Multiz Alignments of 7 Yeasts
 

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Alignment block 1 of 3 in window, 1019316 - 1021678, 2363 bps 
B D  S. cerevisiae  caaatgcagtccatatttttgaattcttcatccatcgaaaaggcgtaatttatttctaaagg---aagtt
            sacPar  caaatgcagtctgcattcttgaatgcttcgtccatcgaaaaagcgtaacttatttctaaagg---aagtt
            sacMik  caaatgt-gtccaaattcttgaacgcttcgtccattgaagatgcatgtattatttctaaagg---atgtt
            sacKud  caagcctagtccacattcttgaatgcttcgtcaatcgaatatgcgtaatttacatctagatgagcaagct
            sacBay  gacacatggtccatattcttgaacgcctcgtccatcgaaaatgcgtaatttacttctagatgagagagct

     S. cerevisiae  ttagttctaccataatgcttgcactgggctcctcgagcaccacaacaactaatttttctcccactaaatc
            sacPar  ttagctccaccatgatacttgcgcttggctcttcaagtaccacaacgactaatttttcccccaccaggtc
            sacMik  tcagctctaccataatactggcgcctggctcttcaagtaccacagtaaccaacttttctccgactagctc
            sacKud  ttagttctaccataatactagcagcgggctcttcaagtaccaccacaactagcttctccttcactagttc
            sacBay  ttaactctaccatgatatttgcgttcgactctttaggtaccaacgcaactagcttttcttttattagctc

     S. cerevisiae  attcactacacttatccaagaaaattgctttagtttctctatagttattgcgggctcccaggcaccgcat
            sacPar  attaactacacttatccaagaaaactgcttcagtttttctatagttatcttgggctcccaggcaccgcat
            sacMik  attgattatacttatccatgagaactgcttcaatatttctatggttatcttgggttcccagacaccgcat
            sacKud  attgaccacacttagccatgataattgcttcagtttctctatggttatttggggctcccatacaccgcag
            sacBay  gttgataacacttatccatgagaagttcttcagcttctctatggttatctggggctcccagacattgcaa

     S. cerevisiae  atgaccttcttaatttcttttgacgccttgtaccctgggttgtcccgcaacatcttcaccatcttaatca
            sacPar  acgaccttcttaatttcttttgatgctttgtagcctgggttgtcccgcaacatcttcaccatcttaatta
            sacMik  attacttttttgatttctcttgatgctttgtaatctgggttgtcctgcaacatcttcaccatcctgatta
            sacKud  accacttttctaatatctttagaagccttgtaatttgggttgtcccgtagcagccgcaccatgttggtta
            sacBay  atcacctctttaatatctctggatgctttgtaacctgggttgtcctgtaacatctgtgtcatcttggtca

     S. cerevisiae  ggacggtctccagagcaagcgtatgacgattcgtgccttcggtttcttgcgccagggtatataaaaatgt
            sacPar  agacagtctccagagcaagcgtgtggcgattcgtgccttcggtttcttgtgccagggtgtataaaaatgt
            sacMik  agagagtctccatagcaagtgtgcggctattcgagccttcagtttcacgcgccaaagtgtataagaatgt
            sacKud  aaacagcatccagcgcaagcgtatgacgattaaggccttcagtctcacgtgccagtgtgtataagaacat
            sacBay  agaggaaatccagcccaagagtatggttattggtaccctcagtttcaagtgccagtgtatacaggaatat

     S. cerevisiae  tctcatcaacagagacattcctataatcttctttgaaatagtttcatccttgaatccgttaatagcttct
            sacPar  tctcatcaatagagacattcccataactttttttgagatagtttcgtctttgaatccgttaatagcttct
            sacMik  cctcaccagtagagacatccctattactttttttgagaatgtttcatctttaaacccgttaattgcttct
            sacKud  tctcattaataaagacatcccgataaccttctttgcaatagcgtcatccttgaacccgttgatagcctct
            sacBay  cctcgccaatagggacatccctataaccctctttgagaaagtgtcatcgttgaacctgccaatggcctct

     S. cerevisiae  gagaaatagcgtggtaccatctcctgtgacactaccaatttacccttttgtagaccacctttccgtacga
            sacPar  gaaaaatagcgtggtaccatctcctgggatgctactggtttacccttttgtagaccacctttccgcagga
            sacMik  gaaaaataacgtggcaccatctcttgggatactactggtttacccttttgtagaccaccttttctgacga
            sacKud  gaaaaataacgcggcagcatttcctgggttttcacgggtttaccctttcgtatgccactctttcctacaa
            sacBay  gaaaaataacgtggtagtatctcctggaatgatacagatttgccctttcgtaaaccgcctctttctacaa

     S. cerevisiae  agtcttttttagaaatttctacggcagcttcacatattttgaatgctttttcagtactaccacttacgtt
            sacPar  agtcatttttagagatttctacggcagtctcacatatcttaaaagctttttcggtactaccacttacgtt
            sacMik  agtcatttttagagatttctacggcaatctcacatattttgaaggcttttttcgtactatcacttatgtt
            sacKud  agtcctttttggagatttccactgccatcttacaaattttgaaagctttctcagtattatcactcagatg
            sacBay  agtcctttttggaggtttccacagccatgtcacatatcttgaaagctttcccagtggtaccactcacatt

     S. cerevisiae  ggctacgttctttgcaataagttgagtgattttgttgttgatcttatgattgattactatcacattatct
            sacPar  cgctacattttttgcaatcagttgaatgattttgttgttgatcttatgattgattgctatcacgttatct
            sacMik  tgctatattttttgcaattagttcagtaattttgctgttaatattgtgatttatcgcgttcacattatct
            sacKud  tgctatattcttcgcgattggttcaatgattttgttgttgatggtgtgggttactgttatcacgcccttt
            sacBay  cgctatattttttgcaattagttctatgattttggtgttgataatatgctctatggcagacacattttct

     S. cerevisiae  ggtattttctggttctgtccttcgcgaatattattgtaaatagtcatttccttcttatcatttactttga
            sacPar  ggtatattttgtttctgtccttcacgaatattattgtaaatagtcatttcctttttatcgtttactttta
            sacMik  ggcaattcttgtttctgtcctccacgaatattgctgtatagagacatttgctttttatcgtttactctta
            sacKud  ggtagcttttgctcctgtttttcgcaactatcattatagatagtcatttcatttttttcgtttactctta
            sacBay  ggtaacttttgtttctctacttcggaaatatcattgtgaagtgccattacctttttgccattcattctca

     S. cerevisiae  catgaaaaggtttcaataaagatttgagtcgcgtgatgatcatttgttgcaattcattcttgtccacctt
            sacPar  cgtagaacggtttcaataaagatttgagtcgcgtaatgatcatttgcagcatttcatctttgtttacctt
            sacMik  catagaacggcttcagtaaggacgtgagatgtgagatgattgcttgtcgtaattcgtctttatttacttt
            sacKud  cgtagaagggtttcagtaaggacttaagatatgggacagtccttcgctgtaaatcgcccttggttacctt
            sacBay  cgtaaaacggcttcaataaggactgaagataggagacgatcattcgttgcaaatcgtcctttgttatctt

     S. cerevisiae  attaagtttgatttcggtaaagtgtgctttgagggagggcattatatttatttgctctctaatcgtcaca
            sacPar  attaagtatgatttcagtaaagtgtggtttgaacgagggcatcacatttatttgttctttaatcatcaca
            sacMik  atcaagtatgattttcttgaagtgcccttgaagtaacggtatcatattaatttgctctgtaatgtcgaca
            sacKud  gtcaagtatgatttcagtgaaatgtggttttaatgagggtgtagcgttaatttgctgtttaatcactgca
            sacBay  gctgagcatgattgaagtaaaatgtgattgaaatgagggcgactcgttcattagcttcttgatcgtctca

     S. cerevisiae  ttatgtccgccaacgcaaatgatagacaattttgaatttttcgaagaaatccatttctcgaaatattgta
            sacPar  ttgtgtccgcctgcacaaacgacagataatttcgaatttttcgaagaaatccatttctcaaagtattgta
            sacMik  t------cgccaatgcaaacggcagacagtttcgaattctctgaagatatccatttgttaaagtgttgaa
            sacKud  ttatctctgccaataccaataacagatagtttcgaattttccgtcgaaatccacttttcaaagtagtgta
            sacBay  ttgttgctgccaacgccaatgatagatagtttggagttctctgaagaaatccacttcccgaagtatcgcg

     S. cerevisiae  aaatcttctcactcaatagattttccggattttgtattaatattagtgtctttctcttttttgctttcgg
            sacPar  atatcttttcattcagtaggtcgtcaagattttggatcaatatcaatgtccttctcttttttgctttcgg
            sacMik  tgatcgttttattcaggcgattgtcgagattttgaattaatatcagtgttcttctctttttcgccttcgg
            sacKud  aggtcttctcgtttaatatattatcgaggtcttgaattaatagcaaagtttttctcttttttgccttcgg
            sacBay  aggtctccttacttgatatgtgatcgaaattttgtactaatatcaaagtccttctcttttttgcctttgg

     S. cerevisiae  gacatttgtaatatagaagtttaaggcctctagtgatatatcaccgcatagattttctttagaaatggcg
            sacPar  aacattagtaatatagaagtttaaggcttccagtgatatatcaccagatagattttctttagagatggag
            sacMik  aacattagtaaaatagaagttcaaagcctccattgatacatcaccggaaagcttatctttagagacagca
            sacKud  aacattgataaaataaaaattcaaagcttctagagatatatcaccggggagcgtttctttagagatggca
            sacBay  aacactagtaaaataaaaatttagagcttccagtgatatgtcaccagaaagcgcatctttggaaatagca

     S. cerevisiae  aaccatattttctcatataatgcatccattcctgccagttccaaggcatcaatatgaatgtaatcgaaaa
            sacPar  gaccatattttctcaaataatgcattcattcctgtcaattccaacgcatcgacatgaatgtaatcgaaaa
            sacMik  gtccatattttctcaaatagtgcattcacttcagtcaattccaacgcatcgatgtaaatgtaatcaaaat
            sacKud  gtccatattctctcgaaaattaccttcatatcagtgaattccaaagcgtcaatataaatataatcaaaaa
            sacBay  gtccatattctctcgaaaaatccttttgtgtcactgtattccaacgcatcgatataaatgtagtcaaaaa

     S. cerevisiae  taggtagttcctttcgggccgaagaggtgatcaactcatccattacatcattcacaagctggaatttagt
            sacPar  ttggtagttccttttgaactgatgaggttacaagctcatccatcacgtcatccactaggctggatttcgt
            sacMik  aaggcagttccttttgggctgatgaggtgaccagctcgttcatgacgtcacacacaagtctagatttagc
            sacKud  taggtaattccttttgcttagaagatatgatcagctcgtccatcacctcttttacaagcctgaattgccc
            sacBay  tgggcaattcgttttgcttcgaagaggtgaccaactcctccattacctctttggcaagcatgaatttcgc

     S. cerevisiae  agaatcatctgcattggtaatataaaatagtttattttgggaagacatcaaactgtcgtaaatcggaagg
            sacPar  agaatcgtctgcattggccacataaaatagtttattttgagaacacattaaactctcgtacattggaaga
            sacMik  aggtacgtctgcattagtcacataaaatagcatattttgagaagaaactaaactatcgtaaatcggaaga
            sacKud  aggttggttttcacttactacataaaatagcttgttttgagaagacattaagctattgtaaatcggaaga
            sacBay  ggacacatcttcattaactatataaaacagcttgttttgagaagacattaaactttcgtatattggaaga

     S. cerevisiae  aatattcttgtaaaatcctccacttgtgattttagtagttctctcttttgtaaagattctctaattgatt
            sacPar  aatagttttatgaaatcctcgacttgtgatttttgtagttctctctttcgtaatgattccctgattaatt
            sacMik  tatacttttataaaatcctcaatctgtgagcttagtagttccttctttcgtaatgattgtttgattaaat
            sacKud  aaaattttaatgaaatcctcaacttgtgaacttaaagactctctcttccctaacgattctctaattgact
            sacBay  aacactttcacaaaatcctcaacttgtggatctagtggtttcctcttttgtagtgtatctctgatcaact

     S. cerevisiae  cctctaaatttatatcagcgttaaaatttgacagaatggtttctcttccagatgaagagcatgcttttct
            sacPar  cttctaagtcgatcttaccattaagctttgacagaatggtttcctttccaggtgtggaacgtgtttttct
            sacMik  cttttaggttgatcccgtcattaagctttgacaaaattgtgtctttttcagatgtagggcttgcttctct
            sacKud  cttttaaatcgatcttaccattaaattttgacagaatagtatctctttcaggcccagggtttatttttct
            sacBay  cctccaaattgttcttactattgagtttcgacaaaatagtatccatttcgggtgtatgatttgttcttct

     S. cerevisiae  aaacttatcctcaaggcctgcaacgtccaagcttgactgttcgtctgttaatttgttcaattgggaggaa
            sacPar  aagcttatcctcgaggcttgcaacgtccagacttgactgttcgtctcttgctctcttcaattgagacaaa
            sacMik  aagcttatcctcgaggtctgcgacgttaaggtttttctgtgtctttgttaccgtcttcaattgagataaa
            sacKud  gaacttatcctcaatatctgcaacatccaaggttgattgtgactctctgacttttttcaactgagttaga
            sacBay  gagcttattttcgagttctgcaacgtccagaactgattgtgtgtctctgacctttttcaactgagaaaga

     S. cerevisiae  tctgttacttgattatctggtgcaaaccggtctaaaattatctgatatttttttttcaactttgacaaag
            sacPar  tctataacttgattacctggagcaaatcggtctaaaatcatctgatatttttttttcaactttgacaaag
            sacMik  tcaacagtttgattctctggagcaaaccgatctaaaattatttgatactttttcttcaacttcgataaag
            sacKud  tcgataatttgattacctggagcaactctgtctaaaaccagctgatattttttcttcaacttcgacaaag
            sacBay  tccataatttgattgcaaggagcaaaccggtccagaattgtttgatactttttctttaactctgacaaag

     S. cerevisiae  tagcgaaatcaatcatctttgcattacctttttctggtgtaggattttcgttcatactatgaattttggt
            sacPar  cagcaaaatcaatcatcttggcattaccttttcttggaatagatttattgttaatactattgtctttggt
            sacMik  caacaaagtcaatcatcttggcactacctctcgcagcaacaggcttcatactcgtattatcgtctctact
            sacKud  cagcaaaatcgatcatttttgcattatctcttgcaggaataggtttatagccgatgttcccgtctttgct
            sacBay  cggcaaaatcgatcacctttgctttatcttttgtaggagacgaatgac------tacccttgcctttgct

     S. cerevisiae  gttgcccctgggaattccaggttttccatttccgttcatttcgttatctg--------------------
            sacPar  actacccatgagcattccaatttttccatttccttctatctcgttatctg--------------------
            sacMik  cctaccctttggaattctagtatttttagttccttttatggtgctatctc--------------------
            sacKud  tctggccttgaaaatttctgccttttcatctctttttgtcttgtcttttgattcatagaatggtagtgcc
            sacBay  actaccctcagttgtcttagttttctcattcacttctgtttttttttctgctttagaagatgccattgtg

     S. cerevisiae  ----------------------------------------------------------------------
            sacPar  ----------------------------------------------------------------------
            sacMik  ----------------------------------------------------------------------
            sacKud  tcattttttccatgattattttgggtttcactttcaacag------------------------------
            sacBay  gcattttgttt--------------------------gagatcatctagggtcttgagaggtttatctct

     S. cerevisiae  -----------------------tttctgtagtgta---atttttagaaaattcttgtgtttcttgaatg
            sacPar  -----------------------tttctgtgtcgtc---attttgaggtagctcttgtgtttcttgaatg
            sacMik  -----------------------ttttaatatcatc---attttgagaaattccttgcgtttcttgaatg
            sacKud  -----ttgcttgttttctgagactttcggtatcatcattatttcgagaaatgtttcgtatttcttgaata
            sacBay  gccgattacttcgcttctggaacttttaatctcatc---attttgggagagttcttgtgtttctgttatg

     S. cerevisiae  tggatttttctaattttactgctcaattcgcttccgtgagcgccacgtcttttatttactggtattattg
            sacPar  tggatttttttagtttttctgctcattttgcttccatgagtcccacgtcttttatttactgcgattattg
            sacMik  ctcatttttctaatttttttgctcattttatcttcctggttcacacgtcttttatttactgcagatatca
            sacKud  tgtatttttctaatctttctgatattattatcgctcagaactccatatctcttatttataacagatgtcg
            sacBay  tgaatttttcgagattttctgctcatgttgtcgccatgagccccacgtcttttgtgtatcaaggatatcg

     S. cerevisiae  cttcatcagaactttctgaactaacttcatctgtttcctcttcaagcccaccatcatcactcacttctgg
            sacPar  cttcaccggaactttcggaggtaaatccatctgtttcctcttcaagttcactatcatcacttactcttgg
            sacMik  cttcatcagaactttcagtagtaaacccatccgattcttcttcgatctcatcatcttgattcactctt--
            sacKud  cttcaccagaactccctgaggcagatgcatctaattcctgtctaggcttcttatctccattcactctcat
            sacBay  cctcacttgaactttcggatgtagtttcatcaatttcctcttcaatttcgctgtctccatccactttgat

     S. cerevisiae  ---attatttgcatatacaaaattctctcggccg---tcaacgagttctgtagatgtcttctctggcttt
            sacPar  tggattgttttcatgtacaaaattctcttggcgg---tgaataaattctgtagatgtattctccaatttt
            sacMik  ---cttat-------------gctatcgtggtga---acatcaaatgttgtaaacccattcgttggtttc
            sacKud  tgaattaccttcgtctacaaaattttcgtggtgc---tcgtaagatcctgtaactccatttttcgtcagt
            sacBay  tgagttatctgcgtccacaaaatcctcacggtggtcatcatcatcttcttcaactccattttctgtcgat

     S. cerevisiae  gaccca--ggtttacttgaaagcacagatg------------tttcattgtttggctc------------
            sacPar  gattcc--ggttgggctgaaatcacagatgattttcgctgaagttcaatgtttggttcccttggttcttc
            sacMik  gaattt--gactggaatgaagataaatatgggtctggctggagtttaccatttcgttctgttggatcttc
            sacKud  gatttcggggtttgccgaatactactcata--------------------------tcattggaatcttc
            sacBay  gatccc--ggttcagctgaaggtggcgattgtgcttgctgaatgtcactattttggtcttttgagtcttc

     S. cerevisiae  ataatcggattcctgttctgaagagtttattggtatttcctctgaaacaattagttcctttgatatagat
            sacPar  attatcggattcttgttctgaggagtttattggtatttcctccgaaacgatcaattcctttgatatagat
            sacMik  atcatcagattcttgctctgacgagtttattggtatttcttccgaaacaaccaactcttttgatatagct
            sacKud  atcgtctgattcctgttctgatgagtttattggtatttcctctgaaacaatcaattcttttgaaataggt
            sacBay  gatttcagactcttgctctgatgaatatattggtatttcctctgagaaaactaattcttttgaaataggt

     S. cerevisiae  cttttttgtaaaattttcgaagaatctgtaggtgatgtgagcgcagaaggggacgccgatgagatgttag
            sacPar  cttttttgtacaatcctcgaagaatctgtgggtgatgttagcgctgtaggtgacgctgatgagctattaa
            sacMik  cttttttttacgaccatcggagtacctgtggatgacgttagcgctgccggtgacgttgatgggctatcaa
            sacKud  cttctttgtacaattcttggagcacttgcgggt------------------gacgctgatgatgcattga
            sacBay  ctcctttgtacaattctcgcagcatcttcacgtggcattgaaattgcaggcgatcctgaaaaggaaagag

     S. cerevisiae  gggaaacagactcttcttggggagaaattgaaccatgagttgttgacgttcctcgctgagacggtatatt
            sacPar  gaaagaaagactttctttcgggagactgtgaaccatacatttctgaggttccctgcttatacgatacatt
            sacMik  ataagatatacttattctcgggaaagggtgagccgtagttttctgagccttcttgctgatacggtacatt
            sacKud  ggaaaatgtcattgctattggaagaaagtggactgttgccttttgagatttctcgtttatatgatgaatt
            sacBay  ttttaaaggagttactctctaaagaacgtgagccattttctgttgagatttttcgattgaacggaaacct

     S. cerevisiae  tccattatttacgtcatcatctgcagagggctcgattttaatttttttcattgaaggtttctttgctagt
            sacPar  tcccttatttgtatcgtcatcagaagagggttcgactttaatttctttcattggaggtttctttgctagt
            sacMik  ccttttatatatatcgtcgtcagaaggaggctcgactttaatttctttcatctgaggcttccttactaat
            sacKud  tttcttcttgaagtcatcatcagaggggggttcgaccttgatttctttcaatggaaatttctttgctagc
            sacBay  gacttttcctaagttaatatctggaggaaactcgactttgatttccttcattggagatttttttgtcagt

     S. cerevisiae  cttt---------ttgaagatctttcaactcccatcttatgcatcacctgtctatttgtcttctgcccac
            sacPar  ctctgctgtctctttacagatctctcaagccctatcttatgtattacctgtctatttgtcttattcaaac
            sacMik  ctttgctgtctctttgttgatctttcgggttctatcttatgcattacttgtttgtttatcttattcgcac
            sacKud  ctttggtgtctctttgcggatctttcaggccctatcttgtgtactgtttgtttgtttgacttattcgcgc
            sacBay  ctttgttgtctctttgctgatctttcaggtgctaccttaggcaccgtctgtttgcttatcttattaacaa

     S. cerevisiae  tcactggtacagatactcttttcaagtattcatcagattgtttgggttccatttcctttactcttcttat
            sacPar  tcactggtgcagatactcttttcaagtattcatcagattgtttgggttccatttccttgactctttttat
            sacMik  tggctggtacagatattcttttcaagtattcatcagattgcttaggttccatttctttgactcttttgat
            sacKud  tttctggggcagatattctttttaaatattcatcagattgcttgggttccatttctttgaccattctgat
            sacBay  ctgctgggactgatattctttttagatattcgtcagattgtttaggttccatttctttaactctcctgat

     S. cerevisiae  gat
            sacPar  gat
            sacMik  gat
            sacKud  aat
            sacBay  aat

Alignment block 2 of 3 in window, 1021679 - 1021685, 7 bps 
B D  S. cerevisiae  ttgaaaa
            sacPar  ttgaaaa
            sacMik  ctgaaaa
            sacKud  ttggaaa
            sacBay  ctggaaa
            sacCas  ttcaata

Alignment block 3 of 3 in window, 1021686 - 1022251, 566 bps 
B D  S. cerevisiae  atatcaattggtacaaacttttccgcagtaggttcgcatgcataacgtactagaaaatctctatcc---t
            sacPar  atatcaattggaacaaacttttctgcagtaggttcgcatgcataacgtactaggaaatctctatcc---t
            sacMik  atatttattgggacaaatctttctgcagtaggttcgcatgcataacgtactagaaaatccctatct---t
            sacKud  atatcaattgggaggaacctttccgcagtaggttcacatgcgtaacgcacgagaaagtccttatta---t
            sacBay  atatcaattggaacaaaattttccgcagtaggttcgcacgcataacgtactaagaaatctttatcc---t
            sacCas  agattaattgggaccacgttgtcagaaatgggactaaatatatatctaacaaagaactcttttttcaagt
            sacKlu  atgtcaatgctggcaaagtttgcaccttgaggttcacaagccctggtaacaaggaaaacatttttc---t

     S. cerevisiae  ctattttatcgatactactatcattccattgtgactctgg--------cagt-----atctgtccaactg
            sacPar  ctattttctcgatactgctatcattccattgtgactctgg--------aagt-----atttgtccaactg
            sacMik  ccaccttttcgattttactatcattccactgcgactctgg--------aatt-----atttgtcctacgg
            sacKud  ctacctttttagtcttttcatcaatccactgtgactctgg--------aaat-----agttgggcgactg
            sacBay  ctacttttttgatcgtgctatcatcccacttagactctgg--------aagt-----atctgcccaactg
            sacCas  ctttttcctcagt------atcgttcaac--caactatcg--------aaattggagactttggctaatg
            sacKlu  ctgttccagaagtaagactactgttgga---aaactcctggtcgtccaggat-----agttgccttat--

     S. cerevisiae  caatgaaatccttaagccaaatctctgatagctcagcagttaaatataactcgctcttatttacttcgtt
            sacPar  caatgaaatccttaagccaaatctctgatagttcagcagttaaatataactcactcttatttacttcgtt
            sacMik  caatgaaatccttaagccaaatttctgataattcagcagttaaatataactcactcttattcacttcgtt
            sacKud  cgatgaaatccttaagccaaatttcagatagttcagcagtcaagtataattcactcttattcacttcttt
            sacBay  cgatgaaatccttaagccaaatttctgatagttcagcagtcaaatatatttcgctcttattcacttcttt
            sacCas  atatgaaattggataatttgagttctgctggttgtaatgtgaaatatagctcgtttttgtccacatcctc
            sacKlu  caaggaagtttttcaagtagatttcagaaagttctggtgtcaaatagatttcgtgtttattggtatcgtt

     S. cerevisiae  gaaaaatttatctttgtaaaattctaaaggatgatcttcctttattagatctggcctgaattgttcgtag
            sacPar  gaaaaatttgtccttgtaaaattccacgggatgattttccttcattatatctggcctgaattgttcgtag
            sacMik  tagaaatttttctttgtaaaaatccacaggatggttttcctttattaaatctggtctgaactgttcgtaa
            sacKud  gaagaatttgtctctgtaaaaatccgtgggatgattttcttttattaaatctggcctaaattgttcgtag
            sacBay  gagaaatttatcgttgtaaaactccatggtttggctttcctcaattaagtctggtctgaattgttcatag
            sacCas  tgccatttttctatttacctcctctcttgtatccagatttttaaccactttgggttcaaaattactgtaa
            sacKlu  agaaaacttttcagcataaaattctgtgggctgatcccctctaagaacctgcggctcgtactgggagtag

     S. cerevisiae  tacagttttggtttgagttcaaaccatctcaagtaagaaaaaacccaaatctccacaacattattaagtg
            sacPar  tataactttggtttgagttcgaaccatcttaagtaagagaaaacccaaatctccacaagattatttagtg
            sacMik  tacagctttggtttgagttcgaaccatctcaaataggagaaaacccaaatctccacgaggttatttaatg
            sacKud  tacaattttggtttgagttcaaaccatcttaggtaagagaagacccagatttctacgagattattcagcg
            sacBay  tacaatttcggtttcagttcgaaccatcttaggtatgagaagacccaaatttccacgagattattcaatg
            sacCas  tatgtgactggatctaattcaaaccatcttaaatacgttagtgcccatagctccaccacattgttcaagg
            sacKlu  tattcactgggattaacctcaaaccaccttaaatagctaaatgcccataactccacgatgtgattcagcg

     S. cerevisiae  tattgagtctgatctcatggatcaagtagacagaatatgtttccgtcacattatcattaaatatcacgct
            sacPar  tattgagtctgatctcgtggatcaagtagacagaatatgtttccgtcacattatcgttgaatattacgct
            sacMik  tattaagtcttatctcgtgaatcagataaacagaatacgtttctgtcacattatcgttgaatattacact
            sacKud  tattgagtctgatttcgtgaatcaaataaacagaatatgtttccgtcacattatcgttgaatatcacact
            sacBay  tgttaagtctaatctcatgaatcaagtagacagaatacgtctcggtgatgctatcgttgaatatcacact
            sacCas  tattcagtctaatatcatgcaccaagtatatcgaataagtatccaacttttcatcgttcataataatgtt
            sacKlu  tattcaatctaatttcatggatcatgtagatcgaaaatgttttactaatactttcatgcataaccaccga

     S. cerevisiae  ctcacccttcccaaaactcaatccatcagaaattcttttcagaaatacgttttctcctcctc------tt
            sacPar  ctcccccttcccaaaactcaatccatcagaaattcttttcagaaacacattttctcctcctc------tt
            sacMik  ttctcctttcccaaagctcaatccatcggaaattcttttcaaaaaaacattctctactcctc------tt
            sacKud  ctctccttttccaaagctcaaaccatcagaaactctctttaagaacacattctctactcctc------tt
            sacBay  ctctcctttcccaaagctgaggccatcggaaattctctgtaaataaacattttctacacctc------tc
            sacCas  gtcaccacgaccaaacctcaatccgtctgattttctttgaaggtagacaagttc--ctcttc------at
            sacKlu  gtcaccgcatccaattcttagaccgtctttttcccgttgtaggtagacatgttctctgcctccagcctcc

     S. cerevisiae  tttcttga-----tcttcttctatt---------------gttgtcgtcaataaccctcccctgatcatc
            sacPar  tttcttga-----tcttcttctatt---------------gttttcgtcaataactctcccctggtcatc
            sacMik  tttcttga-----tcttcttctcct---------------gttttcgtcaatgatccttccttgatcatc
            sacKud  ttccttga-----tcttcttctatt---------------gttctcatcaattatcctccccttatcatc
            sacBay  tttcttga-----tcttcttctatt---------------gttttcctcaatgatcctccccttatcatc
            sacCas  ttcttcgatgacgtcgtcttttctg---------------ggtattatcaataatattaccgaacccatc
            sacKlu  tcacgtgc-----tcttcttctactccttctaaacatctggctttcatcaattaggttacccttgtcatc

     S. cerevisiae  tgtaatgataacttgccaaccgtccaaatctttcaatgttttagccat
            sacPar  tgtaatgataacttgccatccatctagatcttttaatgtttcagccat
            sacMik  agtgatgacgacttgccatccctctagatctctcaacgtttcagccat
            sacKud  ttcaatgacgacttgccacccatccagttcctttaatgttttagccat
            sacBay  tttaataataacttgccacccttccaagtcctttaaagtttcagccat
            sacCas  ggttgttataatttcccagccttccagatccttcaatgaatgcgccat
            sacKlu  agtcttgataatttcccagccgtttaagtcaataagagtttccgccat

View table schema

Go to Conservation track controls

Data last updated at UCSC: 2011-09-01

Description

This track shows a measure of evolutionary conservation in seven species of the genus Saccharomyces based on a phylogenetic hidden Markov model (phastCons). The graphic display shows the alignment projected onto S. cerevisiae.

The genomes were downloaded from:

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 S. cerevisiae 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. Configuration buttons are available to select all of the species (Set all), deselect all of the species (Clear all), or use the default settings (Set defaults). 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 bases or fewer, 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 S. cerevisiae 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.

Downloads for data in this track are available:

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 S. cerevisiae sequence at those alignment positions relative to the longest non-S. cerevisiae 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, depending on the species chosen (Table 2). Species listed in the row labeled "None" do not have species-specific reading frames for gene translation.

Gene TrackSpecies
SGD GenesS. cerevisae
No annotationall the other yeast strains
Table 2. Gene tracks used for codon translation.

Methods

Best-in-genome pairwise alignments were generated for each species using lastz, followed by chaining and netting. The pairwise alignments were then multiply aligned using multiz, and the resulting multiple alignments were assigned conservation scores by phastCons.

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. Note that, unlike many conservation-scoring programs, phastCons does not rely on a sliding window of fixed size, so 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).

PhastCons currently treats alignment gaps as missing data, which sometimes has the effect of producing undesirably high conservation scores in gappy regions of the alignment. We are looking at several possible ways of improving the handling of alignment gaps.

Credits

This track was created at UCSC using the following programs:

  • Lastz (formerly Blastz) and multiz by Minmei Hou, Scott Schwartz and Webb Miller of the Penn State Bioinformatics Group.
  • AxtBest, axtChain, chainNet, netSyntenic, and netClass by Jim Kent at UCSC.
  • PhastCons by Adam Siepel at Cornell University.
  • "Wiggle track" plotting software by Hiram Clawson at UCSC.

The phylogenetic tree is based on the Saccharomyces Phylogeny page from the Department of Genetics at Washington University in St. Louis.

References

Phylo-HMMs and phastCons:

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

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.