Multiz Alignments of 100 Vertebrates
 

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Alignment block 1 of 366 in window, 34988728 - 34988734, 7 bps 
B D                     Human  t-----agg--aga
B D                     Chimp  t-----agg--aga
B D                   Gorilla  t-----agg--aga
B D                 Orangutan  t-----agg--aga
B D                    Gibbon  t-----agg--aga
B D                    Rhesus  t-----agg--aga
B D       Crab-eating macaque  t-----agg--aga
B D                    Baboon  t-----agg--aga
B D              Green monkey  t-----agg--aga
B D                  Marmoset  t---ggggg--aaa
B D           Squirrel monkey  t----gggg--aga
B D                  Bushbaby  t-----agggaaga
           Chinese tree shrew  c----------aga
       Lesser Egyptian jerboa  caagataga--aga
                 Prairie vole  t---attgc--aga
B D           Chinese hamster  t---attgc--aga
               Golden hamster  t---attgc--aga
B D                     Mouse  g---attgc--aga
B D                       Rat  t---attgc--aga
B D            Naked mole-rat  t---agagg--aga
B D                Guinea pig  t---agaga--aga
                   Chinchilla  c---cgagg--aga
             Brush-tailed rat  t---agagg--aga
B D                      Pika  c---cagac--aga
B D                       Pig  t---agggg--agt
B D                    Alpaca  t---agggg--agt
               Bactrian camel  t---agggg--agt
B D                   Dolphin  t---agggg--agc
                 Killer whale  t---agggg--agc
             Tibetan antelope  t---agggg--agc
B D                       Cow  t---agggg--agc
B D                     Sheep  t---agggg--agc
                Domestic goat  t---agggg--agc
B D                     Horse  t---agggg--aga
B D          White rhinoceros  t---agggg--aga
B D                       Cat  t---tgggg--aga
B D                       Dog  t---agggg--aga
B D                   Ferret   t---aggac--aga
B D                     Panda  t---aggag--aga
               Pacific walrus  t---aggag--aga
                 Weddell seal  t---aggag--aga
             Black flying-fox  t---agggg--aga
B D                   Megabat  t---agggg--aga
                Big brown bat  t---ggggg--agc
         David's myotis (bat)  t---aggag--aga
B D                  Microbat  t---aggag--aga
B D                     Shrew  t---aggtg--aga
              Star-nosed mole  t---agggg--ata
B D                  Elephant  t---agggg--a--
          Cape elephant shrew  t---agggg--a--
B D                   Manatee  t---aggag--a--
             Cape golden mole  g---agggg--a--
B D                 Armadillo  c---atggg--a--
B D                   Opossum  t---ggaga--aaa
B D           Tasmanian devil  t--gggaaa--aaa
B D                   Wallaby  t---ggagg--aaa
B D               Zebra finch  c---ggggg--a--
           Tibetan ground jay  c---ggagc--g--
B D                   Chicken  g---ggcac--a--
B D        American alligator  t---agggc--a--
  D            Painted turtle  t---tgggg--a--
B D                  Hedgehog  ==============
B D                    Rabbit  ==============
                    Aardvark  ==============
B D               Stickleback  ==============
B D                    Turkey  ==============
  D              Mallard duck  ==============
  D    White-throated sparrow  ==============
    Mexican tetra (cavefish)  ==============
B D                 Zebrafish  ==============
B D                    Medaka  ==============
B D             X. tropicalis  --------------
B D                Budgerigar  ==============
  D               Rock pigeon  ==============
B D       Medium ground finch  ==============
  D          Peregrine falcon  ==============
  D              Saker falcon  ==============
B D                  Platypus  ==============
B D                    Tenrec  ==============
  D           Green seaturtle  ==============
  D       Collared flycatcher  ==============
B D                  Squirrel  ==============

Inserts between block 1 and 2 in window
            Cape golden mole 1055bp

Alignment block 2 of 366 in window, 34988735 - 34988738, 4 bps 
B D                     Human  tc-gg
B D                     Chimp  tc-gc
B D                   Gorilla  tc-gg
B D                 Orangutan  tc-cg
B D                    Gibbon  tcagg
B D                    Rhesus  tcggg
B D       Crab-eating macaque  tcggg
B D                    Baboon  tcggg
B D              Green monkey  tcagg
B D                  Marmoset  tcagg
B D           Squirrel monkey  tcagg
B D                  Bushbaby  tcacg
           Chinese tree shrew  tc---
       Lesser Egyptian jerboa  tggca
                 Prairie vole  ccaca
B D           Chinese hamster  ccaca
               Golden hamster  ccaca
B D                     Mouse  ctatg
B D                       Rat  ccaca
B D            Naked mole-rat  ccaca
B D                Guinea pig  ccaca
                   Chinchilla  c----
             Brush-tailed rat  ccaaa
B D                      Pika  ccct-
B D                       Pig  tcatg
B D                    Alpaca  tcatg
               Bactrian camel  tcatg
B D                   Dolphin  acatg
                 Killer whale  acatg
             Tibetan antelope  tcatg
B D                       Cow  tcatg
B D                     Sheep  tcatg
                Domestic goat  tcatg
B D                     Horse  ccatg
B D          White rhinoceros  tcatg
B D                       Cat  tcatg
B D                       Dog  ccata
B D                   Ferret   tcata
B D                     Panda  taaca
               Pacific walrus  tcata
                 Weddell seal  tcata
             Black flying-fox  tcatg
B D                   Megabat  tcatg
                Big brown bat  tcata
         David's myotis (bat)  tcata
B D                  Microbat  tcata
B D                     Shrew  tgatg
              Star-nosed mole  tcgtg
B D                  Elephant  --aag
          Cape elephant shrew  --aag
B D                   Manatee  --aag
B D                   Opossum  ----g
B D           Tasmanian devil  ----g
B D                   Wallaby  ----g
B D               Zebra finch  ----a
           Tibetan ground jay  ----a
B D                   Chicken  ----g
B D        American alligator  ----g
  D            Painted turtle  ----g
B D                  Hedgehog  =====
B D                    Rabbit  =====
                    Aardvark  =====
            Cape golden mole  =====
B D               Stickleback  =====
B D                    Turkey  =====
  D              Mallard duck  =====
  D    White-throated sparrow  =====
    Mexican tetra (cavefish)  =====
B D                 Zebrafish  =====
B D                    Medaka  =====
B D             X. tropicalis  -----
B D                Budgerigar  =====
  D               Rock pigeon  =====
B D       Medium ground finch  =====
  D          Peregrine falcon  =====
  D              Saker falcon  =====
B D                  Platypus  =====
B D                    Tenrec  =====
  D           Green seaturtle  =====
  D       Collared flycatcher  =====
B D                  Squirrel  =====
B D                 Armadillo  -----

Inserts between block 2 and 3 in window
B D                 Elephant 1bp
         Cape elephant shrew 230bp
B D                  Manatee 1bp
B D                  Opossum 3bp
B D          Tasmanian devil 3bp
B D                  Wallaby 3bp
B D              Zebra finch 1bp
          Tibetan ground jay 1bp
B D                  Chicken 9bp
B D       American alligator 20bp
  D           Painted turtle 4bp

Alignment block 3 of 366 in window, 34988739 - 34988740, 2 bps 
B D                     Human  g----g
B D                     Chimp  g----g
B D                   Gorilla  g----g
B D                 Orangutan  g----g
B D                    Gibbon  g----g
B D                    Rhesus  g----g
B D       Crab-eating macaque  g----g
B D                    Baboon  g----g
B D              Green monkey  g----t
B D                  Marmoset  g----g
B D           Squirrel monkey  g----g
B D                  Bushbaby  g----a
           Chinese tree shrew  -----g
       Lesser Egyptian jerboa  g----g
                 Prairie vole  g----a
B D           Chinese hamster  g----a
               Golden hamster  g----a
B D                     Mouse  g----a
B D                       Rat  g----a
B D            Naked mole-rat  g----a
B D                Guinea pig  g----a
             Brush-tailed rat  g----a
B D                       Pig  g----g
B D                    Alpaca  g----g
               Bactrian camel  g----g
B D                   Dolphin  g----g
                 Killer whale  g----g
             Tibetan antelope  g----g
B D                       Cow  g----g
B D                     Sheep  g----g
                Domestic goat  g----g
B D                     Horse  g----g
B D          White rhinoceros  g----g
B D                       Cat  g----g
B D                       Dog  g----g
B D                   Ferret   c----a
B D                     Panda  c----g
               Pacific walrus  c----g
                 Weddell seal  c----g
             Black flying-fox  g----g
B D                   Megabat  g----g
                Big brown bat  g----g
         David's myotis (bat)  g----g
B D                  Microbat  g----g
B D                     Shrew  g----g
              Star-nosed mole  gttaaa
          Cape elephant shrew  g----g
B D                   Manatee  a----g
B D                   Opossum  a----g
B D           Tasmanian devil  g----a
B D                   Wallaby  g----g
B D               Zebra finch  g-----
           Tibetan ground jay  g-----
B D                   Chicken  g-----
B D        American alligator  g-----
  D            Painted turtle  g-----
B D                      Pika  ------
B D                  Hedgehog  ======
B D                    Rabbit  ======
                    Aardvark  ======
            Cape golden mole  ======
B D               Stickleback  ======
B D                    Turkey  ======
  D              Mallard duck  ======
  D    White-throated sparrow  ======
    Mexican tetra (cavefish)  ======
B D                 Zebrafish  ======
B D                    Medaka  ======
B D             X. tropicalis  ------
B D                Budgerigar  ======
                  Chinchilla  ------
  D               Rock pigeon  ======
B D       Medium ground finch  ======
  D          Peregrine falcon  ======
  D              Saker falcon  ======
B D                  Platypus  ======
B D                  Elephant  ======
B D                    Tenrec  ======
  D           Green seaturtle  ======
  D       Collared flycatcher  ======
B D                  Squirrel  ======
B D                 Armadillo  ------

Inserts between block 3 and 4 in window
B D                  Manatee 562bp

Alignment block 4 of 366 in window, 34988741 - 34988741, 1 bps 
B D                     Human  t
B D                     Chimp  t
B D                   Gorilla  t
B D                 Orangutan  t
B D                    Gibbon  t
B D                    Rhesus  t
B D       Crab-eating macaque  t
B D                    Baboon  t
B D              Green monkey  t
B D                  Marmoset  t
B D           Squirrel monkey  t
B D                  Bushbaby  t
           Chinese tree shrew  t
       Lesser Egyptian jerboa  g
                 Prairie vole  a
B D           Chinese hamster  a
               Golden hamster  a
B D                     Mouse  a
B D                       Rat  a
B D            Naked mole-rat  g
B D                Guinea pig  t
             Brush-tailed rat  t
B D                       Pig  a
B D                    Alpaca  a
               Bactrian camel  a
B D                   Dolphin  a
                 Killer whale  a
             Tibetan antelope  a
B D                       Cow  a
B D                     Sheep  a
                Domestic goat  a
B D                     Horse  a
B D          White rhinoceros  a
B D                       Cat  a
B D                       Dog  a
B D                   Ferret   a
B D                     Panda  a
               Pacific walrus  a
                 Weddell seal  a
             Black flying-fox  a
B D                   Megabat  a
                Big brown bat  a
         David's myotis (bat)  a
B D                  Microbat  a
B D                     Shrew  c
              Star-nosed mole  a
B D                  Elephant  a
          Cape elephant shrew  a
B D                   Opossum  t
B D           Tasmanian devil  t
B D                   Wallaby  t
B D               Zebra finch  a
           Tibetan ground jay  t
B D                   Chicken  t
B D        American alligator  t
  D            Painted turtle  t
B D                      Pika  -
B D                  Hedgehog  =
B D                    Rabbit  =
                    Aardvark  =
            Cape golden mole  =
B D               Stickleback  =
B D                    Turkey  =
  D              Mallard duck  =
  D    White-throated sparrow  =
    Mexican tetra (cavefish)  =
B D                 Zebrafish  =
B D                    Medaka  =
B D             X. tropicalis  -
B D                Budgerigar  =
                  Chinchilla  -
  D               Rock pigeon  =
B D       Medium ground finch  =
  D          Peregrine falcon  =
  D              Saker falcon  =
B D                  Platypus  =
B D                   Manatee  =
B D                    Tenrec  =
  D           Green seaturtle  =
  D       Collared flycatcher  =
B D                  Squirrel  =
B D                 Armadillo  -

Inserts between block 4 and 5 in window
B D                 Elephant 844bp
B D                  Opossum 3bp
B D          Tasmanian devil 4bp
B D                  Wallaby 4bp

Alignment block 5 of 366 in window, 34988742 - 34988756, 15 bps 
B D                     Human  gt-aaag---aaa-----gaacca
B D                     Chimp  gt-aaag---aaa-----gaacca
B D                   Gorilla  gt-aaag---aaa-----gaacca
B D                 Orangutan  -t-aaag---aaa-----gaacca
B D                    Gibbon  gt-aaag---aaa-----gaacca
B D                    Rhesus  gt-aaag---aaa-----gaacca
B D       Crab-eating macaque  gt-aaag---aaa-----gaacca
B D                    Baboon  gt-aaag---aaa-----gaacca
B D              Green monkey  gt-aaag---aaa-----gaacca
B D                  Marmoset  gt-agag---aaa-----ggacca
B D           Squirrel monkey  gt-cgag---aaa-----ggacca
B D                  Bushbaby  gt-agag---aaa-----ggagta
           Chinese tree shrew  gt-agag---gaa-----ggatta
       Lesser Egyptian jerboa  gcgaggg---aga----tca--ta
                 Prairie vole  at-aggg---aga----taaatta
B D           Chinese hamster  at-aggg---aga----tggatca
               Golden hamster  ac--ggg---aaa----cgaatca
B D                     Mouse  gc-aggg---aat----tgaatta
B D                       Rat  ac-aga-----------tgactta
B D            Naked mole-rat  ccacagg---atagattaagacta
B D                Guinea pig  gcacaag---ata----aagaaca
                   Chinchilla  ---ccgg---gcg----aagacca
             Brush-tailed rat  gcacagg---ata----aagaata
B D                       Pig  gt-aaat---aaa-----ggatta
B D                    Alpaca  gt-a-------aa-----ggatta
               Bactrian camel  gt-a-------aa-----ggatta
B D                   Dolphin  gt-agat----aa-----ggatta
                 Killer whale  gt-agat----aa-----ggatta
             Tibetan antelope  at-aaat----aa-----ggatta
B D                       Cow  at-aaat----aa-----ggatta
B D                     Sheep  at-agat----aa-----ggatta
                Domestic goat  at-agat----aa-----ggatta
B D                     Horse  gt-agat---aaa-----gaatta
B D          White rhinoceros  g-----t---aaa-----gaatta
B D                       Cat  gt-cg-t---aac-----agatta
B D                       Dog  at-agat---aac-----agatta
B D                   Ferret   gt-agat---aac-----ggatta
B D                     Panda  gt-agat---aac-----agatta
               Pacific walrus  gt-agat---aac-----ggatta
                 Weddell seal  gt-agat---aac-----ggatta
             Black flying-fox  gc-ag-----aaa-----gaatta
B D                   Megabat  gc-aa-----aaa-----gaatta
                Big brown bat  gc-ag-----aaa-----gaatta
         David's myotis (bat)  gc-ag-----aaa-----gaatta
B D                  Microbat  gc-ag-----aaa-----gaatta
B D                     Shrew  cg-aggg--gcaa-----ggatt-
              Star-nosed mole  aa-aaaa--aaaa-----agatt-
          Cape elephant shrew  gc-agag---aaa-----agatta
B D                 Armadillo  at-agag---aaa-----ggatta
B D                   Opossum  ac-atggttgaaa-----gaatcg
B D           Tasmanian devil  ac-agggttggaa-----aaagag
B D                   Wallaby  ac-agggttgaaa-----gaaggg
B D               Zebra finch  -----------------ggggaca
           Tibetan ground jay  -----------------gggggtg
B D                   Chicken  -----------------gggggga
B D        American alligator  -----------------gggggtg
  D            Painted turtle  -----------------gcaggtg
B D                      Pika  ------------------------
B D                  Hedgehog  ========================
B D                    Rabbit  ========================
                    Aardvark  ========================
            Cape golden mole  ========================
B D               Stickleback  ========================
B D                    Turkey  ========================
  D              Mallard duck  ========================
  D    White-throated sparrow  ========================
    Mexican tetra (cavefish)  ========================
B D                 Zebrafish  ========================
B D                    Medaka  ========================
B D             X. tropicalis  ------------------------
B D                Budgerigar  ========================
  D               Rock pigeon  ========================
B D       Medium ground finch  ========================
  D          Peregrine falcon  ========================
  D              Saker falcon  ========================
B D                  Platypus  ========================
B D                   Manatee  ========================
B D                  Elephant  ========================
B D                    Tenrec  ========================
  D           Green seaturtle  ========================
  D       Collared flycatcher  ========================
B D                  Squirrel  ========================

Inserts between block 5 and 6 in window
B D           Naked mole-rat 19bp
B D               Guinea pig 19bp
                  Chinchilla 18bp
            Brush-tailed rat 19bp
B D                    Shrew 3bp
             Star-nosed mole 3bp
B D              Zebra finch 2bp
          Tibetan ground jay 11bp
B D                  Chicken 8bp
B D       American alligator 14bp
  D           Painted turtle 11bp

Alignment block 6 of 366 in window, 34988757 - 34988758, 2 bps 
B D                     Human  ag
B D                     Chimp  ag
B D                   Gorilla  ag
B D                 Orangutan  ag
B D                    Gibbon  ag
B D                    Rhesus  ag
B D       Crab-eating macaque  ag
B D                    Baboon  ag
B D              Green monkey  ag
B D                  Marmoset  ag
B D           Squirrel monkey  ag
B D                  Bushbaby  ag
           Chinese tree shrew  ag
B D                  Squirrel  ag
       Lesser Egyptian jerboa  gg
                 Prairie vole  ag
B D           Chinese hamster  ag
               Golden hamster  ag
B D                     Mouse  ag
B D                       Rat  ag
B D            Naked mole-rat  aa
B D                Guinea pig  ag
                   Chinchilla  gg
             Brush-tailed rat  gg
B D                      Pika  gg
B D                       Pig  ag
B D                    Alpaca  aa
               Bactrian camel  aa
B D                   Dolphin  ag
                 Killer whale  ag
             Tibetan antelope  ag
B D                       Cow  ag
B D                     Sheep  ag
                Domestic goat  ag
B D                     Horse  ag
B D          White rhinoceros  ag
B D                       Cat  ag
B D                     Panda  ag
               Pacific walrus  ag
                 Weddell seal  ag
             Black flying-fox  ag
B D                   Megabat  ag
                Big brown bat  ag
         David's myotis (bat)  ag
B D                  Microbat  gg
          Cape elephant shrew  ag
B D                 Armadillo  ag
B D                   Opossum  ag
B D           Tasmanian devil  gg
B D                   Wallaby  ca
           Tibetan ground jay  -a
B D                   Chicken  -g
  D            Painted turtle  -g
B D                     Shrew  ==
B D                  Hedgehog  ==
B D                    Rabbit  ==
                    Aardvark  ==
            Cape golden mole  ==
B D               Stickleback  ==
B D                    Turkey  ==
  D              Mallard duck  ==
B D               Zebra finch  ==
  D    White-throated sparrow  ==
    Mexican tetra (cavefish)  ==
B D                 Zebrafish  ==
B D                    Medaka  ==
B D             X. tropicalis  --
B D        American alligator  ==
B D                Budgerigar  ==
  D               Rock pigeon  ==
B D       Medium ground finch  ==
  D          Peregrine falcon  ==
  D              Saker falcon  ==
B D                  Platypus  ==
B D                   Manatee  ==
B D                  Elephant  ==
B D                    Tenrec  ==
  D           Green seaturtle  ==
B D                   Ferret   --
  D       Collared flycatcher  ==
             Star-nosed mole  ==
B D                       Dog  --

Inserts between block 6 and 7 in window
B D                  Chicken 5bp

Alignment block 7 of 366 in window, 34988759 - 34988762, 4 bps 
B D                     Human  aata
B D                     Chimp  aata
B D                   Gorilla  aata
B D                 Orangutan  aata
B D                    Gibbon  aata
B D                    Rhesus  aata
B D       Crab-eating macaque  aata
B D                    Baboon  aata
B D              Green monkey  aata
B D                  Marmoset  aatg
B D           Squirrel monkey  aatg
B D                  Bushbaby  aaca
           Chinese tree shrew  aata
B D                  Squirrel  gcca
       Lesser Egyptian jerboa  gaca
                 Prairie vole  aata
B D           Chinese hamster  aata
               Golden hamster  aata
B D                     Mouse  aat-
B D                       Rat  aat-
B D            Naked mole-rat  agaa
B D                Guinea pig  aaag
                   Chinchilla  a---
             Brush-tailed rat  aaaa
B D                      Pika  g---
B D                       Pig  aata
B D                    Alpaca  aata
               Bactrian camel  aata
B D                   Dolphin  aata
                 Killer whale  aata
             Tibetan antelope  aata
B D                       Cow  aata
B D                     Sheep  aata
                Domestic goat  aata
B D                     Horse  aata
B D          White rhinoceros  aata
B D                       Cat  gcta
B D                       Dog  -aga
B D                   Ferret   -ata
B D                     Panda  aata
               Pacific walrus  gata
                 Weddell seal  gata
             Black flying-fox  aata
B D                   Megabat  aata
                Big brown bat  acta
         David's myotis (bat)  aata
B D                  Microbat  aata
          Cape elephant shrew  aata
B D                 Armadillo  aata
B D                   Opossum  actg
B D           Tasmanian devil  acgg
B D                   Wallaby  actg
B D                     Shrew  ====
B D                  Hedgehog  ====
B D                    Rabbit  ====
                    Aardvark  ====
            Cape golden mole  ====
B D               Stickleback  ====
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                 Zebrafish  ====
B D                    Medaka  ====
B D             X. tropicalis  ----
  D            Painted turtle  ----
B D        American alligator  ====
B D                Budgerigar  ====
  D               Rock pigeon  ====
B D       Medium ground finch  ====
  D          Peregrine falcon  ====
  D              Saker falcon  ====
B D                  Platypus  ====
B D                   Manatee  ====
B D                  Elephant  ====
B D                    Tenrec  ====
  D           Green seaturtle  ====
  D       Collared flycatcher  ====
             Star-nosed mole  ====

Inserts between block 7 and 8 in window
                  Chinchilla 5bp
B D                      Pig 5bp
B D                   Alpaca 5bp
              Bactrian camel 5bp
B D                  Dolphin 5bp
                Killer whale 5bp
            Tibetan antelope 5bp
B D                      Cow 5bp
B D                    Sheep 5bp
               Domestic goat 5bp
B D                    Horse 5bp
B D         White rhinoceros 5bp
B D                      Cat 5bp
B D                      Dog 5bp
B D                  Ferret  5bp
B D                    Panda 5bp
              Pacific walrus 5bp
                Weddell seal 5bp
            Black flying-fox 5bp
B D                  Megabat 5bp
               Big brown bat 5bp
B D                 Microbat 5bp

Alignment block 8 of 366 in window, 34988763 - 34988771, 9 bps 
B D                     Human  aga-caaaag
B D                     Chimp  aga-caaaac
B D                   Gorilla  aga-caaaac
B D                 Orangutan  gga-caaaac
B D                    Gibbon  gga-caaaac
B D                    Rhesus  gga-taaaac
B D       Crab-eating macaque  gga-taaaac
B D                    Baboon  gga-taaaac
B D              Green monkey  gga-taaaac
B D                  Marmoset  gga-caagac
B D           Squirrel monkey  gga-caagac
B D                  Bushbaby  aga-ccagac
           Chinese tree shrew  gga-caagag
B D                  Squirrel  agacagaaa-
       Lesser Egyptian jerboa  aga-agaga-
                 Prairie vole  agacaaaag-
B D           Chinese hamster  aga-aaaga-
               Golden hamster  aga-ataga-
B D                     Mouse  ----taaga-
B D                       Rat  ----taaga-
B D            Naked mole-rat  aaa-agaaa-
B D                Guinea pig  aag-agaaa-
             Brush-tailed rat  aaa-agaaa-
B D                       Pig  aga-cagag-
B D                    Alpaca  aga-cagag-
               Bactrian camel  aga-cagag-
B D                   Dolphin  aga-cagaa-
                 Killer whale  aga-cagaa-
             Tibetan antelope  agg-caaaa-
B D                       Cow  agg-caaaa-
B D                     Sheep  agg-caaaa-
                Domestic goat  agg-caaaa-
B D                     Horse  agg-cagaa-
B D          White rhinoceros  aga-cagaa-
B D                       Cat  aaa-cagaa-
B D                       Dog  aga-cagaa-
B D                   Ferret   aaa-cggaa-
B D                     Panda  aaa-cagaa-
               Pacific walrus  aaa-cagaa-
                 Weddell seal  aaa-cagaa-
             Black flying-fox  tga-caaaa-
B D                   Megabat  tga-caaaa-
                Big brown bat  agc-cagaa-
B D                  Microbat  agc-cagga-
B D                     Shrew  agg-gaggg-
              Star-nosed mole  gat-aggat-
          Cape elephant shrew  gca-cagga-
B D                 Armadillo  aga-caagg-
B D                   Opossum  aga-caggg-
B D           Tasmanian devil  aga-cagaa-
B D                   Wallaby  aga-caggg-
B D               Zebra finch  gga-tgggg-
B D                   Chicken  ggc-ggggg-
B D        American alligator  ggg-ggtgg-
  D            Painted turtle  --g-tgggg-
B D                      Pika  ----------
B D                  Hedgehog  ==========
B D                    Rabbit  ==========
                    Aardvark  ==========
            Cape golden mole  ==========
B D               Stickleback  ==========
B D                    Turkey  ==========
  D              Mallard duck  ==========
          Tibetan ground jay  ==========
  D    White-throated sparrow  ==========
    Mexican tetra (cavefish)  ==========
B D                 Zebrafish  ==========
B D                    Medaka  ==========
B D             X. tropicalis  ----------
B D                Budgerigar  ==========
                  Chinchilla  ==========
  D               Rock pigeon  ==========
B D       Medium ground finch  ==========
  D          Peregrine falcon  ==========
  D              Saker falcon  ==========
B D                  Platypus  ==========
B D                   Manatee  ==========
B D                  Elephant  ==========
B D                    Tenrec  ==========
  D           Green seaturtle  ==========
  D       Collared flycatcher  ==========
        David's myotis (bat)  NNNNNNNNNN

Inserts between block 8 and 9 in window
      Lesser Egyptian jerboa 328bp
B D           Naked mole-rat 15bp
B D               Guinea pig 31bp
            Brush-tailed rat 14bp
         Cape elephant shrew 1bp
B D                Armadillo 1bp
B D                  Opossum 1bp
B D          Tasmanian devil 1bp
B D                  Wallaby 1bp
B D              Zebra finch 3bp
B D       American alligator 3bp

Alignment block 9 of 366 in window, 34988772 - 34988774, 3 bps 
B D                     Human  gga
B D                     Chimp  gga
B D                   Gorilla  gga
B D                 Orangutan  gga
B D                    Gibbon  gga
B D                    Rhesus  gga
B D       Crab-eating macaque  gga
B D                    Baboon  gga
B D              Green monkey  gga
B D                  Marmoset  aga
B D           Squirrel monkey  aga
B D                  Bushbaby  aga
           Chinese tree shrew  aga
                 Prairie vole  aaa
B D           Chinese hamster  aaa
               Golden hamster  aaa
B D                     Mouse  caa
B D                       Rat  caa
B D            Naked mole-rat  -ag
B D                Guinea pig  -aa
                   Chinchilla  --g
             Brush-tailed rat  -ag
B D                   Opossum  aaa
B D           Tasmanian devil  aga
B D                   Wallaby  gga
B D               Zebra finch  ggg
B D                   Chicken  ggg
B D        American alligator  aaa
      Lesser Egyptian jerboa  ===
B D                      Pika  ---
B D                     Shrew  ---
B D                  Hedgehog  ===
B D                    Rabbit  ===
                    Aardvark  ===
            Cape golden mole  ===
B D                       Pig  ---
B D                   Megabat  ---
B D                   Dolphin  ---
B D               Stickleback  ===
B D                    Turkey  ===
  D              Mallard duck  ===
          Tibetan ground jay  ===
  D    White-throated sparrow  ===
    Mexican tetra (cavefish)  ===
B D                 Zebrafish  ===
B D                    Medaka  ===
B D             X. tropicalis  ---
  D            Painted turtle  ---
B D                Budgerigar  ===
  D               Rock pigeon  ===
B D       Medium ground finch  ===
  D          Peregrine falcon  ===
  D              Saker falcon  ===
         Cape elephant shrew  ===
B D                  Platypus  ===
B D                   Manatee  ===
B D                  Elephant  ===
B D                    Tenrec  ===
  D           Green seaturtle  ===
B D                       Cat  ---
                Weddell seal  ---
B D                   Ferret   ---
               Domestic goat  ---
B D                     Sheep  ---
            Tibetan antelope  ---
  D       Collared flycatcher  ===
             Star-nosed mole  ---
              Bactrian camel  ---
B D                    Alpaca  ---
               Big brown bat  ---
              Pacific walrus  ---
B D                     Panda  ---
B D                       Cow  ---
                Killer whale  ---
B D                       Dog  ---
            Black flying-fox  ---
B D          White rhinoceros  ---
B D                     Horse  ---
B D                  Squirrel  ---
        David's myotis (bat)  NNN
B D                  Microbat  ---
B D                 Armadillo  ===

Inserts between block 9 and 10 in window
B D          Tasmanian devil 5bp
B D                  Wallaby 910bp

Alignment block 10 of 366 in window, 34988775 - 34988775, 1 bps 
B D                     Human  t
B D                     Chimp  t
B D                   Gorilla  t
B D                 Orangutan  t
B D                    Gibbon  t
B D                    Rhesus  t
B D       Crab-eating macaque  t
B D                    Baboon  t
B D              Green monkey  t
B D                  Marmoset  t
B D           Squirrel monkey  t
B D                  Bushbaby  a
           Chinese tree shrew  t
                 Prairie vole  a
B D           Chinese hamster  a
               Golden hamster  a
B D                     Mouse  a
B D                       Rat  a
B D            Naked mole-rat  a
B D                Guinea pig  a
                   Chinchilla  g
             Brush-tailed rat  a
B D                   Opossum  t
B D           Tasmanian devil  t
B D               Zebra finch  g
B D                   Chicken  a
B D        American alligator  t
      Lesser Egyptian jerboa  =
B D                      Pika  -
B D                     Shrew  -
B D                  Hedgehog  =
B D                    Rabbit  =
                    Aardvark  =
            Cape golden mole  =
B D                       Pig  -
B D                   Megabat  -
B D                   Dolphin  -
B D               Stickleback  =
B D                    Turkey  =
  D              Mallard duck  =
          Tibetan ground jay  =
  D    White-throated sparrow  =
    Mexican tetra (cavefish)  =
B D                 Zebrafish  =
B D                    Medaka  =
B D             X. tropicalis  -
  D            Painted turtle  -
B D                Budgerigar  =
  D               Rock pigeon  =
B D       Medium ground finch  =
  D          Peregrine falcon  =
  D              Saker falcon  =
B D                   Wallaby  =
         Cape elephant shrew  =
B D                  Platypus  =
B D                   Manatee  =
B D                  Elephant  =
B D                    Tenrec  =
  D           Green seaturtle  =
B D                       Cat  -
                Weddell seal  -
B D                   Ferret   -
               Domestic goat  -
B D                     Sheep  -
            Tibetan antelope  -
  D       Collared flycatcher  =
             Star-nosed mole  -
              Bactrian camel  -
B D                    Alpaca  -
               Big brown bat  -
              Pacific walrus  -
B D                     Panda  -
B D                       Cow  -
                Killer whale  -
B D                       Dog  -
            Black flying-fox  -
B D          White rhinoceros  -
B D                     Horse  -
B D                  Squirrel  -
        David's myotis (bat)  N
B D                  Microbat  -
B D                 Armadillo  =

Inserts between block 10 and 11 in window
B D                  Opossum 777bp
B D          Tasmanian devil 3bp

Alignment block 11 of 366 in window, 34988776 - 34988789, 14 bps 
B D                     Human  cactgcg-------------------------------------------g-g-----------aagg--
B D                     Chimp  cactgcg-------------------------------------------g-g-----------aagg--
B D                   Gorilla  cactgcg-------------------------------------------g-g-----------aagg--
B D                 Orangutan  cactgca-------------------------------------------g-g-----------aagg--
B D                    Gibbon  cactgcg-------------------------------------------g-g-----------aagg--
B D                    Rhesus  cactgcg-------------------------------------------g-g-----------aagg--
B D       Crab-eating macaque  cactgcg-------------------------------------------g-g-----------aagg--
B D                    Baboon  cactgcg-------------------------------------------g-g-----------aagg--
B D              Green monkey  cactgcg-------------------------------------------g-g-----------aagg--
B D                  Marmoset  cactggg-----------------------------------------------------------gg--
B D           Squirrel monkey  cattggg-----------------------------------------------------------gg--
B D                  Bushbaby  gatcctg-------------------------------------------g-g-----------g-gg--
           Chinese tree shrew  catag-------------------------------------------------------------gg--
B D                  Squirrel  gggtggg-----------gg------------------------------g-a-----------ggacag
                 Prairie vole  aagtaag-----------ga------------------------------a-g-----------atac--
B D           Chinese hamster  aa--aag-----------aa------------------------------a-g-----------atac--
               Golden hamster  aagtaag-----------aa------------------------------a-g-----------atac--
B D                     Mouse  aggcgggag-----atggag------------------------------g-g-----------ggaa--
B D                       Rat  aggtggg------------g------------------------------g-g-----------acga--
B D            Naked mole-rat  agattgg-------------------------------------------g-g-----------tgga--
B D                Guinea pig  agattgg-------------------------------------------g-g-----------tgta--
                   Chinchilla  aggttgg-------------------------------------------g-g-----------tgga--
             Brush-tailed rat  agatggg-------------------------------------------g-g-----------tgga--
B D                      Pika  gggccgg-------------------------------------------g-g-----------tgag--
B D                       Pig  --------------gatgat------------------------------g-a-----------ggga--
B D                    Alpaca  --------------gatcat------------------------------g-g-----------g-ga--
               Bactrian camel  --------------gatcat------------------------------g-g-----------g-ga--
B D                   Dolphin  --------------gatcat------------------------------g-g-----------ggga--
                 Killer whale  --------------gatcat------------------------------g-g-----------ggga--
             Tibetan antelope  --------------gatcat------------------------------g-g-----------gcga--
B D                       Cow  --------------gatcat------------------------------g-g-----------gcga--
B D                     Sheep  --------------gatcac------------------------------g-g-----------gcga--
                Domestic goat  --------------gatcat------------------------------g-g-----------gcga--
B D                     Horse  --------------aattcat-----------------------------g-g-----------ggga--
B D          White rhinoceros  --------------aattctt-----------------------------a-g-----------ggga--
B D                       Cat  --------------gatcat------------------------------g-g-----------gggg--
B D                       Dog  --------------gat----ggggga-----------------------g-t-----------gggg--
B D                   Ferret   --------------gatgcggaggggg-----------------------gcg-----------gggg--
B D                     Panda  --------------gattgggaagatt-----------------------g-g-----------gggg--
               Pacific walrus  --------------gattatgggggcgggggtgggggtgggagtgggggtg-g-----------gggg--
                 Weddell seal  --------------gattatgggggtg-----------------------g-g-----------gggg--
             Black flying-fox  --------------gatcat------------------------------g-g-----------ggga--
B D                   Megabat  --------------gatcat------------------------------g-g-----------ggga--
                Big brown bat  --------------gatctt------------------------------g-g-----------gggg--
B D                  Microbat  --------------gatcttggggg-------------------------g-g-----------gggg--
B D                     Shrew  --------------gaaaat------------------------------g-agagaaccaaggggga--
              Star-nosed mole  --------------taaact------------------------------c-a-----------ggga--
          Cape elephant shrew  -------agaagaggaatga------------------------------g-g-----------cgag--
B D                 Armadillo  -------aga----taatgc------------------------------g-g-----------tggg--
B D           Tasmanian devil  -----------------------------------------------taag-g-----------tggc--
B D               Zebra finch  ----------------------------------------------caccg-a-----------gggg--
B D                   Chicken  ----------------------------------------------catca-c-----------ggga--
B D        American alligator  ----------------------------------------------aattg-t-----------gggt--
  D            Painted turtle  -----------------------------------------------attg-t-----------gggg--
B D             X. tropicalis  -----------------------------------------------actg-a-----------tggg--
      Lesser Egyptian jerboa  ======================================================================
B D                  Hedgehog  ======================================================================
B D                    Rabbit  ======================================================================
                    Aardvark  ======================================================================
            Cape golden mole  ======================================================================
B D               Stickleback  ======================================================================
B D                    Turkey  ======================================================================
  D              Mallard duck  ======================================================================
          Tibetan ground jay  ======================================================================
  D    White-throated sparrow  ======================================================================
    Mexican tetra (cavefish)  ======================================================================
B D                 Zebrafish  ======================================================================
B D                    Medaka  ======================================================================
B D                Budgerigar  ======================================================================
B D                   Opossum  ======================================================================
  D               Rock pigeon  ======================================================================
B D       Medium ground finch  ======================================================================
  D          Peregrine falcon  ======================================================================
  D              Saker falcon  ======================================================================
B D                   Wallaby  ======================================================================
B D                  Platypus  ======================================================================
B D                   Manatee  ======================================================================
B D                  Elephant  ======================================================================
B D                    Tenrec  ======================================================================
  D           Green seaturtle  ======================================================================
  D       Collared flycatcher  ======================================================================
        David's myotis (bat)  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

                        Human  -------a---
                        Chimp  -------a---
                      Gorilla  -------a---
                    Orangutan  -------a---
                       Gibbon  -------a---
                       Rhesus  -------a---
          Crab-eating macaque  -------a---
                       Baboon  -------a---
                 Green monkey  -------a---
                     Marmoset  -------a---
              Squirrel monkey  -------a---
                     Bushbaby  -------a---
           Chinese tree shrew  -------g---
                     Squirrel  tcaggaga---
                 Prairie vole  -------a---
              Chinese hamster  -------a---
               Golden hamster  -------a---
                        Mouse  -------g---
                          Rat  -------g---
               Naked mole-rat  -------g---
                   Guinea pig  -------g---
                   Chinchilla  -------g---
             Brush-tailed rat  -------g---
                         Pika  -------g---
                          Pig  -------a---
                       Alpaca  -------a---
               Bactrian camel  -------a---
                      Dolphin  -------a---
                 Killer whale  -------a---
             Tibetan antelope  -------a---
                          Cow  -------a---
                        Sheep  -------a---
                Domestic goat  -------a---
                        Horse  -------a---
             White rhinoceros  -------a---
                          Cat  -------g---
                          Dog  -------t---
                      Ferret   -------g---
                        Panda  -----------
               Pacific walrus  -------g---
                 Weddell seal  -------g---
             Black flying-fox  -------a---
                      Megabat  -------a---
                Big brown bat  -------a---
                     Microbat  -------g---
                        Shrew  -------a---
              Star-nosed mole  -------a---
          Cape elephant shrew  -------g---
                    Armadillo  -------g---
              Tasmanian devil  -------a---
                  Zebra finch  -------a---
                      Chicken  -------a---
           American alligator  -------g---
               Painted turtle  -------a---
                X. tropicalis  -------aatg
       Lesser Egyptian jerboa  ===========
                     Hedgehog  ===========
                       Rabbit  ===========
                     Aardvark  ===========
             Cape golden mole  ===========
                  Stickleback  ===========
                       Turkey  ===========
                 Mallard duck  ===========
           Tibetan ground jay  ===========
       White-throated sparrow  ===========
     Mexican tetra (cavefish)  ===========
                    Zebrafish  ===========
                       Medaka  ===========
                   Budgerigar  ===========
                      Opossum  ===========
                  Rock pigeon  ===========
          Medium ground finch  ===========
             Peregrine falcon  ===========
                 Saker falcon  ===========
                      Wallaby  ===========
                     Platypus  ===========
                      Manatee  ===========
                     Elephant  ===========
                       Tenrec  ===========
              Green seaturtle  ===========
          Collared flycatcher  ===========
         David's myotis (bat)  NNNNNNNNNNN

Inserts between block 11 and 12 in window
         Cape elephant shrew 32bp
B D                Armadillo 1bp
B D          Tasmanian devil 5bp
B D              Zebra finch 8bp
B D                  Chicken 11bp
B D       American alligator 9bp
  D           Painted turtle 14bp

Alignment block 12 of 366 in window, 34988790 - 34988797, 8 bps 
B D                     Human  agacagg-----a------
B D                     Chimp  agac--------a------
B D                   Gorilla  agacagg-----a------
B D                 Orangutan  agacagg-----a------
B D                    Gibbon  agacagg-----a------
B D                    Rhesus  agacagg-----a------
B D       Crab-eating macaque  agacagg-----a------
B D                    Baboon  agacagg-----a------
B D              Green monkey  agacagg-----a------
B D                  Marmoset  agacagtagatca------
B D           Squirrel monkey  agacagg-----a------
B D                  Bushbaby  aatcagg-----a------
           Chinese tree shrew  caaaatg-----a------
B D                  Squirrel  tgataag-----g------
                 Prairie vole  taaaaag-----a------
B D           Chinese hamster  gaacaag-----a------
               Golden hamster  gaacaag-----a------
B D                     Mouse  taaaaag-----a------
B D                       Rat  ttacagggcc--a------
B D            Naked mole-rat  gaacagg-----a------
B D                Guinea pig  ----agg-----a------
                   Chinchilla  gagcagg-----a------
             Brush-tailed rat  gaacaga-----a------
B D                      Pika  gggcaggcag--a------
B D                       Pig  ggacagg-----a------
B D                    Alpaca  agacagg-----a------
               Bactrian camel  agacagg-----a------
B D                   Dolphin  agacagg-----a------
                 Killer whale  agacagg-----a------
             Tibetan antelope  agacagg-----a------
B D                       Cow  agacagg-----a------
B D                     Sheep  agacagg-----a------
                Domestic goat  aggcagg-----a------
B D                     Horse  agacagg------------
B D          White rhinoceros  aggcagg------------
B D                       Cat  taacagg-----a------
B D                       Dog  aggcaga-----a------
B D                   Ferret   aggcagg-----a------
B D                     Panda  -----gg-----g------
               Pacific walrus  aggcagg-----a------
                 Weddell seal  aggcagg-----a------
             Black flying-fox  agacagg-----a------
B D                   Megabat  agacagg-----a------
                Big brown bat  agactgg-----a------
B D                  Microbat  ggactgg-----a------
B D                     Shrew  agaca--------------
              Star-nosed mole  aga----------------
          Cape elephant shrew  acaaagg-----g------
                     Aardvark  agacagg-----a------
B D                 Armadillo  ---cggg-----g------
B D           Tasmanian devil  ggtcagt------------
B D               Zebra finch  aacgagg-----g------
B D                   Chicken  cgccata-----g------
B D        American alligator  ggccagg-----g------
  D            Painted turtle  ggt-aga-----g------
B D             X. tropicalis  tgatagg-----ggcctta
      Lesser Egyptian jerboa  ===================
B D                  Hedgehog  ===================
B D                    Rabbit  ===================
            Cape golden mole  ===================
B D               Stickleback  ===================
B D                    Turkey  ===================
  D              Mallard duck  ===================
          Tibetan ground jay  ===================
  D    White-throated sparrow  ===================
    Mexican tetra (cavefish)  ===================
B D                 Zebrafish  ===================
B D                    Medaka  ===================
B D                Budgerigar  ===================
B D                   Opossum  ===================
  D               Rock pigeon  ===================
B D       Medium ground finch  ===================
  D          Peregrine falcon  ===================
  D              Saker falcon  ===================
B D                   Wallaby  ===================
B D                  Platypus  ===================
B D                   Manatee  ===================
B D                  Elephant  ===================
B D                    Tenrec  ===================
  D           Green seaturtle  ===================
  D       Collared flycatcher  ===================
        David's myotis (bat)  NNNNNNNNNNNNNNNNNNN

Inserts between block 12 and 13 in window
         Cape elephant shrew 15bp
                    Aardvark 1bp
B D                Armadillo 5bp

Alignment block 13 of 366 in window, 34988798 - 34988826, 29 bps 
B D                     Human  gat---cat--------c-------ta-gggccaa---------gaagg---------------------
B D                     Chimp  gat---cat--------c-------ga-gggccaa---------gaagg---------------------
B D                   Gorilla  gat---cat--------c-------ga-gggccaa---------gaagg---------------------
B D                 Orangutan  gat---ctt--------c-------ga-gggccaa---------gaagg---------------------
B D                    Gibbon  gat---tat--------c-------ga-gggccaa---------gaagg---------------------
B D                    Rhesus  gat---cat--------t-------ga-gggccaa---------gaagg---------------------
B D       Crab-eating macaque  gat---cat--------t-------ga-gggccaa---------gaagg---------------------
B D                    Baboon  gat---cat--------t-------ga-gggccaa---------gaagg---------------------
B D              Green monkey  gat---cat--------t-------ga-gggccaa---------gaagg---------------------
B D                  Marmoset  gat---cct--------c-------ga-gggctaa---------gaagg---------------------
B D           Squirrel monkey  gac---cct--------c-------ga-gggccaa---------gtagg---------------------
B D                  Bushbaby  gtt---cat----------------aa-gggccaa---------gaagg------ggagt----------
           Chinese tree shrew  gat---tat--------a-------gg-gggccga---------gaagg---------------------
B D                  Squirrel  gat---aag--------a-------aa-ggagcaa----------gtaa---------------------
                 Prairie vole  cag---aat--------g-------tt-ggggtga---------gggaa---------------------
B D           Chinese hamster  cag---aat--------a-------tt-ggggtga---------gggga---------------------
               Golden hamster  gag---aat--------a-------tt-ggggtga---------gggaa---------------------
B D                     Mouse  tac---aga--------a-------ca-gggcaga----aatttggtgt---------------------
B D                       Rat  aac---aga--------a-------ca-ggactga----aatttggggt---------------------
B D            Naked mole-rat  gac---cac--------a-------gt-gggc--a---------agaag---------------------
B D                Guinea pig  gat---cac--------t-------gc-------------------aag---------------------
                   Chinchilla  ggt---cgc--------g-------gg-gga--------------agga---------------------
             Brush-tailed rat  gat---cac--------a-------gt-ggg--------------gaag---------------------
B D                      Pika  gac---tgc--------c-------ag-ggccggaagaaagtctgtaaa---------------------
B D                       Pig  gat---cat--------a-------tg-aggccaa---------gatga------gaggatgataaa---
B D                    Alpaca  gat---cat--------a-------ta-gggctaa---------gaaga------ggggacagtaaa---
               Bactrian camel  gat---cat--------a-------ta-gggctaa---------gaaga------ggggatagtaaa---
B D                   Dolphin  gat---cat--------a-------tg-gggccag---------gaatg------ggggggagtaaa---
                 Killer whale  gat---cat--------a-------tg-gggccag---------gaatg------ggggggagtaaa---
             Tibetan antelope  gat---cct--------a-------tg-gggccaa---------gaagg------gaggaaagtcaa---
B D                       Cow  gat---cct--------a-------tg-ggg-caa---------gaagg------gaggaaagtcaa---
B D                     Sheep  gat---cct--------a-------tg-gggccaa---------gaagg------gaggaaagtcaa---
                Domestic goat  gat---cct--------a-------tg-gggccaa---------gaagg------gaggaaagtcaa---
B D                     Horse  ---------------------------------ac---------caaga------ggggaaagtaaa---
B D          White rhinoceros  ---------------------------------ac---------caaga------ggggaaagtaaa---
B D                       Cat  gat----at--------a-------cc-cagccaa---------gaaga------gggggaaaaaag---
B D                       Dog  gat---cag--------a-------cc-cagctac---------aacgc------tggggaagagag---
B D                   Ferret   gat---aat--------a-------tc-cagccaa---------gaaga------ggggaaagaaag---
B D                     Panda  gat---cat--------a-------cc-cagccaa---------gaaga------ggggaaagaaagggg
               Pacific walrus  gat---cat--------a-------cc-cagccaa---------gaaga------ggggaaagaaag--a
                 Weddell seal  gat---cat--------a-------cc-cagccaa---------gaaga------ggggaaagaaag---
             Black flying-fox  gat---cat--------a-------cg-gggccaa---------gaaga------gggaaaaacaaa---
B D                   Megabat  gat---cat--------a-------cg-gggccaa---------gaaga------gggaaaaacaaa---
                Big brown bat  gat---cat--------a-------tg-gggtcaa---------gaaga------gggaaaagtaaa---
         David's myotis (bat)  gat---cac--------a-------tg-gggtcaa---------gaaga------gggaaaagcaag---
B D                  Microbat  gat---cac--------a-------tg-gggtcaa---------gaaga------gggaaaagtaag---
B D                     Shrew  gat---cat--------a-------cc-aggccaa---------gatac------ggatacaaggca---
              Star-nosed mole  --------------------------c-aggccaa---------gaaga------ggggaaagtgaa---
          Cape elephant shrew  tgt---cat--------a-------ta-gggtcac---------tgtgg---------gccagaact---
                     Aardvark  -----------------a-------tt-agggagc---------gaggg---------gacagagcg---
B D                 Armadillo  -----------------a-------ta-gggccaa---------gaaga---------tgttattaa---
B D           Tasmanian devil  gatatgcat--------c-------ta-gcccaga---------gcagt---------------------
B D               Zebra finch  ------gac--------a-------cg-gggcacc---------gaggg---------------------
B D                   Chicken  ------gac--------a-------cgagggcacc---------gcggga--------------------
B D        American alligator  ------ggtggttgtgaa-------tg-gggtctc---------ggagg---------------------
  D            Painted turtle  ------gtg--------a-------tg-gggttca---------ggggtaacggg---------------
B D             X. tropicalis  gat---tgt--------aagctcactg-gggcagg---------gactg---------------------
      Lesser Egyptian jerboa  ======================================================================
B D                  Hedgehog  ======================================================================
B D                    Rabbit  ======================================================================
            Cape golden mole  ======================================================================
B D               Stickleback  ======================================================================
B D                    Turkey  ======================================================================
  D              Mallard duck  ======================================================================
          Tibetan ground jay  ======================================================================
  D    White-throated sparrow  ======================================================================
    Mexican tetra (cavefish)  ======================================================================
B D                 Zebrafish  ======================================================================
B D                    Medaka  ======================================================================
B D                Budgerigar  ======================================================================
B D                   Opossum  ======================================================================
  D               Rock pigeon  ======================================================================
B D       Medium ground finch  ======================================================================
  D          Peregrine falcon  ======================================================================
  D              Saker falcon  ======================================================================
B D                   Wallaby  ======================================================================
B D                  Platypus  ======================================================================
B D                   Manatee  ======================================================================
B D                  Elephant  ======================================================================
B D                    Tenrec  ======================================================================
  D           Green seaturtle  ======================================================================
  D       Collared flycatcher  ======================================================================

                        Human  aa-----agggc-t
                        Chimp  aa-----agggc-t
                      Gorilla  aa-----agggc-t
                    Orangutan  aa-----agggc-t
                       Gibbon  aa-----agggc-t
                       Rhesus  aa-----agggc-t
          Crab-eating macaque  aa-----agggc-t
                       Baboon  aa-----agggc-t
                 Green monkey  aa-----agggc-t
                     Marmoset  aa-----agggc-t
              Squirrel monkey  aa-----agggc-t
                     Bushbaby  aa-----aggac-c
           Chinese tree shrew  ---------ggc-t
                     Squirrel  aa-----agggt-t
                 Prairie vole  gg-----acggg-t
              Chinese hamster  -g-----ctgga-t
               Golden hamster  gg-----ctgga-t
                        Mouse  ga-----gggaa-g
                          Rat  ga-----gggaa-g
               Naked mole-rat  aa-----gggtc-t
                   Guinea pig  ag-----gggtt-t
                   Chinchilla  ag-----cgggc-t
             Brush-tailed rat  ag-----ggggg-t
                         Pika  gg-----gcgag-a
                          Pig  gg-----ggagc-t
                       Alpaca  ag-----ggggc-t
               Bactrian camel  ag-----ggggc-t
                      Dolphin  ag-----gggga-t
                 Killer whale  ag-----gggga-t
             Tibetan antelope  ac-----gggtc-t
                          Cow  ac-----gggtc-t
                        Sheep  ac-----gggtc-t
                Domestic goat  ac-----gggtc-t
                        Horse  ag-----gaggc-t
             White rhinoceros  gg-----ggggc-t
                          Cat  gg-----tgggc-t
                          Dog  gg-----tgggc-t
                      Ferret   gg-----tgggc-t
                        Panda  gg-----ggggc-t
               Pacific walrus  ag-----tgggc-t
                 Weddell seal  ag-----tgggc-t
             Black flying-fox  gg-----ggggt-t
                      Megabat  gg-----ggggt-t
                Big brown bat  aggatggggggtgt
         David's myotis (bat)  ggt---gggggtgt
                     Microbat  ggt----ggggtgt
                        Shrew  gg-----g------
              Star-nosed mole  gg-----ggggc-t
          Cape elephant shrew  aa-----cgagc--
                     Aardvark  ga-----gatcc--
                    Armadillo  aa-----taacc--
              Tasmanian devil  gc-----cgcgc-c
                  Zebra finch  --------------
                      Chicken  --------------
           American alligator  --------------
               Painted turtle  --------------
                X. tropicalis  at-----gggaa-t
       Lesser Egyptian jerboa  ==============
                     Hedgehog  ==============
                       Rabbit  ==============
             Cape golden mole  ==============
                  Stickleback  ==============
                       Turkey  ==============
                 Mallard duck  ==============
           Tibetan ground jay  ==============
       White-throated sparrow  ==============
     Mexican tetra (cavefish)  ==============
                    Zebrafish  ==============
                       Medaka  ==============
                   Budgerigar  ==============
                      Opossum  ==============
                  Rock pigeon  ==============
          Medium ground finch  ==============
             Peregrine falcon  ==============
                 Saker falcon  ==============
                      Wallaby  ==============
                     Platypus  ==============
                      Manatee  ==============
                     Elephant  ==============
                       Tenrec  ==============
              Green seaturtle  ==============
          Collared flycatcher  ==============

Inserts between block 13 and 14 in window
         Cape elephant shrew 20bp
                    Aardvark 7bp
B D                Armadillo 4bp
B D          Tasmanian devil 3bp
B D              Zebra finch 1bp

Alignment block 14 of 366 in window, 34988827 - 34988837, 11 bps 
B D                     Human  aa-------------aacacaggc--
B D                     Chimp  aa-------------aacacaggc--
B D                   Gorilla  aa-------------aacacaggc--
B D                 Orangutan  aa-------------aacacaggc--
B D                    Gibbon  aa-------------aacacaggc--
B D                    Rhesus  aa-------------aacacaggc--
B D       Crab-eating macaque  aa-------------aacacaggc--
B D                    Baboon  aa-------------aacacaggc--
B D              Green monkey  aa-------------aacacaggc--
B D                  Marmoset  aa-------------aacacaagc--
B D           Squirrel monkey  aa-------------aacacaggc--
B D                  Bushbaby  ga-------------aatacagaa--
           Chinese tree shrew  aa-------------aatacagga--
B D                  Squirrel  aa-------------tattcagga--
                 Prairie vole  at-------------cat--------
B D           Chinese hamster  at-------------cata-------
               Golden hamster  at-------------cata-------
B D                     Mouse  ac-----------------cagg---
B D                       Rat  ac-------------cagacaga---
B D            Naked mole-rat  aa-------------tgttcagga--
B D                Guinea pig  aa-------------tgttcagga--
                   Chinchilla  cg-------------cgtccagga--
             Brush-tailed rat  aa-------------tattcagga--
B D                      Pika  ag------------------------
B D                       Pig  aa-------------aacgtggga--
B D                    Alpaca  aa-------------aacgtggga--
               Bactrian camel  aa-------------aacgtggga--
B D                   Dolphin  aa-------------aatgtggga--
                 Killer whale  aa-------------aatgtggga--
             Tibetan antelope  ta-----ggggaagtaagatggga--
B D                       Cow  aaaacatgtgttaccttaatggta--
B D                     Sheep  ta-----ggggaagtaagatggga--
                Domestic goat  ta-----ggggaagtaagatggga--
B D                     Horse  aa-------------aatgcggga--
B D          White rhinoceros  -a-------------aattcgaga--
B D                       Cat  ac-------------aatttggga--
B D                       Dog  aa-------------catttggga--
B D                   Ferret   aa-------------catttggga--
B D                     Panda  aa-------------catttggga--
               Pacific walrus  aa-------------catttggga--
                 Weddell seal  aa-------------catttggga--
             Black flying-fox  aa-------------aatgtaggg--
B D                   Megabat  aa-------------aatgtaggg--
                Big brown bat  aa-------------aatgtagaa--
         David's myotis (bat)  aa-------------aatgtagga--
B D                  Microbat  aa-------------aatgtagga--
B D                     Shrew  ----------------gtgcaggt--
              Star-nosed mole  aa-------------agtgtgggc--
          Cape elephant shrew  aa-------------agtgcagga--
B D                   Manatee  aa-------------aatacgaga--
                     Aardvark  ---------------acgacgggg--
B D                 Armadillo  aa-------------aatgcaggt--
B D           Tasmanian devil  ga-------------aatctggg---
B D                   Chicken  -------------------caggt--
B D        American alligator  -----------------------t--
  D            Painted turtle  ------------------gcaatg--
B D             X. tropicalis  ---------------gggatagggac
      Lesser Egyptian jerboa  ==========================
B D                  Hedgehog  ==========================
B D                    Rabbit  ==========================
            Cape golden mole  ==========================
B D               Stickleback  ==========================
B D                    Turkey  ==========================
  D              Mallard duck  ==========================
          Tibetan ground jay  ==========================
B D               Zebra finch  ==========================
  D    White-throated sparrow  ==========================
    Mexican tetra (cavefish)  ==========================
B D                 Zebrafish  ==========================
B D                    Medaka  ==========================
B D                Budgerigar  ==========================
B D                   Opossum  ==========================
  D               Rock pigeon  ==========================
B D       Medium ground finch  ==========================
  D          Peregrine falcon  ==========================
  D              Saker falcon  ==========================
B D                   Wallaby  ==========================
B D                  Platypus  ==========================
B D                  Elephant  ==========================
B D                    Tenrec  ==========================
  D           Green seaturtle  ==========================
  D       Collared flycatcher  ==========================

Inserts between block 14 and 15 in window
                    Aardvark 2bp
B D                  Chicken 2bp
B D       American alligator 2bp
  D           Painted turtle 2bp

Alignment block 15 of 366 in window, 34988838 - 34988838, 1 bps 
B D                     Human  -a
B D                     Chimp  -a
B D                   Gorilla  -a
B D                 Orangutan  -a
B D                    Gibbon  -a
B D                    Rhesus  -a
B D       Crab-eating macaque  -a
B D                    Baboon  -a
B D              Green monkey  -a
B D                  Marmoset  -a
B D           Squirrel monkey  -a
B D                  Bushbaby  -g
           Chinese tree shrew  -a
B D                  Squirrel  -a
B D            Naked mole-rat  -a
B D                Guinea pig  -a
                   Chinchilla  -a
             Brush-tailed rat  -a
B D                       Pig  -a
B D                    Alpaca  -a
               Bactrian camel  -a
B D                   Dolphin  -a
                 Killer whale  -a
             Tibetan antelope  -a
B D                       Cow  -a
B D                     Sheep  -a
                Domestic goat  -a
B D                     Horse  -a
B D          White rhinoceros  -a
B D                       Cat  -a
B D                       Dog  -g
B D                   Ferret   -a
               Pacific walrus  -a
                 Weddell seal  -a
             Black flying-fox  -a
B D                   Megabat  -a
                Big brown bat  -a
         David's myotis (bat)  -c
B D                  Microbat  -c
B D                     Shrew  -a
              Star-nosed mole  -a
          Cape elephant shrew  -a
B D                   Manatee  -a
             Cape golden mole  -a
B D                    Tenrec  -a
                     Aardvark  -a
B D                 Armadillo  -a
B D           Tasmanian devil  -c
B D               Zebra finch  -g
B D                   Chicken  -a
B D        American alligator  -g
  D            Painted turtle  -t
B D             X. tropicalis  c-
              Golden hamster  --
      Lesser Egyptian jerboa  ==
B D                       Rat  --
                Prairie vole  --
B D                     Mouse  --
B D                      Pika  --
B D                  Hedgehog  ==
B D                    Rabbit  ==
B D               Stickleback  ==
B D                    Turkey  ==
  D              Mallard duck  ==
          Tibetan ground jay  ==
  D    White-throated sparrow  ==
    Mexican tetra (cavefish)  ==
B D                 Zebrafish  ==
B D                    Medaka  ==
B D                Budgerigar  ==
B D                   Opossum  ==
  D               Rock pigeon  ==
B D       Medium ground finch  ==
  D          Peregrine falcon  ==
  D              Saker falcon  ==
B D                   Wallaby  ==
B D                  Platypus  ==
B D                  Elephant  ==
B D           Chinese hamster  --
  D           Green seaturtle  ==
  D       Collared flycatcher  ==
B D                     Panda  --

Alignment block 16 of 366 in window, 34988839 - 34988848, 10 bps 
B D                     Human  ctccag-----gggg-
B D                     Chimp  ttccag-----gggg-
B D                   Gorilla  ctccag-----gggg-
B D                 Orangutan  ctccag-----gggg-
B D                    Gibbon  ctccag-----gggg-
B D                    Rhesus  ctccag-----gggg-
B D       Crab-eating macaque  ctccag-----gggg-
B D                    Baboon  ctccag-----gggg-
B D              Green monkey  ctccag-----gggg-
B D                  Marmoset  ctcaag-----gggg-
B D           Squirrel monkey  ctcaag-----gggg-
B D                  Bushbaby  tccagg-----gagg-
           Chinese tree shrew  ct--------------
B D                  Squirrel  ctctca-----aaga-
                 Prairie vole  -------------gg-
B D           Chinese hamster  -------------gg-
               Golden hamster  -------------gg-
B D                     Mouse  -tatca-----cagg-
B D                       Rat  -tatca-----cagt-
B D            Naked mole-rat  ctcaaa-----tgg--
B D                Guinea pig  ctcaca-----ttg--
                   Chinchilla  ccccag-----cgc--
             Brush-tailed rat  ctccag-----tgg--
B D                       Pig  ctcaaa-----ggaa-
B D                    Alpaca  ctcaaa-----gggg-
               Bactrian camel  ctcaaa-----gggg-
B D                   Dolphin  ctcaaa-----aggg-
                 Killer whale  ctcaaa-----aggg-
             Tibetan antelope  ctcaaa-----gggg-
B D                       Cow  ctcaaa-----gggg-
B D                     Sheep  ctcaaa-----gggg-
                Domestic goat  ctcaaa-----gggg-
B D                     Horse  ctcgaa-----gggg-
B D          White rhinoceros  cacgaa-----gggg-
B D                       Cat  ctcaag-----aggg-
B D                       Dog  atcaag-----gggg-
B D                   Ferret   ctcaaa-----gggg-
               Pacific walrus  ctcaag-----gggg-
                 Weddell seal  ctcaag-----gggg-
             Black flying-fox  ctcaaa-----gggg-
B D                   Megabat  cccaaa-----gggg-
                Big brown bat  ttcaaa-----ggga-
         David's myotis (bat)  ttcaaa-----ggga-
B D                  Microbat  ttcaaa-----ggga-
B D                     Shrew  cgcaaa-----gggg-
              Star-nosed mole  ctcaaa-----gagg-
          Cape elephant shrew  ctcaaa-----ggag-
B D                   Manatee  ctcaaa-----gagg-
             Cape golden mole  ttcaaa-----ggga-
B D                    Tenrec  ttcaaa-----gggg-
                     Aardvark  cgagag-----ggga-
B D                 Armadillo  tccaat-----gagg-
B D           Tasmanian devil  ctagct-----gagg-
B D                  Platypus  cccgga-----gggg-
B D               Zebra finch  cgcgggggaacgagg-
B D                   Chicken  cgccgggg---gggg-
B D        American alligator  cttcat-----gagc-
  D            Painted turtle  cttggggtgcagagg-
B D             X. tropicalis  -ttaga-----ttgta
      Lesser Egyptian jerboa  ================
B D                      Pika  ----------------
B D                  Hedgehog  ================
B D                    Rabbit  ================
B D               Stickleback  ================
B D                    Turkey  ================
  D              Mallard duck  ================
          Tibetan ground jay  ================
  D    White-throated sparrow  ================
    Mexican tetra (cavefish)  ================
B D                 Zebrafish  ================
B D                    Medaka  ================
B D                Budgerigar  ================
B D                   Opossum  ================
  D               Rock pigeon  ================
B D       Medium ground finch  ================
  D          Peregrine falcon  ================
  D              Saker falcon  ================
B D                   Wallaby  ================
B D                  Elephant  ================
  D           Green seaturtle  ================
  D       Collared flycatcher  ================
B D                     Panda  ----------------

Inserts between block 16 and 17 in window
B D                 Squirrel 2bp
                Prairie vole 21bp
B D          Chinese hamster 20bp
              Golden hamster 22bp
B D                    Mouse 38bp
B D                      Rat 32bp
B D                 Platypus 2bp
B D              Zebra finch 14bp
B D                  Chicken 13bp
B D       American alligator 14bp

Alignment block 17 of 366 in window, 34988849 - 34988867, 19 bps 
B D                     Human  ---------aagcagg------------------atgagagactga
B D                     Chimp  ---------aagcagg------------------atgagagactga
B D                   Gorilla  ---------aagcaga------------------atgagagactga
B D                 Orangutan  ---------aagcagg------------------atgagagactga
B D                    Gibbon  ---------aagcagg------------------atgagagactga
B D                    Rhesus  ---------aagcagg------------------atgagagactga
B D       Crab-eating macaque  ---------aagcagg------------------atgagagactga
B D                    Baboon  ---------aagcagg------------------atgagagactga
B D              Green monkey  ---------aagcagg------------------atgagagactga
B D                  Marmoset  ---------aagcagg------------------atgagagactga
B D           Squirrel monkey  ---------aagcagg------------------atgagagactga
B D                  Bushbaby  ---------agtaagg------------------atgaaagattcg
B D                  Squirrel  ---------aagtaaa------------------aggaaaggttga
       Lesser Egyptian jerboa  ---------gaggaag------------------atgaaaggttgg
                 Prairie vole  ---------gacaaag------------------atgaaaggttga
B D           Chinese hamster  ------------aaag------------------atgaaaggttgg
               Golden hamster  ---------gacaaag------------------atgagaggttgg
B D                     Mouse  ---------ggagaag------------------atggaaggttag
B D                       Rat  ---------ggagaag------------------atggaaggttag
B D            Naked mole-rat  ---------aaataaa------------------atgaaaggttgg
B D                Guinea pig  ---------aagtaaa------------------acgaaaggttgg
                   Chinchilla  ---------gag--ac------------------tcgaagggccgg
             Brush-tailed rat  ---------aggtaaa------------------atgaaaggttgg
B D                       Pig  ---------aagaaag------------------atgaaaga----
B D                    Alpaca  ---------aagaagg------------------atgaaaga----
               Bactrian camel  ---------aagaagg------------------atgaaaga----
B D                   Dolphin  ---------aagtagg------------------atgaaaga----
                 Killer whale  ---------aagtagg------------------atgaaaga----
             Tibetan antelope  ---------aagtaag------------------atgaaaga----
B D                       Cow  ---------aagtaaa------------------atgaaaga----
B D                     Sheep  ---------aagtaag------------------atgaaaga----
                Domestic goat  ---------aagtaag------------------atgaaaga----
B D                     Horse  ---------aagtagg------------------gtgaaaga----
B D          White rhinoceros  ---------aagtagg------------------gtgaaaga----
B D                       Cat  ---------aagtgag------------------atgaaaga----
B D                       Dog  ---------aagtagg------------------atgaaagg----
B D                   Ferret   ---------aagtagg------------------atgaaaga----
B D                     Panda  ---------aagtagg------------------atgaaaga----
               Pacific walrus  ---------aagtagg------------------atgaaaga----
                 Weddell seal  ---------aagtagg------------------atgaaaga----
             Black flying-fox  ---------aagtaga------------------atgaaaga----
B D                   Megabat  ---------aagtaga------------------atgaaaga----
                Big brown bat  ---------aagtggg------------------atgaaaaa----
         David's myotis (bat)  ---------aagtggg------------------gtgaaaga----
B D                  Microbat  ---------aagtggg------------------gtgaaaga----
B D                     Shrew  ---------aaggata------------------gaaaca------
              Star-nosed mole  ---------aggaagg------------------atgaca------
          Cape elephant shrew  ---------aagtagg------------------atgaagg-----
B D                   Manatee  ---------aagcagg------------------acgaaggcttaa
             Cape golden mole  ---------aagtaca------------------atgaagac----
B D                    Tenrec  ---------aagcagg------------------atgaagac----
                     Aardvark  ---------acgcagggctccggcctgtgcgggcacga--------
B D                 Armadillo  ---------aagtagg------------------atgaagga----
B D           Tasmanian devil  ---------acggggg------------------gtctgggactat
B D                  Platypus  ---------gtgaaga------------------ccgacagt----
B D               Zebra finch  ----------aagagg------------------aagaagta----
B D                   Chicken  ----------aggagt------------------gccaaaag----
B D        American alligator  ----------aggcag------------------------------
  D            Painted turtle  ----------aggcga------------------gacagaga----
B D             X. tropicalis  agctcactggggcagg------------------gactga------
B D                      Pika  ----------------------------------------------
B D                  Hedgehog  ==============================================
B D                    Rabbit  ==============================================
B D               Stickleback  ==============================================
B D                    Turkey  ==============================================
  D              Mallard duck  ==============================================
          Tibetan ground jay  ==============================================
  D    White-throated sparrow  ==============================================
    Mexican tetra (cavefish)  ==============================================
B D                 Zebrafish  ==============================================
B D                    Medaka  ==============================================
B D                Budgerigar  ==============================================
B D                   Opossum  ==============================================
  D               Rock pigeon  ==============================================
B D       Medium ground finch  ==============================================
  D          Peregrine falcon  ==============================================
  D              Saker falcon  ==============================================
B D                   Wallaby  ==============================================
          Chinese tree shrew  ----------------------------------------------
B D                  Elephant  ==============================================
  D           Green seaturtle  ==============================================
  D       Collared flycatcher  ==============================================

Inserts between block 17 and 18 in window
B D                    Mouse 1bp
B D                      Rat 1bp
                    Aardvark 6bp
B D                Armadillo 4bp
B D                 Platypus 2bp
B D              Zebra finch 5bp
B D                  Chicken 5bp
B D       American alligator 2bp
  D           Painted turtle 5bp

Alignment block 18 of 366 in window, 34988868 - 34988950, 83 bps 
B D                     Human  tta-------------gaaga--gggactgaaatg--gagacc---gc--g---------------g---
B D                     Chimp  tta-------------gaagg--gggactgaaatg--gggacc---gc--g---------------g---
B D                   Gorilla  tta-------------gaagg--aggactgaaatg--gggacc---gc--g---------------g---
B D                 Orangutan  tta-------------gaagg--gggactgaaatg--gggacc---gc--g---------------a---
B D                    Gibbon  tta-------------gaagg--gggactgaaatg--gggacc---gc--g---------------g---
B D                    Rhesus  tta-------------gaaag--gggactgaaatg--ggcacc---gc--g---------------g---
B D       Crab-eating macaque  tta-------------gaaag--gggactgaaatg--ggcacc---gc--g---------------g---
B D                    Baboon  tta-------------gaaag--gggactgaaatg--ggcacc---gc--g---------------g---
B D              Green monkey  tta-------------gaaag--gggactgaaatg--ggcacc---gc--g---------------g---
B D                  Marmoset  tta-------------gaaag--gggactgaaatg--gggacc---gc--g---------------g---
B D           Squirrel monkey  tta-------------gaaag--gggactgaaatg--gggacc---gc--g---------------g---
B D                  Bushbaby  ttatcggcactaaattgaaat--ggggctg---tg--gggact---gc--t---------------gaga
           Chinese tree shrew  ----------------cagcc--gggactgagatg--gggact---gt--g---------------a---
B D                  Squirrel  tta-------------taagt--aacc-tgaaatg--gaagct---gt--g---------------g---
       Lesser Egyptian jerboa  cta-------------taagg--aggtctgaagta--ggcagt---gt--g---------------g---
                 Prairie vole  tta-------------taagg--ggct--------------ct---gt--g---------------g---
B D           Chinese hamster  ttt-------------taagg--ggt---------------ct---gt--g---------------a---
               Golden hamster  tgg-------------taacg--ggtc-tgagctg--ggcact---gt--g---------------a---
B D                     Mouse  tta-------------taacg--aggt-tgaactg--gacact---gt--g---------------g---
B D                       Rat  tta-------------taagg--agtc-tgaactg--gacac-----t--g---------------g---
B D            Naked mole-rat  tta-------------tgagg--cggcctaaaatg--tgaaat---gt--g---------------a---
B D                Guinea pig  tta-------------tgagg--agctctaaa-tg--ggagct---gt--g---------------a---
                   Chinchilla  gcg-------------cgagg--ggctctgaaggg--ggcgct---gt--g---------------a---
             Brush-tailed rat  tta-------------tgagg--ggctttaaatta--ggagct---at--g---------------a---
B D                      Pika  --g-------------cgcgg--ggcctgggaccg--ggag-----gc--g---------------g---
B D                       Pig  tta-------------taggg--ggaactttaatg--gggatt---gt--g---------------g---
B D                    Alpaca  tta-------------taggt--agaactttaata--gggact---gt--g---------------g---
               Bactrian camel  tta-------------taggt--agaactttaata--gggact---gt--g---------------g---
B D                   Dolphin  tta-------------taggg--agaactttaatg--aggatt---gt--g---------------g---
                 Killer whale  tta-------------taggg--agaactttaatg--aggatt---gt--g---------------g---
             Tibetan antelope  tta-------------tagga--agaactttaatg--agtatc---at--g---------------g---
B D                       Cow  taa-------------tagga--agaactttaatg--ggtatc---at--g---------------c---
B D                     Sheep  tta-------------tagga--agaactttaatg--ggtatc---at--g---------------g---
                Domestic goat  tta-------------tagga--agaactttaatg--ggtatc---at--g---------------g---
B D                     Horse  ctg-------------tagag---gaattttaatg--gggatt---gt--g---------------g---
B D          White rhinoceros  tta-------------taggg---gaattttaacg--gggatt---gt--g---------------g---
B D                       Cat  tta-------------tagag--agaatgttactg--aggatt---gt--g---------------g---
B D                       Dog  tta-------------cagag--agaacattaatg--aggatt---gt--g---------------t---
B D                   Ferret   tta-------------cagag--agaacgttaatg--agaatt---gt--g---------------g---
B D                     Panda  tta-------------cagag--aggacgttaatg--aaaatt---gt--g---------------g---
               Pacific walrus  tta-------------cagag--agaacgttaatg--agaatt---gc--g---------------g---
                 Weddell seal  tta-------------cagag--agaacgttaatg--agaatt---gt--g---------------g---
             Black flying-fox  tta-------------t--ag--agaactttaatg--gagatt---gt--g---------------g---
B D                   Megabat  tta-------------t--ag--agaactttaatg--gagatt---gt--g---------------g---
                Big brown bat  tca-------------tagag--agaagtttaatg--gggacg---gt----------------------
         David's myotis (bat)  cca-------------tagag--agaactctaatg--ggggct---gt----------------------
B D                  Microbat  tca-------------tagag--agaactctaata--ggggct---gg----------------------
B D                     Shrew  -ca-------------gaggg--agaatgttcctg--ggggct---gc--g---------------g---
              Star-nosed mole  -tt-------------gtaag--ggaactttaacg--ggggct---g---g---------------g---
B D                  Elephant  ------------------ttg--ggg------------------------g---------------g---
          Cape elephant shrew  ttt-------------aaatg--gagaccaaaata-gaagact---gt--g---------------g---
B D                   Manatee  ------------------acg--gagactgaaata-gaggatt---gt--g---------------g---
             Cape golden mole  -tt-------------aaagg--gagactgaaata--aggatt---gt--g---------------g---
B D                    Tenrec  --t-------------aaagg--gaaccaggaat----gggtt---gg--gggt------------g---
                     Aardvark  ctg-------------caccg--gacgccacagaaggcaggtt---gc--gggcagactgacgtcgg---
B D                 Armadillo  ------------------agg--gtaactgaaggg---gaggt---gt--g---------------g---
B D           Tasmanian devil  -----------------ttca--gggccagggtcg--ggatct---ac--g---------------t---
B D                  Platypus  ---------------------------tttggagc--ggcgca---gccgg---------------g---
B D               Zebra finch  ccg-------------cagcc---ccccagaaatg--gggcacag-gc--a---------------g---
B D                   Chicken  ctg-------------agg-----gcatgggaacg--ttgcagggcgc--g---------------g---
B D        American alligator  ttg-------------tgacc--accatcggggtg--gatttccgtgt--c---------------c---
  D            Painted turtle  tta-------------tggtgcggtcattgagatg--gggc-----gc--c---------------a---
B D             X. tropicalis  ----------------------tgggaatgggata--gggacc---tt--a---------------g---
B D                  Hedgehog  ======================================================================
B D                    Rabbit  ======================================================================
B D               Stickleback  ======================================================================
B D                    Turkey  ======================================================================
  D              Mallard duck  ======================================================================
          Tibetan ground jay  ======================================================================
  D    White-throated sparrow  ======================================================================
    Mexican tetra (cavefish)  ======================================================================
B D                 Zebrafish  ======================================================================
B D                    Medaka  ======================================================================
B D                Budgerigar  ======================================================================
B D                   Opossum  ======================================================================
  D               Rock pigeon  ======================================================================
B D       Medium ground finch  ======================================================================
  D          Peregrine falcon  ======================================================================
  D              Saker falcon  ======================================================================
B D                   Wallaby  ======================================================================
  D           Green seaturtle  ======================================================================
  D       Collared flycatcher  ======================================================================

                        Human  -g-------g-----tcgc--------tg--a-----ag-a--------------------------gg-
                        Chimp  -g-------g-----tcgc--------tg--a-----ag-a--------------------------gg-
                      Gorilla  -g-------g-----tcgc--------tg--a-----ag-a--------------------------gg-
                    Orangutan  -g-------g-----tcgc--------tg--a-----ag-a--------------------------gg-
                       Gibbon  -g-------g-----tcgc--------tg--a-----ag-a--------------------------gg-
                       Rhesus  -g-------g-----tcgc--------tg--a-----gg-a--------------------------gg-
          Crab-eating macaque  -g-------g-----tcgc--------tg--a-----gg-a--------------------------gg-
                       Baboon  -g-------g-----tcgc--------tg--a-----gg-a--------------------------gg-
                 Green monkey  -g-------g-----tcgc--------tg--a-----gg-a--------------------------gg-
                     Marmoset  -a-------g-----tcgc--------tg--a-----gg-a--------------------------gg-
              Squirrel monkey  -a-------g-----tcgc--------tg--a-----gg-a--------------------------gg-
                     Bushbaby  ag-------g-----gggc--------tg--actgctgg-g--------------------------ag-
           Chinese tree shrew  -g-------g----cttgc--------tg--a-----ga-a--------------------------gg-
                     Squirrel  -g------gg-----ttgc--------tg--a-----ga-a--------------------------gc-
       Lesser Egyptian jerboa  -g------ag-----ttgc--------ag--a-----ga-a--------------------------gg-
                 Prairie vole  -gct-ccaag-----tagc--------tg--a-----ga-a--------------------------gt-
              Chinese hamster  -aat-ccaag-----tagc--------tg--a-----ga-a--------------------------gc-
               Golden hamster  -act-ccaag-----tgac--------tg--a-----g--a--------------------------gc-
                        Mouse  -act-ccaag-----tggc--------tg--a-----ga-a--------------------------gc-
                          Rat  -act-ccacg-----tggc--------tg--a-----ga-a--------------------------gc-
               Naked mole-rat  -g------aa-----t-gc--------tc--a-----ga-a--------------------------gg-
                   Guinea pig  -g------ag-----aaat--------gg--t-----ga-a--------------------------ag-
                   Chinchilla  -g------ga-----cggc--------cg--a-----ga-a--------------------------gg-
             Brush-tailed rat  -g------aa-----ttga--------tg--a-----ga-a--------------------------gg-
                         Pika  -a------gg-----aagc--------ac--a-----gt-c--------------------------ca-
                          Pig  -g------gt-----ttgt--------tg--a-----ga-a--------------------------cg-
                       Alpaca  -g------gg-----ttgc--------tg--a-----ga-a--------------------------gg-
               Bactrian camel  -g------gg-----ttgc--------tg--a-----ga-a--------------------------gg-
                      Dolphin  -g------ga-----ttgt--------tg--a-----ga-a--------------------------gg-
                 Killer whale  -g------ga-----ttgt--------tg--a-----ga-a--------------------------gg-
             Tibetan antelope  -g------gg-----ttgc--------tg--a-----ga-a--------------------------gg-
                          Cow  -g------gg-----ttgc--------tg--a-----ga-a--------------------------gg-
                        Sheep  -g------gg-----ttgc--------tg--a-----ga-a--------------------------ggg
                Domestic goat  -g------gg-----ttgc--------tg--a-----ga-a--------------------------gg-
                        Horse  -g------gg-----ttgc--------tg--a-----ga-a--------------------------gg-
             White rhinoceros  -g------ag-----ttgc--------tg--a-----ga-a--------------------------ag-
                          Cat  -g------gg-----ttgc--------tg--g-----gg-a--------------------------gg-
                          Dog  -g------gg-----ttcc--------tt--c-----gg-a--------------------------gg-
                      Ferret   -g------gg-----ttgc--------tg--a-----gg-a--------------------------gg-
                        Panda  -g------gg-----ctgc--------tg--a-----gg-a--------------------------gg-
               Pacific walrus  -g------gg-----ttgc--------tg--a-----ggaa--------------------------ag-
                 Weddell seal  -g------gg-----ttgc--------tg--a-----gg-a--------------------------gg-
             Black flying-fox  -g------ag-----ttgc--------tg--a-----ga-a--------------------------gg-
                      Megabat  -g------ag-----ttgc--------tg--a-----ga-a--------------------------gg-
                Big brown bat  --------------------------------------------------------------------g-
         David's myotis (bat)  --------------------------------------------------------------------g-
                     Microbat  --------------------------------------------------------------------g-
                        Shrew  -a------gg-----ttgc--------tg-----------------------------------------
              Star-nosed mole  -g------gg-----tggc--------tgtct-----gc-a--------------------------gg-
                     Elephant  -g------gg-----ctac--------tg--a-----ga-a--------------------------gg-
          Cape elephant shrew  -g------gg-----ttgc--------tg--a-----aa-a--------------------------gg-
                      Manatee  -g------gg----cctgc--------tg--a-----ga-a--------------------------ag-
             Cape golden mole  -g------gg-----ctgc--------tg--a-----ga-t--------------------------ag-
                       Tenrec  -g------gg-----ctgcttgtgatgtg--g-----ga-t--------------------------ga-
                     Aardvark  -g------gg-----ctgc--------cg--c-----gg-a--------------------------gg-
                    Armadillo  -t------gg-----gtgc--------tg--a-----ga-a--------------------------gg-
              Tasmanian devil  -g------tc-----actc--------tg--t-----gg-a--------------------------gg-
                     Platypus  -a------gg-----gagg--------tg--a-----ga-c--------------------------gg-
                  Zebra finch  -a------gagtccccagc--------tg--g-----gg-gggcagcgcttgtgggaccccggcccggg-
                      Chicken  -a------ga-----cagc--------tg--a-----gg-a------------------------cgtg-
           American alligator  -g------ga--------c--------tg--t-----gg-t---------------------gctcggg-
               Painted turtle  -g------ga--------t--------ca--a-----gg-t------------------------gatg-
                X. tropicalis  -attgtaagc-----tcac--------tg--g-----ggca--------------------------gg-
                     Hedgehog  ======================================================================
                       Rabbit  ======================================================================
                  Stickleback  ======================================================================
                       Turkey  ======================================================================
                 Mallard duck  ======================================================================
           Tibetan ground jay  ======================================================================
       White-throated sparrow  ======================================================================
     Mexican tetra (cavefish)  ======================================================================
                    Zebrafish  ======================================================================
                       Medaka  ======================================================================
                   Budgerigar  ======================================================================
                      Opossum  ======================================================================
                  Rock pigeon  ======================================================================
          Medium ground finch  ======================================================================
             Peregrine falcon  ======================================================================
                 Saker falcon  ======================================================================
                      Wallaby  ======================================================================
              Green seaturtle  ======================================================================
          Collared flycatcher  ======================================================================

                        Human  -------------g------------------------------gc-------gcga-------ggatga
                        Chimp  -------------g------------------------------gc-------gcga-------ggatga
                      Gorilla  -------------g------------------------------gc-------gcga-------ggatga
                    Orangutan  -------------g------------------------------gc-------gcga-------ggatga
                       Gibbon  -------------g------------------------------gc-------gcga-------ggatga
                       Rhesus  -------------g------------------------------gc-------gcga-------ggatga
          Crab-eating macaque  -------------g------------------------------gc-------gcga-------ggatga
                       Baboon  -------------g------------------------------gc-------gcga-------ggatga
                 Green monkey  -------------g------------------------------gc-------gcga-------ggatga
                     Marmoset  -------------g------------------------------gc-------gcga-------ggatga
              Squirrel monkey  -------------g------------------------------gc-------gcga-------ggatga
                     Bushbaby  -------------g------------------------------ga-------gcta-------ggatga
           Chinese tree shrew  -------------ga---ttggtcta---------a-----agaga-------gcta-------tgatga
                     Squirrel  -------------ag---ctactcag---------g-----aggga-------acta-------gggtga
       Lesser Egyptian jerboa  -------------gt---ctgcctgt---------g-----aggga-------gtca-------gcctgc
                 Prairie vole  -------------gg---ccgttcct---------a-----agagagtcaacagcca-------gcgaga
              Chinese hamster  -------------gg---ctgctcct---------a-----agcgagccagcagcca-------tcgtga
               Golden hamster  -------------gg---gcgctcct---------a-----agcgagccagcggcca-------tcgtga
                        Mouse  -------------ca---ctgctcct---------a-----agcga-------gccg-------ctgtga
                          Rat  -------------ca---ctattcct---------a-----agcga-------gccg-------gcgtga
               Naked mole-rat  -------------gg---ctgtttat---------g-----aggga-------gttg-------ggctga
                   Guinea pig  --------------t---ctgttcat---------g-----aggga-------tttg-------ggttga
                   Chinchilla  -------------gc---ctgccggc---------g-----ag-gg-------gctg-------ggagga
             Brush-tailed rat  -------------ct---ctgattgt---------g-----agtga-------gtca-------ggatga
                         Pika  -------------cc---acgcgccg---------a-----cgcgc-------gcc--------------
                          Pig  -------------gg---ctg--cat---------a-----aggga-------gcag-------ggatga
                       Alpaca  -------------gg---ctgctcat---------g-----gagga-------gcag-------ggatga
               Bactrian camel  -------------gg---ctgctcat---------g-----gagaa-------gcag-------ggatga
                      Dolphin  -------------gg---ctgctcat---------g-----aggga-------gcag-------ggatga
                 Killer whale  -------------gg---ctgctcat---------g-----aggga-------gcag-------ggatga
             Tibetan antelope  -------------gg---ctgctcgt---------g-----aggga-------acac-------gaatga
                          Cow  -------------gg---ctgctcat---------g-----aggga-------acac-------gaatga
                        Sheep  gttgctgagaagtgg---ctgctcat---------g-----aggga-------acac-------gaatga
                Domestic goat  -------------gg---ctgctcat---------g-----aggga-------acac-------gaatga
                        Horse  -------------ga---cgccgcag---------g-----aggga-------gcca-------ggatgg
             White rhinoceros  -------------gg---ctgctcat---------g-----aggga-------gccg-------ggatgg
                          Cat  -------------gg---ctgctcat---------a-----aggta-------ggtg-------gtatta
                          Dog  -------------gg---ctgctcac---------g-----aggga-------gctg-------ggatga
                      Ferret   -------------gg---ctgctcac---------a-----aggga-------gctg-------ggatga
                        Panda  -------------gg---ctgctcac---------a-----aggga-------gcta-------ggatga
               Pacific walrus  -------------gg---ctgctcac---------a-----aggga-------gctg-------ggatga
                 Weddell seal  -------------gg---ctgctcac---------a-----aggga-------gctg-------ggatga
             Black flying-fox  -------------gg---ctgctcat---------g-----aagaa-------gctg-------ggatgt
                      Megabat  -------------gg---ctgctcat---------g-----aagaa-------gctg-------ggatgt
                Big brown bat  -------------gg---ctgctcatgcac-----g-----aggca-------gcta-------ggatgt
         David's myotis (bat)  -------------gg---ctgctcgt---------g-----aggca-------gctg-------ggatgc
                     Microbat  -------------gg---ctgctcgt---------g-----aggca-------gctg-------ggatgc
                        Shrew  -------------------------a---------g-----atgga-------gcaa-------agatga
              Star-nosed mole  -------------aa---ctgctctt---------g-----aagga-------gctg-------ggatga
                     Elephant  -------------gg---ctgctcatgggggacgga-----gaagg-------aagt-----taggatac
          Cape elephant shrew  -------------gg---ctgctcac---------a-----gaagg-------aggtttttctaggatta
                      Manatee  -------------gg---tcgcttatagg------g-----gtggg-------gagt-----taggataa
             Cape golden mole  -------------ga---ctgctcatg--------g-----agtgg-------g----------gaatga
                       Tenrec  -------------ga---gggtt------------g-----ggtgg-------gggt--cgctagaatga
                     Aardvark  -------------gg----tgctcga---------g-----ggggc-------gggc-------gagggg
                    Armadillo  -------------gag--ctgttcac---------g-----gggga-------agct--------gataa
              Tasmanian devil  -------------gg-----acctag---------g-----actgg-------gtaa-------ggatgg
                     Platypus  -------------ggagcgggcccaa---------g-----aggct-------gacg-------ggagag
                  Zebra finch  -------------gg---gtgcccgt---------gtgccagtgcc-------ttca-------gcacgg
                      Chicken  -------------gg---gacgctgt---------g-----gggtt-------ttgc-------ggacag
           American alligator  -------------gggctgcggctgc---------ggctccaggtc-------tggg-------acacgg
               Painted turtle  -------------ga-------ttgt---------g-----gggt-------------------------
                X. tropicalis  -------------ga---ctg--------------a-----tggga-------g----------tgatgt
                     Hedgehog  ======================================================================
                       Rabbit  ======================================================================
                  Stickleback  ======================================================================
                       Turkey  ======================================================================
                 Mallard duck  ======================================================================
           Tibetan ground jay  ======================================================================
       White-throated sparrow  ======================================================================
     Mexican tetra (cavefish)  ======================================================================
                    Zebrafish  ======================================================================
                       Medaka  ======================================================================
                   Budgerigar  ======================================================================
                      Opossum  ======================================================================
                  Rock pigeon  ======================================================================
          Medium ground finch  ======================================================================
             Peregrine falcon  ======================================================================
                 Saker falcon  ======================================================================
                      Wallaby  ======================================================================
              Green seaturtle  ======================================================================
          Collared flycatcher  ======================================================================

                        Human  ggg-gctgta---cagagggt-ggg------cg---gg------g---------------g
                        Chimp  ggg-gctgta---cagagggt-ggg------cg---gg------g---------------g
                      Gorilla  ggg-gctgta---cagagggt-ggg------cg---gg------g---------------g
                    Orangutan  ggg-gctcta---cagagggc-ggg------cg---gc------g---------------g
                       Gibbon  ggg-gctgta---cagagggt-agg------cg---gg------g---------------g
                       Rhesus  ggg-gctgta---cagagggt-ggg------cg---gg------g---------------g
          Crab-eating macaque  ggg-gctgta---cagagggt-ggg------cg---gg------g---------------g
                       Baboon  ggg-gctgta---cagagggt-ggg------cg---gg------g---------------g
                 Green monkey  ggg-gctgta---cagagggt-ggg------cg---gg------g---------------g
                     Marmoset  ggg-gctgta---cagagggt-ggg------cg---gg------a---------------g
              Squirrel monkey  ggg-gctgta---cagagggt-ggg------cg---gg------a---------------g
                     Bushbaby  ggg-aat-tacaccagacgat-gga------aa---gg------ggac---tct-----tg
           Chinese tree shrew  gggaactgga---cggtgggt-agaggcatcgg---aa------a---------------g
                     Squirrel  gaggattatt---gagaggat-gga------aa---ggcagtttgctt--ggga-----ag
       Lesser Egyptian jerboa  agggactgaa---cagaagat-gga------ag---tg------act-----aa-----ag
                 Prairie vole  aaggtctaca---cggaagac-gga------ag---gc------agct--ggac-----ag
              Chinese hamster  aaggactaca---cagaggat-gga------gg---gg------agct--ggac-----ag
               Golden hamster  aagcacaaca---cagaggat-gga------gg---ga------agct--ggac-----ag
                        Mouse  aaggact--------gaagat-gga------gg---gc------atct--ggac-----ag
                          Rat  aagcact--------gaagat-gga------ag---gg------atct--ggat-----ag
               Naked mole-rat  agggattata---caggggtt-gga------aa---gg------ggctt-ggaa-----ag
                   Guinea pig  aggtactatt---cagaggtt-gga------aa---ga------ggttg-gaaa-----gg
                   Chinchilla  aggccgca-----cggagggt-gcg------aa---gc------ggctt-gg---------
             Brush-tailed rat  ggttggaa-----aggagctt-gga------aa---ga------gaatt------------
                         Pika  -------------ctggggag-gga------ag---gg------cact-----c-----ga
                          Pig  ggggattata---cagaggat-gaa------aa---gg------ggactc---------ag
                       Alpaca  ggggattata---cagagaat-gaa------aa---gg------agactcagga-----aa
               Bactrian camel  ggggattata---cagaggat-gaa------aa---gg------agactcagaa-----aa
                      Dolphin  ggggattata---cagaggat-gaa------aa---gg------ggactcataa-----ag
                 Killer whale  ggggattata---cagaggat-gaa------aa---gg------ggactcataa-----ag
             Tibetan antelope  gggaaacata---cagag--taaaa------aa---gg------agactcagaa-----ag
                          Cow  gagaaacata---cagaggat-aaa------aa---gg------ggactcagaa-----ag
                        Sheep  gggaaacata---cagag--t-aaa------aa---gg------ggactcagaa-----ag
                Domestic goat  gggaaacata---cagag--t-aaa------aa---gg------ggactcagaa-----ag
                        Horse  ggggataata---cggagaaa-gaa------aa---gg------ggactcagaa-----ag
             White rhinoceros  ggcg-ttata---cagagaac-gaa------aa---gg------ggactcagaa-----ag
                          Cat  ggggattata---cagaggat-gaa------aa---gg------ggactcacaa-----cg
                          Dog  ggggattata---ccga-cac-gaa------ga---gg------agactggcaa-----ag
                      Ferret   gaggattata---cagaggat-gaa------ta---gg------ggactcacaa-----ag
                        Panda  ggggattata---cagaggat-gaa------aa---gg------ggactcacta-----ag
               Pacific walrus  ggggattata---cagaggat-gaa------aa---gg------ggactcacaa-----ag
                 Weddell seal  ggggattata---cagaggat-gaa------aa---gg------ggactcacaa-----ag
             Black flying-fox  agggactata---tagagaat-gaa------aa---gg------agactc---------aa
                      Megabat  agggactata---tagagaat-gaa------aa---gg------agactc---------aa
                Big brown bat  ggggatcatc---cagagaac-gaa------aa---gg------ggactcggaa-----ag
         David's myotis (bat)  gagg-ttata---ccgagaa--gag------aa---gg------ggactcggaa-----ag
                     Microbat  gggc-ttata---ccgagaa--gag------aa---gg------ggactcggaa-----ag
                        Shrew  agggaccata---cagaggat-gac------cg---gg------gg--tctgaa-----ag
              Star-nosed mole  ggggattata---cagaggat-gaa------aa---gg------ggactctgaa-----ag
                     Elephant  gggggtta-----gaatggat-gag------aa---gg------gaactcagaa-----at
          Cape elephant shrew  gagggttacg---gagtggat-gag------ag---gg------ggtcttagaa-----at
                      Manatee  cgggattaca---gagtggtt-gag------aa---gg------ggactcagaa-----at
             Cape golden mole  gaagaataca---gagaagat-gag------aagaggg------gctc-------------
                       Tenrec  ggggaaccca---gagtgcat-gag------gaggagg------ggcctgggga-----ct
                     Aardvark  aggggacgcg---gggtggac-gag------aa---gg------gggctccgaa-----gc
                    Armadillo  aggaattata---gggagggt-aag------ga---gg------ggacacagcc-----ag
              Tasmanian devil  agggtccagc---ctgggtag-gga------tg---ga------gggccacggggtaccag
                     Platypus  gggtggtgag---gcgaaggt-ggg------cg---ga------gggga------------
                  Zebra finch  tgtggccgtg---ggg---------------------------------------------
                      Chicken  tg-ggcggca---gag---------------------------------------------
           American alligator  cgggacagga---gcg---------------------------------------------
               Painted turtle  ----gcaggg---gtg---------------------------------------------
                X. tropicalis  atagtctgtg---cagggg------------------------------------------
                     Hedgehog  =============================================================
                       Rabbit  =============================================================
                  Stickleback  =============================================================
                       Turkey  =============================================================
                 Mallard duck  =============================================================
           Tibetan ground jay  =============================================================
       White-throated sparrow  =============================================================
     Mexican tetra (cavefish)  =============================================================
                    Zebrafish  =============================================================
                       Medaka  =============================================================
                   Budgerigar  =============================================================
                      Opossum  =============================================================
                  Rock pigeon  =============================================================
          Medium ground finch  =============================================================
             Peregrine falcon  =============================================================
                 Saker falcon  =============================================================
                      Wallaby  =============================================================
              Green seaturtle  =============================================================
          Collared flycatcher  =============================================================

Inserts between block 18 and 19 in window
B D              Zebra finch 8bp
B D       American alligator 23bp

Alignment block 19 of 366 in window, 34988951 - 34988952, 2 bps 
B D                     Human  ag
B D                     Chimp  ag
B D                   Gorilla  ag
B D                 Orangutan  gg
B D                    Gibbon  ag
B D                    Rhesus  ag
B D       Crab-eating macaque  ag
B D                    Baboon  ag
B D              Green monkey  ag
B D                  Marmoset  ag
B D           Squirrel monkey  ag
B D                  Bushbaby  ag
           Chinese tree shrew  ag
B D                  Squirrel  ag
       Lesser Egyptian jerboa  ag
                 Prairie vole  ag
B D           Chinese hamster  a-
               Golden hamster  a-
B D                     Mouse  ag
B D                       Rat  ag
B D            Naked mole-rat  ag
B D                Guinea pig  ag
B D                      Pika  gg
B D                       Pig  gg
B D                    Alpaca  gg
               Bactrian camel  gg
B D                   Dolphin  gg
                 Killer whale  gg
             Tibetan antelope  gt
B D                       Cow  gg
B D                     Sheep  gg
                Domestic goat  gg
B D                     Horse  ga
B D          White rhinoceros  ga
B D                       Cat  gg
B D                       Dog  gg
B D                   Ferret   gg
B D                     Panda  gg
               Pacific walrus  ga
                 Weddell seal  gg
             Black flying-fox  ag
B D                   Megabat  ag
                Big brown bat  gg
         David's myotis (bat)  gg
B D                  Microbat  gg
              Star-nosed mole  gg
B D                  Elephant  gg
          Cape elephant shrew  ga
B D                   Manatee  gg
B D                    Tenrec  ga
                     Aardvark  cc
B D                 Armadillo  ga
B D           Tasmanian devil  ag
B D                     Shrew  --
B D                  Hedgehog  ==
B D                    Rabbit  ==
            Cape golden mole  --
B D               Stickleback  ==
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                 Zebrafish  ==
B D                    Medaka  ==
B D             X. tropicalis  ==
  D            Painted turtle  --
B D        American alligator  ==
B D                Budgerigar  ==
B D                   Opossum  ==
                  Chinchilla  --
  D               Rock pigeon  ==
B D       Medium ground finch  ==
  D          Peregrine falcon  ==
  D              Saker falcon  ==
B D                   Wallaby  ==
            Brush-tailed rat  --
B D                  Platypus  ==
  D           Green seaturtle  ==
  D       Collared flycatcher  ==

Alignment block 20 of 366 in window, 34988953 - 34988953, 1 bps 
B D                     Human  a
B D                     Chimp  a
B D                   Gorilla  a
B D                 Orangutan  a
B D                    Gibbon  a
B D                    Rhesus  a
B D       Crab-eating macaque  a
B D                    Baboon  a
B D              Green monkey  a
B D                  Marmoset  a
B D           Squirrel monkey  a
B D                  Bushbaby  a
           Chinese tree shrew  a
B D                  Squirrel  a
       Lesser Egyptian jerboa  a
                 Prairie vole  a
B D                     Mouse  a
B D                       Rat  a
B D            Naked mole-rat  a
B D                Guinea pig  a
B D                      Pika  a
B D                       Pig  a
B D                    Alpaca  a
               Bactrian camel  a
B D                   Dolphin  a
                 Killer whale  a
             Tibetan antelope  a
B D                       Cow  a
B D                     Sheep  a
                Domestic goat  a
B D                       Cat  a
B D                       Dog  a
                 Weddell seal  a
             Black flying-fox  a
B D                   Megabat  a
                Big brown bat  a
         David's myotis (bat)  a
B D                  Microbat  a
              Star-nosed mole  a
B D                  Elephant  a
          Cape elephant shrew  a
B D                   Manatee  a
B D                    Tenrec  a
                     Aardvark  a
B D                 Armadillo  a
B D           Tasmanian devil  a
B D        American alligator  g
  D            Painted turtle  g
              Golden hamster  -
B D                     Shrew  -
B D                  Hedgehog  =
B D                    Rabbit  =
            Cape golden mole  -
B D               Stickleback  =
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                 Zebrafish  =
B D                    Medaka  =
B D             X. tropicalis  =
B D                Budgerigar  =
B D                   Opossum  =
                  Chinchilla  -
  D               Rock pigeon  =
B D       Medium ground finch  =
  D          Peregrine falcon  =
  D              Saker falcon  =
B D                   Wallaby  =
            Brush-tailed rat  -
B D                  Platypus  =
B D           Chinese hamster  -
  D           Green seaturtle  =
B D                   Ferret   -
  D       Collared flycatcher  =
              Pacific walrus  -
B D                     Panda  -
B D          White rhinoceros  -
B D                     Horse  -

Inserts between block 20 and 21 in window
B D                      Cat 7bp
B D                      Dog 5bp
                Weddell seal 3bp

Alignment block 21 of 366 in window, 34988954 - 34988969, 16 bps 
B D                     Human  ttcctggaggc-accg-g
B D                     Chimp  ttcctggaggc-accg-g
B D                   Gorilla  ttcctggaggc-accg-g
B D                 Orangutan  ttcctggaggc-gctg-g
B D                    Gibbon  ttcctggaggc-gccg-g
B D                    Rhesus  ctcctggaggc-gccg-g
B D       Crab-eating macaque  ctcctggaggc-gccg-g
B D                    Baboon  ctcctggaggc-gccg-g
B D              Green monkey  ctcctggaggc-gccg-g
B D                  Marmoset  ctcgtggaggc-accg-g
B D           Squirrel monkey  ctcctggaggc-accg-g
B D                  Bushbaby  gtcctggaggt-gctgca
           Chinese tree shrew  atcctgcaggt-gct--a
B D                  Squirrel  atcatggaggt-gtca--
       Lesser Egyptian jerboa  atcaccgagtt-gtca--
                 Prairie vole  ctcaggaaggt-gtca--
B D           Chinese hamster  ------------atca--
               Golden hamster  ------------atca--
B D                     Mouse  ctcaggaaggt-gtta--
B D                       Rat  ctcacgaaggt-gtta--
B D            Naked mole-rat  atcatggaggt-gccact
B D                Guinea pig  accatgaaggt-gccact
                   Chinchilla  --cgggcgggt-gcc-ct
             Brush-tailed rat  ---atggaggt-gccact
B D                      Pika  ttcccggaggg-gctgcg
B D                       Pig  agcatgaaggt-gctaaa
B D                    Alpaca  attatggaggt-gctaaa
               Bactrian camel  attatggaggt-gctaaa
B D                   Dolphin  atcttggaggt-gctaaa
                 Killer whale  atcttggaggt-gctaaa
             Tibetan antelope  attatggaggt-gctaaa
B D                       Cow  attatggaggt-gctaaa
B D                     Sheep  attatggaggt-gttaaa
                Domestic goat  attatggaggt-gctaaa
B D                     Horse  atcaaggaggtggctaca
B D          White rhinoceros  atcatgggggc-gcta-a
B D                       Cat  atcgtggaggc-gctaaa
B D                       Dog  agttaggacgt-gctaac
B D                   Ferret   aatgaggaggc-gctaaa
B D                     Panda  aatgaggagac-gctaaa
               Pacific walrus  attgaggaggc-gctaaa
                 Weddell seal  aatgaggaggc-gctaaa
             Black flying-fox  cccatggaggt-cccaaa
B D                   Megabat  cccatggaggt-gccaaa
                Big brown bat  atcgtggaggc-gctaca
         David's myotis (bat)  atcagggcggc-gctagg
B D                  Microbat  atcaggg-ggc-gctaga
B D                     Shrew  -----gaagtt-gctaaa
              Star-nosed mole  accatggagat-gctaaa
B D                  Elephant  atcacagaggt-gctgag
          Cape elephant shrew  at---ggagac-gctgag
B D                   Manatee  atcacggaggt-gttgag
             Cape golden mole  ----------t-gctgag
B D                    Tenrec  atcgtggagat-gctaca
                     Aardvark  gtcaccacggg-gctgag
B D                 Armadillo  attgtgcaggt-gctgag
B D           Tasmanian devil  ---tgagagaa-atcaga
B D               Zebra finch  -------atgc-ccggg-
B D        American alligator  agtgtgggtgg-gcggg-
  D            Painted turtle  gtactggggag-atggg-
B D                  Hedgehog  ==================
B D                    Rabbit  ==================
B D               Stickleback  ==================
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  ==================
B D             X. tropicalis  ==================
B D                Budgerigar  ==================
B D                   Opossum  ==================
  D               Rock pigeon  ==================
B D       Medium ground finch  ==================
  D          Peregrine falcon  ==================
  D              Saker falcon  ==================
B D                   Wallaby  ==================
B D                  Platypus  ==================
  D           Green seaturtle  ==================
  D       Collared flycatcher  ==================

Inserts between block 21 and 22 in window
B D                 Squirrel 17bp
      Lesser Egyptian jerboa 17bp
                Prairie vole 12bp
B D          Chinese hamster 23bp
              Golden hamster 61bp
B D                    Mouse 3bp
B D                      Rat 3bp

Alignment block 22 of 366 in window, 34988970 - 34988976, 7 bps 
B D                     Human  -----cct--gggc
B D                     Chimp  -----cct--gggc
B D                   Gorilla  -----cct--gggc
B D                 Orangutan  -----cct--gggc
B D                    Gibbon  -----cct--gggc
B D                    Rhesus  -----cct--gggc
B D       Crab-eating macaque  -----cct--gggc
B D                    Baboon  -----tct--gggc
B D              Green monkey  -----cct--gggc
B D                  Marmoset  -----cct--gcgc
B D           Squirrel monkey  -----cctgcgcgc
B D                  Bushbaby  -----cct--gagc
           Chinese tree shrew  -----tgt--ggga
B D            Naked mole-rat  -----cct--gagg
B D                Guinea pig  -----cct--ggga
                   Chinchilla  -----cct--ggga
             Brush-tailed rat  -----ccc--ggga
B D                      Pika  -----cct--gggg
B D                       Pig  -----cct--gtaa
B D                    Alpaca  -----cct--ttgg
               Bactrian camel  -----cct--ttgg
B D                   Dolphin  -----acc--gtgg
                 Killer whale  -----acc--gtgg
             Tibetan antelope  -----att--gtgg
B D                       Cow  -----att--gtgg
B D                     Sheep  -----att--gtgg
                Domestic goat  -----att--gtgg
B D                     Horse  -----cct--gggg
B D          White rhinoceros  -----ccc--tggg
B D                       Cat  -----att--ggga
B D                       Dog  -----cct--gggg
B D                   Ferret   -----cct--ggaa
B D                     Panda  -----cct--gggg
               Pacific walrus  -----cct--gggg
                 Weddell seal  -----cct--gggg
             Black flying-fox  -----cat--ga--
B D                   Megabat  -----cat--ga--
                Big brown bat  -----cct--gggg
         David's myotis (bat)  -----cct--gggg
B D                  Microbat  -----cct--gggg
B D                     Shrew  -----tcc-----g
              Star-nosed mole  -----cct--g-gg
B D                  Elephant  -----cct--gggg
          Cape elephant shrew  -----cct--gggg
B D                   Manatee  -----cct--gggg
             Cape golden mole  -----cct--gggg
B D                    Tenrec  -----ttt--ggag
                     Aardvark  -----cct--gtgg
B D                 Armadillo  -----gct--gt-g
B D           Tasmanian devil  -----cgc--agaa
B D               Zebra finch  -----gc-------
B D        American alligator  -----cc-------
  D            Painted turtle  actgcgc-------
              Golden hamster  ==============
      Lesser Egyptian jerboa  ==============
B D                       Rat  ==============
                Prairie vole  ==============
B D                     Mouse  ==============
B D                  Hedgehog  ==============
B D                    Rabbit  ==============
B D               Stickleback  ==============
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  ==============
B D             X. tropicalis  ==============
B D                Budgerigar  ==============
B D                   Opossum  ==============
  D               Rock pigeon  ==============
B D       Medium ground finch  ==============
  D          Peregrine falcon  ==============
  D              Saker falcon  ==============
B D                   Wallaby  ==============
B D                  Platypus  ==============
B D           Chinese hamster  ==============
  D           Green seaturtle  ==============
  D       Collared flycatcher  ==============
B D                  Squirrel  ==============

Inserts between block 22 and 23 in window
B D              Zebra finch 3bp
B D       American alligator 1bp
  D           Painted turtle 1bp

Alignment block 23 of 366 in window, 34988977 - 34988983, 7 bps 
B D                     Human  agagcc---a
B D                     Chimp  agagcc---a
B D                   Gorilla  agagcc---a
B D                 Orangutan  agagcc---a
B D                    Gibbon  agagcc---a
B D                    Rhesus  agagcc---a
B D       Crab-eating macaque  agagcc---a
B D                    Baboon  agagcc---a
B D              Green monkey  agagcc---a
B D                  Marmoset  agagct---a
B D           Squirrel monkey  agagct---a
B D                  Bushbaby  cgaact---a
           Chinese tree shrew  agggct---c
B D            Naked mole-rat  agaggc---c
B D                Guinea pig  agagcg---a
                   Chinchilla  agggcc---g
             Brush-tailed rat  aaagcc---a
B D                      Pika  acagcc----
B D                       Pig  agaact---a
B D                    Alpaca  agaaca---a
               Bactrian camel  agaaca---a
B D                   Dolphin  agaact---g
                 Killer whale  agaact---g
             Tibetan antelope  agaact---a
B D                       Cow  agaact---a
B D                     Sheep  agaact---a
                Domestic goat  agaact---a
B D                     Horse  agaaat---a
B D          White rhinoceros  aga------a
B D                       Cat  agaact---a
B D                       Dog  agaagt---a
B D                   Ferret   acaact---a
B D                     Panda  agaact---a
               Pacific walrus  agaact---a
                 Weddell seal  agaact---a
             Black flying-fox  -gaact---a
B D                   Megabat  -gaact---a
                Big brown bat  agaact---a
         David's myotis (bat)  -gagct---a
B D                  Microbat  -gaacc---g
B D                     Shrew  agaacc---a
              Star-nosed mole  agagct---a
B D                  Elephant  agaact---g
          Cape elephant shrew  gcagct---a
B D                   Manatee  agaatt---a
             Cape golden mole  agaagt---a
B D                    Tenrec  ggaaga---g
                     Aardvark  ---acc---a
B D                 Armadillo  agaact---a
B D           Tasmanian devil  aaagtc---a
B D               Zebra finch  -gggac---a
B D        American alligator  --ggac---a
  D           Green seaturtle  agagtc---a
  D            Painted turtle  ggggttggga
              Golden hamster  ==========
      Lesser Egyptian jerboa  ==========
B D                       Rat  ==========
                Prairie vole  ==========
B D                     Mouse  ==========
B D                  Hedgehog  ==========
B D                    Rabbit  ==========
B D               Stickleback  ==========
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  ==========
B D             X. tropicalis  ==========
B D                Budgerigar  ==========
B D                   Opossum  ==========
  D               Rock pigeon  ==========
B D       Medium ground finch  ==========
  D          Peregrine falcon  ==========
  D              Saker falcon  ==========
B D                   Wallaby  ==========
B D                  Platypus  ==========
B D           Chinese hamster  ==========
  D       Collared flycatcher  ==========
B D                  Squirrel  ==========

Inserts between block 23 and 24 in window
B D           Naked mole-rat 1bp
B D               Guinea pig 2bp
                  Chinchilla 1bp
            Brush-tailed rat 1bp
B D          Tasmanian devil 11bp

Alignment block 24 of 366 in window, 34988984 - 34989002, 19 bps 
B D                     Human  tc---cg-----ttt-c-cct---------------cggggg---------------ag
B D                     Chimp  tg---cg-----ttt-c-cct---------------cggggg---------------ag
B D                   Gorilla  tc---ca-----ttt-c-cct---------------cggggg---------------ag
B D                 Orangutan  tc---cg-----ttt-c-cct---------------cagagg---------------ag
B D                    Gibbon  tc---cg-----ttt-c-cct---------------cagggg---------------ag
B D                    Rhesus  tc---cg-----ttt-c-cct---------------caggga---------------ag
B D       Crab-eating macaque  tc---cg-----ttt-c-cct---------------caggga---------------ag
B D                    Baboon  tc---cg-----ttt-c-cct---------------caggga---------------ag
B D              Green monkey  tc---cg-----ttt-c-cct---------------caggga---------------ag
B D                  Marmoset  tc---cc-----ctt-c-cct---------------cacggg---------------ag
B D           Squirrel monkey  cc---cg-----ctt-c-cct---------------cagggg---------------ag
B D                  Bushbaby  tc---ag-----gttac-cct---------------caccgg---------------ag
           Chinese tree shrew  cc---ag-----gtc-a-c-----------------tgacaa---------------ag
B D                  Squirrel  -c---ag-----ttt-a-ctg--------------ataaagg---------------ag
       Lesser Egyptian jerboa  -c---ag-----gtt-atctc------------ctgcaaatg---------------ag
                 Prairie vole  -c---ca-----gtt-a-ctatagt--------gtgcagaga---------------gg
B D           Chinese hamster  ------------------cta------------gtgcagagc---------------gg
B D                     Mouse  ------------gtt-a-cta------------gcgcagag----------------ga
B D                       Rat  ------------gtt-a-cta------------gcacagag----------------gg
B D            Naked mole-rat  -c---ag-----gtt-a-cag------------gggcagg-------------------
B D                Guinea pig  -c---tg-----gtt-a-cag------------acggagg-------------------
                   Chinchilla  -c---ag-----gtt-c-cgc------------gcgcagg-------------------
             Brush-tailed rat  -c---ag-----gtt-a-cag------------gcaaagga------------------
B D                       Pig  cc---ca-----att-a-------------------caaagg---------------ag
B D                    Alpaca  c----gg-----gtt-a-------------------caaaga---------------ag
               Bactrian camel  a----gg-----gtt-a-------------------ca---a---------------ag
B D                   Dolphin  ct---ag-----gtt-a-------------------caaagg---------------ag
                 Killer whale  ct---ag-----gtt-a-------------------caaagg---------------ag
             Tibetan antelope  cc---ag-----gtt-a-------------------caaagg---------------aa
B D                       Cow  cc---ag-----gtt-a-------------------caaaga---------------aa
B D                     Sheep  cc---ag-----gtt-a-------------------caaagg---------------aa
                Domestic goat  cc---ag-----gtt-a-------------------caaagg---------------aa
B D                     Horse  cc---ag-----gtt-a-------------------gaaagg---------------ag
B D          White rhinoceros  cc---tg-----gtt-a-------------------taaagg---------------ag
B D                       Cat  cc---ag-----gtt-a-------------------ccaagg---------------ag
B D                       Dog  cc---ag-----gtt-a-------------------caaagg---------------ag
B D                   Ferret   cc---agtgtaaatt-a-------------------ccaagg---------------ag
B D                     Panda  cc---ag-----gtt-a-------------------caaagg---------------ag
               Pacific walrus  cc---ag-----gtt-a-------------------caaagg---------------ag
                 Weddell seal  cc---ag-----gtt-a-------------------caaagg---------------ag
             Black flying-fox  cc---ag-----gtt-a-------------------caaaag---------------ag
B D                   Megabat  cc---ag-----gtt-a-------------------caaaag---------------ag
                Big brown bat  cc---ag-----gtt-a-------------------caaggg---------------ag
         David's myotis (bat)  cc---ag-----gtt-g-------------------caaagg---------------cg
B D                  Microbat  cc---ag-----gtt-g-------------------ccaagg---------------cg
B D                     Shrew  cc---ag-----gcg-a-------------------cagcgg---------------ag
              Star-nosed mole  ca---ag-----gta-t-------------------caaagg---------------ag
B D                  Elephant  cc---ca-----ggt-g-ctg---------------acaagt---------------gg
          Cape elephant shrew  cc---ca-----ggt-g-ctg---------------atga------------------g
B D                   Manatee  ct---ta-----ggt-g-ctg---------------acaagg---------------ag
             Cape golden mole  cc---ca-----ggt-g-ctg---------------ac-ata---------------gg
B D                    Tenrec  ctgggca-----gga-g-agg---------------ccaagg---------------gg
                     Aardvark  ct---ca-----ggt-a-ccg---------------acaagg---------------gc
B D                 Armadillo  cc---cg-----ggt-a-ctg---------------a-aagg---------------aa
B D           Tasmanian devil  ca---cg-----gtc-c-------------------caaagg---------------ta
B D               Zebra finch  ----------------------cct---ccctctgcctgggg---------------ac
B D        American alligator  ----------------------cctgggctctgtgcggggggtg----ggtctgc--ag
  D           Green seaturtle  ----------------------cacgccggccctgccggtggtggagaaaaacgaggaa
  D            Painted turtle  ----------------------tgtagggggctgcacgggggtgtaggggactgc--at
              Golden hamster  ===========================================================
B D                      Pika  -----------------------------------------------------------
B D                  Hedgehog  ===========================================================
B D                    Rabbit  ===========================================================
B D               Stickleback  ===========================================================
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  ===========================================================
B D             X. tropicalis  ===========================================================
B D                Budgerigar  ===========================================================
B D                   Opossum  ===========================================================
  D               Rock pigeon  ===========================================================
B D       Medium ground finch  ===========================================================
  D          Peregrine falcon  ===========================================================
  D              Saker falcon  ===========================================================
B D                   Wallaby  ===========================================================
B D                  Platypus  ===========================================================
  D       Collared flycatcher  ===========================================================

Alignment block 25 of 366 in window, 34989003 - 34989015, 13 bps 
B D                     Human  aggtcc-gggg-----ggc
B D                     Chimp  aggtcc-gggg-----ggc
B D                   Gorilla  aggtcc-gggg-----ggc
B D                 Orangutan  aggtcc-gggg-----ggc
B D                    Gibbon  aggtcc-ggag-----ggc
B D                    Rhesus  aggtcc-ggag-----ggc
B D       Crab-eating macaque  aggtcc-ggag-----ggc
B D                    Baboon  aggtcc-agag-----ggc
B D              Green monkey  aggtcc-ggag-----ggc
B D                  Marmoset  aggtcc-ggag-----ggc
B D           Squirrel monkey  aggtcc-ggag-----gga
B D                  Bushbaby  agatca-gaaa-----gga
           Chinese tree shrew  agatca-gaag-----ggc
B D                  Squirrel  agagtg-gaag-----ggc
       Lesser Egyptian jerboa  aggtca-cgcg-----ggc
                 Prairie vole  aggtag-caag-----ggc
B D           Chinese hamster  agatcg-caag-----ggc
B D                     Mouse  taatca-cagg-----ggc
B D                       Rat  tgatca-caag-----ggc
B D            Naked mole-rat  ----aa-ggag-----ggc
B D                Guinea pig  --aacg-gaag-----gcc
                   Chinchilla  gcagcg-gggg-----gcc
             Brush-tailed rat  ggaaca-gaaa-----gcc
B D                      Pika  ------------------c
B D                       Pig  agatca-gaaa-----ggt
B D                    Alpaca  aga-ca-ggaa-----ggt
               Bactrian camel  aga-ca-ggaa-----ggt
B D                   Dolphin  agggca-gaag-----ggt
                 Killer whale  agggca-gaag-----agt
             Tibetan antelope  ggcgca-gaag-----agt
B D                       Cow  agagcaggaag-----agt
B D                     Sheep  agagca-gaag-----agt
                Domestic goat  agagca-gaag-----agt
B D                     Horse  ggagta-gaaa-----ggt
B D          White rhinoceros  ggagca-gaat-----ggt
B D                       Cat  agaggg-ggag-----cat
B D                       Dog  aaagcg-gaaa-----ggt
B D                   Ferret   aaagcg-gaag-----ggt
B D                     Panda  aaagcg-gaag-----ggt
               Pacific walrus  aaagca-gaag-----ggt
                 Weddell seal  aaagca-gaag-----ggt
             Black flying-fox  agaggg-gaag-----ggc
B D                   Megabat  agagcg-gaag-----ggc
                Big brown bat  agggca-gaag-----ggc
         David's myotis (bat)  agagca-gaag-----ggc
B D                  Microbat  agagca-gaag-----ggc
B D                     Shrew  aaagag-gagg-----tat
              Star-nosed mole  agagaa-gagt-----act
B D                  Elephant  agatga-aaag-----ggt
          Cape elephant shrew  agatca-taaa-----agt
B D                   Manatee  agatca-aaac-----ggt
             Cape golden mole  a-----------------t
B D                    Tenrec  a-----------------t
                     Aardvark  agatcc-aaag-----gga
B D                 Armadillo  agttcg-gaag-----ggt
B D           Tasmanian devil  ggagct-gacaaagccagg
B D               Zebra finch  cccttg-ggga-----cac
B D        American alligator  gagtgg-ggga-----agc
  D           Green seaturtle  acggct-caga-----aac
  D            Painted turtle  ggggtt-tggg-----gtg
B D             X. tropicalis  aggaaa-gagc-----agc
              Golden hamster  ===================
B D                  Hedgehog  ===================
B D                    Rabbit  ===================
B D               Stickleback  ===================
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  ===================
B D                Budgerigar  ===================
B D                   Opossum  ===================
  D               Rock pigeon  ===================
B D       Medium ground finch  ===================
  D          Peregrine falcon  ===================
  D              Saker falcon  ===================
B D                   Wallaby  ===================
B D                  Platypus  ===================
  D       Collared flycatcher  ===================

Alignment block 26 of 366 in window, 34989016 - 34989025, 10 bps 
B D                     Human  tctgaaaccc
B D                     Chimp  tctgaaaccc
B D                   Gorilla  tctgaaaccc
B D                 Orangutan  tctgaaacct
B D                    Gibbon  tctgaaaccc
B D                    Rhesus  tctgaaaccc
B D       Crab-eating macaque  tctgaaaccc
B D                    Baboon  tctgaaaccc
B D              Green monkey  tctgaaaccc
B D                  Marmoset  ttggaaacca
B D           Squirrel monkey  tcggaaaccc
B D                  Bushbaby  acttaaactc
           Chinese tree shrew  g-tgaaact-
B D                  Squirrel  acttaaactc
       Lesser Egyptian jerboa  acttactctc
                 Prairie vole  acacagactc
B D           Chinese hamster  tc-----ttc
B D                     Mouse  acttagaatc
B D                       Rat  acttagaatc
B D            Naked mole-rat  acttaagcaa
B D                Guinea pig  acttaa----
                   Chinchilla  gcgtgagcga
             Brush-tailed rat  acttaaacaa
B D                      Pika  gctcgcgctc
B D                       Pig  acttaaactc
B D                    Alpaca  actta-actc
               Bactrian camel  actta-actc
B D                   Dolphin  acttaaacta
                 Killer whale  acttaaacta
             Tibetan antelope  ------acta
B D                       Cow  ------acta
B D                     Sheep  ------acta
                Domestic goat  ------acta
B D                     Horse  acttaaaccc
B D          White rhinoceros  acttaaactc
B D                       Cat  gcttaaattc
B D                       Dog  gcttgaattc
B D                   Ferret   gcttaaattc
B D                     Panda  gcttaaattc
               Pacific walrus  gcttaaattc
                 Weddell seal  gcttaaattc
             Black flying-fox  acttaaa--c
B D                   Megabat  acttaaa--c
                Big brown bat  ccttacactc
         David's myotis (bat)  cctcaaactc
B D                  Microbat  cctcaaactc
B D                     Shrew  --tttaa--c
              Star-nosed mole  --ttaaa--c
B D                  Elephant  atttaaact-
          Cape elephant shrew  acttcaagtc
B D                   Manatee  atttaaact-
             Cape golden mole  acttcagcgc
B D                    Tenrec  tcttccactc
                     Aardvark  acctcggttc
B D                 Armadillo  acttaaaatt
B D           Tasmanian devil  actgaaactc
B D                  Platypus  gcagagacca
B D               Zebra finch  --ct--cccc
B D        American alligator  --ccgaacgc
  D           Green seaturtle  --caggcggc
  D            Painted turtle  --tagggggc
B D             X. tropicalis  attaaggttc
              Golden hamster  ==========
B D                  Hedgehog  ==========
B D                    Rabbit  ==========
B D               Stickleback  ==========
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  ==========
B D                Budgerigar  ==========
B D                   Opossum  ==========
  D               Rock pigeon  ==========
B D       Medium ground finch  ==========
  D          Peregrine falcon  ==========
  D              Saker falcon  ==========
B D                   Wallaby  ==========
  D       Collared flycatcher  ==========

Inserts between block 26 and 27 in window
      Lesser Egyptian jerboa 8bp
                Prairie vole 8bp
B D          Chinese hamster 5bp
B D                    Mouse 5bp
B D                      Rat 5bp
B D           Naked mole-rat 6bp
                  Chinchilla 6bp
            Brush-tailed rat 6bp
B D                     Pika 2bp
B D                      Pig 2bp
B D                   Alpaca 2bp
              Bactrian camel 2bp
B D                  Dolphin 2bp
                Killer whale 2bp
            Tibetan antelope 2bp
B D                      Cow 2bp
B D                    Sheep 2bp
               Domestic goat 2bp
B D                    Horse 2bp
B D         White rhinoceros 2bp
B D                      Cat 2bp
B D                      Dog 2bp
B D                  Ferret  2bp
B D                    Panda 2bp
              Pacific walrus 2bp
                Weddell seal 2bp
            Black flying-fox 2bp
B D                  Megabat 2bp
               Big brown bat 2bp
        David's myotis (bat) 2bp
B D                 Microbat 2bp
B D                    Shrew 2bp
             Star-nosed mole 2bp
         Cape elephant shrew 6bp
B D                  Manatee 3bp
            Cape golden mole 6bp
B D                   Tenrec 6bp
                    Aardvark 6bp
B D                Armadillo 6bp
B D                 Platypus 7bp
B D              Zebra finch 5bp
B D       American alligator 10bp
  D          Green seaturtle 11bp
  D           Painted turtle 4bp

Alignment block 27 of 366 in window, 34989026 - 34989036, 11 bps 
B D                     Human  --ggcatccgt----gg
B D                     Chimp  --ggcatccgt----gg
B D                   Gorilla  --ggcatccgt----gg
B D                 Orangutan  --ggcatccgt----gg
B D                    Gibbon  --agcatccgt----gg
B D                    Rhesus  --ggcatccgt----ga
B D       Crab-eating macaque  --ggtatccgt----ga
B D                    Baboon  --ggcatccgt----gg
B D              Green monkey  --ggcatccgt----gg
B D                  Marmoset  --ggggtccgt----ga
B D           Squirrel monkey  ---gggtccgt----ag
B D                  Bushbaby  --tgcgtgtcttttgga
           Chinese tree shrew  ---gcatgtgtatcgag
       Lesser Egyptian jerboa  ---------gtc---cg
                 Prairie vole  ---------gtc---ct
B D           Chinese hamster  ------tctatc---ct
               Golden hamster  ------tctatc---ct
B D                     Mouse  ------tctatc---cg
B D                       Rat  ------tctatc---cg
B D            Naked mole-rat  ------tctacc---cg
                   Chinchilla  ------cccgtc---cg
             Brush-tailed rat  ------tctatt---cg
B D                       Pig  --cacatctac------
B D                    Alpaca  --cacgtctac------
               Bactrian camel  --cacgtctac------
B D                   Dolphin  --ctcatctac------
                 Killer whale  --ctcatctac------
             Tibetan antelope  --cacatctac------
B D                       Cow  --cacatctac------
B D                     Sheep  --cacatctac------
                Domestic goat  --cacatctac------
B D                     Horse  --catgtctac------
B D          White rhinoceros  --catgtcgac------
B D                       Cat  --catgcctac------
B D                       Dog  --catgtctcg------
B D                   Ferret   --catgtctat------
B D                     Panda  --catgtctat------
               Pacific walrus  --catgtctat------
                 Weddell seal  --catgtctat------
             Black flying-fox  --catatctaa------
B D                   Megabat  --catatctaa------
                Big brown bat  --cgtgtct-c------
         David's myotis (bat)  --cgtgtccgc------
B D                  Microbat  --cgtgtccgc------
B D                     Shrew  --cttggcgac------
              Star-nosed mole  --tgcaacgac------
B D                  Elephant  ---ctatcaa-------
          Cape elephant shrew  --actgctga-------
B D                   Manatee  --actatcga-------
             Cape golden mole  --tctatcga-------
B D                    Tenrec  --gctctcg--------
                     Aardvark  --acgctcga-------
B D                 Armadillo  --tctatcaa-------
B D           Tasmanian devil  --ggtgcctgt------
B D                  Platypus  --gagg-----------
B D               Zebra finch  --tgag-----------
B D        American alligator  --tgcg-----------
  D           Green seaturtle  --tgca-----------
  D            Painted turtle  --tggg-----------
B D             X. tropicalis  agggtataaag------
B D                      Pika  =================
B D                  Hedgehog  =================
B D                Guinea pig  -----------------
B D                    Rabbit  =================
B D               Stickleback  =================
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  =================
B D                Budgerigar  =================
B D                   Opossum  =================
  D               Rock pigeon  =================
B D       Medium ground finch  =================
  D          Peregrine falcon  =================
  D              Saker falcon  =================
B D                   Wallaby  =================
  D       Collared flycatcher  =================
B D                  Squirrel  -----------------

Inserts between block 27 and 28 in window
B D                      Pig 3bp
B D                   Alpaca 3bp
              Bactrian camel 3bp
B D                  Dolphin 3bp
                Killer whale 3bp
            Tibetan antelope 3bp
B D                      Cow 3bp
B D                    Sheep 3bp
               Domestic goat 3bp
B D                    Horse 3bp
B D         White rhinoceros 3bp
B D                      Cat 3bp
B D                      Dog 3bp
B D                  Ferret  3bp
B D                    Panda 3bp
              Pacific walrus 3bp
                Weddell seal 3bp
            Black flying-fox 3bp
B D                  Megabat 3bp
               Big brown bat 3bp
        David's myotis (bat) 3bp
B D                 Microbat 3bp
B D                    Shrew 3bp
             Star-nosed mole 3bp
B D          Tasmanian devil 2bp

Alignment block 28 of 366 in window, 34989037 - 34989053, 17 bps 
B D                     Human  ggtctg--------ttagagat---tcc
B D                     Chimp  ggtctg--------ttagagat---tcc
B D                   Gorilla  ggtctg--------ttagagat---tcc
B D                 Orangutan  ggtctg--------ttagagat---tcc
B D                    Gibbon  ggtctg--------ttagagat---tcc
B D                    Rhesus  ggtctg--------ttagagat---tcc
B D       Crab-eating macaque  ggtctg--------ttagagat---tcc
B D                    Baboon  ggtctg--------ttagagat---tcc
B D              Green monkey  ggtctg--------ttagagat---tcc
B D                  Marmoset  agtctg--------ttagagat---tcc
B D           Squirrel monkey  agtctg--------ttagagat---tcc
B D                  Bushbaby  ggtctg-------ctttgagat---cca
           Chinese tree shrew  gtcctt--------tttgagat---tc-
B D                  Squirrel  -tacaa-------acatgagat---tca
       Lesser Egyptian jerboa  ggtctg-------ttttgagtc---aca
                 Prairie vole  ggtctg-------tttcgtgct---acc
B D           Chinese hamster  ggtctg-------ttttgtgtt---aca
               Golden hamster  ggtctg-------tttcgtgtt---aca
B D                     Mouse  gctctg-------ttttgtgtt---aca
B D                       Rat  ggtc-g-------gattgtgtt---aca
B D            Naked mole-rat  ggtctg-------tgctaagat---tca
B D                Guinea pig  tgtctg-------ttctgggat---cca
                   Chinchilla  ggtctg-------tcccgaggt---tca
             Brush-tailed rat  ggtctg-------ttctgagat---taa
B D                      Pika  --tctg-------c----agat---tca
B D                       Pig  agtctg-------ttttgagat---t--
B D                    Alpaca  ggtctg-------ttttgatat---cca
               Bactrian camel  ggtctg-------ttttgatat---cca
B D                   Dolphin  ggtctg-------ttttgagat---tca
                 Killer whale  ggtctg-------ttttgagat---tca
             Tibetan antelope  gttcta-------ttttgagat---tca
B D                       Cow  ggccta-------ttttgagat---tca
B D                     Sheep  gttcta-------ttttgagat---tca
                Domestic goat  gttcta-------ttttgagat---tca
B D                     Horse  ggtctg-------ttttgagat---t--
B D          White rhinoceros  ggtccg-------ttttgaatt---t--
B D                       Cat  ggtctg-------ttttg---t---t--
B D                       Dog  ggtctg-------ttttg---t---t--
B D                   Ferret   ggtctg-------ttttg---t---t--
B D                     Panda  ggtctg-------ttttg---t---t--
               Pacific walrus  ggtctg-------ttttg---t---a--
                 Weddell seal  ggtctg-------ttttg---t---t--
             Black flying-fox  ggtctg-------ttttgaact---tca
B D                   Megabat  ggtctg-------ttttgaact---tca
                Big brown bat  ggcctg-------ttt------------
         David's myotis (bat)  ggcctg-------ctttgaaat---cca
B D                  Microbat  ggcctg-------ttgtgaaat---cca
B D                  Hedgehog  gatctg-------ttttgagat---tca
B D                     Shrew  gctctg-------tttcgacac---tca
              Star-nosed mole  ggcctg-------tttagagat---tca
B D                  Elephant  gatcat-------ttttgagat---tca
          Cape elephant shrew  ggtctt-------atttgacgt---tta
B D                   Manatee  ggtctt-------ttttgagat---tca
             Cape golden mole  ggtctt-------ttttgtgat---tca
B D                    Tenrec  ggtcat-------ttttgagat---tca
                     Aardvark  ggacttg------ccctgagac---tca
B D                 Armadillo  ggtctg-------ttttgcgat---tcg
B D           Tasmanian devil  ttccta-------taatagaac---tct
B D                  Platypus  ------ggcaaagatcagagag---ctg
B D               Zebra finch  ggaccc-------cttggggacacc---
B D        American alligator  gggcga-------ctggggtct------
  D           Green seaturtle  gatgta-------tttgttttt------
  D            Painted turtle  ggtgta-------ggggactcc------
B D             X. tropicalis  -----g-------tacagagac---gac
B D                    Rabbit  ============================
B D               Stickleback  ============================
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  ============================
B D                Budgerigar  ============================
B D                   Opossum  ============================
  D               Rock pigeon  ============================
B D       Medium ground finch  ============================
  D          Peregrine falcon  ============================
  D              Saker falcon  ============================
B D                   Wallaby  ============================
  D       Collared flycatcher  ============================

Inserts between block 28 and 29 in window
B D              Zebra finch 120bp

Alignment block 29 of 366 in window, 34989054 - 34989071, 18 bps 
B D                     Human  gt-t---------a-------------------ggtc-aca----------tcaggcc
B D                     Chimp  gt-t---------a-------------------ggtc-aca----------tcaggcc
B D                   Gorilla  gt-t---------a-------------------ggtc-aca----------tcaggcc
B D                 Orangutan  gt-t---------a-------------------ggtc-acg----------tcaggcc
B D                    Gibbon  gt-t---------a-------------------ggtc-aca----------tcaggcc
B D                    Rhesus  gt-t---------a-------------------ggtc-acg----------tcaggcc
B D       Crab-eating macaque  gt-t---------a-------------------ggtc-acg----------tcaggcc
B D                    Baboon  gt-t---------a-------------------ggtc-acg----------tcaggcc
B D              Green monkey  gt-t---------a-------------------ggtc-acg----------tcaggcc
B D                  Marmoset  gt-t---------a-------------------ggtc-acg----------tcaggcc
B D           Squirrel monkey  gt-t---------a-------------------ggtc-atg----------tcaggcc
B D                  Bushbaby  gt-t---------a-------------------ggtc-atg----------tcaggtc
           Chinese tree shrew  -------------a-------------------ggtg-gtg----------tcagatg
B D                  Squirrel  gt-t---------a-------------------ggcc-atg----------taaggtc
       Lesser Egyptian jerboa  gt-t---------agggccacagtcacagttagggcc-ata----------tcaggtc
                 Prairie vole  gt-t---------a-------------------agcc-atg----------tcaggtc
B D           Chinese hamster  gt-t---------a-------------------agcc-atg----------tcaggtc
               Golden hamster  gt-t---------a-------------------agcc-acg----------tcaggtc
B D                     Mouse  gt-t---------a-------------------aacc-atg----------gcaggtc
B D                       Rat  gt-t---------a-------------------aact-atg----------tcaggtc
B D            Naked mole-rat  ac-t---------a-------------------ggcg-atg----------tcaggtc
B D                Guinea pig  at-t---------a-------------------agtg-atg----------tcagatc
                   Chinchilla  gt-c---------a-------------------ggcg-gcg----------tcgggcc
             Brush-tailed rat  at-t---------t-------------------ggcg-atg----------tcaggtc
B D                      Pika  gt-t---------a------------------gggtc-acc----------tcaggtc
B D                       Pig  gt-t---------a-------------------ggtc-aca----------tcaggtc
B D                    Alpaca  gt-t---------a-------------------ggtc-aca----------tcaggtc
               Bactrian camel  gt-t---------a-------------------ggtc-aca----------tcaggtc
B D                   Dolphin  gt-t---------a-------------------ggtc-ata----------tcaggtc
                 Killer whale  gt-t---------a-------------------ggtc-ata----------tcaggtc
             Tibetan antelope  gt-t---------g-------------------ggtc-aca----------tcaggtc
B D                       Cow  gt-t---------a-------------------ggtc-aca----------tcaggtc
B D                     Sheep  gt-t---------g-------------------ggtc-aca----------tcaggtc
                Domestic goat  gt-t---------g-------------------ggtc-aca----------tcaggtc
B D                     Horse  -------------c-------------------ggtc-acg----------tcaggtc
B D          White rhinoceros  -------------c--------------agttaggtc-acg----------tcaggtc
B D                       Cat  -------------a-------------------ggtc-acc----------tcaggtc
B D                       Dog  -------------a-------------------ggtc-acc----------tcaggtc
B D                   Ferret   -------------a-------------------ggtc-acc----------tcaggtc
B D                     Panda  -------------a-------------------ggtc-acc----------tcaggtc
               Pacific walrus  -------------g-------------------ggtc-acc----------tcaggtc
                 Weddell seal  -------------a-------------------ggtc-acc----------tcaggtc
             Black flying-fox  gt-t---------a-------------------ggtc-acg----------tcaggtc
B D                   Megabat  gt-t---------a-------------------ggtc-acg----------tcaggtc
                Big brown bat  ---------ttaaa-------------------ggtc-gcg----------cc-----
         David's myotis (bat)  gg-cctgtatgaaa-------------------ggtc-acg----------tc-----
B D                  Microbat  gg-cctgtttgaaa-------------------ggtc-acg----------tc-----
B D                  Hedgehog  ct-t---------a-------------------ggtc-aca----------tcgggtc
B D                     Shrew  gt-t---------a-------------------a------------------cgggtc
              Star-nosed mole  gc-t---------a-------------------ggtc-aca----------tcaggtc
B D                  Elephant  gt-t---------g-------------------agtc-atg----------taaggtc
          Cape elephant shrew  gtgt---------g-------------------tgcc-atg----------tcaggtc
B D                   Manatee  gt-t---------t-------------------ggtc-atg----------tcaggtc
             Cape golden mole  gt-t---------g-------------------ggtc-atg----------tcaggtc
B D                    Tenrec  gc-t---------g-------------------ggcc-ttg----------ccaggtc
                     Aardvark  gg-a---------g-------------------ggtc-acg----------tcaggtc
B D                 Armadillo  gt-t---------g-------------------ggtc-atc----------tcaggtc
B D           Tasmanian devil  ta-t---------g-------------------gatctata----------ataca--
B D                  Platypus  ag-g---------a-------------------gcag-cgg----------tcagagg
B D        American alligator  ----------------------------------------ggagggttacagcaggtg
  D           Green seaturtle  ---------------------------------------------------tta---a
  D            Painted turtle  ---------------------------------------------------acagggg
B D             X. tropicalis  -----------------------------------tg-aca----------ccgagac
B D                    Rabbit  ==========================================================
B D               Stickleback  ==========================================================
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                 Zebrafish  ==========================================================
B D                    Medaka  ==========================================================
B D                Budgerigar  ==========================================================
B D                   Opossum  ==========================================================
  D               Rock pigeon  ==========================================================
B D       Medium ground finch  ==========================================================
  D          Peregrine falcon  ==========================================================
  D              Saker falcon  ==========================================================
B D                   Wallaby  ==========================================================
  D       Collared flycatcher  ==========================================================

Inserts between block 29 and 30 in window
B D          Tasmanian devil 10bp
B D       American alligator 1bp
  D          Green seaturtle 1bp
  D           Painted turtle 1bp

Alignment block 30 of 366 in window, 34989072 - 34989072, 1 bps 
B D                     Human  a
B D                     Chimp  a
B D                   Gorilla  a
B D                 Orangutan  a
B D                    Gibbon  a
B D                    Rhesus  a
B D       Crab-eating macaque  a
B D                    Baboon  a
B D              Green monkey  a
B D                  Marmoset  a
B D           Squirrel monkey  a
B D                  Bushbaby  a
           Chinese tree shrew  a
B D                  Squirrel  a
       Lesser Egyptian jerboa  a
                 Prairie vole  g
B D           Chinese hamster  a
               Golden hamster  a
B D                     Mouse  a
B D                       Rat  a
B D            Naked mole-rat  a
B D                Guinea pig  a
                   Chinchilla  a
             Brush-tailed rat  a
B D                      Pika  a
B D                       Pig  a
B D                    Alpaca  a
               Bactrian camel  a
B D                   Dolphin  a
                 Killer whale  a
             Tibetan antelope  a
B D                       Cow  a
B D                     Sheep  a
                Domestic goat  a
B D                     Horse  a
B D          White rhinoceros  a
B D                       Cat  a
B D                       Dog  a
B D                   Ferret   a
B D                     Panda  a
               Pacific walrus  a
                 Weddell seal  a
             Black flying-fox  a
B D                   Megabat  a
B D                  Hedgehog  a
B D                     Shrew  a
              Star-nosed mole  a
B D                  Elephant  a
          Cape elephant shrew  a
B D                   Manatee  a
             Cape golden mole  a
B D                    Tenrec  a
                     Aardvark  a
B D                 Armadillo  a
B D                   Opossum  a
B D           Tasmanian devil  a
B D                  Platypus  a
B D             X. tropicalis  a
B D                    Rabbit  =
B D               Stickleback  =
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                 Zebrafish  =
B D                    Medaka  =
  D            Painted turtle  =
B D        American alligator  =
B D                Budgerigar  =
  D               Rock pigeon  =
B D       Medium ground finch  =
  D          Peregrine falcon  =
  D              Saker falcon  =
B D                   Wallaby  =
  D           Green seaturtle  =
  D       Collared flycatcher  =
               Big brown bat  -
        David's myotis (bat)  -
B D                  Microbat  -

Inserts between block 30 and 31 in window
B D                  Manatee 186bp

Alignment block 31 of 366 in window, 34989073 - 34989087, 15 bps 
B D                     Human  ccgcgggg---tcagga-t
B D                     Chimp  ccgcgggg---tcagga-t
B D                   Gorilla  cggcgggg---tcagga-t
B D                 Orangutan  ccgcgggg---tcagga-t
B D                    Gibbon  ccgcgggg---tcagga-t
B D                    Rhesus  ccgcgggg---tcaggg-t
B D       Crab-eating macaque  ccgcgggg---tcaggg-t
B D                    Baboon  ccgcgggg---tcaggg-t
B D              Green monkey  ccgcgggg---tcaggg-t
B D                  Marmoset  ctgcgggg---tcaggg-t
B D           Squirrel monkey  ccgcgggg---tcaggg-t
B D                  Bushbaby  atat---g---tcagg--t
           Chinese tree shrew  actt-cgg---tcaagg-t
B D                  Squirrel  accccaga---tccaag-t
       Lesser Egyptian jerboa  accccagg---ttaagg-g
                 Prairie vole  acctcaga---acaaga-c
B D           Chinese hamster  accccaga---tcaaga-c
               Golden hamster  accccaga---tcaaga-c
B D                     Mouse  atcccagg---tcaaga-c
B D                       Rat  atcccagg---tcaaga-c
B D            Naked mole-rat  acactagg---ctaagg-t
B D                Guinea pig  actctaaa---tcaagg-t
                   Chinchilla  gccctgcg---tcaagg-c
             Brush-tailed rat  accctaga---gcaagg-t
B D                      Pika  acgcca-------ctgg-c
B D                       Pig  attccggg---tcacgg-t
B D                    Alpaca  actccggg---tcaaga-t
               Bactrian camel  actccggg---tcaaga-t
B D                   Dolphin  actccggg---tcacgg-t
                 Killer whale  actccggg---tcacgg-t
             Tibetan antelope  actccggg---tcacgg-t
B D                       Cow  actccggg---tcacgg-t
B D                     Sheep  actccagg---tcacgg-t
                Domestic goat  actccggg---tcacgg-t
B D                     Horse  attccggg---tcaagg-t
B D          White rhinoceros  attccggg---tcaggg-t
B D                       Cat  gtgccggg---tcaagg-t
B D                       Dog  attccggg---tcacga-t
B D                   Ferret   attctggg---tcaaga-t
B D                     Panda  attccggg---tcaaga-t
               Pacific walrus  attccggg---tcaaga-t
                 Weddell seal  attccggg---tcaaga-t
             Black flying-fox  actctggg---tcaagg-t
B D                   Megabat  actctggg---tcaagg-t
B D                  Hedgehog  actccagg---tcgagt-t
B D                     Shrew  tctccagg---tcaggg-t
              Star-nosed mole  actcctga---tcaagg-t
B D                  Elephant  -atgagga---ccaacg-t
          Cape elephant shrew  -cccacaa---tcaagg-t
             Cape golden mole  -ctcaaga---tcaagg-t
B D                    Tenrec  -ctcagga---tccggg--
                     Aardvark  -ctgagtg---tcaagg-t
B D                 Armadillo  ----a--------------
B D                   Opossum  ---ctgcggtttcaagg-g
B D           Tasmanian devil  ---cgaggtcagcaagg-c
B D                  Platypus  -ctgaggg---gaagag--
B D        American alligator  gcaggggg---tggggga-
  D           Green seaturtle  ctggcgac---tggggg--
  D            Painted turtle  atgcgggg---tagggg--
B D             X. tropicalis  ccacaggg---caacgg-c
B D                    Rabbit  ===================
B D               Stickleback  ===================
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                 Zebrafish  ===================
B D                    Medaka  ===================
B D                Budgerigar  ===================
  D               Rock pigeon  ===================
B D       Medium ground finch  ===================
  D          Peregrine falcon  ===================
  D              Saker falcon  ===================
B D                   Wallaby  ===================
B D                   Manatee  ===================
  D       Collared flycatcher  ===================
               Big brown bat  -------------------
        David's myotis (bat)  -------------------
B D                  Microbat  -------------------

Inserts between block 31 and 32 in window
B D                 Elephant 1bp
         Cape elephant shrew 1bp

Alignment block 32 of 366 in window, 34989088 - 34989107, 20 bps 
B D                     Human  aa----ggta------------------aa----g--------ct----aa--atgagg-t---
B D                     Chimp  aa----ggta------------------aa----g--------ct----aa--atgagg-t---
B D                   Gorilla  aa----ggta------------------aa----g--------ct----aa--atgagg-t---
B D                 Orangutan  aa----ggta------------------aa----g--------ct----aa--atgagg-t---
B D                    Gibbon  aa----ggta------------------aa----g--------ct----aa--atgagg-t---
B D                    Rhesus  aa----ggta------------------aa----g--------ct----aa--atgagg-t---
B D       Crab-eating macaque  aa----ggta------------------aa----g--------ct----aa--atgagg-t---
B D                    Baboon  aa----ggta------------------aa----g--------ct----aa--attagg-t---
B D              Green monkey  aa----ggta------------------aa----g--------ct----aa--atgagg-t---
B D                  Marmoset  aa----ggta------------------aa----g--------ct----aa--atgagg-t---
B D           Squirrel monkey  aa----ggta------------------aa----g--------ct----aa--atgagg-t---
B D                  Bushbaby  aa----ggta------------------aa----g--------ct----aa--atcaga-t---
           Chinese tree shrew  ag----ggta------------------aa----g--------c-----aa--atcagg-t---
B D                  Squirrel  aa----agta------------------aa----c--------tt----aa--atcagg-t---
       Lesser Egyptian jerboa  at----ggta------------------aa----g--------gt----aa--atcagg-t---
                 Prairie vole  aa----agta------------------ag----g--------ct----aa--cccagg-c---
B D           Chinese hamster  ag----ggta------------------aa----g--------ct----ac--accagg-c---
               Golden hamster  ag----ggta------------------aa----a--------ct----ac--accagg-c---
B D                     Mouse  aa----ggga------------------aa----g--------ct----aa--accagg-c---
B D                       Rat  aa----ggta------------------aa----a--------ct----aa--atcagg-c---
B D            Naked mole-rat  aa----aata------------------aa----g--------ct----aa--atcagg-t---
B D                Guinea pig  aa----agtg------------------aa----g--------ct----aa--atcaag-t---
                   Chinchilla  ac----agt--------------------a----g--------ct----aa--accagg-c---
             Brush-tailed rat  ac----agta------------------aa----g--------ct----aa--atcagg-t---
B D                      Pika  ag----gg-g------------------ga----g--------ct----ga--gccagg-t---
B D                       Pig  aa----tata------------------aa----g--------ct----aa--atcagg-t---
B D                    Alpaca  aa----ggta------------------aa----g--------ct----ca--ttcagg-t---
               Bactrian camel  aa----ggta------------------aa----g--------ct----ca--ttcagg-t---
B D                   Dolphin  aa----ggta------------------aa----g--------ct----aa--atcagg-t---
                 Killer whale  aa----ggta------------------aa----g--------ct----aa--atcagg-t---
             Tibetan antelope  aa----ggta------------------aa----g--------ct----aa--atcagg-t---
B D                       Cow  aa----ggta------------------aa----g--------ct----aa--atcagg-t---
B D                     Sheep  aag---ggta------------------aa----g--------ct----aa--atcagg-t---
                Domestic goat  aa----ggta------------------aa----g--------ct----aa--atcagg-t---
B D                     Horse  aa----ggta------------------aa----g--------ct----aa--atcagg-t---
B D          White rhinoceros  aa----ggta------------------aa----g--------ct----aa--atcagg-t---
B D                       Cat  aa----ggta------------------aa----g--------ct----aa--atcagg-t---
B D                       Dog  aa----ggta------------------aa----g--------cc----ga--atcagg-t---
B D                   Ferret   aa----ggta------------------aa----g--------ct----ga--atcagg-t---
B D                     Panda  aa----ggta------------------aa----g--------ct----ga--atcagg-t---
               Pacific walrus  aa----ggtaaagctgaatcaggtc--taa----g--------ct----ga--atcagg-t---
                 Weddell seal  aa----ggtaaagctgaatcaggtc--taa----g--------ct----ga--atcagg-t---
             Black flying-fox  aa----ggta------------------aa----g--------ct----aa--atcagg-t---
B D                   Megabat  aa----ggta------------------aa----g--------ct----aa--atcagg-t---
                Big brown bat  -a----ggta------------------aa----g--------ct----aa--atcagg-t---
         David's myotis (bat)  -a----ggta------------------aa----g--------cg----aa--a------t---
B D                  Microbat  -a----ggta------------------ac----g--------cg----aa--a------t---
B D                  Hedgehog  aa----ggta------------------aa----g--------ct----aa--atcggg-t---
B D                     Shrew  aa----ggta------------------aa----g--------ct----aa--atcagg-t---
              Star-nosed mole  aa----gata------------------aa----g--------ct----aa--atcagg-t---
B D                  Elephant  ----------------------------aa----g--------ct----aa--atcagt-t---
          Cape elephant shrew  ------agca-----------------gaa----g--------ct----ta--atcagg-t---
B D                   Manatee  ------aacg--------------t--aaa----g--------ct----aa--atcagg-t---
             Cape golden mole  ----------------------------aa----ggta--caact----ga--atcagg-t---
B D                    Tenrec  -------------------------------------------ct----ga--cccaggaa---
                     Aardvark  ------------------------------------taggtaacc----ca--gtcagg-t---
B D                 Armadillo  ---------------------------------------acagct----aa--atcagg-t---
B D                   Opossum  ---------------------------gag----g--------at----gagagcgggg-g---
B D           Tasmanian devil  ---------------------------gaa----t--------ct----aaggattggg-g---
B D                  Platypus  ----------------------gccaaaga----g--------ctgtgggg--aatagg-c---
B D        American alligator  ----------------------------aaggcag--------gg----gt--gtgagg-a---
  D           Green seaturtle  ----------------------------------g--------cc----ct--gagcgg-g---
  D            Painted turtle  ----------------------------------g--------ct----gc--ataggg-g---
B D             X. tropicalis  --caggggta------------------aa----t--------ac----ac--cacagg-ggaa
B D                    Rabbit  ================================================================
B D               Stickleback  ================================================================
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                 Zebrafish  ================================================================
B D                    Medaka  ================================================================
B D                Budgerigar  ================================================================
  D               Rock pigeon  ================================================================
B D       Medium ground finch  ================================================================
  D          Peregrine falcon  ================================================================
  D              Saker falcon  ================================================================
B D                   Wallaby  ================================================================
  D       Collared flycatcher  ================================================================

Inserts between block 32 and 33 in window
B D                 Hedgehog 1bp
B D       American alligator 2bp
  D          Green seaturtle 13bp

Alignment block 33 of 366 in window, 34989108 - 34989112, 5 bps 
B D                     Human  cagct-
B D                     Chimp  cagct-
B D                   Gorilla  cagct-
B D                 Orangutan  cagct-
B D                    Gibbon  cagct-
B D                    Rhesus  cagct-
B D       Crab-eating macaque  cagct-
B D                    Baboon  cagct-
B D              Green monkey  cagct-
B D                  Marmoset  cagct-
B D           Squirrel monkey  cagct-
B D                  Bushbaby  caagt-
           Chinese tree shrew  caggt-
B D                  Squirrel  cagga-
       Lesser Egyptian jerboa  ctggt-
                 Prairie vole  caggt-
B D           Chinese hamster  cagat-
               Golden hamster  caggt-
B D                     Mouse  caggt-
B D                       Rat  caggt-
B D            Naked mole-rat  caggt-
B D                Guinea pig  cagat-
                   Chinchilla  caggt-
             Brush-tailed rat  cgagt-
B D                      Pika  caagt-
B D                       Pig  caggg-
B D                    Alpaca  caggg-
               Bactrian camel  caggg-
B D                   Dolphin  caggg-
                 Killer whale  caggg-
             Tibetan antelope  caggg-
B D                       Cow  caggg-
B D                     Sheep  caggg-
                Domestic goat  caggg-
B D                     Horse  caggt-
B D          White rhinoceros  ccggt-
B D                       Cat  ctggt-
B D                       Dog  ctggt-
B D                   Ferret   ctggt-
B D                     Panda  ctggt-
               Pacific walrus  ctggt-
                 Weddell seal  ctggt-
             Black flying-fox  aaggt-
B D                   Megabat  aaggt-
                Big brown bat  caggt-
         David's myotis (bat)  caggt-
B D                  Microbat  caggt-
B D                  Hedgehog  gaggt-
B D                     Shrew  caggt-
              Star-nosed mole  caggt-
B D                  Elephant  caggc-
          Cape elephant shrew  caggt-
B D                   Manatee  caggt-
             Cape golden mole  cagat-
B D                    Tenrec  caggt-
                     Aardvark  cgggc-
B D                 Armadillo  caggt-
B D                   Opossum  gaggg-
B D           Tasmanian devil  cagag-
B D                  Platypus  c-----
B D        American alligator  ct----
  D           Green seaturtle  ca----
B D             X. tropicalis  -gggcc
B D                    Rabbit  ======
B D               Stickleback  ======
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                 Zebrafish  ======
B D                    Medaka  ======
  D            Painted turtle  ======
B D                Budgerigar  ======
  D               Rock pigeon  ======
B D       Medium ground finch  ======
  D          Peregrine falcon  ======
  D              Saker falcon  ======
B D                   Wallaby  ======
  D       Collared flycatcher  ======

Inserts between block 33 and 34 in window
B D                Orangutan 1070bp
B D                  Opossum 5bp

Alignment block 34 of 366 in window, 34989113 - 34989120, 8 bps 
B D                     Human  tgaggtgg
B D                     Chimp  tgaggtgg
B D                   Gorilla  tgatgtgg
B D                    Gibbon  cgaggtgg
B D                    Rhesus  cgaggtgg
B D       Crab-eating macaque  cgaggtgg
B