Multiz Alignments of 100 Vertebrates
 

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Alignment block 1 of 8 in window, 115650245 - 115650257, 13 bps 
B D                     Human  agct----ag-aag------------------aaaa
B D                     Chimp  agct----ag-aag------------------aaaa
B D                   Gorilla  agct----ag-aag------------------aaaa
B D                 Orangutan  agct----ag-aag------------------aaaa
B D                    Gibbon  agct----ag-aag------------------aaaa
B D                    Rhesus  agct----ag-aag------------------aaaa
B D       Crab-eating macaque  agct----ag-aag------------------aaaa
B D                    Baboon  agct----ag-aag------------------aaaa
B D              Green monkey  agct----ag-aag------------------aaaa
B D                  Marmoset  agct----ag-aag------------------aaaa
B D           Squirrel monkey  agct----ag-aag------------------aaaa
B D                  Bushbaby  aggt----ag-agga-----------------aaaa
           Chinese tree shrew  aggt----ag-aag------------------aaaa
B D                  Squirrel  aggt----ag-agg------------------aaaa
       Lesser Egyptian jerboa  aagt----gg-agg------------------aaaa
                 Prairie vole  agat----gg-agg-------------------aaa
B D           Chinese hamster  aggg----gg-agg-------------------aaa
               Golden hamster  aggg----gg-agg-------------------aaa
B D                     Mouse  aggt----gg-aag-------------------aaa
B D                       Rat  aggt----gg-agg-------------------aaa
B D            Naked mole-rat  aggt----ag-agg------------------cacc
B D                Guinea pig  agat----ag-aag------------------cacc
                   Chinchilla  aggt----ag-agg------------------cacc
             Brush-tailed rat  aggt----ag-agg------------------caca
B D                    Rabbit  aga-----gg-aaaa-----------------aaaa
B D                      Pika  agct----ag-aggg-----------------aaaa
B D                       Pig  aggt----agagga------------------aaaa
B D                    Alpaca  aggt----ag-agg------------------aaaa
               Bactrian camel  aggt----ag-agg------------------aaaa
B D                   Dolphin  aggt----agaaga------------------aaaa
                 Killer whale  aggt----agaaga------------------aaaa
             Tibetan antelope  aggt----ag-agg------------------gaaa
B D                       Cow  aggt----ag-agg------------------gaaa
B D                     Sheep  aggt----ag-agg------------------gaaa
                Domestic goat  aggt----ag-agg------------------gaaa
B D                     Horse  aggt----ag-agg------------------aaaa
B D          White rhinoceros  aggt----ag-agg------------------aaaa
B D                       Cat  aggt----ag-aggaa---------------caaaa
B D                       Dog  aggt----ag-agg------------------aaaa
B D                   Ferret   aggt----ag-aga------------------aaaa
B D                     Panda  aggt----ag-agg------------------aaag
               Pacific walrus  aggt----ag-agg------------------aaaa
                 Weddell seal  aggt----ag-agg------------------aaag
             Black flying-fox  agac----ag-agg------------------aaaa
                Big brown bat  aggt----ag-agg------------------aaaa
         David's myotis (bat)  aagt----ag-agg------------------aaga
B D                  Microbat  aaat----ag-agg------------------aaaa
B D                  Hedgehog  aggta---ag-ggg------------------gaaa
B D                     Shrew  aggt----ag-agg------------------aaaa
              Star-nosed mole  aagt----ag-agg------------------aaaa
B D                  Elephant  aggt----ag-agg------------------agaa
B D                   Manatee  aggt----ag-agg------------------aaaa
             Cape golden mole  aggt----ag-agg-----------------aaaaa
B D                    Tenrec  aagt----ag-aag------------------agaa
                     Aardvark  aggt----ag-aggga---------------aaaaa
B D                   Opossum  aggg----ag-tgg------------------ggaa
B D           Tasmanian devil  --------ag-tgg------------------ggaa
B D                   Wallaby  agag----ag-tgg------------------ggaa
  D               Rock pigeon  ---------------taaaagttatattccatatga
  D              Saker falcon  ---------------ttaaagttatgctatatatga
  D          Peregrine falcon  ---------------ttaaagttatgctatatatga
B D               Zebra finch  ---------------------------------tga
           Tibetan ground jay  ---------------------------------taa
B D                Budgerigar  ---------------ttaaagttacattatctctga
  D                    Parrot  ---------------ttaaagttatgttatctatga
  D             Scarlet macaw  ---------------ttaaagttacgttatctatga
  D              Mallard duck  ---------------tttatgttagactatatatga
B D                   Chicken  ---------------ttaaggtt-tcctttatctga
B D                    Turkey  ---------------tttaagttagactttatctga
  D  Chinese softshell turtle  ----------------------tagaatatatttga
  D    Spiny softshell turtle  ----------------------tagaatatatatga
B D                    Lizard  -----------------aaaatcactccttttgggg
B D             X. tropicalis  ---------------------tcgtattcagaatga
        Burton's mouthbreeder  aagtgctcag-aag------------------aaaa
                  Zebra mbuna  aagtgctcag-aag------------------aaaa
          Pundamilia nyererei  aagtgctcag-aag------------------aaaa
B D                 Zebrafish  ------------------------------------
  D           Green seaturtle  ====================================
  D            Painted turtle  ====================================
  D       Collared flycatcher  ====================================
B D       Medium ground finch  ====================================
  D    White-throated sparrow  ====================================
B D        American alligator  ====================================

Inserts between block 1 and 2 in window
       Burton's mouthbreeder 23bp
                 Zebra mbuna 23bp

Alignment block 2 of 8 in window, 115650258 - 115650262, 5 bps 
B D                     Human  atgta
B D                     Chimp  atgta
B D                   Gorilla  atgta
B D                 Orangutan  atgta
B D                    Gibbon  atgta
B D                    Rhesus  atgta
B D       Crab-eating macaque  atgta
B D                    Baboon  atgta
B D              Green monkey  atgta
B D                  Marmoset  atgta
B D           Squirrel monkey  atgta
B D                  Bushbaby  atgta
           Chinese tree shrew  atgta
B D                  Squirrel  atgta
       Lesser Egyptian jerboa  atgta
                 Prairie vole  atgga
B D           Chinese hamster  atgga
               Golden hamster  atgga
B D                     Mouse  gtgga
B D                       Rat  gtgga
B D            Naked mole-rat  atgta
B D                Guinea pig  atgta
                   Chinchilla  atgta
             Brush-tailed rat  atgta
B D                    Rabbit  atgta
B D                      Pika  atgta
B D                       Pig  -tgta
B D                    Alpaca  -tgta
               Bactrian camel  -tgta
B D                   Dolphin  -tgta
                 Killer whale  -tgta
             Tibetan antelope  -tgta
B D                       Cow  -tgta
B D                     Sheep  -tgta
                Domestic goat  -tgta
B D                     Horse  atgta
B D          White rhinoceros  acgta
B D                       Cat  cggac
B D                       Dog  gtgtt
B D                   Ferret   gtgta
B D                     Panda  gtgta
               Pacific walrus  --gtc
                 Weddell seal  gtgtc
             Black flying-fox  -cgta
                Big brown bat  -tgta
         David's myotis (bat)  -tgta
B D                  Microbat  -tgta
B D                  Hedgehog  tttta
B D                     Shrew  atgaa
              Star-nosed mole  atgta
B D                  Elephant  gtgta
B D                   Manatee  atgta
             Cape golden mole  atgta
B D                    Tenrec  atgta
                     Aardvark  atata
B D                   Opossum  -tgtg
B D           Tasmanian devil  -ttta
B D                   Wallaby  -tata
  D               Rock pigeon  gaata
  D              Saker falcon  gaata
  D          Peregrine falcon  gaata
B D               Zebra finch  taata
           Tibetan ground jay  t---a
B D                Budgerigar  gagca
  D                    Parrot  gaaca
  D             Scarlet macaw  gaaca
  D              Mallard duck  gaata
B D                   Chicken  gaata
B D                    Turkey  gaata
B D        American alligator  -aata
  D           Green seaturtle  ---ta
  D  Chinese softshell turtle  gaata
  D    Spiny softshell turtle  gaata
B D                    Lizard  gagaa
B D             X. tropicalis  atgca
        Burton's mouthbreeder  aaata
                  Zebra mbuna  aaata
B D                 Zebrafish  atgta
  D            Painted turtle  =====
  D       Collared flycatcher  =====
B D       Medium ground finch  =====
  D    White-throated sparrow  =====

Alignment block 3 of 8 in window, 115650263 - 115650302, 40 bps 
B D                     Human  cct----------------------------------------------taaa---tttgcat-------
B D                     Chimp  cct----------------------------------------------taaa---tttgcat-------
B D                   Gorilla  cct----------------------------------------------taaa---tttgcat-------
B D                 Orangutan  cct----------------------------------------------taaa---tttgcat-------
B D                    Gibbon  cct----------------------------------------------taaa---tttacat-------
B D                    Rhesus  cct----------------------------------------------taaa---tttgcat-------
B D       Crab-eating macaque  cct----------------------------------------------taaa---tttgcat-------
B D                    Baboon  cct----------------------------------------------taaa---tttgcat-------
B D              Green monkey  cct----------------------------------------------taaa---tttgcat-------
B D                  Marmoset  cct----------------------------------------------taaa---tttacat-------
B D           Squirrel monkey  cct----------------------------------------------taaa---tttgcat-------
B D                  Bushbaby  cct----------------------------------------------taaa---ttcacat-------
           Chinese tree shrew  -ct----------------------------------------------tgaa---gttgcat-------
B D                  Squirrel  cac----------------------------------------------caaa---atttcat-------
       Lesser Egyptian jerboa  ccc----------------------------------------------taag---gttgcat-------
                 Prairie vole  cta----------------------------------------------taag---gttatat-------
B D           Chinese hamster  ccc----------------------------------------------taagtttgttgtat-------
               Golden hamster  gcc----------------------------------------------taag---attgtgt-------
B D                     Mouse  ccc----------------------------------------------taag---gttgcat-------
B D                       Rat  ccc----------------------------------------------gaag---gttgcat-------
B D            Naked mole-rat  ccc----------------------------------------------taaa---tttgcat-------
B D                Guinea pig  ccc----------------------------------------------taaa---tttgcac-------
                   Chinchilla  ccc----------------------------------------------taaa---tttgcat-------
             Brush-tailed rat  ccc----------------------------------------------taaa---ttttcat-------
B D                    Rabbit  cct----------------------------------------------taaa---tttgcat-------
B D                      Pika  cct----------------------------------------------taaa---tatgcat-------
B D                       Pig  cct----------------------------------------------agaa---tttccat-------
B D                    Alpaca  cct----------------------------------------------tgaa---tttccat-------
               Bactrian camel  cct----------------------------------------------tgaa---tttccat-------
B D                   Dolphin  cct----------------------------------------------tgaa---tttccat-------
                 Killer whale  cct----------------------------------------------tgaa---tttccat-------
             Tibetan antelope  cct----------------------------------------------tgaa---tttccat-------
B D                       Cow  cct----------------------------------------------tgaa---tttctat-------
B D                     Sheep  cct----------------------------------------------taaa---tttccat-------
                Domestic goat  cct----------------------------------------------tgaa---tttccat-------
B D                     Horse  cct----------------------------------------------tgaa---tttgcat-------
B D          White rhinoceros  cct----------------------------------------------tgaa---tttgcat-------
B D                       Cat  ctt----------------------------------------------ccaa---tttgcatacc----
B D                       Dog  cct----------------------------------------------tgat---tttgcat-------
B D                   Ferret   cct----------------------------------------------tgat---tttgcat-------
B D                     Panda  cct----------------------------------------------tgat---ttcgcgt-------
               Pacific walrus  cct----------------------------------------------tgat---tttgcat-------
                 Weddell seal  cct----------------------------------------------tgat---tttgcat-------
             Black flying-fox  cct----------------------------------------------taaa---tttgcat-------
                Big brown bat  cct----------------------------------------------taaa---tttgcat-------
         David's myotis (bat)  cct----------------------------------------------taaa---tttgcat-------
B D                  Microbat  cct----------------------------------------------taaa---tttgcat-------
B D                  Hedgehog  ctt----------------------------------------------tcaa---cctgcat-------
B D                     Shrew  ccg----------------------------------------------tgaa---gttgcat-------
              Star-nosed mole  cct----------------------------------------------tgaa---gttgcat-------
B D                  Elephant  cct----------------------------------------------taaa---tttgcat-------
B D                   Manatee  cct----------------------------------------------taaa---tttgcat-------
             Cape golden mole  cct----------------------------------------------tgaa---tttgcat-------
B D                    Tenrec  cct----------------------------------------------taaa---tttgcat-------
                     Aardvark  ccc----------------------------------------------taaa---tttgcat-------
B D                   Opossum  tct----------------------------------------------taaa---ccttcat-------
B D           Tasmanian devil  tcc----------------------------------------------taac---ccttgat-------
B D                   Wallaby  tcg----------------------------------------------taac---ctttcat-------
  D               Rock pigeon  cca----------------------------------------------ccat---acttgga-------
  D              Saker falcon  cca----------------------------------------------ccat---cctttga-------
  D          Peregrine falcon  cca----------------------------------------------ccat---cctttga-------
B D               Zebra finch  cca----------------------------------------------ccat---ccttgga-------
           Tibetan ground jay  cca----------------------------------------------ccat---ccttgga-------
B D                Budgerigar  cca----------------------------------------------ccat---ccttgga-------
  D                    Parrot  cca----------------------------------------------ccat---ccttgga-------
  D             Scarlet macaw  cca----------------------------------------------ccat---ccttgga-------
  D              Mallard duck  caaaaaaaaaagaaagggggtggggggttgtttgtatttttaagttagactat---atatgagaatatca
B D                   Chicken  cca----------------------------------------------ccat---ccttgaa-------
B D                    Turkey  cca----------------------------------------------ccat---ccttgaa-------
B D        American alligator  cca----------------------------------------------tgaa---actcag--------
  D           Green seaturtle  cca---------------------------------------------cctaa---aactcag-------
  D  Chinese softshell turtle  tca--------------------------------------------ccctaa---aattctg-------
  D    Spiny softshell turtle  tca--------------------------------------------ccctaa---aattctg-------
B D                    Lizard  gga----------------------------------------------ccac---cttttgaggca---
B D             X. tropicalis  ttt----------------------------------------------ttg----tctgtat-------
B D                 Zebrafish  ttc----------------------------------------------ttta---tttttat-------
  D            Painted turtle  ======================================================================
  D       Collared flycatcher  ======================================================================
B D       Medium ground finch  ======================================================================
  D    White-throated sparrow  ======================================================================

                        Human  -----------c-ttccc--tct---cata-cc-------caagctgtaaa
                        Chimp  -----------c-ttccc--tct---cata-cc-------caagctgtaaa
                      Gorilla  -----------c-ttccc--tct---cata-cc-------caagctgtaaa
                    Orangutan  -----------c-ttccc--tct---cata-cc-------caagctgtaaa
                       Gibbon  -----------c-ttccc--tct---cata-cc-------caagctgtaaa
                       Rhesus  -----------c-ttccc--tct---cata-cc-------caagctgtaaa
          Crab-eating macaque  -----------c-ttccc--tct---cata-cc-------caagctgtaaa
                       Baboon  -----------c-ttccc--tct---cata-cc-------caagctgtaaa
                 Green monkey  -----------c-ttccc--tct---cata-cc-------caagctgtaaa
                     Marmoset  -----------ctttccc--tct---cata-cc-------taagctgtaaa
              Squirrel monkey  -----------ctttccc--tct---cata-cc-------taagctgtaaa
                     Bushbaby  -----------c-ttcct--tct---cacg-cc-------caagctgcaaa
           Chinese tree shrew  -----------c-atccc--tct---ctca-tc-------caagctgtaca
                     Squirrel  -----------c-tttcc--ttt---caca-ct-------caaaatgtaaa
       Lesser Egyptian jerboa  -----------c-ttctc--tct---caca-cc-------caagctgtaaa
                 Prairie vole  -------------tttcc--cct---caca-cc-------caggctcaaat
              Chinese hamster  -------------ttccc--cct---caca-cc-------caggatcaaat
               Golden hamster  -------------ttccc--gct---caca-cc-------caggat-aaat
                        Mouse  -------------ttccc--cct---caca-cc-------caggctcaaag
                          Rat  -------------ttccc--cct---cata-cc-------caggctcaaat
               Naked mole-rat  -----------c-tttcc--tct---caca-cc-------caagatgtaaa
                   Guinea pig  -----------c-ttccc--tct---caca-cc-------caggatgtaaa
                   Chinchilla  -----------c-tcccc--tct---caca-cc-------caagatgtaaa
             Brush-tailed rat  -----------c-tttcc--tct---caca-ct-------caagatgtgaa
                       Rabbit  -------------cttcc---ct---ctca-cc-------caagctgtaaa
                         Pika  -------------cttcc--tct---cata-cc-------caggctggaaa
                          Pig  -----------c-ttccc--tct---caca-cc-------caacctgtaaa
                       Alpaca  -----------c-ttccc--tct---cata-cc-------caagctgtaaa
               Bactrian camel  -----------c-ttccc--tct---caca-cc-------caagctgtaaa
                      Dolphin  -----------c-ttccc--tct---caca-cc-------gaagctgtaaa
                 Killer whale  -----------c-ttccc--tct---caca-cc-------gaagctgtaaa
             Tibetan antelope  -----------c-ttccc--tcc---caca-ct-------aaagctgtaaa
                          Cow  -----------c-ttctc--tcc---caca-ct-------aaagctgtaaa
                        Sheep  -----------c-ttccc--tcc---caca-ct-------aaagctgtaaa
                Domestic goat  -----------c-ttccc--tcc---caca-ct-------aaagctgtaaa
                        Horse  -----------c-ttccc--tct---caca-cc-------caagctgtaaa
             White rhinoceros  -----------c-ttccc--ttt---caca-cc-------caagctgtaaa
                          Cat  -----------c-tggcc--tct---caca-cc-------caagctgtaaa
                          Dog  -----------c-taccc--tct---caca-cc-------caagctgtaaa
                      Ferret   -----------c-taccc--tct---caca-cc-------caagctgtaaa
                        Panda  -----------c-taccc--tct---caca-cc-------cacgctgtaaa
               Pacific walrus  -----------c-gaccc--tct---caca-cc-------caagttgtaaa
                 Weddell seal  -----------c-caccc--tct---caca-cc-------caagttgtaaa
             Black flying-fox  -----------t-ttccc--cct---caca-cc-------caagctataaa
                Big brown bat  -----------c-ttctc--cct---cata-cc-------caagctgtaaa
         David's myotis (bat)  -----------c-ttctc--cct---cata-ac-------caagctgtaaa
                     Microbat  -----------c-ttctc--cct---cata-ac-------caagctgtaaa
                     Hedgehog  -----------c-ttccc--tct---caca-cc-------ctagctataag
                        Shrew  -----------c-ttccc--tct---caca-cc-------caagctgtaaa
              Star-nosed mole  -----------c-ttcgc--tct---caca-cc-------caagctgtaaa
                     Elephant  -----------c-ttccc--ac------ca-cc-------caagctataaa
                      Manatee  -----------c-ttccc--ac------ca-cc-------taagctgtaaa
             Cape golden mole  -----------c-tgccc--gc------caccc-------caagctgtaaa
                       Tenrec  -----------c-tttct--gc------ca-ca-------caagctgtaaa
                     Aardvark  -----------c-ttccc--ac------ca-cc-------caagctgtaaa
                      Opossum  -----------c-tgctt--ttc---caag---------------tgtgga
              Tasmanian devil  -----------c-tgctt--ttc---c-ag---------------cgtaga
                      Wallaby  -----------c-tgctt--ttc---c-ag---------------tgtaga
                  Rock pigeon  -----------c-ctctc--aga---gtaa-ca-------tacgatatcat
                 Saker falcon  -----------t-ctctt--gca---gtaa-ca-------cgtgatagcat
             Peregrine falcon  -----------t-ctctt--gca---gtaa-ca-------cgtgatagcat
                  Zebra finch  -----------c-ctctt--gca---gtaa-ca-------tatg--atcgt
           Tibetan ground jay  -----------c-ctctt--gca---gtaa-cg-------tatg--atcat
                   Budgerigar  -----------c-ctcac-----------a-cg-------catggcatcac
                       Parrot  -----------c-ctcgc-----------a-tg-------tatggcatcat
                Scarlet macaw  -----------c-ctcgc-----------a-cg-------tatggcatcat
                 Mallard duck  ccatccttggac-tgcac--aca---gtaa-cg---------tgataccat
                      Chicken  -----------c-ttctc--cca---gtaa-ca-------cctgatatcat
                       Turkey  -----------c-ttctc--aca---gtaa-ca-------cctgatatcac
           American alligator  -----------c-ctttc--aca---agaa-ta-------gctgttgtnat
              Green seaturtle  -----------c-ctctctggca---gtag-tggacatttgatggcatccg
     Chinese softshell turtle  -----------c-ctttctggca---ataa-tggacatcttgtgacatcag
       Spiny softshell turtle  -----------c-ctctctggca---gtaa-tggacatcttgtgacatcaa
                       Lizard  -----------t-tcatc--aga---gaac-ca-------aa---------
                X. tropicalis  -----------c-ttgtt--tcaaagcata-ac------------------
                    Zebrafish  -----------t-tgttc--tat---tata-ta-------aaa--------
               Painted turtle  ===================================================
          Collared flycatcher  ===================================================
          Medium ground finch  ===================================================
       White-throated sparrow  ===================================================

Inserts between block 3 and 4 in window
  D              Rock pigeon 26bp
  D             Saker falcon 26bp
  D         Peregrine falcon 26bp
B D              Zebra finch 26bp
          Tibetan ground jay 26bp
B D               Budgerigar 26bp
  D                   Parrot 26bp
  D            Scarlet macaw 26bp
  D             Mallard duck 26bp
B D                  Chicken 26bp
B D                   Turkey 26bp
B D       American alligator 23bp
  D          Green seaturtle 36bp
  D Chinese softshell turtle 37bp
  D   Spiny softshell turtle 37bp
B D                   Lizard 1bp

Alignment block 4 of 8 in window, 115650303 - 115650309, 7 bps 
B D                     Human  ca---attg--a
B D                     Chimp  ca---attg--a
B D                   Gorilla  ca---attg--a
B D                 Orangutan  ca---attg--a
B D                    Gibbon  ca---attg--a
B D                    Rhesus  ca---actg--a
B D       Crab-eating macaque  ca---actg--a
B D                    Baboon  ca---attg--a
B D              Green monkey  ca---attg--a
B D                  Marmoset  ca---attg--a
B D           Squirrel monkey  ca---attg--a
B D                  Bushbaby  ca---tttg--a
           Chinese tree shrew  ca---attg--a
B D                  Squirrel  ca---aaag--a
       Lesser Egyptian jerboa  ct---aagg--a
                 Prairie vole  ca---aatg--g
B D           Chinese hamster  ca---aatg--a
               Golden hamster  ca---aatg--a
B D                     Mouse  ga---aatg--a
B D                       Rat  gg---aatg--a
B D            Naked mole-rat  cg---aatg--a
B D                Guinea pig  ca---aatg---
                   Chinchilla  ca---aagg--a
             Brush-tailed rat  ga---aatg--a
B D                    Rabbit  ca---attg--a
B D                      Pika  ca---aaag--a
B D                       Pig  ca---attg--a
B D                    Alpaca  ca---gttg--a
               Bactrian camel  ca---gttg--a
B D                   Dolphin  ca---attg--a
                 Killer whale  ca---attg--a
             Tibetan antelope  ca---cttg--a
B D                       Cow  ca---cttg--a
B D                     Sheep  ca---cttg--a
                Domestic goat  ca---cttg--a
B D                     Horse  ca---attg--a
B D          White rhinoceros  ca---attg--a
B D                       Cat  ca---attg--a
B D                       Dog  ca---gttg--a
B D                   Ferret   ca---gctg--a
B D                     Panda  ca---attg--a
               Pacific walrus  ca---gctg--a
                 Weddell seal  ca---gctg--a
             Black flying-fox  ca---gttg--a
                Big brown bat  ca---gttgaca
         David's myotis (bat)  cg---gttgaca
B D                  Microbat  ca---gttgaca
B D                  Hedgehog  ta---gctg--a
B D                     Shrew  ca---atgg--a
              Star-nosed mole  ca---attg--a
B D                  Elephant  ca---attg--g
B D                   Manatee  ca---attg--g
             Cape golden mole  ca---attg--a
B D                    Tenrec  ca---attg--a
                     Aardvark  ca---gttg--a
B D                   Opossum  ca---acta--t
B D           Tasmanian devil  caactacta--g
B D                   Wallaby  ca---acta--g
  D               Rock pigeon  -g---aatg--g
  D              Saker falcon  -g---aatg--g
  D          Peregrine falcon  -g---aatg--g
B D               Zebra finch  -g---aatg--g
           Tibetan ground jay  -g---aatg--g
B D                Budgerigar  -g---aacg--g
  D                    Parrot  -a---aaca--g
  D             Scarlet macaw  -g---aacg--g
  D              Mallard duck  -g---aatg--g
B D                   Chicken  -g---aatg--g
B D                    Turkey  -g---aatg--g
B D        American alligator  -g---gatg--g
  D           Green seaturtle  -a---aatg---
  D            Painted turtle  -a---aatg---
  D  Chinese softshell turtle  -a---aatg---
  D    Spiny softshell turtle  -a---aatg---
B D                    Lizard  -c---aatg--c
B D             X. tropicalis  ----catag--a
B D                 Zebrafish  ta---attt--a
  D       Collared flycatcher  ============
B D       Medium ground finch  ============
  D    White-throated sparrow  ============

Inserts between block 4 and 5 in window
  D              Rock pigeon 5bp
  D             Saker falcon 5bp
  D         Peregrine falcon 5bp
B D              Zebra finch 5bp
          Tibetan ground jay 10bp
B D               Budgerigar 6bp
  D                   Parrot 6bp
  D            Scarlet macaw 6bp
  D             Mallard duck 5bp
B D                  Chicken 5bp
B D                   Turkey 5bp
B D       American alligator 5bp
B D            X. tropicalis 1bp

Alignment block 5 of 8 in window, 115650310 - 115650609, 300 bps 
B D                     Human  aata-tt--------ttgtctt-aaa-tcacttggttcaa-------------t--------------ac
B D                     Chimp  aata-tt--------ttgtctt-aaa-tcacttggttcaa-------------t--------------ac
B D                   Gorilla  aata-tt--------ttgtctt-aaa-tcacttggttcaa-------------t--------------ac
B D                 Orangutan  aata-tt--------ttgtctt-aaa-tcacttggttcaa-------------t--------------ac
B D                    Gibbon  aata-tt--------ttgtctt-aaa-tcacttggttcaa-------------t--------------ac
B D                    Rhesus  aata-tt--------ttgtctt-aaa-tcacttggttcaa-------------t--------------ac
B D       Crab-eating macaque  aata-tt--------ttgtctt-aaa-tcacttggttcaa-------------t--------------ac
B D                    Baboon  aata-tt--------ttgtctt-aaa-tcacttggttcaa-------------t--------------ac
B D              Green monkey  aata-tt--------ttgtctt-aaa-tcacttggttcaa-------------t--------------ac
B D                  Marmoset  aata-tt--------ttg---------tcacttggttcaa-------------t--------------ac
B D           Squirrel monkey  aata-tt--------ttg---------tcacttggttcaa-------------t--------------ac
B D                  Bushbaby  aata-tt--------ttgtctt-caa-tcacttggttgaa-------------t--------------ac
           Chinese tree shrew  aata-tt--------ttgtctt-aaa-ttacttgattcaa-------------t--------------ac
B D                  Squirrel  aata-tt--------ttgtct--aaa-tcacttagttcca-------------c--------------at
       Lesser Egyptian jerboa  agtattt--------ttgtctc-caa-tatgtcagttcaa-------------t--------------ac
                 Prairie vole  aata-tt--------ttgtctt-caa-tgagtccgttcga-------------t--------------ac
B D           Chinese hamster  aata-ct--------ttgtctt-caa-tgaatcagttcga-------------c--------------ac
               Golden hamster  aaca-tt--------tttcctt-caa-taaatcagttcga-------------c--------------ac
B D                     Mouse  aata-tt--------ttgtctt-caa-taagttggtccga-------------t--------------ac
B D                       Rat  aata-tt--------ttgtctt-caa-taagtcagtctga-------------t--------------ac
B D            Naked mole-rat  aata-tt--------ttgtctt-aaa-tcacttggttcta-------------t--------------ac
B D                Guinea pig  cata-tt--------ttgtctt-aag-tcacttggttcta-------------t--------------ac
                   Chinchilla  aata-tt--------ttgtctt-aaa-tcacttggttcta-------------t--------------ac
             Brush-tailed rat  aaca-tt--------ttgtctt-aaa-tcacttggttcta-------------t--------------gc
B D                    Rabbit  aata-tt--------ttgtctt-aaa-ttgcttggttcaa-------------t--------------cc
B D                      Pika  aata-tt--------ttgtctt-aaa-ttgcttcattcaa-------------t--------------ac
B D                       Pig  cata-tt--------ggatcct-aaa-acacttggttcaa----------------------------at
B D                    Alpaca  cata-tt--------ttgtcttaaaa-acacttggttcaa-------------t--------------at
               Bactrian camel  cata-tt--------ttgtctt-aaa-acacttggttcaa-------------t--------------at
B D                   Dolphin  cata-tt--------ttgtctt-aaa-acacttggttcaa-------------t--------------at
                 Killer whale  cata-tt--------ttgtctt-aaa-acacttggttcaa-------------t--------------at
             Tibetan antelope  cata-tt--------ttgtcct-gaa-acacttggttcaa-------------t--------------at
B D                       Cow  cata-tt--------ttgtcct-gaa-acacttggttcaa-------------t--------------at
B D                     Sheep  cata-tt--------ttgtcct-gaa-acacttggttcaa-------------t--------------at
                Domestic goat  cata-tt--------ttgtcct-gaa-acacttggttcaa-------------t--------------at
B D                     Horse  cata-tt--------ttgtctt-aaa-acactttgttcaa-------------t--------------at
B D          White rhinoceros  cata-tt--------ttgtctt-aaa-acacttggttcaa-------------t--------------at
B D                       Cat  cgca-tc--------ttatctt-aaa-acacttggttcag-------------t--------------at
B D                       Dog  cata-tt--------ttgtctt-aaa-agacttggttcaa-------------t--------------at
B D                   Ferret   cata-tt--------ttgtctt-cac-acacttggttcca-------------t--------------at
B D                     Panda  cata-tt--------ttgtctt-caa-acccttggttcaa-------------t--------------at
               Pacific walrus  cata-ct--------ttgtctt-caa-acacttggttcca-------------t--------------at
                 Weddell seal  cata-tt--------ttgtctt-caa-acacttggttcca-------------t--------------at
             Black flying-fox  tata-tt--------ttgtctt-aaa-a-acttagttcaa-------------t--------------at
                Big brown bat  tata-tt--------ttgtctt-aaa-acacttggttcaa-------------t--------------tt
         David's myotis (bat)  tata-tt--------ttgtctt-aaa-acacttggttcaa-------------t--------------tt
B D                  Microbat  tata-tt--------ttgtctt-aaa-acacctggttcaa-------------t--------------tt
B D                  Hedgehog  tata-tt--------ttgtctt-caa-atgcttggttcaa-------------t--------------at
B D                     Shrew  cata-tt--------ttgtctt-aaagatgctcgg-tcat-------------t--------------at
              Star-nosed mole  cata-tt--------ttgtctt-aaa-acacttgg-ttca-------------a--------------tt
B D                  Elephant  tcta-tt--------ttgtctt-caa-atacttggttcag-------------t--------------ac
B D                   Manatee  tata-tt--------ttgtctt-aaa-atacttggttcaa-------------t--------------ac
             Cape golden mole  tcta-ta--------ttgtctt-aca-ttacttggttcag-------------t--------------ac
B D                    Tenrec  tata-ct--------ttgtctt-aaa-atacttagttaaa-------------t--------------ac
                     Aardvark  tata-tt--------ttgtctt-aaa-atacttggttcaa-------------t--------------ac
B D                   Opossum  caga-tg-----------ccac-aaa-ctgaacgactt--------------------------------
B D           Tasmanian devil  cagg-tg--------tttccac-ca---------------------------------------------
B D                   Wallaby  cagg-tg--------ttgccac-aaa-ctga---actt--------------------------------
  D               Rock pigeon  aatg-ca--------tttttgt-atg-catcttggttcag--ttctgtgcacct--------------ag
  D              Saker falcon  aatg-ca--------tttttgt-atg-catcttggttcag--ttctgtgcatct--------------ag
  D          Peregrine falcon  aatg-ca--------tttttgt-atg-catcttggttcag--ttctgtgcatct--------------ag
  D       Collared flycatcher  aatg-ca--------tttttgt-atg-catcttggttcag--ttctgtgcacct--------------ag
  D    White-throated sparrow  aatg-ca--------tttttgt-atg-catcttggttcag--ttctgtgcacct--------------ag
B D       Medium ground finch  aatg-ca--------tttttgt-atg-catcttggttcag--ttctgtgcacct--------------ag
B D               Zebra finch  aatg-ca--------tttttgt-atg-catcttggttcag--ttctgtgcacct--------------ag
           Tibetan ground jay  ------a--------tttttgt-atg-catcttggttcgg--ttctgtgcatct--------------ag
B D                Budgerigar  -atg-ca--------tttttgt--tg-catcttggttcag--ttctgtgcacct--------------ag
  D                    Parrot  -atg-ca--------tttttgt--tg-cgtcttggttcag--ttctgtgcacct--------------ag
  D             Scarlet macaw  -atg-ca--------tttttgt--tg-cgtcttggttcag--atctgtgcacct--------------ag
  D              Mallard duck  aatg-ca--------ttttcgt-atg-catcttggttcag--ttgtgtgtacct--------------ag
B D                   Chicken  aatg-ca--------tttttgt-atg-catcttggttcag--ttgtgtgtacct--------------ag
B D                    Turkey  aatg-ca--------tttttgt-atg-catcttggttcag--ttgtgtgtacct--------------ag
B D        American alligator  aatg-cc--------ttttcgt-acg-catcttgattcag--ttgtgtgcacct--------------ag
  D           Green seaturtle  aatg-ca--------tttttgt-acg-catcttggttcaa--ttgtgtgcacct--------------ag
  D            Painted turtle  aatg-ca--------tttttgt-acg-catcttggttcaattttgtgtgcacct--------------ag
  D  Chinese softshell turtle  aatg-ca--------tttttgt-acg-catcttggttcaa--ttgtgtgcacct--------------gc
  D    Spiny softshell turtle  aatg-ca--------tttttgt-acg-catcttggttcaa--ttgtgtgcacct--------------ac
B D                    Lizard  ---------------aatttct-aaa-aatccaacttcgg--ttctgttcgtcttttcccttaggcaccg
B D             X. tropicalis  aata-ttttcttccctttttgt-ata-aggcccgcatgaa-------------c--------------a-
B D                 Zebrafish  ggta-tt--------ttattat-ttt-ctatttattgctt-------------t--------------ta

                        Human  atgcttatt-------------tgttttaaa-a-cctgt-atc-atcaaa--------ctctct------
                        Chimp  atgcttatt-------------tgttttaaa-a-cctgt-atc-atcaaa--------ctctct------
                      Gorilla  atgcttatt-------------tgttttaaa-a-cctgt-atc-atcaaa--------ctctct------
                    Orangutan  atgcttatt-------------tgttttaaa-a-cctgt-atc-atcaaa--------ctctct------
                       Gibbon  gtgcttatt-------------tgttttgaa-a-cctgt-atc-atcaaa--------ctctct------
                       Rhesus  atgcttatt-------------tgttttaaa-g-cctgt-atc-atcaaact------ctctct------
          Crab-eating macaque  atgcttatt-------------tgttttaaa-g-cctgt-atc-atcaaact------ctctct------
                       Baboon  atgcttatt-------------tgttttaaa-g-cctgt-atc-atcaaact------ctctct------
                 Green monkey  atgcttatt-------------tgctttaaa-g-cctgt-atc-atcaaa--------ctctct------
                     Marmoset  ctgcttatt-------------tgttttaaa-a-cctgt-gtc-atcaaa--------ctctct------
              Squirrel monkey  atgcttatt-------------tgttttaaa-a-cctgt-atc-atcaaa--------ctctct------
                     Bushbaby  atgcttatt-------------tgttttaag-a-cctgt-atc-atcata--------ctctct------
           Chinese tree shrew  gtgcttgtt-------------tgtgttaca-a-cctac-atc-accaaa--------ctctct------
                     Squirrel  atgcttatt-------------tgtttggaa-a-cctgt-gtc-ataaaa----------ctct------
       Lesser Egyptian jerboa  atgcttatt-------------tgctctgaa-a-cctgt-atc-atcaag--------ctctct------
                 Prairie vole  ttgcttctt-------------tggtctgaa-a-actta-atc-acagaa----------ctct------
              Chinese hamster  atgcttctt-------------tgttttgaa-c-acttt-atc-acaaaa----------ctct------
               Golden hamster  atgcttctt-------------tgttttgaa-a-acttt-atc-acaaaa----------ctct------
                        Mouse  atgcttgtt-------------tgtttggaa-a-tcttt-atc-acaaaa----------ctct------
                          Rat  atacttctt-------------tgtttggaa-a-tcttt-atc-acaaaa----------ctct------
               Naked mole-rat  atgcttatt-------------tgttttaca-a-cctgt-atc-atcaaa--------ctctct------
                   Guinea pig  atgcttatt-------------tgttttaca-a-cctgc-atc-atcgaa--------ctctct------
                   Chinchilla  atgcttatt-------------tgttttaca-a-cctgc-atc-atcaaa--------ctctct------
             Brush-tailed rat  atgcttctt-------------tgttttaca-a-caagc-atc-atcaaa--------ctctct------
                       Rabbit  atccttatt-------------tgttttaaa-a-ccggt-acc-atcaaa--------ctctct------
                         Pika  gtgcttatt-------------tgttttaaa-a-cctgt-atc-atcaaa--------ctctct------
                          Pig  atgcttatt-------------tgttttaaa-a-cccgt-att-atcaaa--------ttctct------
                       Alpaca  atgcttatt-------------cattttaaa-a-cctgt-atc-atccaa--------ctctct------
               Bactrian camel  atgcttatt-------------cattttaaa-a-cctgt-atc-atccaa--------ctctct------
                      Dolphin  atgcttatt-------------tgttttaaa-a-cctgt-atc-atcaaa--------ctctct------
                 Killer whale  atgcttatt-------------tgttttaaa-a-cctgt-atc-atcaaa--------ctctct------
             Tibetan antelope  atgcttctt-------------tgttttaaa-a-catgt-acc-atcaaa--------ctctct------
                          Cow  atacttctt-------------tgttttaaa-a-catgt-acc-atcaaa--------ttctct------
                        Sheep  atgcttctt-------------tgttttaaa-a-catat-acc-atcaaa--------ctctct------
                Domestic goat  atgcttctt-------------tgttttaaa-a-catgt-acc-atcaaa--------ctctct------
                        Horse  atgcttatt-------------tgttttaaa-a-cctgt-atc-atcaaa--------ctctct------
             White rhinoceros  atgcttatt-------------tgttttaaa-a-cctgt-atc-atcaaa--------ctctct------
                          Cat  acgcttctt-------------tgtgttaca-a-cctgt-atc-ctcagact------ctctct------
                          Dog  atgcttatt-------------tgttttaaa-a-cttgt-atc-atcaaa--------ctctct------
                      Ferret   atgcttatt-------------tgttttaaa-aacttgt-atc-gtcaaa--------ctctct------
                        Panda  atgcttatt-------------tgttttcaa-agcctgt-atc-atcaaa--------ctctct------
               Pacific walrus  atgcttatt-------------tgttttaaa-agcctgt-atc-atcaaa--------ctctct------
                 Weddell seal  atgcttatt-------------tgttttaaa-agcctgt-atc-atcaaa--------ctctct------
             Black flying-fox  ctgcttatt-------------tgttttaaa-a-cctat-atc-atcaaa----------ctct------
                Big brown bat  tggcttatt-------------tgttttaaa-a-cctgt-atc-atcaaa--------ctctct------
         David's myotis (bat)  tggcttatt-------------tgttttaaa-a-cctgt-atc-atcaaa----------ctct------
                     Microbat  tggcttatt-------------tgttttaaa-a-cctgt-atc-atcaaa----------ctct------
                     Hedgehog  atgcttatt-------------tgttttaaa-gacctat-atc-attaaa--------ctctct------
                        Shrew  atgcttatt-------------tgttttgaa-g-cctgt-acc-atcaaa--------ctctct------
              Star-nosed mole  ataattttt-------------tgtcttaaa-a-cctat-acc-atcaaa--------ctctct------
                     Elephant  atgcttctt-------------tttgtt-aa-a-cctgtaatc-atcaag--------ctctct------
                      Manatee  atgcttctt-------------tttgtt-aa-a-cctgt-att-atcaag--------ctctct------
             Cape golden mole  atgcttctt-------------ttttttgaa-a-tctgt-acc-atcaag--------ctctct------
                       Tenrec  atccttctttttgtttttgatattttttgaa-g-cctgt-atc-accaa----------tctct------
                     Aardvark  atgcttct--------------tttgttgaa-a-cctgt-atc-atcaag--------ctctct------
                      Opossum  -catgaatc-------------catttgggg-t-tgggt-ttg-atccaagtcttttccttttt------
              Tasmanian devil  -cgcaaatc-------------ccttttgtg-c-tgtgt-ttg-atccaagtcttttgcttcttttgttt
                      Wallaby  -cacgaatc-------------cattttgtg-a-agcgt-ttg-atctaagtcttctacttttt------
                  Rock pigeon  aaaataatt-------------tttacaaaa-a-tctgc-atg-a--aaa----------ctataac---
                 Saker falcon  aaaataatt-------------tttatgaaa-a-tctgc-atg-a--aaa----------ctataac---
             Peregrine falcon  aaaataatt-------------tttatgaaa-a-tctgc-atg-a--aaa----------ctataac---
          Collared flycatcher  aaaataatt-------------tttacaaaa-a-tctgc-atg-a--aaa----------ctataac---
       White-throated sparrow  aaaataatt-------------tttacaaaa-a-tctgc-atg-a--aaa----------ctataac---
          Medium ground finch  aaaataatt-------------tttacgaaa-a-tctgc-atg-a--aaa----------ctataac---
                  Zebra finch  aaaataatt-------------tttacagaa-a-tttgc-atg-a--aaa----------ctataac---
           Tibetan ground jay  aaaataatt-------------tttacaaaa-a-tctgc-atg-a--aaa----------ctataac---
                   Budgerigar  aaaataagt-------------tttacaaaaga-tctgc-atg-a--aag----------ctctaaggt-
                       Parrot  aaaacaact-------------ttgacaaaaga-tctgc-atg-a--aaa------------cgaagg--
                Scarlet macaw  aaaataact-------------ttgacaaaaga-tctgc-atg-a--gaa----------ctcgaagg--
                 Mallard duck  aacataatt-------------tttacaaga-a-tctgc-atgaa--aaa----------atataactt-
                      Chicken  aacataatt-------------tttacagaa-a-tctgc-atg-a--caa----------atataac---
                       Turkey  aacataatt-------------tttacagaa-a-tctgc-atg-a--gaa----------atataactt-
           American alligator  aaaataatt-------------tttacaaa--g-tctgc-atg-a--aaa----------ctat-ac---
              Green seaturtle  aaaataatt-------------tttacaaa--t-cctgc-atg-t--aaa-------cttctgttac---
               Painted turtle  aaaataatt-------------tttacaaa--t-cctgc-atg-t--aaa-------cttctattac---
     Chinese softshell turtle  aaaataatt-------------tttacaga--a-cctgc-atg-t--aaa-------cttctgttactt-
       Spiny softshell turtle  aaaataatt-------------tttacaga--a-cctgc-atg-t--aaa-------cttctattactt-
                       Lizard  aaacttctt-------------tttag-----a-tctgt-----g--gat--------------------
                X. tropicalis  ----ttatt-------------gttttggtt-t-ttttt-ttt-gtaaca--------attttt------
                    Zebrafish  aagttaatt-------------tattgtat--t-tatgc-ata-ttgaat----------ctcc------

                        Human  --ctctaaa----ttt-aaaatgctgttgaatat-gatac--------------------ttttgagga-
                        Chimp  --ctctaaa----ttt-aaaatgctgttgaatat-gatac--------------------ttttgagga-
                      Gorilla  --ctctaaa----ttt-aaaatgctgttgaatat-gatac--------------------ttttgagga-
                    Orangutan  --ctctaaa----ttt-aaaatgctgttgaatat-gatat--------------------ttttgagga-
                       Gibbon  --ctctaaa----ttt-aaaatgctgttgaatat-gatac--------------------ttttgagga-
                       Rhesus  --ctctaaa----ttt-aaaatgctgttgaatat-gatac--------------------ttttgagga-
          Crab-eating macaque  --ctctaaa----ttt-aaaatgctgttgaatat-gatac--------------------ttttgagga-
                       Baboon  --ctctaaa----ttt-aaaatgctgttgaatat-gatac--------------------ttttgagga-
                 Green monkey  --ctctaaa----ttt-aaaatgctgttgaatat-gatac--------------------ttttgagga-
                     Marmoset  --ctttaaa----ttt-aaaatgctgttgaatat-gatac--------------------ttttgagga-
              Squirrel monkey  --ctttaaa----ttt-aaaatgctgttgaatat-gatac--------------------ttttgagga-
                     Bushbaby  --ctttaaa----ttt-aaaatgctgcggaatag-gacac----------------------ctgagga-
           Chinese tree shrew  --ctttaaa----ttt-aaaatgctggtgactat-gacac--------------------ttttgagga-
                     Squirrel  --ctctttaaattttt-aaaatgctgt-----------------------------------ttgagga-
       Lesser Egyptian jerboa  --ctttcaa----tcg-aaaataccattgaatat-ggccc----------------------ttgagga-
                 Prairie vole  --ctttcaa----tct-aaaattctgttgaacat-gacac--------------------ttaggagga-
              Chinese hamster  --catttga----tct-aaaatgctgttgaatat-gacac--------------------ctttgagga-
               Golden hamster  --cgtttga----tct-aaaatgctgttgaatat-tacac--------------------ttttgggaa-
                        Mouse  --ttttcag----tct-aaaatgctgttgaacat-gacac--------------------ttttgaaga-
                          Rat  --tttt-gg----tct-acaatgctgttgaatat-gacac---------------------tttgaggg-
               Naked mole-rat  --ctttaaa----ttt-aaaatactgttggacaa-gacag----------------------atgggga-
                   Guinea pig  --ctttaaa----ctt-aaaataatgttggacag-gacaa----------------------ttgggga-
                   Chinchilla  --ctttaaa----ttt-aaaatactgttggacag-gacag----------------------ttgggga-
             Brush-tailed rat  --ctttaaa----ttt-aaaatactgttggacag-gacag----------------------ttgggga-
                       Rabbit  --ctttaca----ttt-aaaatgctgttgaatgt-gacac--------------------ttttgagga-
                         Pika  --ctttaca----ttt-aaaatgctgttgactat-gacac--------------------ttctgagga-
                          Pig  --ctttaga----ttt-aaaatggtgttgaatat-gacac--------------------ttttgagga-
                       Alpaca  --ctttaga----ttt-caaatgctgttgagtat-gacat--------------------ctttgagga-
               Bactrian camel  --ctttaga----ttt-caaatgctgttgagtat-gacat--------------------ctttgagga-
                      Dolphin  --ctttaga----ttt-aaagtgctgttgaatat-gacac--------------------ttttgagga-
                 Killer whale  --ctttaga----ttt-aaagtgctgttgaatat-gacac--------------------ttttgagga-
             Tibetan antelope  --ctttaga----ttt-aaaatgctgttgaatat-gacac--------------------ttttgagga-
                          Cow  --ctttaga----ttt-taaatgctgttgaatat-gacac--------------------ttttgagga-
                        Sheep  --ctttaga----ttt-aaaatgctgttgaatat-gacac--------------------ttatgagga-
                Domestic goat  --ctttaga----ttt-aaaatgctgttgaatat-gacac--------------------ttttgagga-
                        Horse  --ctttaga----ttt-aaaatgctgttgactat-gaca---------------------ttttgagga-
             White rhinoceros  --ctttaga----ttt-gaaatgctgttgactat-gaca---------------------ttttgagga-
                          Cat  --ctctgga----tttaaaaatgttgttga--at-gacac--------------------ttttgagga-
                          Dog  --ctttaga----ttg-aaaatgctgttgaatat-gacac--------------------ttttgagga-
                      Ferret   --ctttaga----ttt-aaaatgctgttgaatat-gacac--------------------ttttgagga-
                        Panda  --ctttaga----ttt-aaaatgctgttgaatat-gacac--------------------ttttgagga-
               Pacific walrus  --ctttaga----ttt-aaaatgctgatgaatat-gacac--------------------ttttgagga-
                 Weddell seal  --ctttaga----ttt-aaaatgctgttgaatat-gacac--------------------ttttgagga-
             Black flying-fox  --ctctaga----ttt-aaaatgctattgaatat-gccac--------------------ttctgagga-
                Big brown bat  --ctttaga----ttt-aaaatgctgttgaatat-gacac--------------------tttccagga-
         David's myotis (bat)  --ctttaga----ttt-aaaatgctgttgaatat-gacac--------------------tttcaagga-
                     Microbat  --ctttaga----ttt-aaaatgctgttgaagat-gacac--------------------tttcgagga-
                     Hedgehog  --ctttaga----ttt-aaaacactgttgtgcat-gacac---------------------tttgagga-
                        Shrew  --ctgtaga----ttt-aaaaagctttggagtac-gatgc--------------------ttttgagga-
              Star-nosed mole  --ctttagg----ttt-aaaatgctgttgaatct-gacac--------------------ttttgagga-
                     Elephant  --ctttaaa----ttt-aaaatgctgttgagtat-gacac--------------------ttttcagga-
                      Manatee  --ctttaaa----ttt-aaaatgctgttgaatat-ggtac--------------------ttttcagga-
             Cape golden mole  --ctttaca----ttt-aaaaagctgttgaacag-gacac--------------------ttttgaggg-
                       Tenrec  --ctttaaa----tcg-aaaatgctgttgaatag-gacac--------------------tattgaagg-
                     Aardvark  --ctttcaa----ttt-aaaatactgttgaatat-gacac--------------------cttggaaga-
                      Opossum  --ttaaaaa----ttg-aaaatgctgttgaatag-aagata-------------------tttttaggg-
              Tasmanian devil  tgttttaaa----ttg-aaaatgctgttgaatagtaactat-------------------gtttcaggg-
                      Wallaby  --ttttcat----ttg-aaaa---tgttgaatag-aattct-------------------ttttcaggg-
                  Rock pigeon  --tttttta----ttt-aaaatgctgttggatat-aaaaccatactacattgtggggaggttttatgca-
                 Saker falcon  --tttttta----ttt-aaaatgctgttggatat-aaacccaatatacattgtggggaggttttgtgca-
             Peregrine falcon  --tttttta----ttt-aaaatgctgttggatat-aaacccaatatacattgtggggaggttttgtgca-
          Collared flycatcher  --tttttta----ttt-aaaatgctgttagatac-aaaaccatactacattgtggggaggttttgtgca-
       White-throated sparrow  --tttttta----ttt-aaaatgctgttagatac-aaaaccatactacattgtggagaggttttgtgca-
          Medium ground finch  --tttttta----ttt-aaaatgctgttagatac-aaaaccatactacattgtggagaggttttgtgca-
                  Zebra finch  --tttttta----ttt-aaaatgctgttaaatac-aaaaccatactacattgtggagcggttttgtgca-
           Tibetan ground jay  --tttttta----ttt-aaaatgctgttagatac-aaaaccatactacattgtggagaggttttgtgca-
                   Budgerigar  --tttttta----ttt-aaaacgctgttggatat-aaacccatactccgtgggggggaggttttatgcag
                       Parrot  --ggtttta----ttt-aaaacgctgttggatat-aaacccatgctccgt-ggggggaggttttgtgcag
                Scarlet macaw  --tttttta----ttt-aaaacgctgttggatat-aaacccatgctccgt-ggggggaggttttatgcag
                 Mallard duck  --tttttta----ttt-aaaatgttgttggatat-aaaaccatactacattgtggggaggttttgtgca-
                      Chicken  --tttttta----ttt-aaaatgctgttggatat-aaaaccatactacattgtggggaggttttgtgca-
                       Turkey  --tttttta----ttt-aaaatgctgttgaatat-aaaaccatactacactgtggggaggttttgtgca-
           American alligator  --tttttta----ttt-aaaatgctgttggatat-aaaactacagaacattgtgggcaggttttgtgag-
              Green seaturtle  --tttttta----ttt-aaaatgctgttgggaat-aaaacaataaaacgctgtagggcag--ctatgaa-
               Painted turtle  --tttttta----ttt-aaaattctgttgggaat-aaaacc--------ttgtagggcgg--ttgtgaa-
     Chinese softshell turtle  --tttttta----ttt-aaattgctgttggaact-aaaacaagaaaacattgcagggtgg--ctgagaa-
       Spiny softshell turtle  --tttttta----ttt-aaattgctgttggaact-aaaacaagaaaacattgcagggtgg--ctgtgaa-
                       Lizard  --tttttta----aaa-aaaatgcaat---attt-aagatactattattttcagag------ctagacag
                X. tropicalis  --atttaaa----gtt-atatta--gttataaat-aacat--------------------tcctgtttt-
                    Zebrafish  --ttttcta----ttt-tatgtactatttattgg-tattt--------------------atttaactt-

                        Human  --gagagtg--------tgctcagaac----ttaga---c---ggga-t-----ttggta-ggc------
                        Chimp  --gagagtg--------tgctcagaac----ttaga---c---ggga-t-----ttggta-ggc------
                      Gorilla  --gagagtg--------tgctcaaaac----ttaga---c---ggga-t-----ttggtg-ggc------
                    Orangutan  --gagagtg--------tgctcagaac----ttaga---c---ggga-t-----ttggta-ggc------
                       Gibbon  --gagagtg--------tgctcagaac----ttaga---c---ggga-t-----ttggta-ggc------
                       Rhesus  --gagaatg--------tgctcagaac----ttaga---c---ggga-t-----ttagta-ggc------
          Crab-eating macaque  --gagaatg--------tgctcagaac----ttaga---c---ggga-t-----ttagta-ggc------
                       Baboon  --gagaatg--------tgctcagaac----ttaga---c---ggga-t-----ttagta-ggc------
                 Green monkey  --gagaatg--------tgctcagaac----ttaga---c---ggga-t-----ttagta-ggc------
                     Marmoset  --gagagta--------tgctcagaat----tta----------gga-t-----ttggta-ggc------
              Squirrel monkey  --gagagta--------tgctcagaat----tta----------gga-t-----ttggta-ggc------
                     Bushbaby  --gagagtg--------tgctcagaac----tttga---c---agga-t-----tcggta-ggc------
           Chinese tree shrew  --gagagtg--------tgctcagaac----ttagg---c---agga-t-----ttggta-ggc------
                     Squirrel  --gagagtg--------cattcagaac----ttaaa---t---ggga-t-----tcggta-ggc------
       Lesser Egyptian jerboa  --gagagtg--------aatgcagaac----ttgga---t---gaaa-t-----tgtgta-ggc------
                 Prairie vole  --ggaagtg--------agctcagaat----ttaga---tg--atga-t-----tcaata-agc------
              Chinese hamster  --gagagtg--------ggctcagaat----ttaga---t---ggga-c-----tcaata-agc------
               Golden hamster  --gagagtg--------agctcagaat----ttcaa---tg--ggga-c-----tcaata-agc------
                        Mouse  --gagggtg--------ggctcagaat----ttaga---cg--ggaa-t-----ttgata-agc------
                          Rat  --gagagtg--------ggctcagaat----ttaga---tg--ggaa-t-----ttgata-agc------
               Naked mole-rat  --gagaatg--------aggtcagagt----gtaga---t---ggga-t-----acggta-ggc------
                   Guinea pig  --gagagtg--------aagtcagagt----gtaga---t---ggga-c-----acgata-ggc------
                   Chinchilla  --gagagtg--------aggtcagagt----gtagg---t---ggga-t-----acggta-ggc------
             Brush-tailed rat  --gagagtg--------aggtcagaat----gtaga---t---ggga-t-----atggta-ggc------
                       Rabbit  --gagagta--------tgctcagaac----ttaga---c---agga-t-----tcggta-ggc------
                         Pika  --gagagta--------tgcttggaac----ataga---c---agga-t-----ttagta-gac------
                          Pig  --gagggta--------tgctcagaac----ttagg---c---agga-t-----acagta-ggc------
                       Alpaca  --gagagtg--------tgcgcagaac----ttaga---c---agga-t-----acggta-ggc------
               Bactrian camel  --gagagtg--------tgcacagaac----ttaga---c---agga-t-----acggta-ggc------
                      Dolphin  --gagagtg--------ggctcagaat----ttagg---c---agga-t-----acggta-ggc------
                 Killer whale  --gagagtg--------ggctcagaat----ttagg---c---agga-t-----acggta-ggc------
             Tibetan antelope  --gagagtg--------ggctcagaat----ttagg---a---agga-t-----atggta-ggc------
                          Cow  --gagagtg--------ggctcagaat----ttagg---a---agga-t-----atgata-ggc------
                        Sheep  --gagagtg--------ggctcagaat----ttagg---a---agga-t-----atggta-ggc------
                Domestic goat  --gagagtg--------ggctcagaat----ttagg---a---agga-t-----atggta-ggc------
                        Horse  --gagagtg--------tgctcagaac----tt----------agga-c-----acagta-ggc------
             White rhinoceros  --gagagtg--------tgctcagaac----tt----------agga-t-----acggta-ggc------
                          Cat  --gagagtg--------tgctcggacc----gtaga---c---agga-----------------------
                          Dog  --gagagtg--------tgctcagaac----gtgga---c---agga-t-----acagta-ggc------
                      Ferret   --gagagcg--------tgctcagaat----gtaga---c---agga-g-----acggta-ggc------
                        Panda  --gagagtg--------tgctcagaac----gtaga---c---agta-t-----gtggta-ggc------
               Pacific walrus  --gagagtg--------tgctcagaat----gtaga---c---agga-g-----acggta-ggc------
                 Weddell seal  --gagagtg--------cgctcagaat----gcaga---c---agga-g-----acggta-ggt------
             Black flying-fox  --gagagtg--------tgctcagaac----t-------t---agga-t-----aaggta-ggc------
                Big brown bat  --gagagta--------tgctcagaac----ttaag---t---agga-t-----acagta-ggc------
         David's myotis (bat)  --gagagta--------tgctcagaac----ttagg---t---aggg-t-----gcagta-ggc------
                     Microbat  --gagagta--------tgctcagaac----ttagg---t---agga-t-----gcagta-ggc------
                     Hedgehog  --gagaacc--------tgttcagaac----tt----------agga-t-----acagta-gga------
                        Shrew  --gagagtg--------ggttcagaac----tt----------agga-t-----acagta-gga------
              Star-nosed mole  --gagagta--------tgctcagaac----tt----------agga-t-----acagcc-gga------
                     Elephant  --aagagag--------gactcagaaa----ttagc---t----gga-t-----gcagta-ggc------
                      Manatee  --aagagag--------tactcagaag----ttagc---c---agga-t-----gcagta-ggc------
             Cape golden mole  --aggagag--------tgctcagaag----ttagc---c---gtga-t-----gcagta-ggc------
                       Tenrec  --aagagag--------tgctcagaag----ttagc---c---agga-t-----gcaatagggc------
                     Aardvark  --aagagag--------tgctcagaag----ttagc---c---agga-t-----gcagta-gag------
                      Opossum  --gagggag--------tgctatgaatagctgcagt---t---agtc-t-----agggta-gag------
              Tasmanian devil  --gagggaa--------tgctatgaccagctcaagt---c---agta-g-----caggta-gag------
                      Wallaby  --gagggag--------tactatgaacagcttgagt---ca--agta-g-----ggggta-gag------
                  Rock pigeon  --gggaaaa--------ggcaaatgtt----ataaa---cagtaggg-t-----tcaaca-agctgaata
                 Saker falcon  --gggaaga--------ggcaagtgtc----ataaa---caccaggg-t-----tcaatc-aactgaaca
             Peregrine falcon  --gggaaga--------ggcaagtgtc----ataaa---caccaggg-t-----tcaatc-aactgaaca
          Collared flycatcher  --gggaaga--------ggcaaatggt----ataaa---cagcaggg-t-----tcaata-aagtgaaca
       White-throated sparrow  --gggaaga--------ggcaaatggt----ataaa---cagcaggg-t-----tcaata-aagtgaaca
          Medium ground finch  --gggaaga--------ggcaaatggt----ataaa---cagcaggg-t-----tcaata-aagtgaaca
                  Zebra finch  --gggaaga--------ggcaaatggt----ataaa---cagcaggg-t-----tcaata-aagtgaaca
           Tibetan ground jay  --gggaaga--------ggcaaatggt----ataaa---cagcaggg-t-----tcaata-aagcgaaca
                   Budgerigar  --gggaaga--------ggcaaatgtt----agaaa---cagcaggg-t-----tcaata-aactgaaca
                       Parrot  --gggaaga--------ggcaaatgtt----agaaa---cagcaggg-t-----tcaata-aactgaaca
                Scarlet macaw  --gggaaga--------ggcaaatgtt----agaaa---cagcaggg-t-----tcaata-aactgaaca
                 Mallard duck  --gggaaga--------ggcaaatgtt----gtgaa---cagcaggg-t-----tcaata-aactgaaca
                      Chicken  --gggaaga--------ggcaaatatt----atgaa---cagcaggg-t-----tcaata-aactgaaga
                       Turkey  --gggaaga--------ggcaaatatt----atgaa---cagcaggg-t-----tcaata-aactgaaga
           American alligator  --gggaaga--------agcaaatgtt----acaaa---cagcaggg-t-----tcaata-aactgaaca
              Green seaturtle  --gggaaga--------aacaaatgtt----atgaa---cagcaggg-t-----taagta-atctgaact
               Painted turtle  --gggaaga--------ggcaaatgtt----acaaacagcagcaggg-t-----taagta-atctgaact
     Chinese softshell turtle  --gggaaga--------ggcaaaggtg----tcaca---cagcaggg-taatcaaaggta-atccaaact
       Spiny softshell turtle  --gggaaga--------ggcaaatgtc----acaca---cagcaggg-taatcaaaggta-atccaaact
                       Lizard  atgggacca--------ggtcagtccc----acaaa---catcagggac-----ttaaag-agccaaac-
                X. tropicalis  --atctgga--------aatgctggtt----tcata---c---atgc-c-----acagag-cga------
                    Zebrafish  --tatttaattttcttttgtttaattt----ttaag---tat-gtgt-t-----tatata-aag------

                        Human  -c-aagtatgct-aagtgtac---------a--at--ata---ttt---tttaatttt-----acacctg
                        Chimp  -c-aagtatgct-aagtgtac---------a--at--ata---ttt---tttaatttt-----acaccta
                      Gorilla  -c-aagtatgct-aagtgtac---------a--at--ata---ttt---tttaatttt-----acaccta
                    Orangutan  -c-aagtatgct-aagtgtac---------a--at--ata---ttt---tttaatttt-----acaccta
                       Gibbon  -c-aagtatgct-aagtgtac---------a--at--ata---ttt---tttaatttt-----acaccta
                       Rhesus  -c-gagtatgct-aagtgtac---------a--at--ata---ttt---tttaatttt-----acaccta
          Crab-eating macaque  -c-gagtatgct-aagtgtac---------a--at--ata---ttt---tttaatttt-----acaccta
                       Baboon  -c-gagtatgct-aagtgtac---------a--at--ata---ttt---tttaatttt-----acaccta
                 Green monkey  -c-gagtatgct-aagtgtac---------a--at--ata---ttt---tttaatttt-----acaccta
                     Marmoset  -c-aagtctgct-gagtgtac---------a--at--gta---ttt---ttaaatttt-----acaccta
              Squirrel monkey  -c-aagtatgct-aagtgtac---------a--at--ata---ttt---ttaaatttt-----acaccta
                     Bushbaby  -c-aagtatgct-aagtgtat---------g--at--gta---ttt---tttaatttc-----acaccta
           Chinese tree shrew  -c-gtgtatgct-gtgtgtac---------g--at--ata---ttt---tttaatgtt-----acaccta
                     Squirrel  -c-aactatgct-aagtgtac---------g--at--ata---ttt---tttaatttt-----acaccta
       Lesser Egyptian jerboa  -c-aagtctgct-aagtgtac---------a--at--aca---ttt---ttaaatttt-----actccta
                 Prairie vole  -a-aagaatgcc-aaatgaac---------a--at--aga---ttt---ataaattca-----acactta
              Chinese hamster  -a-aagtatgct-aagtgtac---------a--at--aga---ttt---ttaaattta-----acgcatc
               Golden hamster  -a-aagtatgct-aagtgtac---------a--at--ata---ttt---ttaaattta-----acacata
                        Mouse  -a-aagaatgctaaaatgtac---------a--at--gga---ttt---ttaa-tttt-----acaccta
                          Rat  -a-aagaatgctaaagtgtac---------a--at--ata---tgt---ttaagtttc-----acacctg
               Naked mole-rat  -c-aagtatgat-aagtgtac---------a--at--ata---ttt---tttaatttt-----acaccca
                   Guinea pig  -c-aagtatgct-aagtgtac---------a--at--ata---ttt---tttaatttt-----acaccta
                   Chinchilla  -t-aagcatgct-ctgtgtac---------a--at--ata---ttt---tttaatgtt-----acaccta
             Brush-tailed rat  -c-aagtatgct-ccgtgtac---------a--at--ata---ttt---tttaatttt-----acgccta
                       Rabbit  -c-aagtgtgct-aagtgtac---------a--at--ata---ttt---ttaaatttt-----acatcta
                         Pika  -c-aa-tatgct-aagtgtac---------a--at--ata---ttt---ttaaatttt-----acatcta
                          Pig  -c-aggtatgct-aagtgtat---------a--at--aaa---ttt---tctaatttt-----acaccta
                       Alpaca  -c-aagtatgct-aagtgtac---------a--gt--aaa---ttt---tctaatttt-----acaccta
               Bactrian camel  -c-aagtatgct-aagtgtat---------a--gt--aaa---ttt---tctaatttt-----acaccta
                      Dolphin  -c-aagtatgct-aagtgtat---------a--at--aaa---ttt---tctaatttt-----acaccta
                 Killer whale  -c-aagtatgct-aagtgtat---------a--at--aaa---ttt---tctaatttt-----acaccta
             Tibetan antelope  -c-aagtatgct-aagtgtataattttctaa--tt--aaa---ttt---tctaatttt-----acaccta
                          Cow  -c-aagtatgct-aagtctat---------a--tt--aaa---ttt---tctaatttt-----acaccta
                        Sheep  -c-aagtatgct-aagtgtat---------a--tt--aaa---ttt---tctaatttt-----acaccta
                Domestic goat  -c-aagtatgct-aagtgtat---------a--tt--aaa---ttt---tctaatttt-----acaccta
                        Horse  -c-aagtttgct-aagtgtac---------a--at--aaa---ttt---tctaatttt-----acaccta
             White rhinoceros  -c-aagtttgct-aagtatac---------a--at--aaa---ttt---tctaatttt-----acaccta
                          Cat  ------tatgct-aagtgtac---------c--at--cga---att---tccaatttt-----acaccta
                          Dog  -c-aagcatgct-aagcatac---------c--at--aaa---ttt---tctaatttt-----acaccta
                      Ferret   -c-aagcatgct-aagtgtac---------c--at--aaa---ttt---tctaatttt-----ccaccta
                        Panda  -c-aagcatgct-aaacgtac---------c--at--aaa---ttt---tctaatttt-----ccaccta
               Pacific walrus  -caaagcatgct-aagcgtac---------c--at--aaa---ttt---tctaatttt-----ccaccta
                 Weddell seal  -c-aagcatgct-aagcgtac---------c--at--aaa---ttt---tctaatttt-----ccaccta
             Black flying-fox  -c-aactgtgct-aagtgtaa---------a--at--aga---ttt---tctaatttt-----acaccta
                Big brown bat  -c-aggtatgct-aagtgtac---------a--at--aga---ttt---tctaatttt-----acatcta
         David's myotis (bat)  -c-aggtatgct-aagtgtac---------a--at--aga---ttt---tctaatttt-----acaccta
                     Microbat  -c-aggtatgct-aagtgtac---------a--at--aga---ttt---tctaatttt-----acaccta
                     Hedgehog  -c-caggatgct-aaatatac---------c--ag--agatttttt---tctagaatt-----acaccta
                        Shrew  -c-aggtgtgct-aagtgtac---------a--at--aca---ttt---tctaatttt-----acatctg
              Star-nosed mole  -c-aagtatgct-aagtgtac---------a--at--aaa---ttt---ttgagtttt-----acaccta
                     Elephant  -c-aagtatgct-aagtgtac---------a--at--ac----ttt---tttaatttt-----acaccta
                      Manatee  -c-aagtatgct-aagtgtac---------a--aa--at----ttt---tgtaatttt-----acaccta
             Cape golden mole  -c-aagtatgct-aagtgtac---------aattt--tt----ttt---tttaatttt-----acaccta
                       Tenrec  -c-aagtatgct-aactgtac---------a--ct--gt----ttt---ttcaatttt-----acaccta
                     Aardvark  -c-aagtatgct-aagtgtac---------a--at--at----ttt---ttaaatttt-----acaccta
                      Opossum  -g-cagtgtgct-gattcaaaaagta----a--at--aca---cta---gtgggcttt-----ccaccta
              Tasmanian devil  -c-cagtgtgcc-gattctcgagata----a--at--aca---cc-----------------------ga
                      Wallaby  -c-cagtgtgcc-gattctcaagata----a--at--aca---ctg---------tct-----acacggc
                  Rock pigeon  gc-aaatgtgct-gga---ac---------a--ta--aaa---gta---t----tttt-----acagata
                 Saker falcon  gc-aaatgtgct-gga---ac---------a--ta--aaa---cta---t----tttt-----acagata
             Peregrine falcon  gc-aaatgtgct-gga---ac---------a--ta--aaa---cta---t----tttt-----acagata
          Collared flycatcher  gc-aaatgtgct-gga---at---------a--ta--aaa---tta---t----tttt-----acagata
       White-throated sparrow  gc-aactgtgct-gga---at---------a--ta--aaa---tta---t----tttt-----agagata
          Medium ground finch  gc-aaatgtgct-gga---at---------a--ta--aaa---tta---t----tttt-----agagata
                  Zebra finch  gc-aaatgtgct-gga---at---------a--ta--aag---tta---t----tttt-----agagata
           Tibetan ground jay  gc-aaatgtgct-gga---at---------a--ta--aaa---tta---t----tttt-----acagata
                   Budgerigar  gc-agctgtgct-gga---ac---------a--ta--aaa---cta---t----tttt-----acagata
                       Parrot  gc-aactgtgct-gga---ac---------a--ta--aaa---ctg---t----tttt-----acagata
                Scarlet macaw  gc-aactgtgct-gga---ac---------a--ta--aaa---cta---t----tttt-----acagata
                 Mallard duck  gc-aaatgcgct-gga---at---------a--ta--aaa---tta---t----tttt-----acagaaa
                      Chicken  gc-aaatgtgct-gga---at---------a--ta--aaa---cta---t----tttt-----acagatg
                       Turkey  gc-aaatgtgct-gga---at---------a--ta--gaa---cta---t----tttt-----acagatg
           American alligator  gc-aactgtgcc-gaa---ac---------a--ga--aaa---cta---t----tttt-----gcagaaa
              Green seaturtle  gc-aaa-gtgcc-gag---ac---------c--ta--aaa---cta--tt----tttt-----acaaata
               Painted turtle  gc-aaa-gtgct-gag---ac---------a--ca--aaa---cta--tt----tttt-----acaacta
     Chinese softshell turtle  gc-aaa-gtgcc-gag---ac---------g--ta--aaa---ctg--tt----tttt-----acaacta
       Spiny softshell turtle  gc-aaa-gtgcc-gag---ac---------g--ta--aaa---ctgtttt----tttt-----acaaata
                       Lizard  -------gtgcc-gag---aa---------g--gaagaaa---cta-ttt----tttt-----ataaagg
                X. tropicalis  -a-aactgcaca-tgg----c---------a--gg--aag---ttt---catatctctgcaaaacaaata
                    Zebrafish  -g-aag-atgat-ttgtatat---------a--at--taa---tca---a------tt-----atggat-

                        Human  aaac-------aa----agaaatgtggtcact---aa---------aaata----a-aag---t----at
                        Chimp  aaac-------aa----agaaatgtggtcact---aa---------aaata----a-aag---t----at
                      Gorilla  aaac-------aa----agaaatgtggtcact---aa---------aaata----a-aag---t----at
                    Orangutan  aaac-------ag----agagatgtggtcact---aa---------aaata----a-aag---t----at
                       Gibbon  aaac-------aa----agaaatgtggtcact---aa---------aaata----a-aag---t----at
                       Rhesus  aaac-------aa----agaactgtggtcact---aa---------aaata----a-acg---t----at
          Crab-eating macaque  aaac-------aa----agaactgtggtcact---aa---------aaata----a-acg---t----at
                       Baboon  aaac-------aa----agaactgtggtcact---aa---------aaata----a-acg---t----at
                 Green monkey  aaac-------aa----agaactgtggtcact---aa---------aaata----a-gcg---t----at
                     Marmoset  aaac-------aa----agaaatgtggtcact---aa---------aaata----a-aaa---t----at
              Squirrel monkey  aaac-------aa----agaaatgtggtcact---aa---------aaata----a-aag---t----at
                     Bushbaby  aga--------------aaagatgtcatcact---aa---------aaata----a-aa----t----at
           Chinese tree shrew  aaat-------aa----ggacatgtggtcact---aa---------aagga----a-aaa---t----at
                     Squirrel  aaac-------aa----aaagctgtggtcact-a-aa---------aagta----a-ggt---t----at
       Lesser Egyptian jerboa  taac-------aac---aaaggtatg---------aa---------aagtc----a-aag---t----at
                 Prairie vole  taac-------aa------agatgtggttatg-a-ga---------aagag----a-aag---t----at
              Chinese hamster  taac-------aa----ggagatgtggtcacg-a-aa---------agggg----a-aag---t----at
               Golden hamster  taac-------aa----ggagatgtgatcaca-agaa---------aaggg----a-aag---t----at
                        Mouse  taac-------aa----ggagatgtggtctca-g-aa---------atggg----a-aag---t----at
                          Rat  taac-------aa----ggagatgtggtcaca-a-aa---------atgag----a-aa-----------
               Naked mole-rat  caac-------aa----gaggatgtgatcact-a-aa---------aagta----a-aag---t----at
                   Guinea pig  caac--------------gagatgtggtcact-a-aa---------aagta----a-aag---t----ct
                   Chinchilla  caac-------aa----agagatgtggtcact-a-aa---------aagta----a-aag---t----at
             Brush-tailed rat  caag-------aa----gaagatgtgatcactaa-aa---------aagta----a-aag---t----at
                       Rabbit  aaac-------aa----ggagatgtggtcact---aa---------aattg----a-aaa---t----at
                         Pika  aaac-------aa----gaaaat---gtcact---aa---------aatta----a-aaa---t----at
                          Pig  aaat-------aa----ggaaatgtggtcact---aa---------aaat-------aaa---c----at
                       Alpaca  agac-------aa----ggagatgtggtcact-a-aa---------aaat-------aaa---c----at
               Bactrian camel  agac-------aa----ggagatgtggtcact-a-aa---------aaat-------aaa---c----at
                      Dolphin  agac-------aa----ggagatgcggtcact-a-aa---------aaat-------aaa---c----at
                 Killer whale  agac-------aa----ggagatgtggtcact-a-aa---------aaat-------aaa---c----at
             Tibetan antelope  agat-------aa----ggagatgcggtcact-a-aa---------aaat-------aag---c----at
                          Cow  agat-------aa----ggagatgtggtcact-a-aa---------aaat-------aaa---c----at
                        Sheep  agat-------aa----ggagatgcggtcact-a-aa---------aaat-------aaa---c----at
                Domestic goat  agat-------aa----ggagatgcggtcact-a-aa---------aaat-------aaa---c----at
                        Horse  agac-------aa----ggagatgtgggcact-a-aa---------aaata----a-aaa---t----at
             White rhinoceros  agac-------aa----ggagatgtggtcact-a-aa---------aaata----a-aaa---t----at
                          Cat  agac-------aa----ggagatgtggtcact-a-ga---------gaata----a-aaa---t----at
                          Dog  aaac-------aa----ggagatgaggtcact-a-aa---------aaata----a-aaa---t----ac
                      Ferret   aaac-------aa----ggagatgcggtcgct-a-aa---------aaat-----a-aaa---t----at
                        Panda  aaac-------aa----ggagatgtggtcact-a-aa---------aaata----a-aaa---t----at
               Pacific walrus  aaac-------aa----ggagacgtggtcact-a-aa---------aaata----a-aaa---t----at
                 Weddell seal  aaac-------aa----ggagacgtggtcact-a-aa---------aaata----a-aaa---t----at
             Black flying-fox  agac-------aa----ggagatgtggtcact-a-aa---------a-ata----a-aaa---ttaaaat
                Big brown bat  aggc-------aa----ggagatgtggtcact-a-aa---------acata----a-aaa---t----at
         David's myotis (bat)  agac-------aa----ggagatgtggtcact-a-aa---------acata----a-aaa---tc---at
                     Microbat  agac-------aa----ggagatgtggacact-a-aa---------acata----a-aaa---tt---at
                     Hedgehog  agac-------aa----ggagatatggtcact-c-ag---------atata----a-aaa---c----at
                        Shrew  aaac-------aa----ggagatgtggtcact-a-ag---------gtata----a-aaa---t----ac
              Star-nosed mole  agac-------aa----ggaaatgtggtcact-a-aa---------atata----a-aaa---t----at
                     Elephant  aaac-------aa----ggagatgtggtcact-a-aa---------aaata----a-aag---t----at
                      Manatee  aaac-------aa----ggagatgtggtcact-a-aa---------aaata----a-aag---t----at
             Cape golden mole  aaac--------a----ggagatgtggtcact-a-aa---------atatt----gaaaa---c----tt
                       Tenrec  a-----------------gagatgtggtccct-a-ag---------aaata----g-aaa---t----at
                     Aardvark  aaac-------aa----ggaaatgtggtcact-a-aataaaaaaataaaaa----a-aat---t----at
                      Opossum  aaac-------aa----ggagcagtgatcacc-a-aa---------gaaggaagaa-aaa---t----gt
              Tasmanian devil  aaac-------ga----ggagcagtgctcacc-a-aa---------gaaggaagaa-aaa---t----gt
                      Wallaby  aaac-------ga----ggagcagtgatcacc-a-aa---------gaaggaag-a-taa---t----gt
                  Rock pigeon  a----------aa----ggaagcattgtcgcc-a-aa---------gaagg----a-agatgct----gt
                 Saker falcon  a----------aa----ggaagcattgtcgcc-a-aa---------gaagg----a-agatgct----gt
             Peregrine falcon  a----------aa----ggaagcattgtcgcc-a-aa---------gaagg----a-agatgct----gt
          Collared flycatcher  aatg------gaa----ggaagcattgtcgcc-a-aa---------gaagg----a-agatgct----gt
       White-throated sparrow  aacg------gaa----ggaagcattgtcgcc-a-aa---------gaagg----a-agatgct----gt
          Medium ground finch  aatg------gaa----ggaagcattgtcgcc-a-aa---------gaagg----a-agatgct----gt
                  Zebra finch  aatg------gaa----ggaagcattgtcgcc-a-aa---------gaagg----a-agatgct----gt
           Tibetan ground jay  aatg------gaa----ggaagcattgtcacc-a-aa---------gaagg----a-agatgct----gt
                   Budgerigar  a----------aa----ggaagtgttgtcgcc-a-aa---------gaagg----a-agatgct----gt
                       Parrot  c----------ag----ggaagtgttgtcgcc-a-aa---------gaagg----a-agatgct----gt
                Scarlet macaw  c----------aa----ggaagtgttgtcacc-a-aa---------gaagg----a-agatgct----gt
                 Mallard duck  a----------aa----tgaagtgttgtcgcc-a-aa---------gaagg----a-agattct----gt
                      Chicken  a----------aa----ggaagcattgtcgcc-a-aa---------gaagg----a-agatgct----gt
                       Turkey  a----------aa----ggaagcattgtcgcc-a-aa---------gaagg----a-agatgct----gt
           American alligator  a----------aaaccggaaagtgttgtcacc-a-aa---------gaaga----a-aggagct----gt
              Green seaturtle  t---------gca----ggaagtggtgtcacc-a-aa---------gaagg----a-aggagct----gt
               Painted turtle  t---------gca----ggaagtgatgtcacc-a-aa---------gaagg----a-aggagct----gt
     Chinese softshell turtle  t---------aca----gaaagtggtgtcacc-a-aa---------gaaga----a-aggagct----at
       Spiny softshell turtle  t---------aca----gaaagtgttgtcacc-a-aa---------gaaga----a-aggagct----at
                       Lizard  gaagggggaaaag----gaaagcggcatcacc-a-aa---------gaag-----a-aggcctt----tt
                X. tropicalis  caaa-------aa----agaaaag----cgcc-a-aa---------gattgattta-aacctct----at
                    Zebrafish  -----------at----ggaaagttaataact---at---------aagta----a-ata---t----ac

                        Human  atatg-taggaatta----atgtactct----------tgc-tttgtcaagc-tg-tttg---c--tata
                        Chimp  atatg-taggaatta----atgtactct----------tgc-tttgtcaagc-tg-tttg---c--tata
                      Gorilla  atatg-taggaatta----atgtactct----------tgc-tttgtcaagc-tg-tttg---c--tata
                    Orangutan  atatg-taggaatta----atgtactct----------tgc-tttgtcaagc-tg-tttg---c--tata
                       Gibbon  atatg-taggaatta----atgtactct----------tgc-tttgtcaagc-tg-tttg---c--tata
                       Rhesus  atatg-taggaatta----atgtactct----------tgc-tttgtcaagc-tg-tttg---c--tata
          Crab-eating macaque  atatg-taggaatta----atgtactct----------tgc-tttgtcaagc-tg-tttg---c--tata
                       Baboon  atatg-taggaatta----atgtactct----------tgc-tttgtcaagc-tg-tttg---c--tata
                 Green monkey  atatg-taggaatta----atgtactct----------tgc-tttgtcaagc-tg-tttg---c--tata
                     Marmoset  atatg-taggactta----atgtactct----------tgc-tttgtcaagc-tg-tttg---c--tata
              Squirrel monkey  atatg-taggactta----atgtactct----------tgc-tttgtcaagc-tg-tttg---c--tata
                     Bushbaby  acatg-taggactta----atgtactcc----------tgc-tttgtcaagc-tg-tttg---c--tata
           Chinese tree shrew  aaatg-taggactt-----atgtactct----------tgc-tttgtcaagc-tg-tttg---c--tcta
                     Squirrel  atatg-taggattta----atgtactct----------tgc-tttgtcaagc-tg-tttg---c--tata
       Lesser Egyptian jerboa  gtatg-taggacttg----atgtactct----------tgc-tttgtcaagc-tc-tttg---c--tata
                 Prairie vole  gtatg-tcggacttg----atgttctct----------tgc-tttgtcaagc-tt-tttg---c--tata
              Chinese hamster  gtatg-tcggacttg----atgttctct----------tcc-tttgtcaagc-tt-tttg---c--tgta
               Golden hamster  gtatg-tcagacttg----atgttctct----------tgc-tttgtcaagcttt-tttg---c--tgta
                        Mouse  gtatg-tcggacttg----atgtactct----------tgc-tctgtcaagc-tc-tttg---c--tata
                          Rat  gtatg-tcggacttg----atgtcctct----------tgc-tctgtcaagc-ta-tttg---c--tata
               Naked mole-rat  atatg-taggactta----atgtactct----------tgc-tttgtgaagc-tg-tttg---c--tgta
                   Guinea pig  acgtg-taggactta----acatattct----------tgc-tttgtcaagc-tg-tttg---c--tata
                   Chinchilla  atatg-taggactta----acgtactct----------tgc-tttgtcaaac-tg-tttg---c--tata
             Brush-tailed rat  atatg-taggactta----acatactct----------tgc-tttgtcaagc-tg-tttg---c--tata
                       Rabbit  atatg-taggactta----atgtactcc----------tgc-tttgtcaagc-tg--tta---c--tata
                         Pika  ctacg-taggaccta----atgtactcc----------tgc-tttgtcaagc-tg--ttg---c--tata
                          Pig  atatg-taggacttaatgtatgtactct----------tgc-tttgtcaagc-tg-tttg---c--tcta
                       Alpaca  atatattaggactta----atgtactct----------tgc-tttgtcaagc-tg-tttg---c--tata
               Bactrian camel  atatattaggactta----atgtactct----------tgc-tttgtcaagc-tg-tttg---c--tata
                      Dolphin  atatg-taggactta----atgtactct----------tgc-tttgtcaagc-tg-tttg---c--tata
                 Killer whale  atatg-taggactta----atgtactct----------tgc-tttgtcaagc-tg-tttg---c--tata
             Tibetan antelope  gtatg-taggactta----atgtactctaatgtactc-tgc-tttgtcaagc-tg-tttg---c--tata
                          Cow  gtatg-taggactta----atgtattctaatgtactcttgc-tttgtcaagc-tg-tttg---c--tata
                        Sheep  gtatg-taggactta----atgtactctaatgtactc-tgc-tttgtcaagc-tg-tttg---c--tata
                Domestic goat  gtatg-taggactta----atgtactctaatgtactc-tgc-tttgtcaagc-tg-tttg---c--tata
                        Horse  atatg-taggactta----atgtactct----------tgc-tttgtcaagc-tg-tttg---c--tata
             White rhinoceros  atatg-taggactta----atgtactct----------tgc-tttgtcaagc-ta-tttg---c--tata
                          Cat  gtatg-taggactta----atgtactct----------tgc-tttgtccagc-ta-tttg---c--tata
                          Dog  atatg-taagactta----atgtactct----------tgc-tttgtcaagc-tg-tttg---c--tgta
                      Ferret   gtatg-taggacgta----atgtactct----------tgc-tttgtcaagc-tg-tttg---c--tata
                        Panda  atatg-taggacgta----atgtactct----------tgc-tttgtcaagc-tg-tttg---c--tata
               Pacific walrus  atatg-taggacgta----atgtactct----------tgc-tttgtcaagc-tg-tttg---c--tata
                 Weddell seal  atatg-taggacgta----atgtactct----------tgc-tttgtcaagc-tg-tttg---c--tata
             Black flying-fox  atatg-taagactt-----atgtactct----------tgc-tttgtcaagc-tg-tttg---c--tata
                Big brown bat  atatg-taggactt-----atgtactct----------tgc-tttgtcaagc-tg-tttg---c--tata
         David's myotis (bat)  atatg-taggactt-----atgtactct----------tgc-tttgtcaagc-tg-tttg---c--tata
                     Microbat  atatg-taggactt-----acgtactct----------tgc-tttgtcaagc-tg-tttg---c--tata
                     Hedgehog  acatg-ttagactta----atatactct----------tgcttttattaagc-tg-tttg---c--tata
                        Shrew  atatg-tagaactta----atgtactct----------cgcttttgtcacac-tg-tttg---c--tgta
              Star-nosed mole  atatg-tagaactta----atatactct----------tgcttttgtcaagc-tg-tttg---c--tata
                     Elephant  atatg-tagaactta----atgtactct----------tgc-tgtgtcaagc-tt-tttg---c--tgta
                      Manatee  atatg-tagaactta----atgtactct----------tcc-tctgtcaagc-tt-tttg---c--tata
             Cape golden mole  atatg-tagaactta----atgtactct----------tgc-tgtgtcaagc-tg-tttg---ctatata
                       Tenrec  atatg-tagaactta----atgtactct----------tac-tgtgtcccac-tg-tttg---c--tata
                     Aardvark  atatg-tagaactta----atgtactct----------tgc-tgtgtcaagc-ta-tttg---c--tata
                      Opossum  accca-taggtctta----atgtactct----------tgc-tttggcaagc-tg-tttg---c--tcta
              Tasmanian devil  accca-tacgtctta----atgtactct----------tgc-tttggcaagc-tg-tttg---c--tcta
                      Wallaby  accca-gaagtctta----atgtactct----------tgc-tttggcaagc-tg-tttg---c--tcta
                  Rock pigeon  atctg-taggattta----atattatct----------tgc-tttggcaagc-tg-tttg---c--tgta
                 Saker falcon  atcca-taggattta----atattatct----------tgc-tttggcaagc-tg-tttg---c--tgta
             Peregrine falcon  atcca-taggattta----atattatct----------tgc-tttggcaagc-tg-tttg---c--tgta
          Collared flycatcher  atcca-taggattta----atattctct----------tgc-tttggcaagc-tg-tttg---c--tata
       White-throated sparrow  atcca-taggatttc----ataatctct----------tgc-tttggcaagc-tg-tttg---c--tata
          Medium ground finch  atcca-taggatttc----atattctct----------tgc-tttggcaagc-tg-attg---c--tata
                  Zebra finch  atcca-taggatttc----atattctct----------tgc-tttggcaagc-tg-tttg---c--tata
           Tibetan ground jay  atcca-taggattta----atattctct----------tgc-tttggcaagc-tg-tttg---c--tata
                   Budgerigar  atcca-taggattta----atattatct----------tgc-tttggcaagc-tgttttg---c--tata
                       Parrot  atcca-taggattta----atattatct----------tgc-tttggcaagc-tgttttg---c--tata
                Scarlet macaw  atcca-taggattta----atattatct----------tgc-tttggcaagc-tgttttg---c--tata
                 Mallard duck  atcca-taggagtta----atattatct----------tgc-tttggcaagc-tg-tttg---c--taga
                      Chicken  atcca-taggagtta----atattatct----------tgc-tttggcaagc-tg-tttg---c--tata
                       Turkey  atcca-taggagtta----atattatct----------tgc-tttggcaagc-tg-tttg---c--tata
           American alligator  atcca-taggagtta----atatactct----------tgc-tttggcaagc-tg-tttg---c--tata
              Green seaturtle  atcca-taggagtta----atgtactct----------tgc-tttggcaagc-tg-ttgg---c--tgta
               Painted turtle  atcca-taggagtca----atgtactct----------tgc-tttggcaagc-tg-tttg---c--tata
     Chinese softshell turtle  atcca-taggagttg----atgtactct----------tgc-tttggcaagc-tg-tttg---c--tata
       Spiny softshell turtle  atcca-taggagttg----atgtactct----------tgc-tttggcaagc-tg-tttg---c--tata
                       Lizard  gtccg-ta----------------ctct----------ggc-tttggcaaaa-cg-ttag---c--tatc
                X. tropicalis  ataaa-caggtatta----ctat--ttt----------ggc-tttggcaggc-tg-tttg---c--tagt
                    Zebrafish  acat--taaaattaa----atgtaatttaaattt----tac-tttttaaaaa-tt-gttatatc--acca

                        Human  gtttccaaggt-att-a-tgttactc-taa
                        Chimp  gtttccaaggt-att-a-tgttactc-taa
                      Gorilla  gtttccaaggt-att-a-tgttactc-taa
                    Orangutan  gtttccaaggt-att-a-tgttactc-taa
                       Gibbon  gtttccaaggt-att-a-tgttactc-taa
                       Rhesus  gtttccaaggt-att-a-tgttactc-taa
          Crab-eating macaque  gtttccaaggt-att-a-tgttactc-taa
                       Baboon  gtttccaaggt-att-a-tgttactc-taa
                 Green monkey  gtttccaaggt-att-a-tgttactc-taa
                     Marmoset  gtttccaaggt-att-a-tgttactc-taa
              Squirrel monkey  gtttccaaggt-att-a-tgttactc-taa
                     Bushbaby  gttttcaag---atc-a-tgttactc-taa
           Chinese tree shrew  gtttttaagatcatt-c-tgttactc-taa
                     Squirrel  gttttcaagatcatt-a-tgttactc-taa
       Lesser Egyptian jerboa  gttctcaagatcatt-a-tgttactc-taa
                 Prairie vole  gttctcaagattatt-a-tgttattc-taa
              Chinese hamster  gttctcaagatca-t-a-tgttaatc-taa
               Golden hamster  gttctcaagatca-t-a-tgttaatc-taa
                        Mouse  gttctcaatatcatt-a-tgttaatc-taa
                          Rat  gttttcaagatcatt-a-tgttactc-taa
               Naked mole-rat  gttttcaagatcatt-a-tgttactc-taa
                   Guinea pig  gttctcaacatcatt-a-tgttattc-taa
                   Chinchilla  gttttcaagatgatt-a-tgttactc-taa
             Brush-tailed rat  gttttcaagatcatt-a-tgttattc-taa
                       Rabbit  gtttttgagatcatt-a-tgttactc-taa
                         Pika  gttttcaagatcatt-a-tgttactc-taa
                          Pig  gttttcaagatcata-a-tgttactc-taa
                       Alpaca  gttttcaagaccata-a-tgttactc-taa
               Bactrian camel  gttttcaagaccata-a-tgttactc-taa
                      Dolphin  gttttcaagatcaca-a-tgttactc-taa
                 Killer whale  gttttcaagatcaca-a-tgttactc-taa
             Tibetan antelope  gttttaaagatcata-a-tgttactc-taa
                          Cow  gtttttaagatcata-a-tgttactc-taa
                        Sheep  gtttttaagatcata-a-tgttactc-taa
                Domestic goat  gtttttaagatcata-a-tgttactc-taa
                        Horse  gttttcaggatcata-a-tgttactc-taa
             White rhinoceros  gttttcaagatcata-a-tgttactc-taa
                          Cat  gttttcaagatcata-a-tgttactc-taa
                          Dog  ctttctgagatcata-a-tgttacgc-taa
                      Ferret   gtttccaagatcata-a-tgttactc-taa
                        Panda  gtttccaagatcata-a-tgttactc-taa
               Pacific walrus  gtttccaagatcata-a-tgttactc-taa
                 Weddell seal  gtttccaagatcata-a-tgttactc-taa
             Black flying-fox  gttttcaaggtcata-a-tattactc-taa
                Big brown bat  gtttccaagattata-a-tgttactc-taa
         David's myotis (bat)  gtttccaagattata-a-tgttactc-taa
                     Microbat  gtttccaagattata-a-tgttactc-taa
                     Hedgehog  gttttcaagatcata-attgttattcttaa
                        Shrew  gtattcaagatcata-g-tgttaatc-taa
              Star-nosed mole  gttttcaagatcata-g-tgttactc-taa
                     Elephant  gttttcaagatcata-c-tgttactc-taa
                      Manatee  gttttcaagatcata-a-tgttactc-taa
             Cape golden mole  gttttcaagatcata-a-tgttactc-taa
                       Tenrec  gtttccaacatcata-a-tgttactc-taa
                     Aardvark  gtt--caagatccta-a-tgttactc-taa
                      Opossum  -ttttcaaggtcata-t-tgttattc-taa
              Tasmanian devil  -tttgccagatccta-t-tgttattc-taa
                      Wallaby  -tttgcaagatcata-t-tgttattc-taa
                  Rock pigeon  ---tttgagatcata-t-tgctattc-caa
                 Saker falcon  --ttttgagatcatt-t-tgctattc-cag
             Peregrine falcon  --ttttgagatcatt-t-tgctattc-cag
          Collared flycatcher  --ttttgagatcata-t-tgctattc-caa
       White-throated sparrow  --ttttgagatcata-t-tgctattc-caa
          Medium ground finch  --ttttgagatcata-t-tgctattc-caa
                  Zebra finch  --ttttgagatcata-t-tgctattc-caa
           Tibetan ground jay  --ttttgagatcata-t-tgctattc-caa
                   Budgerigar  --ttttgagatcatatt-tactattc-caa
                       Parrot  --ttttgagatcata-t-tgctattt-caa
                Scarlet macaw  --ttttgagatcata-t-tgctattt-caa
                 Mallard duck  --ttttgagatcata-t-tgctattc-tga
                      Chicken  --ttttgagatcata-t-tgctattc-tga
                       Turkey  --ttttgagatcata-t-tgctattc-tga
           American alligator  --ttttgagatcata-t-tgctattc-tga
              Green seaturtle  --ttttgagatcaca-t-tgctattc-tga
               Painted turtle  --ttttgagatccta-t-tgctattc-tga
     Chinese softshell turtle  --ttttgagatcata-c-tgctattc-tta
       Spiny softshell turtle  --ttttgagatcata-c-tgctattc-tta
                       Lizard  --ccttgaggtcgta-t-tgctgtct-tga
                X. tropicalis  -ttttaaagaccttg-c-tgctattt-taa
                    Zebrafish  ttttttaatgaatgc-a-tgttgttt-cca

Inserts between block 5 and 6 in window
B D                  Opossum 1bp
B D          Tasmanian devil 1bp
B D                  Wallaby 1bp
  D              Rock pigeon 1bp
  D             Saker falcon 1bp
  D         Peregrine falcon 1bp
  D      Collared flycatcher 1bp
  D   White-throated sparrow 1bp
B D      Medium ground finch 1bp
B D              Zebra finch 1bp
          Tibetan ground jay 1bp
B D               Budgerigar 1bp
  D                   Parrot 1bp
  D            Scarlet macaw 1bp
  D             Mallard duck 1bp
B D                  Chicken 1bp
B D                   Turkey 1bp
B D       American alligator 1bp
  D          Green seaturtle 1bp
  D           Painted turtle 1bp
  D Chinese softshell turtle 1bp
  D   Spiny softshell turtle 1bp
B D                   Lizard 1bp

Alignment block 6 of 8 in window, 115650610 - 115650656, 47 bps 
B D                     Human  ctctg------aaaagtgatgtaatctggtagc-aatgtagtagttc-aaataaa
B D                     Chimp  ctctg------aaaagtgatgtaatctggtagc-aatgtagtagttc-aaataaa
B D                   Gorilla  ctctg------aaaagtgatgtaatctggtagc-aatgtagtagttc-aaataaa
B D                 Orangutan  ctctg------aaaagtgatgtaatctggtagc-aatgtagtggttc-aaataaa
B D                    Gibbon  ctctg------aaaagtgatgtaatctggtagc-aatgtagtagttc-aaataaa
B D                    Rhesus  ctctg------aaaagtgatgtaatctggtagc-aatgtagtaattc-aaataaa
B D       Crab-eating macaque  ctctg------aaaagtgatgtaatctggtagc-aatgtagtaattc-aaataaa
B D                    Baboon  ctctg------aaaagtgatgtaatctggtagc-aatgtagtaattc-aaataaa
B D              Green monkey  ctctg------aaaagtgatgtaatctggtagc-aatgtagtaattc-aaataaa
B D                  Marmoset  ctctg------aaaagtgatgtaatctgatagc-aatgtagtagttc-aaataaa
B D           Squirrel monkey  ctctg------aaaagtgatgtaatctgatagc-aatgtagtagttc-aaataaa
B D                  Bushbaby  ctctga-----aaaagtgatgtaatctgatagc-aatgtagtagttc-aaataaa
           Chinese tree shrew  ctctg------aaaagtgatataatctggtagc-aacctagtagttc-caataaa
B D                  Squirrel  ctctggaaaaaaaaactgatgtaatctggtagc-aatgtagtagttc--aataaa
       Lesser Egyptian jerboa  ctctg------aaaagggatgtaatctggtagc-aatgtagtagttcaaaataaa
                 Prairie vole  ctctg------aaacgtgatgtaatttggtagc-aacttagtagttc-aaataaa
B D           Chinese hamster  ctctg------aaaagtgatgtaatctggtagc-aacatagtactcc-aaataaa
               Golden hamster  ctctg------acaagtgatgtaatctggtagt-accatagtagtcc-aaataaa
B D                     Mouse  atctg------aaaagtgatgtaatctggtagc-atcatagtagtcc-aaataaa
B D                       Rat  ctctg------aaaagtgatgtaatctggtagc-aacatagtagtcc-aaataaa
B D            Naked mole-rat  ctctg------aaaagtgatgtaatctggtaga-aatgtagtggttc-aaataaa
B D                Guinea pig  ctctg------aaaagtgatgtaatctggtagc-aatgtagtggttc-aaataaa
                   Chinchilla  ctctg------aaaagtgatgtaatctggtagc-aatgtagtggttc-aaataaa
             Brush-tailed rat  ctctg------aaaagtgatgtaatctggtagc-aatgtagtgcttc-aaataaa
B D                    Rabbit  ctctg------aaaagtgatgtaatctggtagc-aatgtagtagttc-aaataaa
B D                      Pika  ct---------gaaagtgatgtaatctggtagc-tatgtagtacttc-aaataaa
B D                       Pig  ctctg------aaatgtgatgtaatctggtagc-agtgtattagttc-aaataaa
B D                    Alpaca  ctctg------aaaaatgatgtaatctggtagc-agtgtattagttc-aaataaa
               Bactrian camel  ctctg------aaaaatgatgtaatctggtagc-agtgtattagttc-aaataaa
B D                   Dolphin  ctctg------aaaagtgatgtaatctggtagc-aatgtattagttc-aaataaa
                 Killer whale  ctctg------aaaagtgatgtaatctggtagc-aatgtattagttc-aaataaa
             Tibetan antelope  ctctg------aaaagtgatgtaatctggtagc-aatgtattagttc-aaataaa
B D                       Cow  ctctg------aaaagttatgtactctgatagc-aatgtattagttc-aaataaa
B D                     Sheep  ctctg------aaaagtgatgtaatctggtagc-aatgtattagttc-aaataaa
                Domestic goat  ctctg------aaaagtgatgtaatctggtagc-aatgtattagttc-aaataaa
B D                     Horse  ctctg------aaaagtgatgtaatctggtagc-aatgtattagttc-aaataaa
B D          White rhinoceros  ctctg------aaaagtgatgtaatctggtagc-aatgtattagttc-aaataaa
B D                       Cat  ctctg------aaaagtgatgtaatctggtagc-aatgtattagttc-aaataaa
B D                       Dog  ctctg------aaaagtgatgtaatctggtagc-aatgcattagttc-aaataaa
B D                   Ferret   ctctg------aaaagtgatgtaatctggtagc-aatgtattagttc-caataaa
B D                     Panda  ctctg------aaaagtgatgtaatctggtagc-aatgtattagttc-aaataaa
               Pacific walrus  ctctg------aaaagtgatgtaatctggtagc-agtgtattagttc-aaataaa
                 Weddell seal  ctctg------aaaagtgatgtaatctggtagc-aatgtattagttc-aaataaa
             Black flying-fox  ctctg------aaaagtgatgtaatctgaaagc-aatgtattagttc-aaataaa
                Big brown bat  ctctg------aaaaagtatgtaatctgatagc-aatgtattagttc-aaataaa
         David's myotis (bat)  ctctg-------aaaattatgtaatctgatagc-aatgtattagttc-aaataaa
B D                  Microbat  ctctg------aaaaattatgtaatctgatagc-aatgtattagttc-aaataaa
B D                  Hedgehog  ctctg------aaaagtgatgtaatctggtagc-gatgtattagttt-aaataaa
B D                     Shrew  ttctt------aaaagtgatgtaatctggtagc-agtgaattagttt-aaataaa
              Star-nosed mole  ctctg------aaaagtgaagtaatctggtagc-aatgtattcgttg-aaataaa
B D                  Elephant  ctctg------aaaagtgatgtaatcgggtagc-aatgtattagttc-aaataaa
B D                   Manatee  ctctg------aaaagtgatgtaatcgggtagc-aatgtattagttc-aaataaa
             Cape golden mole  ctctg------aaaagcgatgtaatcgggtagc-aatgtattagttc-aaataaa
B D                    Tenrec  ttctg------aaaagtgatgtaatcgggtagc-catgtattagttc-aaataaa
                     Aardvark  ctctg------aaaagtgatgtaatcaggtagc-aatgtactagttc-aaataaa
B D                   Opossum  ctatt------aaaagtgctgtaatttggtgac-aa-atattagttc-aaataaa
B D           Tasmanian devil  ctatt------caaagtgatgtaatttggtggc-aa-atattagttc-aaataaa
B D                   Wallaby  ctatt------aaaagtgatgtaattgggtggc-aa-atattagttc-aagtaaa
  D               Rock pigeon  ctatt------cgaagtgatgtaatatggtggc-aaagcattagttg-aaataaa
  D              Saker falcon  ctatt------caaagtgatgtaatatggtggc-aaagcattagttg-aaataaa
  D          Peregrine falcon  ctatt------caaagtgatgtaatatggtggc-aaagcattagttg-aaataaa
  D       Collared flycatcher  ctatt------caaagtgatgtaatatggtggc-aaagcattagttg-aaataaa
  D    White-throated sparrow  ctatt------caaagtgatgtaatatggtggc-aaagcatcagttg-aaataaa
B D       Medium ground finch  ctatt------caaagtgatgtaatatggtggc-aaagcatcagttg-aaataaa
B D               Zebra finch  ctatt------caaagtgatgtaatatggtggc-aaagcatcagttg-aaataaa
           Tibetan ground jay  ctatt------caaagtgatgtaatatggtggc-aaagcattagttg-aaataaa
B D                Budgerigar  ctatt------caaagtgatgtaatatggtggc-aaagcattagttg-aaataaa
  D                    Parrot  ctatt------caaagtgatgtaatatggtggc-aaagcattcgttg-aaataaa
  D             Scarlet macaw  ctatt------caaagtgat-taatatggtggc-aaagcattcgttg-aaataaa
  D              Mallard duck  ctatt------caaaatgatgtaatatggtggc-aaagcattagttg-aaataaa
B D                   Chicken  ctatt------caaagtgatgtaatatggtggc-aaagcattagttg-aaataaa
B D                    Turkey  ctatt------caaagtgatgtaatatggtggc-aaagcattagttg-aaataaa
B D        American alligator  ctatt------caaagtgatgtaatatggtggc-aaagcgttagttg-aaataaa
  D           Green seaturtle  ctatt------caaa-tgctgtaatatggtggc-aaagccttagttg-aaataaa
  D            Painted turtle  ctatt------caaa-tgatgtaatatggtggc-aaagcattagttg-aaataaa
  D  Chinese softshell turtle  ctatt------caaactgatgtaataaggtggc-aaagcattagttg-aaataaa
  D    Spiny softshell turtle  ctatt------caaactgatgtaataaggtggc-aaagcattagttg-aaataaa
B D                    Lizard  ttact------ccaaatgatgtaatgtggtggcaaaagcaatagtta-aaataaa
B D                 Zebrafish  -------------ctgtgttgtcttgtgattgt-aa-gtaaatgtac-aaataaa

Inserts between block 6 and 7 in window
  D             Mallard duck 5bp
B D                  Chicken 15bp

Alignment block 7 of 8 in window, 115650657 - 115650668, 12 bps 
B D                     Human  ---gg-catttacata
B D                     Chimp  ---gg-catttacata
B D                   Gorilla  ---gg-catttacata
B D                 Orangutan  ---gg-catttacata
B D                    Gibbon  ---gg-catttacata
B D                    Rhesus  ---gg-catttacata
B D       Crab-eating macaque  ---gg-catttacata
B D                    Baboon  ---gg-catttacata
B D              Green monkey  ---gg-catttacata
B D                  Marmoset  ---gg-catttacata
B D           Squirrel monkey  ---gg-catttacatg
B D                  Bushbaby  ---ag-catttacata
           Chinese tree shrew  ---gg-catttacgta
B D                  Squirrel  ---gg-catttatata
       Lesser Egyptian jerboa  ---gg-catttacata
                 Prairie vole  ---gg-catttgcata
B D           Chinese hamster  ---gg-catttgcata
               Golden hamster  ---gg-catttgcata
B D                     Mouse  ---gg-catttgcata
B D                       Rat  ---gg-catttgcata
B D            Naked mole-rat  ---gg-catttacata
B D                Guinea pig  ---gg-catttacata
                   Chinchilla  ---gg-catttacata
             Brush-tailed rat  ---gg-catttacata
B D                    Rabbit  ---gg-catttacata
B D                      Pika  ---gg-catttacata
B D                       Pig  ---gg-catttacgta
B D                    Alpaca  ---gg-catttacata
               Bactrian camel  ---gg-catttacata
B D                   Dolphin  ---gg-catttacata
                 Killer whale  ---gg-catttacata
             Tibetan antelope  ---gg-catttac---
B D                       Cow  ---ag-catttac---
B D                     Sheep  ---gg-catttac---
                Domestic goat  ---gg-catttac---
B D                     Horse  ---gg-catttacata
B D          White rhinoceros  ---gg-catttacata
B D                       Cat  ---gg-catttacata
B D                       Dog  ---gg-catttacata
B D                   Ferret   ---gg-catttacata
B D                     Panda  ---gg-catttacata
               Pacific walrus  ---gg-catttacata
                 Weddell seal  ---gg-catttacata
             Black flying-fox  ---gg-catttacata
                Big brown bat  ---gg-catttacata
         David's myotis (bat)  ---gg-catttacata
B D                  Microbat  ---gg-catttacata
B D                  Hedgehog  ---gg-catttacata
B D                     Shrew  ---gg-catttacata
              Star-nosed mole  ---gt-catttaaata
B D                  Elephant  ---gg-catttacata
B D                   Manatee  ---gg-catttagata
             Cape golden mole  ---gc-catttacata
B D                    Tenrec  ---tg-catttgcata
                     Aardvark  ---gg-catttacata
B D                   Opossum  ---agacatttaatta
B D           Tasmanian devil  ---agacatttaagta
B D                   Wallaby  ---aaacatttaagta
  D               Rock pigeon  ---aa-catttaaata
  D              Saker falcon  ---aa-catttaaata
  D          Peregrine falcon  ---aa-catttaaata
  D       Collared flycatcher  ---aa-catttaaata
  D    White-throated sparrow  ---aa-catttaaata
B D       Medium ground finch  ---aa-catttaaata
B D               Zebra finch  ---aa-catttaaata
           Tibetan ground jay  ---aa-catttaaata
B D                Budgerigar  ---aa-tgtttaaata
  D                    Parrot  ---aa-tgtttaaata
  D             Scarlet macaw  ---aa-catttaaata
  D              Mallard duck  ---ga-catttaaatc
B D                   Chicken  ---ac-catttaaata
B D        American alligator  ---aa-catttaaata
  D           Green seaturtle  ---aa-catttaaat-
  D            Painted turtle  ---aa-catttaaat-
  D  Chinese softshell turtle  ---aa-aggttaaat-
  D    Spiny softshell turtle  ---aa-agtttaaat-
B D                    Lizard  ---ac-cgtttaaata
B D                 Zebrafish  tgtaa-aaattaaat-

Inserts between block 7 and 8 in window
  D              Rock pigeon 3bp
  D             Saker falcon 3bp
  D         Peregrine falcon 3bp
B D               Budgerigar 3bp
  D            Scarlet macaw 3bp

Alignment block 8 of 8 in window, 115650669 - 115650672, 4 bps 
B D                     Human  ataa
B D                     Chimp  ataa
B D                   Gorilla  ataa
B D                 Orangutan  ataa
B D                    Gibbon  ataa
B D                    Rhesus  ataa
B D       Crab-eating macaque  ataa
B D                    Baboon  ataa
B D              Green monkey  ataa
B D                  Marmoset  ataa
B D           Squirrel monkey  ataa
B D                  Bushbaby  ataa
           Chinese tree shrew  atta
B D                  Squirrel  at--
       Lesser Egyptian jerboa  ataa
                 Prairie vole  ataa
B D           Chinese hamster  ataa
               Golden hamster  ttaa
B D                     Mouse  ataa
B D                       Rat  ataa
B D            Naked mole-rat  ataa
B D                Guinea pig  ataa
                   Chinchilla  ataa
             Brush-tailed rat  ataa
B D                    Rabbit  ataa
B D                      Pika  ataa
B D                       Pig  ataa
B D                    Alpaca  ataa
               Bactrian camel  ataa
B D                   Dolphin  ataa
                 Killer whale  ataa
             Tibetan antelope  ataa
B D                       Cow  ataa
B D                     Sheep  ataa
                Domestic goat  ataa
B D                     Horse  ataa
B D          White rhinoceros  ataa
B D                       Cat  ataa
B D                       Dog  atca
B D                   Ferret   ataa
B D                     Panda  ataa
               Pacific walrus  ataa
                 Weddell seal  ataa
             Black flying-fox  ataa
                Big brown bat  ataa
         David's myotis (bat)  ataa
B D                  Microbat  ataa
B D                  Hedgehog  atta
B D                     Shrew  atac
              Star-nosed mole  ataa
B D                  Elephant  ataa
B D                   Manatee  ataa
             Cape golden mole  ataa
B D                    Tenrec  ataa
                     Aardvark  ataa
B D                   Opossum  caaa
B D           Tasmanian devil  caaa
B D                   Wallaby  caaa
  D              Mallard duck  ----
B D                   Chicken  ----
  D           Green seaturtle  acaa
  D            Painted turtle  acag
  D  Chinese softshell turtle  gcag
  D    Spiny softshell turtle  gcag
B D                    Lizard  ----
B D                 Zebrafish  gtaa
  D             Scarlet macaw  ====
B D                Budgerigar  ====
  D          Peregrine falcon  ====
  D              Saker falcon  ====
B D               Zebra finch  ====
  D               Rock pigeon  ====

View table schema

Go to Conservation track controls

Data last updated: 2015-05-06

Downloads for data in this track are available:

Description

This track shows multiple alignments of 100 vertebrate species and measurements of evolutionary conservation using two methods (phastCons and phyloP) from the PHAST package, for all species. The multiple alignments were generated using multiz and other tools in the UCSC/Penn State Bioinformatics comparative genomics alignment pipeline. Conserved elements identified by phastCons are also displayed in this track. PHAST/Multiz are built from chains ("alignable") and nets ("syntenic"), see the documentation of the Chain/Net tracks for a description of the complete alignment process.

PhastCons is a hidden Markov model-based method that estimates the probability that each nucleotide belongs to a conserved element, based on the multiple alignment. It considers not just each individual alignment column, but also its flanking columns. By contrast, phyloP separately measures conservation at individual columns, ignoring the effects of their neighbors. As a consequence, the phyloP plots have a less smooth appearance than the phastCons plots, with more "texture" at individual sites. The two methods have different strengths and weaknesses. PhastCons is sensitive to "runs" of conserved sites, and is therefore effective for picking out conserved elements. PhyloP, on the other hand, is more appropriate for evaluating signatures of selection at particular nucleotides or classes of nucleotides (e.g., third codon positions, or first positions of miRNA target sites).

Another important difference is that phyloP can measure acceleration (faster evolution than expected under neutral drift) as well as conservation (slower than expected evolution). In the phyloP plots, sites predicted to be conserved are assigned positive scores (and shown in blue), while sites predicted to be fast-evolving are assigned negative scores (and shown in red). The absolute values of the scores represent -log p-values under a null hypothesis of neutral evolution. The phastCons scores, by contrast, represent probabilities of negative selection and range between 0 and 1.

Both phastCons and phyloP treat alignment gaps and unaligned nucleotides as missing data, and both were run with the same parameters.

See also: lastz parameters and other details and chain minimum score and gap parameters used in these alignments.

UCSC has repeatmasked and aligned all genome assemblies, and provides all the sequences for download. For genome assemblies not available in the genome browser, there are alternative assembly hub genome browsers. Missing sequence in any assembly is highlighted in the track display by regions of yellow when zoomed out and by Ns when displayed at base level (see Gap Annotation, below).

Primate subset
OrganismSpeciesRelease dateUCSC versionAlignment type
BaboonPapio hamadryasMar 2012Baylor Panu_2.0/papAnu2Reciprocal best net
BushbabyOtolemur garnettiiMar 2011Broad/otoGar3Syntenic net
ChimpPan troglodytesFeb 2011CSAC 2.1.4/panTro4Syntenic net
Crab-eating macaqueMacaca fascicularisJun 2013Macaca_fascicularis_5.0/macFas5Syntenic net
GibbonNomascus leucogenysOct 2012GGSC Nleu3.0/nomLeu3Syntenic net
GorillaGorilla gorilla gorillaMay 2011gorGor3.1/gorGor3Reciprocal best net
Green monkeyChlorocebus sabaeusMar 2014Chlorocebus_sabeus 1.1/chlSab2Syntenic net
HumanHomo sapiensDec 2013GRCh38/hg38reference species
MarmosetCallithrix jacchusMar 2009WUGSC 3.2/calJac3Syntenic net
OrangutanPongo pygmaeus abeliiJuly 2007WUGSC 2.0.2/ponAbe2Reciprocal best net
RhesusMacaca mulattaOct 2010BGI CR_1.0/rheMac3Syntenic net
Squirrel monkeySaimiri boliviensisOct 2011Broad/saiBol1Syntenic net
Euarchontoglires subset
Brush-tailed ratOctodon degusApr 2012OctDeg1.0/octDeg1Syntenic net
ChinchillaChinchilla lanigeraMay 2012 ChiLan1.0/chiLan1Syntenic net
Chinese hamsterCricetulus griseusJul 2013C_griseus_v1.0/criGri1Syntenic net
Chinese tree shrewTupaia chinensisJan 2013TupChi_1.0/tupChi1Syntenic net
Golden hamsterMesocricetus auratusMar 2013MesAur1.0/mesAur1Syntenic net
Guinea pigCavia porcellusFeb 2008Broad/cavPor3Syntenic net
Lesser Egyptian jerboaJaculus jaculusMay 2012JacJac1.0/jacJac1Syntenic net
MouseMus musculusDec 2011GRCm38/mm10Syntenic net
Naked mole-ratHeterocephalus glaberJan 2012Broad HetGla_female_1.0/hetGla2Syntenic net
PikaOchotona princepsMay 2012OchPri3.0/ochPri3Syntenic net
Prairie voleMicrotus ochrogasterOct 2012MicOch1.0/micOch1Syntenic net
RabbitOryctolagus cuniculusApr 2009Broad/oryCun2Syntenic net
RatRattus norvegicusJul 2014RGSC 6.0/rn6Syntenic net
SquirrelSpermophilus tridecemlineatusNov 2011Broad/speTri2Syntenic net
Laurasiatheria subset
AlpacaVicugna pacosMar 2013Vicugna_pacos-2.0.1/vicPac2Syntenic net
Bactrian camelCamelus ferusDec 2011CB1/camFer1Syntenic net
Big brown batEptesicus fuscusJul 2012EptFus1.0/eptFus1Syntenic net
Black flying-foxPteropus alectoAug 2012ASM32557v1/pteAle1Syntenic net
CatFelis catusNov 2014ICGSC Felis_catus 8.0/felCat8Syntenic net
CowBos taurusJun 2014Bos_taurus_UMD_3.1.1/bosTau8Syntenic net
David's myotis batMyotis davidiiAug 2012ASM32734v1/myoDav1Syntenic net
DogCanis lupus familiarisSep 2011Broad CanFam3.1/canFam3Syntenic net
DolphinTursiops truncatusOct 2011Baylor Ttru_1.4/turTru2Reciprocal best net
Domestic goatCapra hircusMay 2012CHIR_1.0/capHir1Syntenic net
Ferret Mustela putorius furoApr 2011MusPutFur1.0/musFur1Syntenic net
HedgehogErinaceus europaeusMay 2012EriEur2.0/eriEur2Syntenic net
HorseEquus caballusSep 2007EquCab3.0/equCab3Syntenic net
Killer whaleOrcinus orcaJan 2013Oorc_1.1/orcOrc1Syntenic net
MegabatPteropus vampyrusJul 2008Broad/pteVam1Reciprocal best net
MicrobatMyotis lucifugusJul 2010Broad Institute Myoluc2.0/myoLuc2Syntenic net
Pacific walrusOdobenus rosmarus divergensJan 2013Oros_1.0/odoRosDiv1Syntenic net
PandaAiluropoda melanoleucaDec 2009BGI-Shenzhen 1.0/ailMel1Syntenic net
PigSus scrofaAug 2011SGSC Sscrofa10.2/susScr3Syntenic net
SheepOvis ariesAug 2012ISGC Oar_v3.1/oviAri3Syntenic net
ShrewSorex araneusAug 2008Broad/sorAra2Syntenic net
Star-nosed moleCondylura cristataMar 2012ConCri1.0/conCri1Syntenic net
Tibetan antelopePantholops hodgsoniiMay 2013PHO1.0/panHod1Syntenic net
Weddell sealLeptonychotes weddelliiMar 2013LepWed1.0/lepWed1Reciprocal best net
White rhinocerosCeratotherium simumMay 2012CerSimSim1.0/cerSim1Syntenic net
Afrotheria subset
AardvarkOrycteropus afer aferMay 2012OryAfe1.0/oryAfe1Syntenic net
Cape elephant shrewElephantulus edwardiiAug 2012EleEdw1.0/eleEdw1Syntenic net
Cape golden moleChrysochloris asiaticaAug 2012ChrAsi1.0/chrAsi1Syntenic net
ElephantLoxodonta africanaJul 2009Broad/loxAfr3Syntenic net
ManateeTrichechus manatus latirostrisOct 2011Broad v1.0/triMan1Syntenic net
TenrecEchinops telfairiNov 2012Broad/echTel2Syntenic net
Mammal subset
ArmadilloDasypus novemcinctusDec 2011Baylor/dasNov3Syntenic net
OpossumMonodelphis domesticaOct 2006Broad/monDom5Net
PlatypusOrnithorhynchus anatinusMar 2007WUGSC 5.0.1/ornAna1Reciprocal best net
Tasmanian devilSarcophilus harrisiiFeb 2011WTSI Devil_ref v7.0/sarHar1Net
WallabyMacropus eugeniiSep 2009TWGS Meug_1.1/macEug2Reciprocal best net
Aves subset
BudgerigarMelopsittacus undulatusSep 2011WUSTL v6.3/melUnd1Net
ChickenGallus gallusNov 2011ICGSC Gallus_gallus-4.0/galGal4Net
Collared flycatcherFicedula albicollisJun 2013FicAlb1.5/ficAlb2Net
Mallard duckAnas platyrhynchosApr 2013BGI_duck_1.0/anaPla1Net
Medium ground finchGeospiza fortisApr 2012GeoFor_1.0/geoFor1Net
ParrotAmazona vittataJan 2013AV1/amaVit1Net
Peregrine falconFalco peregrinusFeb 2013F_peregrinus_v1.0/falPer1Net
Rock pigeonColumba liviaFeb 2013Cliv_1.0/colLiv1Net
Saker falconFalco cherrugFeb 2013F_cherrug_v1.0/falChe1Net
Scarlet macawAra macaoJun 2013SMACv1.1/araMac1Net
Tibetan ground jayPseudopodoces humilisJan 2013PseHum1.0/pseHum1Net
TurkeyMeleagris gallopavoDec 2009TGC Turkey_2.01/melGal1Net
White-throated sparrowZonotrichia albicollisApr 2013ASM38545v1/zonAlb1Net
Zebra finchTaeniopygia guttataFeb 2013WashU taeGut324/taeGut2Net
Sarcopterygii subset
American alligatorAlligator mississippiensisAug 2012allMis0.2/allMis1Net
Chinese softshell turtlePelodiscus sinensisOct 2011PelSin_1.0/pelSin1Net
CoelacanthLatimeria chalumnaeAug 2011Broad/latCha1Net
Green seaturtleChelonia mydasMar 2013CheMyd_1.0/cheMyd1Net
LizardAnolis carolinensisMay 2010Broad AnoCar2.0/anoCar2Net
Painted turtleChrysemys picta belliiMar 2014v3.0.3/chrPic2Net
Spiny softshell turtleApalone spiniferaMay 2013ASM38561v1/apaSpi1Net
X. tropicalisXenopus tropicalisSep 2012JGI 7.0/xenTro7Net
Fish subset
Atlantic codGadus morhuaMay 2010Genofisk GadMor_May2010/gadMor1Net
Burton's mouthbreederHaplochromis burtoniOct 2011AstBur1.0/hapBur1Net
FuguTakifugu rubripesOct 2011FUGU5/fr3Net
LampreyPetromyzon marinusSep 2010WUGSC 7.0/petMar2Net
MedakaOryzias latipesOct 2005NIG/UT MEDAKA1/oryLat2Net
Mexican tetra (cavefish)Astyanax mexicanusApr 2013Astyanax_mexicanus-1.0.2/astMex1Net
Nile tilapiaOreochromis niloticusJan 2011Broad oreNil1.1/oreNil2Net
Princess of BurundiNeolamprologus brichardiMay 2011NeoBri1.0/neoBri1Net
Pundamilia nyerereiPundamilia nyerereiOct 2011PunNye1.0/punNye1Net
Southern platyfishXiphophorus maculatusJan 2012Xiphophorus_maculatus-4.4.2/xipMac1Net
Spotted garLepisosteus oculatusDec 2011LepOcu1/lepOcu1Net
SticklebackGasterosteus aculeatusFeb 2006Broad/gasAcu1Net
TetraodonTetraodon nigroviridisMar 2007Genoscope 8.0/tetNig2Net
Yellowbelly pufferfishTakifugu flavidusMay 2013version 1 of Takifugu flavidus genome/takFla1Net
Zebra mbunaMaylandia zebraMar 2012MetZeb1.1/mayZeb1Net
ZebrafishDanio rerioSep 2014GRCz10/danRer10Net

Table 1. Genome assemblies included in the 100-way Conservation track.

Display Conventions and Configuration

In full and pack display modes, conservation scores are displayed as a wiggle track (histogram) in which the height reflects the size of the score. The conservation wiggles can be configured in a variety of ways to highlight different aspects of the displayed information. Click the Graph configuration help link for an explanation of the configuration options.

Pairwise alignments of each species to the human genome are displayed below the conservation histogram as a grayscale density plot (in pack mode) or as a wiggle (in full mode) that indicates alignment quality. In dense display mode, conservation is shown in grayscale using darker values to indicate higher levels of overall conservation as scored by phastCons.

Checkboxes on the track configuration page allow selection of the species to include in the pairwise display. Note that excluding species from the pairwise display does not alter the the conservation score display.

To view detailed information about the alignments at a specific position, zoom the display in to 30,000 or fewer bases, then click on the alignment.

Gap Annotation

The Display chains between alignments configuration option enables display of gaps between alignment blocks in the pairwise alignments in a manner similar to the Chain track display. The following conventions are used:

  • Single line: No bases in the aligned species. Possibly due to a lineage-specific insertion between the aligned blocks in the human genome or a lineage-specific deletion between the aligned blocks in the aligning species.
  • Double line: Aligning species has one or more unalignable bases in the gap region. Possibly due to excessive evolutionary distance between species or independent indels in the region between the aligned blocks in both species.
  • Pale yellow coloring: Aligning species has Ns in the gap region. Reflects uncertainty in the relationship between the DNA of both species, due to lack of sequence in relevant portions of the aligning species.

Genomic Breaks

Discontinuities in the genomic context (chromosome, scaffold or region) of the aligned DNA in the aligning species are shown as follows:

  • Vertical blue bar: Represents a discontinuity that persists indefinitely on either side, e.g. a large region of DNA on either side of the bar comes from a different chromosome in the aligned species due to a large scale rearrangement.
  • Green square brackets: Enclose shorter alignments consisting of DNA from one genomic context in the aligned species nested inside a larger chain of alignments from a different genomic context. The alignment within the brackets may represent a short misalignment, a lineage-specific insertion of a transposon in the human genome that aligns to a paralogous copy somewhere else in the aligned species, or other similar occurrence.

Base Level

When zoomed-in to the base-level display, the track shows the base composition of each alignment. The numbers and symbols on the Gaps line indicate the lengths of gaps in the human sequence at those alignment positions relative to the longest non-human sequence. If there is sufficient space in the display, the size of the gap is shown. If the space is insufficient and the gap size is a multiple of 3, a "*" is displayed; other gap sizes are indicated by "+".

Codon translation is available in base-level display mode if the displayed region is identified as a coding segment. To display this annotation, select the species for translation from the pull-down menu in the Codon Translation configuration section at the top of the page. Then, select one of the following modes:

  • No codon translation: The gene annotation is not used; the bases are displayed without translation.
  • Use default species reading frames for translation: The annotations from the genome displayed in the Default species to establish reading frame pull-down menu are used to translate all the aligned species present in the alignment.
  • Use reading frames for species if available, otherwise no translation: Codon translation is performed only for those species where the region is annotated as protein coding.
  • Use reading frames for species if available, otherwise use default species: Codon translation is done on those species that are annotated as being protein coding over the aligned region using species-specific annotation; the remaining species are translated using the default species annotation.

Codon translation uses the following gene tracks as the basis for translation:

Gene TrackSpecies
UCSC GenesHuman, Mouse
RefSeq GenesCow, Frog (X. tropicalis)
Ensembl Genes v73Atlantic cod, Bushbaby, Cat, Chicken, Chimp, Coelacanth, Dog, Elephant, Ferret, Fugu, Gorilla, Horse, Lamprey, Lizard, Mallard duck, Marmoset, Medaka, Megabat, Microbat, Orangutan, Panda, Pig, Platypus, Rat, Soft-shell Turtle, Southern platyfish, Squirrel, Tasmanian devil, Tetraodon, Zebrafish
no annotationAardvark, Alpaca, American alligator, Armadillo, Baboon, Bactrian camel, Big brown bat, Black flying-fox, Brush-tailed rat, Budgerigar, Burton's mouthbreeder, Cape elephant shrew, Cape golden mole, Chinchilla, Chinese hamster, Chinese tree shrew, Collared flycatcher, Crab-eating macaque, David's myotis (bat), Dolphin, Domestic goat, Gibbon, Golden hamster, Green monkey, Green seaturtle, Hedgehog, Killer whale, Lesser Egyptian jerboa, Manatee, Medium ground finch, Mexican tetra (cavefish), Naked mole-rat, Nile tilapia, Pacific walrus, Painted turtle, Parrot, Peregrine falcon, Pika, Prairie vole, Princess of Burundi, Pundamilia nyererei, Rhesus, Rock pigeon, Saker falcon, Scarlet Macaw, Sheep, Shrew, Spiny softshell turtle, Spotted gar, Squirrel monkey, Star-nosed mole, Tawny puffer fish, Tenrec, Tibetan antelope, Tibetan ground jay, Wallaby, Weddell seal, White rhinoceros, White-throated sparrow, Zebra Mbuna, Zebra finch
Table 2. Gene tracks used for codon translation.

Methods

Pairwise alignments with the human genome were generated for each species using lastz from repeat-masked genomic sequence. Lineage-specific repeats were removed prior to alignment, then reinserted. Pairwise alignments were then linked into chains using a dynamic programming algorithm that finds maximally scoring chains of gapless subsections of the alignments organized in a kd-tree. The scoring matrix and parameters for pairwise alignment and chaining were tuned for each species based on phylogenetic distance from the reference. High-scoring chains were then placed along the genome, with gaps filled by lower-scoring chains, to produce an alignment net. For more information about the chaining and netting process and parameters for each species, see the description pages for the Chain and Net tracks.

An additional filtering step was introduced in the generation of the 100-way conservation track to reduce the number of paralogs and pseudogenes from the high-quality assemblies and the suspect alignments from the low-quality assemblies: the pairwise alignments of high-quality mammalian sequences (placental and marsupial) were filtered based on synteny; those for 2X mammalian genomes were filtered to retain only alignments of best quality in both the target and query ("reciprocal best").

The resulting best-in-genome pairwise alignments were progressively aligned using multiz/autoMZ, following the tree topology diagrammed above, to produce multiple alignments. The multiple alignments were post-processed to add annotations indicating alignment gaps, genomic breaks, and base quality of the component sequences. The annotated multiple alignments, in MAF format, are available for bulk download. An alignment summary table containing an entry for each alignment block in each species was generated to improve track display performance at large scales. Framing tables were constructed to enable visualization of codons in the multiple alignment display.

Phylogenetic Tree Model

Both phastCons and phyloP are phylogenetic methods that rely on a tree model containing the tree topology, branch lengths representing evolutionary distance at neutrally evolving sites, the background distribution of nucleotides, and a substitution rate matrix. The all-species tree model for this track was generated using the phyloFit program from the PHAST package (REV model, EM algorithm, medium precision) using multiple alignments of 4-fold degenerate sites extracted from the 100-way alignment (msa_view). The 4d sites were derived from the RefSeq (Reviewed+Coding) gene set, filtered to select single-coverage long transcripts.

This same tree model was used in the phyloP calculations; however, the background frequencies were modified to maintain reversibility. The resulting tree model: all species.

PhastCons Conservation

The phastCons program computes conservation scores based on a phylo-HMM, a type of probabilistic model that describes both the process of DNA substitution at each site in a genome and the way this process changes from one site to the next (Felsenstein and Churchill 1996, Yang 1995, Siepel and Haussler 2005). PhastCons uses a two-state phylo-HMM, with a state for conserved regions and a state for non-conserved regions. The value plotted at each site is the posterior probability that the corresponding alignment column was "generated" by the conserved state of the phylo-HMM. These scores reflect the phylogeny (including branch lengths) of the species in question, a continuous-time Markov model of the nucleotide substitution process, and a tendency for conservation levels to be autocorrelated along the genome (i.e., to be similar at adjacent sites). The general reversible (REV) substitution model was used. Unlike many conservation-scoring programs, phastCons does not rely on a sliding window of fixed size; therefore, short highly-conserved regions and long moderately conserved regions can both obtain high scores. More information about phastCons can be found in Siepel et al. 2005.

The phastCons parameters used were: expected-length=45, target-coverage=0.3, rho=0.3.

PhyloP Conservation

The phyloP program supports several different methods for computing p-values of conservation or acceleration, for individual nucleotides or larger elements ( http://compgen.cshl.edu/phast/). Here it was used to produce separate scores at each base (--wig-scores option), considering all branches of the phylogeny rather than a particular subtree or lineage (i.e., the --subtree option was not used). The scores were computed by performing a likelihood ratio test at each alignment column (--method LRT), and scores for both conservation and acceleration were produced (--mode CONACC).

Conserved Elements

The conserved elements were predicted by running phastCons with the --viterbi option. The predicted elements are segments of the alignment that are likely to have been "generated" by the conserved state of the phylo-HMM. Each element is assigned a log-odds score equal to its log probability under the conserved model minus its log probability under the non-conserved model. The "score" field associated with this track contains transformed log-odds scores, taking values between 0 and 1000. (The scores are transformed using a monotonic function of the form a * log(x) + b.) The raw log odds scores are retained in the "name" field and can be seen on the details page or in the browser when the track's display mode is set to "pack" or "full".

Credits

This track was created using the following programs:

  • Alignment tools: lastz (formerly blastz) and multiz by Minmei Hou, Scott Schwartz and Webb Miller of the Penn State Bioinformatics Group
  • Chaining and Netting: axtChain, chainNet by Jim Kent at UCSC
  • Conservation scoring: phastCons, phyloP, phyloFit, tree_doctor, msa_view and other programs in PHAST by Adam Siepel at Cold Spring Harbor Laboratory (original development done at the Haussler lab at UCSC).
  • MAF Annotation tools: mafAddIRows by Brian Raney, UCSC; mafAddQRows by Richard Burhans, Penn State; genePredToMafFrames by Mark Diekhans, UCSC
  • Tree image generator: phyloPng by Galt Barber, UCSC
  • Conservation track display: Kate Rosenbloom, Hiram Clawson (wiggle display), and Brian Raney (gap annotation and codon framing) at UCSC

The phylogenetic tree is based on Murphy et al. (2001) and general consensus in the vertebrate phylogeny community. Thanks to Giacomo Bernardi for help with the fish relationships.

References

Phylo-HMMs, phastCons, and phyloP:

Felsenstein J, Churchill GA. A Hidden Markov Model approach to variation among sites in rate of evolution. Mol Biol Evol. 1996 Jan;13(1):93-104. PMID: 8583911

Pollard KS, Hubisz MJ, Rosenbloom KR, Siepel A. Detection of nonneutral substitution rates on mammalian phylogenies. Genome Res. 2010 Jan;20(1):110-21. PMID: 19858363; PMC: PMC2798823

Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, Rosenbloom K, Clawson H, Spieth J, Hillier LW, Richards S, et al. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 2005 Aug;15(8):1034-50. PMID: 16024819; PMC: PMC1182216

Siepel A, Haussler D. Phylogenetic Hidden Markov Models. In: Nielsen R, editor. Statistical Methods in Molecular Evolution. New York: Springer; 2005. pp. 325-351.

Yang Z. A space-time process model for the evolution of DNA sequences. Genetics. 1995 Feb;139(2):993-1005. PMID: 7713447; PMC: PMC1206396

Chain/Net:

Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784

Multiz:

Blanchette M, Kent WJ, Riemer C, Elnitski L, Smit AF, Roskin KM, Baertsch R, Rosenbloom K, Clawson H, Green ED, et al. Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res. 2004 Apr;14(4):708-15. PMID: 15060014; PMC: PMC383317

Lastz (formerly Blastz):

Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468

Harris RS. Improved pairwise alignment of genomic DNA. Ph.D. Thesis. Pennsylvania State University, USA. 2007.

Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961

Phylogenetic Tree:

Murphy WJ, Eizirik E, O'Brien SJ, Madsen O, Scally M, Douady CJ, Teeling E, Ryder OA, Stanhope MJ, de Jong WW, Springer MS. Resolution of the early placental mammal radiation using Bayesian phylogenetics. Science. 2001 Dec 14;294(5550):2348-51. PMID: 11743200