Multiz Alignments of 100 Vertebrates
 

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Alignment block 1 of 10 in window, 55712373 - 55712883, 511 bps 
B D                   Human  cctgtaatcccagccctttgggaggccgaggcaggcgtatcacctgaggtcaagaattggagaccagcct
B D                   Chimp  cctgtaatcccagccctttgggaggccaaggcaggcatatcacctgaggtcaagaattggagaccagcct
B D                 Gorilla  cctgtaatcccagccctttgggaggccgagggaggcgtatcacctgaggtcaagaattggagaccagcct
B D               Orangutan  cctgtaatcccagccctttgggagg-tgaggcaggcatatcacctgaggtcaagagttggagaccagcct
B D                  Gibbon  cctgtaatcccagcgctttgggagtctgaggcaggcatgtcacctgaggtcaagagttggagaccagcct
B D     Crab-eating macaque  cctgtaatcccagccctttgggaggccgaggcaggcttatcacctgaggtcaagagttggagaccagcct
B D                  Baboon  cctgtaatcccagccctttgggaggccgaggcaggcttatcacctgaggtcaagagttggagaccagcct
B D            Green monkey  cctgtaatcccagccctttgggaggccgaggcaggcttatcacctgaggtcaagagttggagaccagcct
B D                Marmoset  cctataatcctag-actttgggaggccaaggcaggcagatcacctgaggtcaggagttggagataggcct
B D         Squirrel monkey  cttataatcccag-actttgggaggccaaggcaggcagatcacctgaggtcaggagttggagactggcct
B D                Hedgehog  ======================================================================
            Golden hamster  ======================================================================
B D                   Shrew  ======================================================================
       Cape elephant shrew  ======================================================================
              Prairie vole  ======================================================================
           Star-nosed mole  ======================================================================
B D                   Panda  ======================================================================
B D                    Pika  ======================================================================
B D                  Rabbit  ======================================================================
B D          Naked mole-rat  ======================================================================
    Lesser Egyptian jerboa  ======================================================================
B D                 Ferret   ======================================================================
B D                     Dog  ======================================================================
B D                     Cat  ======================================================================
        Chinese tree shrew  ======================================================================
          Brush-tailed rat  ======================================================================
B D                     Rat  ======================================================================
B D                   Mouse  ======================================================================
B D         Chinese hamster  ======================================================================
B D               Armadillo  ======================================================================
B D                  Tenrec  ======================================================================
B D                 Manatee  ======================================================================
B D                Elephant  ======================================================================
B D                Microbat  ======================================================================
      David's myotis (bat)  ======================================================================
             Big brown bat  ======================================================================
             Domestic goat  ======================================================================
B D                   Sheep  ======================================================================
B D                     Cow  ======================================================================
          Tibetan antelope  ======================================================================
                Chinchilla  ======================================================================
B D              Guinea pig  ======================================================================
B D                Squirrel  ======================================================================
            Pacific walrus  ======================================================================
B D                   Horse  ======================================================================
B D        White rhinoceros  ======================================================================
            Bactrian camel  ======================================================================
B D                  Alpaca  ======================================================================
              Killer whale  ======================================================================
          Black flying-fox  ======================================================================
B D                Bushbaby  ======================================================================
B D                 Dolphin  ======================================================================
B D                     Pig  ======================================================================
  D         Green seaturtle  ======================================================================
B D         Tasmanian devil  ======================================================================
B D                 Opossum  ======================================================================
          Cape golden mole  ======================================================================
B D                 Megabat  ======================================================================
                  Aardvark  ======================================================================
              Weddell seal  ======================================================================
B D                  Rhesus  ======================================================================
  D          Painted turtle  ======================================================================
B D                Platypus  ======================================================================

                      Human  ggccaacatggggaaaccctgtctctactaaaaatacaaaaattagccagg--------cactcccctgt
                      Chimp  ggccaacatggggaaaccctgtctctactaaaaatacaaaaattagccagg--------cactcccctgt
                    Gorilla  ggccaacatggggaaaccctgtctctactaaaaatacaaaaattagccagg--------cactcccctgt
                  Orangutan  ggccaacatggggaaaccctgtctctactaaaaatacaaaaattagccagg--------cacacccctgt
                     Gibbon  ggccaacatggggaaacactgtctctactaaaaatacaaaaatcagccagg--------cacacccctgc
        Crab-eating macaque  ggccaacatggggaaaccctgtctctactaaaaatacaaaaattagccagg--------cacacctc--t
                     Baboon  ggccaacatggggaaaccctgtctctactaaaaatacaaaaattagccagg--------cacacctctgt
               Green monkey  ggccaacatggggaaaccctgtctctactaaaaatacaaaaattagccagg--------cacacctctgt
                   Marmoset  ggcaaacatggggaaaccctgtctctactaaaaatacaaaaattagccagatgtggtaacacatgcctgt
            Squirrel monkey  ggccaacatggggaaaccctgtctctactaaaaacacaaaaattagccaggcatggtaacacatgcctgt
                   Hedgehog  ======================================================================
             Golden hamster  ======================================================================
                      Shrew  ======================================================================
        Cape elephant shrew  ======================================================================
               Prairie vole  ======================================================================
            Star-nosed mole  ======================================================================
                      Panda  ======================================================================
                       Pika  ======================================================================
                     Rabbit  ======================================================================
             Naked mole-rat  ======================================================================
     Lesser Egyptian jerboa  ======================================================================
                    Ferret   ======================================================================
                        Dog  ======================================================================
                        Cat  ======================================================================
         Chinese tree shrew  ======================================================================
           Brush-tailed rat  ======================================================================
                        Rat  ======================================================================
                      Mouse  ======================================================================
            Chinese hamster  ======================================================================
                  Armadillo  ======================================================================
                     Tenrec  ======================================================================
                    Manatee  ======================================================================
                   Elephant  ======================================================================
                   Microbat  ======================================================================
       David's myotis (bat)  ======================================================================
              Big brown bat  ======================================================================
              Domestic goat  ======================================================================
                      Sheep  ======================================================================
                        Cow  ======================================================================
           Tibetan antelope  ======================================================================
                 Chinchilla  ======================================================================
                 Guinea pig  ======================================================================
                   Squirrel  ======================================================================
             Pacific walrus  ======================================================================
                      Horse  ======================================================================
           White rhinoceros  ======================================================================
             Bactrian camel  ======================================================================
                     Alpaca  ======================================================================
               Killer whale  ======================================================================
           Black flying-fox  ======================================================================
                   Bushbaby  ======================================================================
                    Dolphin  ======================================================================
                        Pig  ======================================================================
            Green seaturtle  ======================================================================
            Tasmanian devil  ======================================================================
                    Opossum  ======================================================================
           Cape golden mole  ======================================================================
                    Megabat  ======================================================================
                   Aardvark  ======================================================================
               Weddell seal  ======================================================================
                     Rhesus  ======================================================================
             Painted turtle  ======================================================================
                   Platypus  ======================================================================

                      Human  aatcccacctactactcaggaggctgaggtgggagaatcacttgaactcaggaggtggaggttgcagtga
                      Chimp  aatcccacctactactcaggaggctgaggtgggagaattgcttgaactcaggaggtggaggttgcagtga
                    Gorilla  aatcccagctactactcaggaggctgaggtgggagaatcgcttgaactcaggaggtggaggttgcagtga
                  Orangutan  aatcccagctactactcaggaggctggggtgggagaatcgcttgaactcaggaggtggaggttgcagtga
                     Gibbon  aataccagctactactcaggaggctgaggtgggagaatcacttgaactcaggaggtggaggttgcagtga
        Crab-eating macaque  aatcccagctactacttgggaggctgaggtgggataatcgcctgaactcaggaggtggacgttacagtga
                     Baboon  aatcccagctactacttgggaggctgaggtgggataatcgcttgaactcaggaggtggacgttacagtga
               Green monkey  aatcccagctactacttgggagactgaggtgggataatcgcttgaactcaggaggtggacgttacagtga
                   Marmoset  -atcccagctactactccagaggctgaagttggagaatcacttgaactcaggaggtggaggttgcaatga
            Squirrel monkey  aatcccagctaccactcaggaggctgaagtcagagaatcacttgaactcaggaggtggaggttgcaatca
                   Hedgehog  ======================================================================
             Golden hamster  ======================================================================
                      Shrew  ======================================================================
        Cape elephant shrew  ======================================================================
               Prairie vole  ======================================================================
            Star-nosed mole  ======================================================================
                      Panda  ======================================================================
                       Pika  ======================================================================
                     Rabbit  ======================================================================
             Naked mole-rat  ======================================================================
     Lesser Egyptian jerboa  ======================================================================
                    Ferret   ======================================================================
                        Dog  ======================================================================
                        Cat  ======================================================================
         Chinese tree shrew  ======================================================================
           Brush-tailed rat  ======================================================================
                        Rat  ======================================================================
                      Mouse  ======================================================================
            Chinese hamster  ======================================================================
                  Armadillo  ======================================================================
                     Tenrec  ======================================================================
                    Manatee  ======================================================================
                   Elephant  ======================================================================
                   Microbat  ======================================================================
       David's myotis (bat)  ======================================================================
              Big brown bat  ======================================================================
              Domestic goat  ======================================================================
                      Sheep  ======================================================================
                        Cow  ======================================================================
           Tibetan antelope  ======================================================================
                 Chinchilla  ======================================================================
                 Guinea pig  ======================================================================
                   Squirrel  ======================================================================
             Pacific walrus  ======================================================================
                      Horse  ======================================================================
           White rhinoceros  ======================================================================
             Bactrian camel  ======================================================================
                     Alpaca  ======================================================================
               Killer whale  ======================================================================
           Black flying-fox  ======================================================================
                   Bushbaby  ======================================================================
                    Dolphin  ======================================================================
                        Pig  ======================================================================
            Green seaturtle  ======================================================================
            Tasmanian devil  ======================================================================
                    Opossum  ======================================================================
           Cape golden mole  ======================================================================
                    Megabat  ======================================================================
                   Aardvark  ======================================================================
               Weddell seal  ======================================================================
                     Rhesus  ======================================================================
             Painted turtle  ======================================================================
                   Platypus  ======================================================================

                      Human  gctgaaatcttgccactgcactccagcctgggtgacagaacaagactccatctc-------aaaaaattt
                      Chimp  gctgaaatcttgccattgcactccagcctgggtgacagaacaagactccatctc-------aaaaaattt
                    Gorilla  gctgaaatcgtgccactgcactccagcctgggtgacagaacaagactccatctc-------aaaaaattt
                  Orangutan  gctgaaattgtgccactgcactccagcctgggtgacagaacaagactccatctc-------aaaaaattt
                     Gibbon  gctgaaatcgtgccactgcactccagcctgggtgacagaacaagactccatctc-------aaaaaattt
        Crab-eating macaque  gctgaaatcgtgccactgcactccagcctgggtgacagaacaagacttcatctcaaaaaaaaaaaaattt
                     Baboon  gctgaaatcgtgccactgcactccagcctgggtgacagaacaagacttcatctcaaaaaaaaaaaaattt
               Green monkey  gctgaaatcatgccactgcactccagcctgggtgacagaacaagacttcatctcaaaaaaaaaaaaaatt
                   Marmoset  gctgaaattgtgccactgcactccatcctgtgtgacagaacaacactctgtctc-------aaaaaattt
            Squirrel monkey  tctgaaattgtgccactgcactcc----------------------------------------------
                   Hedgehog  ======================================================================
             Golden hamster  ======================================================================
                      Shrew  ======================================================================
        Cape elephant shrew  ======================================================================
               Prairie vole  ======================================================================
            Star-nosed mole  ======================================================================
                      Panda  ======================================================================
                       Pika  ======================================================================
                     Rabbit  ======================================================================
             Naked mole-rat  ======================================================================
     Lesser Egyptian jerboa  ======================================================================
                    Ferret   ======================================================================
                        Dog  ======================================================================
                        Cat  ======================================================================
         Chinese tree shrew  ======================================================================
           Brush-tailed rat  ======================================================================
                        Rat  ======================================================================
                      Mouse  ======================================================================
            Chinese hamster  ======================================================================
                  Armadillo  ======================================================================
                     Tenrec  ======================================================================
                    Manatee  ======================================================================
                   Elephant  ======================================================================
                   Microbat  ======================================================================
       David's myotis (bat)  ======================================================================
              Big brown bat  ======================================================================
              Domestic goat  ======================================================================
                      Sheep  ======================================================================
                        Cow  ======================================================================
           Tibetan antelope  ======================================================================
                 Chinchilla  ======================================================================
                 Guinea pig  ======================================================================
                   Squirrel  ======================================================================
             Pacific walrus  ======================================================================
                      Horse  ======================================================================
           White rhinoceros  ======================================================================
             Bactrian camel  ======================================================================
                     Alpaca  ======================================================================
               Killer whale  ======================================================================
           Black flying-fox  ======================================================================
                   Bushbaby  ======================================================================
                    Dolphin  ======================================================================
                        Pig  ======================================================================
            Green seaturtle  ======================================================================
            Tasmanian devil  ======================================================================
                    Opossum  ======================================================================
           Cape golden mole  ======================================================================
                    Megabat  ======================================================================
                   Aardvark  ======================================================================
               Weddell seal  ======================================================================
                     Rhesus  ======================================================================
             Painted turtle  ======================================================================
                   Platypus  ======================================================================

                      Human  attttgagataattgta-gaatattcagtttgaatgaatctctaatacagagaggtttca-----tttta
                      Chimp  attttgagataattgta-gaatattcagtttgaat----ctctaatacagagaggtttca-----tttta
                    Gorilla  attttgagataattgta-gaatattcagtttgaatgaatctctaatacagagaggtttca-----tttta
                  Orangutan  attttgagataattgta-gaatattcagtttgaatgaatctctaatacagagagatttca-----tttta
                     Gibbon  attttgagataattgta-gaatattcagtttgaatgaatctgtaatacagagagatttca-----tttta
        Crab-eating macaque  attttgagataattgta-gaatattcagtttgaatgaatctctaatacagagagatttcatatactttta
                     Baboon  attttgagataattgta-gaatattcagtttgaatgaatctctaatacagagagatttcatatactttta
               Green monkey  attttgagataattgta-gaatattcagtttgaatgaatctctaatacagagagatttcatatactttta
                   Marmoset  -ttttgagataactgtagaaatattcagtttgaatgaatctctaatacagagacatttcatata-ctttt
            Squirrel monkey  ------------------aaatattcagtttgaatgaatctctaatacagagacatttcatata-cttaa
                   Hedgehog  ======================================================================
             Golden hamster  ======================================================================
                      Shrew  ======================================================================
        Cape elephant shrew  ======================================================================
               Prairie vole  ======================================================================
            Star-nosed mole  ======================================================================
                      Panda  ======================================================================
                       Pika  ======================================================================
                     Rabbit  ======================================================================
             Naked mole-rat  ======================================================================
     Lesser Egyptian jerboa  ======================================================================
                    Ferret   ======================================================================
                        Dog  ======================================================================
                        Cat  ======================================================================
         Chinese tree shrew  ======================================================================
           Brush-tailed rat  ======================================================================
                        Rat  ======================================================================
                      Mouse  ======================================================================
            Chinese hamster  ======================================================================
                  Armadillo  ======================================================================
                     Tenrec  ======================================================================
                    Manatee  ======================================================================
                   Elephant  ======================================================================
                   Microbat  ======================================================================
       David's myotis (bat)  ======================================================================
              Big brown bat  ======================================================================
              Domestic goat  ======================================================================
                      Sheep  ======================================================================
                        Cow  ======================================================================
           Tibetan antelope  ======================================================================
                 Chinchilla  ======================================================================
                 Guinea pig  ======================================================================
                   Squirrel  ======================================================================
             Pacific walrus  ======================================================================
                      Horse  ======================================================================
           White rhinoceros  ======================================================================
             Bactrian camel  ======================================================================
                     Alpaca  ======================================================================
               Killer whale  ======================================================================
           Black flying-fox  ======================================================================
                   Bushbaby  ======================================================================
                    Dolphin  ======================================================================
                        Pig  ======================================================================
            Green seaturtle  ======================================================================
            Tasmanian devil  ======================================================================
                    Opossum  ======================================================================
           Cape golden mole  ======================================================================
                    Megabat  ======================================================================
                   Aardvark  ======================================================================
               Weddell seal  ======================================================================
                     Rhesus  ======================================================================
             Painted turtle  ======================================================================
                   Platypus  ======================================================================

                      Human  gaacat-----ttttattttttaaattgactaataaatatacatattcatggaatacatagtgatatttc
                      Chimp  gaacat-----ttttattttttaaattgactaataaatatacatattcatggaatacatagtgatatttc
                    Gorilla  gaacat-----ttttattttttaaattgagtaataaatatacatattcatggaatacatagtgatatttc
                  Orangutan  gaacat-----ttttattttttaaattgactaataaatgtacgtattcatggaatacatagtgatatttc
                     Gibbon  gaacat-----ttttattttttaaattgactaataaatgtacatattcatggaatacatagtgatatttc
        Crab-eating macaque  gaacat-----ttttattttttaaattgactaataaatgtacatattcatggaatacatagtgatatttc
                     Baboon  gaacat-----ttttattttttaaattgactaataaatgtacatattcatggaatacatagtgatatttc
               Green monkey  gaacatttttattttatttttaaaattgactaataaatgtacatattcatggaatacctagtgatatttc
                   Marmoset  taaaaa-----attaattttttaaattgacaaataaatgtacatattcatggaatacatagtgatatttc
            Squirrel monkey  aaaaat-----ttttactttttaaattgacaaataaatgtacatattcatggaatatatagcgatatttc
                   Hedgehog  ======================================================================
             Golden hamster  ======================================================================
                      Shrew  ======================================================================
        Cape elephant shrew  ======================================================================
               Prairie vole  ======================================================================
            Star-nosed mole  ======================================================================
                      Panda  ======================================================================
                       Pika  ======================================================================
                     Rabbit  ======================================================================
             Naked mole-rat  ======================================================================
     Lesser Egyptian jerboa  ======================================================================
                    Ferret   ======================================================================
                        Dog  ======================================================================
                        Cat  ======================================================================
         Chinese tree shrew  ======================================================================
           Brush-tailed rat  ======================================================================
                        Rat  ======================================================================
                      Mouse  ======================================================================
            Chinese hamster  ======================================================================
                  Armadillo  ======================================================================
                     Tenrec  ======================================================================
                    Manatee  ======================================================================
                   Elephant  ======================================================================
                   Microbat  ======================================================================
       David's myotis (bat)  ======================================================================
              Big brown bat  ======================================================================
              Domestic goat  ======================================================================
                      Sheep  ======================================================================
                        Cow  ======================================================================
           Tibetan antelope  ======================================================================
                 Chinchilla  ======================================================================
                 Guinea pig  ======================================================================
                   Squirrel  ======================================================================
             Pacific walrus  ======================================================================
                      Horse  ======================================================================
           White rhinoceros  ======================================================================
             Bactrian camel  ======================================================================
                     Alpaca  ======================================================================
               Killer whale  ======================================================================
           Black flying-fox  ======================================================================
                   Bushbaby  ======================================================================
                    Dolphin  ======================================================================
                        Pig  ======================================================================
            Green seaturtle  ======================================================================
            Tasmanian devil  ======================================================================
                    Opossum  ======================================================================
           Cape golden mole  ======================================================================
                    Megabat  ======================================================================
                   Aardvark  ======================================================================
               Weddell seal  ======================================================================
                     Rhesus  ======================================================================
             Painted turtle  ======================================================================
                   Platypus  ======================================================================

                      Human  tatacataaaatgtataatgatcagat-------cagggtaattagcatgtccatcacctcaaacatcat
                      Chimp  tatacataaaatgtataatgatcagat-------cagggtaattagcatgtccatcacctcaaacatcat
                    Gorilla  tatacataaaatgtataatgatcagat-------cagggtaatgagcatgtccatcacctcaaacatcat
                  Orangutan  tatacataaaatgtataatgatcagat-------cagggtaattagcgtgtccatcacctcaaacatcat
                     Gibbon  tatacataaaatgtataatgatcagat-------aagggtaattagcatgtccatcacctcaaacatcat
        Crab-eating macaque  ta-acataaaatgtaaaatgatcagat-------cagggtaattagcatgtccatcacctcaaacatcat
                     Baboon  ta-acataaaatgtataatgatcagat-------cagggtaattagcatgtccatcacctcaaacatcat
               Green monkey  ta-acataaaatgtataatgatcagatcattatacagtgtaattagcatgtccatcacctcaaacatcat
                   Marmoset  tatacatataatgtataatgatcagat-------cagggtaattagcacatccatcatctcaaacatcat
            Squirrel monkey  tatacatataatgtataatgatcagat-------cagggtaattagcacatctatcatctcaaacatcat
                   Hedgehog  ======================================================================
             Golden hamster  ======================================================================
                      Shrew  ======================================================================
        Cape elephant shrew  ======================================================================
               Prairie vole  ======================================================================
            Star-nosed mole  ======================================================================
                      Panda  ======================================================================
                       Pika  ======================================================================
                     Rabbit  ======================================================================
             Naked mole-rat  ======================================================================
     Lesser Egyptian jerboa  ======================================================================
                    Ferret   ======================================================================
                        Dog  ======================================================================
                        Cat  ======================================================================
         Chinese tree shrew  ======================================================================
           Brush-tailed rat  ======================================================================
                        Rat  ======================================================================
                      Mouse  ======================================================================
            Chinese hamster  ======================================================================
                  Armadillo  ======================================================================
                     Tenrec  ======================================================================
                    Manatee  ======================================================================
                   Elephant  ======================================================================
                   Microbat  ======================================================================
       David's myotis (bat)  ======================================================================
              Big brown bat  ======================================================================
              Domestic goat  ======================================================================
                      Sheep  ======================================================================
                        Cow  ======================================================================
           Tibetan antelope  ======================================================================
                 Chinchilla  ======================================================================
                 Guinea pig  ======================================================================
                   Squirrel  ======================================================================
             Pacific walrus  ======================================================================
                      Horse  ======================================================================
           White rhinoceros  ======================================================================
             Bactrian camel  ======================================================================
                     Alpaca  ======================================================================
               Killer whale  ======================================================================
           Black flying-fox  ======================================================================
                   Bushbaby  ======================================================================
                    Dolphin  ======================================================================
                        Pig  ======================================================================
            Green seaturtle  ======================================================================
            Tasmanian devil  ======================================================================
                    Opossum  ======================================================================
           Cape golden mole  ======================================================================
                    Megabat  ======================================================================
                   Aardvark  ======================================================================
               Weddell seal  ======================================================================
                     Rhesus  ======================================================================
             Painted turtle  ======================================================================
                   Platypus  ======================================================================

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

Inserts between block 1 and 2 in window
B D               Marmoset 4032bp
B D        Squirrel monkey 5bp

Alignment block 2 of 10 in window, 55712884 - 55713100, 217 bps 
B D                   Human  ctggtaatatattaaatatattctaatatcataatatataataataatatactattaaacattactgcta
B D                   Chimp  ctggtaatatattagatgtattctaatatcataatatataataataatatactattaaacattactgcta
B D                 Gorilla  ctggtaatatattagatgtattctaatatcataatatataataataatatactattaaacattactgcta
B D               Orangutan  ctggtaatatattagatgtattctattatcataatatataataataatatactattaaacattactgcta
B D                  Gibbon  ctggtaatatattagatgtattctattatcatagtatataataataatatactattaaacattactgcta
B D     Crab-eating macaque  ctggtaatatattaaatgtattctattat-----tatataataataatatactattaaacattactgcta
B D                  Baboon  ctggtaatatattaaatgtattctattat-----tatataataataatatactattaaacattactgcta
B D            Green monkey  ctggtaatatattaaatgtattctattat-----tatatcataataatatactattaaacattactgcta
B D         Squirrel monkey  ctgctactatatttgatgtattatgttat--taaaatataat----atatattattaaatattactggta
B D                Hedgehog  ======================================================================
            Golden hamster  ======================================================================
B D                   Shrew  ======================================================================
       Cape elephant shrew  ======================================================================
              Prairie vole  ======================================================================
           Star-nosed mole  ======================================================================
B D                   Panda  ======================================================================
B D                    Pika  ======================================================================
B D                  Rabbit  ======================================================================
B D          Naked mole-rat  ======================================================================
    Lesser Egyptian jerboa  ======================================================================
B D                 Ferret   ======================================================================
B D                     Dog  ======================================================================
B D                     Cat  ======================================================================
        Chinese tree shrew  ======================================================================
          Brush-tailed rat  ======================================================================
B D                     Rat  ======================================================================
B D                   Mouse  ======================================================================
B D         Chinese hamster  ======================================================================
B D               Armadillo  ======================================================================
B D                  Tenrec  ======================================================================
B D                 Manatee  ======================================================================
B D                Elephant  ======================================================================
B D                Microbat  ======================================================================
      David's myotis (bat)  ======================================================================
             Big brown bat  ======================================================================
             Domestic goat  ======================================================================
B D                   Sheep  ======================================================================
B D                     Cow  ======================================================================
          Tibetan antelope  ======================================================================
                Chinchilla  ======================================================================
B D              Guinea pig  ======================================================================
B D                Squirrel  ======================================================================
            Pacific walrus  ======================================================================
B D                   Horse  ======================================================================
B D        White rhinoceros  ======================================================================
            Bactrian camel  ======================================================================
B D                  Alpaca  ======================================================================
              Killer whale  ======================================================================
          Black flying-fox  ======================================================================
B D                Bushbaby  ======================================================================
B D                 Dolphin  ======================================================================
B D                     Pig  ======================================================================
  D         Green seaturtle  ======================================================================
B D         Tasmanian devil  ======================================================================
B D                 Opossum  ======================================================================
          Cape golden mole  ======================================================================
B D                 Megabat  ======================================================================
                  Aardvark  ======================================================================
              Weddell seal  ======================================================================
B D                  Rhesus  ======================================================================
  D          Painted turtle  ======================================================================
B D                Marmoset  ======================================================================
B D                Platypus  ======================================================================

                      Human  aatatagtta-cctacagtgctgtagaacaatagaccgtattcctcctatttagctataattttgtatca
                      Chimp  aatatagtta-cctacagtggtgtagaacaatagaccatattcctcctatttagctataattttgtatca
                    Gorilla  aatatagtta-cctacagtggtgtagaacaatagaccgtattccccctatttagctataattttgtatca
                  Orangutan  aatatagtta-cctacagtggtgtagaacaatagatcatattcctcccatttagctgtaattttgtatca
                     Gibbon  aatatagtta-cctacagtggtgtagaacaatagaccgtattcctcctatttagctctaattttgtatca
        Crab-eating macaque  aatatagtta-cctacagtggtgtagaacaatagacctt-ttcctcctatttagctgtaattttgtatca
                     Baboon  aatatagtta-cctacagtggtgtagaacaatagaccttattcctcctatttagctgtaattttgtatca
               Green monkey  aatatagtta-cctacagtggtgtagaacaatagaccttattcctcctatttagctgtaattttgtatca
            Squirrel monkey  aatatagtaatcctacagtggtgtagaaaaa-agaccttattcctcctacttagctataatttcgtgtca
                   Hedgehog  ======================================================================
             Golden hamster  ======================================================================
                      Shrew  ======================================================================
        Cape elephant shrew  ======================================================================
               Prairie vole  ======================================================================
            Star-nosed mole  ======================================================================
                      Panda  ======================================================================
                       Pika  ======================================================================
                     Rabbit  ======================================================================
             Naked mole-rat  ======================================================================
     Lesser Egyptian jerboa  ======================================================================
                    Ferret   ======================================================================
                        Dog  ======================================================================
                        Cat  ======================================================================
         Chinese tree shrew  ======================================================================
           Brush-tailed rat  ======================================================================
                        Rat  ======================================================================
                      Mouse  ======================================================================
            Chinese hamster  ======================================================================
                  Armadillo  ======================================================================
                     Tenrec  ======================================================================
                    Manatee  ======================================================================
                   Elephant  ======================================================================
                   Microbat  ======================================================================
       David's myotis (bat)  ======================================================================
              Big brown bat  ======================================================================
              Domestic goat  ======================================================================
                      Sheep  ======================================================================
                        Cow  ======================================================================
           Tibetan antelope  ======================================================================
                 Chinchilla  ======================================================================
                 Guinea pig  ======================================================================
                   Squirrel  ======================================================================
             Pacific walrus  ======================================================================
                      Horse  ======================================================================
           White rhinoceros  ======================================================================
             Bactrian camel  ======================================================================
                     Alpaca  ======================================================================
               Killer whale  ======================================================================
           Black flying-fox  ======================================================================
                   Bushbaby  ======================================================================
                    Dolphin  ======================================================================
                        Pig  ======================================================================
            Green seaturtle  ======================================================================
            Tasmanian devil  ======================================================================
                    Opossum  ======================================================================
           Cape golden mole  ======================================================================
                    Megabat  ======================================================================
                   Aardvark  ======================================================================
               Weddell seal  ======================================================================
                     Rhesus  ======================================================================
             Painted turtle  ======================================================================
                   Marmoset  ======================================================================
                   Platypus  ======================================================================

                      Human  tttaacaaatctctctctgtccttaccttccccctattctttatttctatgagagtaa-gtttttttagc
                      Chimp  tttaacaaatctctctctgtccttaccttccccctattctttatttctatgagagtaa-gtttttttagc
                    Gorilla  tttaacaaatctctctctgtccttaccttccccctattctttatttctatgagagtaa-gtttttttagc
                  Orangutan  tttaacaaatctctttctgtccttaccttccccgtattctttatttctatgagattaa-gtttttttagc
                     Gibbon  tttaacaaatctc--tctgtccttaccttccccctattctttatttctatgagattaa-gtttttttagc
        Crab-eating macaque  tgtaacaaa----tctctatgcttaccttccccctattctttatttctatgagattga-gtttttttagc
                     Baboon  tttaacaaatctctctctatccttaccttccccctattctttatttctatgagattga-gtttttttagc
               Green monkey  tttaacaaatctctctctatccttaccttccccctattctttatttctatgagattga-gtttttttagc
            Squirrel monkey  tttaacaaatctctctgtatccttaccttccccctacgctttatttatatgagattaacttttttttaac
                   Hedgehog  ======================================================================
             Golden hamster  ======================================================================
                      Shrew  ======================================================================
        Cape elephant shrew  ======================================================================
               Prairie vole  ======================================================================
            Star-nosed mole  ======================================================================
                      Panda  ======================================================================
                       Pika  ======================================================================
                     Rabbit  ======================================================================
             Naked mole-rat  ======================================================================
     Lesser Egyptian jerboa  ======================================================================
                    Ferret   ======================================================================
                        Dog  ======================================================================
                        Cat  ======================================================================
         Chinese tree shrew  ======================================================================
           Brush-tailed rat  ======================================================================
                        Rat  ======================================================================
                      Mouse  ======================================================================
            Chinese hamster  ======================================================================
                  Armadillo  ======================================================================
                     Tenrec  ======================================================================
                    Manatee  ======================================================================
                   Elephant  ======================================================================
                   Microbat  ======================================================================
       David's myotis (bat)  ======================================================================
              Big brown bat  ======================================================================
              Domestic goat  ======================================================================
                      Sheep  ======================================================================
                        Cow  ======================================================================
           Tibetan antelope  ======================================================================
                 Chinchilla  ======================================================================
                 Guinea pig  ======================================================================
                   Squirrel  ======================================================================
             Pacific walrus  ======================================================================
                      Horse  ======================================================================
           White rhinoceros  ======================================================================
             Bactrian camel  ======================================================================
                     Alpaca  ======================================================================
               Killer whale  ======================================================================
           Black flying-fox  ======================================================================
                   Bushbaby  ======================================================================
                    Dolphin  ======================================================================
                        Pig  ======================================================================
            Green seaturtle  ======================================================================
            Tasmanian devil  ======================================================================
                    Opossum  ======================================================================
           Cape golden mole  ======================================================================
                    Megabat  ======================================================================
                   Aardvark  ======================================================================
               Weddell seal  ======================================================================
                     Rhesus  ======================================================================
             Painted turtle  ======================================================================
                   Marmoset  ======================================================================
                   Platypus  ======================================================================

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

Alignment block 3 of 10 in window, 55713101 - 55713153, 53 bps 
B D                   Human  tgagtgagaacatgtggtgtttaacttctgttcctggtttatctcacttaaca
B D                   Chimp  tgagtgagaacatgtggtgtttaacttctgttcctggtttatctcacttaaca
B D                 Gorilla  tgagtgagaacatgtggtgtttaacttctgttcctggtttatctcacttaaca
B D               Orangutan  tgagtgagaacatgtggtgtttaacttctgttcctggtttatctcacttaaca
B D                  Gibbon  tgagtgagaacatgtggtgtttaacttctgttcctggtttatctcacttaaca
B D                  Rhesus  tgagtgagaacatgtggtgtttaacttctgttcctggtttatctcacttaaca
B D     Crab-eating macaque  tgagtgagaacatgtggtgtttaacttctgttcctggtttatctcacttaaca
B D                  Baboon  tgagtgagaacatgtggtgtttaacttctgttcctggtttatctcacttaaca
B D            Green monkey  tgagtgagaacatgtggtgtttaacttctgttcctggtttatctcacttaaca
B D         Squirrel monkey  tgagtgagaacatgtggtgtttaaattctgttcctggcttatctcacttaaca
B D                Hedgehog  =====================================================
            Golden hamster  =====================================================
B D                   Shrew  =====================================================
       Cape elephant shrew  =====================================================
              Prairie vole  =====================================================
           Star-nosed mole  =====================================================
B D                   Panda  =====================================================
B D                    Pika  =====================================================
B D                  Rabbit  =====================================================
B D          Naked mole-rat  =====================================================
    Lesser Egyptian jerboa  =====================================================
B D                 Ferret   =====================================================
B D                     Dog  =====================================================
B D                     Cat  =====================================================
        Chinese tree shrew  =====================================================
          Brush-tailed rat  =====================================================
B D                     Rat  =====================================================
B D                   Mouse  =====================================================
B D         Chinese hamster  =====================================================
B D               Armadillo  =====================================================
B D                  Tenrec  =====================================================
B D                 Manatee  =====================================================
B D                Elephant  =====================================================
B D                Microbat  =====================================================
      David's myotis (bat)  =====================================================
             Big brown bat  =====================================================
             Domestic goat  =====================================================
B D                   Sheep  =====================================================
B D                     Cow  =====================================================
          Tibetan antelope  =====================================================
                Chinchilla  =====================================================
B D              Guinea pig  =====================================================
B D                Squirrel  =====================================================
            Pacific walrus  =====================================================
B D                   Horse  =====================================================
B D        White rhinoceros  =====================================================
            Bactrian camel  =====================================================
B D                  Alpaca  =====================================================
              Killer whale  =====================================================
          Black flying-fox  =====================================================
B D                Bushbaby  =====================================================
B D                 Dolphin  =====================================================
B D                     Pig  =====================================================
  D         Green seaturtle  =====================================================
B D         Tasmanian devil  =====================================================
B D                 Opossum  =====================================================
          Cape golden mole  =====================================================
B D                 Megabat  =====================================================
                  Aardvark  =====================================================
              Weddell seal  =====================================================
  D          Painted turtle  =====================================================
B D                Marmoset  =====================================================
B D                Platypus  =====================================================

Alignment block 4 of 10 in window, 55713154 - 55713156, 3 bps 
B D                   Human  tat
B D                   Chimp  tat
B D                 Gorilla  tat
B D               Orangutan  tat
B D                  Gibbon  tat
B D                  Rhesus  tat
B D     Crab-eating macaque  tat
B D                  Baboon  tat
B D            Green monkey  tat
B D         Squirrel monkey  tat
B D                Squirrel  tat
B D          Naked mole-rat  tac
                 Chinchilla  tat
           Brush-tailed rat  tat
B D                     Cat  tat
B D                     Dog  tac
B D                 Ferret   tac
B D                Hedgehog  ===
            Golden hamster  ===
B D                   Shrew  ===
       Cape elephant shrew  ===
              Prairie vole  ===
           Star-nosed mole  ===
B D                   Panda  ===
B D                    Pika  ===
B D                  Rabbit  ===
    Lesser Egyptian jerboa  ===
        Chinese tree shrew  ===
B D                     Rat  ===
B D                   Mouse  ===
B D         Chinese hamster  ===
B D               Armadillo  ===
B D                  Tenrec  ===
B D                 Manatee  ===
B D                Elephant  ===
B D                Microbat  ===
      David's myotis (bat)  ===
             Big brown bat  ===
             Domestic goat  ===
B D                   Sheep  ===
B D                     Cow  ===
          Tibetan antelope  ===
B D              Guinea pig  ===
            Pacific walrus  ===
B D                   Horse  ===
B D        White rhinoceros  ===
            Bactrian camel  ===
B D                  Alpaca  ===
              Killer whale  ===
          Black flying-fox  ===
B D                Bushbaby  ===
B D                 Dolphin  ===
B D                     Pig  ===
  D         Green seaturtle  ===
B D         Tasmanian devil  ===
B D                 Opossum  ===
          Cape golden mole  ===
B D                 Megabat  ===
                  Aardvark  ===
              Weddell seal  ===
  D          Painted turtle  ===
B D                Marmoset  ===
B D                Platypus  ===

Alignment block 5 of 10 in window, 55713157 - 55713160, 4 bps 
B D                   Human  ccag
B D                   Chimp  ccag
B D                 Gorilla  ccag
B D               Orangutan  ccag
B D                  Gibbon  ccag
B D                  Rhesus  ccag
B D     Crab-eating macaque  ccag
B D                  Baboon  ccag
B D            Green monkey  ccag
B D         Squirrel monkey  ccag
B D                Squirrel  cctg
B D          Naked mole-rat  cctg
                 Chinchilla  ctag
           Brush-tailed rat  ctag
B D                     Cat  ccag
B D                     Dog  ccag
B D                 Ferret   ccag
             Pacific walrus  ccag
B D                Hedgehog  ====
            Golden hamster  ====
B D                   Shrew  ====
       Cape elephant shrew  ====
              Prairie vole  ====
           Star-nosed mole  ====
B D                   Panda  ====
B D                    Pika  ====
B D                  Rabbit  ====
    Lesser Egyptian jerboa  ====
        Chinese tree shrew  ====
B D                     Rat  ====
B D                   Mouse  ====
B D         Chinese hamster  ====
B D               Armadillo  ====
B D                  Tenrec  ====
B D                 Manatee  ====
B D                Elephant  ====
B D                Microbat  ====
      David's myotis (bat)  ====
             Big brown bat  ====
             Domestic goat  ====
B D                   Sheep  ====
B D                     Cow  ====
          Tibetan antelope  ====
B D              Guinea pig  ====
B D                   Horse  ====
B D        White rhinoceros  ====
            Bactrian camel  ====
B D                  Alpaca  ====
              Killer whale  ====
          Black flying-fox  ====
B D                Bushbaby  ====
B D                 Dolphin  ====
B D                     Pig  ====
  D         Green seaturtle  ====
B D         Tasmanian devil  ====
B D                 Opossum  ====
          Cape golden mole  ====
B D                 Megabat  ====
                  Aardvark  ====
              Weddell seal  ====
  D          Painted turtle  ====
B D                Marmoset  ====
B D                Platypus  ====

Inserts between block 5 and 6 in window
B D               Squirrel 1bp
B D         Naked mole-rat 1bp
                Chinchilla 1bp
          Brush-tailed rat 1bp
B D                    Cat 1bp
B D                    Dog 1bp
B D                Ferret  1bp
            Pacific walrus 1bp

Alignment block 6 of 10 in window, 55713161 - 55713179, 19 bps 
B D                   Human  tttccccaatggtaacatc
B D                   Chimp  tttccccaatggtaacatc
B D                 Gorilla  tttccccaatggtaacatc
B D               Orangutan  tttccccaatggtaacatc
B D                  Gibbon  tttccccaatggtaacatc
B D                  Rhesus  tttccccaatggtaacatc
B D     Crab-eating macaque  tttccccaatggtaacatc
B D                  Baboon  tttccccaatggtaacatc
B D            Green monkey  tttccccaatggtaacatc
B D         Squirrel monkey  tttctccaatggtgacatc
         Chinese tree shrew  tccccccagtgatgctatc
B D                Squirrel  tttccctgatggtaacatc
B D          Naked mole-rat  ttcacctaactgtaacatc
B D              Guinea pig  ttcctttaagagcaacatc
                 Chinchilla  ttcccttcactataacatc
           Brush-tailed rat  ctcccttaatagtaacatc
B D                     Cat  ttcctccaatggtaacatc
B D                     Dog  ttcctccaatgataacatc
B D                 Ferret   ttcctccaatggtaacatc
             Pacific walrus  ttcctccaatggtaacatc
            Star-nosed mole  tttcttcagtggtgacatg
B D                Hedgehog  ===================
            Golden hamster  ===================
B D                   Shrew  ===================
       Cape elephant shrew  ===================
              Prairie vole  ===================
B D                   Panda  ===================
B D                    Pika  ===================
B D                  Rabbit  ===================
    Lesser Egyptian jerboa  ===================
B D                     Rat  ===================
B D                   Mouse  ===================
B D         Chinese hamster  ===================
B D               Armadillo  ===================
B D                  Tenrec  ===================
B D                 Manatee  ===================
B D                Elephant  ===================
B D                Microbat  ===================
      David's myotis (bat)  ===================
             Big brown bat  ===================
             Domestic goat  ===================
B D                   Sheep  ===================
B D                     Cow  ===================
          Tibetan antelope  ===================
B D                   Horse  ===================
B D        White rhinoceros  ===================
            Bactrian camel  ===================
B D                  Alpaca  ===================
              Killer whale  ===================
          Black flying-fox  ===================
B D                Bushbaby  ===================
B D                 Dolphin  ===================
B D                     Pig  ===================
  D         Green seaturtle  ===================
B D         Tasmanian devil  ===================
B D                 Opossum  ===================
          Cape golden mole  ===================
B D                 Megabat  ===================
                  Aardvark  ===================
              Weddell seal  ===================
  D          Painted turtle  ===================
B D                Marmoset  ===================
B D                Platypus  ===================

Alignment block 7 of 10 in window, 55713180 - 55713326, 147 bps 
B D                   Human  ttgcaaaatgatggtacaacattatatccagaatataggcattga-tgca---gtcaagatacagaacag
B D                   Chimp  ttgcaaaatgatggtacaacattatatccagaatataggcattga-tgca---gtcaagatacagaacag
B D                 Gorilla  ttgcaaaatgatggtacaacattatatccagaatataggcattga-tgca---gtcaagatacagaacag
B D               Orangutan  ttgtaaaatgatggtacaacattatatccagaatataggcactga-tgca---gtcaagatacagaacag
B D                  Gibbon  ttgcaaaatgatggtacaacattatatccagaatataggcattga-tgca---gtcaagatacagaacag
B D                  Rhesus  ttgcaaagtgatggtacaacattatatccagaatataggcattga-tgca---gtcaagatacagaacag
B D     Crab-eating macaque  ttgcaaagtgatggtacaacattatatccagaatataggcattga-tgca---gtcaagatacagaacag
B D                  Baboon  ttgcaaagtgatggtacaacattatatccagaatataggcattga-tgca---gtcaagatacagaacag
B D            Green monkey  ttgcaaagtgatggtacaacattatatccagaatataggcattga-tgca---gtcaagatacagaacag
B D         Squirrel monkey  ttgcaaaatgatggtacaacattatatccagaatataggctttga-tgta---gtcaagatacagtaccg
         Chinese tree shrew  ttgaaaaatgatagtaaaccggtacatccaagctgtggacattga-tgca---gtcagggtacagaacag
B D                Squirrel  ttgcaagatgatagtccagtactagattcaaaatatgggctttaattgca---gtcaaaatatagcccag
B D          Naked mole-rat  ttgtaaaatgctagtccaatgttccatccacgatgtgagcattga-tgca---gtcaggatataaatcag
B D              Guinea pig  ttacaaaatgataatgcaacagtccatccaagataagagcattga-tgca---ttcagggtgtacaccag
                 Chinchilla  ttacaaaataatagtctgaaattccatctaagacacgagcgttgg-tgca---gtcaggatgtacaccag
           Brush-tailed rat  ttactaaatgatagtgcaacattccattcaagaagtgagcattgg-taca---gttgggagctataccag
B D                  Rabbit  ttaagaaaacataatagtacattatatctaaaatgtgag-attga-tgta---gtcaagataaagaacaa
B D                     Cat  ttgcaaaatgatagaacaacttcacaaataggatatggacattaa-tgtagttgtcaagatatacaacgg
B D                     Dog  ttgcaaaatgatagaacaacttcacaaataggatatggacattaa-tgta---gtcaagatacagaa-ag
B D                 Ferret   ttgcaaaatgatagaacaatttcatgaataggatatggacattaa-tgtt---gtaaagattcagaa-ag
             Pacific walrus  ttgcaaaacgatagaaacacttcatgaataggatatggacattaa-tgta---atcaagatacagaa-ag
            Star-nosed mole  tagcaaaacactaacccaacttcataaccagaacatggatattag-ttca---gtcaagatacaggacat
B D                Hedgehog  ======================================================================
            Golden hamster  ======================================================================
B D                   Shrew  ======================================================================
       Cape elephant shrew  ======================================================================
              Prairie vole  ======================================================================
B D                   Panda  ======================================================================
B D                    Pika  ======================================================================
    Lesser Egyptian jerboa  ======================================================================
B D                     Rat  ======================================================================
B D                   Mouse  ======================================================================
B D         Chinese hamster  ======================================================================
B D               Armadillo  ======================================================================
B D                  Tenrec  ======================================================================
B D                 Manatee  ======================================================================
B D                Elephant  ======================================================================
B D                Microbat  ======================================================================
      David's myotis (bat)  ======================================================================
             Big brown bat  ======================================================================
             Domestic goat  ======================================================================
B D                   Sheep  ======================================================================
B D                     Cow  ======================================================================
          Tibetan antelope  ======================================================================
B D                   Horse  ======================================================================
B D        White rhinoceros  ======================================================================
            Bactrian camel  ======================================================================
B D                  Alpaca  ======================================================================
              Killer whale  ======================================================================
          Black flying-fox  ======================================================================
B D                Bushbaby  ======================================================================
B D                 Dolphin  ======================================================================
B D                     Pig  ======================================================================
  D         Green seaturtle  ======================================================================
B D         Tasmanian devil  ======================================================================
B D                 Opossum  ======================================================================
          Cape golden mole  ======================================================================
B D                 Megabat  ======================================================================
                  Aardvark  ======================================================================
              Weddell seal  ======================================================================
  D          Painted turtle  ======================================================================
B D                Marmoset  ======================================================================
B D                Platypus  ======================================================================

                      Human  cctattcaccacaaagattcctcatgtttctcatttaaaacagcattcaccttcctccttcctgctcag-
                      Chimp  cctattcaccacaaagattcctcatgtttctcatttaaaacagcattcaccttcctccttcctgctcag-
                    Gorilla  cctattcaccacaaagattcctcatgtttctcatttaaaacagcattcaccttcctccttcctgctcag-
                  Orangutan  cctattcaccacaaagattcctcatgtttctcatttaaaacagcatttaccttcctccttcctgctcag-
                     Gibbon  cctattcaccacaaagattcctcatgtttctcatttaaaacagcattcaccttcctccttcctgctcag-
                     Rhesus  tctattcaccacaaagattcctcatgtttctcatttaaaacagcattcacctttctccttcctgctcag-
        Crab-eating macaque  tctattcaccacaaagattcctcatgtttctcatttaaaacagcattcacctttctccttcctgctcag-
                     Baboon  tctattcaccacaaagattcctcatgtttctcatttaaaacagcattcacctttctccttcctgctcag-
               Green monkey  tctattcaccacaaagattcctcatgtttctcatttaaaacagcattcacctttctccttcctgctcag-
            Squirrel monkey  cctattcaccacaaagattcctcatgtttctcatttaaaacagtattcaccttcctcctttctactcag-
         Chinese tree shrew  ctca-taattacaggga------atatttctcattttcaattatatgaatcctctttcttcctgctcaa-
                   Squirrel  cttc-tcgccacaatgatccttcatatttctcctctacagtgacatctaccattctctttaccgcttgg-
             Naked mole-rat  ctca-tcacc-cagtgatcc-tcatttttctcatttacaatggcacccaccctcctcttttctgcttga-
                 Guinea pig  ccca-ccatcacaccgattc-tcatacttgtcacttacagtggtatccatttcctctttttttgcttgt-
                 Chinchilla  tcca-ccatcacaatggtcc-tcatacttctcctttataatggcatccaccttcttcttttctacttgg-
           Brush-tailed rat  ctca-ccaccacagcagtct-tcggatttctcatttacaatggcagtcatcctcctcttttccactcgg-
                     Rabbit  ccca-tcactaccaagatccttcatgtttctcacttactgggacaatcaccctcctcctctctgctcag-
                        Cat  ttca-tcgccataggggcccctcatgtttctctttaataaccatctttattct----ctctctgctcctg
                        Dog  ttca-tcaccataggg-cccctcatgttggtctttaa-aaccatctttgttct----ctctcagattct-
                    Ferret   ttta-ttaccataggggtccctcgtgttattctttaataaccacctttgtttt----ctctcagctcct-
             Pacific walrus  ttta-tcaccatagggaccccttatgttactctttaataaccatctttgttct----ctctcagctcct-
            Star-nosed mole  ttca-tcatcacaaggagccctaatattacttttttataaaaacatctattct-----tcttcccacct-
                   Hedgehog  ======================================================================
             Golden hamster  ======================================================================
                      Shrew  ======================================================================
        Cape elephant shrew  ======================================================================
               Prairie vole  ======================================================================
                      Panda  ======================================================================
                       Pika  ======================================================================
     Lesser Egyptian jerboa  ======================================================================
                        Rat  ======================================================================
                      Mouse  ======================================================================
            Chinese hamster  ======================================================================
                  Armadillo  ======================================================================
                     Tenrec  ======================================================================
                    Manatee  ======================================================================
                   Elephant  ======================================================================
                   Microbat  ======================================================================
       David's myotis (bat)  ======================================================================
              Big brown bat  ======================================================================
              Domestic goat  ======================================================================
                      Sheep  ======================================================================
                        Cow  ======================================================================
           Tibetan antelope  ======================================================================
                      Horse  ======================================================================
           White rhinoceros  ======================================================================
             Bactrian camel  ======================================================================
                     Alpaca  ======================================================================
               Killer whale  ======================================================================
           Black flying-fox  ======================================================================
                   Bushbaby  ======================================================================
                    Dolphin  ======================================================================
                        Pig  ======================================================================
            Green seaturtle  ======================================================================
            Tasmanian devil  ======================================================================
                    Opossum  ======================================================================
           Cape golden mole  ======================================================================
                    Megabat  ======================================================================
                   Aardvark  ======================================================================
               Weddell seal  ======================================================================
             Painted turtle  ======================================================================
                   Marmoset  ======================================================================
                   Platypus  ======================================================================

                      Human  cccctatttcta
                      Chimp  cccctatttcta
                    Gorilla  cccctatttcta
                  Orangutan  cccctatttcta
                     Gibbon  cccctatttcta
                     Rhesus  cccatatttcta
        Crab-eating macaque  cccgtatttcta
                     Baboon  cccctatttcta
               Green monkey  cgcgtatttcta
            Squirrel monkey  tccctatttcta
         Chinese tree shrew  ccc-tggaccta
                   Squirrel  ccccaattctaa
             Naked mole-rat  tcaatgtccctg
                 Guinea pig  gccacgtccatg
                 Chinchilla  gccacatcccta
           Brush-tailed rat  tccgaatccctg
                     Rabbit  cccctgtcccca
                        Cat  tcctta------
                        Dog  ccctta------
                    Ferret   tcctta------
             Pacific walrus  tcctta------
            Star-nosed mole  aaccta------
                   Hedgehog  ============
             Golden hamster  ============
                      Shrew  ============
        Cape elephant shrew  ============
               Prairie vole  ============
                      Panda  ============
                       Pika  ============
     Lesser Egyptian jerboa  ============
                        Rat  ============
                      Mouse  ============
            Chinese hamster  ============
                  Armadillo  ============
                     Tenrec  ============
                    Manatee  ============
                   Elephant  ============
                   Microbat  ============
       David's myotis (bat)  ============
              Big brown bat  ============
              Domestic goat  ============
                      Sheep  ============
                        Cow  ============
           Tibetan antelope  ============
                      Horse  ============
           White rhinoceros  ============
             Bactrian camel  ============
                     Alpaca  ============
               Killer whale  ============
           Black flying-fox  ============
                   Bushbaby  ============
                    Dolphin  ============
                        Pig  ============
            Green seaturtle  ============
            Tasmanian devil  ============
                    Opossum  ============
           Cape golden mole  ============
                    Megabat  ============
                   Aardvark  ============
               Weddell seal  ============
             Painted turtle  ============
                   Marmoset  ============
                   Platypus  ============

Alignment block 8 of 10 in window, 55713327 - 55713346, 20 bps 
B D                   Human  gcccctgacaataatc-----------------------------------------agta
B D                   Chimp  gcccctgacaataatc-----------------------------------------agta
B D                 Gorilla  gcccctgacaataatc-----------------------------------------agta
B D               Orangutan  gcccctgacaataatc-----------------------------------------agtc
B D                  Gibbon  gcccctgacaataatc-----------------------------------------agtc
B D                  Rhesus  acccctgacaataacc-----------------------------------------agtc
B D     Crab-eating macaque  acccctgacaataacc-----------------------------------------agtc
B D                  Baboon  acccctgacaataacc-----------------------------------------agtc
B D            Green monkey  acccctgacaataacc-----------------------------------------agtc
B D         Squirrel monkey  acccctgacaataacc-----------------------------------------agtc
         Chinese tree shrew  atctctgacaatggtc-----------------------------------------aatt
B D                Squirrel  acccttgacaataacc-----------------------------------------aatc
B D          Naked mole-rat  accc-tggcaacaact-----------------------------------------cagc
B D              Guinea pig  acacccagcaacaatctgttgctgttcctgttatctgttctctattctgttctctattatc
                 Chinchilla  acccttggcagcaact-----------------------------------------tctc
           Brush-tailed rat  acccttggcaacaacc-----------------------------------------tacc
B D                  Rabbit  gtccctgaaaacagcc-----------------------------------------aatg
B D                    Pika  gttcatgaaaacagcc-----------------------------------------aatc
B D                     Cat  acttctggcaaccttc-----------------------------------------aatc
B D                     Dog  aattctagcaatgacc-----------------------------------------actc
B D                 Ferret   acttctggcaaccacc-----------------------------------------agtc
             Pacific walrus  acttctggcaaccact-----------------------------------------aatc
            Star-nosed mole  aatcctggcacata-----------------------------------------------
B D                Hedgehog  =============================================================
            Golden hamster  =============================================================
B D                   Shrew  =============================================================
       Cape elephant shrew  =============================================================
              Prairie vole  =============================================================
B D                   Panda  =============================================================
    Lesser Egyptian jerboa  =============================================================
B D                     Rat  =============================================================
B D                   Mouse  =============================================================
B D         Chinese hamster  =============================================================
B D               Armadillo  =============================================================
B D                  Tenrec  =============================================================
B D                 Manatee  =============================================================
B D                Elephant  =============================================================
B D                Microbat  =============================================================
      David's myotis (bat)  =============================================================
             Big brown bat  =============================================================
             Domestic goat  =============================================================
B D                   Sheep  =============================================================
B D                     Cow  =============================================================
          Tibetan antelope  =============================================================
B D                   Horse  =============================================================
B D        White rhinoceros  =============================================================
            Bactrian camel  =============================================================
B D                  Alpaca  =============================================================
              Killer whale  =============================================================
          Black flying-fox  =============================================================
B D                Bushbaby  =============================================================
B D                 Dolphin  =============================================================
B D                     Pig  =============================================================
  D         Green seaturtle  =============================================================
B D         Tasmanian devil  =============================================================
B D                 Opossum  =============================================================
          Cape golden mole  =============================================================
B D                 Megabat  =============================================================
                  Aardvark  =============================================================
              Weddell seal  =============================================================
  D          Painted turtle  =============================================================
B D                Marmoset  =============================================================
B D                Platypus  =============================================================

Alignment block 9 of 10 in window, 55713347 - 55713381, 35 bps 
B D                   Human  tgctctccatattta-taattttgtc------atttcaagaa
B D                   Chimp  tgctctccatattta-taattttgtc------atttcaagaa
B D                 Gorilla  tgctctccatattta-taattttgtc------atttcaagaa
B D               Orangutan  tgctctccatattta-taattttgtc------atttcaagaa
B D                  Gibbon  tgctctccatattta-taattttgtc------atttcaagaa
B D                  Rhesus  tgctctccatattta-taattttgtc------atctcaagaa
B D     Crab-eating macaque  tgctctccatattta-taattttgtc------atctcaagaa
B D                  Baboon  tgctctccatattta-taattttgtc------atctcaagaa
B D            Green monkey  tgctctccatattta-taattttgtc------atctcaagaa
B D         Squirrel monkey  tgctctccataatta-tagttttgtc------atttcaagaa
         Chinese tree shrew  tgttctacattttta-tagttctgtc------atttcaagaa
B D                Squirrel  ttttttcaattttta-taatattatc------actttaagat
B D          Naked mole-rat  agttctctatttcta-taatgttacc------atttcaagaa
B D              Guinea pig  tgttctctattcctg-tcactttagc------atttggagaa
                 Chinchilla  ggttctctattccta-caattttacc------atttcaggaa
           Brush-tailed rat  tcttctctattccta-taattttacc------atttcaagaa
B D                  Rabbit  tcttctccatttctatattttttgtc------atttcaagaa
B D                    Pika  tctaccctatttaga-accttgggtc------gtttcaagaa
B D                     Cat  tgttctctattttta-taattttgtc------attttaagat
B D                     Dog  tgttctctatttcta-taattttgtc------atttcaagat
B D                 Ferret   tgttctctatttcta-taattttgtc------atttcaagtt
             Pacific walrus  tgttctctagttcta-taattttttttataaattttataggt
               Weddell seal  tgttctctatttctg-taattttttc------atttaaagat
            Star-nosed mole  ---tgtccactttta-t-atttcatc------acttaaagat
B D                Hedgehog  ==========================================
            Golden hamster  ==========================================
B D                   Shrew  ==========================================
       Cape elephant shrew  ==========================================
              Prairie vole  ==========================================
B D                   Panda  ==========================================
    Lesser Egyptian jerboa  ==========================================
B D                     Rat  ==========================================
B D                   Mouse  ==========================================
B D         Chinese hamster  ==========================================
B D               Armadillo  ==========================================
B D                  Tenrec  ==========================================
B D                 Manatee  ==========================================
B D                Elephant  ==========================================
B D                Microbat  ==========================================
      David's myotis (bat)  ==========================================
             Big brown bat  ==========================================
             Domestic goat  ==========================================
B D                   Sheep  ==========================================
B D                     Cow  ==========================================
          Tibetan antelope  ==========================================
B D                   Horse  ==========================================
B D        White rhinoceros  ==========================================
            Bactrian camel  ==========================================
B D                  Alpaca  ==========================================
              Killer whale  ==========================================
          Black flying-fox  ==========================================
B D                Bushbaby  ==========================================
B D                 Dolphin  ==========================================
B D                     Pig  ==========================================
  D         Green seaturtle  ==========================================
B D         Tasmanian devil  ==========================================
B D                 Opossum  ==========================================
          Cape golden mole  ==========================================
B D                 Megabat  ==========================================
                  Aardvark  ==========================================
  D          Painted turtle  ==========================================
B D                Marmoset  ==========================================
B D                Platypus  ==========================================

Inserts between block 9 and 10 in window
          Brush-tailed rat 255bp

Alignment block 10 of 10 in window, 55713382 - 55713408, 27 bps 
B D                   Human  tattacataagttgaatcccacagtat
B D                   Chimp  tattacataagttgaatcccacagtat
B D                 Gorilla  tattacataagttgaatcccacagtat
B D               Orangutan  tattacataagttgaatcccacagtat
B D                  Gibbon  tattacataagttgaatcccacagtat
B D                  Rhesus  tattacataagttgaatcacacagtat
B D     Crab-eating macaque  tattacataagttgaatcacacagtat
B D                  Baboon  tattacataagttgaatcacacagtat
B D            Green monkey  tattacataagttgaatcacacagtat
B D         Squirrel monkey  tattgcataagttgaatcatatagtat
         Chinese tree shrew  tgttacataaattgaatcaaacagtat
B D                Squirrel  tattacataagttgaatcatccagtat
B D          Naked mole-rat  tatcacataaattgaatcataca----
B D              Guinea pig  tattacataaaatgaaccatacaatat
                 Chinchilla  tattacataaaatgaatcatacagtgt
           Brush-tailed rat  tattacataaaatgaatcatacagtgt
B D                  Rabbit  tattacataacttgaatcataccatat
B D                    Pika  tatttcccaagttgaatcatactg-at
B D                     Cat  tgttatgtaaactgaatcatacagaat
B D                     Dog  ttttatgaaaactgaatcatacagaat
B D                 Ferret   tgttatgtaaacggaatcatacagaat
             Pacific walrus  tgttatgtaaactgaatcatacagaat
               Weddell seal  tgttatgtaaactgaatcatacaaaat
            Star-nosed mole  gaaaatgtaaattgattcatataatat
B D                Hedgehog  ===========================
            Golden hamster  ===========================
B D                   Shrew  ===========================
       Cape elephant shrew  ===========================
              Prairie vole  ===========================
B D                   Panda  ===========================
    Lesser Egyptian jerboa  ===========================
B D                     Rat  ===========================
B D                   Mouse  ===========================
B D         Chinese hamster  ===========================
B D               Armadillo  ===========================
B D                  Tenrec  ===========================
B D                 Manatee  ===========================
B D                Elephant  ===========================
B D                Microbat  ===========================
      David's myotis (bat)  ===========================
             Big brown bat  ===========================
             Domestic goat  ===========================
B D                   Sheep  ===========================
B D                     Cow  ===========================
          Tibetan antelope  ===========================
B D                   Horse  ===========================
B D        White rhinoceros  ===========================
            Bactrian camel  ===========================
B D                  Alpaca  ===========================
              Killer whale  ===========================
          Black flying-fox  ===========================
B D                Bushbaby  ===========================
B D                 Dolphin  ===========================
B D                     Pig  ===========================
  D         Green seaturtle  ===========================
B D         Tasmanian devil  ===========================
B D                 Opossum  ===========================
          Cape golden mole  ===========================
B D                 Megabat  ===========================
                  Aardvark  ===========================
  D          Painted turtle  ===========================
B D                Marmoset  ===========================
B D                Platypus  ===========================

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