Multiz Alignments of 100 Vertebrates
 

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Alignment block 1 of 14 in window, 98321131 - 98321145, 15 bps 
B D                     Human  atcatagagtgtact
B D                     Chimp  atcatagagtgtact
B D                   Gorilla  atcatagagtgtact
B D                 Orangutan  atcacagagtgtact
B D                    Gibbon  atcatagagtgtact
B D       Crab-eating macaque  atcatagagtgtact
B D                    Baboon  atcatagagtgtact
B D              Green monkey  atcatagagtgtact
           Chinese tree shrew  ataactaagtgcact
B D                       Rat  ===============
                Prairie vole  ===============
              Golden hamster  ===============
B D                     Mouse  ===============
      Lesser Egyptian jerboa  ===============
B D                      Pika  ===============
                Weddell seal  ---------------
B D                  Hedgehog  ===============
B D                     Shrew  ===============
B D                Guinea pig  ===============
B D                       Pig  ===============
B D                    Rabbit  ===============
            Cape golden mole  NNNNNNNNNNNNNNN
                    Aardvark  ===============
B D                   Megabat  ===============
B D                   Dolphin  ---------------
B D                    Rhesus  ===============
B D             X. tropicalis  ===============
                 Spotted gar  ===============
B D                    Turkey  ===============
B D                   Chicken  ===============
  D              Mallard duck  ---------------
          Tibetan ground jay  ===============
B D               Zebra finch  ===============
  D    White-throated sparrow  ===============
B D           Tasmanian devil  ===============
  D            Painted turtle  ===============
  D           Green seaturtle  ===============
B D        American alligator  ===============
  D             Scarlet macaw  ===============
B D                Budgerigar  ===============
B D                   Opossum  ===============
B D            Naked mole-rat  ===============
  D               Rock pigeon  ===============
  D       Collared flycatcher  ===============
B D       Medium ground finch  ===============
B D                    Lizard  ===============
  D          Peregrine falcon  ===============
  D              Saker falcon  ===============
  D                    Parrot  ===============
            Brush-tailed rat  ===============
                  Chinchilla  ===============
         Cape elephant shrew  ===============
B D                  Platypus  ===============
B D                   Wallaby  ===============
B D                   Manatee  ===============
B D                  Elephant  ===============
B D           Chinese hamster  ===============
B D                    Tenrec  ===============
B D                       Cat  ===============
B D                  Bushbaby  ===============
  D  Chinese softshell turtle  ===============
B D                   Ferret   ---------------
             Star-nosed mole  ===============
               Domestic goat  ===============
B D                     Sheep  ===============
            Tibetan antelope  ===============
              Bactrian camel  ---------------
B D                    Alpaca  ---------------
              Pacific walrus  ---------------
B D                     Panda  ---------------
                Killer whale  ---------------
B D                       Dog  ---------------
            Black flying-fox  ===============
B D          White rhinoceros  ===============
B D                     Horse  ---------------
B D                  Squirrel  ===============
B D                 Armadillo  ===============
        David's myotis (bat)  ===============
               Big brown bat  ===============
B D                  Microbat  ===============
B D           Squirrel monkey  ---------------
B D                  Marmoset  ---------------
B D                       Cow  ===============

Inserts between block 1 and 2 in window
          Chinese tree shrew 219bp

Alignment block 2 of 14 in window, 98321146 - 98321547, 402 bps 
B D                     Human  tacatgaacct-aatgatacagcttaccacatacttagcctgtatattatagactattgcctctgtgcta
B D                     Chimp  tacatgaacct-aatgatacagcttaccacatacttagcctgtatattatagactattgcctctgtgcta
B D                   Gorilla  tacatgaacct-aatgatacagcttaccacatacttagcctgtatattatagactattgcctctgtgcta
B D                 Orangutan  tacatgaacct-aatgatatagcttaccacatacctagcctgtatattatagactattgcctgtgtgcta
B D                    Gibbon  tacatgaacct-aatgatatagcttaccacatacctagcctgtatattatagactattgcctctgtgcta
B D       Crab-eating macaque  tacatgaacctaaatgatatagcttaccacatacctaggctgtatattatagcttattgcccc--tgcta
B D                    Baboon  tacatgaacctaaatgatatagcttaccacatacctaggctgtatattatagcttattgcccc--tgcta
B D              Green monkey  tacatgaacctaaatgatatagcttaccacatacctaggctatatattatagcttattgcccc--tgcta
B D                       Rat  ======================================================================
                Prairie vole  ======================================================================
              Golden hamster  ======================================================================
B D                     Mouse  ======================================================================
      Lesser Egyptian jerboa  ======================================================================
B D                      Pika  ======================================================================
                Weddell seal  ----------------------------------------------------------------------
B D                  Hedgehog  ======================================================================
B D                     Shrew  ======================================================================
B D                Guinea pig  ======================================================================
B D                       Pig  ======================================================================
B D                    Rabbit  ======================================================================
            Cape golden mole  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
                    Aardvark  ======================================================================
B D                   Megabat  ======================================================================
B D                   Dolphin  ----------------------------------------------------------------------
B D                    Rhesus  ======================================================================
B D             X. tropicalis  ======================================================================
                 Spotted gar  ======================================================================
B D                    Turkey  ======================================================================
B D                   Chicken  ======================================================================
  D              Mallard duck  ----------------------------------------------------------------------
          Tibetan ground jay  ======================================================================
B D               Zebra finch  ======================================================================
  D    White-throated sparrow  ======================================================================
B D           Tasmanian devil  ======================================================================
  D            Painted turtle  ======================================================================
  D           Green seaturtle  ======================================================================
B D        American alligator  ======================================================================
  D             Scarlet macaw  ======================================================================
B D                Budgerigar  ======================================================================
B D                   Opossum  ======================================================================
B D            Naked mole-rat  ======================================================================
  D               Rock pigeon  ======================================================================
  D       Collared flycatcher  ======================================================================
B D       Medium ground finch  ======================================================================
B D                    Lizard  ======================================================================
  D          Peregrine falcon  ======================================================================
  D              Saker falcon  ======================================================================
  D                    Parrot  ======================================================================
            Brush-tailed rat  ======================================================================
                  Chinchilla  ======================================================================
         Cape elephant shrew  ======================================================================
          Chinese tree shrew  ======================================================================
B D                  Platypus  ======================================================================
B D                   Wallaby  ======================================================================
B D                   Manatee  ======================================================================
B D                  Elephant  ======================================================================
B D           Chinese hamster  ======================================================================
B D                    Tenrec  ======================================================================
B D                       Cat  ======================================================================
B D                  Bushbaby  ======================================================================
  D  Chinese softshell turtle  ======================================================================
B D                   Ferret   ----------------------------------------------------------------------
             Star-nosed mole  ======================================================================
               Domestic goat  ======================================================================
B D                     Sheep  ======================================================================
            Tibetan antelope  ======================================================================
              Bactrian camel  ----------------------------------------------------------------------
B D                    Alpaca  ----------------------------------------------------------------------
              Pacific walrus  ----------------------------------------------------------------------
B D                     Panda  ----------------------------------------------------------------------
                Killer whale  ----------------------------------------------------------------------
B D                       Dog  ----------------------------------------------------------------------
            Black flying-fox  ======================================================================
B D          White rhinoceros  ======================================================================
B D                     Horse  ----------------------------------------------------------------------
B D                  Squirrel  ======================================================================
B D                 Armadillo  ======================================================================
        David's myotis (bat)  ======================================================================
               Big brown bat  ======================================================================
B D                  Microbat  ======================================================================
B D           Squirrel monkey  ----------------------------------------------------------------------
B D                  Marmoset  ----------------------------------------------------------------------
B D                       Cow  ======================================================================

                        Human  caaacctgtacagaagttactgcaccgtaggcaactgtaacacaatggtaagtatttatgtatctaaatg
                        Chimp  caaacctgtacagaagttactgcactgtgggcaactgtaacacaatggta----tttatgtatctaaatg
                      Gorilla  caaacctgtacaggagttactgcactgtaggcaactgtaacacaatggtaagtatttatgtatctaaatg
                    Orangutan  caaacctgtacagaagttattgcaccgtgggcaactgtaacacaatggtaagtatttatgtgtctaaatg
                       Gibbon  caaacctgtacagaagttactgcactgtaggcaactgtaacacaatggtaagtatttatgtatctaaatg
          Crab-eating macaque  caaacctgtacagaagttactgcagtgtaggcaactgtaatacgatggtaagtatttatgtgtctaaaca
                       Baboon  caagcctgtacagaagttactgcagtgtaggcaactgtaatacgatggtaagtatttatgtgtctaaaca
                 Green monkey  caaacctgtacagaagttactgcagtgtaggcaactgtaatacgatggtaagtatttatgtgtctaaaca
                          Rat  ======================================================================
                 Prairie vole  ======================================================================
               Golden hamster  ======================================================================
                        Mouse  ======================================================================
       Lesser Egyptian jerboa  ======================================================================
                         Pika  ======================================================================
                 Weddell seal  ----------------------------------------------------------------------
                     Hedgehog  ======================================================================
                        Shrew  ======================================================================
                   Guinea pig  ======================================================================
                          Pig  ======================================================================
                       Rabbit  ======================================================================
             Cape golden mole  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
                     Aardvark  ======================================================================
                      Megabat  ======================================================================
                      Dolphin  ----------------------------------------------------------------------
                       Rhesus  ======================================================================
                X. tropicalis  ======================================================================
                  Spotted gar  ======================================================================
                       Turkey  ======================================================================
                      Chicken  ======================================================================
                 Mallard duck  ----------------------------------------------------------------------
           Tibetan ground jay  ======================================================================
                  Zebra finch  ======================================================================
       White-throated sparrow  ======================================================================
              Tasmanian devil  ======================================================================
               Painted turtle  ======================================================================
              Green seaturtle  ======================================================================
           American alligator  ======================================================================
                Scarlet macaw  ======================================================================
                   Budgerigar  ======================================================================
                      Opossum  ======================================================================
               Naked mole-rat  ======================================================================
                  Rock pigeon  ======================================================================
          Collared flycatcher  ======================================================================
          Medium ground finch  ======================================================================
                       Lizard  ======================================================================
             Peregrine falcon  ======================================================================
                 Saker falcon  ======================================================================
                       Parrot  ======================================================================
             Brush-tailed rat  ======================================================================
                   Chinchilla  ======================================================================
          Cape elephant shrew  ======================================================================
           Chinese tree shrew  ======================================================================
                     Platypus  ======================================================================
                      Wallaby  ======================================================================
                      Manatee  ======================================================================
                     Elephant  ======================================================================
              Chinese hamster  ======================================================================
                       Tenrec  ======================================================================
                          Cat  ======================================================================
                     Bushbaby  ======================================================================
     Chinese softshell turtle  ======================================================================
                      Ferret   ----------------------------------------------------------------------
              Star-nosed mole  ======================================================================
                Domestic goat  ======================================================================
                        Sheep  ======================================================================
             Tibetan antelope  ======================================================================
               Bactrian camel  ----------------------------------------------------------------------
                       Alpaca  ----------------------------------------------------------------------
               Pacific walrus  ----------------------------------------------------------------------
                        Panda  ----------------------------------------------------------------------
                 Killer whale  ----------------------------------------------------------------------
                          Dog  ----------------------------------------------------------------------
             Black flying-fox  ======================================================================
             White rhinoceros  ======================================================================
                        Horse  ----------------------------------------------------------------------
                     Squirrel  ======================================================================
                    Armadillo  ======================================================================
         David's myotis (bat)  ======================================================================
                Big brown bat  ======================================================================
                     Microbat  ======================================================================
              Squirrel monkey  ----------------------------------------------------------------------
                     Marmoset  ----------------------------------------------------------------------
                          Cow  ======================================================================

                        Human  aatctaaacataaaaatgtacagtaaaattgtaagtcaatgagagaagtggtatgtgctatatatacttt
                        Chimp  tatctaaacataaaaatgtacagtaaaattgtaagtcaatgagagaagtggtatgtgctatatatacttt
                      Gorilla  tatctaaacataaaaatgtacagtaaaattgtaagtcaatgagagaagtggtatgtgctatatatacttt
                    Orangutan  tatctaaacataaaaatgtatagtaaaa---taagtcaatgagagaagtggtatgtgctatatatacttt
                       Gibbon  tatctaaacataaaaatgtacagtaaaattataagtcaatgagagaagtggtatgtgctatatatgcttt
          Crab-eating macaque  tatctaaacat-aaaatgtacagtaaaattataagtcagtgagagaagtggtatgggctatatatacttt
                       Baboon  tatctaaacat-aaaatgtacagtaaaattataagtcagtgagagaagtggtatgggctatatatacttt
                 Green monkey  tatctaaacat-aaaatgtacagtaaaattataagtcagtgagagaagtggtatgtgctatatatacttt
                          Rat  ======================================================================
                 Prairie vole  ======================================================================
               Golden hamster  ======================================================================
                        Mouse  ======================================================================
       Lesser Egyptian jerboa  ======================================================================
                         Pika  ======================================================================
                 Weddell seal  ----------------------------------------------------------------------
                     Hedgehog  ======================================================================
                        Shrew  ======================================================================
                   Guinea pig  ======================================================================
                          Pig  ======================================================================
                       Rabbit  ======================================================================
             Cape golden mole  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
                     Aardvark  ======================================================================
                      Megabat  ======================================================================
                      Dolphin  ----------------------------------------------------------------------
                       Rhesus  ======================================================================
                X. tropicalis  ======================================================================
                  Spotted gar  ======================================================================
                       Turkey  ======================================================================
                      Chicken  ======================================================================
                 Mallard duck  ----------------------------------------------------------------------
           Tibetan ground jay  ======================================================================
                  Zebra finch  ======================================================================
       White-throated sparrow  ======================================================================
              Tasmanian devil  ======================================================================
               Painted turtle  ======================================================================
              Green seaturtle  ======================================================================
           American alligator  ======================================================================
                Scarlet macaw  ======================================================================
                   Budgerigar  ======================================================================
                      Opossum  ======================================================================
               Naked mole-rat  ======================================================================
                  Rock pigeon  ======================================================================
          Collared flycatcher  ======================================================================
          Medium ground finch  ======================================================================
                       Lizard  ======================================================================
             Peregrine falcon  ======================================================================
                 Saker falcon  ======================================================================
                       Parrot  ======================================================================
             Brush-tailed rat  ======================================================================
                   Chinchilla  ======================================================================
          Cape elephant shrew  ======================================================================
           Chinese tree shrew  ======================================================================
                     Platypus  ======================================================================
                      Wallaby  ======================================================================
                      Manatee  ======================================================================
                     Elephant  ======================================================================
              Chinese hamster  ======================================================================
                       Tenrec  ======================================================================
                          Cat  ======================================================================
                     Bushbaby  ======================================================================
     Chinese softshell turtle  ======================================================================
                      Ferret   ----------------------------------------------------------------------
              Star-nosed mole  ======================================================================
                Domestic goat  ======================================================================
                        Sheep  ======================================================================
             Tibetan antelope  ======================================================================
               Bactrian camel  ----------------------------------------------------------------------
                       Alpaca  ----------------------------------------------------------------------
               Pacific walrus  ----------------------------------------------------------------------
                        Panda  ----------------------------------------------------------------------
                 Killer whale  ----------------------------------------------------------------------
                          Dog  ----------------------------------------------------------------------
             Black flying-fox  ======================================================================
             White rhinoceros  ======================================================================
                        Horse  ----------------------------------------------------------------------
                     Squirrel  ======================================================================
                    Armadillo  ======================================================================
         David's myotis (bat)  ======================================================================
                Big brown bat  ======================================================================
                     Microbat  ======================================================================
              Squirrel monkey  ----------------------------------------------------------------------
                     Marmoset  ----------------------------------------------------------------------
                          Cow  ======================================================================

                        Human  tatatgac-----tagaagtaggtttgtttacaccagcatatgag--------------------taatg
                        Chimp  tatatgac-----tagaagtaggtttgtttacaccagcacatgag--------------------caatg
                      Gorilla  tatatgac-----tagaagtaggtttgtttacaccagcacatgag--------------------taatg
                    Orangutan  tatatgac-----tagaagtaggtttgtttacaccagcacatgag--------------------taatg
                       Gibbon  tatatgac-----tagaagtaggtttgtttacaccagcacatgag--------------------taatg
          Crab-eating macaque  tttatgactagaatagaagtaggtttgttt-caccagcacatgagtaatgcattgcactctgatataatg
                       Baboon  tttatggctagaatagaagtaggtttgttt-caccagcacatgagtaatgcattgcactctgatataatg
                 Green monkey  tttatgactagaatagaagtaggtttgttt-caccagcacatgagtaatgcattgcactctgatctaatg
                          Rat  ======================================================================
                 Prairie vole  ======================================================================
               Golden hamster  ======================================================================
                        Mouse  ======================================================================
       Lesser Egyptian jerboa  ======================================================================
                         Pika  ======================================================================
                 Weddell seal  ----------------------------------------------------------------------
                     Hedgehog  ======================================================================
                        Shrew  ======================================================================
                   Guinea pig  ======================================================================
                          Pig  ======================================================================
                       Rabbit  ======================================================================
             Cape golden mole  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
                     Aardvark  ======================================================================
                      Megabat  ======================================================================
                      Dolphin  ----------------------------------------------------------------------
                       Rhesus  ======================================================================
                X. tropicalis  ======================================================================
                  Spotted gar  ======================================================================
                       Turkey  ======================================================================
                      Chicken  ======================================================================
                 Mallard duck  ----------------------------------------------------------------------
           Tibetan ground jay  ======================================================================
                  Zebra finch  ======================================================================
       White-throated sparrow  ======================================================================
              Tasmanian devil  ======================================================================
               Painted turtle  ======================================================================
              Green seaturtle  ======================================================================
           American alligator  ======================================================================
                Scarlet macaw  ======================================================================
                   Budgerigar  ======================================================================
                      Opossum  ======================================================================
               Naked mole-rat  ======================================================================
                  Rock pigeon  ======================================================================
          Collared flycatcher  ======================================================================
          Medium ground finch  ======================================================================
                       Lizard  ======================================================================
             Peregrine falcon  ======================================================================
                 Saker falcon  ======================================================================
                       Parrot  ======================================================================
             Brush-tailed rat  ======================================================================
                   Chinchilla  ======================================================================
          Cape elephant shrew  ======================================================================
           Chinese tree shrew  ======================================================================
                     Platypus  ======================================================================
                      Wallaby  ======================================================================
                      Manatee  ======================================================================
                     Elephant  ======================================================================
              Chinese hamster  ======================================================================
                       Tenrec  ======================================================================
                          Cat  ======================================================================
                     Bushbaby  ======================================================================
     Chinese softshell turtle  ======================================================================
                      Ferret   ----------------------------------------------------------------------
              Star-nosed mole  ======================================================================
                Domestic goat  ======================================================================
                        Sheep  ======================================================================
             Tibetan antelope  ======================================================================
               Bactrian camel  ----------------------------------------------------------------------
                       Alpaca  ----------------------------------------------------------------------
               Pacific walrus  ----------------------------------------------------------------------
                        Panda  ----------------------------------------------------------------------
                 Killer whale  ----------------------------------------------------------------------
                          Dog  ----------------------------------------------------------------------
             Black flying-fox  ======================================================================
             White rhinoceros  ======================================================================
                        Horse  ----------------------------------------------------------------------
                     Squirrel  ======================================================================
                    Armadillo  ======================================================================
         David's myotis (bat)  ======================================================================
                Big brown bat  ======================================================================
                     Microbat  ======================================================================
              Squirrel monkey  ----------------------------------------------------------------------
                     Marmoset  ----------------------------------------------------------------------
                          Cow  ======================================================================

                        Human  cattgcattatgatataatgcattgcactattgatgaccataatgtcactggacaatagatatttttcca
                        Chimp  cattgcattatgatataatgcattgcactattgatgaccataatgtcactggacaatagatatttttcca
                      Gorilla  cattgcattatgacataatgcattgcactattgatgaccataatgtcactggacaatagatatttttcca
                    Orangutan  cattgcattatgatataatgcattgcactattgatggccataatgtcactggacaatagagatttttcca
                       Gibbon  cactgcattacgatataatgcattgcactattgatggccataatgtcactggacaatagagatttttcca
          Crab-eating macaque  cattgcactctgatataatgcattgcactattgatggccataatgtcactggatgatagaagtttttcca
                       Baboon  cattgcactctgatataatgcattgcactattgatggccataatgtcactggatgatagaagtttttcca
                 Green monkey  cattgcactctgatacaatgcattgcactattgatgg-cattatgtcactggatgatagaagtttttcca
                          Rat  ======================================================================
                 Prairie vole  ======================================================================
               Golden hamster  ======================================================================
                        Mouse  ======================================================================
       Lesser Egyptian jerboa  ======================================================================
                         Pika  ======================================================================
                 Weddell seal  ----------------------------------------------------------------------
                     Hedgehog  ======================================================================
                        Shrew  ======================================================================
                   Guinea pig  ======================================================================
                          Pig  ======================================================================
                       Rabbit  ======================================================================
             Cape golden mole  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
                     Aardvark  ======================================================================
                      Megabat  ======================================================================
                      Dolphin  ----------------------------------------------------------------------
                       Rhesus  ======================================================================
                X. tropicalis  ======================================================================
                  Spotted gar  ======================================================================
                       Turkey  ======================================================================
                      Chicken  ======================================================================
                 Mallard duck  ----------------------------------------------------------------------
           Tibetan ground jay  ======================================================================
                  Zebra finch  ======================================================================
       White-throated sparrow  ======================================================================
              Tasmanian devil  ======================================================================
               Painted turtle  ======================================================================
              Green seaturtle  ======================================================================
           American alligator  ======================================================================
                Scarlet macaw  ======================================================================
                   Budgerigar  ======================================================================
                      Opossum  ======================================================================
               Naked mole-rat  ======================================================================
                  Rock pigeon  ======================================================================
          Collared flycatcher  ======================================================================
          Medium ground finch  ======================================================================
                       Lizard  ======================================================================
             Peregrine falcon  ======================================================================
                 Saker falcon  ======================================================================
                       Parrot  ======================================================================
             Brush-tailed rat  ======================================================================
                   Chinchilla  ======================================================================
          Cape elephant shrew  ======================================================================
           Chinese tree shrew  ======================================================================
                     Platypus  ======================================================================
                      Wallaby  ======================================================================
                      Manatee  ======================================================================
                     Elephant  ======================================================================
              Chinese hamster  ======================================================================
                       Tenrec  ======================================================================
                          Cat  ======================================================================
                     Bushbaby  ======================================================================
     Chinese softshell turtle  ======================================================================
                      Ferret   ----------------------------------------------------------------------
              Star-nosed mole  ======================================================================
                Domestic goat  ======================================================================
                        Sheep  ======================================================================
             Tibetan antelope  ======================================================================
               Bactrian camel  ----------------------------------------------------------------------
                       Alpaca  ----------------------------------------------------------------------
               Pacific walrus  ----------------------------------------------------------------------
                        Panda  ----------------------------------------------------------------------
                 Killer whale  ----------------------------------------------------------------------
                          Dog  ----------------------------------------------------------------------
             Black flying-fox  ======================================================================
             White rhinoceros  ======================================================================
                        Horse  ----------------------------------------------------------------------
                     Squirrel  ======================================================================
                    Armadillo  ======================================================================
         David's myotis (bat)  ======================================================================
                Big brown bat  ======================================================================
                     Microbat  ======================================================================
              Squirrel monkey  ----------------------------------------------------------------------
                     Marmoset  ----------------------------------------------------------------------
                          Cow  ======================================================================

                        Human  ctccattataactttatgggacgactgttttatatgcagtctgtcattgactgaaacatcattatgttgt
                        Chimp  ctccattataactttatgggacgactgttttatatgcagtctgtcattgactgaaacatcattatgttgt
                      Gorilla  ctccattataactttatgggacgactgttttatatgcagtctgtcattgactgaaacatcattatgttgt
                    Orangutan  ctccattataactttatgggacgactgttttatatgcagtctgtcattgactgaaacatcattatgttgt
                       Gibbon  ccccatgataactttataggacgactgttttatatgcagtctgtcattgactgaaacatcattatgttgt
          Crab-eating macaque  ctccattataactttatgggatgactgttttacatgcagtctgtcattgactggagcatcattatgttgt
                       Baboon  ctccattataactttatgggatgactgttttacatgcagtctgtcattgactgaagcatcattatgttgt
                 Green monkey  ctccattataactttatgggatgactgttttacatgcagtctgtcattgactgaagcatcattatgttgt
                          Rat  ======================================================================
                 Prairie vole  ======================================================================
               Golden hamster  ======================================================================
                        Mouse  ======================================================================
       Lesser Egyptian jerboa  ======================================================================
                         Pika  ======================================================================
                 Weddell seal  ----------------------------------------------------------------------
                     Hedgehog  ======================================================================
                        Shrew  ======================================================================
                   Guinea pig  ======================================================================
                          Pig  ======================================================================
                       Rabbit  ======================================================================
             Cape golden mole  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
                     Aardvark  ======================================================================
                      Megabat  ======================================================================
                      Dolphin  ----------------------------------------------------------------------
                       Rhesus  ======================================================================
                X. tropicalis  ======================================================================
                  Spotted gar  ======================================================================
                       Turkey  ======================================================================
                      Chicken  ======================================================================
                 Mallard duck  ----------------------------------------------------------------------
           Tibetan ground jay  ======================================================================
                  Zebra finch  ======================================================================
       White-throated sparrow  ======================================================================
              Tasmanian devil  ======================================================================
               Painted turtle  ======================================================================
              Green seaturtle  ======================================================================
           American alligator  ======================================================================
                Scarlet macaw  ======================================================================
                   Budgerigar  ======================================================================
                      Opossum  ======================================================================
               Naked mole-rat  ======================================================================
                  Rock pigeon  ======================================================================
          Collared flycatcher  ======================================================================
          Medium ground finch  ======================================================================
                       Lizard  ======================================================================
             Peregrine falcon  ======================================================================
                 Saker falcon  ======================================================================
                       Parrot  ======================================================================
             Brush-tailed rat  ======================================================================
                   Chinchilla  ======================================================================
          Cape elephant shrew  ======================================================================
           Chinese tree shrew  ======================================================================
                     Platypus  ======================================================================
                      Wallaby  ======================================================================
                      Manatee  ======================================================================
                     Elephant  ======================================================================
              Chinese hamster  ======================================================================
                       Tenrec  ======================================================================
                          Cat  ======================================================================
                     Bushbaby  ======================================================================
     Chinese softshell turtle  ======================================================================
                      Ferret   ----------------------------------------------------------------------
              Star-nosed mole  ======================================================================
                Domestic goat  ======================================================================
                        Sheep  ======================================================================
             Tibetan antelope  ======================================================================
               Bactrian camel  ----------------------------------------------------------------------
                       Alpaca  ----------------------------------------------------------------------
               Pacific walrus  ----------------------------------------------------------------------
                        Panda  ----------------------------------------------------------------------
                 Killer whale  ----------------------------------------------------------------------
                          Dog  ----------------------------------------------------------------------
             Black flying-fox  ======================================================================
             White rhinoceros  ======================================================================
                        Horse  ----------------------------------------------------------------------
                     Squirrel  ======================================================================
                    Armadillo  ======================================================================
         David's myotis (bat)  ======================================================================
                Big brown bat  ======================================================================
                     Microbat  ======================================================================
              Squirrel monkey  ----------------------------------------------------------------------
                     Marmoset  ----------------------------------------------------------------------
                          Cow  ======================================================================

                        Human  atgtcact
                        Chimp  atgtcact
                      Gorilla  atgtcact
                    Orangutan  atgtcact
                       Gibbon  atgtcact
          Crab-eating macaque  atgtcact
                       Baboon  atgtcact
                 Green monkey  atgtcact
                          Rat  ========
                 Prairie vole  ========
               Golden hamster  ========
                        Mouse  ========
       Lesser Egyptian jerboa  ========
                         Pika  ========
                 Weddell seal  --------
                     Hedgehog  ========
                        Shrew  ========
                   Guinea pig  ========
                          Pig  ========
                       Rabbit  ========
             Cape golden mole  NNNNNNNN
                     Aardvark  ========
                      Megabat  ========
                      Dolphin  --------
                       Rhesus  ========
                X. tropicalis  ========
                  Spotted gar  ========
                       Turkey  ========
                      Chicken  ========
                 Mallard duck  --------
           Tibetan ground jay  ========
                  Zebra finch  ========
       White-throated sparrow  ========
              Tasmanian devil  ========
               Painted turtle  ========
              Green seaturtle  ========
           American alligator  ========
                Scarlet macaw  ========
                   Budgerigar  ========
                      Opossum  ========
               Naked mole-rat  ========
                  Rock pigeon  ========
          Collared flycatcher  ========
          Medium ground finch  ========
                       Lizard  ========
             Peregrine falcon  ========
                 Saker falcon  ========
                       Parrot  ========
             Brush-tailed rat  ========
                   Chinchilla  ========
          Cape elephant shrew  ========
           Chinese tree shrew  ========
                     Platypus  ========
                      Wallaby  ========
                      Manatee  ========
                     Elephant  ========
              Chinese hamster  ========
                       Tenrec  ========
                          Cat  ========
                     Bushbaby  ========
     Chinese softshell turtle  ========
                      Ferret   --------
              Star-nosed mole  ========
                Domestic goat  ========
                        Sheep  ========
             Tibetan antelope  ========
               Bactrian camel  --------
                       Alpaca  --------
               Pacific walrus  --------
                        Panda  --------
                 Killer whale  --------
                          Dog  --------
             Black flying-fox  ========
             White rhinoceros  ========
                        Horse  --------
                     Squirrel  ========
                    Armadillo  ========
         David's myotis (bat)  ========
                Big brown bat  ========
                     Microbat  ========
              Squirrel monkey  --------
                     Marmoset  --------
                          Cow  ========

Alignment block 3 of 14 in window, 98321548 - 98321557, 10 bps 
B D                     Human  gtaattacat
B D                     Chimp  gtaattacat
B D                   Gorilla  gtaattacat
B D                 Orangutan  gtaattgcat
B D                    Gibbon  gtaattacat
B D       Crab-eating macaque  gtaattgcat
B D                    Baboon  gtaattgcat
B D              Green monkey  gtaattgcat
           Chinese tree shrew  atatttgcaa
B D                  Squirrel  gtaattgcaa
B D                       Rat  ==========
                Prairie vole  ==========
              Golden hamster  ==========
B D                     Mouse  ==========
      Lesser Egyptian jerboa  ==========
B D                      Pika  ==========
                Weddell seal  ----------
B D                  Hedgehog  ==========
B D                     Shrew  ==========
B D                Guinea pig  ==========
B D                       Pig  ==========
B D                    Rabbit  ==========
            Cape golden mole  NNNNNNNNNN
                    Aardvark  ==========
B D                   Megabat  ==========
B D                   Dolphin  ----------
B D                    Rhesus  ==========
B D             X. tropicalis  ==========
                 Spotted gar  ==========
B D                    Turkey  ==========
B D                   Chicken  ==========
  D              Mallard duck  ----------
          Tibetan ground jay  ==========
B D               Zebra finch  ==========
  D    White-throated sparrow  ==========
B D           Tasmanian devil  ==========
  D            Painted turtle  ==========
  D           Green seaturtle  ==========
B D        American alligator  ==========
  D             Scarlet macaw  ==========
B D                Budgerigar  ==========
B D                   Opossum  ==========
B D            Naked mole-rat  ==========
  D               Rock pigeon  ==========
  D       Collared flycatcher  ==========
B D       Medium ground finch  ==========
B D                    Lizard  ==========
  D          Peregrine falcon  ==========
  D              Saker falcon  ==========
  D                    Parrot  ==========
            Brush-tailed rat  ==========
                  Chinchilla  ==========
         Cape elephant shrew  ==========
B D                  Platypus  ==========
B D                   Wallaby  ==========
B D                   Manatee  ==========
B D                  Elephant  ==========
B D           Chinese hamster  ==========
B D                    Tenrec  ==========
B D                       Cat  ==========
B D                  Bushbaby  ==========
  D  Chinese softshell turtle  ==========
B D                   Ferret   ----------
             Star-nosed mole  ==========
               Domestic goat  ==========
B D                     Sheep  ==========
            Tibetan antelope  ==========
              Bactrian camel  ----------
B D                    Alpaca  ----------
              Pacific walrus  ----------
B D                     Panda  ----------
                Killer whale  ----------
B D                       Dog  ----------
            Black flying-fox  ==========
B D          White rhinoceros  ==========
B D                     Horse  ----------
B D                 Armadillo  ==========
        David's myotis (bat)  ==========
               Big brown bat  ==========
B D                  Microbat  ==========
B D           Squirrel monkey  ----------
B D                  Marmoset  ----------
B D                       Cow  ==========

Alignment block 4 of 14 in window, 98321558 - 98321678, 121 bps 
B D                     Human  aaggtgcttctaat-aaaggactgttattcaaaa-acacaaagatttcataaagctcaacaataaa-aaa
B D                     Chimp  aaggtgcttctaat-aaaggactgttattcaaaa-acacaaagatttcataaagctcaacaataaa-aaa
B D                   Gorilla  aaggtgcttctaat-aaaggactgttattcaaaa-acacgaagatttcataaagctcaacaataaa-aaa
B D                 Orangutan  aaggtacttctaat-aaaagactgttattcaaaa-acacaaaggtttcataaaactcaacaataaa-aaa
B D                    Gibbon  aaggtgcttctaat-aaaggactgttactcaaaa-aca--aagatttcataaagctcaacaataaa-aaa
B D       Crab-eating macaque  aaggtgcttctaat-aaaggactgttactcaaaatacacaaagatttcataaagctcaacaataaa----
B D                    Baboon  aaggtgcttctaat-aaaggactgttattgaaaatacacaaagatttcataaagctcaacaataaa----
B D              Green monkey  aaggtgcttctaat-aaaggactgttattcaaaatacacaaagatttcataaaactcaacaataaa----
           Chinese tree shrew  aatgcacttctgat-cactt-ctgttatttacaatatataagtaaatcttaaaacttaaaaataag-a--
B D                  Squirrel  aagatacttctaataaaagagcttatatctaaaatataggaggaactc---aaactctgctataagtaaa
B D            Naked mole-rat  aaaacacttatgat-aaagaactgttacccaaaacata----caactcctaaaactcaccaataagtaaa
B D                       Rat  ======================================================================
                Prairie vole  ======================================================================
              Golden hamster  ======================================================================
B D                     Mouse  ======================================================================
      Lesser Egyptian jerboa  ======================================================================
B D                      Pika  ======================================================================
                Weddell seal  ----------------------------------------------------------------------
B D                  Hedgehog  ======================================================================
B D                     Shrew  ======================================================================
B D                Guinea pig  ======================================================================
B D                       Pig  ======================================================================
B D                    Rabbit  ======================================================================
            Cape golden mole  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
                    Aardvark  ======================================================================
B D                   Megabat  ======================================================================
B D                   Dolphin  ----------------------------------------------------------------------
B D                    Rhesus  ======================================================================
B D             X. tropicalis  ======================================================================
                 Spotted gar  ======================================================================
B D                    Turkey  ======================================================================
B D                   Chicken  ======================================================================
  D              Mallard duck  ----------------------------------------------------------------------
          Tibetan ground jay  ======================================================================
B D               Zebra finch  ======================================================================
  D    White-throated sparrow  ======================================================================
B D           Tasmanian devil  ======================================================================
  D            Painted turtle  ======================================================================
  D           Green seaturtle  ======================================================================
B D        American alligator  ======================================================================
  D             Scarlet macaw  ======================================================================
B D                Budgerigar  ======================================================================
B D                   Opossum  ======================================================================
  D               Rock pigeon  ======================================================================
  D       Collared flycatcher  ======================================================================
B D       Medium ground finch  ======================================================================
B D                    Lizard  ======================================================================
  D          Peregrine falcon  ======================================================================
  D              Saker falcon  ======================================================================
  D                    Parrot  ======================================================================
            Brush-tailed rat  ======================================================================
                  Chinchilla  ======================================================================
         Cape elephant shrew  ======================================================================
B D                  Platypus  ======================================================================
B D                   Wallaby  ======================================================================
B D                   Manatee  ======================================================================
B D                  Elephant  ======================================================================
B D           Chinese hamster  ======================================================================
B D                    Tenrec  ======================================================================
B D                       Cat  ======================================================================
B D                  Bushbaby  ======================================================================
  D  Chinese softshell turtle  ======================================================================
B D                   Ferret   ----------------------------------------------------------------------
             Star-nosed mole  ======================================================================
               Domestic goat  ======================================================================
B D                     Sheep  ======================================================================
            Tibetan antelope  ======================================================================
              Bactrian camel  ----------------------------------------------------------------------
B D                    Alpaca  ----------------------------------------------------------------------
              Pacific walrus  ----------------------------------------------------------------------
B D                     Panda  ----------------------------------------------------------------------
                Killer whale  ----------------------------------------------------------------------
B D                       Dog  ----------------------------------------------------------------------
            Black flying-fox  ======================================================================
B D          White rhinoceros  ======================================================================
B D                     Horse  ----------------------------------------------------------------------
B D                 Armadillo  ======================================================================
        David's myotis (bat)  ======================================================================
               Big brown bat  ======================================================================
B D                  Microbat  ======================================================================
B D           Squirrel monkey  ----------------------------------------------------------------------
B D                  Marmoset  ----------------------------------------------------------------------
B D                       Cow  ======================================================================

                        Human  caaacaacccaatgtgaaagtaagccaaagactttaacagatacctcaccaaag
                        Chimp  caaacaacccaatgtgaaagtaagccaaagactttaacagatacctcaccaaag
                      Gorilla  caaacaacccaatgtgaaagtaagccaaagactttaacagatacctcaccaaag
                    Orangutan  caaacaacccaatgtgaaattaagccaaagactttaacagatacctcaccaaag
                       Gibbon  caaacaacccaatgtgaaagtaagccacagactttaacagatacctcaccaaag
          Crab-eating macaque  -aaacaacccaatgtgaaagtaagccaaagactttaacagatacctcactaaag
                       Baboon  -aaacaacccaatgtgaaagtaagccaaagactttaacagatacctcactaaag
                 Green monkey  -aaacaacccaatgtgaaagtaagccaaagactttaacagatacctcactaaag
           Chinese tree shrew  -aaacaacccaatttaaaagtgtgccaaatattttaatagacatctcatctaag
                     Squirrel  caaacaatccaatttaaaaatagtccacagatgttaacagtctgttcaccaaag
               Naked mole-rat  caaacaattcaatttaaacatggggcagaagctctcatagacacctcaccaatt
                          Rat  ======================================================
                 Prairie vole  ======================================================
               Golden hamster  ======================================================
                        Mouse  ======================================================
       Lesser Egyptian jerboa  ======================================================
                         Pika  ======================================================
                 Weddell seal  ------------------------------------------------------
                     Hedgehog  ======================================================
                        Shrew  ======================================================
                   Guinea pig  ======================================================
                          Pig  ======================================================
                       Rabbit  ======================================================
             Cape golden mole  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
                     Aardvark  ======================================================
                      Megabat  ======================================================
                      Dolphin  ------------------------------------------------------
                       Rhesus  ======================================================
                X. tropicalis  ======================================================
                  Spotted gar  ======================================================
                       Turkey  ======================================================
                      Chicken  ======================================================
                 Mallard duck  ------------------------------------------------------
           Tibetan ground jay  ======================================================
                  Zebra finch  ======================================================
       White-throated sparrow  ======================================================
              Tasmanian devil  ======================================================
               Painted turtle  ======================================================
              Green seaturtle  ======================================================
           American alligator  ======================================================
                Scarlet macaw  ======================================================
                   Budgerigar  ======================================================
                      Opossum  ======================================================
                  Rock pigeon  ======================================================
          Collared flycatcher  ======================================================
          Medium ground finch  ======================================================
                       Lizard  ======================================================
             Peregrine falcon  ======================================================
                 Saker falcon  ======================================================
                       Parrot  ======================================================
             Brush-tailed rat  ======================================================
                   Chinchilla  ======================================================
          Cape elephant shrew  ======================================================
                     Platypus  ======================================================
                      Wallaby  ======================================================
                      Manatee  ======================================================
                     Elephant  ======================================================
              Chinese hamster  ======================================================
                       Tenrec  ======================================================
                          Cat  ======================================================
                     Bushbaby  ======================================================
     Chinese softshell turtle  ======================================================
                      Ferret   ------------------------------------------------------
              Star-nosed mole  ======================================================
                Domestic goat  ======================================================
                        Sheep  ======================================================
             Tibetan antelope  ======================================================
               Bactrian camel  ------------------------------------------------------
                       Alpaca  ------------------------------------------------------
               Pacific walrus  ------------------------------------------------------
                        Panda  ------------------------------------------------------
                 Killer whale  ------------------------------------------------------
                          Dog  ------------------------------------------------------
             Black flying-fox  ======================================================
             White rhinoceros  ======================================================
                        Horse  ------------------------------------------------------
                    Armadillo  ======================================================
         David's myotis (bat)  ======================================================
                Big brown bat  ======================================================
                     Microbat  ======================================================
              Squirrel monkey  ------------------------------------------------------
                     Marmoset  ------------------------------------------------------
                          Cow  ======================================================

Alignment block 5 of 14 in window, 98321679 - 98321738, 60 bps 
B D                     Human  aagatatacagatggcaaataaccatatgaaaatatgttccacat--catat--gtcattaggg
B D                     Chimp  aagatatatggatggcaaataaccatatgaaaacatgttccacat--catat--gtcattaggg
B D                   Gorilla  aagatatacggatggcaaataaccatatgaaaacatgttccacat--catat--gtcattaggg
B D                 Orangutan  aagatacatggatggcaaataaccatatgaaaacatgttacatat--catat--gtcattaggg
B D                    Gibbon  aagatatatggatggcaaataaccatatgaaaacatgttccacat--catat--gtcattaggg
B D       Crab-eating macaque  aaggtatacagatggcaaataaccatatgaaaacatgttccacat--catat--gtcattaggg
B D                    Baboon  aaggtatacagatggcaaataaccataggaaaacatgttccacat--catat--gtcattaggg
B D              Green monkey  aaggtatacagatggcaaataaccatatgaaaacatgttccacat--catat--gtcattaggg
           Chinese tree shrew  aaaatatatagatggaaaataaacata-gaaaagacactctacat--catag--gtcatcagga
B D                  Squirrel  gggatgtatagatggc-aataagcatataaaaatatgttccacac-atacat--gttatcagga
B D            Naked mole-rat  aaaatatattga--ga-attaagcatatgaaaatatgttcaaaataatacataggtaatcagga
B D                      Pika  aaaatatatcaa------gtaaatatatgaaaggacgatcaacat--tatat--gtcattgaga
B D                       Rat  ================================================================
                Prairie vole  ================================================================
              Golden hamster  ================================================================
B D                     Mouse  ================================================================
      Lesser Egyptian jerboa  ================================================================
                Weddell seal  ----------------------------------------------------------------
B D                  Hedgehog  ================================================================
B D                     Shrew  ================================================================
B D                Guinea pig  ================================================================
B D                       Pig  ================================================================
B D                    Rabbit  ================================================================
            Cape golden mole  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
                    Aardvark  ================================================================
B D                   Megabat  ================================================================
B D                   Dolphin  ----------------------------------------------------------------
B D                    Rhesus  ================================================================
B D             X. tropicalis  ================================================================
                 Spotted gar  ================================================================
B D                    Turkey  ================================================================
B D                   Chicken  ================================================================
  D              Mallard duck  ----------------------------------------------------------------
          Tibetan ground jay  ================================================================
B D               Zebra finch  ================================================================
  D    White-throated sparrow  ================================================================
B D           Tasmanian devil  ================================================================
  D            Painted turtle  ================================================================
  D           Green seaturtle  ================================================================
B D        American alligator  ================================================================
  D             Scarlet macaw  ================================================================
B D                Budgerigar  ================================================================
B D                   Opossum  ================================================================
  D               Rock pigeon  ================================================================
  D       Collared flycatcher  ================================================================
B D       Medium ground finch  ================================================================
B D                    Lizard  ================================================================
  D          Peregrine falcon  ================================================================
  D              Saker falcon  ================================================================
  D                    Parrot  ================================================================
            Brush-tailed rat  ================================================================
                  Chinchilla  ================================================================
         Cape elephant shrew  ================================================================
B D                  Platypus  ================================================================
B D                   Wallaby  ================================================================
B D                   Manatee  ================================================================
B D                  Elephant  ================================================================
B D           Chinese hamster  ================================================================
B D                    Tenrec  ================================================================
B D                       Cat  ================================================================
B D                  Bushbaby  ================================================================
  D  Chinese softshell turtle  ================================================================
B D                   Ferret   ----------------------------------------------------------------
             Star-nosed mole  ================================================================
               Domestic goat  ================================================================
B D                     Sheep  ================================================================
            Tibetan antelope  ================================================================
              Bactrian camel  ----------------------------------------------------------------
B D                    Alpaca  ----------------------------------------------------------------
              Pacific walrus  ----------------------------------------------------------------
B D                     Panda  ----------------------------------------------------------------
                Killer whale  ----------------------------------------------------------------
B D                       Dog  ----------------------------------------------------------------
            Black flying-fox  ================================================================
B D          White rhinoceros  ================================================================
B D                     Horse  ----------------------------------------------------------------
B D                 Armadillo  ================================================================
        David's myotis (bat)  ================================================================
               Big brown bat  ================================================================
B D                  Microbat  ================================================================
B D           Squirrel monkey  ----------------------------------------------------------------
B D                  Marmoset  ----------------------------------------------------------------
B D                       Cow  ================================================================

Alignment block 6 of 14 in window, 98321739 - 98321803, 65 bps 
B D                     Human  aaatgcaaatt--aaagcaatagtaagatactattaaatacctcttagaatcccccaaatttggaag
B D                     Chimp  aaatgcaaatt--aaagcaatagtaagatactattaaatgcctcttagaatcccccaaatttggaag
B D                   Gorilla  aaatgcaaatt--aaagcaatagtaagatactattaaatacctcttagaacctcccaaatttggaag
B D                 Orangutan  aaatgcaaatt--aaagcaatagtaagatactattaaataccccttagaatcccccaaatttgggag
B D                    Gibbon  aaatgcaaatt--aaagcaatagtaagatactattaaatacctcttagaatcccccaaatttggaag
B D       Crab-eating macaque  aaatgcaaatt--aagacaatagtgagatactattaaatacctcttagaatccccaaaatttggaac
B D                    Baboon  aaatgcaaatt--aagacaatagtgagatactattaaatacctcttagaatccccaaaatttggaac
B D              Green monkey  aaatgcaaatt--aagacaatagtgagatactattaaatacctcttagaatccccaaaatttggaac
           Chinese tree shrew  aaatgcaaact--aaaacaa---tgagataccattatatgcctgtggacataaccaaaatctgaaac
B D                  Squirrel  aaatgcatatt--aacacaacaaacagataccactgtgtgcctattagaatcaccaaaattttgcac
B D            Naked mole-rat  tgatagaaatc--caaacaa-----agatgccactacctacctatgagaatgactaaaatgttgaac
B D                    Rabbit  aaataaaaaataaataacagtggtgagataccaacctaaatctactagaatggtaaaaatctgaaac
B D                      Pika  aactacaaatt--ttaacagtggtgagatgttactgtatgtctactaggatcacagaaatccaaagt
B D                       Rat  ===================================================================
                Prairie vole  ===================================================================
              Golden hamster  ===================================================================
B D                     Mouse  ===================================================================
      Lesser Egyptian jerboa  ===================================================================
                Weddell seal  -------------------------------------------------------------------
B D                  Hedgehog  ===================================================================
B D                     Shrew  ===================================================================
B D                Guinea pig  ===================================================================
B D                       Pig  ===================================================================
            Cape golden mole  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
                    Aardvark  ===================================================================
B D                   Megabat  ===================================================================
B D                   Dolphin  -------------------------------------------------------------------
B D                    Rhesus  ===================================================================
B D             X. tropicalis  ===================================================================
                 Spotted gar  ===================================================================
B D                    Turkey  ===================================================================
B D                   Chicken  ===================================================================
  D              Mallard duck  -------------------------------------------------------------------
          Tibetan ground jay  ===================================================================
B D               Zebra finch  ===================================================================
  D    White-throated sparrow  ===================================================================
B D           Tasmanian devil  ===================================================================
  D            Painted turtle  ===================================================================
  D           Green seaturtle  ===================================================================
B D        American alligator  ===================================================================
  D             Scarlet macaw  ===================================================================
B D                Budgerigar  ===================================================================
B D                   Opossum  ===================================================================
  D               Rock pigeon  ===================================================================
  D       Collared flycatcher  ===================================================================
B D       Medium ground finch  ===================================================================
B D                    Lizard  ===================================================================
  D          Peregrine falcon  ===================================================================
  D              Saker falcon  ===================================================================
  D                    Parrot  ===================================================================
            Brush-tailed rat  ===================================================================
                  Chinchilla  ===================================================================
         Cape elephant shrew  ===================================================================
B D                  Platypus  ===================================================================
B D                   Wallaby  ===================================================================
B D                   Manatee  ===================================================================
B D                  Elephant  ===================================================================
B D           Chinese hamster  ===================================================================
B D                    Tenrec  ===================================================================
B D                       Cat  ===================================================================
B D                  Bushbaby  ===================================================================
  D  Chinese softshell turtle  ===================================================================
B D                   Ferret   -------------------------------------------------------------------
             Star-nosed mole  ===================================================================
               Domestic goat  ===================================================================
B D                     Sheep  ===================================================================
            Tibetan antelope  ===================================================================
              Bactrian camel  -------------------------------------------------------------------
B D                    Alpaca  -------------------------------------------------------------------
              Pacific walrus  -------------------------------------------------------------------
B D                     Panda  -------------------------------------------------------------------
                Killer whale  -------------------------------------------------------------------
B D                       Dog  -------------------------------------------------------------------
            Black flying-fox  ===================================================================
B D          White rhinoceros  ===================================================================
B D                     Horse  -------------------------------------------------------------------
B D                 Armadillo  ===================================================================
        David's myotis (bat)  ===================================================================
               Big brown bat  ===================================================================
B D                  Microbat  ===================================================================
B D           Squirrel monkey  -------------------------------------------------------------------
B D                  Marmoset  -------------------------------------------------------------------
B D                       Cow  ===================================================================

Alignment block 7 of 14 in window, 98321804 - 98321876, 73 bps 
B D                     Human  actgacaacaccaaatgctggtga---tgtagagcaacaggaactctcattcatta--------------
B D                     Chimp  gctgacaacaccaaatgctggtga---tgtagagcaacaggaactctcattcatta--------------
B D                   Gorilla  actgacaccaccaaatgctggtga---tgtagagcaacaggaactctcattcattt--------------
B D                 Orangutan  actgacaacaccaaatgctggtga---tgtagagcaacgggaactctcattcatta--------------
B D                    Gibbon  actgacaacaccaaatgctggtga---tgtagagcaacaggaactctcattcatta--------------
B D       Crab-eating macaque  actgacaacaccaaatgctggtga---tgtagagcaacaggaactctcattcatta--------------
B D                    Baboon  actgacaacaccaaatgctggtga---tgtagagcaacaggaactctcattcatta--------------
B D              Green monkey  actgacaacaccaaatgctggtga---tgtagagcaacaggaactctcattcatta--------------
B D                  Marmoset  actgacatcaccaaaagctggtga---tacagagcaataggaattctcattcatta--------------
B D           Squirrel monkey  actgacaacgccaaaggctggtga---tacagagcaacaggaattctcattcatta--------------
           Chinese tree shrew  gttgacaacaccaagtgttgacaaacctatggagcaacagga----------agaa--------------
B D                  Squirrel  actgacattaccaaatgcttatga---ggatataaaacagatattctcatttattgccaaaatggtatag
B D            Naked mole-rat  actgacaacaccaaatgtcggtga---aagtatggaacaagaactcacatttgttg--------------
B D                    Rabbit  actggcaacatcaaatcctgatga---ggagatgaaggg-------------------------------
B D                      Pika  agtgataacatcaattgctggtga---ggacatggagga-------------------------------
B D                       Rat  ======================================================================
                Prairie vole  ======================================================================
              Golden hamster  ======================================================================
B D                     Mouse  ======================================================================
      Lesser Egyptian jerboa  ======================================================================
                Weddell seal  ----------------------------------------------------------------------
B D                  Hedgehog  ======================================================================
B D                     Shrew  ======================================================================
B D                Guinea pig  ======================================================================
B D                       Pig  ======================================================================
            Cape golden mole  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
                    Aardvark  ======================================================================
B D                   Megabat  ======================================================================
B D                   Dolphin  ----------------------------------------------------------------------
B D                    Rhesus  ======================================================================
B D             X. tropicalis  ======================================================================
                 Spotted gar  ======================================================================
B D                    Turkey  ======================================================================
B D                   Chicken  ======================================================================
  D              Mallard duck  ----------------------------------------------------------------------
          Tibetan ground jay  ======================================================================
B D               Zebra finch  ======================================================================
  D    White-throated sparrow  ======================================================================
B D           Tasmanian devil  ======================================================================
  D            Painted turtle  ======================================================================
  D           Green seaturtle  ======================================================================
B D        American alligator  ======================================================================
  D             Scarlet macaw  ======================================================================
B D                Budgerigar  ======================================================================
B D                   Opossum  ======================================================================
  D               Rock pigeon  ======================================================================
  D       Collared flycatcher  ======================================================================
B D       Medium ground finch  ======================================================================
B D                    Lizard  ======================================================================
  D          Peregrine falcon  ======================================================================
  D              Saker falcon  ======================================================================
  D                    Parrot  ======================================================================
            Brush-tailed rat  ======================================================================
                  Chinchilla  ======================================================================
         Cape elephant shrew  ======================================================================
B D                  Platypus  ======================================================================
B D                   Wallaby  ======================================================================
B D                   Manatee  ======================================================================
B D                  Elephant  ======================================================================
B D           Chinese hamster  ======================================================================
B D                    Tenrec  ======================================================================
B D                       Cat  ======================================================================
B D                  Bushbaby  ======================================================================
  D  Chinese softshell turtle  ======================================================================
B D                   Ferret   ----------------------------------------------------------------------
             Star-nosed mole  ======================================================================
               Domestic goat  ======================================================================
B D                     Sheep  ======================================================================
            Tibetan antelope  ======================================================================
              Bactrian camel  ----------------------------------------------------------------------
B D                    Alpaca  ----------------------------------------------------------------------
              Pacific walrus  ----------------------------------------------------------------------
B D                     Panda  ----------------------------------------------------------------------
                Killer whale  ----------------------------------------------------------------------
B D                       Dog  ----------------------------------------------------------------------
            Black flying-fox  ======================================================================
B D          White rhinoceros  ======================================================================
B D                     Horse  ----------------------------------------------------------------------
B D                 Armadillo  ======================================================================
        David's myotis (bat)  ======================================================================
               Big brown bat  ======================================================================
B D                  Microbat  ======================================================================
B D                       Cow  ======================================================================

                        Human  ------------------------------atggtgggaatgcaaagtag
                        Chimp  ------------------------------acggtgggaatgcgaagtag
                      Gorilla  ------------------------------ccggtgggaatgcaaagtag
                    Orangutan  ------------------------------ccggtgggaatgcaaagtag
                       Gibbon  ------------------------------ctggtgggaatgcaaagtag
          Crab-eating macaque  ------------------------------ctggtgggaatgcaaaatag
                       Baboon  ------------------------------ctggtgggaatgcaaaatag
                 Green monkey  ------------------------------ctggtggaaatgcaaaatag
                     Marmoset  ------------------------------ctggtgggaatgcaacacag
              Squirrel monkey  ------------------------------ctgctgggaatgcaaaatag
           Chinese tree shrew  ------------------------------ctggtgaaaatgcaaaattc
                     Squirrel  ctccttgaaatatatatatatatatatatattgatattgatatgaggaat
               Naked mole-rat  ------------------------------ttagtaagaatacaaaatgt
                       Rabbit  --------------------------------------aaagcaagatag
                         Pika  --------------------------------------aatgaaaaatat
                          Rat  ==================================================
                 Prairie vole  ==================================================
               Golden hamster  ==================================================
                        Mouse  ==================================================
       Lesser Egyptian jerboa  ==================================================
                 Weddell seal  --------------------------------------------------
                     Hedgehog  ==================================================
                        Shrew  ==================================================
                   Guinea pig  ==================================================
                          Pig  ==================================================
             Cape golden mole  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
                     Aardvark  ==================================================
                      Megabat  ==================================================
                      Dolphin  --------------------------------------------------
                       Rhesus  ==================================================
                X. tropicalis  ==================================================
                  Spotted gar  ==================================================
                       Turkey  ==================================================
                      Chicken  ==================================================
                 Mallard duck  --------------------------------------------------
           Tibetan ground jay  ==================================================
                  Zebra finch  ==================================================
       White-throated sparrow  ==================================================
              Tasmanian devil  ==================================================
               Painted turtle  ==================================================
              Green seaturtle  ==================================================
           American alligator  ==================================================
                Scarlet macaw  ==================================================
                   Budgerigar  ==================================================
                      Opossum  ==================================================
                  Rock pigeon  ==================================================
          Collared flycatcher  ==================================================
          Medium ground finch  ==================================================
                       Lizard  ==================================================
             Peregrine falcon  ==================================================
                 Saker falcon  ==================================================
                       Parrot  ==================================================
             Brush-tailed rat  ==================================================
                   Chinchilla  ==================================================
          Cape elephant shrew  ==================================================
                     Platypus  ==================================================
                      Wallaby  ==================================================
                      Manatee  ==================================================
                     Elephant  ==================================================
              Chinese hamster  ==================================================
                       Tenrec  ==================================================
                          Cat  ==================================================
                     Bushbaby  ==================================================
     Chinese softshell turtle  ==================================================
                      Ferret   --------------------------------------------------
              Star-nosed mole  ==================================================
                Domestic goat  ==================================================
                        Sheep  ==================================================
             Tibetan antelope  ==================================================
               Bactrian camel  --------------------------------------------------
                       Alpaca  --------------------------------------------------
               Pacific walrus  --------------------------------------------------
                        Panda  --------------------------------------------------
                 Killer whale  --------------------------------------------------
                          Dog  --------------------------------------------------
             Black flying-fox  ==================================================
             White rhinoceros  ==================================================
                        Horse  --------------------------------------------------
                    Armadillo  ==================================================
         David's myotis (bat)  ==================================================
                Big brown bat  ==================================================
                     Microbat  ==================================================
                          Cow  ==================================================

Inserts between block 7 and 8 in window
B D                 Squirrel 167bp

Alignment block 8 of 14 in window, 98321877 - 98322015, 139 bps 
B D                     Human  tacaga---------cacttgggaagacaatttggtt-------gtttcttataaaactgaagatactct
B D                     Chimp  tacaga---------cacttgggaagacaatttggtt-------gtttcttataaaactgaagctactct
B D                   Gorilla  tacaga---------cacttgggaagacaatttggtt-------gtttcttataaaactgaagatactct
B D                 Orangutan  tacaga---------cacttgggaagacaatttggtt-------gtttcttataaaactgaagatactct
B D                    Gibbon  tacaga---------cactt-ggaagataatttggtt-------gtttcttataaaactgaagatactct
B D       Crab-eating macaque  tacaga---------cacttggaaagacaatttggtt-------gtttcttatagaactaaagttactct
B D                    Baboon  tacaga---------cacttggaaagacaatttggtt-------gtttcttatagaactaaagttactct
B D              Green monkey  t------------------------gagaatttggtt-------gtttcttatagaactaaagttactct
B D                  Marmoset  tacaga---------tccttgggaagataatttgata-------gtttcttataaaactaaaggtactct
B D           Squirrel monkey  tacaga---------tacttgggaagataatttgata-------gtttcttataaaactgtaggtactct
           Chinese tree shrew  tacagc---------tactttagaagacaatttggtt-------gtttctcatgaagctaaacatactc-
B D                  Squirrel  tacagccttacccagctccttagaatataatttggtggttcttttttttttataaaattaaacatactct
B D            Naked mole-rat  tatagc---------cactttggaagacaatttaaca-------ctttcttataaaactaaacatgttct
B D                    Rabbit  tacaga---------ccctttggaagacagtttggtg-------gcttcttacaaaactaagaatatgct
B D                      Pika  tttggc---------tcttttggaagacaagctagtg-------gcttctt-----actaaatatgttcc
B D                       Rat  ======================================================================
                Prairie vole  ======================================================================
              Golden hamster  ======================================================================
B D                     Mouse  ======================================================================
      Lesser Egyptian jerboa  ======================================================================
                Weddell seal  ----------------------------------------------------------------------
B D                  Hedgehog  ======================================================================
B D                     Shrew  ======================================================================
B D                Guinea pig  ======================================================================
B D                       Pig  ======================================================================
            Cape golden mole  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
                    Aardvark  ======================================================================
B D                   Megabat  ======================================================================
B D                   Dolphin  ----------------------------------------------------------------------
B D                    Rhesus  ======================================================================
B D             X. tropicalis  ======================================================================
                 Spotted gar  ======================================================================
B D                    Turkey  ======================================================================
B D                   Chicken  ======================================================================
  D              Mallard duck  ----------------------------------------------------------------------
          Tibetan ground jay  ======================================================================
B D               Zebra finch  ======================================================================
  D    White-throated sparrow  ======================================================================
B D           Tasmanian devil  ======================================================================
  D            Painted turtle  ======================================================================
  D           Green seaturtle  ======================================================================
B D        American alligator  ======================================================================
  D             Scarlet macaw  ======================================================================
B D                Budgerigar  ======================================================================
B D                   Opossum  ======================================================================
  D               Rock pigeon  ======================================================================
  D       Collared flycatcher  ======================================================================
B D       Medium ground finch  ======================================================================
B D                    Lizard  ======================================================================
  D          Peregrine falcon  ======================================================================
  D              Saker falcon  ======================================================================
  D                    Parrot  ======================================================================
            Brush-tailed rat  ======================================================================
                  Chinchilla  ======================================================================
         Cape elephant shrew  ======================================================================
B D                  Platypus  ======================================================================
B D                   Wallaby  ======================================================================
B D                   Manatee  ======================================================================
B D                  Elephant  ======================================================================
B D           Chinese hamster  ======================================================================
B D                    Tenrec  ======================================================================
B D                       Cat  ======================================================================
B D                  Bushbaby  ======================================================================
  D  Chinese softshell turtle  ======================================================================
B D                   Ferret   ----------------------------------------------------------------------
             Star-nosed mole  ======================================================================
               Domestic goat  ======================================================================
B D                     Sheep  ======================================================================
            Tibetan antelope  ======================================================================
              Bactrian camel  ----------------------------------------------------------------------
B D                    Alpaca  ----------------------------------------------------------------------
              Pacific walrus  ----------------------------------------------------------------------
B D                     Panda  ----------------------------------------------------------------------
                Killer whale  ----------------------------------------------------------------------
B D                       Dog  ----------------------------------------------------------------------
            Black flying-fox  ======================================================================
B D          White rhinoceros  ======================================================================
B D                     Horse  ----------------------------------------------------------------------
B D                 Armadillo  ======================================================================
        David's myotis (bat)  ======================================================================
               Big brown bat  ======================================================================
B D                  Microbat  ======================================================================
B D                       Cow  ======================================================================

                        Human  t-accatatgat----cagc---------tgt-----ttggtatttacc---------------------
                        Chimp  t-accatatgat----cagc---------tgt-----ttggtatttacc---------------------
                      Gorilla  t-accatatgat----cagc---------tgt-----ttggtatttacc---------------------
                    Orangutan  t-accgtatgat----cagc---------tgt-----ttggtatttacc---------------------
                       Gibbon  t-atcatatgat----ccac---------tgt-----ttggtatttacc---------------------
          Crab-eating macaque  t-atagtatgat----cagc---------tgt-----ttggtatttacc---------------------
                       Baboon  t-atagtatgat----cagc---------tgt-----ttggtattcacc---------------------
                 Green monkey  t-atagtatgat----cagc---------tgt-----ttggtatttacc---------------------
                     Marmoset  t-accacgtgat----cagc---------tgt-----ctggtgtttacc---------------------
              Squirrel monkey  t-accacataat----cagc---------tgt-----ctgatgtttacc---------------------
           Chinese tree shrew  --atcaaataattcagcaac---------tgtgctccttggtatttacc---------------------
                     Squirrel  t-accgtacagc----ctac-cattacactcc-----ttggtattcacc---------------------
               Naked mole-rat  taaccatacaat----gcacaaaatgcactcc-----ttgatatttaat---------------------
                       Rabbit  t-accatatgat----ccagtaatagtgttct-----tttgtgtttatg---------------------
                         Pika  t-acaatatgat----ccagtgataatgttct-----tatgtatgtatgtgtttgcatatatacatatat
                          Rat  ======================================================================
                 Prairie vole  ======================================================================
               Golden hamster  ======================================================================
                        Mouse  ======================================================================
       Lesser Egyptian jerboa  ======================================================================
                 Weddell seal  ----------------------------------------------------------------------
                     Hedgehog  ======================================================================
                        Shrew  ======================================================================
                   Guinea pig  ======================================================================
                          Pig  ======================================================================
             Cape golden mole  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
                     Aardvark  ======================================================================
                      Megabat  ======================================================================
                      Dolphin  ----------------------------------------------------------------------
                       Rhesus  ======================================================================
                X. tropicalis  ======================================================================
                  Spotted gar  ======================================================================
                       Turkey  ======================================================================
                      Chicken  ======================================================================
                 Mallard duck  ----------------------------------------------------------------------
           Tibetan ground jay  ======================================================================
                  Zebra finch  ======================================================================
       White-throated sparrow  ======================================================================
              Tasmanian devil  ======================================================================
               Painted turtle  ======================================================================
              Green seaturtle  ======================================================================
           American alligator  ======================================================================
                Scarlet macaw  ======================================================================
                   Budgerigar  ======================================================================
                      Opossum  ======================================================================
                  Rock pigeon  ======================================================================
          Collared flycatcher  ======================================================================
          Medium ground finch  ======================================================================
                       Lizard  ======================================================================
             Peregrine falcon  ======================================================================
                 Saker falcon  ======================================================================
                       Parrot  ======================================================================
             Brush-tailed rat  ======================================================================
                   Chinchilla  ======================================================================
          Cape elephant shrew  ======================================================================
                     Platypus  ======================================================================
                      Wallaby  ======================================================================
                      Manatee  ======================================================================
                     Elephant  ======================================================================
              Chinese hamster  ======================================================================
                       Tenrec  ======================================================================
                          Cat  ======================================================================
                     Bushbaby  ======================================================================
     Chinese softshell turtle  ======================================================================
                      Ferret   ----------------------------------------------------------------------
              Star-nosed mole  ======================================================================
                Domestic goat  ======================================================================
                        Sheep  ======================================================================
             Tibetan antelope  ======================================================================
               Bactrian camel  ----------------------------------------------------------------------
                       Alpaca  ----------------------------------------------------------------------
               Pacific walrus  ----------------------------------------------------------------------
                        Panda  ----------------------------------------------------------------------
                 Killer whale  ----------------------------------------------------------------------
                          Dog  ----------------------------------------------------------------------
             Black flying-fox  ======================================================================
             White rhinoceros  ======================================================================
                        Horse  ----------------------------------------------------------------------
                    Armadillo  ======================================================================
         David's myotis (bat)  ======================================================================
                Big brown bat  ======================================================================
                     Microbat  ======================================================================
                          Cow  ======================================================================

                        Human  ------------------caaaa-agtttaaaact-------------------aat---gtccacac-a
                        Chimp  ------------------caaaa-agtttaaaact-------------------aat---gtccacac-a
                      Gorilla  ------------------caaaa-agtttaaaact-------------------aat---gtccacac-a
                    Orangutan  ------------------caaaa-agtttaaaact-------------------aat---gtccacag-a
                       Gibbon  ------------------caaaa-agtttaaaact-------------------aat---gtccacac-a
          Crab-eating macaque  ------------------caaaa-agtttaaaact-------------------aat---gtccacac-a
                       Baboon  ------------------caaaa-agtttaaaact-------------------aat---gtccacac-a
                 Green monkey  ------------------caaaa-agtttaaaact-------------------aat---gtccacac-a
                     Marmoset  ------------------caaaa-agtttaaaagt-------------------gat---gtccacac-a
              Squirrel monkey  ------------------caaaa-agtttaaaagt-------------------gat---gtccacac-a
           Chinese tree shrew  ------------------acagg-aattgaaaatg-------------------tat---gtccacac-a
                     Squirrel  ------------------ctaagaagttgaaaac---------------------at---atccacaaaa
               Naked mole-rat  ------------------caaag-agttgtaaact-------------------tat---gtccacacaa
                       Rabbit  ------------------aaaaggtgttgaagtct-------------------taa---gtccacac--
                         Pika  atgcatatgtatatatatataatgtatatacatatgtgtatatatatatatatataaaatgtccacacaa
                          Rat  ======================================================================
                 Prairie vole  ======================================================================
               Golden hamster  ======================================================================
                        Mouse  ======================================================================
       Lesser Egyptian jerboa  ======================================================================
                 Weddell seal  ----------------------------------------------------------------------
                     Hedgehog  ======================================================================
                        Shrew  ======================================================================
                   Guinea pig  ======================================================================
                          Pig  ======================================================================
             Cape golden mole  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
                     Aardvark  ======================================================================
                      Megabat  ======================================================================
                      Dolphin  ----------------------------------------------------------------------
                       Rhesus  ======================================================================
                X. tropicalis  ======================================================================
                  Spotted gar  ======================================================================
                       Turkey  ======================================================================
                      Chicken  ======================================================================
                 Mallard duck  ----------------------------------------------------------------------
           Tibetan ground jay  ======================================================================
                  Zebra finch  ======================================================================
       White-throated sparrow  ======================================================================
              Tasmanian devil  ======================================================================
               Painted turtle  ======================================================================
              Green seaturtle  ======================================================================
           American alligator  ======================================================================
                Scarlet macaw  ======================================================================
                   Budgerigar  ======================================================================
                      Opossum  ======================================================================
                  Rock pigeon  ======================================================================
          Collared flycatcher  ======================================================================
          Medium ground finch  ======================================================================
                       Lizard  ======================================================================
             Peregrine falcon  ======================================================================
                 Saker falcon  ======================================================================
                       Parrot  ======================================================================
             Brush-tailed rat  ======================================================================
                   Chinchilla  ======================================================================
          Cape elephant shrew  ======================================================================
                     Platypus  ======================================================================
                      Wallaby  ======================================================================
                      Manatee  ======================================================================
                     Elephant  ======================================================================
              Chinese hamster  ======================================================================
                       Tenrec  ======================================================================
                          Cat  ======================================================================
                     Bushbaby  ======================================================================
     Chinese softshell turtle  ======================================================================
                      Ferret   ----------------------------------------------------------------------
              Star-nosed mole  ======================================================================
                Domestic goat  ======================================================================
                        Sheep  ======================================================================
             Tibetan antelope  ======================================================================
               Bactrian camel  ----------------------------------------------------------------------
                       Alpaca  ----------------------------------------------------------------------
               Pacific walrus  ----------------------------------------------------------------------
                        Panda  ----------------------------------------------------------------------
                 Killer whale  ----------------------------------------------------------------------
                          Dog  ----------------------------------------------------------------------
             Black flying-fox  ======================================================================
             White rhinoceros  ======================================================================
                        Horse  ----------------------------------------------------------------------
                    Armadillo  ======================================================================
         David's myotis (bat)  ======================================================================
                Big brown bat  ======================================================================
                     Microbat  ======================================================================
                          Cow  ======================================================================

                        Human  aaacctgcactttatt-gttt-taagagc
                        Chimp  aaacctgcactttaat-gtttataagagc
                      Gorilla  aaacctgcactttaat-gtttataagagc
                    Orangutan  aaacctgcactttaat-gtttataagagc
                       Gibbon  aaacctgcactttaat-gtttataagagc
          Crab-eating macaque  aaacctgcactttaat-gtttctaacagc
                       Baboon  aaacctgcactttaat-gtttctaacagc
                 Green monkey  aaacctgcactttaat-gtttctaagagc
                     Marmoset  aaacctacactttaatgatttataacagc
              Squirrel monkey  aaacctacactttaatcgtttataacagc
           Chinese tree shrew  aaacctgcacatggtt-gtttacagcagc
                     Squirrel  tatcctgcacattgct-atttatagcaat
               Naked mole-rat  aatcttgcccatgaat-attcatagcagc
                       Rabbit  --atgtacataaggat-gtttacagaagc
                         Pika  aaatatgcacatggga-ttttatagaagc
                          Rat  =============================
                 Prairie vole  =============================
               Golden hamster  =============================
                        Mouse  =============================
       Lesser Egyptian jerboa  =============================
                 Weddell seal  -----------------------------
                     Hedgehog  =============================
                        Shrew  =============================
                   Guinea pig  =============================
                          Pig  =============================
             Cape golden mole  NNNNNNNNNNNNNNNNNNNNNNNNNNNNN
                     Aardvark  =============================
                      Megabat  =============================
                      Dolphin  -----------------------------
                       Rhesus  =============================
                X. tropicalis  =============================
                  Spotted gar  =============================
                       Turkey  =============================
                      Chicken  =============================
                 Mallard duck  -----------------------------
           Tibetan ground jay  =============================
                  Zebra finch  =============================
       White-throated sparrow  =============================
              Tasmanian devil  =============================
               Painted turtle  =============================
              Green seaturtle  =============================
           American alligator  =============================
                Scarlet macaw  =============================
                   Budgerigar  =============================
                      Opossum  =============================
                  Rock pigeon  =============================
          Collared flycatcher  =============================
          Medium ground finch  =============================
                       Lizard  =============================
             Peregrine falcon  =============================
                 Saker falcon  =============================
                       Parrot  =============================
             Brush-tailed rat  =============================
                   Chinchilla  =============================
          Cape elephant shrew  =============================
                     Platypus  =============================
                      Wallaby  =============================
                      Manatee  =============================
                     Elephant  =============================
              Chinese hamster  =============================
                       Tenrec  =============================
                          Cat  =============================
                     Bushbaby  =============================
     Chinese softshell turtle  =============================
                      Ferret   -----------------------------
              Star-nosed mole  =============================
                Domestic goat  =============================
                        Sheep  =============================
             Tibetan antelope  =============================
               Bactrian camel  -----------------------------
                       Alpaca  -----------------------------
               Pacific walrus  -----------------------------
                        Panda  -----------------------------
                 Killer whale  -----------------------------
                          Dog  -----------------------------
             Black flying-fox  =============================
             White rhinoceros  =============================
                        Horse  -----------------------------
                    Armadillo  =============================
         David's myotis (bat)  =============================
                Big brown bat  =============================
                     Microbat  =============================
                          Cow  =============================

Inserts between block 8 and 9 in window
B D                   Rabbit 2bp
B D                     Pika 2bp

Alignment block 9 of 14 in window, 98322016 - 98322022, 7 bps 
B D                     Human  tatgttc
B D                     Chimp  tatgttc
B D                   Gorilla  tatgttc
B D                 Orangutan  tatgttc
B D                    Gibbon  tatgttc
B D       Crab-eating macaque  tgtgttc
B D                    Baboon  tgtgttc
B D              Green monkey  tgtgttc
B D                  Marmoset  tatattc
B D           Squirrel monkey  tatattc
           Chinese tree shrew  tttattc
B D                  Squirrel  tatgttc
B D           Chinese hamster  tactctc
B D            Naked mole-rat  tatcttc
B D                    Rabbit  tatat--
B D                      Pika  tatat--
B D                       Rat  =======
                Prairie vole  =======
              Golden hamster  =======
B D                     Mouse  =======
      Lesser Egyptian jerboa  =======
                Weddell seal  -------
B D                  Hedgehog  =======
B D                     Shrew  =======
B D                Guinea pig  =======
B D                       Pig  =======
            Cape golden mole  NNNNNNN
                    Aardvark  =======
B D                   Megabat  =======
B D                   Dolphin  -------
B D                    Rhesus  =======
B D             X. tropicalis  =======
                 Spotted gar  =======
B D                    Turkey  =======
B D                   Chicken  =======
  D              Mallard duck  -------
          Tibetan ground jay  =======
B D               Zebra finch  =======
  D    White-throated sparrow  =======
B D           Tasmanian devil  =======
  D            Painted turtle  =======
  D           Green seaturtle  =======
B D        American alligator  =======
  D             Scarlet macaw  =======
B D                Budgerigar  =======
B D                   Opossum  =======
  D               Rock pigeon  =======
  D       Collared flycatcher  =======
B D       Medium ground finch  =======
B D                    Lizard  =======
  D          Peregrine falcon  =======
  D              Saker falcon  =======
  D                    Parrot  =======
            Brush-tailed rat  =======
                  Chinchilla  =======
         Cape elephant shrew  =======
B D                  Platypus  =======
B D                   Wallaby  =======
B D                   Manatee  =======
B D                  Elephant  =======
B D                    Tenrec  =======
B D                       Cat  =======
B D                  Bushbaby  =======
  D  Chinese softshell turtle  =======
B D                   Ferret   -------
             Star-nosed mole  =======
               Domestic goat  =======
B D                     Sheep  =======
            Tibetan antelope  =======
              Bactrian camel  -------
B D                    Alpaca  -------
              Pacific walrus  -------
B D                     Panda  -------
                Killer whale  -------
B D                       Dog  -------
            Black flying-fox  =======
B D          White rhinoceros  =======
B D                     Horse  -------
B D                 Armadillo  =======
        David's myotis (bat)  =======
               Big brown bat  =======
B D                  Microbat  =======
B D                       Cow  =======

Inserts between block 9 and 10 in window
B D          Chinese hamster 4bp

Alignment block 10 of 14 in window, 98322023 - 98322305, 283 bps 
B D                     Human  ataattgccaaaacttggaag--aagcaagat---gtcttgcagtatataaatggataaattaactgtgg
B D                     Chimp  ataattgccaaaacttggaag--aagcaagat---gtcttgcagtatataaatggataaattaactgtgg
B D                   Gorilla  ataattgccaaaacttggaag--aagcaagat---gtcttgcagtatataaatggataaattaactgtgg
B D                 Orangutan  ataattgccaaaacttggaag--aagcaagat---gtcttgcggtatataaatggataaattaactgtgg
B D                    Gibbon  ataattgccaaaacttggaag--aagcaagat---gtcttgcagtatataaatggataaattaactgtgg
B D       Crab-eating macaque  ataattgccaaaacttggaagc-aagcgtgat---gtccttcagtatataaagggataaattaactgcgg
B D                    Baboon  ataattgccaaaacttggaagc-aagcgtgat---gtccttcagtatataaagggataaattaactgcgg
B D              Green monkey  ataattgccaaaacttggaagc-aagcacgat---gtccttcagtatataaagggataaattaactgtgg
B D                  Marmoset  ataattgccaaaacatggaagc-aagcaagat---gtctt-cagtatatacatgg-tatat--actgtgg
B D           Squirrel monkey  ataattgccaaaacatggaagc-aagcaagat---gtctt-cagtatatacatgt-tatat--actgtgg
           Chinese tree shrew  ataattgccaaaacttggaggc-aagcaagat---gtgcttcactaagtgaatggttacataaactatgg
B D                  Squirrel  atagttgccaaaacatggaagc-aattgtgat---gtccttcaacagatgaatggatagataatttgtga
B D           Chinese hamster  atgaggacccaaactgggaagc-agctgtgatgacgtccttccatgtgtgaatgaataaa----ctgggg
               Golden hamster  ataaggatccaaactgggaagc-agctgtgatgctgtccttcaatatgtgaatgaataaa----ctggga
B D            Naked mole-rat  ataattgtcaaaacttggaagc-aaccacaat---gtccttaagtaggtgagtggttaaataatctgtgg
B D                    Rabbit  ataatttccaaaacctggaaacaaaccaagat---atcatttagtagatgaatagataaataaactgtga
B D                      Pika  gtaaaatccaata-ttggaagcaagccaagat---attatgtaatagatatatagacaactaaattgtag
B D                       Rat  ======================================================================
                Prairie vole  ======================================================================
B D                     Mouse  ======================================================================
      Lesser Egyptian jerboa  ======================================================================
                Weddell seal  ----------------------------------------------------------------------
B D                  Hedgehog  ======================================================================
B D                     Shrew  ======================================================================
B D                Guinea pig  ======================================================================
B D                       Pig  ======================================================================
            Cape golden mole  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
                    Aardvark  ======================================================================
B D                   Megabat  ======================================================================
B D                   Dolphin  ----------------------------------------------------------------------
B D                    Rhesus  ======================================================================
B D             X. tropicalis  ======================================================================
                 Spotted gar  ======================================================================
B D                    Turkey  ======================================================================
B D                   Chicken  ======================================================================
  D              Mallard duck  ----------------------------------------------------------------------
          Tibetan ground jay  ======================================================================
B D               Zebra finch  ======================================================================
  D    White-throated sparrow  ======================================================================
B D           Tasmanian devil  ======================================================================
  D            Painted turtle  ======================================================================
  D           Green seaturtle  ======================================================================
B D        American alligator  ======================================================================
  D             Scarlet macaw  ======================================================================
B D                Budgerigar  ======================================================================
B D                   Opossum  ======================================================================
  D               Rock pigeon  ======================================================================
  D       Collared flycatcher  ======================================================================
B D       Medium ground finch  ======================================================================
B D                    Lizard  ======================================================================
  D          Peregrine falcon  ======================================================================
  D              Saker falcon  ======================================================================
  D                    Parrot  ======================================================================
            Brush-tailed rat  ======================================================================
                  Chinchilla  ======================================================================
         Cape elephant shrew  ======================================================================
B D                  Platypus  ======================================================================
B D                   Wallaby  ======================================================================
B D                   Manatee  ======================================================================
B D                  Elephant  ======================================================================
B D                    Tenrec  ======================================================================
B D                       Cat  ======================================================================
B D                  Bushbaby  ======================================================================
  D  Chinese softshell turtle  ======================================================================
B D                   Ferret   ----------------------------------------------------------------------
             Star-nosed mole  ======================================================================
               Domestic goat  ======================================================================
B D                     Sheep  ======================================================================
            Tibetan antelope  ======================================================================
              Bactrian camel  ----------------------------------------------------------------------
B D                    Alpaca  ----------------------------------------------------------------------
              Pacific walrus  ----------------------------------------------------------------------
B D                     Panda  ----------------------------------------------------------------------
                Killer whale  ----------------------------------------------------------------------
B D                       Dog  ----------------------------------------------------------------------
            Black flying-fox  ======================================================================
B D          White rhinoceros  ======================================================================
B D                     Horse  ----------------------------------------------------------------------
B D                 Armadillo  ======================================================================
        David's myotis (bat)  ======================================================================
               Big brown bat  ======================================================================
B D                  Microbat  ======================================================================
B D                       Cow  ======================================================================

                        Human  tacatccagacaatggagcattactcagtgctaaaaag------------aaataatatctattaggcca
                        Chimp  tgcatccagacaatggaacattactcagtgctaaaaag------------aaataatatctattaggcca
                      Gorilla  tacatccagacaatggaacattactcagtgctaaaaag------------aaataatatctattaggcca
                    Orangutan  tacatccagacaatggaacattactcagtgctaaaaag------------aaatagtatctattaggcca
                       Gibbon  tacatccagacaatggaacattactcagtgctaaaaag------------aaatcctatctattaggcca
          Crab-eating macaque  tacatccagacaatgggacattactcagtgctagaaag------------aaataatatctattaggcag
                       Baboon  tacatccagacaatggaacattactcagtgctagaaag------------aaataatatctattaggcag
                 Green monkey  tacatccagacaatggaacattactcagtgctagaaag------------aaataatatctattagacag
                     Marmoset  taagtccagacaacggaacattactcagtgctaaaaag------------aaataa----tattaagcca
              Squirrel monkey  tacctccaggcaatggaacattactcagtgctaaaaag------------aaataa----tattaagcca
           Chinese tree shrew  cacatacagatgatggagtactgttcaatgcta-------------------------------------
                     Squirrel  tacatagagacaaatgaatattatccagtcctaaggaa------------aaatga--cct----aatca
              Chinese hamster  cacat-tagacag--------------------aaaaagaagaaaaacaaaaacaa--gctgtgaaatca
               Golden hamster  cacat-tagacagtagaatactagccagtgcaaaaaaaaaaaaagaaagcaaacaa--gctgtgaaatca
               Naked mole-rat  taatt-tagacaaaagaatattatctagtcttaaaaag------------aaatga--gctatcaaatca
                       Rabbit  tacattcagacaggggaatattgcttggtgctaaaaaa------------aaatga--gctatcaagtca
                         Pika  tacattcacagagtagaatattattcaatgctaaaacg------------taatga--gctatcaagtca
                          Rat  ======================================================================
                 Prairie vole  ======================================================================
                        Mouse  ======================================================================
       Lesser Egyptian jerboa  ======================================================================
                 Weddell seal  ----------------------------------------------------------------------
                     Hedgehog  ======================================================================
                        Shrew  ======================================================================
                   Guinea pig  ======================================================================
                          Pig  ======================================================================
             Cape golden mole  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
                     Aardvark  ======================================================================
                      Megabat  ======================================================================
                      Dolphin  ----------------------------------------------------------------------
                       Rhesus  ======================================================================
                X. tropicalis  ======================================================================
                  Spotted gar  ======================================================================
                       Turkey  ======================================================================
                      Chicken  ======================================================================
                 Mallard duck  ----------------------------------------------------------------------
           Tibetan ground jay  ======================================================================
                  Zebra finch  ======================================================================
       White-throated sparrow  ======================================================================
              Tasmanian devil  ======================================================================
               Painted turtle  ======================================================================
              Green seaturtle  ======================================================================
           American alligator  ======================================================================
                Scarlet macaw  ======================================================================
                   Budgerigar  ======================================================================
                      Opossum  ======================================================================
                  Rock pigeon  ======================================================================
          Collared flycatcher  ======================================================================
          Medium ground finch  ======================================================================
                       Lizard  ======================================================================
             Peregrine falcon  ======================================================================
                 Saker falcon  ======================================================================
                       Parrot  ======================================================================
             Brush-tailed rat  ======================================================================
                   Chinchilla  ======================================================================
          Cape elephant shrew  ======================================================================
                     Platypus  ======================================================================
                      Wallaby  ======================================================================
                      Manatee  ======================================================================
                     Elephant  ======================================================================
                       Tenrec  ======================================================================
                          Cat  ======================================================================
                     Bushbaby  ======================================================================
     Chinese softshell turtle  ======================================================================
                      Ferret   ----------------------------------------------------------------------
              Star-nosed mole  ======================================================================
                Domestic goat  ======================================================================
                        Sheep  ======================================================================
             Tibetan antelope  ======================================================================
               Bactrian camel  ----------------------------------------------------------------------
                       Alpaca  ----------------------------------------------------------------------
               Pacific walrus  ----------------------------------------------------------------------
                        Panda  ----------------------------------------------------------------------
                 Killer whale  ----------------------------------------------------------------------
                          Dog  ----------------------------------------------------------------------
             Black flying-fox  ======================================================================
             White rhinoceros  ======================================================================
                        Horse  ----------------------------------------------------------------------
                    Armadillo  ======================================================================
         David's myotis (bat)  ======================================================================
                Big brown bat  ======================================================================
                     Microbat  ======================================================================
                          Cow  ======================================================================

                        Human  tgaaaagacatggaag-accttaaatgcatattatt-agtgaaagaagccaaccaaa-----------aa
                        Chimp  tgaaaagacatgaaag-accttaaatgcatattatt-agtgaaagaagccaac-aaa-----------aa
                      Gorilla  tgaaaagacatggaag-accttaaatgcatattatt-agtgaaagaagccaaccaaa-----------aa
                    Orangutan  tgaaaagacatggaagaaccttaaatgcatgttatt-agtgaaagaagccaaccaaa-----------aa
                       Gibbon  tgaaaagacatggaagaaccttaaatgcatattatt-agtgaaagaagccaaccaaa-----------aa
          Crab-eating macaque  tgaaaagacatggaagaaccttaaatgcatattatt-agtgaaagaagccaaccaaa-----------aa
                       Baboon  tgaaaagacatggaagaatcttaaatgcatattatt-agtgaaagaagccaaccaaa-----------aa
                 Green monkey  tgaaaagacatggaagaaccttaaatgcatattatt-agtgaaagaagccaaccaaa-----------aa
                     Marmoset  tgagaagacatggaaaaaccttaaatgcatattatg-agtgaaagaagccaacccca-----------aa
              Squirrel monkey  tgagaagacatggaaaaaccttaaatgcatattatt-agtgaaagaagccaacccaa-----------aa
           Chinese tree shrew  -------------------cttaaacatacattattaagtgaaataaactggtttgagtccctgacccaa
                     Squirrel  tgaaaaggcatgggggaaacttcaatgcatgttactgagagaaaaaaa--aatctga-----------aa
              Chinese hamster  tgaaaagcaatagtggaaacttcaatgcatgttgctaagtgaaagaagccaatctaa-----------aa
               Golden hamster  caaaaaacaatagtggagacttcaatgcacattgctaactgaaagaagccagtctaa-----------aa
               Naked mole-rat  tgaaaagacatgtgggaaccttaaatgaatattaccaagtgaaagaagtcaatatga-----------aa
                       Rabbit  tgaaaagacatgaaggaaccttaaatgcatattactaagtgaacaaagctaatctga-----------aa
                         Pika  cgaaataacatgaaggagccttaaatgtgtattacaaggtgaacaaatccaatctga-----------aa
                          Rat  ======================================================================
                 Prairie vole  ======================================================================
                        Mouse  ======================================================================
       Lesser Egyptian jerboa  ======================================================================
                 Weddell seal  ----------------------------------------------------------------------
                     Hedgehog  ======================================================================
                        Shrew  ======================================================================
                   Guinea pig  ======================================================================
                          Pig  ======================================================================
             Cape golden mole  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
                     Aardvark  ======================================================================
                      Megabat  ======================================================================
                      Dolphin  ----------------------------------------------------------------------
                       Rhesus  ======================================================================
                X. tropicalis  ======================================================================
                  Spotted gar  ======================================================================
                       Turkey  ======================================================================
                      Chicken  ======================================================================
                 Mallard duck  ----------------------------------------------------------------------
           Tibetan ground jay  ======================================================================
                  Zebra finch  ======================================================================
       White-throated sparrow  ======================================================================
              Tasmanian devil  ======================================================================
               Painted turtle  ======================================================================
              Green seaturtle  ======================================================================
           American alligator  ======================================================================
                Scarlet macaw  ======================================================================
                   Budgerigar  ======================================================================
                      Opossum  ======================================================================
                  Rock pigeon  ======================================================================
          Collared flycatcher  ======================================================================
          Medium ground finch  ======================================================================
                       Lizard  ======================================================================
             Peregrine falcon  ======================================================================
                 Saker falcon  ======================================================================
                       Parrot  ======================================================================
             Brush-tailed rat  ======================================================================
                   Chinchilla  ======================================================================
          Cape elephant shrew  ======================================================================
                     Platypus  ======================================================================
                      Wallaby  ======================================================================
                      Manatee  ======================================================================
                     Elephant  ======================================================================
                       Tenrec  ======================================================================
                          Cat  ======================================================================
                     Bushbaby  ======================================================================
     Chinese softshell turtle  ======================================================================
                      Ferret   ----------------------------------------------------------------------
              Star-nosed mole  ======================================================================
                Domestic goat  ======================================================================
                        Sheep  ======================================================================
             Tibetan antelope  ======================================================================
               Bactrian camel  ----------------------------------------------------------------------
                       Alpaca  ----------------------------------------------------------------------
               Pacific walrus  ----------------------------------------------------------------------
                        Panda  ----------------------------------------------------------------------
                 Killer whale  ----------------------------------------------------------------------
                          Dog  ----------------------------------------------------------------------
             Black flying-fox  ======================================================================
             White rhinoceros  ======================================================================
                        Horse  ----------------------------------------------------------------------
                    Armadillo  ======================================================================
         David's myotis (bat)  ======================================================================
                Big brown bat  ======================================================================
                     Microbat  ======================================================================
                          Cow  ======================================================================

                        Human  gagct------tcatacta--tata-------------------a-tccaactatgtg---acattctgg
                        Chimp  tagct------tcatactg--tata-------------------a-tccaactatgtg---acattctgg
                      Gorilla  tagct------tcacactg--tata-------------------a-tccaactatgtg---acattctgg
                    Orangutan  tagct------tcatactg--tata-------------------a-tccaactatgtg---acattctgg
                       Gibbon  tagct------tcatactg--tata-------------------a-tccaactatgtg---acattctgg
          Crab-eating macaque  tagtt------tcatactg--tata-------------------a-tccaactatgtg---acattctgg
                       Baboon  tagtt------tcatactg--tata-------------------a-tccaactatgtg---acattctgg
                 Green monkey  tagtt------tcatactg--tata-------------------a-tccaactatgtg---acattgtgg
                     Marmoset  tagct------tcatactg--tata-------------------a-tccaactatgtg---acattctgg
              Squirrel monkey  tagct------tcatactg--tata-------------------a-tccaactatgta---acattctgg
           Chinese tree shrew  tggcttgaaaatcatgctg--gacgtgtgtgtgtgtgtgtgtgtg-tgtgtgtgtgtgtccaaaatcttg
                     Squirrel  tggct------acacacag--tata-------------------attccaatttacc----ccatgctgg
              Chinese hamster  ttcgt------acccaaag--tatg-------------------attcca--------------------
               Golden hamster  tttct------acccaaag--catg-------------------attcca--------------------
               Naked mole-rat  tggct------acacattgtatatg-------------------attccaactttctg---atgttctag
                       Rabbit  aggct------acacacta--tttg-------------------attccaactttatg---acattctgg
                         Pika  aagct------acacacaa--tttg-------------------attccaactttatg---acattcggg
                          Rat  ======================================================================
                 Prairie vole  ======================================================================
                        Mouse  ======================================================================
       Lesser Egyptian jerboa  ======================================================================
                 Weddell seal  ----------------------------------------------------------------------
                     Hedgehog  ======================================================================
                        Shrew  ======================================================================
                   Guinea pig  ======================================================================
                          Pig  ======================================================================
             Cape golden mole  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
                     Aardvark  ======================================================================
                      Megabat  ======================================================================
                      Dolphin  ----------------------------------------------------------------------
                       Rhesus  ======================================================================
                X. tropicalis  ======================================================================
                  Spotted gar  ======================================================================
                       Turkey  ======================================================================
                      Chicken  ======================================================================
                 Mallard duck  ----------------------------------------------------------------------
           Tibetan ground jay  ======================================================================
                  Zebra finch  ======================================================================
       White-throated sparrow  ======================================================================
              Tasmanian devil  ======================================================================
               Painted turtle  ======================================================================
              Green seaturtle  ======================================================================
           American alligator  ======================================================================
                Scarlet macaw  ======================================================================
                   Budgerigar  ======================================================================
                      Opossum  ======================================================================
                  Rock pigeon  ======================================================================
          Collared flycatcher  ======================================================================
          Medium ground finch  ======================================================================
                       Lizard  ======================================================================
             Peregrine falcon  ======================================================================
                 Saker falcon  ======================================================================
                       Parrot  ======================================================================
             Brush-tailed rat  ======================================================================
                   Chinchilla  ======================================================================
          Cape elephant shrew  ======================================================================
                     Platypus  ======================================================================
                      Wallaby  ======================================================================
                      Manatee  ======================================================================
                     Elephant  ======================================================================
                       Tenrec  ======================================================================
                          Cat  ======================================================================
                     Bushbaby  ======================================================================
     Chinese softshell turtle  ======================================================================
                      Ferret   ----------------------------------------------------------------------
              Star-nosed mole  ======================================================================
                Domestic goat  ======================================================================
                        Sheep  ======================================================================
             Tibetan antelope  ======================================================================
               Bactrian camel  ----------------------------------------------------------------------
                       Alpaca  ----------------------------------------------------------------------
               Pacific walrus  ----------------------------------------------------------------------
                        Panda  ----------------------------------------------------------------------
                 Killer whale  ----------------------------------------------------------------------
                          Dog  ----------------------------------------------------------------------
             Black flying-fox  ======================================================================
             White rhinoceros  ======================================================================
                        Horse  ----------------------------------------------------------------------
                    Armadillo  ======================================================================
         David's myotis (bat)  ======================================================================
                Big brown bat  ======================================================================
                     Microbat  ======================================================================
                          Cow  ======================================================================

                        Human  aaaaggcaaaacta---tgaa-tacagtaa-aaagatcagtggttgccaggagg-----------gaggc
                        Chimp  aaaaggcaaaacta---tgaa-tacagtaa-aaagatcagtggttgccaggagg-----------gaggc
                      Gorilla  aaaaggcaaaacta---tgaa-tacagtaa-aaagatcagtggttgccaggagg-----------gaggc
                    Orangutan  aaaaggcaaaacta---tgaa-tacagtaa-aaagatcagtggttgccaggagg-----------gaggc
                       Gibbon  aaaaggcaaaacta---tgaa-tacagtaa-aaagatcagtggttgccaggagg-----------gaggc
          Crab-eating macaque  aaaagggaaaacta---tgaa-tatagtaa-aaagatcagtggttgccaggagg-----------gaggc
                       Baboon  -aaagggaaaacta---tgaa-tatagtaa-aaagatcagtggttgccaggagg-----------gaggc
                 Green monkey  aaaagggaaaacta---tgaa-tatagtaa-aaagatcagtggttgccaggagg-----------gaggc
                     Marmoset  aaaatgcaaaac-----tgaa-tacagtaa-aaagatcagtggttg-caggagg-----------gaggc
              Squirrel monkey  aaaatgaaaaacta---tgaa-tacagtaa-aaaggtcagtggttg-caggagg-----------gaggc
           Chinese tree shrew  agaggagaggagaa---tggattgtggtat-ggccataacccctgacggggggg-----------gtagg
                     Squirrel  aaaaagtaaaattatattgaa-gatag-ga-aaaaattgttgtttcttggggtttggttgggggg-----
              Chinese hamster  ----------------------------------------------------------------------
               Golden hamster  ----------------------------------------------------------------------
               Naked mole-rat  aaaagataaaactg---tgaa-gatggtta-aagaagcaccggttactaggggttggat-----------
                       Rabbit  aaaaggcagaacta---tgga-gagagtaa-agagaccaatggttgccagaagt----------------
                         Pika  aaaaggctaaacta---tgaa-aagagtgattgaaaagagtggttgccaagagt----------------
                          Rat  ======================================================================
                 Prairie vole  ======================================================================
                        Mouse  ======================================================================
       Lesser Egyptian jerboa  ======================================================================
                 Weddell seal  ----------------------------------------------------------------------
                     Hedgehog  ======================================================================
                        Shrew  ======================================================================
                   Guinea pig  ======================================================================
                          Pig  ======================================================================
             Cape golden mole  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
                     Aardvark  ======================================================================
                      Megabat  ======================================================================
                      Dolphin  ----------------------------------------------------------------------
                       Rhesus  ======================================================================
                X. tropicalis  ======================================================================
                  Spotted gar  ======================================================================
                       Turkey  ======================================================================
                      Chicken  ======================================================================
                 Mallard duck  ----------------------------------------------------------------------
           Tibetan ground jay  ======================================================================
                  Zebra finch  ======================================================================
       White-throated sparrow  ======================================================================
              Tasmanian devil  ======================================================================
               Painted turtle  ======================================================================
              Green seaturtle  ======================================================================
           American alligator  ======================================================================
                Scarlet macaw  ======================================================================
                   Budgerigar  ======================================================================
                      Opossum  ======================================================================
                  Rock pigeon  ======================================================================
          Collared flycatcher  ======================================================================
          Medium ground finch  ======================================================================
                       Lizard  ======================================================================
             Peregrine falcon  ======================================================================
                 Saker falcon  ======================================================================
                       Parrot  ======================================================================
             Brush-tailed rat  ======================================================================
                   Chinchilla  ======================================================================
          Cape elephant shrew  ======================================================================
                     Platypus  ======================================================================
                      Wallaby  ======================================================================
                      Manatee  ======================================================================
                     Elephant  ======================================================================
                       Tenrec  ======================================================================
                          Cat  ======================================================================
                     Bushbaby  ======================================================================
     Chinese softshell turtle  ======================================================================
                      Ferret   ----------------------------------------------------------------------
              Star-nosed mole  ======================================================================
                Domestic goat  ======================================================================
                        Sheep  ======================================================================
             Tibetan antelope  ======================================================================
               Bactrian camel  ----------------------------------------------------------------------
                       Alpaca  ----------------------------------------------------------------------
               Pacific walrus  ----------------------------------------------------------------------
                        Panda  ----------------------------------------------------------------------
                 Killer whale  ----------------------------------------------------------------------
                          Dog  ----------------------------------------------------------------------
             Black flying-fox  ======================================================================
             White rhinoceros  ======================================================================
                        Horse  ----------------------------------------------------------------------
                    Armadillo  ======================================================================
         David's myotis (bat)  ======================================================================
                Big brown bat  ======================================================================
                     Microbat  ======================================================================
                          Cow  ======================================================================

                        Human  agt-ggggggt
                        Chimp  agttggggggt
                      Gorilla  agt-ggggggt
                    Orangutan  agc-ggggggt
                       Gibbon  agc-agggggt
          Crab-eating macaque  aac-ggggggt
                       Baboon  aac-ggggggt
                 Green monkey  aac-ggggggt
                     Marmoset  a----------
              Squirrel monkey  g----------
           Chinese tree shrew  aga-atggatt
                     Squirrel  -----------
              Chinese hamster  -----------
               Golden hamster  -----------
               Naked mole-rat  -----------
                       Rabbit  -----------
                         Pika  -----------
                          Rat  ===========
                 Prairie vole  ===========
                        Mouse  ===========
       Lesser Egyptian jerboa  ===========
                 Weddell seal  -----------
                     Hedgehog  ===========
                        Shrew  ===========
                   Guinea pig  ===========
                          Pig  ===========
             Cape golden mole  NNNNNNNNNNN
                     Aardvark  ===========
                      Megabat  ===========
                      Dolphin  -----------
                       Rhesus  ===========
                X. tropicalis  ===========
                  Spotted gar  ===========
                       Turkey  ===========
                      Chicken  ===========
                 Mallard duck  -----------
           Tibetan ground jay  ===========
                  Zebra finch  ===========
       White-throated sparrow  ===========
              Tasmanian devil  ===========
               Painted turtle  ===========
              Green seaturtle  ===========
           American alligator  ===========
                Scarlet macaw  ===========
                   Budgerigar  ===========
                      Opossum  ===========
                  Rock pigeon  ===========
          Collared flycatcher  ===========
          Medium ground finch  ===========
                       Lizard  ===========
             Peregrine falcon  ===========
                 Saker falcon  ===========
                       Parrot  ===========
             Brush-tailed rat  ===========
                   Chinchilla  ===========
          Cape elephant shrew  ===========
                     Platypus  ===========
                      Wallaby  ===========
                      Manatee  ===========
                     Elephant  ===========
                       Tenrec  ===========
                          Cat  ===========
                     Bushbaby  ===========
     Chinese softshell turtle  ===========
                      Ferret   -----------
              Star-nosed mole  ===========
                Domestic goat  ===========
                        Sheep  ===========
             Tibetan antelope  ===========
               Bactrian camel  -----------
                       Alpaca  -----------
               Pacific walrus  -----------
                        Panda  -----------
                 Killer whale  -----------
                          Dog  -----------
             Black flying-fox  ===========
             White rhinoceros  ===========
                        Horse  -----------
                    Armadillo  ===========
         David's myotis (bat)  ===========
                Big brown bat  ===========
                     Microbat  ===========
                          Cow  ===========

Inserts between block 10 and 11 in window
B D                 Squirrel 111bp

Alignment block 11 of 14 in window, 98322306 - 98322509, 204 bps 
B D                     Human  gggg---------------ggacggtgtgaat------------------------------cagcagag
B D                     Chimp  gggg---------------ggacggtgtgaat------------------------------cagcagag
B D                   Gorilla  gggg---------------ggacggtgtgaat------------------------------cagcagag
B D                 Orangutan  -ggg---------------ggagggtgtgaat------------------------------tagcagag
B D                    Gibbon  gggg---------------gcagggtatgaat------------------------------cagcagag
B D       Crab-eating macaque  gggg--------------aggagggtgtgaat------------------------------cagcagag
B D                    Baboon  gggg--------------aggagggtgtgaat------------------------------cagcagag
B D              Green monkey  gggg--------------aggagggtgtgaat------------------------------cagcagag
B D                  Marmoset  -------------------ggggtgtgtgaat------------------------------cagcagaa
B D           Squirrel monkey  -------------------ggagtgtgtgaat------------------------------cagcagaa
           Chinese tree shrew  gtagtatggccataacccctgggggaatgatttctcactttctctgtctctctctgtccctccagca-ag
B D           Chinese hamster  -----------------------------aat------------------------------cc------
               Golden hamster  -----------------------------aat------------------------------cc------
B D            Naked mole-rat  gagg---------------gtgagggatgaat------------------------------atggagag
B D                    Rabbit  -ggg---------------agggagggtgaat------------------------------ctgttaaa
B D                      Pika  -acg---------------agggagagtgaat------------------------------ctgtggaa
B D                       Rat  ======================================================================
                Prairie vole  ======================================================================
B D                     Mouse  ======================================================================
      Lesser Egyptian jerboa  ======================================================================
                Weddell seal  ----------------------------------------------------------------------
B D                  Hedgehog  ======================================================================
B D                     Shrew  ======================================================================
B D                Guinea pig  ======================================================================
B D                       Pig  ======================================================================
            Cape golden mole  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
                    Aardvark  ======================================================================
B D                   Megabat  ======================================================================
B D                   Dolphin  ----------------------------------------------------------------------
B D                    Rhesus  ======================================================================
B D             X. tropicalis  ======================================================================
                 Spotted gar  ======================================================================
B D                    Turkey  ======================================================================
B D                   Chicken  ======================================================================
  D              Mallard duck  ----------------------------------------------------------------------
          Tibetan ground jay  ======================================================================
B D               Zebra finch  ======================================================================
  D    White-throated sparrow  ======================================================================
B D           Tasmanian devil  ======================================================================
  D            Painted turtle  ======================================================================
  D           Green seaturtle  ======================================================================
B D        American alligator  ======================================================================
  D             Scarlet macaw  ======================================================================
B D                Budgerigar  ======================================================================
B D                   Opossum  ======================================================================
  D               Rock pigeon  ======================================================================
  D       Collared flycatcher  ======================================================================
B D       Medium ground finch  ======================================================================
B D                    Lizard  ======================================================================
  D          Peregrine falcon  ======================================================================
  D              Saker falcon  ======================================================================
  D                    Parrot  ======================================================================
            Brush-tailed rat  ======================================================================
                  Chinchilla  ======================================================================
         Cape elephant shrew  ======================================================================
B D                  Platypus  ======================================================================
B D                   Wallaby  ======================================================================
B D                   Manatee  ======================================================================
B D                  Elephant  ======================================================================
B D                    Tenrec  ======================================================================
B D                       Cat  ======================================================================
B D                  Bushbaby  ======================================================================
  D  Chinese softshell turtle  ======================================================================
B D                   Ferret   ----------------------------------------------------------------------
             Star-nosed mole  ======================================================================
               Domestic goat  ======================================================================
B D                     Sheep  ======================================================================
            Tibetan antelope  ======================================================================
              Bactrian camel  ----------------------------------------------------------------------
B D                    Alpaca  ----------------------------------------------------------------------
              Pacific walrus  ----------------------------------------------------------------------
B D                     Panda  ----------------------------------------------------------------------
                Killer whale  ----------------------------------------------------------------------
B D                       Dog  ----------------------------------------------------------------------
            Black flying-fox  ======================================================================
B D          White rhinoceros  ======================================================================
B D                     Horse  ----------------------------------------------------------------------
B D                  Squirrel  ======================================================================
B D                 Armadillo  ======================================================================
        David's myotis (bat)  ======================================================================
               Big brown bat  ======================================================================
B D                  Microbat  ======================================================================
B D                       Cow  ======================================================================

                        Human  caca-------------gaagat-----tttcagggcagtgaaaatacagcatctgtatgatac-----t
                        Chimp  caca-------------gaagat-----tttcagggcagtgaaaatacagcatctgtatgatac-----t
                      Gorilla  caca-------------gaagat-----tttcagggcagtgaaaatacagcatctgtatgatac-----t
                    Orangutan  caca-------------gaggat-----tttcagggcagtgaaaatacagcatctgtatgatac-----t
                       Gibbon  caca-------------gaggat-----tttcagggcagtgaaaatacagcatctgtatgatac-----t
          Crab-eating macaque  taca-------------gaggat-----tttcagggcagtgaaaatatagcatctgtatgatac-----t
                       Baboon  taca-------------gaggat-----tttcagggcagtgaaaatatagcatctgtatgatac-----t
                 Green monkey  taca-------------gaggat-----tttcagggcagtgaaaatatagcatctgtatgatac-----t
                     Marmoset  caca-------------gaggat-----tttcagggcagtgaaactataatatctgtatgatac-----t
              Squirrel monkey  caca-------------gaggat-----tttcagggcagtgaaactataatatctgtatgatac-----t
           Chinese tree shrew  tacatgcaccgtattgcaaaaatctctctctctctctaataaaagaatagtatctgtatgatcc-----t
              Chinese hamster  -----------------------------------acagtggagat------------tgataggcctct
               Golden hamster  -----------------------------------atagtg----------------------ggcctct
               Naked mole-rat  cacc-------------g----------ttttagggcagtgaaaatattatatatatatgatag-----t
                       Rabbit  catg-------------gga--------tgttagggcattgaaaaggtagtatcactgtgagac-----a
                         Pika  catg-------------gga--t-----ttttagggcactgaaaaggtggtgtcagtataagac-----a
                          Rat  ======================================================================
                 Prairie vole  ======================================================================
                        Mouse  ======================================================================
       Lesser Egyptian jerboa  ======================================================================
                 Weddell seal  ----------------------------------------------------------------------
                     Hedgehog  ======================================================================
                        Shrew  ======================================================================
                   Guinea pig  ======================================================================
                          Pig  ======================================================================
             Cape golden mole  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
                     Aardvark  ======================================================================
                      Megabat  ======================================================================
                      Dolphin  ----------------------------------------------------------------------
                       Rhesus  ======================================================================
                X. tropicalis  ======================================================================
                  Spotted gar  ======================================================================
                       Turkey  ======================================================================
                      Chicken  ======================================================================
                 Mallard duck  ----------------------------------------------------------------------
           Tibetan ground jay  ======================================================================
                  Zebra finch  ======================================================================
       White-throated sparrow  ======================================================================
              Tasmanian devil  ======================================================================
               Painted turtle  ======================================================================
              Green seaturtle  ======================================================================
           American alligator  ======================================================================
                Scarlet macaw  ======================================================================
                   Budgerigar  ======================================================================
                      Opossum  ======================================================================
                  Rock pigeon  ======================================================================
          Collared flycatcher  ======================================================================
          Medium ground finch  ======================================================================
                       Lizard  ======================================================================
             Peregrine falcon  ======================================================================
                 Saker falcon  ======================================================================
                       Parrot  ======================================================================
             Brush-tailed rat  ======================================================================
                   Chinchilla  ======================================================================
          Cape elephant shrew  ======================================================================
                     Platypus  ======================================================================
                      Wallaby  ======================================================================
                      Manatee  ======================================================================
                     Elephant  ======================================================================
                       Tenrec  ======================================================================
                          Cat  ======================================================================
                     Bushbaby  ======================================================================
     Chinese softshell turtle  ======================================================================
                      Ferret   ----------------------------------------------------------------------
              Star-nosed mole  ======================================================================
                Domestic goat  ======================================================================
                        Sheep  ======================================================================
             Tibetan antelope  ======================================================================
               Bactrian camel  ----------------------------------------------------------------------
                       Alpaca  ----------------------------------------------------------------------
               Pacific walrus  ----------------------------------------------------------------------
                        Panda  ----------------------------------------------------------------------
                 Killer whale  ----------------------------------------------------------------------
                          Dog  ----------------------------------------------------------------------
             Black flying-fox  ======================================================================
             White rhinoceros  ======================================================================
                        Horse  ----------------------------------------------------------------------
                     Squirrel  ======================================================================
                    Armadillo  ======================================================================
         David's myotis (bat)  ======================================================================
                Big brown bat  ======================================================================
                     Microbat  ======================================================================
                          Cow  ======================================================================

                        Human  gtaatgatggataca-tgttattat--------------------acatttgctcaaagccatagaatgg
                        Chimp  gtaatgatggataca-tgttat-----------------------acatttgctcaaagccatagaatgg
                      Gorilla  gtaatgatggataca-tgttattat--------------------acatttgctcaaagccatacaatgg
                    Orangutan  gtaatgatggataca-ttttattac--------------------acgttttctcaaagccatcgaatgg
                       Gibbon  gtaatgatagataca-tgttattat--------------------acatttgctcaaagccatagaatgg
          Crab-eating macaque  gtattgatggataca-tgttattat--------------------acaattgctcaaagccatagaatgg
                       Baboon  gtattgatggataca-tgttattat--------------------acaattgctcaaagccatagaatgg
                 Green monkey  gtattgatggataca-tgttattat--------------------acaattgctcaaagccatagaatgg
                     Marmoset  gtaatgatggataca-tgt--ttat--------------------acatttgctcaaagccacagaatgg
              Squirrel monkey  gtaatgatggataca-tgt--ttat--------------------acatttgctcaaagccacagaatgg
           Chinese tree shrew  acaataatggataca-tattattatatttttatataatattttagacatgtgtccaaaaccatagaatgt
              Chinese hamster  acaatggcaatcaca-ttttattct--------------------gtactttctccaaatcatagaatag
               Golden hamster  acaatggcaatcacagggttattct--------------------gtactttctccaaatcataggatag
               Naked mole-rat  gtaatgataaatgca-agtcattat--------------------acatttttcaaaagt----------
                       Rabbit  acaacgctg-ttgga-tgctattac--------------------atgtttatccaatgccacagaatgg
                         Pika  ggaatgatgactaca-cactgttac--------------------acatttg-ccaaagccttagaatat
                          Rat  ======================================================================
                 Prairie vole  ======================================================================
                        Mouse  ======================================================================
       Lesser Egyptian jerboa  ======================================================================
                 Weddell seal  ----------------------------------------------------------------------
                     Hedgehog  ======================================================================
                        Shrew  ======================================================================
                   Guinea pig  ======================================================================
                          Pig  ======================================================================
             Cape golden mole  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
                     Aardvark  ======================================================================
                      Megabat  ======================================================================
                      Dolphin  ----------------------------------------------------------------------
                       Rhesus  ======================================================================
                X. tropicalis  ======================================================================
                  Spotted gar  ======================================================================
                       Turkey  ======================================================================
                      Chicken  ======================================================================
                 Mallard duck  ----------------------------------------------------------------------
           Tibetan ground jay  ======================================================================
                  Zebra finch  ======================================================================
       White-throated sparrow  ======================================================================
              Tasmanian devil  ======================================================================
               Painted turtle  ======================================================================
              Green seaturtle  ======================================================================
           American alligator  ======================================================================
                Scarlet macaw  ======================================================================
                   Budgerigar  ======================================================================
                      Opossum  ======================================================================
                  Rock pigeon  ======================================================================
          Collared flycatcher  ======================================================================
          Medium ground finch  ======================================================================
                       Lizard  ======================================================================
             Peregrine falcon  ======================================================================
                 Saker falcon  ======================================================================
                       Parrot  ======================================================================
             Brush-tailed rat  ======================================================================
                   Chinchilla  ======================================================================
          Cape elephant shrew  ======================================================================
                     Platypus  ======================================================================
                      Wallaby  ======================================================================
                      Manatee  ======================================================================
                     Elephant  ======================================================================
                       Tenrec  ======================================================================
                          Cat  ======================================================================
                     Bushbaby  ======================================================================
     Chinese softshell turtle  ======================================================================
                      Ferret   ----------------------------------------------------------------------
              Star-nosed mole  ======================================================================
                Domestic goat  ======================================================================
                        Sheep  ======================================================================
             Tibetan antelope  ======================================================================
               Bactrian camel  ----------------------------------------------------------------------
                       Alpaca  ----------------------------------------------------------------------
               Pacific walrus  ----------------------------------------------------------------------
                        Panda  ----------------------------------------------------------------------
                 Killer whale  ----------------------------------------------------------------------
                          Dog  ----------------------------------------------------------------------
             Black flying-fox  ======================================================================
             White rhinoceros  ======================================================================
                        Horse  ----------------------------------------------------------------------
                     Squirrel  ======================================================================
                    Armadillo  ======================================================================
         David's myotis (bat)  ======================================================================
                Big brown bat  ======================================================================
                     Microbat  ======================================================================
                          Cow  ======================================================================

                        Human  a---caccaaaagcaaacactaatacaaacttttg-acctgggtgattctgatgtgtcaatataatttta
                        Chimp  a---caccaaaagcaaacactaatacaaacttttg-acttgggtgattctgatgtgtcaatataatttta
                      Gorilla  a---caccaaaagcaaacactaatacaaacttttg-acttgggtgattctgatgtgtcaatataatttta
                    Orangutan  a---caccaaaagcaaacactaatacaaacatttg-acttgggtgattctgatgtgtcaatataatttta
                       Gibbon  a---caccaaaagcaaacactaatacaaactttcg-acttgggtgattctgatgtgtcaatataatttaa
          Crab-eating macaque  a---caccaagagcaaatgctaatacagactttcg-acttgggtgattctgatgtgtcag----------
                       Baboon  a---caccaagagcaaatgctaatacagactttcg-acttgggtgattctgatgtgtcag----------
                 Green monkey  a---caccaaaagcaaatgctaatacagactttcg-acttgggtgattc---------------------
                     Marmoset  a---caccagatgtaaatactaatacaaactttag-acttgagtgattctgatgtgtcaa----------
              Squirrel monkey  a---caccaaaagtaaatactaatacaaactttag-acttgagtgattctgatgtgtcac----------
           Chinese tree shrew  acagcaccaagagtgaactctaatgttaactatagaatttgggtgattatgatgtat-------------
              Chinese hamster  acaacaccgagtgttaactctaatgtaaagtgtggaaatgaagaaattataatggctaactgtattttca
               Golden hamster  acaacactgagagttaactctaacgtaaagtgtggaaatgaagaaattatgatggctaactatattttca
               Naked mole-rat  acaacactgagattgatctcttatgtaaactat-aattttaggtgattgtgctgtgaaattctaacttca
                       Rabbit  ccaacatcaacagtgagcactaatgtaaaccatga--------------------atcaatacagtttta
                         Pika  tcaaaaccaagagtgaacactaatgtaaaccatgcattttggt---ttatagtgtatcaacacacttaca
                          Rat  ======================================================================
                 Prairie vole  ======================================================================
                        Mouse  ======================================================================
       Lesser Egyptian jerboa  ======================================================================
                 Weddell seal  ----------------------------------------------------------------------
                     Hedgehog  ======================================================================
                        Shrew  ======================================================================
                   Guinea pig  ======================================================================
                          Pig  ======================================================================
             Cape golden mole  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
                     Aardvark  ======================================================================
                      Megabat  ======================================================================
                      Dolphin  ----------------------------------------------------------------------
                       Rhesus  ======================================================================
                X. tropicalis  ======================================================================
                  Spotted gar  ======================================================================
                       Turkey  ======================================================================
                      Chicken  ======================================================================
                 Mallard duck  ----------------------------------------------------------------------
           Tibetan ground jay  ======================================================================
                  Zebra finch  ======================================================================
       White-throated sparrow  ======================================================================
              Tasmanian devil  ======================================================================
               Painted turtle  ======================================================================
              Green seaturtle  ======================================================================
           American alligator  ======================================================================
                Scarlet macaw  ======================================================================
                   Budgerigar  ======================================================================
                      Opossum  ======================================================================
                  Rock pigeon  ======================================================================
          Collared flycatcher  ======================================================================
          Medium ground finch  ======================================================================
                       Lizard  ======================================================================
             Peregrine falcon  ======================================================================
                 Saker falcon  ======================================================================
                       Parrot  ======================================================================
             Brush-tailed rat  ======================================================================
                   Chinchilla  ======================================================================
          Cape elephant shrew  ======================================================================
                     Platypus  ======================================================================
                      Wallaby  ======================================================================
                      Manatee  ======================================================================
                     Elephant  ======================================================================
                       Tenrec  ======================================================================
                          Cat  ======================================================================
                     Bushbaby  ======================================================================
     Chinese softshell turtle  ======================================================================
                      Ferret   ----------------------------------------------------------------------
              Star-nosed mole  ======================================================================
                Domestic goat  ======================================================================
                        Sheep  ======================================================================
             Tibetan antelope  ======================================================================
               Bactrian camel  ----------------------------------------------------------------------
                       Alpaca  ----------------------------------------------------------------------
               Pacific walrus  ----------------------------------------------------------------------
                        Panda  ----------------------------------------------------------------------
                 Killer whale  ----------------------------------------------------------------------
                          Dog  ----------------------------------------------------------------------
             Black flying-fox  ======================================================================
             White rhinoceros  ======================================================================
                        Horse  ----------------------------------------------------------------------
                     Squirrel  ======================================================================
                    Armadillo  ======================================================================
         David's myotis (bat)  ======================================================================
                Big brown bat  ======================================================================
                     Microbat  ======================================================================
                          Cow  ======================================================================

                        Human  tcaatta-----------------------------taacaaatgt
                        Chimp  tcaatta-----------------------------taacaaatgt
                      Gorilla  tcaattataacaaatgcacaggagatgttgatgtattaacaaatgt
                    Orangutan  tcaatta-----------------------------taacaaatgt
                       Gibbon  tcaattg-----------------------------taacaaatat
          Crab-eating macaque  ----------------------------------------------
                       Baboon  ----------------------------------------------
                 Green monkey  ----------------------------------------------
                     Marmoset  ----------------------------------------------
              Squirrel monkey  ----------------------------------------------
           Chinese tree shrew  ----------------------------------------------
              Chinese hamster  acatttg-----------------------------taacaaattt
               Golden hamster  tcatttg-----------------------------taacaaattt
               Naked mole-rat  a---ttg-----------------------------tatcaaatgt
                       Rabbit  tcagttg-----------------------------taacaaatgt
                         Pika  acaattg-----------------------------tgacaagtat
                          Rat  ==============================================
                 Prairie vole  ==============================================
                        Mouse  ==============================================
       Lesser Egyptian jerboa  ==============================================
                 Weddell seal  ----------------------------------------------
                     Hedgehog  ==============================================
                        Shrew  ==============================================
                   Guinea pig  ==============================================
                          Pig  ==============================================
             Cape golden mole  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
                     Aardvark  ==============================================
                      Megabat  ==============================================
                      Dolphin  ----------------------------------------------
                       Rhesus  ==============================================
                X. tropicalis  ==============================================
                  Spotted gar  ==============================================
                       Turkey  ==============================================
                      Chicken  ==============================================
                 Mallard duck  ----------------------------------------------
           Tibetan ground jay  ==============================================
                  Zebra finch  ==============================================
       White-throated sparrow  ==============================================
              Tasmanian devil  ==============================================
               Painted turtle  ==============================================
              Green seaturtle  ==============================================
           American alligator  ==============================================
                Scarlet macaw  ==============================================
                   Budgerigar  ==============================================
                      Opossum  ==============================================
                  Rock pigeon  ==============================================
          Collared flycatcher  ==============================================
          Medium ground finch  ==============================================
                       Lizard  ==============================================
             Peregrine falcon  ==============================================
                 Saker falcon  ==============================================
                       Parrot  ==============================================
             Brush-tailed rat  ==============================================
                   Chinchilla  ==============================================
          Cape elephant shrew  ==============================================
                     Platypus  ==============================================
                      Wallaby  ==============================================
                      Manatee  ==============================================
                     Elephant  ==============================================
                       Tenrec  ==============================================
                          Cat  ==============================================
                     Bushbaby  ==============================================
     Chinese softshell turtle  ==============================================
                      Ferret   ----------------------------------------------
              Star-nosed mole  ==============================================
                Domestic goat  ==============================================
                        Sheep  ==============================================
             Tibetan antelope  ==============================================
               Bactrian camel  ----------------------------------------------
                       Alpaca  ----------------------------------------------
               Pacific walrus  ----------------------------------------------
                        Panda  ----------------------------------------------
                 Killer whale  ----------------------------------------------
                          Dog  ----------------------------------------------
             Black flying-fox  ==============================================
             White rhinoceros  ==============================================
                        Horse  ----------------------------------------------
                     Squirrel  ==============================================
                    Armadillo  ==============================================
         David's myotis (bat)  ==============================================
                Big brown bat  ==============================================
                     Microbat  ==============================================
                          Cow  ==============================================

Inserts between block 11 and 12 in window
              Golden hamster 118bp
B D           Naked mole-rat 3bp

Alignment block 12 of 14 in window, 98322510 - 98322512, 3 bps 
B D                     Human  ttg--
B D                     Chimp  ttg--
B D                   Gorilla  ttg--
B D                 Orangutan  ttg--
B D                    Gibbon  ttg--
B D           Chinese hamster  --ggg
B D                    Rabbit  ----g
B D                      Pika  ----g
B D                       Rat  =====
                Prairie vole  =====
              Golden hamster  =====
B D                     Mouse  =====
      Lesser Egyptian jerboa  =====
                Weddell seal  -----
B D                  Hedgehog  =====
B D                     Shrew  =====
B D                Guinea pig  =====
B D                    Baboon  -----
B D                       Pig  =====
            Cape golden mole  NNNNN
                    Aardvark  =====
B D                   Megabat  =====
B D                   Dolphin  -----
B D              Green monkey  -----
B D       Crab-eating macaque  -----
B D                    Rhesus  =====
B D             X. tropicalis  =====
                 Spotted gar  =====
B D                    Turkey  =====
B D                   Chicken  =====
  D              Mallard duck  -----
          Tibetan ground jay  =====
B D               Zebra finch  =====
  D    White-throated sparrow  =====
B D           Tasmanian devil  =====
  D            Painted turtle  =====
  D           Green seaturtle  =====
B D        American alligator  =====
  D             Scarlet macaw  =====
B D                Budgerigar  =====
B D                   Opossum  =====
B D            Naked mole-rat  =====
  D               Rock pigeon  =====
  D       Collared flycatcher  =====
B D       Medium ground finch  =====
B D                    Lizard  =====
  D          Peregrine falcon  =====
  D              Saker falcon  =====
  D                    Parrot  =====
            Brush-tailed rat  =====
                  Chinchilla  =====
         Cape elephant shrew  =====
          Chinese tree shrew  -----
B D                  Platypus  =====
B D                   Wallaby  =====
B D                   Manatee  =====
B D                  Elephant  =====
B D                    Tenrec  =====
B D                       Cat  =====
B D                  Bushbaby  =====
  D  Chinese softshell turtle  =====
B D                   Ferret   -----
             Star-nosed mole  =====
               Domestic goat  =====
B D                     Sheep  =====
            Tibetan antelope  =====
              Bactrian camel  -----
B D                    Alpaca  -----
              Pacific walrus  -----
B D                     Panda  -----
                Killer whale  -----
B D                       Dog  -----
            Black flying-fox  =====
B D          White rhinoceros  =====
B D                     Horse  -----
B D                  Squirrel  =====
B D                 Armadillo  =====
        David's myotis (bat)  =====
               Big brown bat  =====
B D                  Microbat  =====
B D           Squirrel monkey  -----
B D                  Marmoset  -----
B D                       Cow  =====

Inserts between block 12 and 13 in window
B D                     Pika 2bp

Alignment block 13 of 14 in window, 98322513 - 98322517, 5 bps 
B D                     Human  ctaat
B D                     Chimp  ctaat
B D                   Gorilla  ctaat
B D                 Orangutan  ctaat
B D                    Gibbon  ctaat
B D                  Squirrel  ctaac
B D           Chinese hamster  caggt
B D                      Pika  ---gt
B D                       Rat  =====
                Prairie vole  =====
              Golden hamster  =====
B D                     Mouse  =====
      Lesser Egyptian jerboa  =====
                Weddell seal  -----
B D                  Hedgehog  =====
B D                     Shrew  =====
B D                Guinea pig  =====
B D                    Baboon  -----
B D                       Pig  =====
B D                    Rabbit  -----
            Cape golden mole  NNNNN
                    Aardvark  =====
B D                   Megabat  =====
B D                   Dolphin  -----
B D              Green monkey  -----
B D       Crab-eating macaque  -----
B D                    Rhesus  =====
B D             X. tropicalis  =====
                 Spotted gar  =====
B D                    Turkey  =====
B D                   Chicken  =====
  D              Mallard duck  -----
          Tibetan ground jay  =====
B D               Zebra finch  =====
  D    White-throated sparrow  =====
B D           Tasmanian devil  =====
  D            Painted turtle  =====
  D           Green seaturtle  =====
B D        American alligator  =====
  D             Scarlet macaw  =====
B D                Budgerigar  =====
B D                   Opossum  =====
B D            Naked mole-rat  =====
  D               Rock pigeon  =====
  D       Collared flycatcher  =====
B D       Medium ground finch  =====
B D                    Lizard  =====
  D          Peregrine falcon  =====
  D              Saker falcon  =====
  D                    Parrot  =====
            Brush-tailed rat  =====
                  Chinchilla  =====
         Cape elephant shrew  =====
          Chinese tree shrew  -----
B D                  Platypus  =====
B D                   Wallaby  =====
B D                   Manatee  =====
B D                  Elephant  =====
B D                    Tenrec  =====
B D                       Cat  =====
B D                  Bushbaby  =====
  D  Chinese softshell turtle  =====
B D                   Ferret   -----
             Star-nosed mole  =====
               Domestic goat  =====
B D                     Sheep  =====
            Tibetan antelope  =====
              Bactrian camel  -----
B D                    Alpaca  -----
              Pacific walrus  -----
B D                     Panda  -----
                Killer whale  -----
B D                       Dog  -----
            Black flying-fox  =====
B D          White rhinoceros  =====
B D                     Horse  -----
B D                 Armadillo  =====
        David's myotis (bat)  =====
               Big brown bat  =====
B D                  Microbat  =====
B D           Squirrel monkey  -----
B D                  Marmoset  -----
B D                       Cow  =====

Inserts between block 13 and 14 in window
B D          Chinese hamster 282bp
B D                     Pika 1bp

Alignment block 14 of 14 in window, 98322518 - 98322572, 55 bps 
B D                     Human  acaaacttttgacttgggtcattctgatgtgtcaatataattttatcaattataa
B D                     Chimp  acaaacttttgacttgggtcattctgatgtgtcaatataattttatcaattataa
B D                   Gorilla  acaaacttttgacttgggtcattccgatgtgtcaatataattttatcaattataa
B D                 Orangutan  acgaactttcgacttgggtcattctgatgtgtcaatataattttatcaattataa
B D                    Gibbon  acaaacttttgacttgcgttattctgatgtgtcaatataattttatcaattataa
B D       Crab-eating macaque  -----------------------------------tataattttatcaattatag
B D                    Baboon  -----------------------------------tataattttatcaattatag
B D              Green monkey  ------------------------tgatgtgtcagtataattttatcgattatag
B D                  Marmoset  -----------------------------------tataattttatcaactataa
B D           Squirrel monkey  -----------------------------------tataattttatcaattataa
           Chinese tree shrew  -----------------------------------cataatttcatcaattgtaa
B D                  Squirrel  ataaactaggactgtaagttattatgatgtgtcaatgtagtttcatcaattgttg
B D                       Rat  =======================================================
                Prairie vole  =======================================================
              Golden hamster  =======================================================
B D                     Mouse  =======================================================
      Lesser Egyptian jerboa  =======================================================
B D                      Pika  =======================================================
                Weddell seal  -------------------------------------------------------
B D                  Hedgehog  =======================================================
B D                     Shrew  =======================================================
B D                Guinea pig  =======================================================
B D                       Pig  =======================================================
B D                    Rabbit  -------------------------------------------------------
            Cape golden mole  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
                    Aardvark  =======================================================
B D                   Megabat  =======================================================
B D                   Dolphin  -------------------------------------------------------
B D                    Rhesus  =======================================================
B D             X. tropicalis  =======================================================
                 Spotted gar  =======================================================
B D                    Turkey  =======================================================
B D                   Chicken  =======================================================
  D              Mallard duck  -------------------------------------------------------
          Tibetan ground jay  =======================================================
B D               Zebra finch  =======================================================
  D    White-throated sparrow  =======================================================
B D           Tasmanian devil  =======================================================
  D            Painted turtle  =======================================================
  D           Green seaturtle  =======================================================
B D        American alligator  =======================================================
  D             Scarlet macaw  =======================================================
B D                Budgerigar  =======================================================
B D                   Opossum  =======================================================
B D            Naked mole-rat  =======================================================
  D               Rock pigeon  =======================================================
  D       Collared flycatcher  =======================================================
B D       Medium ground finch  =======================================================
B D                    Lizard  =======================================================
  D          Peregrine falcon  =======================================================
  D              Saker falcon  =======================================================
  D                    Parrot  =======================================================
            Brush-tailed rat  =======================================================
                  Chinchilla  =======================================================
         Cape elephant shrew  =======================================================
B D                  Platypus  =======================================================
B D                   Wallaby  =======================================================
B D                   Manatee  =======================================================
B D                  Elephant  =======================================================
B D           Chinese hamster  =======================================================
B D                    Tenrec  =======================================================
B D                       Cat  =======================================================
B D                  Bushbaby  =======================================================
  D  Chinese softshell turtle  =======================================================
B D                   Ferret   -------------------------------------------------------
             Star-nosed mole  =======================================================
               Domestic goat  =======================================================
B D                     Sheep  =======================================================
            Tibetan antelope  =======================================================
              Bactrian camel  -------------------------------------------------------
B D                    Alpaca  -------------------------------------------------------
              Pacific walrus  -------------------------------------------------------
B D                     Panda  -------------------------------------------------------
                Killer whale  -------------------------------------------------------
B D                       Dog  -------------------------------------------------------
            Black flying-fox  =======================================================
B D          White rhinoceros  =======================================================
B D                     Horse  -------------------------------------------------------
B D                 Armadillo  =======================================================
        David's myotis (bat)  =======================================================
               Big brown bat  =======================================================
B D                  Microbat  =======================================================
B D                       Cow  =======================================================

View table schema

Go to Conservation track controls

Data last updated: 2015-05-07

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