Multiz Alignments of 100 Vertebrates
 

Capitalize exons based on show bases
Place cursor over species for alignment detail. Click on 'B' to link to browser for aligned species, click on 'D' to get DNA for aligned species.
Alignment block 1 of 9 in window, 16223174 - 16223199, 26 bps 
B D                     Human  tcattaaac--------------caaccaatcattcaggt
B D                     Chimp  tcattaaac--------------caaccaatcattcaggt
B D                   Gorilla  tcattaaac--------------caaccaatcattcaggt
B D                 Orangutan  tcattaaac--------------caaccaatcattcaggt
B D                    Gibbon  tcattaaac--------------caaccaatcattcaagt
B D                    Rhesus  tcattaaac--------------caaccaatcattcaggt
B D       Crab-eating macaque  tcattaaac--------------caaccaatcattcaggt
B D                    Baboon  tcattaaac--------------caaccaatcattcaggt
B D              Green monkey  tcattaaac--------------caaccaatcattcaggt
B D                  Marmoset  tcattaagc--------------catccaatcattcaggt
B D           Squirrel monkey  tcattaagc--------------catccaatcattcaggt
B D                  Bushbaby  tcattaagc--------------cagcc-atcattcaggt
           Chinese tree shrew  ttattaaac--------------caacc----attcaggt
B D                  Squirrel  tcagtaaattatctaatcttcaataaccagtcattcaggt
       Lesser Egyptian jerboa  t----aact--------------gagccaatcatttcagg
                 Prairie vole  tcttgaagc--------------cgaccaatcatttc---
B D           Chinese hamster  acctgaagc--------------caaccaatcatttc---
               Golden hamster  acttgaagc--------------caaccaatcatttc---
B D                     Mouse  acttgaagc--------------cagccactcattca--t
B D                       Rat  acttgaagc--------------caaccactcatttaagt
B D            Naked mole-rat  tcattaagc--------------caatcaatcattcagat
B D                Guinea pig  tcattaagc--------------caaccaacaattcagat
                   Chinchilla  tcattaagc--------------caaccaatcattcagat
             Brush-tailed rat  tcattaagc--------------caaccaatcattcagat
B D                      Pika  tcattaagc--------------cattccataattcaggt
B D                       Pig  ttattaagc--------------caaacaataatttgggt
B D                    Alpaca  ttattaagg--------------caactaataattcaggt
               Bactrian camel  ttattaagg--------------caactaataattcaggt
B D                   Dolphin  ttattaagc--------------caaacaataattcagtt
                 Killer whale  ttattaagc--------------caaacaataattcagtt
             Tibetan antelope  ttattaagc--------------caaagaataattcaggt
B D                       Cow  ttattaagc--------------caaacaataattcaggt
B D                     Sheep  ttattaagc--------------caaagaataattcaggt
                Domestic goat  ttattaagc--------------caaagaataattcaggt
B D          White rhinoceros  ttgttaagt--------------caaccaacaattcaggt
B D                       Cat  ttattaagc--------------ca---aataattcaggt
B D                       Dog  ttattagga--------------caaccaattattcaggt
B D                   Ferret   ttattagga--------------caaccagtaattcagat
B D                     Panda  ttattagga--------------caacaaataattcaggt
               Pacific walrus  ttattagga--------------caaccaataattcaggt
                 Weddell seal  ttattaaga--------------caaccaataattcaggt
             Black flying-fox  tcatttagt--------------caagcaataatttaggt
B D                   Megabat  tcatttagt--------------caagcaataatttaggt
                Big brown bat  ttcttaaat--------------caaccaataactcgggt
         David's myotis (bat)  ttcttaaat--------------caagcaataactcagat
B D                  Microbat  ttcttaaat--------------caaccaataactcagat
B D                     Shrew  tcattaagg--------------tgactaataattcaggt
B D                  Elephant  ttattaagc--------------taaccggtcattcgggt
B D                   Manatee  ttattaagc--------------taaccagtcactcaggt
             Cape golden mole  ttattaagc--------------taactaatcttccaggt
B D                    Tenrec  ttattaagc--------------taaccaat----caggt
                     Aardvark  tta-taagc--------------taaccactcactcatgt
B D                 Armadillo  tcattaagt--------------caacaaaccatttaaat
           Southern platyfish  gtttggaaa--------------acatctgtcaatctgac
             Star-nosed mole  ========================================
         Cape elephant shrew  ========================================
B D                  Hedgehog  ========================================
B D                    Rabbit  ========================================
B D              Nile tilapia  ========================================
B D                     Horse  ========================================
B D              Atlantic cod  ========================================
B D                 Tetraodon  ========================================
                 Spotted gar  ========================================
B D                 Zebrafish  ========================================
B D               Stickleback  ========================================
B D                    Medaka  ========================================
      Yellowbelly pufferfish  ========================================
         Pundamilia nyererei  ========================================
                 Zebra mbuna  ========================================
       Burton's mouthbreeder  ========================================
         Princess of Burundi  ========================================
B D                Coelacanth  ========================================
B D             X. tropicalis  ========================================
B D                    Lizard  ========================================
  D  Chinese softshell turtle  ========================================
  D            Painted turtle  ========================================
  D           Green seaturtle  ========================================
B D                    Turkey  ========================================
B D                   Chicken  ========================================
  D              Mallard duck  ========================================
  D             Scarlet macaw  ========================================
  D                    Parrot  ========================================
B D                Budgerigar  ========================================
          Tibetan ground jay  ========================================
B D               Zebra finch  ========================================
B D       Medium ground finch  ========================================
  D    White-throated sparrow  ========================================
  D       Collared flycatcher  ========================================
  D          Peregrine falcon  ========================================
  D              Saker falcon  ========================================
  D               Rock pigeon  ========================================
B D                  Platypus  ========================================
B D                   Wallaby  ========================================
    Mexican tetra (cavefish)  ========================================
B D                      Fugu  ========================================
B D        American alligator  ========================================
B D                   Opossum  ========================================
B D           Tasmanian devil  ========================================

Alignment block 2 of 9 in window, 16223200 - 16223252, 53 bps 
B D                     Human  aat-aca--gaga--tgctgggct----aaaagt---------------ctctaaatcagtga-------
B D                     Chimp  aat-aca--gaga--tgctgggct----aaaagt---------------ctctaaatcagtga-------
B D                   Gorilla  aat-aca--gaga--tgctgggct----aaaagt---------------ctctaaatcagtga-------
B D                 Orangutan  aat-ata--gaga--tgctgggct----aaaagt---------------ctctatatcagtga-------
B D                    Gibbon  aat-ata--gaga--tgctgggct----aaaagt---------------ctctaaatcagtaa-------
B D                    Rhesus  aat-ata--gaga--tgctgggct----aaaagt---------------ctctaaatcagtga-------
B D       Crab-eating macaque  aat-ata--gaga--tgctgggct----aaaagt---------------ctctaaatcagtga-------
B D                    Baboon  aat-ata--gaga--tgctgggct----aaaagt---------------ctctaaatcagtga-------
B D              Green monkey  aat-ata--gaga--tgctgggct----aaaagt---------------ctctaaatcagtga-------
B D                  Marmoset  aat-ata--gaaa--tgcttggct----aaaagt---------------ctctgaatcagtga-------
B D           Squirrel monkey  aat-ata--gaga--tgctagact----aaaagt---------------ctctaaatcagtga-------
B D                  Bushbaby  aac-aca--gaga--aggcatgct----aaaagt---------------ttctaattcagtga-------
           Chinese tree shrew  aac-aga--gagg--agctaaact----aaaagt---------------ctctaaatcaatga-------
B D                  Squirrel  att-ttt--tagagaagttaagct----aaaagt---------------ttctaaatccccat-------
       Lesser Egyptian jerboa  aat-ata--a-----agttaggct----aaatgt---------------ctttaagatggtgaccccctt
                 Prairie vole  ---------------agataagtt----g-cact---------------ctctacatggctga-------
B D           Chinese hamster  ---------------agataagct----g-------------------------catggttga-------
               Golden hamster  ---------------agatcaact----gcaagt---------------ctcaacatggttga-------
B D                     Mouse  atc-atg--aggaa-tgctgagcc----gcaagt---------------ctctcagtggctga-------
B D                       Rat  atc-ata--aggag-agctaagct----ccaagt---------------ctctacatgactga-------
B D            Naked mole-rat  aat-aca--gaga--agctagtct----aaaagt---------------ctctaagttagtaa-------
B D                Guinea pig  aat-aca--aaga--agctagtgt----aaaagt---------------ctctaagtcagtaa-------
                   Chinchilla  aat-aca--gaga--agctagtct----acaagt---------------ttctaagtcagtaa-------
             Brush-tailed rat  agt--ca--gaga--agctagtcc----aaaagt---------------ctctaattcaataa-------
B D                      Pika  act-cta--gaga--agctaagat----aaaagt---------------cttcaaatcagtga-------
B D                       Pig  aat-aag--gaga--agttatgctaaaaaaaagc---------------ctctaaatcaatga-------
B D                    Alpaca  aat-acg--gaga--aactatgct----aaaagc---------------ctctaaatcagtga-------
               Bactrian camel  aat-acg--gaga--aactatgct----aaaagc---------------ctctaaatcagtga-------
B D                   Dolphin  aat-ata--gaga--agctatgct----gaaagc---------------ctctaaattagtga-------
                 Killer whale  aat-ata--gaga--agctatgct----gaaagc---------------ctctaaattagtga-------
             Tibetan antelope  aat-ata--gaga--agctgt-----------gc---------------cgctaaattagtga-------
B D                       Cow  aat-ata--gaga--agctgt-----------gc---------------ctctaaattagtga-------
B D                     Sheep  aat-ata--gaga--agctgt-----------gc---------------ctctaaattagtga-------
                Domestic goat  aat-ata--gaga--agctgt-----------gc---------------ctctaaattagtga-------
B D          White rhinoceros  aat-atg--gaga--cactatgct----aaaagt---------------ctctaaatcagtga-------
B D                       Cat  aat-atg--gaga--tgctatgct----aaaagt---------------ctctgaatcagtga-------
B D                       Dog  aac-atg--gaga--tgctatgcc----agaagt---------------ctctgaatcagtga-------
B D                   Ferret   aat-atg--gaga--tgctatgct----aaaagt---------------ctctgaatcggtga-------
B D                     Panda  aat-atg--gaga--tgccatgct----aaaagt---------------ctctgagtaggtga-------
               Pacific walrus  aac-atg--gaga--tgccatgct----taaagt---------------ccctagatcggtga-------
                 Weddell seal  aac-atg--gaga--tgccatgct----taaagt---------------ctctggatcggtga-------
             Black flying-fox  aat-ctg--gaaa--agctatgct----aaaagt---------------ctctaaatcagtga-------
B D                   Megabat  aat-ctg--gaaa--agctatgct----aaaagt---------------ctctaaatcagtga-------
                Big brown bat  att-atg--aaga--agctatgaa----aaaagt---------------ttccaaatcagtga-------
         David's myotis (bat)  a-g-atg--aaga--agctatgaa----aaaagt---------------ctccaaatcagtga-------
B D                  Microbat  a-a-atg--aaga--agctatgaa----aaaagt---------------ctccaaatcagtga-------
B D                     Shrew  --t-aaatgaaaa--agtaatgct----aaaagt---------------ctctgaatcaat-t-------
              Star-nosed mole  aat-aaa--gaga--agtcatact----aaacat---------------ctctaaattagt-a-------
B D                  Elephant  aat-aga--gaga--aactaggct----aaaagt---------------ctccacgtcagtga-------
B D                   Manatee  aat-aga--gaga--aactaggct----aaaatt---------------ctccacatcattga-------
             Cape golden mole  tcacaga--gagc--agcta---t----catagt------------------cacattagtga-------
B D                    Tenrec  aatcgaa--gtta--tgcta---------aaagt---------------ctccatgtcagtta-------
                     Aardvark  aac-------aga--aactatact----aaaagt---------------ctccacatcaatga-------
B D                 Armadillo  aat-ata--gaag--agctagttt----aaaaat--------------cctccaaatcaatga-------
           Southern platyfish  act-gca--taga--tgtcactct----gagaattgttgctgactatttctatcaatttatgg-------
         Cape elephant shrew  ======================================================================
B D                  Hedgehog  ======================================================================
B D                    Rabbit  ======================================================================
B D              Nile tilapia  ======================================================================
B D                     Horse  ======================================================================
B D              Atlantic cod  ======================================================================
B D                 Tetraodon  ======================================================================
                 Spotted gar  ======================================================================
B D                 Zebrafish  ======================================================================
B D               Stickleback  ======================================================================
B D                    Medaka  ======================================================================
      Yellowbelly pufferfish  ======================================================================
         Pundamilia nyererei  ======================================================================
                 Zebra mbuna  ======================================================================
       Burton's mouthbreeder  ======================================================================
         Princess of Burundi  ======================================================================
B D                Coelacanth  ======================================================================
B D             X. tropicalis  ======================================================================
B D                    Lizard  ======================================================================
  D  Chinese softshell turtle  ======================================================================
  D            Painted turtle  ======================================================================
  D           Green seaturtle  ======================================================================
B D                    Turkey  ======================================================================
B D                   Chicken  ======================================================================
  D              Mallard duck  ======================================================================
  D             Scarlet macaw  ======================================================================
  D                    Parrot  ======================================================================
B D                Budgerigar  ======================================================================
          Tibetan ground jay  ======================================================================
B D               Zebra finch  ======================================================================
B D       Medium ground finch  ======================================================================
  D    White-throated sparrow  ======================================================================
  D       Collared flycatcher  ======================================================================
  D          Peregrine falcon  ======================================================================
  D              Saker falcon  ======================================================================
  D               Rock pigeon  ======================================================================
B D                  Platypus  ======================================================================
B D                   Wallaby  ======================================================================
    Mexican tetra (cavefish)  ======================================================================
B D                      Fugu  ======================================================================
B D        American alligator  ======================================================================
B D                   Opossum  ======================================================================
B D           Tasmanian devil  ======================================================================

                        Human  --cccca--tttct-----ccca
                        Chimp  --cccca--tttct-----ccca
                      Gorilla  --cccca--tttct-----ccca
                    Orangutan  --cccca--tttct-----ccca
                       Gibbon  --cccca--tttct-----ccca
                       Rhesus  --cccca--tttct-----ccca
          Crab-eating macaque  --cccca--tttct-----ccca
                       Baboon  --cccca--tttct-----ccca
                 Green monkey  --cccca--tttct-----ccca
                     Marmoset  --cccca--tttct-----ccca
              Squirrel monkey  --cccca--tttct-----ccca
                     Bushbaby  --cccca--ctttt-----tcca
           Chinese tree shrew  --tccca--tttct-----tcta
                     Squirrel  --ctttc--tcactataata---
       Lesser Egyptian jerboa  tctccta--ccacaatgggc---
                 Prairie vole  --ttcta--cctccatggaatca
              Chinese hamster  --ttcta--cctcgatggaatca
               Golden hamster  --tccta--cctcgatggaatca
                        Mouse  --tg--g--actctgtggac---
                          Rat  --tgcca--cctctgtgaactca
               Naked mole-rat  --ttgta--tttct-----ccca
                   Guinea pig  --tacta--tttct-----ccca
                   Chinchilla  --ttcta--tttct-----ccca
             Brush-tailed rat  --ttcta--tttct-----ccca
                         Pika  --ccccc--tttgt-----ccaa
                          Pig  --cccca--tt--t-----ccca
                       Alpaca  --cccca--tttct-----ccca
               Bactrian camel  --cccca--tttct-----ccca
                      Dolphin  --cccca--tttct-----ccca
                 Killer whale  --cccca--tttct-----ccca
             Tibetan antelope  --cccca--ttcct-----ccca
                          Cow  --cccca--ttcct-----ccca
                        Sheep  --cccca--ttcct-----ccca
                Domestic goat  --cccca--ttcct-----ccca
             White rhinoceros  --cccca--attct-----ccca
                          Cat  --cccca--tatct-----ccca
                          Dog  --cccca--tttct-----ccta
                      Ferret   --cccca--tttct-----ccca
                        Panda  --accca--tttct-----ccca
               Pacific walrus  --cccca--tttct-----ccca
                 Weddell seal  --cccca--tttct-----ccca
             Black flying-fox  --cccca--cttct-----atca
                      Megabat  --cccca--cttct-----atca
                Big brown bat  --tccca--tttct-----acca
         David's myotis (bat)  --cccca--tttct-----acca
                     Microbat  --cccca--tttct-----acca
                        Shrew  --accca--tttct-----ccca
              Star-nosed mole  --tcccattttttt-----ccca
                     Elephant  --cccca--tttct-----ccca
                      Manatee  --cccca--tttct-----ccca
             Cape golden mole  --ctccc--tttct-----ccca
                       Tenrec  --gtcca--tttct-----ccca
                     Aardvark  --ctcta--tttct-----ccca
                    Armadillo  --cccca--ttttt-----ccca
           Southern platyfish  --ctgca--gtgca-----ccca
          Cape elephant shrew  =======================
                     Hedgehog  =======================
                       Rabbit  =======================
                 Nile tilapia  =======================
                        Horse  =======================
                 Atlantic cod  =======================
                    Tetraodon  =======================
                  Spotted gar  =======================
                    Zebrafish  =======================
                  Stickleback  =======================
                       Medaka  =======================
       Yellowbelly pufferfish  =======================
          Pundamilia nyererei  =======================
                  Zebra mbuna  =======================
        Burton's mouthbreeder  =======================
          Princess of Burundi  =======================
                   Coelacanth  =======================
                X. tropicalis  =======================
                       Lizard  =======================
     Chinese softshell turtle  =======================
               Painted turtle  =======================
              Green seaturtle  =======================
                       Turkey  =======================
                      Chicken  =======================
                 Mallard duck  =======================
                Scarlet macaw  =======================
                       Parrot  =======================
                   Budgerigar  =======================
           Tibetan ground jay  =======================
                  Zebra finch  =======================
          Medium ground finch  =======================
       White-throated sparrow  =======================
          Collared flycatcher  =======================
             Peregrine falcon  =======================
                 Saker falcon  =======================
                  Rock pigeon  =======================
                     Platypus  =======================
                      Wallaby  =======================
     Mexican tetra (cavefish)  =======================
                         Fugu  =======================
           American alligator  =======================
                      Opossum  =======================
              Tasmanian devil  =======================

Inserts between block 2 and 3 in window
          Southern platyfish 4234bp

Alignment block 3 of 9 in window, 16223253 - 16223261, 9 bps 
B D                     Human  ccacagtgc
B D                     Chimp  ccacagtgc
B D                   Gorilla  ccacagtgc
B D                 Orangutan  ccacaatgc
B D                    Gibbon  ccacaatgc
B D                    Rhesus  ccacaatgc
B D       Crab-eating macaque  ccacaatgc
B D                    Baboon  ccccaatgc
B D              Green monkey  ccacaatgc
B D                  Marmoset  ccgcaatgc
B D           Squirrel monkey  caacaatgc
B D                  Bushbaby  ccataatga
           Chinese tree shrew  ctacaatgc
                 Prairie vole  tcaaaatgt
B D           Chinese hamster  acaaaattc
               Golden hamster  tccaaactc
B D                     Mouse  tcaagac--
B D                       Rat  tcaagacaa
B D            Naked mole-rat  tcataatgc
B D                Guinea pig  tcacaaggc
                   Chinchilla  ccctaatgc
             Brush-tailed rat  ccatagggc
B D                      Pika  atataatgt
B D                       Pig  ccataatgc
B D                    Alpaca  ctagaatgc
               Bactrian camel  ctagaatgc
B D                   Dolphin  ctataatgc
                 Killer whale  ctataatgc
             Tibetan antelope  ttatattgc
B D                       Cow  ttacattgc
B D                     Sheep  ttatattgc
                Domestic goat  ttatattgc
B D          White rhinoceros  ctataatgc
B D                       Cat  aaacaatgc
B D                       Dog  caacaatgc
B D                   Ferret   caacaatgc
B D                     Panda  caacaatgc
               Pacific walrus  caacaatac
                 Weddell seal  caacaatgc
             Black flying-fox  agataatgt
B D                   Megabat  agataatgt
                Big brown bat  acataacaa
         David's myotis (bat)  acataacaa
B D                  Microbat  acataacaa
B D                     Shrew  ctataatgc
              Star-nosed mole  ctgtaatgc
B D                  Elephant  atacaatgc
B D                   Manatee  acataatgt
             Cape golden mole  atagcatgc
B D                    Tenrec  acacagtgc
                     Aardvark  atatactgc
B D                 Armadillo  ccatgat--
         Cape elephant shrew  =========
B D                  Hedgehog  =========
B D                    Rabbit  =========
      Lesser Egyptian jerboa  ---------
B D              Nile tilapia  =========
B D                     Horse  =========
B D                  Squirrel  ---------
B D              Atlantic cod  =========
B D                 Tetraodon  =========
                 Spotted gar  =========
          Southern platyfish  =========
B D                 Zebrafish  =========
B D               Stickleback  =========
B D                    Medaka  =========
      Yellowbelly pufferfish  =========
         Pundamilia nyererei  =========
                 Zebra mbuna  =========
       Burton's mouthbreeder  =========
         Princess of Burundi  =========
B D                Coelacanth  =========
B D             X. tropicalis  =========
B D                    Lizard  =========
  D  Chinese softshell turtle  =========
  D            Painted turtle  =========
  D           Green seaturtle  =========
B D                    Turkey  =========
B D                   Chicken  =========
  D              Mallard duck  =========
  D             Scarlet macaw  =========
  D                    Parrot  =========
B D                Budgerigar  =========
          Tibetan ground jay  =========
B D               Zebra finch  =========
B D       Medium ground finch  =========
  D    White-throated sparrow  =========
  D       Collared flycatcher  =========
  D          Peregrine falcon  =========
  D              Saker falcon  =========
  D               Rock pigeon  =========
B D                  Platypus  =========
B D                   Wallaby  =========
    Mexican tetra (cavefish)  =========
B D                      Fugu  =========
B D        American alligator  =========
B D                   Opossum  =========
B D           Tasmanian devil  =========

Alignment block 4 of 9 in window, 16223262 - 16223290, 29 bps 
B D                     Human  agag-taagtgagaattaagtttatgtcct
B D                     Chimp  agag-taagtgagacttaagtttatgtcct
B D                   Gorilla  agag-taagtgagacttaagtttatgtcct
B D                 Orangutan  agag-taagtgagacttaagtttatgtcct
B D                    Gibbon  agag-taagtgagacttaagtttatgtcct
B D                    Rhesus  agag-taaatcagacttaggtttatgtcct
B D       Crab-eating macaque  agag-taaatcagacttaggtttatgtcct
B D                    Baboon  agag-taaatcagacttaggtttatgtcct
B D              Green monkey  agag-taaatcagacttaggtttatgtcct
B D                  Marmoset  agaa-taagtcagacttaagtttatatcct
B D           Squirrel monkey  agaa-taagtcagacttaagtttatgtcct
B D                  Bushbaby  agaa-taagtcagacttaagtttatgtcct
           Chinese tree shrew  aaaa-taaatcagac-----ttcacattct
B D                  Squirrel  aata-taagtcagatttaagtttatgcctt
       Lesser Egyptian jerboa  ---------taagaaatggg-------cta
                 Prairie vole  agag-taagtaaaacttgaatagatgtctt
B D           Chinese hamster  agag-taagtaaaacttaaattgatgtctt
               Golden hamster  agag-taagtaaaacctaatt---tgtctt
B D                     Mouse  ------aagtcagacttgggttagtgtctt
B D                       Rat  agag-taagtcagacttaggttgatgtctt
B D            Naked mole-rat  agag-taaagcagacttaagtttatgtctt
B D                Guinea pig  agag-taaatcagatttaaacttatgtctt
                   Chinchilla  agag-taagtcagatttaagtttatgtcgt
             Brush-tailed rat  acag-taagttagatttaagtttatgtctt
B D                      Pika  aggg-taaacccaactttgttttatgcctg
B D                       Pig  agag-taagtcacacttaagcttatgtcct
B D                    Alpaca  ---a-tcagtcagacttcagttcacgtcct
               Bactrian camel  ---a-tcagtcagacttcagttcatgtcct
B D                   Dolphin  agaa-taagccagacttaaatttatgtcct
                 Killer whale  agaa-taagccagacttaaatttatgtcct
             Tibetan antelope  aaaa-taagtcaaacttaactttacgt-ct
B D                       Cow  aaaa-taagttaaagttaactttatgt-ct
B D                     Sheep  aaaa-taagtcaaacttaactttatgt-ct
                Domestic goat  aaaa-taagtcaaacttaactttatgt-ct
B D          White rhinoceros  agag-taaatcagacttaagtttatgtcct
B D                       Cat  agag-taagccagacttaaatttatgtcct
B D                       Dog  agag-tcagtcagacttaaatttatgtcct
B D                   Ferret   agaa-tgagtcaaacttaaatttatgtcct
B D                     Panda  agag-ccagtcaa-----------------
               Pacific walrus  --ag-tcagtcaaacttaaatttatgtcct
                 Weddell seal  agag-tcagtcaaacttaaatttatgtcct
             Black flying-fox  aga-----gtcagatttgaatttatgtcct
B D                   Megabat  aga-----gtcagatttaaatttatgtcct
                Big brown bat  agg-------tagacttaagtttatgtcct
         David's myotis (bat)  a----------------------------t
B D                  Microbat  a----------------------------t
B D                  Hedgehog  aaaa-taagtcagactgaatgttatgttct
B D                     Shrew  agagttaagtcagacttaagtttatgt-tt
              Star-nosed mole  aaag-taaatcagacttaagctcatgtcct
B D                  Elephant  agag-taattaagac--aaatttatgacct
B D                   Manatee  agag-taagtaagacttaagttaatgacct
             Cape golden mole  agag-caagtcagacttaagtttataacct
B D                    Tenrec  acat---agtaagacttaaatgtttgatgc
                     Aardvark  agag-taattaagacttaagtttatgacct
B D                 Armadillo  -------aaacagacttaggtttatgtcct
         Cape elephant shrew  ==============================
B D                    Rabbit  ==============================
B D              Nile tilapia  ==============================
B D                     Horse  ==============================
B D              Atlantic cod  ==============================
B D                 Tetraodon  ==============================
                 Spotted gar  ==============================
          Southern platyfish  ==============================
B D                 Zebrafish  ==============================
B D               Stickleback  ==============================
B D                    Medaka  ==============================
      Yellowbelly pufferfish  ==============================
         Pundamilia nyererei  ==============================
                 Zebra mbuna  ==============================
       Burton's mouthbreeder  ==============================
         Princess of Burundi  ==============================
B D                Coelacanth  ==============================
B D             X. tropicalis  ==============================
B D                    Lizard  ==============================
  D  Chinese softshell turtle  ==============================
  D            Painted turtle  ==============================
  D           Green seaturtle  ==============================
B D                    Turkey  ==============================
B D                   Chicken  ==============================
  D              Mallard duck  ==============================
  D             Scarlet macaw  ==============================
  D                    Parrot  ==============================
B D                Budgerigar  ==============================
          Tibetan ground jay  ==============================
B D               Zebra finch  ==============================
B D       Medium ground finch  ==============================
  D    White-throated sparrow  ==============================
  D       Collared flycatcher  ==============================
  D          Peregrine falcon  ==============================
  D              Saker falcon  ==============================
  D               Rock pigeon  ==============================
B D                  Platypus  ==============================
B D                   Wallaby  ==============================
    Mexican tetra (cavefish)  ==============================
B D                      Fugu  ==============================
B D        American alligator  ==============================
B D                   Opossum  ==============================
B D           Tasmanian devil  ==============================

Inserts between block 4 and 5 in window
B D                      Pig 1622bp

Alignment block 5 of 9 in window, 16223291 - 16223306, 16 bps 
B D                     Human  cggaggca-tttt--catt
B D                     Chimp  cggaggca-tttt--catt
B D                   Gorilla  cggaggca-tttt--catt
B D                 Orangutan  cggaggca-tttt--catt
B D                    Gibbon  cggaggca-tttt--catt
B D                    Rhesus  tggaggca-tttt--catt
B D       Crab-eating macaque  tggaggca-tttt--catt
B D                    Baboon  tagaggca-tttt--catt
B D              Green monkey  tggaggca-tttt--catt
B D                  Marmoset  cagaggca-tt------tt
B D           Squirrel monkey  cataggca-tt------tt
B D                  Bushbaby  aggaggca-tgtt--catt
           Chinese tree shrew  gagaggca-tttt--cact
B D                  Squirrel  gggagaca-tttt--cact
       Lesser Egyptian jerboa  ggaagcat-ttta------
                 Prairie vole  ggaagaca-tatt------
B D           Chinese hamster  ggaagaca-tttt------
               Golden hamster  ggaagaca-tttt------
B D                     Mouse  ggaaggtg-tttc------
B D                       Rat  ggaaggtg-tttc------
B D            Naked mole-rat  tggagatg-tttt--cact
B D                Guinea pig  tggagacg-tttt--ctct
                   Chinchilla  gggagtca-tttt--cact
             Brush-tailed rat  aggagaca-tttt--cact
B D                      Pika  gggaggcc-tttt--ctct
B D                    Alpaca  acaaggta-tttt--cact
               Bactrian camel  acaaggta-tttt--caat
B D                   Dolphin  gtgaggta-tttt--cact
                 Killer whale  gtgaggta-tttt--cact
             Tibetan antelope  gtaagata-tttt--cact
B D                       Cow  atgagata-tttt--cact
B D                     Sheep  atgagata-tttt--cact
                Domestic goat  ataagata-tttt--cact
B D          White rhinoceros  gagaggta-tttt--catt
B D                       Cat  gtaaggta-tttt--cact
B D                       Dog  gtaaggta-tttt--cact
B D                   Ferret   gtaaagtg-tttt--tcct
               Pacific walrus  gtaaggtg-tttt--cact
                 Weddell seal  gtaaggtg-tttt--cact
             Black flying-fox  gtgaggta-cttt--tatt
B D                   Megabat  gtgaggta-cttt--tatt
                Big brown bat  gtgaggta-tttt--cact
         David's myotis (bat)  gtgaggta-tttt--cact
B D                  Microbat  gtgaggta-tttt--cact
B D                  Hedgehog  aagaggta-tttt--cact
B D                     Shrew  gaaaagtattttt--tact
              Star-nosed mole  ggaaggta-tttt--tact
B D                  Elephant  gggagaca-ctgt--cgct
B D                   Manatee  gggaggca-ctgt--catt
             Cape golden mole  gggagcca-ttat--cact
B D                    Tenrec  gggaggcc-tggt--ccct
                     Aardvark  ggaaggca-gtgtcacact
B D                 Armadillo  gggag-ca-ttgt--cact
         Cape elephant shrew  ===================
B D                    Rabbit  ===================
B D                       Pig  ===================
B D                     Panda  -------------------
B D              Nile tilapia  ===================
B D                     Horse  ===================
B D              Atlantic cod  ===================
B D                 Tetraodon  ===================
                 Spotted gar  ===================
          Southern platyfish  ===================
B D                 Zebrafish  ===================
B D               Stickleback  ===================
B D                    Medaka  ===================
      Yellowbelly pufferfish  ===================
         Pundamilia nyererei  ===================
                 Zebra mbuna  ===================
       Burton's mouthbreeder  ===================
         Princess of Burundi  ===================
B D                Coelacanth  ===================
B D             X. tropicalis  ===================
B D                    Lizard  ===================
  D  Chinese softshell turtle  ===================
  D            Painted turtle  ===================
  D           Green seaturtle  ===================
B D                    Turkey  ===================
B D                   Chicken  ===================
  D              Mallard duck  ===================
  D             Scarlet macaw  ===================
  D                    Parrot  ===================
B D                Budgerigar  ===================
          Tibetan ground jay  ===================
B D               Zebra finch  ===================
B D       Medium ground finch  ===================
  D    White-throated sparrow  ===================
  D       Collared flycatcher  ===================
  D          Peregrine falcon  ===================
  D              Saker falcon  ===================
  D               Rock pigeon  ===================
B D                  Platypus  ===================
B D                   Wallaby  ===================
    Mexican tetra (cavefish)  ===================
B D                      Fugu  ===================
B D        American alligator  ===================
B D                   Opossum  ===================
B D           Tasmanian devil  ===================

Inserts between block 5 and 6 in window
            Cape golden mole 8bp

Alignment block 6 of 9 in window, 16223307 - 16223324, 18 bps 
B D                     Human  taacac----tca---a-----------cttgtctc
B D                     Chimp  taacac----tca---a-----------cttgtctc
B D                   Gorilla  taacac----tca---a-----------cttgtctc
B D                 Orangutan  taacac----tca---a-----------cttgtctc
B D                    Gibbon  taacac----tca---a-----------cttgtctc
B D                    Rhesus  taacac----tca---a-----------cttttctc
B D       Crab-eating macaque  taacac----tca---a-----------cttttctc
B D                    Baboon  taacac----tca---a-----------cttttctc
B D              Green monkey  taacac----tca---a-----------cttttctc
B D                  Marmoset  taacac----tca---a-----------cttttctc
B D           Squirrel monkey  taacac----tca---a-----------cttttctc
B D                  Bushbaby  taacac----tca---c-----------tttttctc
           Chinese tree shrew  taacac----tca---g-----------tttttctc
B D                  Squirrel  taacat----tca---g-----------attttctc
       Lesser Egyptian jerboa  --atac----tca---aatgtt------tttttttt
                 Prairie vole  --acac----tca---g-----------ttcttctc
B D           Chinese hamster  --atac----tca---acttatactcagttcttctc
               Golden hamster  --atac----tca---a-----------ttcttctc
B D                     Mouse  --acac----tca---a-----------tttttct-
B D                       Rat  --gcac----tcg---a-----------tttttctc
B D            Naked mole-rat  taatac----tca---g-----------ctcttctc
B D                Guinea pig  taacac----tca---g-----------ctttcctc
                   Chinchilla  tgaccc----tca---g-----------cttttccc
             Brush-tailed rat  taacac----tca---g-----------cttttctc
B D                    Rabbit  taacct----tcaaatg-----------atctgaca
B D                      Pika  taaaac----tca---g-----------ctttgata
B D                    Alpaca  taacac----tta---g-----------ctttgttt
               Bactrian camel  taacac----tta---g-----------ctttgctt
B D                   Dolphin  taacac----tca---g-----------ctttgctt
                 Killer whale  taacac----tca---g-----------ctttgctt
             Tibetan antelope  tttcac----tca---g-----------ctttgctt
B D                       Cow  tttcac----tca---g-----------ctttgctt
B D                     Sheep  tttcac----tca---g-----------ctttgctt
                Domestic goat  tttcac----tca---g-----------ctttgctt
B D          White rhinoceros  taacac----tca---g-----------cttcgctt
B D                       Cat  taacac----tca---a-----------ctttgttt
B D                       Dog  tgatag----tca---g-----------ctttgctt
B D                   Ferret   tgacag----tca---g-----------ctttgctt
B D                     Panda  --acag----tca---g-----------ctttgctt
               Pacific walrus  tgacag----tca---g-----------ctttgctt
                 Weddell seal  tgacag----tca---g-----------ctttgctt
             Black flying-fox  taacat----tca---g-----------ctttgctt
B D                   Megabat  taacat----tca---g-----------ctttgctt
                Big brown bat  tcacac----cca---g-----------gtttgctt
         David's myotis (bat)  taacac----tca---g-----------ctttgctt
B D                  Microbat  taacac----tca---g-----------ctttgctt
B D                  Hedgehog  aaccct-----ca---a-----------ctttgttt
B D                     Shrew  taacattcattca---g-----------cttggctt
              Star-nosed mole  taacat------a---g-----------ttttcttt
B D                  Elephant  -cacgt----tca---c-----------ctttgctc
B D                   Manatee  -tacat----tca---c-----------ctttgctc
             Cape golden mole  -catac----tta---t-----------ctttattc
B D                    Tenrec  -tacac----tca---c-----------ttttattc
                     Aardvark  -cacac----tca---c-----------ctttgctc
B D                 Armadillo  -----------------------------------c
         Cape elephant shrew  ====================================
B D                       Pig  ====================================
B D              Nile tilapia  ====================================
B D                     Horse  ====================================
B D              Atlantic cod  ====================================
B D                 Tetraodon  ====================================
                 Spotted gar  ====================================
          Southern platyfish  ====================================
B D                 Zebrafish  ====================================
B D               Stickleback  ====================================
B D                    Medaka  ====================================
      Yellowbelly pufferfish  ====================================
         Pundamilia nyererei  ====================================
                 Zebra mbuna  ====================================
       Burton's mouthbreeder  ====================================
         Princess of Burundi  ====================================
B D                Coelacanth  ====================================
B D             X. tropicalis  ====================================
B D                    Lizard  ====================================
  D  Chinese softshell turtle  ====================================
  D            Painted turtle  ====================================
  D           Green seaturtle  ====================================
B D                    Turkey  ====================================
B D                   Chicken  ====================================
  D              Mallard duck  ====================================
  D             Scarlet macaw  ====================================
  D                    Parrot  ====================================
B D                Budgerigar  ====================================
          Tibetan ground jay  ====================================
B D               Zebra finch  ====================================
B D       Medium ground finch  ====================================
  D    White-throated sparrow  ====================================
  D       Collared flycatcher  ====================================
  D          Peregrine falcon  ====================================
  D              Saker falcon  ====================================
  D               Rock pigeon  ====================================
B D                  Platypus  ====================================
B D                   Wallaby  ====================================
    Mexican tetra (cavefish)  ====================================
B D                      Fugu  ====================================
B D        American alligator  ====================================
B D                   Opossum  ====================================
B D           Tasmanian devil  ====================================

Alignment block 7 of 9 in window, 16223325 - 16223351, 27 bps 
B D                     Human  a-tttctttatcgagataag-aaaat--------------g---ct
B D                     Chimp  a-tttctttattgagataag-aaaat--------------g---ct
B D                   Gorilla  a-tttctttattgagataag-aaaat--------------g---ct
B D                 Orangutan  a-tttctttattgagataag-aaaat--------------g---ct
B D                    Gibbon  a-tttctttgt-----taag-aaaat--------------g---ct
B D                    Rhesus  a-tttctttattgagataag-aaaatnnnnnnnnnnnnnnn---nn
B D       Crab-eating macaque  a-tttctttattgagataag-aaaat--------------g---ct
B D                    Baboon  a-tttctttattgagataag-aaaat--------------g---ct
B D              Green monkey  a-tttctttattgagataag-aaaat--------------g---ct
B D                  Marmoset  a-tatctttattcagataag-aaaat--------------g---ct
B D           Squirrel monkey  a-tatccttattgagttaag-aaaat--------------g---ct
B D                  Bushbaby  a-tttctttattgagtcaag-aaaat--------------g---ct
           Chinese tree shrew  a-tttttttatcaagatgag-aaaa---------------------
B D                  Squirrel  a-ttttttcatggagatagg-agaat--------------g---ct
       Lesser Egyptian jerboa  a---tttttatgtagataa---------------------------
                 Prairie vole  a---ctttgatgaacatgg---------------------------
B D           Chinese hamster  a---cttttatggagatgg---------------------------
               Golden hamster  ----cttatatggagatgg---------------------------
B D                     Mouse  ----cttttatggaggtgg---------------------------
B D                       Rat  a---cttttgtggagatgg---------------------------
B D            Naked mole-rat  atttcttttatggttacagg-aaaat--------------g---ct
B D                Guinea pig  a--ctttttatggtgaaagg-aaaat--------------g---ct
                   Chinchilla  a--ctttttatggtgatagg-aaaat--------------g---ct
             Brush-tailed rat  a-tttttttaaggtgata-g-aaaac--------------g---ct
B D                    Rabbit  -------ttattgaaatagg-aaaat--------------g---ct
B D                      Pika  g-tttcttcaacaaaatagg-aaaat--------------g---ct
B D                    Alpaca  -atctcattactgagataag-aatat--------------g---ct
               Bactrian camel  -atctcattattgagataag-aatat--------------g---ct
B D                   Dolphin  -atctctttattggggtaag-aagat--------------g---ct
                 Killer whale  -atctctttattggggtaag-aagat--------------g---ct
             Tibetan antelope  -acctctttattgagat----aatat--------------g---ct
B D                       Cow  -acctctttattgagat----aatat--------------g---ct
B D                     Sheep  -acctctttattgagat----aatat--------------g---ct
                Domestic goat  -acctctttattgagct----aatat--------------g---ct
B D                     Horse  -atctcttttttgagataaa-aagat--------------a---ct
B D          White rhinoceros  -atctctttattgagataag-aagat--------------g---ct
B D                       Cat  -atttctttattgtgataag-aagat--------------g---ct
B D                       Dog  -atctcttcattgagattag-aagat--------------g---ct
B D                   Ferret   -atctctttattgagataag-aagat--------------g---ct
B D                     Panda  -atctctttattgagatagg-aagat--------------g---ct
               Pacific walrus  -atctttttattgagataag-aagat--------------g---ct
                 Weddell seal  -atctctttattgagataag-aagat--------------g---ct
             Black flying-fox  -atctctttatagaagt----aagat--------------g---ct
B D                   Megabat  -atctctttatagaagt----aagat--------------g---ct
                Big brown bat  -attcctttattgagat----aagat--------------g---ct
         David's myotis (bat)  -attcctttattgagat----aagat--------------g---ct
B D                  Microbat  -attcctttattgagat----aagat--------------g---ct
B D                  Hedgehog  -ctctctttattgagttaa----gat--------------g---tt
B D                     Shrew  -ttctctttattgagataag-aggat--------------g---ct
              Star-nosed mole  -acatctacacttggaaaag-aagat--------------gctact
B D                  Elephant  -atctctttactgagataag-agggt--------------a---ct
B D                   Manatee  -atctctttgtttagataag-aggat--------------g---ct
             Cape golden mole  -atatctttactgagattag-aagat--------------g---ct
B D                    Tenrec  -atctctttactgagataagaaagag--------------g---ct
                     Aardvark  -atctctttactgagataag-aagat--------------g---ca
B D                 Armadillo  -atctctttcttgagataag-aaatt--------------t---ct
         Cape elephant shrew  ==============================================
B D                       Pig  ==============================================
B D              Nile tilapia  ==============================================
B D              Atlantic cod  ==============================================
B D                 Tetraodon  ==============================================
                 Spotted gar  ==============================================
          Southern platyfish  ==============================================
B D                 Zebrafish  ==============================================
B D               Stickleback  ==============================================
B D                    Medaka  ==============================================
      Yellowbelly pufferfish  ==============================================
         Pundamilia nyererei  ==============================================
                 Zebra mbuna  ==============================================
       Burton's mouthbreeder  ==============================================
         Princess of Burundi  ==============================================
B D                Coelacanth  ==============================================
B D             X. tropicalis  ==============================================
B D                    Lizard  ==============================================
  D  Chinese softshell turtle  ==============================================
  D            Painted turtle  ==============================================
  D           Green seaturtle  ==============================================
B D                    Turkey  ==============================================
B D                   Chicken  ==============================================
  D              Mallard duck  ==============================================
  D             Scarlet macaw  ==============================================
  D                    Parrot  ==============================================
B D                Budgerigar  ==============================================
          Tibetan ground jay  ==============================================
B D               Zebra finch  ==============================================
B D       Medium ground finch  ==============================================
  D    White-throated sparrow  ==============================================
  D       Collared flycatcher  ==============================================
  D          Peregrine falcon  ==============================================
  D              Saker falcon  ==============================================
  D               Rock pigeon  ==============================================
B D                  Platypus  ==============================================
B D                   Wallaby  ==============================================
    Mexican tetra (cavefish)  ==============================================
B D                      Fugu  ==============================================
B D        American alligator  ==============================================
B D                   Opossum  ==============================================
B D           Tasmanian devil  ==============================================

Inserts between block 7 and 8 in window
B D                   Alpaca 1bp
              Bactrian camel 1bp
B D                  Dolphin 1bp
                Killer whale 1bp
            Tibetan antelope 1bp
B D                      Cow 1bp
B D                    Sheep 1bp
               Domestic goat 1bp
B D                    Horse 1bp
B D         White rhinoceros 1bp
B D                      Cat 1bp
B D                      Dog 1bp
B D                  Ferret  1bp
B D                    Panda 1bp
              Pacific walrus 1bp
                Weddell seal 1bp
            Black flying-fox 1bp
B D                  Megabat 1bp
               Big brown bat 1bp
        David's myotis (bat) 1bp
B D                 Microbat 1bp
B D                 Hedgehog 1bp
B D                    Shrew 1bp
             Star-nosed mole 1bp

Alignment block 8 of 9 in window, 16223352 - 16223434, 83 bps 
B D                     Human  ac--aaaaatgggactaaatttaccaccccaaaatgttatgaaatc-agcattct-aagttat---agaa
B D                     Chimp  ac--aaaaatgggactaaatttaccaccccaaaatgttatgaaatc-agcattct-aagttat---agaa
B D                   Gorilla  ac--aaaaatgggactaaatttaccaccccaaaatgttatgaaatc-agcattct-aagttat---agaa
B D                 Orangutan  ac--aaaaatgggactaaatttaccatcccaaaatgttatgaaatc-agcattct-aagttat---agaa
B D                    Gibbon  ac--aaaaatgggactaaatttaccaccccaaaatgttatgaaatc-agcattct-aagttat---agaa
B D                    Rhesus  nn--nnaaatgggactaaatttactat-ccaaaatgttatgaaatc-agcattct-aagttat---agaa
B D       Crab-eating macaque  ac--aaaaatgggactaaatttactat-ccaaaatgttatgaaatc-agcattct-aagttat---agaa
B D                    Baboon  ac--aaaaatgggactaaatttactat-ccaaaatgttatgaaatc-agctttct-aagttat---agaa
B D              Green monkey  ac--aaaaatgggactaaatttactat-ccaaaatgttatgacatc-agcattct-aagttat---agaa
B D                  Marmoset  ac--aaaaatgggactaaatttaccaccaaaaaatgttatgaaatc-ggcattca-aagttataggagaa
B D           Squirrel monkey  ac--aaaaattggactaaatttaccaccccaaaatgttatgaaatc-agcattcc-aagttataggagaa
B D                  Bushbaby  act-aaaaatgggacttacttcaccaccccaaaatgttatataatc-agc---cc-aagttat---agga
           Chinese tree shrew  ----aaaaatgggactaaactcaccaccccaaaa--atgtaaaatc-agcattcc-aagttct---agaa
B D                  Squirrel  aca-aaaaatgaggtgaaatttaccacccaaaaa---tgtgaaatg-atcactcc-aattcat---aaga
       Lesser Egyptian jerboa  ----gaaaataagacatagtttgtcactcaacaattttgtgaaatc-atcctttc-aagtccc---agaa
                 Prairie vole  ----aaaactgtgac--------------------gatgaga------------------------gcga
B D           Chinese hamster  ----aaaaatgagaccgaatttgccacccaacaatgttgtgaaat--atcatacc-aacctct---gaga
               Golden hamster  ----aaaaatgagactgaatttgccacccaacaatgttgtgaaat--atcgtgcc-aacctct---g---
B D                     Mouse  ----aaagatgaggctgaactttccacccaacagtgttgtaaaatc-accatgcc-agcctcc---gaga
B D                       Rat  ----aaagatgagactgaatttgccacccaacagtgttgtcgaatc-atcatgcc-agcctct---gaga
B D            Naked mole-rat  act-aaaaatggcactcaatttaccacccaaaaa---tgtgaaatt-atcattcc-aagtcat---aaaa
B D                Guinea pig  act-aaaaatggcattcaatttgccacccaaaac---tgtgaaaataatcattcc-aacttat---c---
                   Chinchilla  gct-aaaaatggcattcaatttgccacccaaaat---tgtgaaat---tcactcc-aacttat---a---
             Brush-tailed rat  act-aaaaattccattccatttgccaccccaaat---tgtgaaatt-atcattccaaacttac---a---
B D                    Rabbit  tct-aaaagtggtactaacttcaccacacaaacatgttgtaaaatc-agcattcc-aagtaat---g--a
B D                      Pika  act-aaaagtggtactaactttgccacacag--attttgtgaaatc-agcattcc-aattaat---g--a
B D                       Pig  -at-aaaaatgggactaaattcatcac-ccaaaatgttgtgaaata-agcattcc-aagttac---aaga
B D                    Alpaca  -ct-aaaaatgagactaagttcaccac-ccaaaatgttgtgaaatc-agcattcc-aagttat---aaga
               Bactrian camel  -ct--aaagtgagactaagttcaccac-tcaaaatgttgtgaaatc-agcattcc-aagttat---aaga
B D                   Dolphin  -ct-aaaaatgggactaaattcact-a-cccaaatgttatgaaatc-agcattcc-aagttat---aaga
                 Killer whale  -ct-aaaaatgggactaaattcact-a-cctaaatgttatgaaatc-agcattcc-aagttat---aaga
             Tibetan antelope  -ct-aaaaatggaactaaattcaccaa-ccaaaatgttgtgaaatc-aatattcc-aagatat---aaga
B D                       Cow  -ct-aaaaatggaactaaattcaccaa-ccaaaatactgtgaaatc-agtattcc-aagttat---aaga
B D                     Sheep  -ct-aaaaatggaactaaattcaccaa-ccaaaatgttgtgaaatc-agtattcc-aagatat---aaga
                Domestic goat  -ct-aaaaatggaactaaattcaccaa-ccaaaatgttgtgaaatc-agtattcc-aagatat---aaga
B D                     Horse  -ct-aaaacttggactaaattcaccac-ccaaaatgttgtgaaatg-agcatccc-aacttat---agga
B D          White rhinoceros  -ct-aaaaatgggactaaattcgccac-ccaaagtgttgtgaaatg-agcattcc-aaattgt---agga
B D                       Cat  -ct-aaaaacgggactacattcacctc-tcaaaatgttgtgaaatc-agcattcc-aagttat---ggaa
B D                       Dog  -ctaaaaaatgggactaaattcaccat-tcaaaatgttgtgaaatc-agcattcc-aagttat---agaa
B D                   Ferret   -ct-aaaaatgggactaaattcaccac-tcaaaatgttgtgaaatc-agcattcc-aagttat---agaa
B D                     Panda  -ct-aaaaatgggactaaattcaccac-tcaaaatgttgtgaaatc-agcattcc-aagttat---agaa
               Pacific walrus  -ct-aaaaatgggactaaactcaccac-tcaaaatgttgtgaaatc-agcattcc-aagttat---agaa
                 Weddell seal  -ct-aaaaatggtattaaattcaccac-tcaaaatgttgtgaaatc-agcattcc-aagttat---agaa
             Black flying-fox  -at-aaaaataggactaaattcaccac-ccaaaatgttgtgaaatc-agcatgcc-aagttat---agga
B D                   Megabat  -at-aaaaataggactaaattcaccac-ccaaaatgttgtgaaatc-agcatgcc-aagttat---agga
                Big brown bat  -ct-aaaaacgggactaaatttaccac-ccaaaatattgtgaaatc-agcattcc-aagttat---agga
         David's myotis (bat)  -ct-aaaaatgggactaaacttaccac-ctaaaatattgtgaaatc-agcattcc-aagttat---agga
B D                  Microbat  -ct-aaaaatgggactaaacttaccac-ccaaaatattgtgaaatc-agcattcc-aacttat---agga
B D                  Hedgehog  -ct-taaaatagggctaaattcatcat-caaaag---tgtaaaata-agcagtcc-aggctac---aaga
B D                     Shrew  -tt-aaaaataagactaaattcaacac-ccaaagtatcataaaatc-agcagtcc-atgttct---agg-
              Star-nosed mole  -ct-aaaaatagaactaaactcactac-caaaa----tgtgaaatc-agtattcc-aagtaat---ag--
B D                  Elephant  act-aaaaatgggactaaattcaccac-ccaaaatgttgtgaaatc-agcattcc-aagttat-----ga
B D                   Manatee  act-aaaaatgggactaaattcaccac-ccaaaatgtggtgaaatc-agcatttc-aagttat---aaga
             Cape golden mole  act-aaaaatgggactaaactcactac-tcaaaacgttatgaaatc-agaattcc-aagtcat---aaga
B D                    Tenrec  tct-aaaaatgggtctaaacttactac-cccaaatcttatgaaatc-agtgtttc-aaattat---gaga
                     Aardvark  act-aaaaattggactaaattcaccac-ctaaaacgttgtgaaatc-agcattcc-aagttgt---aaga
B D                 Armadillo  act-a--------------------------aaatgttgtgaaatc-aacatt-c-acatttt---aaga
         Cape elephant shrew  ======================================================================
B D              Nile tilapia  ======================================================================
B D              Atlantic cod  ======================================================================
B D                 Tetraodon  ======================================================================
                 Spotted gar  ======================================================================
          Southern platyfish  ======================================================================
B D                 Zebrafish  ======================================================================
B D               Stickleback  ======================================================================
B D                    Medaka  ======================================================================
      Yellowbelly pufferfish  ======================================================================
         Pundamilia nyererei  ======================================================================
                 Zebra mbuna  ======================================================================
       Burton's mouthbreeder  ======================================================================
         Princess of Burundi  ======================================================================
B D                Coelacanth  ======================================================================
B D             X. tropicalis  ======================================================================
B D                    Lizard  ======================================================================
  D  Chinese softshell turtle  ======================================================================
  D            Painted turtle  ======================================================================
  D           Green seaturtle  ======================================================================
B D                    Turkey  ======================================================================
B D                   Chicken  ======================================================================
  D              Mallard duck  ======================================================================
  D             Scarlet macaw  ======================================================================
  D                    Parrot  ======================================================================
B D                Budgerigar  ======================================================================
          Tibetan ground jay  ======================================================================
B D               Zebra finch  ======================================================================
B D       Medium ground finch  ======================================================================
  D    White-throated sparrow  ======================================================================
  D       Collared flycatcher  ======================================================================
  D          Peregrine falcon  ======================================================================
  D              Saker falcon  ======================================================================
  D               Rock pigeon  ======================================================================
B D                  Platypus  ======================================================================
B D                   Wallaby  ======================================================================
    Mexican tetra (cavefish)  ======================================================================
B D                      Fugu  ======================================================================
B D        American alligator  ======================================================================
B D                   Opossum  ======================================================================
B D           Tasmanian devil  ======================================================================

                        Human  g----ttcttt----tga--tttacctaaa
                        Chimp  g----ttcttt----taa--tttacctaaa
                      Gorilla  g----ttcttt----taa--tttacctaaa
                    Orangutan  g----ttcttt----taa--tttacctaaa
                       Gibbon  g----ttcttt----taa--tttacctaaa
                       Rhesus  a----ttcctt----taa--tttacctaaa
          Crab-eating macaque  a----ttcctt----taa--tttacctaaa
                       Baboon  a----ttcctt----taa--tttacctaaa
                 Green monkey  a----ttcctt----taa--tttacctaaa
                     Marmoset  g----ttcttt----taa--tttccctaaa
              Squirrel monkey  g----ttcttt----taa--tttccctaaa
                     Bushbaby  gaagtttcttt----cca--tttgcccaaa
           Chinese tree shrew  g---tttctct----caa--tttgcccaaa
                     Squirrel  aaagtttccat----caa--tttgcctaaa
       Lesser Egyptian jerboa  aaaattacttt----caa--gttgtcc--a
                 Prairie vole  gctgtctcatt----cag--tttgactaga
              Chinese hamster  gcagttttttt----cag--tttgactaaa
               Golden hamster  ------------------------------
                        Mouse  gcagcctcttt----cag--t--------a
                          Rat  gcagcgtcttt----cgg--t--------a
               Naked mole-rat  gaagtttcttt----caa--ttgactcaaa
                   Guinea pig  ----ttcctct----caa--tggactccaa
                   Chinchilla  --agcttcttt----caa--ccgattcaaa
             Brush-tailed rat  --agtttcttt----caa--ctgactcaaa
                       Rabbit  aaaattacttt----caa--ttttcccaaa
                         Pika  aaatttacctt----gca--tttgctccca
                          Pig  gaaatttcttt----caa--tttttccaaa
                       Alpaca  aaaatttcttt----cag--tttgcccaaa
               Bactrian camel  aaaatttcttt----cag--tttgcccaaa
                      Dolphin  gaagtttcttt----caa--tatgcccaaa
                 Killer whale  gaagtttcttt----caa--tatgcccaaa
             Tibetan antelope  taaatttattt----caa--tatgccccaa
                          Cow  gaaatttcttt----caa--tatgccccaa
                        Sheep  taaatttcttt----caa--tatgccccaa
                Domestic goat  taaatttcttt----caa--tatgccccaa
                        Horse  gaaatttc-tt----caa--tttacccaaa
             White rhinoceros  gaaatttc-tt----caa--tttgcgcaaa
                          Cat  gaaatt--ttt----cta--tttgcccaaa
                          Dog  gaaatttcttt----caa--tttgcccaaa
                      Ferret   gaaatttc----------------------
                        Panda  gaaattacttt----caa--tttgcccaaa
               Pacific walrus  gaaatttcttt----caa--tttgcccaaa
                 Weddell seal  gaaatttcttt----caa--tttgcccaaa
             Black flying-fox  gaaatttcttt----cag--tttgcccaaa
                      Megabat  gaaatttcttt----cag--tttgcccaaa
                Big brown bat  gaaattccttt----caa--tttgcccaag
         David's myotis (bat)  gaaatttcttt----caa--tttgcccaaa
                     Microbat  gaaatttcttt----caa--tttgcccaaa
                     Hedgehog  aaaatttcttt----caatttttttcccaa
                        Shrew  agaaattcttt----cag--tttgtcaaat
              Star-nosed mole  -aaatttattt----caa--tttgcccata
                     Elephant  gaagtttcttt----caa--tttgcttgag
                      Manatee  gacgtttcatt----caa--tttgctcaag
             Cape golden mole  gaagtttcttt----gaa--cttgcccaag
                       Tenrec  gaaatttctttcaagaaa--tttgtacaag
                     Aardvark  gaagtttcttt----caa--tttgctcaag
                    Armadillo  aaagtttcttt----taa--attacccaa-
          Cape elephant shrew  ==============================
                 Nile tilapia  ==============================
                 Atlantic cod  ==============================
                    Tetraodon  ==============================
                  Spotted gar  ==============================
           Southern platyfish  ==============================
                    Zebrafish  ==============================
                  Stickleback  ==============================
                       Medaka  ==============================
       Yellowbelly pufferfish  ==============================
          Pundamilia nyererei  ==============================
                  Zebra mbuna  ==============================
        Burton's mouthbreeder  ==============================
          Princess of Burundi  ==============================
                   Coelacanth  ==============================
                X. tropicalis  ==============================
                       Lizard  ==============================
     Chinese softshell turtle  ==============================
               Painted turtle  ==============================
              Green seaturtle  ==============================
                       Turkey  ==============================
                      Chicken  ==============================
                 Mallard duck  ==============================
                Scarlet macaw  ==============================
                       Parrot  ==============================
                   Budgerigar  ==============================
           Tibetan ground jay  ==============================
                  Zebra finch  ==============================
          Medium ground finch  ==============================
       White-throated sparrow  ==============================
          Collared flycatcher  ==============================
             Peregrine falcon  ==============================
                 Saker falcon  ==============================
                  Rock pigeon  ==============================
                     Platypus  ==============================
                      Wallaby  ==============================
     Mexican tetra (cavefish)  ==============================
                         Fugu  ==============================
           American alligator  ==============================
                      Opossum  ==============================
              Tasmanian devil  ==============================

Inserts between block 8 and 9 in window
                    Aardvark 220bp

Alignment block 9 of 9 in window, 16223435 - 16223505, 71 bps 
B D                     Human  ca----catttcactctcagattcata----ttattctgatgttaccctgtc-atctc-tcattcc-act
B D                     Chimp  ca----catttcactctcagattcata----ttattctgatgttaccctgtc-atctc-tcattcc-act
B D                   Gorilla  ca----catttcactctcagattcata----ttattctgatgttaccctgtc-atctc-tcattcc-act
B D                 Orangutan  ca----catttcactctcagattcata----ttattctgatgttaccctgtc-atctc-tcattcc-act
B D                    Gibbon  ca----catttcactctcagattcata----ttattctgatgttaccctgtc-atctc-tcattcc-act
B D                    Rhesus  ca----catttcactctcagattcgta----ttattctgacgttaccctgtc-atctc-tcattcc-act
B D       Crab-eating macaque  ca----catttcactctcagattcata----ttattctgacgttaccctgtc-atctc-tcattcc-act
B D                    Baboon  ca----catttcactctcagattcgta----ttattctgacgttaccctgtc-atctc-tcattcc-act
B D              Green monkey  ca----catttcactctcagattcgta----ttattctgacgttaccctgtc-atctc-tcattcc-act
B D                  Marmoset  ca----catttcactcacagattcgta----ttattctgatattaccctgtc-atctc-tcattcc-act
B D           Squirrel monkey  ca----tatttcactcacaaattcata----ttattctgatattaccctgtc-atctc-tcactcc-act
B D                  Bushbaby  ca----cattttacttccagagtc-------ctattccaatgttaccctatc-atctc-----tcc-act
           Chinese tree shrew  ct----catttcactcccagattccta----ctgttctgatgttatcctgtc-atctc-tcattcc-act
B D                  Squirrel  ca----catttcactcccagattc-cc----cttgtt----ctttctctgtc-atctc-tcattcc-act
       Lesser Egyptian jerboa  agcacacatctcccatggttctcc-ca----gttgtga----------tgcc-a----------------
                 Prairie vole  cgtgc-cattgtgcttgcagaccc-ct----c-ttgtacagtga-ccctgtt-a----------------
B D           Chinese hamster  tgtgc-cattccatgtgtagaccc-ct----gtttttacaaagatccctggt-a----------------
               Golden hamster  ----------ccat--------cc-ct----ctttttacaaaaatccctggc-a----------------
B D                     Mouse  agcac-cacaccacatacagatcc-ct----ctctttacaacatccc-catc-a----------------
B D                       Rat  agctc-cactccacatgcagatcc-ct----ccggtcacaatgccccttgtg-g----------------
B D            Naked mole-rat  ca----catttcactcccagatcc-ga-----tgttcc---ataacactgtc-atctc-tcattcc-act
B D                Guinea pig  ca----cattgcactcccggatcc-ta----ctgttc-----------tgtc-atctc-tc-atcc-act
                   Chinchilla  ca----caactcactcccagatcc-ta----ttgttct---gtaaccatgtc-atctc-tc---------
             Brush-tailed rat  ca----cacttcactctcagaacc-ta----tttttct---gtaatcctgtc-atctc-tccttcc-aca
B D                    Rabbit  ga----catttcac-tgtaattcc-tt----ttgttccaaggatatcctgtc-atctc-tcattcc-agt
B D                      Pika  cc----catctcac-tgtgattcc-ta----ttgttctgaagttatcctgac-attgc-tcactca-act
B D                       Pig  ca----catttcactcccagat-------------tctgctgctatcctgtc-atctc-ttattct-act
B D                    Alpaca  ca----catttccttcccagatttcta----tagttctgctgttaccctgtc-atctc-gtatgcc-agt
               Bactrian camel  ca----cacttccttccgagatttcta----tagttctgctgttaccctgtc-atctc-gtatgcc-agt
B D                   Dolphin  ca----catttcattcccagattccta----cagctctgctgttaccctctcaatctcgttattgctatt
                 Killer whale  ca----catttcatttccagattccta----cagctctgctgttaccctctc-atctc-ttattgc-act
             Tibetan antelope  ta----catttcattcccaaattccta----tagctctgctgttaccctgcc-atctc-ttattcc-act
B D                       Cow  ta----catttcattcccagattccta----taactctgctgttaccctgct-gtctc-ttattcc-act
B D                     Sheep  ta----catttcatccccagattccta----tagctctgctgttaccctgcc-atctc-ctattcc-act
                Domestic goat  ta----catttcattcccagattccta----tagctttgctgttaccctgcc-atctc-ttattcc-act
B D                     Horse  ca----catttcactcccagattccta----ttgttctgctgttatcctacc-atctc-atattcc-ac-
B D          White rhinoceros  ca----catttcactcccagattccta----ttgttctgctatgatcctacc-atctc-ttattcc-ac-
B D                       Cat  ca----catttcacttccagattcctactgtctgttcttctgttaccctatc-atctc-ttattcc-act
B D                       Dog  ca----catttcacttccagattccca----ctgtttttccgttaccctgtc-atctc-tcattct-gct
B D                     Panda  ca----catttcacttccaggttccta----ctgttcgtccgttaccctgtc-atctc-ttattcc-act
               Pacific walrus  ca----catttcacttccagattccta----ctgttcttccattaccatgtc-atctc-ttattcc-act
                 Weddell seal  ca----catttcacttccagattccta----ctgttcttctgttatcgtgtc-atctc-ttattcc-act
             Black flying-fox  ca----tattttaatcccagattccta----ttcttctg--------ctgtc-atccc-ttatttc-ac-
B D                   Megabat  ca----tattttaatcccagattccta----ttcttctg--------ctgtc-atccc-ttatttc-ac-
                Big brown bat  ca----catttcactcccagattccta----ttgttctgctgtcaccctgtc-atctc-ttattcc-act
         David's myotis (bat)  ca----catttcactcccagattccta----ttgttctgctgttaccctgtc-atctc-ttattcc-act
B D                  Microbat  ca----catttcactcccagattccta----ttgttctgctgtcaccctgtc-atctc-ttattcc-act
B D                  Hedgehog  ta----catttcagtcctag--------------------------------------------------
B D                     Shrew  ca----tgtttcactctcaa-ttccta----ctgctttgcatctactctatg-ttctc-ttatttc-atg
              Star-nosed mole  ta----tatttcactcccag-cttata----at--tatgctgttaccctatt-atatc-ttatttc-act
B D                  Elephant  aa----catttcacttccatattccca----ctgttttgatgttaccgtgtt-atctc-ttattct-act
B D                   Manatee  ca----catttcactcccacagtccca----ttgttttcatgttaccctatt-ttctc-ttattct-act
             Cape golden mole  cattt-tcattcacttacgca--ctca----ctgttttgatgtt--tttgtt-atctc-atattct-cca
B D                    Tenrec  ta------------------------------cattttaatggtaccctatt-acctt--tattgt-tca
                     Aardvark  ---ta-catttcacttctatattccca----ttgttttgatgttactctgtt-agctc-ttaacct-act
B D                 Armadillo  ---tg-catttcactcctacattctta----ttgttctgatgttgccatgtc-atcac-ttattcc-act
         Cape elephant shrew  ======================================================================
B D              Nile tilapia  ======================================================================
B D                   Ferret   ----------------------------------------------------------------------
B D              Atlantic cod  ======================================================================
B D                 Tetraodon  ======================================================================
                 Spotted gar  ======================================================================
          Southern platyfish  ======================================================================
B D                 Zebrafish  ======================================================================
B D               Stickleback  ======================================================================
B D                    Medaka  ======================================================================
      Yellowbelly pufferfish  ======================================================================
         Pundamilia nyererei  ======================================================================
                 Zebra mbuna  ======================================================================
       Burton's mouthbreeder  ======================================================================
         Princess of Burundi  ======================================================================
B D                Coelacanth  ======================================================================
B D             X. tropicalis  ======================================================================
B D                    Lizard  ======================================================================
  D  Chinese softshell turtle  ======================================================================
  D            Painted turtle  ======================================================================
  D           Green seaturtle  ======================================================================
B D                    Turkey  ======================================================================
B D                   Chicken  ======================================================================
  D              Mallard duck  ======================================================================
  D             Scarlet macaw  ======================================================================
  D                    Parrot  ======================================================================
B D                Budgerigar  ======================================================================
          Tibetan ground jay  ======================================================================
B D               Zebra finch  ======================================================================
B D       Medium ground finch  ======================================================================
  D    White-throated sparrow  ======================================================================
  D       Collared flycatcher  ======================================================================
  D          Peregrine falcon  ======================================================================
  D              Saker falcon  ======================================================================
  D               Rock pigeon  ======================================================================
B D                  Platypus  ======================================================================
B D                   Wallaby  ======================================================================
    Mexican tetra (cavefish)  ======================================================================
B D                      Fugu  ======================================================================
B D        American alligator  ======================================================================
B D                   Opossum  ======================================================================
B D           Tasmanian devil  ======================================================================

                        Human  atgagtcataa---t
                        Chimp  atgagtcataa---t
                      Gorilla  atgagtcataa---t
                    Orangutan  atgagtcataa---t
                       Gibbon  atgagtcataa---t
                       Rhesus  aagagtcataa---t
          Crab-eating macaque  aagagtcataa---t
                       Baboon  aagagtcataa---t
                 Green monkey  aagagtcataa---t
                     Marmoset  gtgagtcataa---t
              Squirrel monkey  atgagtcataa---t
                     Bushbaby  atgagtcatac---t
           Chinese tree shrew  ctgagtcatac---t
                     Squirrel  atgagtcatac---t
       Lesser Egyptian jerboa  ctgcctcctccgctt
                 Prairie vole  gtgagttctac---t
              Chinese hamster  gtgagtccaac---t
               Golden hamster  gtgagtct-ac---t
                        Mouse  ctgagccctac---t
                          Rat  ctgtgacctac---t
               Naked mole-rat  atgagtcatac---t
                   Guinea pig  gtgagtcacac---t
                   Chinchilla  ---attcacac---t
             Brush-tailed rat  atgagtcatgc---t
                       Rabbit  atgagtct-ac---t
                         Pika  attagtcc-ac---t
                          Pig  atgagtcacat---g
                       Alpaca  aagagtcacag---t
               Bactrian camel  a--agtcacag---t
                      Dolphin  ga-agtcacac---c
                 Killer whale  g--agtcacac---c
             Tibetan antelope  aagagtcaaat---t
                          Cow  aagagtcacat---t
                        Sheep  aagagtcaaat---t
                Domestic goat  aagagtcaaat---t
                        Horse  -tgagccatac---a
             White rhinoceros  -tgaatcatac---t
                          Cat  atgagccatac---c
                          Dog  atgaaccatac---c
                        Panda  atgagccgtgc---t
               Pacific walrus  atgagccatac---t
                 Weddell seal  atgagccatac---t
             Black flying-fox  -tgagtcatat---t
                      Megabat  -tgagtcatat---t
                Big brown bat  atgggtcatat---t
         David's myotis (bat)  atgagtcatat---t
                     Microbat  atgagtcatat---t
                     Hedgehog  ---------ag---t
                        Shrew  ataaatcagac---t
              Star-nosed mole  gtgaatcacac---t
                     Elephant  acaagttttac---t
                      Manatee  acaagttacac---t
             Cape golden mole  ---aattacat---t
                       Tenrec  attaattatac---t
                     Aardvark  acaagttatac---t
                    Armadillo  atgagt---------
          Cape elephant shrew  ===============
                 Nile tilapia  ===============
                      Ferret   ---------------
                 Atlantic cod  ===============
                    Tetraodon  ===============
                  Spotted gar  ===============
           Southern platyfish  ===============
                    Zebrafish  ===============
                  Stickleback  ===============
                       Medaka  ===============
       Yellowbelly pufferfish  ===============
          Pundamilia nyererei  ===============
                  Zebra mbuna  ===============
        Burton's mouthbreeder  ===============
          Princess of Burundi  ===============
                   Coelacanth  ===============
                X. tropicalis  ===============
                       Lizard  ===============
     Chinese softshell turtle  ===============
               Painted turtle  ===============
              Green seaturtle  ===============
                       Turkey  ===============
                      Chicken  ===============
                 Mallard duck  ===============
                Scarlet macaw  ===============
                       Parrot  ===============
                   Budgerigar  ===============
           Tibetan ground jay  ===============
                  Zebra finch  ===============
          Medium ground finch  ===============
       White-throated sparrow  ===============
          Collared flycatcher  ===============
             Peregrine falcon  ===============
                 Saker falcon  ===============
                  Rock pigeon  ===============
                     Platypus  ===============
                      Wallaby  ===============
     Mexican tetra (cavefish)  ===============
                         Fugu  ===============
           American alligator  ===============
                      Opossum  ===============
              Tasmanian devil  ===============

View table schema

Go to Conservation track controls

Data last updated: 2015-05-06

Downloads for data in this track are available:

Description

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

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

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

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

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

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

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

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

Display Conventions and Configuration

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

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

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

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

Gap Annotation

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

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

Genomic Breaks

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

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

Base Level

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

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

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

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

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

Methods

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

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

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

Phylogenetic Tree Model

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

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

PhastCons Conservation

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

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

PhyloP Conservation

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

Conserved Elements

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

Credits

This track was created using the following programs:

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

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

References

Phylo-HMMs, phastCons, and phyloP:

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

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

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

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

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

Chain/Net:

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

Multiz:

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

Lastz (formerly Blastz):

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

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

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

Phylogenetic Tree:

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