpaca  NNNNNNNNNNNNNNNNNNNNNN
                Weddell seal  ======================
        David's myotis (bat)  ======================
B D           Squirrel monkey  NNNNNNNNNNNNNNNNNNNNNN

Inserts between block 11 and 12 in window
B D                      Cat 21bp

Alignment block 12 of 1479 in window, 49539247 - 49539249, 3 bps 
B D                     Human  ctc
B D                     Chimp  ctc
B D                   Gorilla  ctc
B D                 Orangutan  ctc
B D       Crab-eating macaque  ctc
B D                    Baboon  ctc
B D              Green monkey  ctc
B D                  Marmoset  ctt
B D                  Bushbaby  ctc
B D                  Squirrel  ctt
       Lesser Egyptian jerboa  ctc
                 Prairie vole  ctc
               Golden hamster  ctc
B D                     Mouse  ctt
B D                       Rat  ctc
B D            Naked mole-rat  ctc
B D                Guinea pig  ctc
             Brush-tailed rat  ctc
B D                    Rabbit  ctc
B D                      Pika  cca
B D                       Pig  ctc
B D                   Dolphin  ctt
                 Killer whale  ctt
B D                       Cow  ctt
B D                     Sheep  ctt
B D                     Horse  ctt
B D          White rhinoceros  ctt
B D                       Dog  ctc
               Pacific walrus  ctc
             Black flying-fox  caa
B D                   Megabat  caa
                Big brown bat  ctc
B D                  Microbat  ctc
B D                  Elephant  ctc
          Cape elephant shrew  ctc
             Cape golden mole  ctc
                     Aardvark  ctt
B D                 Armadillo  ctc
B D           Tasmanian devil  atc
B D                   Wallaby  ctc
B D                  Platypus  ctc
  D               Rock pigeon  tcc
  D              Saker falcon  ttt
  D          Peregrine falcon  ttt
  D       Collared flycatcher  gga
  D    White-throated sparrow  cct
B D               Zebra finch  ccg
           Tibetan ground jay  cgc
B D                Budgerigar  ctg
  D             Scarlet macaw  ctg
  D              Mallard duck  ccg
B D                   Chicken  ccc
B D                    Turkey  ctc
B D        American alligator  cct
  D           Green seaturtle  ccc
  D            Painted turtle  ccc
  D  Chinese softshell turtle  cag
B D                    Lizard  cat
B D             X. tropicalis  --c
B D                 Tetraodon  cac
B D                      Fugu  cac
B D              Nile tilapia  ctc
          Princess of Burundi  ctc
        Burton's mouthbreeder  ctt
                  Zebra mbuna  ctc
          Pundamilia nyererei  ctc
B D                    Medaka  cgc
           Southern platyfish  cgc
B D               Stickleback  cgc
B D              Atlantic cod  ctc
B D                 Zebrafish  cac
     Mexican tetra (cavefish)  ccc
                  Spotted gar  tcc
B D                   Lamprey  ctc
B D                  Hedgehog  NNN
B D                Coelacanth  ===
B D                     Shrew  NNN
B D                    Rhesus  NNN
B D                    Gibbon  NNN
B D                   Opossum  ---
                  Chinchilla  NNN
          Chinese tree shrew  NNN
B D                   Manatee  NNN
B D           Chinese hamster  ---
B D                    Tenrec  NNN
B D                       Cat  ===
B D                   Ferret   NNN
B D                     Panda  ===
               Domestic goat  NNN
            Tibetan antelope  NNN
             Star-nosed mole  NNN
              Bactrian camel  NNN
B D                    Alpaca  NNN
                Weddell seal  ===
        David's myotis (bat)  ===
B D           Squirrel monkey  NNN

Inserts between block 12 and 13 in window
B D                 Platypus 3bp
B D            X. tropicalis 2bp

Alignment block 13 of 1479 in window, 49539250 - 49539255, 6 bps 
B D                     Human  gc------------g-------------cgc--
B D                     Chimp  gc------------g-------------cgc--
B D                   Gorilla  gc------------g-------------cgc--
B D                 Orangutan  gc------------g-------------cgc--
B D       Crab-eating macaque  gc------------g-------------cgc--
B D                    Baboon  gc------------g-------------cgc--
B D              Green monkey  gc------------g-------------cgc--
B D                  Marmoset  gc------------g-------------cgc--
B D                  Bushbaby  ga------------g-------------cgc--
B D                  Squirrel  gc------------g-------------cgc--
                 Prairie vole  gt------------g-------------cgc--
               Golden hamster  gc------------g-------------cgc--
B D                     Mouse  gt------------g-------------cgc--
B D                       Rat  gc------------g-------------cgc--
B D            Naked mole-rat  tc------------g-------------cac--
B D                Guinea pig  tc------------g-------------cgc--
             Brush-tailed rat  cc------------g-------------cgc--
B D                    Rabbit  gc------------g-------------cac--
B D                      Pika  gc------------g-------------cac--
B D                       Pig  gc------------t-------------cgc--
B D                   Dolphin  gc------------g-------------cgc--
                 Killer whale  gc------------g-------------cgc--
B D                       Cow  gc------------g-------------cgc--
B D                     Sheep  gc------------g-------------cgc--
B D                     Horse  gc------------g-------------cgc--
B D          White rhinoceros  gc------------g-------------cgc--
B D                       Dog  gc------------g-------------cgc--
               Pacific walrus  gc------------g-------------cac--
             Black flying-fox  ac------------g-------------cgc--
B D                   Megabat  ac------------g-------------cgc--
                Big brown bat  gc------------g-------------cgc--
B D                  Microbat  gc------------g-------------cgc--
B D                  Elephant  gc------------g-------------cgc--
          Cape elephant shrew  gc------------g-------------tgt--
             Cape golden mole  gc------------g-------------cgc--
                     Aardvark  gc------------g-------------cgc--
B D                 Armadillo  gc------------g-------------cgc--
B D                  Platypus  gg------------g-------------agc--
  D               Rock pigeon  -c------------c-------------atc--
  D              Saker falcon  -c-----------tt-------------ctc--
  D          Peregrine falcon  -c-----------tt-------------ctc--
  D       Collared flycatcher  -c--------agagc-------------agg--
  D    White-throated sparrow  -c------------c-------------ttc--
B D               Zebra finch  -c------------t-------------cgc--
           Tibetan ground jay  -ctccaacccagagc-------------ccc--
B D                Budgerigar  -c--------agggctggggactccgtgtgg--
  D             Scarlet macaw  -c--------ggggctggaca-------tgt--
  D              Mallard duck  -g------------c-------------tgt--
B D                   Chicken  -g------------g-------------tgc--
B D                    Turkey  -a------------c-------------tgc--
B D        American alligator  -g------------c-------------ccc--
  D           Green seaturtle  -c------------c-------------agg--
  D            Painted turtle  -c------------c-------------cgg--
  D  Chinese softshell turtle  -a------------c-------------ggg--
B D                    Lizard  -c--------ctcat-------------cct--
B D             X. tropicalis  --------------g-------------ggt--
B D                 Tetraodon  -------------gg-------------tgg--
B D                      Fugu  -------------gg-------------ttg--
B D              Nile tilapia  -------------gg-------------tgg--
          Princess of Burundi  -------------gg-------------tgg--
        Burton's mouthbreeder  -------------gg-------------tgg--
                  Zebra mbuna  -------------gg-------------tgg--
          Pundamilia nyererei  -------------gg-------------tgg--
B D                    Medaka  -------------ag-------------c----
           Southern platyfish  -------------gg-------------tgc--
B D               Stickleback  -------------gg-------------tgg--
B D                 Zebrafish  -------------gc-------------tac--
     Mexican tetra (cavefish)  -------------gc-------------cgc--
                  Spotted gar  -------------gt-------------ccg--
B D                   Lamprey  ---------------------------tcgcac
B D                  Hedgehog  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D                Coelacanth  =================================
B D                     Shrew  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D                    Rhesus  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D              Atlantic cod  ---------------------------------
B D                    Gibbon  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D           Tasmanian devil  ---------------------------------
B D                   Opossum  ---------------------------------
                  Chinchilla  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
      Lesser Egyptian jerboa  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
          Chinese tree shrew  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D                   Wallaby  ---------------------------------
B D                   Manatee  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D           Chinese hamster  ---------------------------------
B D                    Tenrec  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D                       Cat  =================================
B D                   Ferret   NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D                     Panda  =================================
               Domestic goat  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
            Tibetan antelope  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
             Star-nosed mole  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
              Bactrian camel  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D                    Alpaca  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
                Weddell seal  =================================
        David's myotis (bat)  =================================
B D           Squirrel monkey  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

Inserts between block 13 and 14 in window
B D                Tetraodon 1bp
B D                     Fugu 1bp
B D             Nile tilapia 1bp
         Princess of Burundi 1bp
       Burton's mouthbreeder 1bp
                 Zebra mbuna 1bp
         Pundamilia nyererei 1bp
          Southern platyfish 1bp
B D              Stickleback 1bp
B D                Zebrafish 9bp
    Mexican tetra (cavefish) 108bp
                 Spotted gar 7bp

Alignment block 14 of 1479 in window, 49539256 - 49539285, 30 bps 
B D                     Human  cag-cgt------------ccg------g--------c---g---------------cgaccc---c---
B D                     Chimp  cag-cgt------------ccg------g--------c---g---------------cgaccc---c---
B D                   Gorilla  cag-cgt------------ccg------g--------c---g---------------cgaccc---c---
B D                 Orangutan  ccg-cgt------------ccg------g--------c---g---------------ggaccc---c---
B D       Crab-eating macaque  ccg-cgg------------ccg------g--------c---g---------------cgaccc---g---
B D                    Baboon  ccg-cgg------------ccg------g--------c---g---------------cgaccc---g---
B D              Green monkey  ccg-cgg------------ccg------g--------c---g---------------cgaccc---g---
B D                  Marmoset  ccg-cgg------------ccg------g--------c---g---------------cgacct---g---
B D                  Bushbaby  tgg-ggg------------ctt------g--------c---g---------------ggacct---g---
B D                  Squirrel  tgg-cgg------------ctg------g--------c---g---------------ggtcct---g---
                 Prairie vole  cgg-ccg------------ctg------g--------t---g---------------gggcct---g---
               Golden hamster  cgg-ccg------------ccg------g--------t---g---------------gggcct---g---
B D                     Mouse  cgg-cag------------ctg------c--------t---g---------------gggcct---g---
B D                       Rat  cggccag------------ctg------c--------t---g---------------gggcct---a---
B D            Naked mole-rat  cgg-cgg------------ctg------g--------c---g---------------gggcct---g---
B D                Guinea pig  cgg-cgg------------ccg------a--------c---a---------------gggccc---a---
             Brush-tailed rat  ccg-cgg------------ctg------g--------c---g---------------gggccc---g---
B D                    Rabbit  ccc-cgg------------cca------g--------c---c---------------gggcct---g---
B D                      Pika  ccg-cgg------------ctg------g--------c---g---------------gggcct---t---
B D                       Pig  agg-cgg------------ctg------g--------a---g---------------ggacct---g---
B D                   Dolphin  ggg-cgg------------ctg------g--------c---g---------------ggacct---g---
                 Killer whale  ggg-cgg------------ctg------g--------c---g---------------ggacct---g---
B D                       Cow  ggg-cgg------------ctg------g--------c---a---------------ggacct---g---
B D                     Sheep  gga-cgg------------ctg------g--------c---a---------------ggacct---g---
B D                     Horse  ggg-cgg------------ctg------g--------c---g---------------gggcct---g---
B D          White rhinoceros  ggg-cgg------------ctg------g--------c---g---------------gggcct---g---
B D                       Dog  cgg-ctg------------ccg------g--------c---c---------------cggcct---g---
               Pacific walrus  cgg-ctg------------ctg------g--------c---c---------------gggcct---g---
             Black flying-fox  gga-cgg------------ctg------g--------a---g---------------gggcct---g---
B D                   Megabat  gga-cgg------------ctg------g--------a---g---------------gggcct---g---
                Big brown bat  ggg-cgg------------ccg------g--------t---g---------------gggcct---g---
B D                  Microbat  ggg-cgg------------ccg------g--------c---g---------------gggccc---g---
B D                  Elephant  ggg-ctg------------ccg------g--------c---g---------------gggcct---g---
          Cape elephant shrew  ggg-cag------------ccg------a--------t---g---------------gggcct---a---
             Cape golden mole  cgg-cgg------------ctg------a--------c---g---------------gaacct---g---
                     Aardvark  ggg-cgg------------ccg------g--------c---g---------------gggcct---g---
B D                 Armadillo  ggg-cgg------------ccg------g--------c---g---------------gggcgt---g---
B D                   Opossum  ---------------------g------a--------a---a---------------gggaag---g---
B D           Tasmanian devil  -------------------gca------c--------t---g---------------gggcct---c---
B D                   Wallaby  -------------------gca------c--------t---g---------------gggccg---g---
B D                  Platypus  tcc-cgg------------tcc------g--------a---g---------------gggagc---g---
  D               Rock pigeon  atc-atc------------ctc-------------------------------------ctcc---t---
  D              Saker falcon  cct-gag------------ctc------g--------g---a---------------agctcc---t---
  D          Peregrine falcon  cct-gag------------ctc------g--------g---a---------------agctcc---t---
  D       Collared flycatcher  cac-aac------------ctg------g--------g---a---------------tgatcc---t---
  D    White-throated sparrow  tcc-tcc------------ct--------------------------------------atcc---c---
B D               Zebra finch  ccc-gcg------------ctg------g--------g---a---------------cagtcc---c---
           Tibetan ground jay  ccc-ggg------------cc-------a--------g---a---------------ccgccc---cacc
B D                Budgerigar  ctg-gcg------------ctgacgaacg--------g---g---------------gggctc---c---
  D             Scarlet macaw  ccc-acc------------ttgctg---g--------g---a---------------gggacc---a---
  D              Mallard duck  gcg-ggc------------tgg------gtgtcaggtg---c---------------cagtgt---c---
B D                   Chicken  ccg-ggg------------cgg------g--------g---c---------------tggggg---c---
B D                    Turkey  cc---------------------------------------c---------------tctttc---c---
B D        American alligator  gcg-gcg------------cta------g--------g---g---------------ctcctc---c---
  D           Green seaturtle  gta-gggctccccccaccccag------t--------g---c---------------ctcccc---c---
  D            Painted turtle  ctc-tgg------------cag------g--------a---c----------------------------
  D  Chinese softshell turtle  cgc-ttg------------ccg------g--------g---cgaggcgaagtcgtagcggccc---c---
B D                    Lizard  ctt-gtc------------ctc------c--------g---t---------------ggcttc---c---
B D             X. tropicalis  gcg-ggg------------ctg------t--------ctcgg---------------cgactt---t---
B D                 Tetraodon  -------------------------------------------cggtgtccgcgcccggaccg---t---
B D                      Fugu  -------------------------------------------cggtgcccgctgccggaccg---t---
B D              Nile tilapia  -------------------------------------------cggtggtcagctttggaccg---t---
          Princess of Burundi  -------------------------------------------cggtggtcagctttggaccg---t---
        Burton's mouthbreeder  -------------------------------------------cggtggtcagctttggaccg---t---
                  Zebra mbuna  -------------------------------------------cggtggtcagctttggaccg---t---
          Pundamilia nyererei  -------------------------------------------cggtggtcagctttggaccg---t---
B D                    Medaka  ----------------------------------------------------------------------
           Southern platyfish  -------------------------------------------cggcggaaac-----------------
B D               Stickleback  -------------------------------------------ccgtggtcgccgtagcaccg---t---
B D              Atlantic cod  -------------------------------------------ctgaaactggaaaccgctcg---t---
B D                 Zebrafish  -------------------------------------------caatagatggcgctgtttcg---c---
                  Spotted gar  -------------------------------------------ccgcctccagccggggctcggttc---
B D                   Lamprey  ------------------------------------------------------tcgggttca---g---
B D                  Hedgehog  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D                Coelacanth  ======================================================================
B D                     Shrew  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D                    Rhesus  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D                    Gibbon  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
    Mexican tetra (cavefish)  ======================================================================
                  Chinchilla  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
      Lesser Egyptian jerboa  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
          Chinese tree shrew  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D                   Manatee  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D           Chinese hamster  ----------------------------------------------------------------------
B D                    Tenrec  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D                       Cat  ======================================================================
B D                   Ferret   NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D                     Panda  ======================================================================
               Domestic goat  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
            Tibetan antelope  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
             Star-nosed mole  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
              Bactrian camel  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D                    Alpaca  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
                Weddell seal  ======================================================================
        David's myotis (bat)  ======================================================================
B D           Squirrel monkey  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

                        Human  --------ggat------cccg--------gtc--------------------------
                        Chimp  --------ggat------cccg--------gtc--------------------------
                      Gorilla  --------ggat------cctg--------gtc--------------------------
                    Orangutan  --------agat------cccg--------gtc--------------------------
          Crab-eating macaque  --------agat------cccg--------gtc--------------------------
                       Baboon  --------agat------cccg--------gtc--------------------------
                 Green monkey  --------agat------cccg--------gtc--------------------------
                     Marmoset  --------ggat------ccca--------gcc--------------------------
                     Bushbaby  --------cgag------cccg--------gac--------------------------
                     Squirrel  --------cgag------accc--------tgt--------------------------
                 Prairie vole  --------cgag------cctg--------ggc--------------------------
               Golden hamster  --------cgag------cctg--------ggc--------------------------
                        Mouse  --------cgag------cctg--------ggc--------------------------
                          Rat  --------cgag------cctg--------ggc--------------------------
               Naked mole-rat  --------caag------ccct--------ggc--------------------------
                   Guinea pig  --------cgag------ccct--------ggc--------------------------
             Brush-tailed rat  --------cgag------ccct--------ggc--------------------------
                       Rabbit  --------cgag------cctt--------ggc--------------------------
                         Pika  --------caag------tccg--------cgc--------------------------
                          Pig  --------cgag------cccc--------ggg--------------------------
                      Dolphin  --------cgag------tccg--------ggg--------------------------
                 Killer whale  --------cgag------tccg--------ggg--------------------------
                          Cow  --------cgag------cccg--------ggg--------------------------
                        Sheep  --------cgag------cccg--------ggg--------------------------
                        Horse  --------cgag------cccg--------ggg--------------------------
             White rhinoceros  --------cgag------cctg--------ggg--------------------------
                          Dog  --------cgaa------cccg--------ggc--------------------------
               Pacific walrus  --------cgaa------cccg--------ggg--------------------------
             Black flying-fox  --------caag------ccgg--------ggg--------------------------
                      Megabat  --------caag------ccgg--------ggg--------------------------
                Big brown bat  --------cgag------cccg--------ggg--------------------------
                     Microbat  --------cgag------tctg--------ggg--------------------------
                     Elephant  --------cgaa------gcct--------ggc--------------------------
          Cape elephant shrew  --------cgag------gcgg--------ggc--------------------------
             Cape golden mole  --------cgtg------gctg--------gac--------------------------
                     Aardvark  --------cgag------gcca--------ggt--------------------------
                    Armadillo  --------cggg------tgcg--------cac--------------------------
                      Opossum  --------aggc------aggc--------gca--------------------------
              Tasmanian devil  --------ggag------ctgc--------ggc--------------------------
                      Wallaby  --------ggag------ctgt--------ggc--------------------------
                     Platypus  --------agag------agcg--------gac--------------------------
                  Rock pigeon  --------------------------------c--------------------------
                 Saker falcon  --------gggg------acaa--------ggg--------------------------
             Peregrine falcon  --------gggg------acaa--------ggg--------------------------
          Collared flycatcher  -----------g------tgat--------cgt--------------------------
       White-throated sparrow  -----------------------------------------------------------
                  Zebra finch  ---ggcaagggg------acgg--------cga--------------------------
           Tibetan ground jay  cgcgggcgggga------acgg--------tgc--------------------------
                   Budgerigar  -ctgcgtcgggg------gcgg--------cgc--------------------------
                Scarlet macaw  -gta---cgagc------acgg--------cac--------------------------
                 Mallard duck  --------acag------cagg--------tgt--------------------------
                      Chicken  --------ggag------ccga--------agc--------------------------
                       Turkey  --------tcag------atgatccagaccagc--------------------------
           American alligator  ------cgcggg------gcgg--------ggc--------------------------
              Green seaturtle  -----ctctagg------gcca--------tgc--------------------------
               Painted turtle  ---------agg------ggct--------cgg--------------------------
     Chinese softshell turtle  -----tgctctg------cccc--------ctt--------------------------
                       Lizard  --------tggt------ccca--------cct--------------------------
                X. tropicalis  --------gtgc------cgct--------gtc--------------------------
                    Tetraodon  --------ggag------tccc--------ggg--------------------------
                         Fugu  --------ggag------tccc--------gag--------------------------
                 Nile tilapia  --------ggag------tccc--------ggg--------------------------
          Princess of Burundi  --------ggag------tccc--------ggg--------------------------
        Burton's mouthbreeder  --------ggag------tccc--------ggg--------------------------
                  Zebra mbuna  --------ggag------tccc--------ggg--------------------------
          Pundamilia nyererei  --------ggag------tccc--------ggg--------------------------
                       Medaka  ------------------ccgc--------ctg--------------------------
           Southern platyfish  ----------aa------ccac--------ggg--------------------------
                  Stickleback  --------ggag------tccc--------ggg--------------------------
                 Atlantic cod  --------gcagcccaactctc--------ccg--------------------------
                    Zebrafish  --------caga------c----------------------------------------
                  Spotted gar  --------gggg------tccc--------ggt--------------------------
                      Lamprey  --------cgaa------gcct--------ccgatgaacaccgtgccagaaactcgctg
                     Hedgehog  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
                   Coelacanth  ===========================================================
                        Shrew  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
                       Rhesus  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
                       Gibbon  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
     Mexican tetra (cavefish)  ===========================================================
                   Chinchilla  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
       Lesser Egyptian jerboa  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
           Chinese tree shrew  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
                      Manatee  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
              Chinese hamster  -----------------------------------------------------------
                       Tenrec  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
                          Cat  ===========================================================
                      Ferret   NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
                        Panda  ===========================================================
                Domestic goat  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
             Tibetan antelope  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
              Star-nosed mole  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
               Bactrian camel  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
                       Alpaca  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
                 Weddell seal  ===========================================================
         David's myotis (bat)  ===========================================================
              Squirrel monkey  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

Inserts between block 14 and 15 in window
B D                      Rat 2bp
B D               Budgerigar 1bp
  D            Scarlet macaw 5bp
B D                Tetraodon 11bp
B D                     Fugu 11bp
B D             Nile tilapia 9bp
         Princess of Burundi 9bp
       Burton's mouthbreeder 9bp
                 Zebra mbuna 9bp
         Pundamilia nyererei 9bp
B D                   Medaka 25bp
          Southern platyfish 24bp
B D              Stickleback 9bp
B D             Atlantic cod 10bp
                 Spotted gar 27bp

Alignment block 15 of 1479 in window, 49539286 - 49539307, 22 bps 
B D                     Human  tgcgcat----tgc--------------c--c------------c-----------ccg----ac-ggct
B D                     Chimp  tgcgcat----tgc--------------c--c------------c-----------ccg----ac-ggct
B D                   Gorilla  tgcgcat----tgc--------------c--c------------c-----------ccg----ac-ggct
B D                 Orangutan  tgggcat----tgc--------------c--c------------c-----------ccg----ac-ggct
B D       Crab-eating macaque  tgggcat----tgc--------------c--c------------c-----------ccg----ac-ggct
B D                    Baboon  tgggcat----tgc--------------c--c------------c-----------ccg----ac-ggct
B D              Green monkey  tgggcat----tgc--------------c--c------------c-----------ccg----ac-ggct
B D                  Marmoset  tgggcat----tgc--------------c--c------------c-----------ccg----ac-ggct
B D                  Bushbaby  tgggcat----tgt--------------c--c------------c-----------ccg----ac-ggct
B D                  Squirrel  tgggcat----tgc--------------c--c------------c-----------ccg----ac-ggct
                 Prairie vole  cgggcat----tgc--------------c--c------------c-----------ccg----ac-ggct
               Golden hamster  cgggcat----tgc--------------c--c------------c-----------ccg----ac-ggct
B D                     Mouse  cgggcat----agc--------------c--c------------c-----------ccg----ac-ggct
B D                       Rat  cgggcat----ag-------------------------------------------ccg----ac-ggct
B D            Naked mole-rat  tgggcat----tgc--------------c--t------------c-----------ccc----ac-ggct
B D                Guinea pig  tgggcat----tgc--------------c--c------------c-----------ccg----ac-ggct
             Brush-tailed rat  tgggcat----tgc--------------c--c------------c-----------ccg----ac-aact
B D                    Rabbit  caagctc----tgc--------------c--c------------t-----------tcg----ac-ggct
B D                      Pika  cgggctc----tgc--------------g--c------------t-----------tcg----ac-ggct
B D                       Pig  taggcac----tgc--------------g--c------------c-----------ccg----ac-ggct
B D                   Dolphin  tgggcat----tgc--------------c--c------------c-----------ccg----ac-ggct
                 Killer whale  tgggcat----tgc--------------c--c------------c-----------ccg----ac-ggct
B D                       Cow  tgggcat----cgc--------------c--c------------c-----------ccg----ac-ggct
B D                     Sheep  tgggcat----cga--------------c--c------------c-----------tcg----ac-ggct
B D                     Horse  tgggcat----tgc--------------c--c------------c-----------tcg----ac-ggcc
B D          White rhinoceros  tgggcat----tgc--------------c--c------------c-----------ccg----ac-ggct
B D                       Dog  ggggctc----ggg--------------c--g------------t-----------ccg----ac-ggcc
               Pacific walrus  tgggctt----cgg--------------c--c------------t-----------ccg----ac-ggct
             Black flying-fox  agggcat----tgc--------------c--c------------c-----------ccg----ac-ggct
B D                   Megabat  tgggcat----tgc--------------c--c------------c-----------ccg----ac-ggct
                Big brown bat  tgggcac----tgt--------------c--c------------c-----------ccg----ac-agct
B D                  Microbat  tgggcat----tgt--------------c--c------------c-----------ccg----ac-agcc
B D                  Elephant  tgggcat----tgc--------------t--c------------c-----------ccg----ac-ggct
          Cape elephant shrew  tgggcgt----cgc--------------t--t------------c-----------ccg----ag-ggct
             Cape golden mole  tgggcat----tgc--------------t--c------------c-----------ccg----ac-ggct
                     Aardvark  tgggcat----tgc--------------t--c------------c-----------tcg----ac-ggct
B D                 Armadillo  ccggcct----tgc--------------c--c------------c-----------ccg----ac-ggct
B D                   Opossum  tggggcg----ccc--------------cggc------------c-----------cag----cc-ggca
B D           Tasmanian devil  tgggctg----cgc--------------c--c------------c-----------cag----cc-acct
B D                   Wallaby  tgggctg----cgc--------------c--c------------c-----------cag----ac-agct
B D                  Platypus  t------------c--------------c--c------------g-----------gag----ac-agaa
  D               Rock pigeon  cctgtcc----ttt--------------c--c------------t-----------ccc----tc-ctcc
  D              Saker falcon  cctgcac----cct--------------c--c------------c-----------tgt----cc-ga--
  D          Peregrine falcon  cctgcac----cct--------------c--c------------c-----------tgt----cc-ga--
  D       Collared flycatcher  tttgctg----ctt--------------c--t------------t-----------acc-----------
  D    White-throated sparrow  tccgcct----cct--------------c--c------------c-----------tcc----ct-ac--
B D               Zebra finch  tttgcgg----cat--------------c--c------------c-----------ggc----cc-gcac
           Tibetan ground jay  tcgacgg----tgc--------------c--g------------a-----------ggc-----------
B D                Budgerigar  gcggcat----ccc--------------c--a------------t-----------cct----cc-tcct
  D             Scarlet macaw  tctgtat----tcc--------------c--c------------t-----------ccc----ac-agca
  D              Mallard duck  cgggcgt----a-------------------c--------------------------------------
B D                   Chicken  ccagggt----ggg--------------c--c--------------------------------------
B D                    Turkey  cggacgc----tga--------------t--c--------------------------------------
B D        American alligator  agcgcgc----cat--------------g--c------------a-----------cct----gc-gg--
  D           Green seaturtle  tctgcag----tgt--------------g--t------------a-----------gcc----ac-accc
  D            Painted turtle  tctccgc----cgc--------------t--t------------g-----------gcc-----------
  D  Chinese softshell turtle  tccccgc----ccc--------------c--t------------g-----------cct----cc-cctc
B D                    Lizard  tacgcct----cga--------------c--g------------g-------------------------
B D             X. tropicalis  tcagcgc----tga--------------t--g------------c-----------cgg----tt-----
B D                 Tetraodon  --ggcgc----cct--------------c--c------------t-----------cca----gg-g---
B D                      Fugu  --ggcgc----cct--------------c--c------------t-----------cca----gg-g---
       Yellowbelly pufferfish  --ggcga----ctt--------------c--ccgactgttgtcat-----------cct----ca-g---
B D              Nile tilapia  tcggcgc----cct--------------c--c------------t-----------cca----gg-g---
          Princess of Burundi  tcggcgc----cct--------------c--c------------t-----------cca----gg-g---
        Burton's mouthbreeder  tcggcgc----cct--------------c--c------------t-----------cca----gg-g---
                  Zebra mbuna  tcggcgc----cct--------------c--c------------t-----------cca----gg-g---
          Pundamilia nyererei  tcggcgc----cct--------------c--c------------t-----------cca----gg-g---
B D                    Medaka  acagagag---gca--------------g--c------------t-----------cca----gacg---
           Southern platyfish  tcggcgc----cct--------------c--c------------t-----------cca----gg-g---
B D               Stickleback  tcggcgc----cct--------------c--c------------t-----------cca----gg-g---
B D              Atlantic cod  cggtcat----tcc--------------t--c------------a-----------ccg----gg-g---
B D                 Zebrafish  -------tatgcct--------------g--c------------tatagcggaggatca----gt-g---
                  Spotted gar  tacggtc----ccc--------------c--c------------t-----------ccggcccgg-a---
B D                   Lamprey  cgaacgt----cgcgttttcttttgcatc--t------------c-----------acg----at-agca
B D                  Hedgehog  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D                Coelacanth  ======================================================================
B D                     Shrew  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D                    Rhesus  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D                    Gibbon  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
    Mexican tetra (cavefish)  ======================================================================
                  Chinchilla  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
      Lesser Egyptian jerboa  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
          Chinese tree shrew  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D                   Manatee  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D           Chinese hamster  ----------------------------------------------------------------------
B D                    Tenrec  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D                       Cat  ======================================================================
B D                   Ferret   NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D                     Panda  ======================================================================
               Domestic goat  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
            Tibetan antelope  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
             Star-nosed mole  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
              Bactrian camel  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D                    Alpaca  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
                Weddell seal  ======================================================================
        David's myotis (bat)  ======================================================================
B D           Squirrel monkey  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

Inserts between block 15 and 16 in window
  D              Rock pigeon 12bp
  D             Saker falcon 14bp
  D         Peregrine falcon 521bp
  D      Collared flycatcher 9bp
  D   White-throated sparrow 9bp
B D              Zebra finch 11bp
          Tibetan ground jay 7bp
B D               Budgerigar 11bp
  D            Scarlet macaw 11bp
  D          Green seaturtle 2bp
  D Chinese softshell turtle 2bp

Alignment block 16 of 1479 in window, 49539308 - 49539312, 5 bps 
B D                     Human  gcgct
B D                     Chimp  gcgct
B D                   Gorilla  gcgct
B D                 Orangutan  gcgct
B D       Crab-eating macaque  gcgct
B D                    Baboon  gcgct
B D              Green monkey  gcgct
B D                  Marmoset  gcgct
B D                  Bushbaby  gcgct
B D                  Squirrel  gctct
                 Prairie vole  actct
               Golden hamster  actct
B D                     Mouse  actct
B D                       Rat  atcta
B D            Naked mole-rat  gcgct
B D                Guinea pig  gcgct
             Brush-tailed rat  gcgct
B D                    Rabbit  gcgct
B D                      Pika  gcgct
B D                       Pig  gcgct
B D                   Dolphin  gcgct
                 Killer whale  gcgct
B D                       Cow  gcgct
B D                     Sheep  gcgct
B D                     Horse  gcgct
B D          White rhinoceros  gtgct
B D                       Dog  gcgct
               Pacific walrus  tcgct
             Black flying-fox  gcgct
B D                   Megabat  gcgct
                Big brown bat  gcggt
B D                  Microbat  gcgct
B D                  Elephant  gcgct
          Cape elephant shrew  gcgct
             Cape golden mole  gcact
                     Aardvark  gcact
B D                 Armadillo  gcgct
B D                   Opossum  gc---
B D           Tasmanian devil  gccct
B D                   Wallaby  accct
B D                  Platypus  gagcg
  D               Rock pigeon  cctcc
  D          Peregrine falcon  gcgtc
  D              Mallard duck  gtgtc
B D                   Chicken  gggtc
B D                    Turkey  gagtc
  D           Green seaturtle  --g--
  D            Painted turtle  --g--
B D             X. tropicalis  gcccc
B D                 Tetraodon  --gct
B D                      Fugu  --gct
       Yellowbelly pufferfish  --gat
B D              Nile tilapia  --gtt
          Princess of Burundi  --gtt
        Burton's mouthbreeder  --gtt
                  Zebra mbuna  --gtt
          Pundamilia nyererei  --gtt
B D                    Medaka  --cac
           Southern platyfish  --ctt
B D               Stickleback  --gtt
B D              Atlantic cod  --atc
B D                 Zebrafish  --ggg
                  Spotted gar  --aag
B D                   Lamprey  acagt
B D                  Hedgehog  NNNNN
B D                Coelacanth  =====
B D                     Shrew  NNNNN
B D                    Rhesus  NNNNN
B D                    Gibbon  NNNNN
          Tibetan ground jay  =====
B D               Zebra finch  =====
  D    White-throated sparrow  =====
    Mexican tetra (cavefish)  =====
B D        American alligator  -----
  D             Scarlet macaw  =====
B D                Budgerigar  =====
                  Chinchilla  NNNNN
      Lesser Egyptian jerboa  NNNNN
  D       Collared flycatcher  =====
B D                    Lizard  -----
  D              Saker falcon  =====
          Chinese tree shrew  NNNNN
B D                   Manatee  NNNNN
B D           Chinese hamster  -----
B D                    Tenrec  NNNNN
B D                       Cat  =====
  D  Chinese softshell turtle  =====
B D                   Ferret   NNNNN
B D                     Panda  =====
               Domestic goat  NNNNN
            Tibetan antelope  NNNNN
             Star-nosed mole  NNNNN
              Bactrian camel  NNNNN
B D                    Alpaca  NNNNN
                Weddell seal  =====
        David's myotis (bat)  =====
B D           Squirrel monkey  NNNNN

Inserts between block 16 and 17 in window
  D              Rock pigeon 10bp
B D                Tetraodon 2bp
B D                     Fugu 2bp
      Yellowbelly pufferfish 2bp
B D             Nile tilapia 2bp
         Princess of Burundi 2bp
       Burton's mouthbreeder 2bp
                 Zebra mbuna 2bp
         Pundamilia nyererei 2bp
B D                   Medaka 2bp
          Southern platyfish 2bp
B D              Stickleback 2bp
B D             Atlantic cod 2bp
B D                Zebrafish 2bp
                 Spotted gar 2bp

Alignment block 17 of 1479 in window, 49539313 - 49539313, 1 bps 
B D                     Human  -a
B D                     Chimp  -a
B D                   Gorilla  -a
B D                 Orangutan  -a
B D       Crab-eating macaque  -a
B D                    Baboon  -a
B D              Green monkey  -a
B D                  Marmoset  -a
B D                  Bushbaby  -a
B D                  Squirrel  -a
                 Prairie vole  -a
               Golden hamster  -a
B D                     Mouse  -a
B D                       Rat  -g
B D            Naked mole-rat  -a
B D                Guinea pig  -a
             Brush-tailed rat  -a
B D                    Rabbit  -a
B D                      Pika  -a
B D                       Pig  -a
B D                   Dolphin  -a
                 Killer whale  -a
B D                       Cow  -a
B D                     Sheep  -a
B D                     Horse  -a
B D          White rhinoceros  -a
B D                       Dog  -a
               Pacific walrus  -a
             Black flying-fox  -a
B D                   Megabat  -a
                Big brown bat  -a
B D                  Microbat  -a
B D                  Elephant  -a
          Cape elephant shrew  -a
             Cape golden mole  -a
                     Aardvark  -g
B D                 Armadillo  -a
B D           Tasmanian devil  -a
B D                   Wallaby  -a
B D                  Platypus  -g
B D                 Tetraodon  -g
B D                      Fugu  -g
       Yellowbelly pufferfish  -g
B D              Nile tilapia  -g
          Princess of Burundi  -g
        Burton's mouthbreeder  -g
                  Zebra mbuna  -g
          Pundamilia nyererei  -g
B D                    Medaka  -c
           Southern platyfish  -g
B D               Stickleback  -g
B D              Atlantic cod  -c
B D                 Zebrafish  -g
                  Spotted gar  -g
B D                   Lamprey  t-
B D                  Hedgehog  NN
B D                Coelacanth  ==
B D                     Shrew  NN
B D                    Rhesus  NN
B D                    Gibbon  NN
B D                    Turkey  --
B D                   Chicken  --
  D              Mallard duck  --
          Tibetan ground jay  ==
B D               Zebra finch  ==
  D    White-throated sparrow  ==
    Mexican tetra (cavefish)  ==
B D             X. tropicalis  --
  D            Painted turtle  --
  D           Green seaturtle  --
B D        American alligator  --
  D             Scarlet macaw  ==
B D                Budgerigar  ==
B D                   Opossum  --
                  Chinchilla  NN
      Lesser Egyptian jerboa  NN
  D               Rock pigeon  ==
  D       Collared flycatcher  ==
B D                    Lizard  --
  D          Peregrine falcon  --
  D              Saker falcon  ==
          Chinese tree shrew  NN
B D                   Manatee  NN
B D           Chinese hamster  --
B D                    Tenrec  NN
B D                       Cat  ==
  D  Chinese softshell turtle  ==
B D                   Ferret   NN
B D                     Panda  ==
               Domestic goat  NN
            Tibetan antelope  NN
             Star-nosed mole  NN
              Bactrian camel  NN
B D                    Alpaca  NN
                Weddell seal  ==
        David's myotis (bat)  ==
B D           Squirrel monkey  NN

Inserts between block 17 and 18 in window
B D          Tasmanian devil 40bp
B D                  Wallaby 6bp
B D                 Platypus 6bp

Alignment block 18 of 1479 in window, 49539314 - 49539318, 5 bps 
B D                     Human  gggag
B D                     Chimp  gggag
B D                   Gorilla  gggag
B D                 Orangutan  gggag
B D       Crab-eating macaque  gggag
B D                    Baboon  gggag
B D              Green monkey  gggag
B D                  Marmoset  gggag
B D                  Bushbaby  gaggg
B D                  Squirrel  ggggg
                 Prairie vole  ggggg
               Golden hamster  ggggg
B D                     Mouse  ggggg
B D                       Rat  gggcg
B D            Naked mole-rat  ggggg
B D                Guinea pig  agggg
             Brush-tailed rat  ggggg
B D                    Rabbit  ggggg
B D                      Pika  ggggt
B D                       Pig  ggggg
B D                   Dolphin  ggggg
                 Killer whale  ggggg
B D                       Cow  ggggg
B D                     Sheep  ggggg
B D                     Horse  ggggg
B D          White rhinoceros  ggggg
B D                       Dog  ggggg
               Pacific walrus  ggggg
             Black flying-fox  ggggg
B D                   Megabat  ggggg
                Big brown bat  agggg
B D                  Microbat  agggg
              Star-nosed mole  ggggg
B D                  Elephant  ggggg
          Cape elephant shrew  ggggg
             Cape golden mole  ggggg
                     Aardvark  agggg
B D                 Armadillo  ggggg
B D                   Opossum  gcg--
B D           Tasmanian devil  gcg--
B D                   Wallaby  gcg--
B D                  Platypus  ggaag
  D          Peregrine falcon  ----a
  D              Mallard duck  ----a
B D                   Chicken  ----g
B D                    Turkey  ----t
B D        American alligator  aggga
  D           Green seaturtle  ----a
  D            Painted turtle  ----a
B D                    Lizard  ----a
B D                 Tetraodon  aggag
B D                      Fugu  aggag
       Yellowbelly pufferfish  cagag
B D              Nile tilapia  aggag
          Princess of Burundi  aggag
        Burton's mouthbreeder  aggag
                  Zebra mbuna  aggag
          Pundamilia nyererei  aggag
B D                    Medaka  agcac
           Southern platyfish  aggag
B D               Stickleback  gggag
B D              Atlantic cod  agtgg
B D                 Zebrafish  aggag
                  Spotted gar  agcaa
B D                   Lamprey  --gcg
B D                  Hedgehog  NNNNN
B D                Coelacanth  =====
B D                     Shrew  NNNNN
B D                    Rhesus  NNNNN
B D                    Gibbon  NNNNN
          Tibetan ground jay  =====
B D               Zebra finch  =====
  D    White-throated sparrow  =====
    Mexican tetra (cavefish)  =====
B D             X. tropicalis  -----
  D             Scarlet macaw  =====
B D                Budgerigar  =====
                  Chinchilla  NNNNN
      Lesser Egyptian jerboa  NNNNN
  D               Rock pigeon  =====
  D       Collared flycatcher  =====
  D              Saker falcon  =====
          Chinese tree shrew  NNNNN
B D                   Manatee  NNNNN
B D           Chinese hamster  -----
B D                    Tenrec  NNNNN
B D                       Cat  =====
  D  Chinese softshell turtle  =====
B D                   Ferret   NNNNN
B D                     Panda  =====
               Domestic goat  NNNNN
            Tibetan antelope  NNNNN
              Bactrian camel  NNNNN
B D                    Alpaca  NNNNN
                Weddell seal  =====
        David's myotis (bat)  =====
B D           Squirrel monkey  NNNNN

Inserts between block 18 and 19 in window
B D                  Opossum 8bp
B D          Tasmanian devil 6bp
B D                  Wallaby 30bp
B D             Atlantic cod 17bp
B D                Zebrafish 9bp

Alignment block 19 of 1479 in window, 49539319 - 49539322, 4 bps 
B D                     Human  cgcg
B D                     Chimp  cgcg
B D                   Gorilla  cgcg
B D                 Orangutan  cgcg
B D       Crab-eating macaque  cgcg
B D                    Baboon  cgcg
B D              Green monkey  cgcg
B D                  Marmoset  cgtg
B D                  Bushbaby  cgcg
           Chinese tree shrew  cgtg
B D                  Squirrel  cgca
                 Prairie vole  cgcg
               Golden hamster  cgcg
B D                     Mouse  cgcg
B D                       Rat  cgcg
B D            Naked mole-rat  cgcg
B D                Guinea pig  cgcg
             Brush-tailed rat  cgcg
B D                    Rabbit  cgcg
B D                      Pika  tgcg
B D                       Pig  cgcg
B D                   Dolphin  cgcg
                 Killer whale  cgcg
B D                       Cow  cgcg
B D                     Sheep  cgcg
B D                     Horse  cgcg
B D          White rhinoceros  cgcg
B D                       Dog  cgtc
               Pacific walrus  cgcg
             Black flying-fox  cgcg
B D                   Megabat  cgcg
                Big brown bat  cgcg
B D                  Microbat  cgcg
              Star-nosed mole  cgcg
B D                  Elephant  cgcg
          Cape elephant shrew  tgcg
             Cape golden mole  cgcg
                     Aardvark  cgcg
B D                 Armadillo  cgcg
B D                   Opossum  tgcc
B D           Tasmanian devil  ggcc
B D                   Wallaby  ggcg
B D                  Platypus  ggtg
  D          Peregrine falcon  ggga
  D       Collared flycatcher  ---g
  D    White-throated sparrow  ---g
B D               Zebra finch  ---g
           Tibetan ground jay  ---g
B D                Budgerigar  ---t
  D             Scarlet macaw  ---g
  D              Mallard duck  ccgc
B D                   Chicken  ggcc
B D                    Turkey  gctg
B D        American alligator  gccg
  D           Green seaturtle  gtga
  D            Painted turtle  gggg
B D                    Lizard  gtgg
B D                 Tetraodon  cgcc
B D                      Fugu  cgcc
       Yellowbelly pufferfish  agct
B D              Nile tilapia  cgcc
          Princess of Burundi  cgcc
        Burton's mouthbreeder  cgcc
                  Zebra mbuna  cgcc
          Pundamilia nyererei  cgcc
B D                    Medaka  cgct
           Southern platyfish  cgcc
B D               Stickleback  cgcc
B D              Atlantic cod  tgcc
B D                 Zebrafish  cgcg
                  Spotted gar  cgcg
B D                   Lamprey  -g--
B D                  Hedgehog  NNNN
B D                Coelacanth  ====
B D                     Shrew  NNNN
B D                    Rhesus  NNNN
B D                    Gibbon  NNNN
    Mexican tetra (cavefish)  ====
B D             X. tropicalis  ----
                  Chinchilla  NNNN
      Lesser Egyptian jerboa  NNNN
  D               Rock pigeon  ====
  D              Saker falcon  ====
B D                   Manatee  NNNN
B D           Chinese hamster  ----
B D                    Tenrec  NNNN
B D                       Cat  ====
  D  Chinese softshell turtle  ====
B D                   Ferret   NNNN
B D                     Panda  ====
               Domestic goat  NNNN
            Tibetan antelope  NNNN
              Bactrian camel  NNNN
B D                    Alpaca  NNNN
                Weddell seal  ====
        David's myotis (bat)  ====
B D           Squirrel monkey  NNNN

Inserts between block 19 and 20 in window
B D                Tetraodon 4bp
B D                     Fugu 4bp
      Yellowbelly pufferfish 4bp
B D             Nile tilapia 4bp
         Princess of Burundi 4bp
       Burton's mouthbreeder 4bp
                 Zebra mbuna 4bp
         Pundamilia nyererei 4bp
          Southern platyfish 4bp
B D              Stickleback 4bp
B D             Atlantic cod 4bp
B D                Zebrafish 32bp
                 Spotted gar 15bp

Alignment block 20 of 1479 in window, 49539323 - 49539328, 6 bps 
B D                     Human  g----------gg------c-----cc-
B D                     Chimp  g----------gg------c-----cc-
B D                   Gorilla  g----------gg------c-----cc-
B D                 Orangutan  g----------gg------c-----cc-
B D       Crab-eating macaque  g----------gg------c-----cc-
B D                    Baboon  g----------gg------c-----cc-
B D              Green monkey  g----------gg------c-----cc-
B D                  Marmoset  g----------gg------c-----cc-
B D                  Bushbaby  g----------gg------c-----tc-
           Chinese tree shrew  g----------gg------c-----cg-
B D                  Squirrel  g----------gg------c-----cc-
                 Prairie vole  g----------gg------c-----cc-
               Golden hamster  g----------gg------c-----cc-
B D                     Mouse  g----------gg------c-----cc-
B D                       Rat  g----------gg------c-----cc-
B D            Naked mole-rat  g----------gg------c-----cc-
B D                Guinea pig  g----------gg------c-----cc-
             Brush-tailed rat  g----------gg------c-----cc-
B D                    Rabbit  g----------gg------c-----cc-
B D                      Pika  g----------gg------c-----cc-
B D                       Pig  g----------gg------c-----cc-
B D                   Dolphin  g----------gg------c-----cc-
                 Killer whale  g----------gg------c-----cc-
B D                       Cow  g----------gg------c-----cc-
B D                     Sheep  g----------gg------c-----cc-
B D                     Horse  g----------gg-----cc-----cc-
B D          White rhinoceros  g----------gg------c-----cc-
B D                       Dog  c----------cc------g-----cc-
               Pacific walrus  g----------gg------c-----cg-
             Black flying-fox  g----------gg------c-----cc-
B D                   Megabat  g----------gg------c-----cc-
                Big brown bat  g----------gg------c-----cc-
B D                  Microbat  g----------gg------c-----cc-
              Star-nosed mole  g----------gg------c-----cc-
B D                  Elephant  g----------gg------c-----cc-
          Cape elephant shrew  g----------gg------c-----cc-
             Cape golden mole  g----------gg------c-----cc-
                     Aardvark  g----------gg------c-----cc-
B D                 Armadillo  g----------gg------c-----gc-
B D                   Opossum  c----------gg------c-----cg-
B D           Tasmanian devil  t----------gg------c-----gg-
B D                   Wallaby  cccgctggactgg------c-----gg-
B D                  Platypus  a----------gg------t-----ga-
  D              Saker falcon  -----------gg------c-----tg-
  D          Peregrine falcon  g----------cg------c-----tg-
  D       Collared flycatcher  a----------tg------c-----tc-
  D    White-throated sparrow  g----------cg------c-----cc-
B D               Zebra finch  g----------gg------c-----ag-
           Tibetan ground jay  g----------tg------c-----cg-
B D                Budgerigar  g----------cc------t-----cc-
  D             Scarlet macaw  g----------ag------c-----at-
  D              Mallard duck  g----------ag------c------g-
B D                   Chicken  g----------ag------c-----cg-
B D                    Turkey  a----------cg------c-----ag-
B D        American alligator  g----------cg------c-----tc-
  D           Green seaturtle  g----------cg------tggacacg-
  D            Painted turtle  g----------gg------t-----cg-
  D  Chinese softshell turtle  -------------------------cc-
B D                    Lizard  a----------ct------c-----tc-
B D                 Tetraodon  ------------g------c-----ta-
B D                      Fugu  ------------g------c-----ta-
       Yellowbelly pufferfish  ------------g------g-----gg-
B D              Nile tilapia  ------------g------c-----at-
          Princess of Burundi  ------------g------c-----at-
        Burton's mouthbreeder  ------------g------c-----at-
                  Zebra mbuna  ------------g------c-----at-
          Pundamilia nyererei  ------------g------c-----at-
B D                    Medaka  -------------------------cc-
           Southern platyfish  ------------a------a-----ct-
B D               Stickleback  ------------a------c-----ct-
B D              Atlantic cod  ------------a------c-----ga-
B D                 Zebrafish  ------------g------c-----ag-
     Mexican tetra (cavefish)  ------------gaccaccc-----ag-
                  Spotted gar  ------------c------g-----ct-
B D                   Lamprey  -----------gg------a-----ttt
B D                  Hedgehog  NNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D                Coelacanth  ============================
B D                     Shrew  NNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D                    Rhesus  NNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D                    Gibbon  NNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D             X. tropicalis  ----------------------------
                  Chinchilla  NNNNNNNNNNNNNNNNNNNNNNNNNNNN
      Lesser Egyptian jerboa  NNNNNNNNNNNNNNNNNNNNNNNNNNNN
  D               Rock pigeon  ============================
B D                   Manatee  NNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D           Chinese hamster  ----------------------------
B D                    Tenrec  NNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D                       Cat  ============================
B D                   Ferret   NNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D                     Panda  ============================
               Domestic goat  NNNNNNNNNNNNNNNNNNNNNNNNNNNN
            Tibetan antelope  NNNNNNNNNNNNNNNNNNNNNNNNNNNN
              Bactrian camel  NNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D                    Alpaca  NNNNNNNNNNNNNNNNNNNNNNNNNNNN
                Weddell seal  ============================
        David's myotis (bat)  ============================
B D           Squirrel monkey  NNNNNNNNNNNNNNNNNNNNNNNNNNNN

Inserts between block 20 and 21 in window
B D                  Opossum 1bp
  D             Saker falcon 5bp
  D         Peregrine falcon 5bp
  D      Collared flycatcher 61bp
  D   White-throated sparrow 49bp
          Tibetan ground jay 19bp
B D               Budgerigar 3bp
  D            Scarlet macaw 3bp
B D                  Chicken 27bp
B D                   Turkey 24bp
B D       American alligator 12bp
B D                   Lizard 10bp
B D                Tetraodon 6bp
B D                     Fugu 6bp
      Yellowbelly pufferfish 6bp
B D             Nile tilapia 6bp
         Princess of Burundi 6bp
       Burton's mouthbreeder 6bp
                 Zebra mbuna 6bp
         Pundamilia nyererei 6bp
B D                   Medaka 6bp
          Southern platyfish 6bp
B D              Stickleback 6bp
B D             Atlantic cod 28bp
B D                Zebrafish 11bp
    Mexican tetra (cavefish) 6bp
                 Spotted gar 6bp

Alignment block 21 of 1479 in window, 49539329 - 49539334, 6 bps 
B D                     Human  ggcggg
B D                     Chimp  ggcggg
B D                   Gorilla  ggcggg
B D                 Orangutan  ggcggg
B D       Crab-eating macaque  ggcggg
B D                    Baboon  ggcggg
B D              Green monkey  ggcggg
B D                  Marmoset  ggcggg
B D                  Bushbaby  ggcggg
           Chinese tree shrew  gggggg
B D                  Squirrel  ggaggg
                 Prairie vole  ggcgga
               Golden hamster  ggcggg
B D                     Mouse  ggcggg
B D                       Rat  ggc-gg
B D            Naked mole-rat  ggcggg
B D                Guinea pig  ggcggg
             Brush-tailed rat  ggtggg
B D                    Rabbit  ggcggg
B D                      Pika  ggcggg
B D                       Pig  ggcggg
B D                   Dolphin  ggcggg
                 Killer whale  ggcggg
B D                       Cow  ggtggg
B D                     Sheep  ggcggg
B D                     Horse  ggcggg
B D          White rhinoceros  ggcggg
B D                       Dog  gtcggg
               Pacific walrus  ggcggg
             Black flying-fox  ggagga
B D                   Megabat  ggagga
                Big brown bat  ggcggg
B D                  Microbat  ggcggg
              Star-nosed mole  ggcggg
B D                  Elephant  ggcggg
          Cape elephant shrew  ggcgag
             Cape golden mole  ggcggg
                     Aardvark  ggcggg
B D                 Armadillo  ggcggc
B D           Tasmanian devil  ggcggg
B D                   Wallaby  ggcggg
B D                  Platypus  ggtcgg
  D              Saker falcon  cctgcg
  D          Peregrine falcon  tgcgtg
B D                 Tetraodon  ag----
B D                      Fugu  ag----
       Yellowbelly pufferfish  ac----
B D              Nile tilapia  gg----
          Princess of Burundi  gg----
        Burton's mouthbreeder  gg----
                  Zebra mbuna  gg----
          Pundamilia nyererei  gg----
B D                    Medaka  ag----
           Southern platyfish  gg----
B D               Stickleback  gg----
B D              Atlantic cod  cg----
B D                 Zebrafish  cg----
     Mexican tetra (cavefish)  cg----
                  Spotted gar  gg----
B D                   Lamprey  tgtggg
B D                  Hedgehog  NNNNNN
B D                Coelacanth  ======
B D                     Shrew  NNNNNN
B D                    Rhesus  NNNNNN
B D                    Gibbon  NNNNNN
B D                    Turkey  ======
B D                   Chicken  ======
  D              Mallard duck  ======
          Tibetan ground jay  ======
  D    White-throated sparrow  ======
B D             X. tropicalis  ------
  D            Painted turtle  ------
  D           Green seaturtle  ------
B D        American alligator  ======
  D             Scarlet macaw  ======
B D                Budgerigar  ======
B D                   Opossum  ======
                  Chinchilla  NNNNNN
      Lesser Egyptian jerboa  NNNNNN
  D               Rock pigeon  ======
  D       Collared flycatcher  ======
B D                    Lizard  ======
B D                   Manatee  NNNNNN
B D           Chinese hamster  ------
B D                    Tenrec  NNNNNN
B D                       Cat  ======
  D  Chinese softshell turtle  ------
B D                   Ferret   NNNNNN
B D                     Panda  ======
               Domestic goat  NNNNNN
            Tibetan antelope  NNNNNN
              Bactrian camel  NNNNNN
B D                    Alpaca  NNNNNN
                Weddell seal  ======
        David's myotis (bat)  ======
B D           Squirrel monkey  NNNNNN

Inserts between block 21 and 22 in window
B D          Tasmanian devil 5bp
B D                  Wallaby 5bp
B D                Tetraodon 5bp
B D                     Fugu 5bp
      Yellowbelly pufferfish 2bp
B D             Nile tilapia 5bp
         Princess of Burundi 5bp
       Burton's mouthbreeder 5bp
                 Zebra mbuna 5bp
         Pundamilia nyererei 5bp
B D                   Medaka 5bp
          Southern platyfish 5bp
B D              Stickleback 5bp
B D             Atlantic cod 5bp
B D                Zebrafish 8bp
    Mexican tetra (cavefish) 8bp
                 Spotted gar 34bp

Alignment block 22 of 1479 in window, 49539335 - 49539335, 1 bps 
B D                     Human  g
B D                     Chimp  g
B D                   Gorilla  g
B D                 Orangutan  g
B D       Crab-eating macaque  g
B D                    Baboon  g
B D              Green monkey  g
B D                  Marmoset  g
B D           Squirrel monkey  g
B D                  Bushbaby  g
           Chinese tree shrew  g
B D                  Squirrel  g
                 Prairie vole  g
               Golden hamster  g
B D                     Mouse  g
B D                       Rat  g
B D            Naked mole-rat  g
B D                Guinea pig  g
             Brush-tailed rat  g
B D                    Rabbit  g
B D                      Pika  g
B D                       Pig  g
B D                   Dolphin  g
                 Killer whale  g
B D                       Cow  g
B D                     Sheep  g
B D                     Horse  g
B D          White rhinoceros  g
B D                       Dog  g
               Pacific walrus  g
             Black flying-fox  g
B D                   Megabat  g
                Big brown bat  g
B D                  Microbat  g
              Star-nosed mole  g
B D                  Elephant  g
          Cape elephant shrew  g
             Cape golden mole  g
                     Aardvark  g
B D                 Armadillo  g
B D           Tasmanian devil  g
B D                   Wallaby  g
B D                  Platypus  g
  D              Saker falcon  t
  D          Peregrine falcon  t
B D                    Lizard  g
B D                   Lamprey  a
B D                  Hedgehog  N
B D                Coelacanth  =
B D                     Shrew  N
B D                    Rhesus  N
B D              Atlantic cod  =
B D                    Gibbon  N
                 Spotted gar  =
B D               Stickleback  =
          Southern platyfish  =
      Yellowbelly pufferfish  =
B D                      Fugu  =
B D                 Tetraodon  =
B D                    Turkey  =
B D                   Chicken  =
  D              Mallard duck  =
          Tibetan ground jay  =
  D    White-throated sparrow  =
    Mexican tetra (cavefish)  =
B D                 Zebrafish  =
B D                    Medaka  =
         Pundamilia nyererei  =
                 Zebra mbuna  =
       Burton's mouthbreeder  =
         Princess of Burundi  =
B D              Nile tilapia  =
B D             X. tropicalis  -
  D            Painted turtle  -
  D           Green seaturtle  -
B D        American alligator  =
  D             Scarlet macaw  =
B D                Budgerigar  =
B D                   Opossum  =
                  Chinchilla  N
      Lesser Egyptian jerboa  N
  D               Rock pigeon  =
  D       Collared flycatcher  =
B D                   Manatee  N
B D           Chinese hamster  -
B D                    Tenrec  N
B D                       Cat  =
  D  Chinese softshell turtle  -
B D                   Ferret   N
B D                     Panda  =
               Domestic goat  N
            Tibetan antelope  N
              Bactrian camel  N
B D                    Alpaca  N
                Weddell seal  =
        David's myotis (bat)  =

Inserts between block 22 and 23 in window
B D                      Dog 335bp

Alignment block 23 of 1479 in window, 49539336 - 49539337, 2 bps 
B D                     Human  gg
B D                     Chimp  gg
B D                   Gorilla  gg
B D                 Orangutan  gg
B D       Crab-eating macaque  gg
B D                    Baboon  gg
B D              Green monkey  gg
B D                  Marmoset  gg
B D           Squirrel monkey  gg
B D                  Bushbaby  gg
           Chinese tree shrew  gc
B D                  Squirrel  gg
                 Prairie vole  gg
               Golden hamster  gg
B D                     Mouse  gg
B D                       Rat  gg
B D            Naked mole-rat  gg
B D                Guinea pig  gg
             Brush-tailed rat  gg
B D                    Rabbit  gg
B D                      Pika  gg
B D                       Pig  gg
B D                   Dolphin  gg
                 Killer whale  gg
B D                       Cow  gg
B D                     Sheep  gg
B D                     Horse  gc
B D          White rhinoceros  gg
               Pacific walrus  gg
             Black flying-fox  gg
B D                   Megabat  gg
                Big brown bat  gg
B D                  Microbat  gg
              Star-nosed mole  gg
B D                  Elephant  gg
          Cape elephant shrew  gc
             Cape golden mole  gg
                     Aardvark  gg
B D                 Armadillo  gg
B D           Tasmanian devil  cg
B D                   Wallaby  cg
B D                  Platypus  gc
  D              Saker falcon  gc
  D          Peregrine falcon  gg
B D                    Lizard  gc
B D                   Lamprey  gg
B D                  Hedgehog  NN
B D                Coelacanth  ==
B D                     Shrew  NN
B D                    Rhesus  NN
B D              Atlantic cod  ==
B D                    Gibbon  NN
                 Spotted gar  ==
B D               Stickleback  ==
          Southern platyfish  ==
      Yellowbelly pufferfish  ==
B D                      Fugu  ==
B D                 Tetraodon  ==
B D                    Turkey  ==
B D                   Chicken  ==
  D              Mallard duck  ==
          Tibetan ground jay  ==
  D    White-throated sparrow  ==
    Mexican tetra (cavefish)  ==
B D                 Zebrafish  ==
B D                    Medaka  ==
         Pundamilia nyererei  ==
                 Zebra mbuna  ==
       Burton's mouthbreeder  ==
         Princess of Burundi  ==
B D              Nile tilapia  ==
B D             X. tropicalis  --
  D            Painted turtle  --
  D           Green seaturtle  --
B D        American alligator  ==
  D             Scarlet macaw  ==
B D                Budgerigar  ==
B D                   Opossum  ==
                  Chinchilla  NN
      Lesser Egyptian jerboa  NN
  D               Rock pigeon  ==
  D       Collared flycatcher  ==
B D                   Manatee  NN
B D           Chinese hamster  --
B D                    Tenrec  NN
B D                       Cat  ==
  D  Chinese softshell turtle  --
B D                   Ferret   NN
B D                     Panda  ==
               Domestic goat  NN
            Tibetan antelope  NN
              Bactrian camel  NN
B D                    Alpaca  NN
                Weddell seal  ==
        David's myotis (bat)  ==
B D                       Dog  ==

Inserts between block 23 and 24 in window
B D                  Lamprey 104bp

Alignment block 24 of 1479 in window, 49539338 - 49539339, 2 bps 
B D                     Human  cg
B D                     Chimp  cg
B D                   Gorilla  cg
B D                 Orangutan  cg
B D       Crab-eating macaque  cg
B D                    Baboon  cg
B D              Green monkey  cg
B D                  Marmoset  ca
B D           Squirrel monkey  cg
B D                  Bushbaby  cg
           Chinese tree shrew  cg
B D                  Squirrel  cg
                 Prairie vole  cg
               Golden hamster  cg
B D                     Mouse  cg
B D                       Rat  cg
B D            Naked mole-rat  cg
B D                Guinea pig  cg
             Brush-tailed rat  cg
B D                    Rabbit  cg
B D                      Pika  cg
B D                       Pig  cg
B D                   Dolphin  cg
                 Killer whale  cg
B D                       Cow  cg
B D                     Sheep  cg
B D                     Horse  cg
B D          White rhinoceros  cg
               Pacific walrus  cg
             Black flying-fox  ag
B D                   Megabat  ag
                Big brown bat  cg
B D                  Microbat  cg
              Star-nosed mole  tg
B D                  Elephant  cg
          Cape elephant shrew  ca
             Cape golden mole  cg
                     Aardvark  gg
B D                 Armadillo  cg
B D           Tasmanian devil  cg
B D                   Wallaby  cg
B D                  Platypus  tg
  D              Saker falcon  ct
  D          Peregrine falcon  ct
B D                    Lizard  tt
B D                  Hedgehog  NN
B D                   Lamprey  ==
B D                Coelacanth  ==
B D                     Shrew  NN
B D                    Rhesus  NN
B D              Atlantic cod  ==
B D                    Gibbon  NN
                 Spotted gar  ==
B D               Stickleback  ==
          Southern platyfish  ==
      Yellowbelly pufferfish  ==
B D                      Fugu  ==
B D                 Tetraodon  ==
B D                    Turkey  ==
B D                   Chicken  ==
  D              Mallard duck  ==
          Tibetan ground jay  ==
  D    White-throated sparrow  ==
    Mexican tetra (cavefish)  ==
B D                 Zebrafish  ==
B D                    Medaka  ==
         Pundamilia nyererei  ==
                 Zebra mbuna  ==
       Burton's mouthbreeder  ==
         Princess of Burundi  ==
B D              Nile tilapia  ==
B D             X. tropicalis  --
  D            Painted turtle  --
  D           Green seaturtle  --
B D        American alligator  ==
  D             Scarlet macaw  ==
B D                Budgerigar  ==
B D                   Opossum  ==
                  Chinchilla  NN
      Lesser Egyptian jerboa  NN
  D               Rock pigeon  ==
  D       Collared flycatcher  ==
B D                   Manatee  NN
B D           Chinese hamster  --
B D                    Tenrec  NN
B D                       Cat  ==
  D  Chinese softshell turtle  --
B D                   Ferret   NN
B D                     Panda  ==
               Domestic goat  NN
            Tibetan antelope  NN
              Bactrian camel  NN
B D                    Alpaca  NN
                Weddell seal  ==
        David's myotis (bat)  ==
B D                       Dog  ==

Inserts between block 24 and 25 in window
B D                 Platypus 2bp

Alignment block 25 of 1479 in window, 49539340 - 49539341, 2 bps 
B D                     Human  gc
B D                     Chimp  gc
B D                   Gorilla  gc
B D                 Orangutan  gc
B D       Crab-eating macaque  gc
B D                    Baboon  gc
B D              Green monkey  gc
B D                  Marmoset  gc
B D           Squirrel monkey  gc
B D                  Bushbaby  gc
           Chinese tree shrew  gc
       Lesser Egyptian jerboa  gc
                 Prairie vole  gc
               Golden hamster  gc
B D                     Mouse  gc
B D                       Rat  gg
B D            Naked mole-rat  gc
B D                Guinea pig  gc
             Brush-tailed rat  gc
B D                    Rabbit  gc
B D                      Pika  gc
B D                       Pig  gc
B D                   Dolphin  tc
                 Killer whale  gc
B D                       Cow  gc
B D                     Sheep  gc
B D                     Horse  gc
B D          White rhinoceros  gc
               Pacific walrus  gc
             Black flying-fox  gc
B D                   Megabat  gc
                Big brown bat  gc
B D                  Microbat  gc
              Star-nosed mole  gc
B D                  Elephant  gc
          Cape elephant shrew  gc
             Cape golden mole  tc
                     Aardvark  gc
B D                 Armadillo  gc
B D           Tasmanian devil  gc
B D                   Wallaby  gc
B D                  Platypus  ac
  D              Saker falcon  gc
  D          Peregrine falcon  gg
  D           Green seaturtle  gc
  D            Painted turtle  gg
  D  Chinese softshell turtle  gg
B D                    Lizard  gc
B D             X. tropicalis  -c
B D                 Tetraodon  cc
B D                      Fugu  cc
B D              Nile tilapia  gc
          Princess of Burundi  gc
        Burton's mouthbreeder  gc
                  Zebra mbuna  gc
          Pundamilia nyererei  gc
B D                    Medaka  gt
           Southern platyfish  gc
B D               Stickleback  gc
B D              Atlantic cod  gt
B D                 Zebrafish  ac
     Mexican tetra (cavefish)  ac
                  Spotted gar  gc
B D                  Hedgehog  NN
B D                   Lamprey  ==
B D                Coelacanth  ==
B D                     Shrew  NN
B D                    Rhesus  NN
B D                    Gibbon  NN
      Yellowbelly pufferfish  ==
B D                    Turkey  ==
B D                   Chicken  ==
  D              Mallard duck  ==
          Tibetan ground jay  ==
  D    White-throated sparrow  ==
B D        American alligator  ==
  D             Scarlet macaw  ==
B D                Budgerigar  ==
B D                   Opossum  ==
                  Chinchilla  NN
  D               Rock pigeon  ==
  D       Collared flycatcher  ==
B D                   Manatee  NN
B D           Chinese hamster  --
B D                    Tenrec  NN
B D                       Cat  ==
B D                   Ferret   NN
B D                     Panda  ==
               Domestic goat  NN
            Tibetan antelope  NN
              Bactrian camel  NN
B D                    Alpaca  NN
B D                  Squirrel  --
                Weddell seal  ==
        David's myotis (bat)  ==
B D                       Dog  ==

Inserts between block 25 and 26 in window
  D             Saker falcon 7bp
  D         Peregrine falcon 8bp
  D          Green seaturtle 13bp
  D           Painted turtle 13bp
  D Chinese softshell turtle 13bp
B D                   Lizard 6bp

Alignment block 26 of 1479 in window, 49539342 - 49539345, 4 bps 
B D                     Human  cgag
B D                     Chimp  cgag
B D                   Gorilla  cgag
B D                 Orangutan  cgag
B D       Crab-eating macaque  cgag
B D                    Baboon  cgag
B D              Green monkey  cgag
B D                  Marmoset  cgag
B D           Squirrel monkey  cgag
B D                  Bushbaby  cgaa
           Chinese tree shrew  caag
       Lesser Egyptian jerboa  ctag
                 Prairie vole  ccag
               Golden hamster  cgag
B D                     Mouse  cgag
B D                       Rat  cgag
B D            Naked mole-rat  cgaa
B D                Guinea pig  cgaa
             Brush-tailed rat  cgaa
B D                    Rabbit  cgag
B D                      Pika  cgag
B D                       Pig  cgag
B D                   Dolphin  cgag
                 Killer whale  cgag
B D                       Cow  cgac
B D                     Sheep  cgac
B D                     Horse  ctag
B D          White rhinoceros  caag
               Pacific walrus  cgag
             Black flying-fox  cgag
B D                   Megabat  cgag
                Big brown bat  cgag
B D                  Microbat  cgag
              Star-nosed mole  ctta
B D                  Elephant  cgag
          Cape elephant shrew  cgag
             Cape golden mole  cgag
                     Aardvark  cgag
B D                 Armadillo  cgag
B D           Tasmanian devil  aggg
B D                   Wallaby  aggg
B D                  Platypus  cgat
  D              Saker falcon  aggg
  D          Peregrine falcon  cgag
  D       Collared flycatcher  tggg
B D               Zebra finch  cggg
           Tibetan ground jay  cggg
B D                Budgerigar  tctt
  D             Scarlet macaw  tggg
B D                   Chicken  --ag
B D                    Turkey  --ag
B D        American alligator  cgag
  D           Green seaturtle  tg--
  D            Painted turtle  ta--
  D  Chinese softshell turtle  ct--
B D                    Lizard  tgag
B D             X. tropicalis  cgtg
B D                 Tetraodon  cggg
B D                      Fugu  cggg
       Yellowbelly pufferfish  cagc
B D              Nile tilapia  cggg
          Princess of Burundi  cggg
        Burton's mouthbreeder  cggg
                  Zebra mbuna  cggg
          Pundamilia nyererei  cggg
B D                    Medaka  ccgg
           Southern platyfish  cggg
B D               Stickleback  cggg
B D              Atlantic cod  gagg
B D                 Zebrafish  cgga
     Mexican tetra (cavefish)  cggg
                  Spotted gar  ccgg
B D                  Hedgehog  NNNN
B D                   Lamprey  ====
B D                Coelacanth  ====
B D                     Shrew  NNNN
B D                    Rhesus  NNNN
B D                    Gibbon  NNNN
  D              Mallard duck  ====
  D    White-throated sparrow  ====
B D                   Opossum  ====
                  Chinchilla  NNNN
  D               Rock pigeon  ====
B D                   Manatee  NNNN
B D           Chinese hamster  ----
B D                    Tenrec  NNNN
B D                       Cat  ====
B D                   Ferret   NNNN
B D                     Panda  ====
               Domestic goat  NNNN
            Tibetan antelope  NNNN
              Bactrian camel  NNNN
B D                    Alpaca  NNNN
B D                  Squirrel  ----
                Weddell seal  ====
        David's myotis (bat)  ====
B D                       Dog  ====

Inserts between block 26 and 27 in window
  D             Saker falcon 1bp
  D         Peregrine falcon 1bp
  D      Collared flycatcher 11bp
B D              Zebra finch 10bp
          Tibetan ground jay 13bp
B D               Budgerigar 12bp
  D            Scarlet macaw 19bp
B D                  Chicken 6bp
B D                   Turkey 4bp
B D       American alligator 1bp
  D          Green seaturtle 41bp
  D           Painted turtle 16bp
  D Chinese softshell turtle 18bp
B D                   Lizard 1bp
B D                   Medaka 13bp
          Southern platyfish 28bp

Alignment block 27 of 1479 in window, 49539346 - 49539348, 3 bps 
B D                     Human  ctg
B D                     Chimp  ctg
B D                   Gorilla  ctg
B D                 Orangutan  ctg
B D       Crab-eating macaque  ctg
B D                    Baboon  ctg
B D              Green monkey  ctg
B D                  Marmoset  ctg
B D           Squirrel monkey  ctg
B D                  Bushbaby  ctg
           Chinese tree shrew  cgg
       Lesser Egyptian jerboa  ccg
                 Prairie vole  cca
               Golden hamster  cca
B D                     Mouse  cca
B D                       Rat  cca
B D            Naked mole-rat  tcg
B D                Guinea pig  ctg
             Brush-tailed rat  gcg
B D                    Rabbit  cgg
B D                      Pika  ctg
B D                       Pig  ctg
B D                   Dolphin  ttg
                 Killer whale  ttg
B D                       Cow  ttg
B D                     Sheep  ttg
B D                     Horse  ctg
B D          White rhinoceros  ctg
               Pacific walrus  ttg
             Black flying-fox  tag
B D                   Megabat  tag
                Big brown bat  ctg
B D                  Microbat  ctg
              Star-nosed mole  ttg
B D                  Elephant  ctg
          Cape elephant shrew  cgg
             Cape golden mole  ctg
                     Aardvark  ctg
B D                 Armadillo  ccg
B D           Tasmanian devil  cag
B D                   Wallaby  cag
B D                  Platypus  g--
  D               Rock pigeon  ccg
  D              Saker falcon  cga
  D          Peregrine falcon  gga
B D       Medium ground finch  ccg
           Tibetan ground jay  ccg
B D                Budgerigar  ccg
  D                    Parrot  ccg
  D             Scarlet macaw  ctg
  D              Mallard duck  ccg
B D                   Chicken  cgg
B D                    Turkey  cag
B D        American alligator  cgc
  D           Green seaturtle  agg
  D            Painted turtle  ggg
  D  Chinese softshell turtle  ggg
B D             X. tropicalis  cgg
B D                 Tetraodon  ctt
B D                      Fugu  gtt
       Yellowbelly pufferfish  atc
B D              Nile tilapia  ctt
          Princess of Burundi  ctt
        Burton's mouthbreeder  ctt
                  Zebra mbuna  ctt
          Pundamilia nyererei  ctt
B D               Stickleback  ctt
B D              Atlantic cod  gcg
B D                 Zebrafish  ga-
     Mexican tetra (cavefish)  gag
                  Spotted gar  ctt
B D                  Hedgehog  NNN
B D                   Lamprey  ===
B D                Coelacanth  ===
B D                     Shrew  NNN
B D                    Rhesus  NNN
B D                    Gibbon  NNN
          Southern platyfish  ===
B D               Zebra finch  ===
  D    White-throated sparrow  ===
B D                    Medaka  ===
B D                   Opossum  ===
                  Chinchilla  NNN
  D       Collared flycatcher  ===
B D                    Lizard  ===
B D                   Manatee  NNN
B D           Chinese hamster  ---
B D                    Tenrec  NNN
B D                       Cat  ===
B D                   Ferret   NNN
B D                     Panda  ===
               Domestic goat  NNN
            Tibetan antelope  NNN
              Bactrian camel  NNN
B D                    Alpaca  NNN
B D                  Squirrel  ---
                Weddell seal  ===
        David's myotis (bat)  ===
B D                       Dog  ===

Alignment block 28 of 1479 in window, 49539349 - 49539351, 3 bps 
B D                     Human  gg--c
B D                     Chimp  gg--c
B D                   Gorilla  gg--c
B D                 Orangutan  gg--c
B D       Crab-eating macaque  gg--c
B D                    Baboon  gg--c
B D              Green monkey  gg--c
B D                  Marmoset  gg--c
B D           Squirrel monkey  gg--c
B D                  Bushbaby  gg--c
           Chinese tree shrew  gg--c
B D                  Squirrel  gg--c
       Lesser Egyptian jerboa  gg--c
                 Prairie vole  gg--c
               Golden hamster  gg--c
B D                     Mouse  gg--c
B D                       Rat  gg--c
B D            Naked mole-rat  gg--c
B D                Guinea pig  gg--c
             Brush-tailed rat  gg--c
B D                    Rabbit  gg--c
B D                      Pika  gg--c
B D                       Pig  ga--c
B D                   Dolphin  gg--c
                 Killer whale  gg--c
B D                       Cow  gg--c
B D                     Sheep  gg--c
B D                     Horse  gg--c
B D          White rhinoceros  gg--c
               Pacific walrus  gg--c
             Black flying-fox  gg--c
B D                   Megabat  gg--c
                Big brown bat  gg--c
B D                  Microbat  gg--c
              Star-nosed mole  gg--c
B D                  Elephant  gg--c
          Cape elephant shrew  gg--c
B D                   Manatee  gg--c
             Cape golden mole  gg--c
                     Aardvark  gg--c
B D                 Armadillo  gg--c
B D           Tasmanian devil  ag--c
B D                   Wallaby  ag--a
B D                  Platypus  gg--c
  D               Rock pigeon  gg--c
  D              Saker falcon  gg--t
  D          Peregrine falcon  gg--c
B D       Medium ground finch  gg--c
B D               Zebra finch  gg--c
           Tibetan ground jay  ggatc
B D                Budgerigar  gg--c
  D                    Parrot  gg--c
  D             Scarlet macaw  gg--c
  D              Mallard duck  gg--c
B D                   Chicken  ag--g
B D                    Turkey  gt--g
B D        American alligator  gg--c
  D           Green seaturtle  ag--c
  D            Painted turtle  gg--c
  D  Chinese softshell turtle  ta--a
B D             X. tropicalis  -a--c
B D                 Tetraodon  cg--t
B D                      Fugu  cg--t
       Yellowbelly pufferfish  ag--c
B D              Nile tilapia  cg--t
          Princess of Burundi  cg--t
        Burton's mouthbreeder  cg--t
                  Zebra mbuna  cg--t
          Pundamilia nyererei  cg--t
B D               Stickleback  tg--t
B D              Atlantic cod  cg--c
B D                 Zebrafish  cg--c
     Mexican tetra (cavefish)  cg--g
                  Spotted gar  cg--g
B D                  Hedgehog  NNNNN
B D                   Lamprey  =====
B D                Coelacanth  =====
B D                     Shrew  NNNNN
B D                    Rhesus  NNNNN
B D                    Gibbon  NNNNN
          Southern platyfish  =====
  D    White-throated sparrow  =====
B D                    Medaka  =====
B D                   Opossum  =====
                  Chinchilla  NNNNN
  D       Collared flycatcher  =====
B D                    Lizard  =====
B D           Chinese hamster  -----
B D                    Tenrec  NNNNN
B D                       Cat  =====
B D                   Ferret   NNNNN
B D                     Panda  =====
               Domestic goat  NNNNN
            Tibetan antelope  NNNNN
              Bactrian camel  NNNNN
B D                    Alpaca  NNNNN
                Weddell seal  =====
        David's myotis (bat)  =====
B D                       Dog  =====

Inserts between block 28 and 29 in window
B D          Tasmanian devil 11bp
B D                  Wallaby 11bp
  D            Scarlet macaw 1bp
B D            X. tropicalis 1bp
                 Spotted gar 19bp

Alignment block 29 of 1479 in window, 49539352 - 49539353, 2 bps 
B D                     Human  gc
B D                     Chimp  gc
B D                   Gorilla  gc
B D                 Orangutan  gc
B D       Crab-eating macaque  gc
B D                    Baboon  gc
B D              Green monkey  gc
B D                  Marmoset  gc
B D           Squirrel monkey  gc
B D                  Bushbaby  gc
           Chinese tree shrew  gc
B D                  Squirrel  gc
       Lesser Egyptian jerboa  gc
                 Prairie vole  gc
               Golden hamster  gc
B D                     Mouse  gc
B D                       Rat  gc
B D            Naked mole-rat  gc
B D                Guinea pig  gc
                   Chinchilla  gc
             Brush-tailed rat  gc
B D                    Rabbit  gc
B D                      Pika  gc
B D                       Pig  gc
B D                   Dolphin  gc
                 Killer whale  gc
B D                       Cow  gc
B D                     Sheep  gc
B D                     Horse  gc
B D          White rhinoceros  gc
               Pacific walrus  gc
             Black flying-fox  tc
B D                   Megabat  tc
                Big brown bat  gc
B D                  Microbat  gc
              Star-nosed mole  gc
B D                  Elephant  gc
          Cape elephant shrew  cc
B D                   Manatee  gc
             Cape golden mole  gc
                     Aardvark  gc
B D                 Armadillo  ac
B D                   Opossum  gc
B D           Tasmanian devil  gc
B D                   Wallaby  gc
B D                  Platypus  g-
  D               Rock pigeon  gc
  D              Saker falcon  gt
  D          Peregrine falcon  gg
B D       Medium ground finch  gc
B D               Zebra finch  ag
           Tibetan ground jay  ag
B D                Budgerigar  gc
  D                    Parrot  gc
  D             Scarlet macaw  gg
  D              Mallard duck  gc
B D                   Chicken  gg
B D                    Turkey  gg
B D        American alligator  ag
  D           Green seaturtle  ag
  D            Painted turtle  gg
  D  Chinese softshell turtle  ag
B D             X. tropicalis  tc
B D                 Tetraodon  gg
B D                      Fugu  gg
       Yellowbelly pufferfish  ag
B D              Nile tilapia  gt
          Princess of Burundi  at
        Burton's mouthbreeder  gt
                  Zebra mbuna  gt
          Pundamilia nyererei  gt
B D               Stickleback  gg
B D              Atlantic cod  tc
B D                 Zebrafish  g-
     Mexican tetra (cavefish)  g-
B D                  Hedgehog  NN
B D                   Lamprey  ==
B D                Coelacanth  ==
B D                     Shrew  NN
B D                    Rhesus  NN
B D                    Gibbon  NN
                 Spotted gar  ==
          Southern platyfish  ==
  D    White-throated sparrow  ==
B D                    Medaka  ==
  D       Collared flycatcher  ==
B D                    Lizard  ==
B D           Chinese hamster  --
B D                    Tenrec  NN
B D                       Cat  ==
B D                   Ferret   NN
B D                     Panda  ==
               Domestic goat  NN
            Tibetan antelope  NN
              Bactrian camel  NN
B D                    Alpaca  NN
                Weddell seal  ==
        David's myotis (bat)  ==
B D                       Dog  ==

Inserts between block 29 and 30 in window
B D                  Opossum 4bp
B D          Tasmanian devil 4bp
B D                  Wallaby 2bp
B D                Zebrafish 12bp
    Mexican tetra (cavefish) 15bp

Alignment block 30 of 1479 in window, 49539354 - 49539358, 5 bps 
B D                     Human  cctcc
B D                     Chimp  cctcc
B D                   Gorilla  cctcc
B D                 Orangutan  cctcc
B D       Crab-eating macaque  cctcc
B D                    Baboon  cctcc
B D              Green monkey  cctcc
B D                  Marmoset  tctcc
B D           Squirrel monkey  cctcc
B D                  Bushbaby  cctcc
           Chinese tree shrew  cctcc
B D                  Squirrel  cctcc
       Lesser Egyptian jerboa  cgtcc
                 Prairie vole  cctcc
               Golden hamster  cctcc
B D                     Mouse  cctcc
B D                       Rat  cctcg
B D            Naked mole-rat  cctcc
B D                Guinea pig  cctcc
                   Chinchilla  cctcc
             Brush-tailed rat  cctcc
B D                    Rabbit  cctcc
B D                      Pika  cctcc
B D                       Pig  cctcc
B D                   Dolphin  cctcc
                 Killer whale  cctcc
B D                       Cow  cctcc
B D                     Sheep  cctcc
B D                     Horse  cctcc
B D          White rhinoceros  cctcc
B D                       Cat  cctcc
               Pacific walrus  cctcc
             Black flying-fox  cctcc
B D                   Megabat  cctcc
                Big brown bat  cctcc
B D                  Microbat  cctcc
              Star-nosed mole  cctcc
B D                  Elephant  cctcc
          Cape elephant shrew  cctcc
B D                   Manatee  cctcc
             Cape golden mole  cctcc
                     Aardvark  cctcc
B D                 Armadillo  cctcc
B D                   Opossum  cctcc
B D           Tasmanian devil  cctct
B D                   Wallaby  cccct
B D                  Platypus  --t--
  D               Rock pigeon  ----c
  D              Saker falcon  ----c
  D          Peregrine falcon  ----c
B D       Medium ground finch  ----c
B D               Zebra finch  ----c
           Tibetan ground jay  ----c
B D                Budgerigar  ----c
  D                    Parrot  ----c
  D             Scarlet macaw  ----c
  D              Mallard duck  ----c
B D                   Chicken  ----t
B D                    Turkey  ----t
B D        American alligator  ----c
  D           Green seaturtle  ----c
  D            Painted turtle  ----c
  D  Chinese softshell turtle  ----t
B D             X. tropicalis  tcagc
B D                 Tetraodon  ccacc
B D                      Fugu  ccact
       Yellowbelly pufferfish  -caca
B D              Nile tilapia  caacc
          Princess of Burundi  caacc
        Burton's mouthbreeder  caacc
                  Zebra mbuna  caacc
          Pundamilia nyererei  caacc
B D               Stickleback  ccccc
B D              Atlantic cod  tgcac
B D                  Hedgehog  NNNNN
B D                   Lamprey  =====
B D                Coelacanth  =====
B D                     Shrew  NNNNN
B D                    Rhesus  NNNNN
B D                    Gibbon  NNNNN
                 Spotted gar  =====
          Southern platyfish  =====
  D    White-throated sparrow  =====
    Mexican tetra (cavefish)  =====
B D                 Zebrafish  =====
B D                    Medaka  =====
  D       Collared flycatcher  =====
B D                    Lizard  =====
B D           Chinese hamster  -----
B D                    Tenrec  NNNNN
B D                   Ferret   NNNNN
B D                     Panda  =====
               Domestic goat  NNNNN
            Tibetan antelope  NNNNN
              Bactrian camel  NNNNN
B D                    Alpaca  NNNNN
                Weddell seal  =====
        David's myotis (bat)  =====
B D                       Dog  =====

Inserts between block 30 and 31 in window
  D              Rock pigeon 2bp
  D         Peregrine falcon 7bp
B D      Medium ground finch 2bp
B D              Zebra finch 2bp
          Tibetan ground jay 3bp
B D               Budgerigar 2bp
  D                   Parrot 2bp
  D            Scarlet macaw 2bp
  D             Mallard duck 2bp
B D                  Chicken 2bp
B D                   Turkey 8bp
B D       American alligator 2bp
  D          Green seaturtle 27bp
  D           Painted turtle 21bp
  D Chinese softshell turtle 11bp

Alignment block 31 of 1479 in window, 49539359 - 49539362, 4 bps 
B D                     Human  cccg---
B D                     Chimp  cccg---
B D                   Gorilla  cccg---
B D                 Orangutan  cccg---
B D       Crab-eating macaque  cccg---
B D                    Baboon  cccg---
B D              Green monkey  cccg---
B D                  Marmoset  cccg---
B D           Squirrel monkey  cccg---
B D                  Bushbaby  cccg---
           Chinese tree shrew  ctcg---
B D                  Squirrel  ccgg---
       Lesser Egyptian jerboa  cccg---
                 Prairie vole  cccg---
               Golden hamster  ccgg---
B D                     Mouse  cccg---
B D                       Rat  cccg---
B D            Naked mole-rat  cccg---
B D                Guinea pig  cgcg---
                   Chinchilla  cccg---
             Brush-tailed rat  cccg---
B D                    Rabbit  cccg---
B D                      Pika  cccg---
B D                       Pig  cccg---
B D                   Dolphin  cccg---
                 Killer whale  cccg---
B D                       Cow  cccg---
B D                     Sheep  cccg---
B D                     Horse  cccg---
B D          White rhinoceros  cccg---
B D                       Cat  cccg---
               Pacific walrus  cccg---
                 Weddell seal  cccg---
             Black flying-fox  cccg---
B D                   Megabat  cccg---
                Big brown bat  tccg---
B D                  Microbat  cccg---
              Star-nosed mole  cccg---
B D                  Elephant  tccg---
          Cape elephant shrew  cccg---
B D                   Manatee  tccg---
             Cape golden mole  cccg---
                     Aardvark  cccg---
B D                 Armadillo  cccg---
B D                   Opossum  ccc----
B D           Tasmanian devil  ccc----
B D                   Wallaby  tcc----
B D                  Platypus  ---g---
  D               Rock pigeon  ct-----
  D              Saker falcon  ca-----
  D          Peregrine falcon  cc-----
B D       Medium ground finch  ct-----
B D               Zebra finch  cg-----
           Tibetan ground jay  cg-----
B D                Budgerigar  ct-----
  D                    Parrot  ct-----
  D             Scarlet macaw  ct-----
  D              Mallard duck  ct-----
B D                   Chicken  cg-----
B D                    Turkey  ct-----
B D        American alligator  cc-----
B D                    Lizard  cc-----
B D             X. tropicalis  ---g---
B D                 Tetraodon  ---gccg
B D                      Fugu  ---gccg
       Yellowbelly pufferfish  ---agcg
B D              Nile tilapia  ---gccg
          Princess of Burundi  ---gcga
        Burton's mouthbreeder  ---gcca
                  Zebra mbuna  ---gcca
          Pundamilia nyererei  ---gcca
B D               Stickleback  ---gccg
B D              Atlantic cod  ---atca
B D                  Hedgehog  NNNNNNN
B D                   Lamprey  =======
B D                Coelacanth  =======
B D                     Shrew  NNNNNNN
B D                    Rhesus  NNNNNNN
B D                    Gibbon  NNNNNNN
                 Spotted gar  =======
          Southern platyfish  =======
  D    White-throated sparrow  =======
    Mexican tetra (cavefish)  =======
B D                 Zebrafish  =======
B D                    Medaka  =======
  D            Painted turtle  =======
  D           Green seaturtle  =======
  D       Collared flycatcher  =======
B D           Chinese hamster  -------
B D                    Tenrec  NNNNNNN
  D  Chinese softshell turtle  =======
B D                   Ferret   NNNNNNN
B D                     Panda  =======
               Domestic goat  NNNNNNN
            Tibetan antelope  NNNNNNN
              Bactrian camel  NNNNNNN
B D                    Alpaca  NNNNNNN
        David's myotis (bat)  =======
B D                       Dog  =======

Inserts between block 31 and 32 in window
B D                 Platypus 3bp
B D            X. tropicalis 3bp

Alignment block 32 of 1479 in window, 49539363 - 49539364, 2 bps 
B D                     Human  gc
B D                     Chimp  gc
B D                   Gorilla  gc
B D                 Orangutan  gc
B D       Crab-eating macaque  gc
B D                    Baboon  gc
B D              Green monkey  gc
B D                  Marmoset  gc
B D           Squirrel monkey  gt
B D                  Bushbaby  gt
           Chinese tree shrew  gc
B D                  Squirrel  gc
       Lesser Egyptian jerboa  gc
                 Prairie vole  gc
               Golden hamster  gc
B D                     Mouse  gc
B D                       Rat  gc
B D            Naked mole-rat  gc
B D                Guinea pig  gc
                   Chinchilla  cc
             Brush-tailed rat  gc
B D                    Rabbit  gc
B D                      Pika  gc
B D                       Pig  gc
B D                   Dolphin  gc
                 Killer whale  gc
B D                       Cow  gc
B D                     Sheep  gc
B D                     Horse  gc
B D          White rhinoceros  gc
B D                       Cat  gc
               Pacific walrus  gt
                 Weddell seal  gt
             Black flying-fox  gc
B D                   Megabat  gc
                Big brown bat  gc
B D                  Microbat  gc
B D                  Hedgehog  gc
              Star-nosed mole  gc
B D                  Elephant  gc
          Cape elephant shrew  gc
B D                   Manatee  gc
             Cape golden mole  gc
                     Aardvark  gc
B D                 Armadillo  gc
B