Multiz Alignments of 100 Vertebrates
 

Capitalize exons based on show bases
Place cursor over species for alignment detail. Click on 'B' to link to browser for aligned species, click on 'D' to get DNA for aligned species.
Alignment block 1 of 1 in window, 25621106 - 25640645, 19540 bps 
B D  Human  gatatttggaccactctgtgtccttcgttcgagacgggtatatcttcacacgacatctagacagaagctt
B D  Chimp  ======================================================================

     Human  tctcagaaaattctttgggatgattgagttgaactcacagagctgaacattccttgcgatgtagcagttt
     Chimp  ======================================================================

     Human  agaaacacactttctgcagaatctgcaagtgcatatttagacctctctgaggaattcgttggaaacggga
     Chimp  ======================================================================

     Human  taatttcagctgactaaacagaagcattctcagaaccttcttcgtgatgtctgcattcaactcacagtgt
     Chimp  ======================================================================

     Human  ggaacctttctttgatagttcaggtttgaaacactctttttgtagaaactgcaaggggataattgcactt
     Chimp  ======================================================================

     Human  ctttgaggcctaccgtagcaaaagaaataacttcctataaaaagaagacagaagcattctcagaaccttc
     Chimp  ======================================================================

     Human  ttcgtgatgtttgcattcaactcacagtgctgaacctttctttgatagttcagctttgaaacactctttt
     Chimp  ======================================================================

     Human  tgtagaaacagcaagtggatatttcgtcctctctgaggatttcgttggaaacgggataaaccgcacagaa
     Chimp  ======================================================================

     Human  ctaaacagaagcattcacagaaaactcttggtgacgactgagtttaactcacagagctgaacattccttt
     Chimp  ======================================================================

     Human  ggatggagcagtttcgaaacacactatttgtagaatgtgcaagtggatatgtgggcctctctgaggattt
     Chimp  ======================================================================

     Human  cgttggaaacgggataaaccgcacagaactaaacagaagcattctcagaaactactttgtgatgattgca
     Chimp  ======================================================================

     Human  ttcaagtcacagagttgaacattccctttgacagagcagtttggaaactctctttgtgtagaatctgcaa
     Chimp  ======================================================================

     Human  gtggagatatggaccgctttgaggcctatggtagtaaaggaaatagcttcatataaaagctagacagtag
     Chimp  ======================================================================

     Human  cattctcagaaacttctttgtgatgcttgcattcaactcacagagttgaactttcctttcgagagagaag
     Chimp  ======================================================================

     Human  ccttgaaacactctttttccagaatctgcaagtggacatttggagggctttgaggcctgtggtggaaaag
     Chimp  ======================================================================

     Human  gaattatcttcccgtaaaagctagatagaagcattgtcagaaacttctttgtgatgattgcattcaactc
     Chimp  ======================================================================

     Human  acagagttgaaggttccttttcaaagagcagtttccaatcactctttctgtggaatctgcaagtggatat
     Chimp  ======================================================================

     Human  ttggacctctttgaagatttcgttggaaacgggagaatcttcacagaaaagctaaacagaagcattctca
     Chimp  ======================================================================

     Human  gaaacttctctgtgatgtttgtgttcaactcccagagtttcacattgcttttcatagagtagttctgaaa
     Chimp  ======================================================================

     Human  catgcttttcgtagtgtctacaagtggacatttggagcgctttcaggcctgtggtggaaaacgaattatg
     Chimp  ======================================================================

     Human  gtcacataaaaactggagagaagccttctcagaaacttctctgtgatgattgcattcaactcacagagtt
     Chimp  ======================================================================

     Human  gaaccctcctatggatagagcagtgttgaaactctctttttgtggaatctgcaagtggatatgtggacct
     Chimp  ======================================================================

     Human  ctccgaagatgtctttggaaacgggaatatcttcacataaaaactaaacagaagcattctcagaaacttc
     Chimp  ======================================================================

     Human  ttggtgatgtttgcattcaaatcccagagttgaaccttcctttgatagttcaggtttgaaacactctttt
     Chimp  ======================================================================

     Human  tgtaggatctgcaagtggatatttggaccactctgtggccttcgttcgaaacgggtatatcttcgcataa
     Chimp  ======================================================================

     Human  aatctagacagaagcattctcagaaaatactttgtgatgattgagtttaactcacagagctgaacatttc
     Chimp  ======================================================================

     Human  tttggatggagcaggtttgagacacaccttttgtagaatctacaagtggatatttggacctctctgagga
     Chimp  ======================================================================

     Human  tttcgttggaaacgggataactgcacctaactaaacggaagcattctcagaaactgctttgtgatgattg
     Chimp  ======================================================================

     Human  cattcacctcacagagttgaacattcctattgatagagcagtttggaaacactcttgttgtggaatgtgc
     Chimp  ======================================================================

     Human  aagtggagatttggagcgctttgaggcctatggtagtaaagggaatagcttcatagaaaaactagacaga
     Chimp  ======================================================================

     Human  tgcattctcaggaactttttggtgatgtttgtattcaactcccagagttgaactttcctttggaaagagc
     Chimp  ======================================================================

     Human  agctatgaaacactctttttctagaatctgcaagtggacgtttggagggctttgtggtttgtggtggaaa
     Chimp  ======================================================================

     Human  aggaaatatcttcacttaaatactagatagaagcattctcagaagcttctctgtgatgactgcattcaac
     Chimp  ======================================================================

     Human  tcacggagttgaacactccttttgagagcgcagttttgaaactctctttctgtggcatccgcaaggggac
     Chimp  ======================================================================

     Human  atgtggacctctttgaaggtttcgttggaaacggaatcatcttcacataaaaactatacagaagcagtct
     Chimp  ======================================================================

     Human  cagaatcttctttgtgatgtttgcattcaaatcccagagttgaacttgcctttcaaagttcacgtttgaa
     Chimp  ======================================================================

     Human  acactctttttgcaggatctacaagtggatatttggaccactctgtgtccttcgttcgaaacgggtatat
     Chimp  ======================================================================

     Human  cttcacatgacatctagacagaagctttctcagaaaattctttgggatgattgagtggaactcacagagc
     Chimp  ======================================================================

     Human  tgaacattccttgcgatgtagcagtttagaaacacactttctgcagaatctgcaagtgcatatttggacc
     Chimp  ======================================================================

     Human  tctctgaggaattcgttggatacgggataatttcagctgactaaacagaagcattctcagaaccttcttc
     Chimp  ======================================================================

     Human  gtgatgtctgcattcaactcacagtgtggaacctttctttgatagttcaggtttgaaacactctttttgt
     Chimp  ======================================================================

     Human  agaaactgcaaggggataattgcacttctttgaggcctaccgtagtaaaggaaataacttcctatagaaa
     Chimp  ======================================================================

     Human  gaagacagaagcattctcagaaccctcttcgtgatgtttgcattcaactcacagtgctgaacctttcttt
     Chimp  ======================================================================

     Human  gatagttcagctttgaaacactcttcttgtagaaactgcaagtggatatttggtcctctctgaggatttc
     Chimp  ======================================================================

     Human  gttggaaacgggataaaccgcacagaactaaacagaagaattctcagagccctattcgtgatgtttgcat
     Chimp  ======================================================================

     Human  tcaactcacagtgctgaacctttctttgatagtgcagctttgaaacactctttttgtagaaactgcaagt
     Chimp  ======================================================================

     Human  cgatatttggtcctctctgaggatttcgttggaaacgggataaaccgcacagaactaaaacagaagcatt
     Chimp  ======================================================================

     Human  cacagaaaactcttggtgacgactgagtttaactcacagagctgaacattcctttggatggagcagtttc
     Chimp  ======================================================================

     Human  gaaacacactatttgtagaatctgcaagtggatatttgggcctctctgaggatttcgttggaaacgggat
     Chimp  ======================================================================

     Human  aaaccgcacagaactaaaacagaagcattctcagaaactactttgtgatgattgcattcaagtcacagag
     Chimp  ======================================================================

     Human  ttgaacattccctttgacagagcagtttggaaactctctttgtgtagaatctgcaagtggagatatggac
     Chimp  ======================================================================

     Human  cgctttgaggcctatggtagtaaaggaaatagcttcatataaaagctagacagtagcattctcagaaact
     Chimp  ======================================================================

     Human  tctttgtgatgcttgcattcaactcacagagttgaactttcctttcgagagagaagctttgaaacactct
     Chimp  ======================================================================

     Human  ttttccagaatctgcaagtggacatttggagggctttgaggcctgtggtggaaaaggaattaacttcccg
     Chimp  ======================================================================

     Human  taaaagctagatagaagcattgtcagaaacttctttgtgatgattgcattcaactcacggagatgaaggt
     Chimp  ======================================================================

     Human  tcctttacaaacagcagtttccaaacactctttctgtggaatctgcaagtggatatttggacctctttga
     Chimp  ======================================================================

     Human  agatttcgttggaaacgggagaatcttcacagaaaatctaaacagaagcattctcagaaacttctctgtg
     Chimp  ======================================================================

     Human  atgtttgtgttcaactcccagagtgtcacattgcttttcatagagtagttctgaaacgtgcttttcgtag
     Chimp  ======================================================================

     Human  tgtctgcaagtggacatttggagcgctttcaggcctgtggtggaaaacgaattatggtcacataaaaact
     Chimp  ======================================================================

     Human  ggagagaagccttctcagaaacttctctgtgatgattgcattcaactcacagagttgaaccctcctatgg
     Chimp  ======================================================================

     Human  atagagcagtgttgaaactctctttttgtggaatctgcaagtggatatgtggacctctccgaagatgtct
     Chimp  ======================================================================

     Human  ttggaaacgggaatatcttcacataaaaactacacagaagcattctcagaaacttcttggtgatgtttgc
     Chimp  ======================================================================

     Human  attcacatcgcagagttgatccttcctttgatagttcaggtttgaaacactctttttgtaggatctgcaa
     Chimp  ======================================================================

     Human  gtggatatttggaccactctgtggccttcgttcgaaacgggtacatcttcgcataaaatctagacagaag
     Chimp  ======================================================================

     Human  cattctcagaaaatactttgtgatgattgagtttaactcacagagctgaacattcctttggatggagcag
     Chimp  ======================================================================

     Human  gttcgagacacactttttgtaggatctacaagtggatatttggacctctctgaggatttcgttggaaacg
     Chimp  ======================================================================

     Human  ggataactgcaccgaactaaacggaagcattctcagaaactgctttgtgatgattgcattcacctcacag
     Chimp  ======================================================================

     Human  agttgaacattcctattgatagagcagtttggaaacactcttgttgtggaatgtgcaagtggagatttgg
     Chimp  ======================================================================

     Human  agcgctttgaggcctatggtagtaaagggaatagcttcatagaaaaactagacagatgcattctcaggaa
     Chimp  ======================================================================

     Human  ctttttggtgatgtttgtattcaactcccagagttgaactttcctttggaaagagcagctatgaaacact
     Chimp  ======================================================================

     Human  ctttttctagaatctgcaagtggacgtttggagggctttgtggtttgtggtggaaaaggaaatatcttca
     Chimp  ======================================================================

     Human  cctaaatactaggatagaagcatcctcagaagcttttctgtgatgactgcattcaactcacggagttgaa
     Chimp  ======================================================================

     Human  cactccttttgagagcgcagttttgaaactctctttctgtggcatccgcaaggggacatgtggacctctt
     Chimp  ======================================================================

     Human  tgaagatttcgttggaaacggaatcatcttcacataaaaattatacagaagcagtctcagaatcttcttt
     Chimp  ======================================================================

     Human  gtgatgtttgcattcaaatccccgagttgaactttcctttcaaagttcacgtttgaaacactctttttgc
     Chimp  ======================================================================

     Human  aggatctacaagtggatatttggaccactctgtgtccttcgttcgaaacgggtatatcttcacatgacat
     Chimp  ======================================================================

     Human  ctagacagaagctttctcagaaaattctttgggatgattgagttgaactcacagagctgagcattccttg
     Chimp  ======================================================================

     Human  cgatgtagcagtttagaaacacactttctgcagaatctgcaagtgcatatttggacctctgtgaggaatt
     Chimp  ======================================================================

     Human  cgttggaaacgggataatttcagctgactaaacagaagcattctcagaaccttcttcatgatgtctgcat
     Chimp  ======================================================================

     Human  tcaactcacagtgtggaacctttctttgatagttcaggtttgaaacactctttttgtagaaactgcaagg
     Chimp  ======================================================================

     Human  ggataattgcactctttgaggagtaccgtagtaaaggaaataacttcctataaaaagaagacagaagcat
     Chimp  ======================================================================

     Human  tctcagaaccctcttcgtgatgtttgcattcaactcacagtgctgaacctttctttgatagttcagcttt
     Chimp  ======================================================================

     Human  gaaacactctttttgtagaaactgcaagtggatatttggtcctctctgaggatttcgttggaaacgggat
     Chimp  ======================================================================

     Human  aaactgcacagaactaaacagaagcattctcagaaccttcttcgtgatgtttgcattcaactcacagtgt
     Chimp  ======================================================================

     Human  tgaacctttctttgatagttcaggtttgaaacggtctttctgtagaaactgcaagtagatatttggacct
     Chimp  ======================================================================

     Human  ctctgaggatttcgttggaaacgggataacccgcacagaactaaaacagaagcattcacagaaaactctt
     Chimp  ======================================================================

     Human  ggtgacgactgagtttaactcacagagctgaacattcctttggatggagcagtttcgaaacacactattt
     Chimp  ======================================================================

     Human  gtagaatgtgcaagtggatatttaggcctctctgaggatttcgttggaaacgggataaaccgcacagaac
     Chimp  ======================================================================

     Human  taaacagaagcattctcagaaactactttgtgatgattgcattcaagtcacagagttgaacattcccttt
     Chimp  ======================================================================

     Human  gacagagcagtttggaaactctctttgtgtagaatctgcaagtggagatatggaccgctttgaggcctat
     Chimp  ======================================================================

     Human  ggtagtaaaggaaatagcttcatataaaacctagacagtagcattctcagaaacttctttgtgatgcttg
     Chimp  ======================================================================

     Human  cattcaactcacagagttgaactttcctttcgagagagaagctttgaaacactctttttccagaatgtgc
     Chimp  ======================================================================

     Human  aagtggacatttggggagctttgaggcctgtggaggaaaaggaattatcttcccgtaaaagctagataga
     Chimp  ======================================================================

     Human  agcattgtcagaaacttctttgtgatgattgcattcaactcacagagttgaaggttccttttcaaacagc
     Chimp  ======================================================================

     Human  agtttccaatcactctttctgtggaatctgcaagtggatatttcgacctctttgaagatttcgttggaaa
     Chimp  ======================================================================

     Human  cgggagaatcttcacagaaaagctaaacagaagcattctcagaaacttctctgtgatgtttgtgttcaac
     Chimp  ======================================================================

     Human  tcccagagtttcacattgcttttcatagagtagttctgaaacatgcttttcgtagtgtctacaagtggac
     Chimp  ======================================================================

     Human  atttggagcgctttcaggcctgtggtggaaaacgaattatggtcacataaaaactggagagaagccttct
     Chimp  ======================================================================

     Human  cagaaacttctctgtgatgattgcattcaactcacagagttgaaccctcctatggatagagcagtgttga
     Chimp  ======================================================================

     Human  aactctctttttgtggaatctgcaagtggatatgtggacctctccgaagatgtctttggaaacgggaata
     Chimp  ======================================================================

     Human  tcttcacataaaaactaaacagaagcattctcagaaacttcttggtgatgtttgcattcaaatcccagag
     Chimp  ======================================================================

     Human  ttgaaccttcctttgatagttcaggtttgaaacactctttttgtaggatctgcaagtggatatttggacc
     Chimp  ======================================================================

     Human  actctgtggccttcgttcgaaacgggtacatcttcgcataaaatctagacagaagcattctcagaaaata
     Chimp  ======================================================================

     Human  ctttgtgatgattgagtttaactcacagagctgaacattcctttggatggagcaggtttgagacacactt
     Chimp  ======================================================================

     Human  tttgtagaatctacaagtggatatttggacctctctgaggatttcgttggaaacgggataactgcaccta
     Chimp  ======================================================================

     Human  actaaacggaagcattctcagaaactgcttgtgatgattgcattcaactcacagagttgaacattcctat
     Chimp  ======================================================================

     Human  tgatagagcagtttggaaacactcttgttgtggaatgtgcaagtggagatttggagcgctttgaggccta
     Chimp  ======================================================================

     Human  tggtagtaaagggaatagcttcatagaaaaactagacagatgcattctcaggaactttttggtgatgttt
     Chimp  ======================================================================

     Human  gtattcaactcccagagttgaacttttcctttggaaagagcagctatgaaacactgtttttctagaatct
     Chimp  ======================================================================

     Human  gcaagtggacgtttggagggctttgtggtttgtggtggaaaaggaaatatcttcacctaaatactagata
     Chimp  ======================================================================

     Human  gaagcattctcagaagcttctctgtgatgactgcattcaactcacggagttgaacactccttttgagagc
     Chimp  ======================================================================

     Human  gcagttttgaaactctctttctgtggcatctgcaaggggacatgtagacctctttgaagatttcgttgga
     Chimp  ======================================================================

     Human  aacggaatcatcttcacataaaaactatacagaagcagtctcagaatcttctttgtgatgtttgcattca
     Chimp  ======================================================================

     Human  aatcccagagttgaactttcctttcaaagttcacgtttgaagcactctttttgcaggatctacaagtgga
     Chimp  ======================================================================

     Human  tatttggaccactctgtgtccttcgttcgaaacgggtatatcttcacatgacatctagacagaagctttc
     Chimp  ======================================================================

     Human  tcagaaaattctttgggatgattgagttgagcaaacagagctgaacactccttgcgatgtagcagtttag
     Chimp  ======================================================================

     Human  aaacacactttctgcagaatctgcaagtgcatatgtggacctctctgaggaattcgttggaaatgggata
     Chimp  ======================================================================

     Human  atttcagctgactaaacagaagcattctcagaaccttcttcgtgatgtctgcattcaactcacagtgtgg
     Chimp  ======================================================================

     Human  aacctttctttgatagttcaggtttgaaacactctttttgtagaaactgcaaggggatcattgcacttct
     Chimp  ======================================================================

     Human  ttgaggcctaccgtagtaaaggagataagttcctataaaaagaagacagaagaattctcagagccctctt
     Chimp  ======================================================================

     Human  cgtgatgtttgcattcaactcacagtgctgaacctttctttgatagtgcagctttgaaacactctttttg
     Chimp  ======================================================================

     Human  tagaaactgcaagtggatgtttggtcctctctgaggatttcgttggaaacgggataaaccgcacagaact
     Chimp  ======================================================================

     Human  aaaacagagcattgtcagaaacttctttgtgatgattgcattcaactcacagagttgaaggttccttttc
     Chimp  ======================================================================

     Human  aaacagcagtttccaatcactctttctgtggaatctgcaagtggatatttgggcctctctgaggatttcg
     Chimp  ======================================================================

     Human  ttggaaacgggataaaacgcacagaactaaaacagaagcattctcagaaacttctctgtgatgtttgtgt
     Chimp  ======================================================================

     Human  tcaactcccagagtttcacgttgcttttcatagagtagttctgaaacatgcttttcgtagtgtctgcaag
     Chimp  ======================================================================

     Human  tggacatttggagcgctttcaggcctgtggtggaaaacgaattatggtcacataaaaactggagagaagc
     Chimp  ======================================================================

     Human  cttctcagaaacttttctgtgatgattgcattcaactcacagagttgaaccctcctatggacagagcagt
     Chimp  ======================================================================

     Human  gttgaaactctctttttgtggaatctgcaagtggatatgtggacctctccgaagatgtctttggaaacgg
     Chimp  ======================================================================

     Human  gaatatcttcacataaaaactaaacagaagcattctcagaaagttcttggtgatgtttgcattgcaatcc
     Chimp  ======================================================================

     Human  cagagttgaaccttcctttgatagttcaggtttgaaacactctttttgtaggatctgcaagtggatattt
     Chimp  ======================================================================

     Human  ggaccactctgtggccttcgttcgaaacgggtacatcttcgcataaaatctagagagaagcattctcaga
     Chimp  ======================================================================

     Human  aaatattttgtgatgattgagttgaactcacagagctgaacattcctttcgatggagcaggtttgaaaca
     Chimp  ======================================================================

     Human  cactttttgtagaatctacaggtggatatttggacctctctgaagatttcgttggaaacgggataactgc
     Chimp  ======================================================================

     Human  acctaactaaacggaagcattgtcagaaactgctttgtgatgattgcattcacctcacagagttgaacat
     Chimp  ======================================================================

     Human  tcctattgatagagcagtttggaaacactcttcttgtggaatgtgcaagtggagatttggagcgctttga
     Chimp  ======================================================================

     Human  ggcctatggtagtaaagggaatagcttcatagaaaaactagacagatgcattctcaggaactttttggtg
     Chimp  ======================================================================

     Human  atgtttgtattcaactcccagagttgaactttcctttgaaaagagcagctatgaaacactctttttctag
     Chimp  ======================================================================

     Human  aatctgcaagtggacgtttggaggtcttttttggtttgtggtggaaaaggaaatatcttcacctaaatac
     Chimp  ======================================================================

     Human  tagatagaagcattctcagaagcttctctgtgatgactgcattcaactcacggagttgaacactcctttt
     Chimp  ======================================================================

     Human  gagagcgcagttttgaatctctctttctgtggcatctgcaaggggacatgtagacctctttgaagatttc
     Chimp  ======================================================================

     Human  gttggaaacggaatcatcttcacataaaaactatacagaagcagtctcagaatcttcttggtgatgtttg
     Chimp  ======================================================================

     Human  cattcaaatcccataactgaactttcctttcaaagttcacgtttgaaacactctttttgcaggatctaca
     Chimp  ======================================================================

     Human  agtggatatttggaccactctgtgtccttcgttcgaaacgggtatatcttcacatgacatctagacagaa
     Chimp  ======================================================================

     Human  gctttatcagaaaattctttgggatgattgagttgaactcacagagctgaacattccttgcgatgtagca
     Chimp  ======================================================================

     Human  gtttagaaacacactttctgcagaatctgcaagtgcatatttggacctctctgaggaattcgttggaaac
     Chimp  ======================================================================

     Human  gggataatttcagctgactaaacagaagcattctcagaaccttcttcgtgatgtctgcattcaactcaca
     Chimp  ======================================================================

     Human  gtgtggaacctttctttgatagttcaggtttgaaacactctttttgtagaaactgcaaggggataattgc
     Chimp  ======================================================================

     Human  acttctttgaggcctaccgtagtaaaggaaataacttcctataaaaagaagacagaagcattctcagaac
     Chimp  ======================================================================

     Human  cctcttcgtgatgtttgcattcaactcacggtgctgaacctttctttgatagttcagctttgaaacactc
     Chimp  ======================================================================

     Human  tttttgtagaaactgcaagtggatatttggtcctctctgaggatttcgttggaaacgggataaaccgcac
     Chimp  ======================================================================

     Human  agaactaaacagaagcattctcagaacattcttcgtgatgtttacattcaactcaaagggttgaaccttt
     Chimp  ======================================================================

     Human  ctttgatagttcaggtttgaaacggtctttctgtagaaactgcaagtagatatttggacctctctgagga
     Chimp  ======================================================================

     Human  tttcgttggaaacgggataaaccgcacagaactaaaacagaagcattcacagaaaactcttggtgacgac
     Chimp  ======================================================================

     Human  tgagtttaactcacagagctgaacattcctttggatggagcagtttcgaaacacactatttctagaaggt
     Chimp  ======================================================================

     Human  gcaagtggatatgtgggcctctctgaggatttcgttggaaacgggataaaccgcacagaactaaacagaa
     Chimp  ======================================================================

     Human  gcattctcagaaactactttgtgatgattgcattcaagtcacagagttgaacattccctttgacagagca
     Chimp  ======================================================================

     Human  gtttggaaactctctttgtgtagaatctgcaagtggagatatggaccgctttgaggcctatggtagtaaa
     Chimp  ======================================================================

     Human  ggaaatagcttcatataaaagctagacagtagcattctcagaaacttctttgtgatgcttgcattcaact
     Chimp  ======================================================================

     Human  cacagagttgaactttcctttcgagagagaagctttgaaacactctttttccagaatctgcaagtggaca
     Chimp  ======================================================================

     Human  tttggagggctttgaggcctgtggtggaaaaggaattatcttcctgtaaaagctagatagaagcattgtc
     Chimp  ======================================================================

     Human  agaaacttctttgtgatgattgcattcaactcacagagttgaaggttccttttcaaagagcagtttccaa
     Chimp  ======================================================================

     Human  tcactctttctgtggaatctgcaagtggatatttggacctctttgaagatttcgttggaaacgggagaat
     Chimp  ======================================================================

     Human  cttcacagaaaagctaaacagaagcattctcagaaacttctctgtgatgtttgtgttcaactcccagagt
     Chimp  ======================================================================

     Human  ttcacattgcttctcatagagtagttctgaaacatgcttttcgtagtgtctgcaagtggacatttggagc
     Chimp  ======================================================================

     Human  gctttcaggcctgtggtggaaaacgaattatggtcacatgaaaactggagagaagccttctcagaaactt
     Chimp  ======================================================================

     Human  ctctgtgatgattgcattcaactcacagagttgaaccctcctatggatagagcagtgttgaaactctctt
     Chimp  ======================================================================

     Human  tttgtggaatctgcaagcggatatgtggacctctccgaagatgtctttggaaacgggaatatcttcacat
     Chimp  ======================================================================

     Human  aaaaactaaacagaagcattctcagaaacttcttggtgatgtttgcattcaaatcccagagttgaacctt
     Chimp  ======================================================================

     Human  cctttgagagttcaggtttgaaacactctttttgtaggatctgcaagtggatatttggaccactctgtgg
     Chimp  ======================================================================

     Human  ccttcgttcgaaacgggtacatcttcgcaaaaaatctagacagaagcattctcagaaaatactttgtgat
     Chimp  ======================================================================

     Human  gattgagtttaaatcacagagctgaccattcctttggatggagcaggtttgagacacactttttgtagaa
     Chimp  ======================================================================

     Human  tctacaagtggatatttggacctctctgaggatttcgttggaaacgggataactgcacctaactaaacgg
     Chimp  ======================================================================

     Human  aagcattctcagaaactgctttgtgatgattgcattcacctcacagagttgaacattcctattgatagag
     Chimp  ======================================================================

     Human  cagtttggaaacactcttgttgtggaatgtgcaagtggagatttggagcgctttgaggcctatggtagta
     Chimp  ======================================================================

     Human  aagggaatagcttcatagaaaaactagacagatgcattctcaggaactttttggtgatgtttgtattcaa
     Chimp  ======================================================================

     Human  ctcccagagttgaactttcctttggaaagagcagctatgaaacactctttttctagaatctgcaagtgga
     Chimp  ======================================================================

     Human  cgtttggagggctttgtggtttgtggtggaaaaggaaatatcttcacctaaatactagatagaagcattc
     Chimp  ======================================================================

     Human  tcagaagcttctctgtgatgactgcattcaactcacggaattgaacactccttttgagagcgcagttttg
     Chimp  ======================================================================

     Human  aaactctctttctgtggcatctgcaaggggacatgtagacctctttgaagatttcgttggaaacggaatc
     Chimp  ======================================================================

     Human  atcttcacataaaaactatacagaagcagtctcagaatcttctttgtgatgtttgcattcaaatcccaga
     Chimp  ======================================================================

     Human  gttgaactttcctttcaaagttcacgtttgaaatactctttttgcaggatctacaagtggatatttggac
     Chimp  ======================================================================

     Human  cactctgtggccttcgttcgaaacgggtatatcttcacatgacatctagacagaagctttctcagaaaat
     Chimp  ======================================================================

     Human  tctttgggatgattgagttgaactcacagagctgagcattccttgcgatgtagcagtttagaaacacact
     Chimp  ======================================================================

     Human  ttctgcagaatctgcaagtgcatatttggacctctgtgaggaattcgttggaaacgggataatttcagct
     Chimp  ======================================================================

     Human  gactaaacagaagcattctcagaaccttcttcgtgatgtctgcattcaactcacagtgtggaacctttct
     Chimp  ======================================================================

     Human  ttgatagttcaggtttgaaacactctttttgtagaaactgcaaggggataattgcactctttgaggagta
     Chimp  ======================================================================

     Human  ccgtagtaaaggaaataacttcctataaaaagaagacagaagcattctcagaaccctcttcgtgatgttt
     Chimp  ======================================================================

     Human  gcattcaactcacagtgcgtgaacctttctttgatagttcagctttgaaacactcttcttgtagaaactg
     Chimp  ======================================================================

     Human  caagtggatatttggtcctctctgaggatttcattggaaacgggataaaccgcacagaactaaacagaag
     Chimp  ======================================================================

     Human  cattctcagaaccttcttcgtgatgtttgcattcaactcacagtgttgaacctttctttgatagttcagg
     Chimp  ======================================================================

     Human  tttgaaacggtctttctgtagaaactgcaagtagatatttggacctctctgaggatttcgttggaaacgg
     Chimp  ======================================================================

     Human  gataacccgcacagaactaaaacagaagcattcacagaaaactcttggtgacgactgagtttaactcaca
     Chimp  ======================================================================

     Human  gagctgaacattcctttggatggagcagtttcgaaacacactatttgtagaatgtgcaagtggatattta
     Chimp  ======================================================================

     Human  ggcctctctgaggatttcgttggaaacgggataaaccgcacagaactaaacagaagcattctcagaaact
     Chimp  ======================================================================

     Human  actttgtgatgattgcattcaagtcacagagttgtacattccctttgacagagcagtttggaaactctct
     Chimp  ======================================================================

     Human  ttgtgtagaatctgcaagtggagatatggaccgctttgaggcctatggtagtaaaggaaatagcttcata
     Chimp  ======================================================================

     Human  taaaagctagacagtggcattctcagaaacttctttgtaatgtttgcattcaactcacagagttgaactt
     Chimp  ======================================================================

     Human  tccttttgagagacaagctttgaaacactctttctctagaatctgcaagtggatatttggagggatttga
     Chimp  ======================================================================

     Human  ggcctgtggtggaaagggaattatcttcccgtaaaaactagatggaagcattgtcagaaacttctttgtg
     Chimp  ======================================================================

     Human  atgattgcattcaactcacagagatgaaggttccttttcaaacagcagtttccaaacactctttctgtgg
     Chimp  ======================================================================

     Human  aatctgcaagtggatatttggatctctttgaagatttcgttggaaacgggagaatcttcacagaaaagct
     Chimp  ======================================================================

     Human  aaacagaagcattctcagaaacttctctgtgatgtttgtgttcaactcccagaagtttcacattgctttt
     Chimp  ======================================================================

     Human  catagagtagttctgaaacatgcttttcgtagtgtctgcaagtggacatttggagcgctttcaggcctgt
     Chimp  ======================================================================

     Human  ggtgcaaaacgaattatggtcccataaaaactggaaagaagccttctcagaaacttctctgtgatgattg
     Chimp  ======================================================================

     Human  cattcaactcacaggtttgaaccctcctatggatagagcagtgttgaaactctctttttgtggaatctgc
     Chimp  ======================================================================

     Human  aagtggatatgtggacctctccgaagatgtctttggaaacgggaatatcttcacataaaaactaaacaga
     Chimp  ======================================================================

     Human  agcattctcagaaacttcttggtgatgtttgcattcaaatcccagagttgaaccttcctgtgatagttca
     Chimp  ======================================================================

     Human  ggtttgaaacactctttttgtaggatcttcaagtggatatttggaccactctgtggccttcgttcgaaac
     Chimp  ======================================================================

     Human  gggtacatcttcacataaaatctagacagaagcattctcagaaaatactttgtgatgattgagtttaact
     Chimp  ======================================================================

     Human  cacagagctgaacattcctttggatggagcaggtttgagacacactttttgtagaatctacaagtggata
     Chimp  ======================================================================

     Human  tttggacctctctgaggatttcgttggaaacgggataactgcacctaactaaacggaagcattctcagaa
     Chimp  ======================================================================

     Human  actgctttgtgatgattgcattcacctcacagagttgaacattcctattgatagagcagtttggaaacac
     Chimp  ======================================================================

     Human  tcttgttgtggaatgtgcaagtggagatttggagcgctttgaggcctatggtagtaaagggaatagcttc
     Chimp  ======================================================================

     Human  atagaaaaactagacagatgcattctcaggaactttttggtgatgtttgtattcaactcccagagttgaa
     Chimp  ======================================================================

     Human  ctttcctttggaaagagcagctatgaaacactgtttctctagaatctgcaagtggacgtttggagggctt
     Chimp  ======================================================================

     Human  tgtggtttgtggtggaaaaggaaatatcttcacctaaatactagatagaagcattctcagaagcttctct
     Chimp  ======================================================================

     Human  gtgatgactgcattcaactcacggagttgaacactccttttgagagcgcagttttgaaactctctttctg
     Chimp  ======================================================================

     Human  tggcatctgcaaggggacatgtagacctctttgaagatttcgttggaaacggaatcatcttcacataaaa
     Chimp  ======================================================================

     Human  actatacagaagcagtctcagaatcttctttgtgatgtttgcattcaaatcccagagttgaactttcctt
     Chimp  ======================================================================

     Human  tcaaagttcacgtttgaaacactctttttgcaggatctacaagtggatatttggaccactctgtgtcctt
     Chimp  ======================================================================

     Human  cgttcgaaacgggtatatcttcacatgacatctagacagaagctttctcagaaaattctttgggatgatt
     Chimp  ======================================================================

     Human  gagtggaactcacagagctgaacattccttgcgatggagcagtttagaaacacactttctgcagaatctg
     Chimp  ======================================================================

     Human  caagtgcatatttggacctctctgaggaattcgttggaaacgggataatttcagctgactaaacagaagc
     Chimp  ======================================================================

     Human  attctcagaaccttcttcgtgatgtctgcattcaactcacagtgtggaacctttctttgatagttcaggt
     Chimp  ======================================================================

     Human  ttgaaacactctttttgtagaaactgcaaggggataattgcacttctttgaggcctaccgtagtaaagga
     Chimp  ======================================================================

     Human  aataacttcctatagaaagaagacagaagcattctcagaaccctcttcgtgatgtttgcattcaactcac
     Chimp  ======================================================================

     Human  agtgctgaacctttctttgatagttcagctttgaaacactcttcttgtagaaactgcaagtggatatttg
     Chimp  ======================================================================

     Human  gtcctctctgaggatttcgttggaaacgggataaaccgcacagaactaaacagaagcattctcagaacct
     Chimp  ======================================================================

     Human  tcttcgtgatgtttgcattcaaatcacagtgctgaacgtttctttgatagttcagctttgaaacactctt
     Chimp  ======================================================================

     Human  tttgtagaaactgcaagtggatatttggtcctctgtgaggattttgttggaagcgggataaaccgcacag
     Chimp  ======================================================================

     Human  aactaaacagaagcattcacagaaaactcttggtgacgactgagtttaactcacagagctgaacatctct
     Chimp  ======================================================================

     Human  ttggatggagcagtttcgaaacacactatttgtagaatgtgcaagtggatattggggcctctctgaggat
     Chimp  ======================================================================

     Human  ttcgttggaaacgggataaaccgcacagaactaaacagaagcattctcagaaactactttgtgatgattg
     Chimp  ======================================================================

     Human  cattcaagtcacagagttgaacattccctttgacagagcagtttggaaactctctttgtgtagaatctgc
     Chimp  ======================================================================

     Human  aagtggagatatggaccactttgaggactatggtagtaaaggaaatagcttcatataaaagctaaacagt
     Chimp  ======================================================================

     Human  agcattctcagaaacttctttgtgatgcttgcattcaactcacagagttgaactttcctttcgagagaga
     Chimp  ======================================================================

     Human  agctttgaaacactctttttccagaatctgcaagtggacatttggagggctttgaggcctgtggtggaaa
     Chimp  ======================================================================

     Human  aggaattatcttcccgtaaaagctagatagaagcattgtcagaaacttctttgtgatgattgcattcaac
     Chimp  ======================================================================

     Human  tcacagagttgaaggttccttttcaaagagcagtttccaatcactctttctgtggaatctgcaagtggat
     Chimp  ======================================================================

     Human  atttggacctctttgaagatttcgttggaaacgggagaatcttcacagaaaagctaaacagaagcattct
     Chimp  ======================================================================

     Human  cagaaacttctctgtgatgtttgtgttcaactcccagagtttcacattgcttctcatagagtagttctga
     Chimp  ======================================================================

     Human  aacatgcttttcgtagtgtctgcaagtggacatttggagcgctttcaggcctgtggtggaaaacgaatta
     Chimp  ======================================================================

     Human  tggtcacataaaaactggagagaagccttctcagaaacttctctgtgatgattgcattcaactcacagag
     Chimp  ======================================================================

     Human  ttgaaccctcctatggatagagcagtgttgaaactctctttttgtggaatctgcaagtggatatgtggac
     Chimp  ======================================================================

     Human  ctctccgaagatgtctttggaaacgggaatatcttcacataaaaactaaacagaagcattctcagaaact
     Chimp  ======================================================================

     Human  tcttggtgatgtttgcattcaaatcccagagttgaaccttcctttgatagttcaggtttgaaacactctt
     Chimp  ======================================================================

     Human  tttgtaggatctgcaagtggatatttggaccactctgtggccttcgttcgaaacgggtacatcttcgcat
     Chimp  ======================================================================

     Human  aaaatctagacagaagcattctcagaaaatactttgtgatgattgagtttaactcacagagctgaacatt
     Chimp  ======================================================================

     Human  cctttggatggagcacgtttgagacacactttttgtagaatctacaagtggatatttggacctctctgag
     Chimp  ======================================================================

     Human  gatttcgttggaaacgggataactgcacctaactaagcggaagcattctcagaaactgctttgtgatgat
     Chimp  ======================================================================

     Human  tgcattcacctcacagagttgaacattcctattgatagagcagtttggaaacactcttgttgtggaatgt
     Chimp  ======================================================================

     Human  gcaagtggagatttggagcgctttgaggcctatggtagtaaagggaatagcttcatagaaaaactagaca
     Chimp  ======================================================================

     Human  gatgcattctcaggaacttctttttggtgatgtttgtattcaactcccagagttgaactttcctttggaa
     Chimp  ======================================================================

     Human  agagcagctatgaaacactctttttctagaatctgcaagtggacgtttggagggctttgtggtttgtggt
     Chimp  ======================================================================

     Human  ggaaaaggaaatatcttcacctaaatactagatagaagcattctcagaagcttctctgtgatgactgcat
     Chimp  ======================================================================

     Human  tcaactcatggagttgaacactccttttgagagcgcagttttgaaactctctttctgtggcatctgcaag
     Chimp  ======================================================================

     Human  gggacatgtagacctctttgaagatttcgttggaaacggaatcatcttcacataaaaactatacagaagc
     Chimp  ======================================================================

     Human  agtctcagaatcttctttgtgatgtttgcattcaaatcccagagttgaactttcctttcaaagttcacgt
     Chimp  ======================================================================

     Human  ttgaaacactctttttgcaggatctacaagtggatatttggaccactctgtgtccttcgttcgaaacggg
     Chimp  ======================================================================

     Human  tatatcttcacacgacatctagacagaagctttctcagaaaattctttgggatgattgagtggaactcac
     Chimp  ======================================================================

     Human  agtagctgaacattccttgcgatggagcagtttagaaacacactttctgcagaatctgcaagtgcatatt
     Chimp  ======================================================================

     Human  tggacctctctgaggaattcgttggaaacgggataatttcagctgactaaacagaagcattctcagaacc
     Chimp  ======================================================================

     Human  ttcttcgtgatgtctgcattcaactcacagtgtggaacctttctttgatagttcaggtttgaaacactct
     Chimp  ======================================================================

     Human  ttttgtagaaactgcaaggggataattgcacttctttgaggcctaccgtagtaaaggaaataacttccta
     Chimp  ======================================================================

     Human  tagaaagaagacagaagcattctcagaaccctcttcgtgatgtttgcattcaactcacagtgctgaacct
     Chimp  ======================================================================

     Human  ttctttgatagttcagctttgaaacactcttcttgtagaaactgcaagtggatattttgtcctctctgag
     Chimp  ======================================================================

     Human  gatttcgttgtaaacgggataaaccgcacggaaataaacagaagcattctcagaaccttcttcgtgatgt
     Chimp  ======================================================================

     Human  ttgcattcaactcacagtgttgaacctttctttgatagttcaggtttgaaacggtctttctgtagaaact
     Chimp  ======================================================================

     Human  gcaagtagatatttggacctctctgaggatttcgttggaaacgggataaaccgcacagaactaaacagaa
     Chimp  ======================================================================

     Human  gcattcacagaaaactcttggtgacgactgagtttaactcacagagctgaacattcctttggatggagca
     Chimp  ======================================================================

     Human  gtttcgaaccacactatttgtagaatctgcaagtggatatgtgggcctctctgaggatttcgttggaaac
     Chimp  ======================================================================

     Human  gggataaaacgcatagaactaaaacagaagcattctcagaaactactttgtgatgattgcattcaagtca
     Chimp  ======================================================================

     Human  cagagttgaacattccctttgacagagcagtttggaaactctctttgtgtagaatctgcaagtggagata
     Chimp  ======================================================================

     Human  tggaccgctttgaggcctatggtagtaaaggaaatatcttcatataaaagctagacagtagcattctcag
     Chimp  ======================================================================

     Human  aaacttctttgtgatgcttgcattcaactcacagagttgaactttcctttcgagagagaagctttgaaac
     Chimp  ======================================================================

     Human  actctttttccagaatgtgcaagtggacatttggagggctttgaggcctgtggtggaaaaggaattatct
     Chimp  ======================================================================

     Human  tcccgtaaaagctagatagaagcattgtcagaaacttctttgtgatgattgcattcaactcacagagttg
     Chimp  ======================================================================

     Human  aaggttccttttcaaagagcagtttccaatcactctttctgtggaatctgcaagtggatatttggaccta
     Chimp  ======================================================================

     Human  ttttgaagat
     Chimp  ==========

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