Multiz Alignments of 100 Vertebrates
 

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Alignment block 1 of 10 in window, 6510222 - 6510222, 1 bps 
B D                     Human  g
B D                     Chimp  g
B D                   Gorilla  g
B D                 Orangutan  g
B D                    Gibbon  g
B D                    Rhesus  g
B D       Crab-eating macaque  g
B D                    Baboon  g
B D              Green monkey  g
B D                  Marmoset  g
B D           Squirrel monkey  g
B D                  Bushbaby  g
           Chinese tree shrew  g
B D                  Squirrel  g
       Lesser Egyptian jerboa  g
                 Prairie vole  g
B D           Chinese hamster  g
               Golden hamster  g
B D                     Mouse  g
B D                       Rat  g
B D            Naked mole-rat  g
B D                Guinea pig  g
                   Chinchilla  g
             Brush-tailed rat  g
B D                    Rabbit  g
B D                      Pika  g
B D                    Alpaca  g
               Bactrian camel  g
B D                   Dolphin  g
                 Killer whale  g
             Tibetan antelope  g
B D                       Cow  g
B D                     Sheep  g
                Domestic goat  g
B D                     Horse  g
B D          White rhinoceros  g
B D                       Cat  g
B D                       Dog  g
B D                   Ferret   g
B D                     Panda  g
               Pacific walrus  g
                 Weddell seal  g
             Black flying-fox  g
B D                   Megabat  g
                Big brown bat  g
         David's myotis (bat)  g
B D                  Microbat  g
B D                  Hedgehog  g
B D                     Shrew  g
              Star-nosed mole  g
B D                  Elephant  g
          Cape elephant shrew  g
B D                   Manatee  g
             Cape golden mole  g
B D                    Tenrec  g
                     Aardvark  g
B D                 Armadillo  g
B D                   Opossum  g
B D           Tasmanian devil  g
B D                   Wallaby  g
B D                  Platypus  g
  D               Rock pigeon  g
  D              Saker falcon  g
  D          Peregrine falcon  g
  D       Collared flycatcher  g
  D    White-throated sparrow  g
B D       Medium ground finch  g
B D               Zebra finch  g
           Tibetan ground jay  g
B D                Budgerigar  g
  D                    Parrot  g
  D              Mallard duck  g
B D                    Turkey  g
B D        American alligator  g
  D           Green seaturtle  g
  D            Painted turtle  g
  D  Chinese softshell turtle  g
  D    Spiny softshell turtle  g
B D                    Lizard  g
B D                Coelacanth  a
B D              Nile tilapia  t
          Princess of Burundi  t
        Burton's mouthbreeder  t
                  Zebra mbuna  t
          Pundamilia nyererei  t
           Southern platyfish  c
B D               Stickleback  t
B D              Atlantic cod  =
                 Spotted gar  =
      Yellowbelly pufferfish  =
B D                      Fugu  =
B D                 Tetraodon  =
B D                   Chicken  -
B D                 Zebrafish  =
B D                    Medaka  =
B D             X. tropicalis  =
B D                       Pig  =

Inserts between block 1 and 2 in window
B D             Nile tilapia 6bp
         Princess of Burundi 6bp
       Burton's mouthbreeder 6bp
                 Zebra mbuna 6bp
         Pundamilia nyererei 6bp
          Southern platyfish 5bp
B D              Stickleback 5bp

Alignment block 2 of 10 in window, 6510223 - 6510281, 59 bps 
B D                     Human  ccacatgatgatatcaaggctg---ttgtgattcagttggttt----ggcta-agccc-aggg-acctt
B D                     Chimp  ccacatgatgatatcaaggctg---ttgtgattcagttggttt----ggcta-agccc-aggg-acctt
B D                   Gorilla  ccacatgatgatatcaaggctg---ttgtgattcagttggttt----ggcta-agccc-aggg-acctt
B D                 Orangutan  ccacatgatgatatcaaggctg---ttgtgattcagttggttt----ggcta-agccc-aggg-acctt
B D                    Gibbon  ccacatgatgatatcaaggctg---ttgtgattcagttggttt----ggcta-agccc-aggg-acctt
B D                    Rhesus  ccacatgatgatatcaaggctg---ttgtgattcagttggttt----ggcta-agccc-aggg-acctt
B D       Crab-eating macaque  ccacatgatgatatcaaggctg---ttgtgattcagttggttt----ggcta-agccc-aggg-acctt
B D                    Baboon  ccacatgatgatatcaaggctg---ttgtgattcagttggttt----ggcta-agccc-aggg-acctt
B D              Green monkey  ccacatgatgatatcaaggctg---ttgtgattcagttggttt----ggcta-agccc-aggg-acctt
B D                  Marmoset  ccacatgatgatatcaaggctg---ttgtgattcagttggttt----ggcta-agccc-aggg-acctt
B D           Squirrel monkey  ccacatgatgatatcaaggctg---ttgtgattcagttggttt----ggcta-agccc-aggg-acgtt
B D                  Bushbaby  ccacatgatgatatcaaggctg---ttgtgattcagttggttt----ggcta-agtcc-aagg-atctc
           Chinese tree shrew  ccaggtgatgataaccaggctg---ctgtgactcggctggtcg----ggccg-agccc-aggg-acctc
B D                  Squirrel  ccacatgatgatatcaaggctg---ttgtgattcagttggttt----ggcta-agcct-ggga-acctt
       Lesser Egyptian jerboa  ccacgtgatgatatcaaggctg---ttgtgattcagttggtct----ggcca-agccc-ggag-acctt
                 Prairie vole  ccatgtgatgatatcaaggctg---ttgtgattcagttggttt----ggcta-agtcc-gggg-acctc
B D           Chinese hamster  ccatgtgatgatatcaaggctg---ttgtgattcagtcggttt----ggcta-agtcc-aggg--tctc
               Golden hamster  ccatgtgatgatatcaaggctg---ttgtgattcagtcggttt----ggcta-agtcc-ggggaacctc
B D                     Mouse  ccatgtgatgatatcaaggctg---ttgtgattcagttggttt----agcta-agtcc-aggg-acctc
B D                       Rat  ccatgtgatgatatcaaggctg---ttgtgattcagttggttt----ggcta-agtcc-aggg-acctc
B D            Naked mole-rat  ccacgtgatgatatcaaggctg---ttgtgattcagttggtcg----gacta-agccc-ggga-t---c
B D                Guinea pig  ccatgtgatgataccaaggctg---ttgtgattcagtcggtct----gagta-agccc-ggga-a-cct
                   Chinchilla  ccacatgatgataccaaggctg---ttgtgattcagttggcct----gacta-agcct-gggg-accct
             Brush-tailed rat  ccatgtgatgataccaaggctg---ttgtgattcagttggtct----gacta-agcct-ggga-accct
B D                    Rabbit  ccacatgatgatatcaaggctg---ttgtgattcagttggtct----ggcta-agccc-tggg-acctt
B D                      Pika  ccatgtgatgatatgaaggctg---ttgtgattcagctggctt----ggcta-agccc-tggg-gcccc
B D                    Alpaca  ccagatgatgatatcaaggctg---tggtgattcagttggttt----ggctg-agcct-gggg-acctc
               Bactrian camel  ccagatgatgatatcaaggctg---tggtgattcagttggttt----ggcta-agcct-gggg-acctc
B D                   Dolphin  ccacatgatgatatcaaggctg---tggtgattcagttggttt----ggcta-agccc-aggg-acctc
                 Killer whale  ccacatgatgatatcaaggctg---tggtgattcagttggttt----ggcta-agccc-gggg-acctc
             Tibetan antelope  ccacatgatgacatcgaggctg---tggtgaatcagttggttt----ggctg-agccc--ggg-acccc
B D                       Cow  ccatgtgatgatatcaaggctg---tggtgaatcagttggttt----ggcta-agccc--ggg-acctc
B D                     Sheep  ccatgtgatgatatcaaggctg---tggtgaatcagttggttt----ggcta-agccc--ggg-acccc
                Domestic goat  ccatgtgatgatatcaaggctg---tggtgaatcagttggttt----ggcta-agccc--ggg-acccc
B D                     Horse  ccacatgatgatatcaaggctg---tggtgattcagttggttt----ggcta-agccc-gggg-acctt
B D          White rhinoceros  ccacatgatgatatcaaggctg---tagtgattcagttggttt----ggcta-agcct-gggg-acctt
B D                       Cat  ccacgtgatgatatcaaggctg---tggtgattcagttggttt----ggcta-agccc-gggg-acctt
B D                       Dog  ccatgtgatgatatcaaggctg---tggtgattcagttggttt----ggcta-agcct-gggg-acctt
B D                   Ferret   ccatgtgatgatatcaaggctg---tggtgattcagttggttt----ggcta-agccc-aggg-acctt
B D                     Panda  ccatgtgatgatatcaaggctg---tggtgattcagttggttt----ggcta-agccc-gggg-acctt
               Pacific walrus  ccacgtgatgatatgaaggctg---tggtgattcaggtggttt----ggcta-agccc-gggt-acctt
                 Weddell seal  ccacatgatgatatcaaggctg---tggtgattcagttggttt----ggcta-agccc-aggg-acctt
             Black flying-fox  ccacatgatgatatcaaggctg---tggtgattcagttggttt----ggcta-agtcc-aggg-acctt
B D                   Megabat  ccacatgatgatatcaaggctg---tggtgattcagttggttt----ggcta-agtcc-aggg-acctt
                Big brown bat  ccacatgatgatatcaaggcta---tggtgattcagttggttt----ggcta-agccc-aggg-acctt
         David's myotis (bat)  ccacatgatgatatcaaggctt---tggtgattcagttggttt----ggcta-agccc-aggg-acctt
B D                  Microbat  ccacatgatgatatcaaggctt---tggtgattcagttggttt----ggcta-agccc-aggg-acctt
B D                  Hedgehog  ccacatgatgatgtcaaggctg---tggtgattcagctggctt----agcta-agcccaggaa-acctt
B D                     Shrew  ccatgtgatgatatcaaggctg---tggtgattcagctggttt----ggctc-agtct-gggg-acctt
              Star-nosed mole  ccacttgatgatatcaaggctg---tggtgattcagttggttt----ggcta-agcct-gaga-gcctt
B D                  Elephant  ccacatgatgatatcaaggctg---ttgtgattcagttggttt----ggcta-agtcc-tagg-acctt
          Cape elephant shrew  ccatatgatgatatcaaggctg---ttgtgattcagtaggttt----gacta-agccc-tggg-acctt
B D                   Manatee  ccacatgatgatatcaaggctg---ttgtgattcagttggttt----ggcta-agtcc-cggg-acctt
             Cape golden mole  ccacatgatgatatccaggctg---ttgtgattcagttggttt----ggcta-agtcc-aggg-acctt
B D                    Tenrec  ccatatgatgatatcaaggctg---ttgtgattcag-tgggtt----gacta-agtcc-aggg-acctg
                     Aardvark  ccacatgatgatatcaaggctg---ttgtgattcagttggttt----ggcta-agtcc-tagg-acctt
B D                 Armadillo  ccacatgatgatatcagggctg---ttgtgattcagttggttt----ggtta-agtct-gggg-acctt
B D                   Opossum  ccatatgatgatatcaaggcta---ttgttacttggctggtct----tacta-agccc-tagg-acc-c
B D           Tasmanian devil  ccatatgatgataccaaggcta---ttgttacttggctggtct----ggttg-agccc-tagg-acc-c
B D                   Wallaby  ccatttgatgatatcaaggctg---ttgttacttggctggtct----ggttg-agccc-tagg-acc-c
B D                  Platypus  cctcgtgatgatgtgcggctta---gggtgactcgaccggccc----ggctc-agtcc-cggg-gcc-c
  D               Rock pigeon  ttcaatgatgacataaaggcta---atgtgacttgactagctg----ggttg-caccc-tcgg-cccat
  D              Saker falcon  ctcggtgatgatataaaggcta---atgtgacttgaccagctg----ggttg-cactt-t---------
  D          Peregrine falcon  ctcggtgatgatataaaggcta---atgtgacttgaccagctg----ggttg-cactt-t---------
  D       Collared flycatcher  ctcaatgatgatacaaaggcta---atgtgactcggccagctg----ggctg-caccc-tcag-cccgc
  D    White-throated sparrow  ctcaatgatgatataaaggcta---atgtgactcggccagctg----ggctg-caccc-tcag-cccac
B D       Medium ground finch  ctcaatgatgatataaaggcta---atgtgactcggccagctg----ggctg-caccc-tcag-cccac
B D               Zebra finch  ctcaatgatgatataaaggcta---atgtgactcggccagctg----ggctg-caccc-tcag-cccac
           Tibetan ground jay  ctccgtgatgatataaaggcta---atgtgactcggccagctg----ggctg-caccc-tcag-cccac
B D                Budgerigar  ttcagtgatgatataaaggcta---atgtgacttgaccagctg----ggttg-caccc-tcag-cccat
  D                    Parrot  ctcagtgatgatataaaggcta---atgtgacttgaccagctg----ggttg-caccc-tcag-cccat
  D              Mallard duck  ctccatgatgatataaaggcta---atgtgacttggccagctg----ggttg-cgccc-tcag-cccat
B D                   Chicken  ----atgatgatgtaaaggcta---atgtgactcaaccagcag----ggttg-ctcct-tcag-cccat
B D                    Turkey  tttgatgatgatataaaggcta---atgcgactcaaccagcag----ggttg-ctcct-tcag-cccat
B D        American alligator  ctgtatgatgaaat-aaggcaa---atgtgacttcactggcag----ggctg-catcc-tcaa-ccca-
  D           Green seaturtle  ctttatgatgatatgaaggcaa---atgtgaccccattggccg----ggctg-caccc-tc-a-cccat
  D            Painted turtle  ctttatgatgatataaaggcaa---atgtgaccccattggctg----ggctg-caccc-tc-a-cccat
  D  Chinese softshell turtle  ctctatgatgatatgaaggcaa---atgtgatctcattggctg----ggctg-caccc-tcaa-cccgt
  D    Spiny softshell turtle  ctctatgatgatatgaaggcaa---atgtgacctcattggctg----ggctg-caccc-tcaa-cccat
B D                    Lizard  cttcatgatgacatcaaggcga---atgtgacctcaatagc-a----ggctg-ctccc-tcaa-tctgt
B D             X. tropicalis  ccaagtgatga-accaaggcaa---atctgactctcccttctg----agtgt-gacct-c---------
B D                Coelacanth  ----atgatgataccaaggcga---atgtgatcttattggctg----ggagc-ggccg-ttga-cctt-
B D              Nile tilapia  ccac-tgatgag-ctttgacaagctttatgattcagtcagactaagatatta-agtct-c---------
          Princess of Burundi  ccac-tgatgag-ctttgactagctttatgattcagtcaaactaagagattg-agtct-c---------
        Burton's mouthbreeder  ccac-tgatgag-ctttaactagctttatgattcagtcaaactaagagattg-agtct-c---------
                  Zebra mbuna  ccac-tgatgag-ctttaactagctttatgattcagtcaaactaagagattg-agttt-c---------
          Pundamilia nyererei  ccac-tgatgag-ctttaactagctttatgattcagtcaaactaagagattg-agtct-c---------
           Southern platyfish  ccag-tgatgagaccttggcattatttatgatctgattacacttagaaactgtggttc-t---------
B D               Stickleback  ccgtatgatgatatcatggcaagtttgatgagtccgtcagacccagagattgttgctt-c---------
B D              Atlantic cod  =====================================================================
                 Spotted gar  =====================================================================
      Yellowbelly pufferfish  =====================================================================
B D                      Fugu  =====================================================================
B D                 Tetraodon  =====================================================================
B D                 Zebrafish  =====================================================================
B D                    Medaka  =====================================================================
B D                       Pig  =====================================================================

Inserts between block 2 and 3 in window
  D             Saker falcon 8bp
  D         Peregrine falcon 8bp

Alignment block 3 of 10 in window, 6510282 - 6510358, 77 bps 
B D                     Human  tggcc---t-------gtta-a---a--------------ggtctgtaatcttggtgg-gcgatacagag
B D                     Chimp  tggcc---t-------gtta-a---a--------------ggtctgtaatcttggtgg-gcgatacagag
B D                   Gorilla  tggcc---t-------gtta-a---a--------------ggtctgtaatcttggtgg-gcgatacagag
B D                 Orangutan  tggcc---t-------gtta-a---a--------------ggtctgtaatcttggtgg-gcgatacagag
B D                    Gibbon  tggcc---t-------gtta-a---a--------------ggtctgtaatcttggtgg-gcgatacagag
B D                    Rhesus  tggcc---t-------gtta-a---a--------------ggtctgtaatcttggtgg-gcaatacagag
B D       Crab-eating macaque  tggcc---t-------gtta-a---a--------------ggtctgtaatcttggtgg-gcaatacagag
B D                    Baboon  tggcc---t-------gtta-a---a--------------ggtctgtaatcttggtgg-gcaatacagag
B D              Green monkey  tggcc---t-------gtta-a---a--------------ggtctgtaatcttggtgg-gcaatacagag
B D                  Marmoset  tggcc---t--------tta-a---a--------------ggtctgtaatcttggtgg-gcaatacagag
B D           Squirrel monkey  tggcc---t-------gtta-a---a--------------ggtctgtaatcttggtgg-gcgatacagag
B D                  Bushbaby  tgacc---t-------att--a---a--------------ggtctgtaatcttggtgg-gcaatacagag
           Chinese tree shrew  tgacc---c-------gtt--g---a--------------ggtctgtaatcttggtgg-gtgatacagag
B D                  Squirrel  tgacc---t-------att--a---t--------------ggtctgtaatcttggtgg-gtgatacagag
       Lesser Egyptian jerboa  tgacc---t-------act--a---a--------------ggtctgtaatcttggtgg-gtcatacagag
                 Prairie vole  tggct---t-------atc--c---a--------------ggtctgtaatcttggtgg-tcgatacagag
B D           Chinese hamster  tgacc---t-------act--c---a--------------ggtctgtaatcttggtgg-tcgatacagag
               Golden hamster  tgacc---t-------gtt--g---ag-------------ggtctgtaatcttggtgg-tcgatacagag
B D                     Mouse  tgacc---t-------att--c---a--------------ggtctgtaatcttggtgg-tcgatacagag
B D                       Rat  tgacc---t-------att--t---t--------------ggtctgtaatcttggtgg-tcgatacaaag
B D            Naked mole-rat  aggcc---c-------ctg--a---c--------------ggtctgtaatcttggtgg-gtgatgcagag
B D                Guinea pig  ggacc---t-------gtt--a---c--------------ggtctgtaatcttggtgg-gtgatacagag
                   Chinchilla  ggacc---t-------gtt--a---t--------------ggtctgtaatcttggtgg-gtgatacagag
             Brush-tailed rat  ggcct---t-------gtt--a---c--------------ggtctgtaatcttggtgg-gtgatacagag
B D                    Rabbit  tgaca---t-------ctt--a---a--------------ggtctgtaatcttggtgg-gcgatacagag
B D                      Pika  tgaca---t-------ctg--c---a--------------ggtctgtaatcttggtgg-gcgatacagag
B D                    Alpaca  tgacc---t-------att--a---a--------------ggtctgtaatcttggtgg-gcactacagag
               Bactrian camel  tgacc---t-------att--a---a--------------ggtctgtaatcttggtgg-gcaatacagag
B D                   Dolphin  tgacc---t-------a-t------a--------------ggtctgtaatcttggtgg-gcaatacagag
                 Killer whale  tgacc---t-------a-t------a--------------ggtctgtaatcttggtgg-gcaatacagag
             Tibetan antelope  tgacc---t-------acc------a--------------ggtctgtaatcttggtgg-gcgacacagag
B D                       Cow  tgacc---t-------act------a--------------ggtctgtaatcttggtgg-gcgatacagag
B D                     Sheep  tgacc---t-------act------a--------------ggtctgtaatcttggtgg-gcgatacagag
                Domestic goat  tgacc---t-------act------a--------------ggtctgtaatcttggtgg-gcgatacagag
B D                     Horse  tgacc---t-------gtt--a---a--------------ggtctgtaatcttggtgg-gcaatacagag
B D          White rhinoceros  tgacc---t-------gtt--a---a--------------ggtctgtaatcttggtgg-gcaatacagag
B D                       Cat  tgacc---t-------att--a---a--------------ggtctgtaatcttggtgg-acaatacagag
B D                       Dog  tgacc---t-------att--a---a--------------ggtctgtaatcttggtgg-gcaatacagag
B D                   Ferret   tgacc---t-------att--a---a--------------ggtctgtaatcttggtgg-gcaatacagag
B D                     Panda  tgacc---t-------att--a---a--------------ggtctgtaatcttggtgg-gcaatacagag
               Pacific walrus  tgacc---t-------att--a---a--------------ggtctgtaatcttggtgg-gcaatacagag
                 Weddell seal  tgacc---t-------att--a---a--------------ggtctgtaatcttggtgg-gcaatacagag
             Black flying-fox  tgatc---t-------att--a---a--------------ggtctgtaatcttggtgg-tcaacacagag
B D                   Megabat  tgatc---t-------att--a---a--------------ggtctgtaatcttggtgg-tcaacacagag
                Big brown bat  tgacc---t-------att------a--------------ggtctgtaatcttggtgg-gcaatacagag
         David's myotis (bat)  tgacc---t-------att------a--------------ggtctgtaatcttggtgg-gcaatacagag
B D                  Microbat  tgacc---t-------att------a--------------ggtctgtaatcttggtgg-gcaatacagag
B D                  Hedgehog  tgacc---c-------att--a---a--------------ggtctgtaatcttggtgg-gc-atacagag
B D                     Shrew  tgact---c-------g-----------------------ggtctgtaatcttggtgg-acaataccgag
              Star-nosed mole  tgacc---t-------att--a---c--------------ggtctgtaatcttggtgg-gcaatacagag
B D                  Elephant  tggccatct-------att--a---a--------------ggtctgtaatcttggtga-gcgatacagag
          Cape elephant shrew  tggccttct-------att--a---a--------------ggtctgtaatcttggtgg-acgatacagag
B D                   Manatee  tgaccttct-------att--a---a--------------ggtctgtaatcttggtgg-atgatacagag
             Cape golden mole  tgacctat---------ta--a---a--------------ggtctgtaatcttggtgg-gtgatacaaag
B D                    Tenrec  tggcccttc-------atg--a---a--------------ggtctgtaatcttggtgg-gcgatacagag
                     Aardvark  tgaccttct-------att--a---a--------------ggtctgtaatcttggtgg-gcgaaacagag
B D                 Armadillo  tgacc---t-------att--a---a--------------ggtctggaatcttggtgg-acaatacagag
B D                   Opossum  tgact---ttcc----atc--t---a--------------ggtctgtaatcttggtgg-gcaatacagag
B D           Tasmanian devil  tgact---ttac----atc--c---a--------------ggtctgtaatcttggtgg-gcaatacagag
B D                   Wallaby  tgacc---tttc----atc--c---a--------------ggtctgtaatcttggtgg-gcaatacagag
B D                  Platypus  cgacc---c-------atc--aacca--------------ggtcagtaatcttggcgg-gcgctgcagag
  D               Rock pigeon  ---------tccagtaata--c---g--------------ggtctgtaatcttggtga-acaatgctgag
  D              Saker falcon  ---------tccagtaata--t---g--------------ggcctgtaatcttggtgg-acaatgctgag
  D          Peregrine falcon  ---------tccagtaata--t---g--------------ggcctgtaatcttggtgg-acaatgctgag
  D       Collared flycatcher  ---------tcctgtcata--c---g--------------ggtctgtaatcttggtgg-acgatgctgag
  D    White-throated sparrow  ---------tcctatcata--c---g--------------ggtctgtaatcttggtgg-atgatgctgag
B D       Medium ground finch  ---------tcctgtcata--c---g--------------ggtctgtaatcttggtgg-acgatgctgag
B D               Zebra finch  ---------tcctgtcata--c---g--------------ggtctgtaatcttggtgg-acgatgctgag
           Tibetan ground jay  ---------tcctgtcata--c---g--------------ggtctgtaatcttggtgg-acagtgctgag
B D                Budgerigar  ---------tccagtaata--c---g--------------ggcctgtaatcttggtgg-acaatgctgag
  D                    Parrot  ---------tccagtaata--c---g--------------ggcctgtaatcttggtgg-acgatgctgag
  D             Scarlet macaw  ---------tggcttaata--c---g--------------ggcctgtaatcttggtgg-acaatgctgag
  D              Mallard duck  ---------tcctgt-gta--g---g--------------ggtctgtaatcttggtgg-gcagcgcagag
B D                   Chicken  ---------tccagt-ata--c---a--------------ggtctgtaatcttggtgg-acaatgcagag
B D                    Turkey  ---------tccagt-ata--c---g--------------ggtctgtaatcttggtgg-acaacacagag
B D        American alligator  ---------tttccttaga--c---g--------------ggtttgtaatcttggcag-acaatgcagag
  D           Green seaturtle  -----------ccctgata--c---a--------------ggtctgtaatcttggcag-gcagtgcagag
  D            Painted turtle  -----------ccctgata--c---a--------------ggtctgtaatcttggcag-gcagtgcagag
  D  Chinese softshell turtle  -----------ccctgata--t---a--------------ggtctgtaatcttggcag-gcagtgcagag
  D    Spiny softshell turtle  -----------ccctgata--t---a--------------ggtctgtaatcttggcag-gcagtgcagag
B D                    Lizard  ---------tgctcatata--a---c--------------ggtctgtaatcttggtgg-gcaatacaaag
B D             X. tropicalis  --------------------------tagccttcactcttggtctgtaatcttggtgg-ctgctgagaag
B D                Coelacanth  tgacc---t-------tct--g---g--------------tgtccgtaatcttggtgg-gcatgttgaag
B D              Nile tilapia  tagcc---t-------gttgtt---a--------------tgtgggtaatcttggttgtgtggtagagtg
          Princess of Burundi  tagcc---t-------gttgtt---a--------------tgtgggtagtcttggttgtgtggtagagtg
        Burton's mouthbreeder  tagcc---t-------gttgtt---a--------------tgtgggtagtcttggttgtgtggtagagtg
                  Zebra mbuna  tagcc---t-------gttgtt---a--------------tgtggttattcttggttgtgtggtagagtg
          Pundamilia nyererei  tagcc---t-------gttgtt---a--------------tgtgggtagtcttggttgtgtggtagagtg
           Southern platyfish  tagtc---a-------gctgtt---t--------------ggtgagtagtcttggtagtgtgattgagtt
B D               Stickleback  tagcc---t-------gctgtt---t--------------ggtgggtaatcttggtggtgtggtagagtt
B D              Atlantic cod  ======================================================================
                 Spotted gar  ======================================================================
      Yellowbelly pufferfish  ======================================================================
B D                      Fugu  ======================================================================
B D                 Tetraodon  ======================================================================
B D                 Zebrafish  ======================================================================
B D                    Medaka  ======================================================================
B D                       Pig  ======================================================================

                        Human  -ttatgtgtgttcactgtaagggcagaccaacaaga--a-
                        Chimp  -ttatatgtgttcactgtaagggcagaccaacaaga--a-
                      Gorilla  -ttatgtgtgttcactgtaagggcagaccaacaaga--a-
                    Orangutan  -ttatgtgtgttcactgtaagggcagaccaacaaga--a-
                       Gibbon  -ttatgtgtgttcactgtaagggcagaccaacaaga--a-
                       Rhesus  -ttatgtgtgttcactgtaagggcagaccaacaaga--a-
          Crab-eating macaque  -ttatgtgtgttcactgtaagggcagaccaacaaga--a-
                       Baboon  -ttatgtgtgttcactgtaagggcagaccaacaaga--a-
                 Green monkey  -ttatgtgtgttcactgtaagggcagaccaacaaga--a-
                     Marmoset  -ttatgtgtgttcactgtaagggcagaccaacaaga--a-
              Squirrel monkey  -ttatgtgtgttcactgtaagggcagaccaacaaga--a-
                     Bushbaby  -ttatgtatgttcactgtaagggcagaccaacaaga--a-
           Chinese tree shrew  -tggtgtgcattcgctgtaagggcagaccaacaaga--a-
                     Squirrel  -ttatgtgcattcactgtaagggcagaccaacaaga--a-
       Lesser Egyptian jerboa  -gtatgtgtgctcactgtaagggcagaccaacaggaata-
                 Prairie vole  -tgatgtgcgatcgctgtaagggcggaccaacagaa--a-
              Chinese hamster  -taatgtgcgttcactgtaagggcggaccaacaaaa--g-
               Golden hamster  -taatgtgcgttcactgtaagggcggaccaacaaaa--g-
                        Mouse  -taatgtgcgttcactgtaagggcggaccgacaaaa--a-
                          Rat  -taatgtgcgttcactgtaagggcggaccaacaaaa--a-
               Naked mole-rat  -ttatgtgcgtccgctgtaagggcagaccaacaaga--a-
                   Guinea pig  -ttatgtgcatccactgtaaggccagaccaacaaaa--a-
                   Chinchilla  -ttatgtgcatccactgtaaggccagaccaacaaga--a-
             Brush-tailed rat  -ttatgtgctcccactgtaaggccagaccaacaaga--a-
                       Rabbit  -tagtgtgcgttcgctgtaagggcagaccaacacaa--a-
                         Pika  -cagtgtccgtccgctgtaagggcagaccaacagaa--a-
                       Alpaca  -ttatgtgtgttcactgtaagggcagaccaacaata--a-
               Bactrian camel  -ttatgtgtgttcactgtaagggcagaccaacaata--a-
                      Dolphin  -ttatgtgtgttcactgtaagggcagaccaacaata--a-
                 Killer whale  -ttatgtgtgttcactgtaagggcagaccaacaata--a-
             Tibetan antelope  -cagtgtgtgttcactgtaagggcggaccgacaac-----
                          Cow  -caatgtgtgttcactgtaagggcagaccgacaat-----
                        Sheep  -caatgtgtgttcactgtaagggcagaccgacaac-----
                Domestic goat  -caatgtgtgttcactgtaagggcagaccgacaac-----
                        Horse  -ttatgtgtgttcgctgtaagggcagaccaacaaga--a-
             White rhinoceros  -ttatgtttgttcgctgtaagggcagaccaacaaga--a-
                          Cat  -ttgtgtgtgttcgctgtaagggcagaccaacaaga--a-
                          Dog  -ttatgtgtgttcgctgtaagggcagaccaacaaga--a-
                      Ferret   -ttgtgtgtgttcgctgtaagggcagaccaacaaga--a-
                        Panda  -ttgtgtgtgttcgctgtaagggcagaccaacaaga--a-
               Pacific walrus  -ttgtgtgtgttcgctgtaagggcagaccaacaaga--a-
                 Weddell seal  -ttgtgtgtgttcgctgtaagggcagaccaacaaga--a-
             Black flying-fox  -ttatgtgtgttcactgtaagggcagaccaacaaga--a-
                      Megabat  -ttatgtgtgttcactgtaagggcagaccaacaaga--a-
                Big brown bat  -ttatgtgtgttcactgtaagggcagaccaacaaga--a-
         David's myotis (bat)  -ttacgtgtgttcactgtaagggcagaccaacaaga--a-
                     Microbat  -ttatgtgtgttcactgtaagggcagaccaacaaga--a-
                     Hedgehog  -ccatgtgtgtccgctgtaagggcagaccaacatga--t-
                        Shrew  -ct-tgtgtgttcgctgtaagggcagaccaatagat--a-
              Star-nosed mole  -ttatgtgtgttcgctgtaagggcagaccaacaaga--a-
                     Elephant  -ttgtgtgcgttcgctgtaagggcagacccacagga--a-
          Cape elephant shrew  -ttgtgtgcgtttgctgtaagggcagaccgacaaga--a-
                      Manatee  -ttgtgtgctttcgctgtaagggcagaccaacagga--a-
             Cape golden mole  -ttgtgtgcactcgctgtaagggcagaccaacaaga--a-
                       Tenrec  -ttgtgtgcgttcgctgtaagggcagaccaacaaga--a-
                     Aardvark  -ttatgtgcgttcgctgtaagggcagaccaacaaga--a-
                    Armadillo  -ttatgtgtgttcactgtaagggcggaccaataaga--a-
                      Opossum  -ctgtgtttgtttgctgtaagggcagaccaacagga--a-
              Tasmanian devil  -ctgtgtttgtttgctgtaagggcagaccaacagga--a-
                      Wallaby  -atgtgtttgtttgctgtaagggcagaccaacagga--a-
                     Platypus  -ccgtgcgcgctggctgtaagggcagaccgaaagca--a-
                  Rock pigeon  -ctgtgcatgttcgctgtaagggcaggccgacaaaa--a-
                 Saker falcon  -ctgtgcatgtttgctgtaagggcaggccgacagaa--a-
             Peregrine falcon  -ctgtgcatgtttgctgtaagggcaggccgacagaa--a-
          Collared flycatcher  -ctgtgcatgttcgctgtaagggcagaccgacagaa--a-
       White-throated sparrow  -ttgtgcatgttcgctgtaagggcagaccgacagaa--a-
          Medium ground finch  -ttgtgcatgttcgctgtaagggcagaccgacagaa--a-
                  Zebra finch  -ttgtgcatgttcgctgtaagggcagaccaacagaa--a-
           Tibetan ground jay  -ttgtgcgtgttcgctgtaagggcagaccgacagaa--a-
                   Budgerigar  -ttgtgtatgttcgctgtaagggcaggccgacaaaa--a-
                       Parrot  -ctgtgcatgtttgctgtaagggcaggccgacaaaa--a-
                Scarlet macaw  -ctgtgcatgtttgctgtaagggcaggccgacaaaa--a-
                 Mallard duck  -ccgtgcgtgctcgctgtaagggcaggccgacagaa--a-
                      Chicken  -ctgtgcgtgttcgctgtaagggcaggccgacagaa--a-
                       Turkey  -ctgtgcgtgttcgctgtaagggcaggccgacagaa--a-
           American alligator  -ttgtgtgtgtttgctgtaagggcagaccaacagaa--a-
              Green seaturtle  -tcgtgtgcgttcgctgtaagggcagaccgacagga--a-
               Painted turtle  -ttgtgtgcgttcgctgtaagggcagaccaacagga--a-
     Chinese softshell turtle  tttgtgtgcgtttgctgtaagggcagaccgacataa--a-
       Spiny softshell turtle  tttgtgtgcgtttgctgtaagggcagaccgacatga--a-
                       Lizard  -taatgtttgtttgctgtaagggcagacctacagaa--t-
                X. tropicalis  -cttctcactgttgctgtaagggcagaccaatagca--g-
                   Coelacanth  -cttggcgcgcccgctgtaaggccggacccacagca--a-
                 Nile tilapia  -ttat-tgcatt-actgtaagggcccacccagagtg--aa
          Princess of Burundi  -ttat-tgtact-gctgtaagggcccacccagagtg--aa
        Burton's mouthbreeder  -ttat-tgcact-gctgtaagggcccacccagagtg--aa
                  Zebra mbuna  -ttat-tgcact-gctgtaagggcccacccagagtg--aa
          Pundamilia nyererei  -ttat-tgcact-gctgtaagggcccacccagagtg--aa
           Southern platyfish  -ttat-tacact-gctgtaagggctcacctacagtc--aa
                  Stickleback  -ttat-tgcagc-gctgtaagggcccatccacagta--aa
                 Atlantic cod  ========================================
                  Spotted gar  ========================================
       Yellowbelly pufferfish  ========================================
                         Fugu  ========================================
                    Tetraodon  ========================================
                    Zebrafish  ========================================
                       Medaka  ========================================
                          Pig  ========================================

Inserts between block 3 and 4 in window
B D                 Platypus 733bp
  D              Rock pigeon 5bp
  D             Saker falcon 5bp
  D         Peregrine falcon 5bp
  D      Collared flycatcher 5bp
  D   White-throated sparrow 5bp
B D      Medium ground finch 5bp
B D              Zebra finch 5bp
          Tibetan ground jay 5bp
B D               Budgerigar 5bp
  D                   Parrot 5bp
  D            Scarlet macaw 5bp
  D             Mallard duck 5bp
B D                  Chicken 5bp
B D                   Turkey 5bp
B D       American alligator 5bp
  D          Green seaturtle 5bp
  D           Painted turtle 5bp
  D Chinese softshell turtle 5bp
  D   Spiny softshell turtle 5bp
B D                   Lizard 5bp

Alignment block 4 of 10 in window, 6510359 - 6510383, 25 bps 
B D                     Human  cttt---t--tccta--ct---tttgagct-ac-ctc
B D                     Chimp  cttt---t--tccta--ct---tttgagct-ac-ctc
B D                   Gorilla  cttt---t--tccta--ct---tttgagct-ac-ctc
B D                 Orangutan  cttt---t--tccta--ct---tttgagct-ac-ctc
B D                    Gibbon  cttt---t--tccta--ct---tttgagct-ac-ctc
B D                    Rhesus  cttt---t--tccta--ct---tttgaact-ac-ctc
B D       Crab-eating macaque  cttt---t--tccta--ct---tttgaact-ac-ctc
B D                    Baboon  cttt---t--tccta--ct---tttgaact-ac-ctc
B D              Green monkey  cttt---t--tccta--ct---tttgaact-ac-ctc
B D                  Marmoset  cttt---t--tccta--ct---tttgagtt-ac-ctc
B D           Squirrel monkey  cttt---t--tccta--ct---tttgagct-ac-ctc
B D                  Bushbaby  cttt---t--tccta--ct---tttgagct-ac-ctc
           Chinese tree shrew  tgtt---g--tccta--ct---tttgaact-ac-ttc
B D                  Squirrel  --ct---ttctccta--ct---tttgaacc-ac-ctc
       Lesser Egyptian jerboa  --tt---g--tccta--ct---tttgaacc-gc-ctt
                 Prairie vole  --tt---t--tcctg--ct---tttgaacc-ac-ctc
B D           Chinese hamster  --tt---t--tcctg--ct---tctgaacc-ac-ctc
               Golden hamster  --at---t--tccta--ct---tctgaacc-tc-ctc
B D                     Mouse  --at---t--tccta--ct--ctttaaatt-ac-ctc
B D                       Rat  --tt---t--tccta--ct--ttttgaacc-ac-ctc
B D            Naked mole-rat  c-tt---t--tccta--ct---ttcaagcc-a-----
B D                Guinea pig  cttt---t--tccta--ct---ttcaaatc-ac-ttc
                   Chinchilla  cttt---t--tccta--ct---ttcaaccc-ac-ttc
             Brush-tailed rat  cttt---t--tcctg--ct---ttcagatc-ac-ttc
B D                    Rabbit  ctactgtt--tccta--ct---tttgagct-gc-ctc
B D                      Pika  cgac---t--tcctg--ct---ttggagct--t-atc
B D                    Alpaca  attc---t--tccta--cc---ctccaact-gc-ctt
               Bactrian camel  attc---t--tccta--cc---ctccaact-gc-ctc
B D                   Dolphin  attc---t--tccca--ct---cttgaact-gc-ctc
                 Killer whale  attc---t--tccca--ct---cttgaact-gc-ctc
             Tibetan antelope  attc---t--tccta--ct---tgggggct-gc-ctc
B D                       Cow  attc---t--tccta--ct---tgtgggct-gc-ctc
B D                     Sheep  attc---t--tccta--ct---tgtgggct-gc-ctc
                Domestic goat  attc---t--tccta--ct---tgcgggct-gc-ctc
B D                     Horse  attc---t--tccta--ct---tttgaact-ac-ctc
B D          White rhinoceros  attc---t--tccta--ct---tttgaatt-ac-ctc
B D                       Cat  atat---t--tccta--ct---tttgaatt-gc-ctc
B D                       Dog  atat---t--tccta--ct---tttgaact-ac-ctc
B D                   Ferret   ctat---t--tccta--ct---cttgaact-ac-ccc
B D                     Panda  atat---t--tccta--ct---tttgaact-ac-ctc
               Pacific walrus  atat---t--cccta--ct---tttgaact-ac-ctc
                 Weddell seal  atat---t--tccta--ct---tttgaact-ac-ctc
             Black flying-fox  attc---t--ccctg--ct---tttgaact-ac-ctc
B D                   Megabat  attc---t--ccctg--ct---tttgaact-ac-ctc
                Big brown bat  attc---t--tcctg--ct---tttgaact-at-ctc
         David's myotis (bat)  attc---t--tcctg--ct---tttgaact-at-ctc
B D                  Microbat  attc---t--tcctg--ct---tttgaact-at-ctc
B D                  Hedgehog  act--------ccta--ct---tctgaact-ac---c
B D                     Shrew  atct---c---ccta--ct---ttcgaacg-ac-gtc
              Star-nosed mole  attt---c--tccta--ct---tttgagct-ac---c
B D                  Elephant  tttt---g--tccta--ct---tttgaact-ac---c
          Cape elephant shrew  gttt---a--tccta--ct---tttgaact-ac---c
B D                   Manatee  gttt---g--tccta--ct---tttgaact-ac---c
             Cape golden mole  gttt---g--tcctg--ct---tttgaact-ac---c
B D                    Tenrec  gtta---a--cccta--ct---tttgagct-cc---c
                     Aardvark  gttt---g--ttcta--ct---tttgaact-ac---c
B D                 Armadillo  tttt---t--tccta--ct---tttgagct-ac-ctc
B D                   Opossum  gttc---t--gcctc--tc---ttactctt-at-ctc
B D           Tasmanian devil  gtgc---c--acctc--tt---ttgctcct-gt-ctt
B D                   Wallaby  gttc---c--acctctttt---ttgctccc-at-ctt
  D               Rock pigeon  cttc---c--ccaag--tc---cctggaaa-at-aca
  D              Saker falcon  cttc---c--ctgtg--tc---cctggaaa-at-aca
  D          Peregrine falcon  cttc---c--ctgtg--tc---cctggaaa-at-aca
  D       Collared flycatcher  cttg---c--ccatg--tc---cctggaaa-at-aca
  D    White-throated sparrow  cttg---c--ccctg--tc---cccggaaa-at-gaa
B D       Medium ground finch  cgtg---c--ccctg--tc---cctggaaa-at-aca
B D               Zebra finch  ctt----------tg--tc---cctggaaa-ataaca
           Tibetan ground jay  cttg---c--ccttg--tc---cctggaaa-at-aca
B D                Budgerigar  cttc---t--ccgca--tc---cctggaaa-at-aca
  D                    Parrot  cttc---t--ccgcg--tc---cctggaaa-at-aca
  D             Scarlet macaw  cttc---t--ccgca--tc---cctggaaa-at-gca
  D              Mallard duck  cttc---c--ccaca--tc---cctggaaaggc-aaa
B D                   Chicken  cttc---c--ccgtg--tc---cctgggaa-at-aaa
B D                    Turkey  cttc---c--ctgtg--tc---tctgggaa-at-aaa
B D        American alligator  attt---c--ctgtt----------------at-cca
  D           Green seaturtle  attt---t--ccatt--tcattcctggcag-ga----
  D            Painted turtle  attt---t--ccatt--tcattcctggagg-ga----
  D  Chinese softshell turtle  attt---t--ccatt--tcattcctcgaag-gg----
  D    Spiny softshell turtle  attt---t--ccatt--ttattccttgaag-gg----
B D                    Lizard  attc-ttc--ctcct--tc---catttaga-ag----
B D             X. tropicalis  ---t---g--ctcaa--tg---cgtggccc-ac-aac
B D                Coelacanth  --------------------------accc-gc-gcc
B D              Nile tilapia  --at---t--gacat--tt---tctatgct-gt-gcc
          Princess of Burundi  --ct---t--gacac--tt---tctatgct-gt-gcc
        Burton's mouthbreeder  --at---t--gacac--tt---tctatgct-gt-gcc
                  Zebra mbuna  --at---t--gacac--tt---tctatgct-gt-gcc
          Pundamilia nyererei  --at---t--gacac--tt---tctatgct-gt-gcc
           Southern platyfish  --ac---g--tccat----------------------
B D               Stickleback  --ct---t--gatac--tt---tccttaac-ct-c--
B D              Atlantic cod  =====================================
                 Spotted gar  =====================================
      Yellowbelly pufferfish  =====================================
B D                      Fugu  =====================================
B D                 Tetraodon  =====================================
B D                 Zebrafish  =====================================
B D                    Medaka  =====================================
B D                  Platypus  =====================================
B D                       Pig  =====================================

Inserts between block 4 and 5 in window
B D                  Wallaby 1bp
B D             Nile tilapia 226bp
B D              Stickleback 3bp

Alignment block 5 of 10 in window, 6510384 - 6510397, 14 bps 
B D                     Human  t-t----ttt-aataggggt
B D                     Chimp  t-t----ttt-aataggggt
B D                   Gorilla  t-t----ttt-aataggggt
B D                 Orangutan  t-t----ttt-aataggggt
B D                    Gibbon  t-t----ttt-aataggggt
B D                    Rhesus  t-t----ttt-aatgggggt
B D       Crab-eating macaque  t-t----ttt-aatgggggt
B D                    Baboon  t-t----ttt-aatgggggt
B D              Green monkey  t-t----ttt-aatgggggt
B D                  Marmoset  t-t----tat-aataggggt
B D           Squirrel monkey  t-t----ttt-aataggggt
B D                  Bushbaby  t-t----ttt-aataggggt
           Chinese tree shrew  t-c----ttt-aacgtaaga
B D                  Squirrel  t-t----ttt-aataggggt
       Lesser Egyptian jerboa  --t----ctt-aggaggggt
                 Prairie vole  --c----cca-agtaggggt
B D           Chinese hamster  a-c----tcc-agtagggtt
               Golden hamster  a-c----tcc-agtaggg--
B D                     Mouse  a-c----tcc-agtcggggt
B D                       Rat  a-ctccatcc-agttggggt
B D            Naked mole-rat  g-c----tct-tgtagggtc
B D                Guinea pig  t-c----ttt-cgtaggggt
                   Chinchilla  t-c----ttt-cgtaggggt
             Brush-tailed rat  t-c----ttt-cgtgggggt
B D                    Rabbit  t-c----ttg-aatagaggt
B D                      Pika  t-c----tct-gaccgaggt
B D                    Alpaca  t-------tc-aatagaggc
               Bactrian camel  t-------tc-aataaaggc
B D                   Dolphin  t-c----ttc-aatagaggc
                 Killer whale  t-c----ttc-aatagaggc
             Tibetan antelope  t-c----ttc-agtggaggc
B D                       Cow  t-c----ttc-aatggaggc
B D                     Sheep  t-c----gtc-aatggaggc
                Domestic goat  t-c----gtc-aatggaggc
B D                     Horse  t-c----ttt-agtagaggt
B D          White rhinoceros  t-c----ttt-aatagaggt
B D                       Cat  t-c----ttt-aatagaggt
B D                       Dog  t-c----ttt-aata-agag
B D                   Ferret   t-c----ttt-aatagaggc
B D                     Panda  t-c----ttt-aaaagaggt
               Pacific walrus  t-c----ttt-aacagaggt
                 Weddell seal  t-t----ttt-aacagaggt
             Black flying-fox  t-c----ttt-aatagaggt
B D                   Megabat  t-c----ttt-aatagaggt
                Big brown bat  ---------t-catggagat
         David's myotis (bat)  t-c----ttt-catggagat
B D                  Microbat  t-c----ttt-catggagat
B D                  Hedgehog  t-c----t------------
B D                     Shrew  t-c----ttt-cacagaggc
              Star-nosed mole  t-c----ttt-aacagaggt
B D                  Elephant  t-c----ttt-gataggggt
          Cape elephant shrew  t-t----ttt-aatagaggt
B D                   Manatee  a-c----tgt-aacaggggt
             Cape golden mole  t-c----ttt-aataggggt
B D                    Tenrec  t-c----ctt-aatgggggg
                     Aardvark  t-c----ttt-aataggggt
B D                 Armadillo  t-c----ttt-aataggggt
B D                   Opossum  t-c----cct-aagtggagt
B D           Tasmanian devil  c-c----cct-aaggggaga
B D                   Wallaby  c-c----cct-aaggggagt
  D               Rock pigeon  t-c----ttt-----gggat
  D              Saker falcon  t-c----ctt-----gggat
  D          Peregrine falcon  t-c----ctt-----gggat
  D       Collared flycatcher  t-c----tgt-----gggat
  D    White-throated sparrow  t-c----tgt-----gggat
B D       Medium ground finch  t-c----tgt-----gggat
B D               Zebra finch  t-c----tgt-----gggat
           Tibetan ground jay  t-c----tgt-----gggac
B D                Budgerigar  t-c----ttt-----gggat
  D                    Parrot  t-c----ttt-----gggat
  D             Scarlet macaw  t-c----ttt-----gggat
  D              Mallard duck  t-c----ctg-----ggggt
B D                   Chicken  t-c----ctt-----gggac
B D                    Turkey  t-c----ctt-----gggat
B D        American alligator  t-c----tc-----------
  D           Green seaturtle  -----------------gat
  D            Painted turtle  -----------------gat
  D  Chinese softshell turtle  -----------------agt
  D    Spiny softshell turtle  -----------------agc
B D                    Lizard  ---------------gaaat
B D             X. tropicalis  tga----ttt-aatatctgt
B D                Coelacanth  t-t----tcc-tgtaccgtc
          Princess of Burundi  -ac----ttc-aagagaaat
        Burton's mouthbreeder  -ac----ttc-aagagaaat
                  Zebra mbuna  -ac----ttc-aagagaaat
          Pundamilia nyererei  -ac----ttc-aagagaaat
           Southern platyfish  --c----ttctaaaacgtat
B D               Stickleback  -tc----ccc-aagagc---
B D              Atlantic cod  ====================
                 Spotted gar  ====================
      Yellowbelly pufferfish  ====================
B D                      Fugu  ====================
B D                 Tetraodon  ====================
B D                 Zebrafish  ====================
B D                    Medaka  ====================
B D              Nile tilapia  ====================
B D                  Platypus  ====================
B D                       Pig  ====================

Inserts between block 5 and 6 in window
               Big brown bat 1bp
         Princess of Burundi 272bp
       Burton's mouthbreeder 5bp
                 Zebra mbuna 5bp
         Pundamilia nyererei 5bp
          Southern platyfish 1bp
B D              Stickleback 8bp

Alignment block 6 of 10 in window, 6510398 - 6510428, 31 bps 
B D                     Human  ga-ttctt-ccagttgctgga-gagaaat-----------tgtgg
B D                     Chimp  ga-ttctt-ccagttgctgga-gagaaat-----------tgtgg
B D                   Gorilla  ga-ttctt-ccagttgctgga-gagaaat-----------tgtgg
B D                 Orangutan  ga-ttctt-ccagttgctgga-gagaaat-----------tgtgg
B D                    Gibbon  ga-ttctt-ccagttgctgga-gagaaat-----------tgtgg
B D                    Rhesus  ga-ttctt-ccagttgctgga-gagaaat-----------tgtgg
B D       Crab-eating macaque  ga-ttctt-ccagttgctgga-gagaaat-----------tgtgg
B D                    Baboon  ga-ttctt-ccagttgctgga-gagaaat-----------tgtgg
B D              Green monkey  ga-ttctt-ccagttgctgga-gagaaat-----------tgtgg
B D                  Marmoset  ga-ttctt-ccagttgctgga-gagaaat-----------tttgg
B D           Squirrel monkey  ga-ttctt-ccagttgctgga-gagaaat-----------tgcgg
B D                  Bushbaby  g--ttctt-ccagttgccagg-aagaaac-----------agtgg
           Chinese tree shrew  ga-ttctc-ccagttgccagg-aaggaat-----------tgcgg
B D                  Squirrel  ga-ttctt-ccagttgccaga-gagaaat-----------tgtgg
       Lesser Egyptian jerboa  gg-ttctt-ccagttgccaga-gagaaat-----------tgtgg
                 Prairie vole  ga-ttc-t-cca-ttgcctgc-aaggact-----------t---g
B D           Chinese hamster  gg-ttc-t-ccaggtgccagg-gaggact-----------tgtgg
               Golden hamster  gg-ttc-t-ccaggtgccagg-gaggact-----------tgtgg
B D                     Mouse  ga-ttc-t-ccagctgccagg-gaggaat-----------tgtgg
B D                       Rat  ga-ttc-t-ctagctgccagg-gaggaat-----------tgtgg
B D            Naked mole-rat  ---ttctc-ccaggtgccagg-gagaaat-----------cgtgg
B D                Guinea pig  ga-tcctt-ccagttgccagg-gagaaat-----------tgtgc
                   Chinchilla  ga-ctctt-ccagttgccagg-gagaaat------------gtgc
             Brush-tailed rat  ga-ttctt-ccaggtgcctgg-gagaaac-------------tgc
B D                    Rabbit  ca-atctt-ccagttgccagg-gag-aat-----------tg-gg
B D                      Pika  ca-ctctt-ccggttgctggg-gag-agt-----------tgtgg
B D                    Alpaca  agtttctt-ccggttgcc--a-gagaagc-----------tgggg
               Bactrian camel  agtttctt-ctggttgcc--a-gagaagc-----------tgggg
B D                   Dolphin  ag-ttctt-cctgttgccaga-gagaaat-----------cgggg
                 Killer whale  ag-ttctt-cctgttgccaga-gagaaat-----------tgggg
             Tibetan antelope  tg-ttctt-cccgttgccgga-gagaacg-----------tgggg
B D                       Cow  tg-ttctt-cccgttgccaga-gagaaca-----------tgggg
B D                     Sheep  tg-ttctt-cccgttgccaga-gagaaca-----------tgggg
                Domestic goat  tg-ttctt-cccgttgccaga-gagaacg-----------tgggg
B D                     Horse  ga-ttttt-ccagttgccagg-gagaact-----------tctgg
B D          White rhinoceros  ga-ttttt-ccagttgccagg-gagaact-----------tctgg
B D                       Cat  ag-ttctt-ccagttgccaag-gagaaac-----------tgggg
B D                       Dog  gg-ttctt-ccagttgccaga-gagaaac-----------taggg
B D                   Ferret   gg-ttctt-ctagtcaccaga-gagaaac-----------tggga
B D                     Panda  gg-ttcct-ccagttgccaga-gagaaac-----------tgggg
               Pacific walrus  ga-ttctt-ccagtctccaga-gagaaac-----------tgggg
                 Weddell seal  gg-ttctt-ccagtctccaga-gagaaac-----------tgggg
             Black flying-fox  ga-ttctt-ccagttgccagg-gagaaat-----------tgtgg
B D                   Megabat  ga-ttctt-ccagttgccagg-gagaaat-----------tgtgg
                Big brown bat  at-ttcttcccagttgccagg-aagaaat-----------tgtgg
         David's myotis (bat)  at-ttcttcccagctgccaga-aagaaat-----------tgtgg
B D                  Microbat  at-ttcttcccagttgccagg-aagaaat-----------tgtgg
B D                  Hedgehog  ---------ccagctgccagc-gagaaat-----------tctgg
B D                     Shrew  gg-ccctg-ccagtggccaga-gagaaaa-----------c-tgg
              Star-nosed mole  ga-ttctt-ccagttgccagt-aagaaat-----------tgtgg
B D                  Elephant  ga-ttctt-ccagttaccaga-gagaaac-----------catgg
          Cape elephant shrew  ga-ttctt-tctgttgccaga-gagaaac-----------tttgg
B D                   Manatee  ga-tta-t-ccagttgccaga-aagaaac-----------cgtgg
             Cape golden mole  ag-tcttt-ccagttgccagg-gagaaac-------------tgg
B D                    Tenrec  at-tc-tt-ccagttgcca-g-gagaaaa-------------tgg
                     Aardvark  ca-ttctt-ccagttgccagg-gagaaac-----------tgtgg
B D                 Armadillo  aa-ttctt-ccagttgccagg-gagaaat-----------tgtgg
B D                   Opossum  ga-t---t-ttggctgccact-gaaagat-----------cctgg
B D           Tasmanian devil  gg-t---c-ctggctgccact-gaaagat-----------cctgg
B D                   Wallaby  ga-t---c-ctggttaccaca-gaaagat-----------gctgg
  D               Rock pigeon  gc-----a-tcagctttgcgt-gagtgtt-----------tcgtt
  D              Saker falcon  gc-----a-tcagctctgagg-gagtatt-----------tctgt
  D          Peregrine falcon  gc-----a-tcagctctgagg-gagtatt-----------tctgt
  D       Collared flycatcher  gt-----a-tcagctcagagt-gagtttt-----------cctct
  D    White-throated sparrow  gt-----t-tcagctcagagt-gagtgtt-----------tctct
B D       Medium ground finch  gt-----a-tcagctcagagc-gagtgtt-----------tctct
B D               Zebra finch  gt-----a-tcagctcagagc-gagtgtt-----------tctct
           Tibetan ground jay  ga-----a-tcagctcagagt-gagtgtt-----------tctct
B D                Budgerigar  gt-----a-tcagctctgagc-gagtgtt-----------tccat
  D                    Parrot  gc-----a-tcagctctgagc-aagtgtt-----------tccat
  D             Scarlet macaw  gc-----a-tcagctctgagc-gagtgtt-----------tccat
  D              Mallard duck  gc-----a-tcagctccgagt-gagtgct-----------tctcg
B D                   Chicken  gt-----g-tcagctctgagc-aagtgct-----------tctag
B D                    Turkey  gt-----g-tcagctctgagc-aagtgct-----------tctag
B D        American alligator  -------------ctcctagctaagaggt-----------actag
  D           Green seaturtle  at-----g-cctgcccctagc-aagtggt-----------cctag
  D            Painted turtle  at-----g-cctgcccctagc-aagtgat-----------cctag
  D  Chinese softshell turtle  at-----g-cctgcccttagc-aagtggt-----------cctag
  D    Spiny softshell turtle  at-----g-cctgcccctagc-aagtggt-----------cctag
B D                    Lizard  g------g-ccattcctttgc-aaagcat-----------cataa
B D             X. tropicalis  gc-gt--a-cgagcgaccgtg-cagatct-----------cagct
B D                Coelacanth  tg-tcgct-tcaagaaacagc-agcagat-----------cacag
        Burton's mouthbreeder  ------------agtataagc-aggagctgtcaaacaatgtgtgg
                  Zebra mbuna  ------------agtataagc-agaagctgtcaaacaatgtgtgg
          Pundamilia nyererei  ------------agtataagc-aggagctgtcaaacaatgtgtgg
           Southern platyfish  ------------cctatgatg-agaa----------atttcgtgg
B D               Stickleback  ------------tggtcaggt-gggagatatcagacagtgtgtga
B D              Atlantic cod  =============================================
                 Spotted gar  =============================================
      Yellowbelly pufferfish  =============================================
B D                      Fugu  =============================================
B D                 Tetraodon  =============================================
B D                 Zebrafish  =============================================
B D                    Medaka  =============================================
         Princess of Burundi  =============================================
B D              Nile tilapia  =============================================
B D                  Platypus  =============================================
B D                       Pig  =============================================

Inserts between block 6 and 7 in window
       Burton's mouthbreeder 235bp
                 Zebra mbuna 235bp
         Pundamilia nyererei 235bp
B D              Stickleback 1bp

Alignment block 7 of 10 in window, 6510429 - 6510437, 9 bps 
B D                     Human  taactgga---g-
B D                     Chimp  taactgga---g-
B D                   Gorilla  taactgga---g-
B D                 Orangutan  taactgga---g-
B D                    Gibbon  taactgga---g-
B D                    Rhesus  taactgga---g-
B D       Crab-eating macaque  taactgga---g-
B D                    Baboon  taactgga---g-
B D              Green monkey  taactgga---g-
B D                  Marmoset  taactgga---g-
B D           Squirrel monkey  taactgga---g-
B D                  Bushbaby  taactgga---g-
           Chinese tree shrew  taactgga---g-
B D                  Squirrel  taactgga---g-
       Lesser Egyptian jerboa  taactggc---a-
                 Prairie vole  tcattgga---a-
B D           Chinese hamster  taactgga---a-
               Golden hamster  taactgga---a-
B D                     Mouse  taactgga---a-
B D                       Rat  taactgga---a-
B D            Naked mole-rat  tacctgga---g-
B D                Guinea pig  taactgga---a-
                   Chinchilla  tgactgga---g-
             Brush-tailed rat  tgactgga---g-
B D                    Rabbit  taactgga---g-
B D                      Pika  taactgga---g-
B D                    Alpaca  taactgga---g-
               Bactrian camel  taactgga---g-
B D                   Dolphin  taactgga---g-
                 Killer whale  taactgga---g-
             Tibetan antelope  taac--ga---g-
B D                       Cow  taac--ga---g-
B D                     Sheep  taac--ga---g-
                Domestic goat  taac--ga---g-
B D                     Horse  taactgga---g-
B D          White rhinoceros  taactaga---g-
B D                       Cat  tagctggc---c-
B D                       Dog  tagctgga---g-
B D                   Ferret   tggttgga---g-
B D                     Panda  taactgga---g-
               Pacific walrus  tagctgga---g-
                 Weddell seal  tagctgga---g-
             Black flying-fox  taactgga---a-
B D                   Megabat  taactgga---a-
                Big brown bat  taacagga---g-
         David's myotis (bat)  taactgga---g-
B D                  Microbat  taactgga---g-
B D                  Hedgehog  tgcctgga---a-
B D                     Shrew  tgactggt---g-
              Star-nosed mole  taactgga---g-
B D                  Elephant  tagctgga---g-
          Cape elephant shrew  taactaga---a-
B D                   Manatee  tagctgga---g-
             Cape golden mole  taactgga---g-
B D                    Tenrec  taactaaa---g-
                     Aardvark  tagctgga---g-
B D                 Armadillo  taactgga---g-
B D                   Opossum  tagctaga---g-
B D           Tasmanian devil  tagctaga---a-
B D                   Wallaby  tagctaga---g-
  D               Rock pigeon  gagctgat---a-
  D              Saker falcon  gagctgac---a-
  D          Peregrine falcon  gagctgac---a-
  D       Collared flycatcher  gagctgat---g-
  D    White-throated sparrow  gagccgac---g-
B D       Medium ground finch  gagctgac---a-
B D               Zebra finch  gagctgac---g-
           Tibetan ground jay  gagctga----g-
B D                Budgerigar  gagctggc---a-
  D                    Parrot  gagctggc---a-
  D             Scarlet macaw  gagctggc---a-
  D              Mallard duck  cagctgac--gg-
B D                   Chicken  gaactgac---t-
B D                    Turkey  gggctgac---t-
B D        American alligator  gagttga----g-
  D           Green seaturtle  gagctggg-----
  D            Painted turtle  gagctggg-----
  D  Chinese softshell turtle  gggctggactga-
  D    Spiny softshell turtle  gggctgggctga-
B D                    Lizard  ggaatggt---a-
B D             X. tropicalis  gggcctac---a-
B D                Coelacanth  gaagtgcc---g-
           Southern platyfish  -gatatgt---ag
B D               Stickleback  -tgtttgt---g-
B D              Atlantic cod  =============
                 Spotted gar  =============
      Yellowbelly pufferfish  =============
B D                      Fugu  =============
B D                 Tetraodon  =============
B D                 Zebrafish  =============
B D                    Medaka  =============
         Pundamilia nyererei  =============
                 Zebra mbuna  =============
       Burton's mouthbreeder  =============
         Princess of Burundi  =============
B D              Nile tilapia  =============
B D                  Platypus  =============
B D                       Pig  =============

Inserts between block 7 and 8 in window
                    Aardvark 1bp
          Southern platyfish 64bp

Alignment block 8 of 10 in window, 6510438 - 6510486, 49 bps 
B D                     Human  ----t----gagagagtaggaacagg-gcatgt-t----ca-ggg-tatca----g---ggccaagggtc
B D                     Chimp  ----t----gagagagtaggaacagg-gcatgt-t----ca-ggg-tatca----g---ggccaagggtc
B D                   Gorilla  ----t----gagagagtaggaacagg-gcatgt-t----ca-ggg-tatca----g---ggccaagggtc
B D                 Orangutan  ----t----gagagagtaggaacagg-gcatgt-t----ca-ggg-tatca----g---ggccaagggtc
B D                    Gibbon  ----t----gagagagtaggaacagg-gcatgt-g----ca-ggg-tatca----g---ggccaagggtc
B D                    Rhesus  ----t----gagagagtaggaacagg-gcatgt-t----ca-ggc-tatca----g---ggccaagggtc
B D       Crab-eating macaque  ----t----gagagagtaggaacagg-gcatgt-t----ca-ggc-tatca----g---ggccaagggtc
B D                    Baboon  ----t------aagagtaggaacagg-gcatgt-t----ca-ggc-tatca----g---ggccaagggtc
B D              Green monkey  ----t----gagagagtaggaacagg-gcatgt-t----ca-ggc-tatca----g---ggccaagggtc
B D                  Marmoset  ----g----gagagagtaggaacagg-gcatgt-t----ca-ggg-tatca----t---ggccaagggtc
B D           Squirrel monkey  ----g----aagagagtaggaacagg-gcgtgt-t----ca-ggg-tttca----t---ggccaagggtc
B D                  Bushbaby  ----t----caaagagtaggaacagg-gcatgt-t----ca-agg-tat----------ggtcaagggtt
           Chinese tree shrew  ----t----gagaaggtgggaacagg-gcatgt-t----ct-ggg-tctca----g---gatcaggggtc
B D                  Squirrel  ----t----gag--ggtagaaacagg-gcatgt-t----tg-aga-tatca----g---ggtcaggggtt
       Lesser Egyptian jerboa  ----t----gag--agtgggaacaga--gatat-t----ca-agg-tatca--------ggtcaggggtc
                 Prairie vole  ----t----gaa--agtaggaacagg-ctctat-c----tc-a-a-tacag----g---ggtcaggggtc
B D           Chinese hamster  ----t----caa--agtaggaacagg-ctgtat-t----aa-aga-tacaa----g---ggtcaggggtc
               Golden hamster  ----t----gga--agtaggaacagg-ctatat-t----ca-aga-tacaa----g---ggtcaggggtc
B D                     Mouse  ----t----gaa--agtaggaacagtcttatat-t----cg-agg-tgcca----g---ggtcagtggtc
B D                       Rat  ----t----gaa--agtaggaatagg-ttatat-t----cg-aga-tgcca----g---ggttgggagtc
B D            Naked mole-rat  ----t----gag--agtaggaacagg-gcatgt-t----cc-agg-tttcaattgg---ggtccagg-tc
B D                Guinea pig  ----t----gag--agtagaaacagg-gcatgt-t----cc-acg-tttcgatggg---ggtcaaggttc
                   Chinchilla  ----t----gag--agtaggaacagg-gcatgt-t----cc-ggg-tttcagctgg---ggccaagggtc
             Brush-tailed rat  ----t----gag--agtaggaatagg-acatgt-t----cc-agg-tttcacttgg---ggctgagggtc
B D                    Rabbit  ----t----gagagagcaggaacaga-gcacgt-t----cg-ggt-tgtca---gg---agtcagaggtc
B D                      Pika  ----t----gagaaagcagggacagg-gcaca--t----ct-cgt-tagct---gg---agtcaggggtc
B D                    Alpaca  ----t----gggagagtagggatagg-acacat-t----ca-gga-tgtca----g---ggtcgggggtc
               Bactrian camel  ----t----gggagagtagggatagg-gcacgt-t----ca-gga-tgtca----g---ggtcaggggtc
B D                   Dolphin  ----t----gagagagtagggatagg-gcatgt-t----ca-gga-tatca----g---ggtcaggggtc
                 Killer whale  ----t----gagagagtagggatagg-gcatgt-t----ca-gga-tatca----g---ggtcaggggtc
             Tibetan antelope  ----t----gagagagtagggacagg-gcgtgc-t----tg-gga-cgtca----g---ggtcaggggt-
B D                       Cow  ----t----aagagagtagggatagg-gcatgc-t----cg-gga-catca----g---ggtcaggtgt-
B D                     Sheep  ----t----gagagagtagggatagg-gcgtgc-t----tg-gga-catca----g---gggcaggggt-
                Domestic goat  ----t----gagagagtagggatagg-gcatgc-t----tg-gga-catca----g---gggcaggggt-
B D                     Horse  ----t----gagagagtggggacagg-gcatg--t----ca-gag-tat-g----g---ggtcaggggtc
B D          White rhinoceros  ----t----gagagagtggggacagg-gcgtg--t----ca-ggg-tat-g----g---ggttaggggtc
B D                       Cat  ----t----gagagagtggggacagg-gcgtgt-t----ca-gcg-tgtcg----g---ggtcaggggtc
B D                       Dog  ----t----gagagagtggggacagg-gcatgt-t----ca-ggg-taaag----a---gatcaggggtc
B D                   Ferret   ----t----gagagagtggggacagg-gcacat-t----ca-ggg-cgtcg----a---ggtcaggggtc
B D                     Panda  ----t----gagagagtggggacagg-gcatgt-t----ca-ggg-tatca----a---ggtcagggctc
               Pacific walrus  ----tgagagagagagtggggacagg-gcatgt-t----ca-ggg-tatcg----a---ggtcggaggtc
                 Weddell seal  ----t----gagagagtggggacaag-gcatgt-t----ca-ggg-tatca----a---ggtcgggggtc
             Black flying-fox  ----t----gagagagtagggacagg-acatgt-t----ca-cgg-tatca----g---ggtcaggggtt
B D                   Megabat  ----t----gagagagtagggacagg-atatgt-t----ca-cag-tatca----g---ggtcaggggtc
                Big brown bat  ----t----gagtagggagagacaag-gcatgt-t----cg-tgg-tatca----a---ggtcaagggtc
         David's myotis (bat)  ----t----gagtagggagggacaag-gcatgt-t----ca-tgg-tatca----g---ggtcaagggtc
B D                  Microbat  ----t----gagtaggga-ggacaag-gcatgt-t----ca-tgg-tatca----g---ggtcaagggtc
B D                  Hedgehog  ----t----gaggaagtagggacagg-gcatat-t-------cgg-gaatt----g---agtcggggctc
B D                     Shrew  ----t----caaggagtagggacagg-gcgttt-t----cc-ggg-caccg----g---ggtcggggctc
              Star-nosed mole  ----t----gaa--agtagggacagg-gcatat-gaacaca-tgg-tattt----g---ggtcaagggtt
B D                  Elephant  ----c----gagagagtagggacagg-gcatgt---------------tca----g---ggtcaggggtc
          Cape elephant shrew  ----t----gagagagtagggacatg-gcatgc-t----ca-ggg-agtca----g---ggtcaagggtc
B D                   Manatee  ----t----gagagagtagggacagg-gtatgt-t----ca-ggg-tacct----g---ggtcagaggtc
             Cape golden mole  ----t----gagagagtaggaacagg-gcatat-t----aatggg-tatca----g---gatcaagggtc
B D                    Tenrec  ----c----tagagagtagggacaag-gcaggt-t----ga-ggt-gatgc----g---ggtcagggctc
                     Aardvark  ----t----gaaaaagtaggaacagg-gcacat-t----ca-cgg-tatca----g---ggtcaggggac
B D                 Armadillo  ----t----gagagagtagggata-g-gtatat-t----ta-ggg-tatcg----g---ggtcaagggtc
B D                   Opossum  ----c----agtgcagaggtaacagg-acaagc-c----ta-gag-tattg----a---agtcaaggacc
B D           Tasmanian devil  ----t----agagcagaggtaacagg-acaagc-c----ta-agc-tattg----a---ggtcaagggtc
B D                   Wallaby  ----t----tgggcagaggtaacagg-gcaagc-c----ta-ggg-tatgg----a---ggtccagggtc
  D               Rock pigeon  ----t----ggggttgtggagatagg-acagga------ca-gcg-cttcc----a---aggtttgggtt
  D              Saker falcon  ----t----ggggctgtggggatagg-atgggg------ca-gcg-catcc----a---aggtttgggtt
  D          Peregrine falcon  ----t----ggggctgtggggatagg-atgggg------ca-gcg-catcc----a---aggtttgggtt
  D       Collared flycatcher  ----g----agggctgtcgggatagg-acaaga------ca-gca-tgccc----a---aggtctgggtt
  D    White-throated sparrow  ----g----agggctgtggggatagg-acaaga------ca-gtg-tgccc----a---aggtctgggct
B D       Medium ground finch  ----g----agggctgtggggatagg-acaaga------ca-gtg-tgccc----a---aggtctgggtt
B D               Zebra finch  ----g----agggctgtggggatagg-acaaga------ca-gca-cgccc----a---aggtctgggtt
           Tibetan ground jay  ----g----agggctgtggggatagg-acaaga------ca-gca-tgccc----c---aggcctgggtt
B D                Budgerigar  ----a----ggggctatggggatagg-ataggc------ta-gag-aaaaa----aaacaggtttgggtt
  D                    Parrot  ----a----ggggctatggggatagg-ataggc------ca-gtg-aaaaa----aaacaggtttgggtt
  D             Scarlet macaw  ----a----gaggctatggggatagg-ataggc------ca-gtg-agaaa----aaccaggtttgggtt
  D              Mallard duck  ----g----ggggctgcgggaacagg-gttgga------ga-gcg--ctcc----c---aggtttgggtt
B D                   Chicken  ----g----gtgactg-gggaacagg-atggga------aa-gtg-cctcc----g---aggttttggtt
B D                    Turkey  ----g----gtgactg-gggaacagg-atggga------aa-gtg-cctct----g---aggttttggct
B D        American alligator  ----t----aaggttatggggacagg-gtgcac------tg-atggtgtcc----a---aggtgtggg-t
  D           Green seaturtle  ---------caggatgtggggacagg-gtaaac-t----ta-gca-tctct----g---ggtcctgggtc
  D            Painted turtle  ---------caggggatggggacagg-gtgaac-t----ta-gca-tctct----g---ggtcctgggtc
  D  Chinese softshell turtle  ----g----cagggcatggggacaga-atgaac-t----tg-gtg-tcttt----g---ggtcctgggtc
  D    Spiny softshell turtle  ----t----cagggcatggggacaga-atgaac-t----tg-gtg-tcttt----g---ggtcctgggtc
B D                    Lizard  ----a----aggga-atggggacagg-gccaac-t----tc-ata-cgcct----g---ggctataggtt
B D             X. tropicalis  ----t----gatggtgtaagagggaa-ggatg-------ca-gaa-ca--g----a---ggtcattgctc
B D                Coelacanth  ----a----cattttttggggggggg-ttactc-t----tt-agg-t-caa----a---ggtcaagtgtg
B D               Stickleback  tgtct----aacgatgttggatgaat-gtacatgt----ca-gca-ggcaa----g---aagct------
B D              Atlantic cod  ======================================================================
                 Spotted gar  ======================================================================
          Southern platyfish  ======================================================================
      Yellowbelly pufferfish  ======================================================================
B D                      Fugu  ======================================================================
B D                 Tetraodon  ======================================================================
B D                 Zebrafish  ======================================================================
B D                    Medaka  ======================================================================
         Pundamilia nyererei  ======================================================================
                 Zebra mbuna  ======================================================================
       Burton's mouthbreeder  ======================================================================
         Princess of Burundi  ======================================================================
B D              Nile tilapia  ======================================================================
B D                  Platypus  ======================================================================
B D                       Pig  ======================================================================

                        Human  ct
                        Chimp  ct
                      Gorilla  ct
                    Orangutan  cc
                       Gibbon  cc
                       Rhesus  cc
          Crab-eating macaque  cc
                       Baboon  cc
                 Green monkey  cc
                     Marmoset  cc
              Squirrel monkey  cc
                     Bushbaby  ct
           Chinese tree shrew  cc
                     Squirrel  tc
       Lesser Egyptian jerboa  tc
                 Prairie vole  cc
              Chinese hamster  cc
               Golden hamster  cc
                        Mouse  tc
                          Rat  tc
               Naked mole-rat  tc
                   Guinea pig  tc
                   Chinchilla  tc
             Brush-tailed rat  tc
                       Rabbit  cc
                         Pika  tc
                       Alpaca  cc
               Bactrian camel  cc
                      Dolphin  cc
                 Killer whale  cc
             Tibetan antelope  cc
                          Cow  cc
                        Sheep  cc
                Domestic goat  cc
                        Horse  cc
             White rhinoceros  cc
                          Cat  cc
                          Dog  cc
                      Ferret   cc
                        Panda  cc
               Pacific walrus  cc
                 Weddell seal  cc
             Black flying-fox  ct
                      Megabat  ct
                Big brown bat  cc
         David's myotis (bat)  cc
                     Microbat  cc
                     Hedgehog  ct
                        Shrew  cc
              Star-nosed mole  ca
                     Elephant  cc
          Cape elephant shrew  cc
                      Manatee  ct
             Cape golden mole  tc
                       Tenrec  cc
                     Aardvark  cc
                    Armadillo  cc
                      Opossum  ct
              Tasmanian devil  cc
                      Wallaby  cc
                  Rock pigeon  gc
                 Saker falcon  gc
             Peregrine falcon  gc
          Collared flycatcher  gc
       White-throated sparrow  gc
          Medium ground finch  gc
                  Zebra finch  gc
           Tibetan ground jay  gc
                   Budgerigar  gt
                       Parrot  gt
                Scarlet macaw  gt
                 Mallard duck  gc
                      Chicken  gc
                       Turkey  gt
           American alligator  at
              Green seaturtle  ac
               Painted turtle  ac
     Chinese softshell turtle  tc
       Spiny softshell turtle  ac
                       Lizard  gc
                X. tropicalis  ta
                   Coelacanth  tc
                  Stickleback  --
                 Atlantic cod  ==
                  Spotted gar  ==
           Southern platyfish  ==
       Yellowbelly pufferfish  ==
                         Fugu  ==
                    Tetraodon  ==
                    Zebrafish  ==
                       Medaka  ==
          Pundamilia nyererei  ==
                  Zebra mbuna  ==
        Burton's mouthbreeder  ==
          Princess of Burundi  ==
                 Nile tilapia  ==
                     Platypus  ==
                          Pig  ==

Alignment block 9 of 10 in window, 6510487 - 6510548, 62 bps 
B D                     Human  aaaggac-----ttagcttg-tgttatggccactgagagatgaaacacagatctttggtaatctgatg
B D                     Chimp  aaaggac-----ttagcttg-tgttatggccactgagagatgaaacacagatctttggtaatctgatg
B D                   Gorilla  aaaggac-----ttagcttg-tgttacggccactgagagatgaaacacagatctttggtaatctgatg
B D                 Orangutan  aaaggac-----ttagcttg-tgttatggccactgagagatgaaacacagatctttggtaatctgatg
B D                    Gibbon  aaaggac-----ttagcttg-tgttatggccactgagagatgaaacacagatctttggtaatctgatg
B D                    Rhesus  aaaggac-----ttagcttg-tattatggccactgagagatgaaacacagatctttggtaatctgatg
B D       Crab-eating macaque  aaaggac-----ttagcttg-tattatggccactgagagatgaaacacagatctttggtaatctgatg
B D                    Baboon  aaaggac-----ttagcttg-tgttatggccactgagagatgaaacacagatctttggtaatctgatg
B D              Green monkey  aaaggac-----ttagcttg-tgttatggccactgagagatgaaacacagatctttggtaatctgatg
B D                  Marmoset  aaaggac-----ttagctcg-tattatgaccactgagagatgaaacatagatctttggtaatctgatg
B D           Squirrel monkey  aaaggac-----ttagcttg-tattatgaccgctgagagatgaaacacagatctttggtaatctgatg
B D                  Bushbaby  aaaggac-----ttagctta-tgttatggccactgagagatgaaacacagatctttggtaatctgatg
           Chinese tree shrew  taaggac-----tcagccgg-cgtggtggccaccgagagatgaggcacagatctttggtaatctgatg
B D                  Squirrel  aaaggac-----ttagcta--tattttgaccactgagagatgaaacacagatctttggtaatctgatg
       Lesser Egyptian jerboa  aaaggac-----ttggcta--tgttgtgaccactgagagatgaaacacagatctttggtaatctgatg
                 Prairie vole  aaaggac-----ttagctg--tgtcatggccactgagagatgatacacagatctttggtaatctgatg
B D           Chinese hamster  aaaggac-----ttagcta--tatcatggccactgagagatgacacacagatctttggtaatctgatg
               Golden hamster  aaaggac-----ttagctg--tgtcataaccactgagagatgacacacagatctttggtaatctgatg
B D                     Mouse  aaaggac-----ttagctg--tgtcatggccactgagagatgacacacagatctttggtaatctgatg
B D                       Rat  aaaggac-----ttagctg--cgtcatggccactgagagatgacacacagatctttggtaatctgatg
B D            Naked mole-rat  aaagggc-----ttagctc--tc--atggccactgagagatgaaacacagatctttggtaatctgatg
B D                Guinea pig  caaggac-----ttagctc--tcttatggccactgagagatgaaacatagatctttggtaatctgatg
                   Chinchilla  caaggtc-----ttagctc--tc-tatggccactgagagatgaaacatagatctttggtaatctgatg
             Brush-tailed rat  caaggtc-----ttagctc--tcttatggccactgagagatgaaacatagatctttggtaatctgatg
B D                    Rabbit  aaaggac-----ttagctta-tagcatggccactgagagatgaaacacagatctttggtaatctgatg
B D                      Pika  tgaggac-----ttagctcattagcacggccgctgagagatgaaacacagatctttggtaatctgatg
B D                    Alpaca  aaagggc-----ttagcttg-tgttgtggccactgagagatgaaacacagatctttggtaatctgatg
               Bactrian camel  aaagggc-----ttagtttg-tgttgtggccactgagagatgaaacacagatctttggtaatctgatg
B D                   Dolphin  agaggat-----ttagcttg-tgttgtagccactgagagatgaaacacagatctttggtaatctgatg
                 Killer whale  agaggac-----ttagcttg-tgttgtagccactgagagatgaaacacagatctttggtaatctgatg
             Tibetan antelope  agaggac-----ttggcctg-tgctgtggccactgagagatgagacacagatctttggtaatctgatg
B D                       Cow  agaggac-----ttagcctg-tgctgtggccactgagagatgaaacacagatctttggtaatctgatg
B D                     Sheep  agaggac-----ttggcctg-tgctgtggccactgagagatgagacacagatctttggtaatctgatg
                Domestic goat  agaggac-----ttggcctg-tgctgtggccactgagagatgagacacagatctttggtaatctgatg
B D                     Horse  aaaggac-----ttagcttg-tcttgtggccactgagagatgaaacacagatctttggtaatctgatg
B D          White rhinoceros  aaaggac-----ttagctta-tattatggccactgagagatgaaacacagatctttggtaatctgatg
B D                       Cat  aaaggac-----ttggcttg-tgttgtggccactgagagatgaaacacagatctttggtaatctgatg
B D                       Dog  aaaggat-----ttagcttg-tgttgtggccactgagagatgaaacacagatctttggtaatctgatg
B D                   Ferret   aaaggac-----ttggcttg-tgttgtgaccactgagagatgaaacacagatctttggtaatctgatg
B D                     Panda  aaaggac-----ttggcttg-tgttgtgaccactgagagatgaaacacagatctttggtaatctgatg
               Pacific walrus  aaaggac-----ttggcttg-tgttgtgaccactgagagatgaaacacagatctttggtaatctgatg
                 Weddell seal  aaaggac-----ttggcttg-tgttgtgaccactgagagatgaaacacagatctttggtaatctgatg
             Black flying-fox  aaaggac-----ttagcttg-tatcgtagccactgagagatgaaacacagatctttggtaatctgatg
B D                   Megabat  aaaggac-----ttagcttg-tatcgtagccactgagagatgaaacacagatctttggtaatctgatg
                Big brown bat  aaaggac-----ttagcttg-tgttgtggccactgagaaatgaaacacagatctttggtaatctgatg
         David's myotis (bat)  aaaggac-----ttagctgg-tgttgtggccactgagaaatgaaacacagatctttggtaatctgatg
B D                  Microbat  aaaggac-----ttagctgg-tgttgtggccactgagaaatgaaacacagatctttggtaatctgatg
B D                  Hedgehog  gaagggc-----ttagcttg-tgtcatggccactgagagatgaaatacatatctttggtaatctgatg
B D                     Shrew  gagagac-----ttggcctg-tgctgtggccgctg-gagatg-aacacagatctttggtaatctgatg
              Star-nosed mole  aag-gac-----ttagtctg-cgttatagccactgagagatgaaacatagatctttggtaatctgatg
B D                  Elephant  aaaggac-----ttagcttg-tattgtgaccactgagagatgaaacacagatctttggtaatctgatg
          Cape elephant shrew  -aaggac-----ttagcttc-tattgtgaccgctgagaaatgaaacacatatctttggtaatctgatg
B D                   Manatee  aaaggac-----ttagcttg-tattgtgaccactgagagatgagacacagatctttggtaatctgatg
             Cape golden mole  aaaggac-----ttagctga-tattgtgaccactgagagatgaaacacagatctttggtaatctgatg
B D                    Tenrec  aaaggac-----atagtctg-tattgtgaccactgagagatgaaacacatatctttggtaatctgatg
                     Aardvark  aaaggac-----ttggcttc-tattgtgaccactgagaaatgaaacacagatctttggtaatctgatg
B D                 Armadillo  aaaagac-----ttagcttg-tgctatggccactgagagatgaaacacagatctttggtaatctgatg
B D                   Opossum  agaaggc-----ttagcatg-tgatatagccgccaagagatgag-cacagatctttggtaatctgatg
B D           Tasmanian devil  agaaggc-----ttagcttt-tgttatagccaccaagagatgag-cacagatctttggtaatctgatg
B D                   Wallaby  agaaggc-----ttagctta-tattatagccaccaagagatgag-cacagatctttggtaatctgatg
  D               Rock pigeon  agggggc-------agccct-tgttacagctgtcaagatgtgag-cacacatctttggtaatctgatg
  D              Saker falcon  agggggc-------agccct-tattacagctggtaagatgtgag-cac--gtctttggtaatctgatg
  D          Peregrine falcon  agggggc-------agccct-tattacagctggtaagatgtgag-cac--gtctttggtaatctgatg
  D       Collared flycatcher  agggggc-------agccca-tgttacagctggtgagatgtgag-cacacatctttggtaatctgatg
  D    White-throated sparrow  agggggc-------agcccg-tgttacagctggtgagatgtgag-cacacatctttggtaatctgatg
B D       Medium ground finch  agggggc-------agcccg-tgttacagctgatgagatgtgag-cacacatctttggtaatctgatg
B D               Zebra finch  agggggc-------agccca-tgttacagctggtgagatgtgag-cacacatctttggtaatctgatg
           Tibetan ground jay  agggggc-------agccca-cgttacagctggtgagatgtgag-cacacatctttggtaatctgatg
B D                Budgerigar  aggaggc-------agccca-tattacagctggtgagatgtgag-cacatgtctttggtaatctgatg
  D                    Parrot  agggggc-------agccca-cattacagctggtgagatgtgag-cacacatctttggtaatctgatg
  D             Scarlet macaw  agggggc-------agccca-cgttacagctggtgagatgtgag-cacacatctttggtaatctgatg
  D              Mallard duck  agggggc-------agcc-----ttgcagctggcaagatgtgag-cacacatctttggtaatctgatg
B D                   Chicken  agggggc-------agccca-tgttacagctggtgagacgtgag-cacacatctttggtaatctgatg
B D                    Turkey  aggaggc-------agccca-tgttac-gctggtgagatgtgag-cacacatctttggtaatctgatg
B D        American alligator  gggatgt-------ggccca-ggtcaaagctggtgagagatgag-cacaggtctttggtaatctgatg
  D           Green seaturtle  cgggtgt-------agccca-aattatggctggtgaggcatgag-cacagttctttggtaatctgatg
  D            Painted turtle  agggtgt-------agccca-aattatggctggtgaggcatgag-cacagttctttggtaatctgatg
  D  Chinese softshell turtle  agggtgt-------agtcca-gattatggccagtgaggcatgag-cacagttctttggtaatctgagg
  D    Spiny softshell turtle  agggtgt-------agtcca-gattatggccagtgaggcatgag-cacagttctttggtaatctgatg
B D                    Lizard  tgggtgc-------tgccag-aatgctggctgttggggcatgag-cacaagtctttggtaatctgaaa
B D             X. tropicalis  ataggga-----gaggtaca-catgacag------------------tgcatctttggtaatctgatg
B D                Coelacanth  a-------------agtcta-c-cgatagccagtagggcatgag-ctcatatctttggtaatctgatg
           Southern platyfish  -aaaggctgtagtctatggc-aggtttgacagat-----atgaa-cagtcatctttggtaatctgagg
B D               Stickleback  -aacgtc-----tctacagg-ggttttgaccatt-----atgaa-ttacagtctttggtaacctgagg
B D              Atlantic cod  ====================================================================
                 Spotted gar  ====================================================================
      Yellowbelly pufferfish  ====================================================================
B D                      Fugu  ====================================================================
B D                 Tetraodon  ====================================================================
B D                 Zebrafish  ====================================================================
B D                    Medaka  ====================================================================
         Pundamilia nyererei  ====================================================================
                 Zebra mbuna  ====================================================================
       Burton's mouthbreeder  ====================================================================
         Princess of Burundi  ====================================================================
B D              Nile tilapia  ====================================================================
B D                  Platypus  ====================================================================
B D                       Pig  ====================================================================

Inserts between block 9 and 10 in window
          Southern platyfish 102bp

Alignment block 10 of 10 in window, 6510549 - 6510551, 3 bps 
B D                     Human  gct
B D                     Chimp  gct
B D                   Gorilla  gct
B D                 Orangutan  gct
B D                    Gibbon  gct
B D                    Rhesus  gct
B D       Crab-eating macaque  gct
B D                    Baboon  gct
B D              Green monkey  gct
B D                  Marmoset  gct
B D           Squirrel monkey  gct
B D                  Bushbaby  gct
           Chinese tree shrew  gcg
B D                  Squirrel  gct
       Lesser Egyptian jerboa  gct
                 Prairie vole  gct
B D           Chinese hamster  gct
               Golden hamster  gct
B D                     Mouse  gct
B D                       Rat  gct
B D            Naked mole-rat  gcc
B D                Guinea pig  gct
                   Chinchilla  gcc
             Brush-tailed rat  gct
B D                    Rabbit  gct
B D                      Pika  gct
B D                    Alpaca  gct
               Bactrian camel  gct
B D                   Dolphin  gct
                 Killer whale  gct
             Tibetan antelope  gct
B D                       Cow  gct
B D                     Sheep  gct
                Domestic goat  gct
B D                     Horse  gct
B D          White rhinoceros  gct
B D                       Cat  gct
B D                       Dog  gct
B D                   Ferret   gct
B D                     Panda  gct
               Pacific walrus  gct
                 Weddell seal  gct
             Black flying-fox  gtt
B D                   Megabat  gtt
                Big brown bat  gct
         David's myotis (bat)  gct
B D                  Microbat  gct
B D                  Hedgehog  gct
B D                     Shrew  gct
              Star-nosed mole  gct
B D                  Elephant  gct
          Cape elephant shrew  gct
B D                   Manatee  gct
             Cape golden mole  gct
B D                    Tenrec  gct
                     Aardvark  gct
B D                 Armadillo  gct
B D                   Opossum  gct
B D           Tasmanian devil  gct
B D                   Wallaby  gct
  D               Rock pigeon  act
  D              Saker falcon  gct
  D          Peregrine falcon  gct
  D       Collared flycatcher  act
  D    White-throated sparrow  gct
B D       Medium ground finch  gct
B D               Zebra finch  gct
           Tibetan ground jay  act
B D                Budgerigar  act
  D                    Parrot  act
  D             Scarlet macaw  act
  D              Mallard duck  gct
B D                   Chicken  act
B D                    Turkey  act
B D        American alligator  gct
  D           Green seaturtle  gct
  D            Painted turtle  gct
  D  Chinese softshell turtle  gct
  D    Spiny softshell turtle  gct
B D                    Lizard  gct
B D             X. tropicalis  g--
B D                Coelacanth  gcc
B D               Stickleback  g--
B D              Atlantic cod  ===
                 Spotted gar  ===
          Southern platyfish  ===
      Yellowbelly pufferfish  ===
B D                      Fugu  ===
B D                 Tetraodon  ===
B D                 Zebrafish  ===
B D                    Medaka  ===
         Pundamilia nyererei  ===
                 Zebra mbuna  ===
       Burton's mouthbreeder  ===
         Princess of Burundi  ===
B D              Nile tilapia  ===
B D                  Platypus  ===
B D                       Pig  ===

View table schema

Go to Conservation track controls

Data last updated: 2015-05-07

Downloads for data in this track are available:

Description

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

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

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

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

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

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

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

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

Display Conventions and Configuration

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

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

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

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

Gap Annotation

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

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

Genomic Breaks

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

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

Base Level

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

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

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

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

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

Methods

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

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

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

Phylogenetic Tree Model

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

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

PhastCons Conservation

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

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

PhyloP Conservation

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

Conserved Elements

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

Credits

This track was created using the following programs:

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

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

References

Phylo-HMMs, phastCons, and phyloP:

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

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

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

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

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

Chain/Net:

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

Multiz:

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

Lastz (formerly Blastz):

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

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

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

Phylogenetic Tree:

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