Multiz Alignments of 100 Vertebrates
 

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Alignment block 1 of 17 in window, 49146637 - 49146642, 6 bps 
B D                   Human  tatata----
B D                   Chimp  tatata----
B D               Orangutan  tatata----
B D                  Gibbon  tatata----
B D                  Rhesus  tatat-----
B D     Crab-eating macaque  tatata----
B D            Green monkey  tatata----
B D                Marmoset  tatata----
B D         Squirrel monkey  tatgta----
B D                Bushbaby  tatata----
         Chinese tree shrew  tattta----
B D                Squirrel  taaata----
     Lesser Egyptian jerboa  catata----
               Prairie vole  cagata----
B D         Chinese hamster  cagata----
B D                   Mouse  tatata----
B D          Naked mole-rat  cctaga----
B D              Guinea pig  cctata----
                 Chinchilla  cctata----
           Brush-tailed rat  cccata----
B D                  Alpaca  tatatg----
               Killer whale  tatatg----
           Tibetan antelope  tatatg----
B D                     Cow  catatg----
B D                   Sheep  tatatg----
              Domestic goat  tatatg----
B D                   Horse  catata----
B D        White rhinoceros  catat-----
B D                     Cat  catgtc----
B D                     Dog  tatatt----
B D                 Ferret   tgtgtt----
B D                   Panda  tatttt----
             Pacific walrus  tgtgtg----
B D                Elephant  catat-----
B D                 Manatee  ---at-----
B D                  Tenrec  tatat-----
                   Aardvark  tatat-----
B D                 Opossum  tacatg----
  D            Saker falcon  tttttt----
  D        Peregrine falcon  tttttt----
  D  Spiny softshell turtle  tgtatt----
B D              Coelacanth  cataca----
B D               Tetraodon  ----cattgc
     Yellowbelly pufferfish  ----tagtat
        Princess of Burundi  ----tgatga
      Burton's mouthbreeder  ----tgatga
                Zebra mbuna  ----tgatga
        Pundamilia nyererei  ----tgatga
B D               Zebrafish  ----tatt--
B D                    Pika  ==========
B D                     Rat  ----------
B D                  Rabbit  ==========
          Black flying-fox  ----------
B D                  Baboon  ==========
B D                     Pig  ==========
B D                 Dolphin  ==========
              Weddell seal  ==========
B D                 Megabat  ----------
             Big brown bat  ----------
B D                Microbat  ----------
      David's myotis (bat)  ----------
B D               Armadillo  ==========
            Bactrian camel  ==========
B D      American alligator  ==========
B D                 Gorilla  ==========
          Cape golden mole  ==========

Inserts between block 1 and 2 in window
        Chinese tree shrew 777bp
B D               Squirrel 2bp
    Lesser Egyptian jerboa 3bp
              Prairie vole 5bp
B D        Chinese hamster 5bp
B D                  Mouse 3bp
B D                  Horse 3bp
B D       White rhinoceros 2bp
B D                    Cat 3bp
B D                    Dog 6bp
B D                Ferret  6bp
B D                  Panda 3bp
            Pacific walrus 3bp
B D             Coelacanth 1bp
B D              Tetraodon 3bp
    Yellowbelly pufferfish 9bp
       Princess of Burundi 1bp
     Burton's mouthbreeder 1bp
               Zebra mbuna 1bp
       Pundamilia nyererei 1bp

Alignment block 2 of 17 in window, 49146643 - 49146646, 4 bps 
B D                   Human  atat
B D                   Chimp  atat
B D               Orangutan  atat
B D                  Gibbon  atat
B D                  Rhesus  atat
B D     Crab-eating macaque  atat
B D            Green monkey  atat
B D                Marmoset  ttat
B D         Squirrel monkey  atat
B D                Bushbaby  at-t
B D                  Alpaca  -tac
               Killer whale  -tac
           Tibetan antelope  -tac
B D                     Cow  -tac
B D                   Sheep  -tac
              Domestic goat  -tac
B D                   Horse  acat
B D        White rhinoceros  acgc
B D                     Cat  atac
B D                     Dog  attt
B D                 Ferret   atat
B D                   Panda  agaa
             Pacific walrus  gtgt
           Black flying-fox  -cat
B D                 Megabat  -cat
              Big brown bat  -cac
       David's myotis (bat)  -cac
B D                Microbat  -cac
B D                Elephant  --at
B D                 Manatee  --at
B D                  Tenrec  --at
                   Aardvark  --ac
B D                 Opossum  ccag
  D            Saker falcon  --at
  D        Peregrine falcon  --at
B D      American alligator  ---t
  D  Spiny softshell turtle  --at
B D              Coelacanth  atat
B D               Tetraodon  acac
     Yellowbelly pufferfish  aaat
B D            Nile tilapia  --at
        Princess of Burundi  gcat
      Burton's mouthbreeder  gcat
                Zebra mbuna  gcat
        Pundamilia nyererei  gcat
B D                    Pika  ====
B D                   Mouse  ====
              Prairie vole  ====
B D                     Rat  ----
B D         Chinese hamster  ====
B D                  Rabbit  ====
    Lesser Egyptian jerboa  ====
          Brush-tailed rat  ----
                Chinchilla  ----
B D              Guinea pig  ----
B D                  Baboon  ====
B D                     Pig  ====
B D                 Dolphin  ====
              Weddell seal  ====
B D               Armadillo  ====
            Bactrian camel  ====
B D                Squirrel  ====
        Chinese tree shrew  ====
B D          Naked mole-rat  ----
B D               Zebrafish  ----
B D                 Gorilla  ====
          Cape golden mole  ====

Inserts between block 2 and 3 in window
B D               Elephant 2bp
B D                Manatee 2bp
B D                 Tenrec 14bp
                  Aardvark 4bp
  D           Saker falcon 2bp
  D       Peregrine falcon 2bp
B D     American alligator 2bp
  D Spiny softshell turtle 2bp

Alignment block 3 of 17 in window, 49146647 - 49146653, 7 bps 
B D                   Human  tcaac--------tt-----
B D                   Chimp  tcaac--------tt-----
B D               Orangutan  tcaac--------tt-----
B D                  Gibbon  tcaac--------tt-----
B D                  Rhesus  tcaac--------tt-----
B D     Crab-eating macaque  tcaac--------tt-----
B D            Green monkey  tcaac--------tt-----
B D                Marmoset  acaac--------tt-----
B D         Squirrel monkey  tcaac--------tt-----
B D                Bushbaby  tcaac--------tt-----
               Prairie vole  --------------c-----
B D         Chinese hamster  --------------c-----
B D                 Opossum  tacaa--------gt-----
  D            Saker falcon  tgtat---------------
  D        Peregrine falcon  tgtat---------------
B D      American alligator  tgaat---------------
  D  Spiny softshell turtle  tcaaagaacga---------
B D              Coelacanth  --------ctttttt-----
B D               Tetraodon  -------------tcaaaat
     Yellowbelly pufferfish  -------------gtaaaat
B D            Nile tilapia  -------------ttctcat
        Princess of Burundi  -------------ttcacat
      Burton's mouthbreeder  -------------ttcacat
                Zebra mbuna  -------------ttcacat
        Pundamilia nyererei  -------------ttcacat
B D                    Pika  ====================
B D                   Mouse  ====================
B D                     Rat  --------------------
B D                  Rabbit  ====================
          Black flying-fox  --------------------
    Lesser Egyptian jerboa  ====================
B D                  Tenrec  ====================
          Brush-tailed rat  --------------------
                Chinchilla  --------------------
B D              Guinea pig  --------------------
B D                  Baboon  ====================
B D                     Pig  ====================
B D                 Dolphin  ====================
              Weddell seal  ====================
B D                 Megabat  --------------------
              Killer whale  --------------------
B D                   Panda  --------------------
             Big brown bat  --------------------
B D                     Cow  --------------------
             Domestic goat  --------------------
B D                   Sheep  --------------------
          Tibetan antelope  --------------------
B D                Microbat  --------------------
      David's myotis (bat)  --------------------
B D               Armadillo  ====================
B D                 Manatee  ====================
B D                Elephant  ====================
B D        White rhinoceros  --------------------
B D                   Horse  --------------------
            Bactrian camel  ====================
B D                  Alpaca  --------------------
B D                Squirrel  ====================
        Chinese tree shrew  ====================
B D          Naked mole-rat  --------------------
B D                     Dog  --------------------
B D                 Ferret   --------------------
B D                     Cat  --------------------
            Pacific walrus  --------------------
B D               Zebrafish  --------------------
B D                 Gorilla  ====================
          Cape golden mole  ====================
                  Aardvark  ====================

Inserts between block 3 and 4 in window
B D     American alligator 4bp
  D Spiny softshell turtle 3bp

Alignment block 4 of 17 in window, 49146654 - 49146655, 2 bps 
B D                   Human  ta
B D                   Chimp  ta
B D               Orangutan  ta
B D                  Gibbon  ta
B D                  Rhesus  ta
B D     Crab-eating macaque  ta
B D            Green monkey  ta
B D                Marmoset  ta
B D         Squirrel monkey  ta
B D                Bushbaby  ta
B D                Squirrel  -c
     Lesser Egyptian jerboa  -t
               Prairie vole  cc
B D         Chinese hamster  at
B D                   Mouse  -g
B D          Naked mole-rat  -a
B D              Guinea pig  -a
                 Chinchilla  -g
           Brush-tailed rat  -a
B D                 Opossum  tt
  D            Saker falcon  tc
  D        Peregrine falcon  tc
  D     Collared flycatcher  tg
B D      American alligator  tt
B D              Coelacanth  tg
B D               Tetraodon  ag
     Yellowbelly pufferfish  tg
B D            Nile tilapia  tg
        Princess of Burundi  tg
      Burton's mouthbreeder  tg
                Zebra mbuna  tg
        Pundamilia nyererei  tg
B D                    Pika  ==
B D                     Rat  --
B D                  Rabbit  ==
          Black flying-fox  --
B D                  Tenrec  ==
B D                  Baboon  ==
B D                     Pig  ==
B D                 Dolphin  ==
              Weddell seal  ==
B D                 Megabat  --
              Killer whale  --
B D                   Panda  --
             Big brown bat  --
B D                     Cow  --
             Domestic goat  --
B D                   Sheep  --
          Tibetan antelope  --
B D                Microbat  --
      David's myotis (bat)  --
B D               Armadillo  ==
B D                 Manatee  ==
B D                Elephant  ==
B D        White rhinoceros  --
B D                   Horse  --
            Bactrian camel  ==
B D                  Alpaca  --
        Chinese tree shrew  ==
B D                     Dog  --
B D                 Ferret   --
B D                     Cat  --
            Pacific walrus  --
B D               Zebrafish  --
  D  Spiny softshell turtle  ==
B D                 Gorilla  ==
          Cape golden mole  ==
                  Aardvark  ==

Inserts between block 4 and 5 in window
  D           Saker falcon 22bp
  D       Peregrine falcon 22bp
B D     American alligator 1bp

Alignment block 5 of 17 in window, 49146656 - 49146669, 14 bps 
B D                   Human  ttt-----------------------caaat--------at-----------acca------------
B D                   Chimp  ttt-----------------------caaat--------at-----------acca------------
B D               Orangutan  ttt-----------------------caaat--------at-----------acca------------
B D                  Gibbon  ttt-----------------------caaat--------at-----------acca------------
B D                  Rhesus  ttt-----------------------caaat--------at-----------acca------------
B D     Crab-eating macaque  ttt-----------------------caaat--------at-----------acca------------
B D            Green monkey  ttt-----------------------caaat--------at-----------acca------------
B D                Marmoset  ttt-----------------------caaat--------at-----------gcca------------
B D         Squirrel monkey  ttt-----------------------caaat--------at-----------acca------------
B D                Bushbaby  ttt-----------------------tcagc--------tt-----------atca------------
B D                Squirrel  tcc-----------------------cacat---ttat-tt-----------ctta------------
     Lesser Egyptian jerboa  ccc-----------------------cacca--------tt-----------tact------------
               Prairie vole  gat-----------------------cataaaatctcatat-----------attt------------
B D         Chinese hamster  aat-----------------------cataaaatctca-ac-----------ctgt------------
B D                   Mouse  ctc-----------------------catag---ttcc-at-----------aggg------------
B D                     Rat  -tc-----------------------cacaa--------at-----------cagt------------
B D          Naked mole-rat  tct-----------------------cac----------ac-----------tttt------------
B D              Guinea pig  tct-----------------------cac----------ac-----------tttt------------
                 Chinchilla  tct-----------------------cac----------gc-----------tttt------------
           Brush-tailed rat  tct-----------------------cac----------gc-----------tttt------------
B D                  Alpaca  ---------------------------------------ac-----------aagt------------
               Killer whale  ---------------------------------------at-----------aact------------
           Tibetan antelope  ---------------------------------------ac-----------aact------------
B D                     Cow  ---------------------------------------ac-----------aact------------
B D                   Sheep  ---------------------------------------ac-----------aact------------
              Domestic goat  ---------------------------------------ac-----------aact------------
B D                   Horse  ---------------------------------------ac-----------aact------------
B D        White rhinoceros  ---------------------------------------ac-----------aact------------
B D                     Cat  ---------------------------------------atacacatatacatagt------------
B D                     Dog  ---------------------------------------tt-----------tagt------------
B D                 Ferret   ---------------------------------------tt-----------tagt------------
B D                   Panda  ---------------------------------------ac-----------cagt------------
             Pacific walrus  ---------------------------------------ac--------gtgtatt------------
           Black flying-fox  ---------------------------------------ac-----------aact------------
B D                 Megabat  ---------------------------------------ac-----------aact------------
              Big brown bat  ---------------------------------------ac-----------aact------------
       David's myotis (bat)  ---------------------------------------ac-----------aact------------
B D                Microbat  ---------------------------------------ac-----------aact------------
B D                Elephant  ---------------------------------------cc-----------gact------------
B D                 Manatee  ---------------------------------------cc-----------aatt------------
B D                  Tenrec  ---------------------------------------cc-----------aact------------
                   Aardvark  ---------------------------------------aa-----------ggtt------------
B D               Armadillo  ---------------------------------------cc-----------atct------------
B D                 Opossum  gtt-----------------------gagat--------at-----------tccc------------
  D            Saker falcon  ttt-----------------------taaat--------ac-----------tcgg------------
  D        Peregrine falcon  ttt-----------------------taaat--------ac-----------tcgg------------
  D     Collared flycatcher  ttt-----------------------caaat--------gc-----------tcca------------
  D  White-throated sparrow  ttt-----------------------caagt--------gc-----------tcca------------
B D             Zebra finch  ttt-----------------------caaat--------gc-----------tcca------------
B D      American alligator  tttggtaataaccctactcatgttggtaaat--------gc-----------tcta------------
  D  Spiny softshell turtle  ttttaacataattctgctcatatctctaaat--------gc-----------tctg------------
B D              Coelacanth  ----------------------------------------c-----------taca------------
B D               Tetraodon  ----------------------------------------------------ttac---------aat
     Yellowbelly pufferfish  ----------------------------------------------------tttt-----tgtaagt
B D            Nile tilapia  ----------------------------------------------------ttcttcaggtctaggt
        Princess of Burundi  ----------------------------------------------------ttctgcaggtctagat
      Burton's mouthbreeder  ----------------------------------------------------ttctgcaggtctaggt
                Zebra mbuna  ----------------------------------------------------ttctgcaggtctaggt
        Pundamilia nyererei  ----------------------------------------------------ttctgcaggtctaggt
B D               Zebrafish  ------------------------------------------------------------ctataagt
B D                    Pika  ====================================================================
B D                  Rabbit  ====================================================================
B D                  Baboon  ====================================================================
B D                     Pig  ====================================================================
B D                 Dolphin  ====================================================================
              Weddell seal  ====================================================================
            Bactrian camel  ====================================================================
        Chinese tree shrew  ====================================================================
B D                 Gorilla  ====================================================================
          Cape golden mole  ====================================================================

Inserts between block 5 and 6 in window
B D                 Alpaca 12bp
              Killer whale 2bp
          Tibetan antelope 2bp
B D                    Cow 2bp
B D                  Sheep 2bp
             Domestic goat 2bp
B D                  Horse 12bp
B D       White rhinoceros 12bp
B D                    Cat 13bp
B D                    Dog 11bp
B D                Ferret  11bp
B D                  Panda 36bp
            Pacific walrus 15bp
          Black flying-fox 12bp
B D                Megabat 12bp
             Big brown bat 12bp
      David's myotis (bat) 12bp
B D               Microbat 13bp
B D               Elephant 3bp
B D                Manatee 2bp
                  Aardvark 8bp
B D              Armadillo 2bp
B D             Coelacanth 3bp

Alignment block 6 of 17 in window, 49146670 - 49146679, 10 bps 
B D                   Human  at-------tttaaaat
B D                   Chimp  at-------tttaaaat
B D               Orangutan  at-------tttaaaat
B D                  Gibbon  at-------tttaaaat
B D                  Rhesus  at-------tttaaaat
B D     Crab-eating macaque  at-------tttaaaat
B D            Green monkey  at-------tttaaaat
B D                Marmoset  at-------tttaaaat
B D         Squirrel monkey  at-------tttaaaat
B D                Bushbaby  atatattcatttttaat
B D                Squirrel  at---------------
     Lesser Egyptian jerboa  at---------------
               Prairie vole  at---------------
B D         Chinese hamster  at---------------
B D                   Mouse  at---------------
B D                     Rat  tt---------------
B D          Naked mole-rat  at---------------
B D              Guinea pig  at---------------
                 Chinchilla  at---------------
           Brush-tailed rat  a----------------
             Bactrian camel  ---------------at
               Killer whale  ---------------at
           Tibetan antelope  ---------------ac
B D                     Cow  ---------------ac
B D                   Sheep  ---------------ac
              Domestic goat  ---------------ac
B D                Elephant  --------ttttttagt
B D                 Manatee  --------ttttttagt
B D                  Tenrec  --------tttttgagg
                   Aardvark  --------ttttttctt
B D               Armadillo  --------gttttgagt
B D                 Opossum  -------------caat
  D            Saker falcon  ---------ttt-----
  D        Peregrine falcon  ---------ttt-----
  D     Collared flycatcher  ---------tttttaag
  D  White-throated sparrow  ---------tttttaaa
B D             Zebra finch  ---------tttttaag
B D      American alligator  ---------tttctgat
  D  Spiny softshell turtle  ---------tttttgag
B D              Coelacanth  -------actttat---
B D               Tetraodon  -------aatatttag-
     Yellowbelly pufferfish  -------cattttaaa-
B D            Nile tilapia  -------gttctggaaa
        Princess of Burundi  -------gttctggaaa
      Burton's mouthbreeder  -------gttctggaaa
                Zebra mbuna  -------gttctggaaa
        Pundamilia nyererei  -------gttctggaaa
B D               Zebrafish  -------cacctcttaa
B D                    Pika  =================
B D                  Rabbit  =================
          Black flying-fox  =================
B D                  Baboon  =================
B D                     Pig  =================
B D                 Dolphin  =================
              Weddell seal  =================
B D                 Megabat  =================
B D                   Panda  =================
             Big brown bat  =================
B D                Microbat  =================
      David's myotis (bat)  =================
B D        White rhinoceros  =================
B D                   Horse  =================
B D                  Alpaca  =================
        Chinese tree shrew  =================
B D                     Dog  =================
B D                 Ferret   =================
B D                     Cat  =================
            Pacific walrus  =================
B D                 Gorilla  =================
          Cape golden mole  =================

Inserts between block 6 and 7 in window
            Bactrian camel 8bp
              Killer whale 8bp
          Tibetan antelope 8bp
B D                    Cow 8bp
B D                  Sheep 8bp
             Domestic goat 8bp
B D                Opossum 7bp
  D           Saker falcon 1bp
  D       Peregrine falcon 1bp
  D    Collared flycatcher 3bp
  D White-throated sparrow 3bp
B D            Zebra finch 3bp
B D     American alligator 3bp
  D Spiny softshell turtle 3bp
B D             Coelacanth 1bp

Alignment block 7 of 17 in window, 49146680 - 49146681, 2 bps 
B D                   Human  --tt
B D                   Chimp  --tt
B D               Orangutan  --tt
B D                  Gibbon  --tt
B D                  Rhesus  --tt
B D     Crab-eating macaque  --tt
B D            Green monkey  --tt
B D                Marmoset  --tt
B D         Squirrel monkey  --tt
B D                Bushbaby  --tt
         Chinese tree shrew  --tt
B D                Squirrel  --tt
     Lesser Egyptian jerboa  --tt
               Prairie vole  --tt
B D         Chinese hamster  --tt
B D                   Mouse  --tt
B D                     Rat  --tt
B D          Naked mole-rat  --tt
B D              Guinea pig  --tt
                 Chinchilla  --tt
           Brush-tailed rat  --tt
B D                  Alpaca  --tt
             Bactrian camel  --tt
               Killer whale  --tt
           Tibetan antelope  --tt
B D                     Cow  --tt
B D                   Sheep  --tt
              Domestic goat  --tt
B D                   Horse  --tt
B D        White rhinoceros  --tt
B D                     Cat  --tt
           Black flying-fox  --tt
B D                 Megabat  --tt
              Big brown bat  --tt
       David's myotis (bat)  --tt
B D                Microbat  --tt
B D                Elephant  --ct
B D                 Manatee  --ct
B D                  Tenrec  --tt
                   Aardvark  --ct
B D               Armadillo  --tt
B D                 Opossum  --c-
  D            Saker falcon  --tc
  D        Peregrine falcon  --tc
  D     Collared flycatcher  --tc
  D  White-throated sparrow  --tc
B D             Zebra finch  --tc
B D      American alligator  --tt
  D  Spiny softshell turtle  --tc
B D              Coelacanth  --t-
B D            Nile tilapia  ac--
        Princess of Burundi  ac--
      Burton's mouthbreeder  ac--
                Zebra mbuna  ac--
        Pundamilia nyererei  ac--
B D               Zebrafish  ga--
B D                    Pika  ====
B D                  Rabbit  ====
B D                  Baboon  ====
B D                     Pig  ====
B D                 Dolphin  ====
              Weddell seal  ====
B D                   Panda  ====
B D                     Dog  ====
B D                 Ferret   ====
            Pacific walrus  ====
B D               Tetraodon  ----
    Yellowbelly pufferfish  ----
B D                 Gorilla  ====
          Cape golden mole  ====

Inserts between block 7 and 8 in window
  D           Saker falcon 8bp
  D       Peregrine falcon 8bp
  D    Collared flycatcher 8bp
  D White-throated sparrow 8bp
B D            Zebra finch 8bp
B D     American alligator 7bp
  D Spiny softshell turtle 7bp
B D             Coelacanth 5bp

Alignment block 8 of 17 in window, 49146682 - 49146692, 11 bps 
B D                   Human  ------atcaatatac-c
B D                   Chimp  ------atcaatatac-c
B D               Orangutan  ------atcaatatac-c
B D                  Gibbon  ------atcaatatac-c
B D                  Rhesus  ------atcaatatac-c
B D     Crab-eating macaque  ------atcaatatac-c
B D            Green monkey  ------atcaatatac-c
B D                Marmoset  ------atcaatatac-c
B D         Squirrel monkey  ------atcagtatac-c
B D                Bushbaby  ------ataaatatac-c
         Chinese tree shrew  ------atcaatatac-c
B D                Squirrel  ------gtcaattgat--
     Lesser Egyptian jerboa  ------attcattaat--
               Prairie vole  ------ttctatatag--
B D         Chinese hamster  ------ttctatatag--
B D          Naked mole-rat  ------ttcagt------
B D              Guinea pig  ------ttcagt------
                 Chinchilla  ------ttcagt------
           Brush-tailed rat  ------ttcagt------
B D                    Pika  ------atgaatatggc-
B D                  Alpaca  ------atcaatacat-a
             Bactrian camel  ------atcaatacat-a
               Killer whale  ------atctgtacat-c
           Tibetan antelope  ------atcaatacat-c
B D                     Cow  ------atcaattcat-c
B D                   Sheep  ------atcaatacat-c
              Domestic goat  ------atcaatacat-c
B D                   Horse  ------atcaatacat-c
B D        White rhinoceros  ------atcagtgcac-c
B D                     Cat  ------accaatacac-c
B D                     Dog  ---------aatacag-c
B D                 Ferret   ---------aatatgc-c
B D                   Panda  ---------aatacac-c
             Pacific walrus  ---------aatatgc-c
           Black flying-fox  ------atcagtgctc-c
B D                 Megabat  ------atcagtgctc-c
              Big brown bat  ------gtcaatacag-c
       David's myotis (bat)  ------gtcaatacac-c
B D                Microbat  ------gtcaatacac-c
B D                Elephant  ------atcaacatgg-c
B D                 Manatee  ------atcagtatgc-c
B D                  Tenrec  ------atcagtatgt-c
                   Aardvark  ------atcagtatgg-c
B D               Armadillo  ------attaacacat-c
B D                 Opossum  ------atccattttg-c
  D            Saker falcon  ------gtc---------
  D        Peregrine falcon  ------gtc---------
  D     Collared flycatcher  ------gtc---------
  D  White-throated sparrow  ------gtc---------
B D             Zebra finch  ------gtc---------
B D      American alligator  ------gtt---------
  D  Spiny softshell turtle  ------gtc---------
B D              Coelacanth  ------aacaat------
B D               Tetraodon  ---caggaaaa-------
     Yellowbelly pufferfish  ---ctgattta-------
B D            Nile tilapia  atccaaataaa-------
        Princess of Burundi  atccagataaa-------
      Burton's mouthbreeder  atccagataaa-------
                Zebra mbuna  atccagataaa-------
        Pundamilia nyererei  atccagataaa-------
B D               Zebrafish  gccagaccaaa-------
B D                   Mouse  ------------------
B D                     Rat  ------------------
B D                  Rabbit  ==================
B D                  Baboon  ==================
B D                     Pig  ==================
B D                 Dolphin  ==================
              Weddell seal  ==================
B D                 Gorilla  ==================
          Cape golden mole  ==================

Alignment block 9 of 17 in window, 49146693 - 49146706, 14 bps 
B D                   Human  cattacgatt----cttt------
B D                   Chimp  cattatgatt----cttt------
B D               Orangutan  cattatgatt----cttt------
B D                  Gibbon  cattatggtt----cttt------
B D                  Rhesus  cattctgatt----cttt------
B D     Crab-eating macaque  cattctgatt----cttt------
B D            Green monkey  cattatgatt----cttt------
B D                Marmoset  caccatgatt----cttt------
B D         Squirrel monkey  cgctgttatt----cttt------
B D                Bushbaby  tgtcatgatt----cttt------
         Chinese tree shrew  caccatgatt----ctt-------
     Lesser Egyptian jerboa  ---------------gta------
               Prairie vole  ---------------gtt------
B D         Chinese hamster  ---------------gtc------
B D                  Rabbit  cactatggtt----cttt------
B D                    Pika  cattatgatt----cttt------
B D                  Alpaca  catcatgatt----cttc------
             Bactrian camel  catcatgatt----cttc------
               Killer whale  caacatgatt----cttt------
           Tibetan antelope  caacatgttt----cttt------
B D                     Cow  caacatgatt----cttt------
B D                   Sheep  caacatgatt----cttt------
              Domestic goat  caacatgatt----cttt------
B D                   Horse  catcacgatt----cttt------
B D        White rhinoceros  catcatgatt----cttt------
B D                     Cat  at----------------------
B D                     Dog  tttcatgatt----ct--------
B D                 Ferret   ttttatgatt----cttt------
B D                   Panda  tttcatgatt----cttt------
             Pacific walrus  tttcacgatt----cttt------
           Black flying-fox  catgaagatt----cttt------
B D                 Megabat  catgaagatt----cttt------
              Big brown bat  catgaggatt----cttt------
       David's myotis (bat)  catgaggatt----cttt------
B D                Microbat  catgaggatt----cttt------
B D                Elephant  catgatgatt----cttt------
B D                 Manatee  caggatgatt----cttt------
B D                  Tenrec  tgtagtgatt----tctt------
                   Aardvark  catgatgatt----cttt------
B D               Armadillo  catgatggtt----cttt------
B D                 Opossum  tatcaggcat----ttt-------
  D            Saker falcon  -acacatagt----cttc------
  D        Peregrine falcon  -acacatagt----cttc------
  D     Collared flycatcher  -acatttagt----ctcc------
  D  White-throated sparrow  -acgtttagt----cttt------
B D             Zebra finch  -agatttagt----cttc------
B D      American alligator  -gaat-cagtagaaattc------
  D  Spiny softshell turtle  -aactccagt----ct--------
B D              Coelacanth  attcataact----cggc------
B D               Tetraodon  --tat----t----ccttattgtt
     Yellowbelly pufferfish  --tag----t----cc----catc
B D            Nile tilapia  --catggact----cccatctgtg
        Princess of Burundi  --catgggtt----ctcatgtgtg
      Burton's mouthbreeder  --catggatt----cccatgtgtg
                Zebra mbuna  --catggatt----cccatgtgtg
        Pundamilia nyererei  --catggatt----cccatgtgtg
B D               Zebrafish  --tctcaagt----cccttatagt
B D                   Mouse  ------------------------
B D                     Rat  ------------------------
          Brush-tailed rat  ------------------------
                Chinchilla  ------------------------
B D              Guinea pig  ------------------------
B D                  Baboon  ========================
B D                     Pig  ========================
B D                 Dolphin  ========================
              Weddell seal  ========================
B D                Squirrel  ------------------------
B D          Naked mole-rat  ------------------------
B D                 Gorilla  ========================
          Cape golden mole  ========================

Inserts between block 9 and 10 in window
  D           Saker falcon 1bp
  D       Peregrine falcon 1bp
  D    Collared flycatcher 1bp
  D White-throated sparrow 1bp
B D            Zebra finch 1bp
B D     American alligator 1bp

Alignment block 10 of 17 in window, 49146707 - 49146708, 2 bps 
B D                   Human  ct
B D                   Chimp  ct
B D               Orangutan  at
B D                  Gibbon  ct
B D                  Rhesus  ct
B D     Crab-eating macaque  ct
B D                  Baboon  ct
B D            Green monkey  ct
B D                Marmoset  ct
B D         Squirrel monkey  ct
B D                Bushbaby  ct
         Chinese tree shrew  ct
     Lesser Egyptian jerboa  ca
               Prairie vole  ct
B D         Chinese hamster  at
B D                  Rabbit  ct
B D                    Pika  ct
B D                  Alpaca  -c
             Bactrian camel  -c
B D                 Dolphin  -c
               Killer whale  -c
           Tibetan antelope  -c
B D                     Cow  -c
B D                   Sheep  -c
              Domestic goat  -c
B D                   Horse  -c
B D        White rhinoceros  -c
B D                 Ferret   -c
B D                   Panda  -c
             Pacific walrus  -c
               Weddell seal  -c
           Black flying-fox  -c
B D                 Megabat  -c
              Big brown bat  -c
       David's myotis (bat)  -c
B D                Microbat  -c
B D                Elephant  -c
B D                 Manatee  -c
B D                  Tenrec  -t
                   Aardvark  -c
B D               Armadillo  -c
B D                 Opossum  ct
  D            Saker falcon  tt
  D        Peregrine falcon  tt
  D     Collared flycatcher  tt
  D  White-throated sparrow  ct
B D             Zebra finch  ct
B D      American alligator  ct
B D              Coelacanth  tt
B D               Tetraodon  ac
     Yellowbelly pufferfish  ac
B D            Nile tilapia  tt
        Princess of Burundi  tt
      Burton's mouthbreeder  tt
                Zebra mbuna  tt
        Pundamilia nyererei  tt
B D               Zebrafish  ca
B D                   Mouse  --
B D                     Rat  --
          Brush-tailed rat  --
                Chinchilla  --
B D              Guinea pig  --
B D                     Pig  ==
B D                Squirrel  --
B D          Naked mole-rat  --
B D                     Dog  --
B D                     Cat  --
  D  Spiny softshell turtle  --
B D                 Gorilla  ==
          Cape golden mole  ==

Inserts between block 10 and 11 in window
B D                 Baboon 291bp
B D                 Alpaca 1bp
            Bactrian camel 1bp
B D                Dolphin 288bp
              Killer whale 1bp
B D                  Horse 1bp
B D       White rhinoceros 1bp
B D                Ferret  1bp
B D                  Panda 1bp
            Pacific walrus 1bp
              Weddell seal 287bp
          Black flying-fox 1bp
B D                Megabat 1bp
             Big brown bat 1bp
      David's myotis (bat) 1bp
B D               Microbat 1bp
B D               Elephant 1bp
B D                Manatee 1bp
B D                 Tenrec 1bp
                  Aardvark 1bp
B D              Armadillo 1bp

Alignment block 11 of 17 in window, 49146709 - 49146717, 9 bps 
B D                   Human  -gagtg-------acat
B D                   Chimp  -gagtg-------acat
B D               Orangutan  -gggtg-------tcaa
B D                  Gibbon  -gagtg-------acat
B D                  Rhesus  -gaatg-------acat
B D     Crab-eating macaque  -gaatg-------acat
B D            Green monkey  -gaatg-------acat
B D                Marmoset  -gagtg-------atat
B D         Squirrel monkey  -gagtg-------atat
B D                Bushbaby  -gagtg-------atct
         Chinese tree shrew  -gagtg-------gtat
B D                Squirrel  ---------------at
     Lesser Egyptian jerboa  -cagtg-------acat
               Prairie vole  -cccaa-------taat
B D         Chinese hamster  -cccaa-------taat
B D          Naked mole-rat  ---------------gt
B D              Guinea pig  ---------------gt
                 Chinchilla  ---------------gg
           Brush-tailed rat  ---------------gt
B D                  Rabbit  -gactg-------atat
B D                    Pika  -gattg-------acac
B D                  Alpaca  -gcctg-------atgc
             Bactrian camel  -gcctg-------atgc
               Killer whale  -gagtg-------atac
           Tibetan antelope  ----tg-------atac
B D                     Cow  ----tg-------attc
B D                   Sheep  ----tg-------atac
              Domestic goat  ----tg-------atac
B D                   Horse  -gagtg-------atat
B D        White rhinoceros  -gagtg-------atat
B D                     Cat  --agtg-------atat
B D                     Dog  -gagtg-------acag
B D                 Ferret   -gagcg-------acag
B D                   Panda  -gagtg-------atag
             Pacific walrus  -gagtg-------atag
           Black flying-fox  -gagtg-------atag
B D                 Megabat  -gagtgatagaccatag
              Big brown bat  -gagca-------acag
       David's myotis (bat)  -gagtg-------acag
B D                Microbat  -gagtg-------acag
B D                Elephant  -------------gagt
B D                 Manatee  -------------gagt
B D                  Tenrec  -------------aggt
                   Aardvark  -------------gagt
B D               Armadillo  -------------gagt
B D                 Opossum  -gaaag-------atgc
  D            Saker falcon  -----g-------atga
  D        Peregrine falcon  -----g-------atga
  D     Collared flycatcher  -----g-------atga
  D  White-throated sparrow  -----g-------acga
B D             Zebra finch  -----g-------atga
B D      American alligator  -----g-----------
B D              Coelacanth  -----------gtacat
B D               Tetraodon  attttg-------ggt-
     Yellowbelly pufferfish  aaccac-------ggt-
B D            Nile tilapia  gaactg-------gaa-
        Princess of Burundi  aaactg-------gag-
      Burton's mouthbreeder  gaactg-------gag-
                Zebra mbuna  gaactg-------gag-
        Pundamilia nyererei  gaactg-------gag-
B D               Zebrafish  ctattg-------tat-
B D                   Mouse  -----------------
B D                     Rat  -----------------
B D                  Baboon  =================
B D                     Pig  =================
B D                 Dolphin  =================
              Weddell seal  =================
  D  Spiny softshell turtle  -----------------
B D                 Gorilla  =================
          Cape golden mole  =================

Inserts between block 11 and 12 in window
  D           Saker falcon 4bp
  D       Peregrine falcon 4bp
  D    Collared flycatcher 4bp
  D White-throated sparrow 4bp
B D            Zebra finch 4bp
B D     American alligator 3bp
B D             Coelacanth 3bp

Alignment block 12 of 17 in window, 49146718 - 49146727, 10 bps 
B D                   Human  acca----cacaaa
B D                   Chimp  acca----cacaaa
B D               Orangutan  acca----cacata
B D                  Gibbon  acca----cacaaa
B D                  Rhesus  acca----cacaaa
B D     Crab-eating macaque  acca----cacaaa
B D            Green monkey  acca----cacaaa
B D                Marmoset  atc-----cacaaa
B D         Squirrel monkey  atc-----cacaaa
B D                Bushbaby  acca----tacaaa
         Chinese tree shrew  acca----taccaa
B D                Squirrel  acca----tacaaa
     Lesser Egyptian jerboa  acca----caccaa
               Prairie vole  atca----taccta
B D         Chinese hamster  atca----taccta
B D          Naked mole-rat  atca----tagcag
B D              Guinea pig  atca----cagcca
                 Chinchilla  atca----cagcag
           Brush-tailed rat  ctca----cagcgg
B D                  Rabbit  acca----tacaaa
B D                    Pika  gcca----catcga
B D                  Alpaca  gtcg----caccag
             Bactrian camel  gtcg----caccag
               Killer whale  atca----tactaa
           Tibetan antelope  atca----taccaa
B D                     Cow  atca----ttccaa
B D                   Sheep  atca----taccaa
              Domestic goat  atca----taccaa
B D                   Horse  acga----caccaa
B D        White rhinoceros  acca----taccaa
B D                     Cat  acc-----taccta
B D                     Dog  acca----tcccta
B D                 Ferret   acca----caccta
B D                   Panda  acca----taccta
             Pacific walrus  acca----taccta
           Black flying-fox  acca----taccaa
B D                 Megabat  acca----taccaa
              Big brown bat  ---a----taccaa
       David's myotis (bat)  ---a----tactaa
B D                Microbat  ---a----tactaa
B D                Elephant  aatt----caccaa
B D                 Manatee  aatt----catcaa
B D                  Tenrec  cgtt----tactaa
                   Aardvark  aact----caccaa
B D               Armadillo  aatt----caccaa
B D                 Opossum  tcag----ctttta
B D                Platypus  accc----cacaaa
  D            Saker falcon  gttg----ttgata
  D        Peregrine falcon  gttg----ttgata
  D     Collared flycatcher  attg----tctata
  D  White-throated sparrow  attg----ctcata
B D             Zebra finch  attg----ttcata
B D              Coelacanth  ttct----tgaata
B D               Tetraodon  gttt----------
     Yellowbelly pufferfish  agct----caaaac
B D            Nile tilapia  atgt----tataat
        Princess of Burundi  atct----tataat
      Burton's mouthbreeder  atct----tataat
                Zebra mbuna  atct----tataat
        Pundamilia nyererei  atct----tataat
B D               Zebrafish  gtttagagtactat
B D                   Mouse  --------------
B D                     Rat  --------------
B D                  Baboon  ==============
B D                     Pig  ==============
B D                 Dolphin  ==============
              Weddell seal  ==============
  D  Spiny softshell turtle  --------------
B D      American alligator  ==============
B D                 Gorilla  ==============
          Cape golden mole  ==============

Inserts between block 12 and 13 in window
B D             Coelacanth 1bp

Alignment block 13 of 17 in window, 49146728 - 49146734, 7 bps 
B D                   Human  --ttcaa-ta
B D                   Chimp  --ttcaa-ta
B D               Orangutan  --ttcaa-ta
B D                  Gibbon  --ttcaa-ta
B D                  Rhesus  --ttcaa-ta
B D     Crab-eating macaque  --ttcaa-ta
B D            Green monkey  --ttcag-ta
B D                Marmoset  --ttcat-tg
B D         Squirrel monkey  --ttcaa-tg
B D                Bushbaby  --ttcag-ta
         Chinese tree shrew  --ttcaa-ta
B D                Squirrel  --ttcaa-cc
     Lesser Egyptian jerboa  --ctcaa-tg
               Prairie vole  --ctaaa-ta
B D         Chinese hamster  --ctaaa-ta
B D                   Mouse  --------tg
B D                     Rat  --------ta
B D          Naked mole-rat  --ttcaa-ca
B D              Guinea pig  --ttcag-ca
                 Chinchilla  --ttcag-ca
           Brush-tailed rat  --gtcag-ca
B D                  Rabbit  --ttcag-tt
B D                    Pika  --ttcag-ca
B D                  Alpaca  --ctcag-tg
             Bactrian camel  --ctcag-tg
               Killer whale  --ttca---a
           Tibetan antelope  --ttcag-ta
B D                     Cow  --ttcag-ta
B D                   Sheep  --ttcag-ta
              Domestic goat  --ctcag-ta
B D                   Horse  --ttcaa-ta
B D        White rhinoceros  --atcaa-ta
B D                     Cat  --ttcaa-ca
B D                     Dog  --tttaa-ta
B D                 Ferret   --gtcag-ta
B D                   Panda  --ttcaa-ag
             Pacific walrus  --ttcaa-ta
           Black flying-fox  --ttcaa--a
B D                 Megabat  --ttcaa--a
              Big brown bat  --ctcaa-ct
       David's myotis (bat)  --ttcaa-ta
B D                Microbat  --ttcaa-ta
B D                Elephant  --ctcag-ta
B D                 Manatee  --ctcag-ta
B D                  Tenrec  --ttcaa-ta
                   Aardvark  --ctcaa-ta
B D               Armadillo  --ttcaa-tg
B D                 Opossum  --catgc-ta
B D                Platypus  --ccc-----
  D            Saker falcon  --------t-
  D        Peregrine falcon  --------t-
  D     Collared flycatcher  --------t-
  D  White-throated sparrow  --------t-
B D             Zebra finch  --------t-
  D          Painted turtle  --ttcactt-
  D  Spiny softshell turtle  --ttcactt-
B D              Coelacanth  --cttat-ga
     Yellowbelly pufferfish  --tcaga---
B D            Nile tilapia  tgtcaaa---
        Princess of Burundi  tgtcaag---
      Burton's mouthbreeder  tgtcaaa---
                Zebra mbuna  tgtcaaa---
        Pundamilia nyererei  tgtcaaa---
B D               Zebrafish  tatttag---
B D                  Baboon  ==========
B D                     Pig  ==========
B D                 Dolphin  ==========
              Weddell seal  ==========
B D               Tetraodon  ----------
B D      American alligator  ==========
B D                 Gorilla  ==========
          Cape golden mole  ==========

Inserts between block 13 and 14 in window
B D                Opossum 3bp
  D White-throated sparrow 1bp
B D            Zebra finch 1bp

Alignment block 14 of 17 in window, 49146735 - 49146741, 7 bps 
B D                   Human  cggattc
B D                   Chimp  tggattc
B D               Orangutan  cagattc
B D                  Gibbon  cagattc
B D                  Rhesus  tggattc
B D     Crab-eating macaque  tggattc
B D            Green monkey  tggattc
B D                Marmoset  tgggttc
B D         Squirrel monkey  tggattc
B D                Bushbaby  tgaattc
         Chinese tree shrew  cgggttc
B D                Squirrel  tgaggtt
     Lesser Egyptian jerboa  cttgctc
               Prairie vole  tggactc
B D         Chinese hamster  gggattc
B D                   Mouse  tg-attc
B D                     Rat  tgaattc
B D          Naked mole-rat  ggacctt
B D              Guinea pig  ggacctc
                 Chinchilla  ggccctc
           Brush-tailed rat  ggacctg
B D                  Rabbit  tgtgttc
B D                    Pika  cacactg
B D                  Alpaca  tgtgttc
             Bactrian camel  tgtgttc
               Killer whale  cgtgttc
           Tibetan antelope  tgcattt
B D                     Cow  tgcattt
B D                   Sheep  tgcgttt
              Domestic goat  tgtgttt
B D                   Horse  caaggtc
B D        White rhinoceros  tgggttc
B D                     Cat  cgggttc
B D                     Dog  tgagttc
B D                 Ferret   tgggttc
B D                   Panda  aaggatc
             Pacific walrus  cgggttc
           Black flying-fox  tggattc
B D                 Megabat  tggattc
              Big brown bat  tgtgttc
       David's myotis (bat)  tgggttc
B D                Microbat  tgggttc
B D                Elephant  tgggctc
B D                 Manatee  tgggttc
           Cape golden mole  agggctc
B D                  Tenrec  ttaactc
                   Aardvark  tgggctc
B D               Armadillo  -caggtc
B D                 Opossum  catgc--
B D                Platypus  caaatcc
B D                  Turkey  ---cgca
B D      American alligator  ---atta
  D          Painted turtle  ctgagta
  D  Spiny softshell turtle  ttgatta
B D              Coelacanth  ctggttc
B D               Tetraodon  ----ttc
     Yellowbelly pufferfish  ataatta
B D            Nile tilapia  ttaagta
        Princess of Burundi  ttaatta
      Burton's mouthbreeder  ttaatta
                Zebra mbuna  ttaatta
        Pundamilia nyererei  ttaatta
B D               Zebrafish  ttgtgta
B D                  Baboon  =======
B D                     Pig  =======
B D                 Dolphin  =======
              Weddell seal  =======
B D             Zebra finch  =======
  D  White-throated sparrow  =======
  D     Collared flycatcher  -------
  D        Peregrine falcon  -------
  D            Saker falcon  -------
B D                 Gorilla  =======

Inserts between block 14 and 15 in window
          Cape golden mole 393bp

Alignment block 15 of 17 in window, 49146742 - 49146742, 1 bps 
B D                   Human  t
B D                   Chimp  t
B D               Orangutan  t
B D                  Gibbon  t
B D                  Rhesus  t
B D     Crab-eating macaque  t
B D            Green monkey  t
B D                Marmoset  t
B D         Squirrel monkey  t
B D                Bushbaby  t
         Chinese tree shrew  g
B D                Squirrel  t
     Lesser Egyptian jerboa  t
               Prairie vole  t
B D         Chinese hamster  t
B D                   Mouse  t
B D                     Rat  t
B D          Naked mole-rat  t
B D              Guinea pig  t
                 Chinchilla  t
           Brush-tailed rat  c
B D                  Rabbit  t
B D                    Pika  t
B D                  Alpaca  t
             Bactrian camel  t
               Killer whale  c
           Tibetan antelope  t
B D                     Cow  t
B D                   Sheep  t
              Domestic goat  t
B D                   Horse  t
B D        White rhinoceros  t
B D                     Cat  t
B D                     Dog  t
B D                 Ferret   t
B D                   Panda  t
             Pacific walrus  t
           Black flying-fox  t
B D                 Megabat  t
              Big brown bat  t
       David's myotis (bat)  t
B D                Microbat  t
B D                Elephant  t
B D                 Manatee  t
B D                  Tenrec  t
                   Aardvark  t
B D               Armadillo  t
B D                 Opossum  t
B D                Platypus  t
B D                  Turkey  t
B D      American alligator  t
  D          Painted turtle  t
  D  Spiny softshell turtle  t
B D              Coelacanth  t
B D               Tetraodon  c
     Yellowbelly pufferfish  c
B D            Nile tilapia  t
        Princess of Burundi  c
      Burton's mouthbreeder  c
                Zebra mbuna  c
        Pundamilia nyererei  c
B D               Zebrafish  t
B D                  Baboon  =
B D                     Pig  =
B D                 Dolphin  =
              Weddell seal  =
B D             Zebra finch  =
  D  White-throated sparrow  =
  D     Collared flycatcher  -
  D        Peregrine falcon  -
  D            Saker falcon  -
B D                 Gorilla  =
          Cape golden mole  =

Inserts between block 15 and 16 in window
                  Aardvark 1734bp
B D              Armadillo 4bp
B D                 Turkey 4bp
B D     American alligator 4bp
  D         Painted turtle 4bp
  D Spiny softshell turtle 4bp

Alignment block 16 of 17 in window, 49146743 - 49146745, 3 bps 
B D                   Human  cta
B D                   Chimp  cta
B D               Orangutan  cta
B D                  Gibbon  cta
B D                  Rhesus  cta
B D     Crab-eating macaque  cta
B D            Green monkey  cta
B D                Marmoset  cta
B D         Squirrel monkey  cta
B D                Bushbaby  cta
         Chinese tree shrew  cta
B D                Squirrel  cta
     Lesser Egyptian jerboa  ctg
               Prairie vole  ttg
B D         Chinese hamster  ctg
B D                   Mouse  gta
B D                     Rat  gta
B D          Naked mole-rat  ttt
B D              Guinea pig  ttc
                 Chinchilla  ttt
           Brush-tailed rat  ctt
B D                  Rabbit  cta
B D                    Pika  ctg
B D                  Alpaca  ctg
             Bactrian camel  ctg
               Killer whale  cca
           Tibetan antelope  acg
B D                     Cow  aca
B D                   Sheep  acg
              Domestic goat  acg
B D                   Horse  tgg
B D        White rhinoceros  ctg
B D                     Cat  ctg
B D                     Dog  cag
B D                 Ferret   ctg
B D                   Panda  ctg
             Pacific walrus  ctg
           Black flying-fox  cta
B D                 Megabat  cta
              Big brown bat  cca
       David's myotis (bat)  cca
B D                Microbat  cca
B D                Elephant  tga
B D                 Manatee  caa
B D                  Tenrec  tgc
B D               Armadillo  aga
B D                 Opossum  ctg
B D                Platypus  ccc
B D                  Turkey  cca
B D      American alligator  ctg
  D          Painted turtle  ctg
  D  Spiny softshell turtle  ctg
B D               Tetraodon  ata
     Yellowbelly pufferfish  ctt
B D            Nile tilapia  ata
        Princess of Burundi  ata
      Burton's mouthbreeder  aca
                Zebra mbuna  aca
        Pundamilia nyererei  aca
B D               Zebrafish  aga
B D                  Baboon  ===
B D                     Pig  ===
B D                 Dolphin  ===
              Weddell seal  ===
B D              Coelacanth  ---
B D             Zebra finch  ===
  D  White-throated sparrow  ===
  D     Collared flycatcher  ---
  D        Peregrine falcon  ---
  D            Saker falcon  ---
B D                 Gorilla  ===
          Cape golden mole  ===
                  Aardvark  ===

Inserts between block 16 and 17 in window
B D                 Turkey 4bp
B D     American alligator 2023bp
  D         Painted turtle 2bp
  D Spiny softshell turtle 2bp
B D              Zebrafish 9bp

Alignment block 17 of 17 in window, 49146746 - 49146748, 3 bps 
B D                   Human  aag
B D                   Chimp  aag
B D               Orangutan  aag
B D                  Gibbon  aag
B D                  Rhesus  aag
B D     Crab-eating macaque  aag
B D            Green monkey  aag
B D                Marmoset  gag
B D         Squirrel monkey  aag
B D                Bushbaby  gag
         Chinese tree shrew  aag
B D                Squirrel  gag
     Lesser Egyptian jerboa  cag
               Prairie vole  aag
B D         Chinese hamster  aag
B D                   Mouse  gaa
B D                     Rat  aag
B D          Naked mole-rat  cag
B D              Guinea pig  cag
                 Chinchilla  cga
           Brush-tailed rat  cag
B D                  Rabbit  agg
B D                    Pika  agg
B D                  Alpaca  aag
             Bactrian camel  aag
               Killer whale  aag
           Tibetan antelope  aag
B D                     Cow  aag
B D                   Sheep  aag
              Domestic goat  aag
B D                   Horse  aag
B D        White rhinoceros  aag
B D                     Cat  aag
B D                     Dog  aag
B D                 Ferret   aag
B D                   Panda  aag
             Pacific walrus  aag
           Black flying-fox  cag
B D                 Megabat  cag
              Big brown bat  cag
       David's myotis (bat)  cag
B D                Microbat  cag
B D                Elephant  atg
B D                 Manatee  acg
B D                  Tenrec  aaa
B D               Armadillo  acg
B D                 Opossum  gc-
B D                Platypus  ggg
B D           X. tropicalis  -aa
B D                  Baboon  ===
B D                     Pig  ===
B D                 Dolphin  ===
              Weddell seal  ===
B D            Nile tilapia  ---
B D               Tetraodon  ---
B D               Zebrafish  ===
    Yellowbelly pufferfish  ---
       Pundamilia nyererei  ---
               Zebra mbuna  ---
     Burton's mouthbreeder  ---
       Princess of Burundi  ---
B D              Coelacanth  ---
  D  Spiny softshell turtle  ===
  D          Painted turtle  ===
B D                  Turkey  ===
B D             Zebra finch  ===
  D  White-throated sparrow  ===
  D     Collared flycatcher  ---
  D        Peregrine falcon  ---
  D            Saker falcon  ---
B D      American alligator  ===
B D                 Gorilla  ===
          Cape golden mole  ===
                  Aardvark  ===

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