melanogaster  TGATTGTCGT-------CGTTCGGTTT-GGT--------TGGAT---CATCGGATGCCTGAG------T--TGCCGGTGCT-GTTGAGCTCCCC-AAGT-----ATCTGCTCCTCTTGCA
       simulans  TGATTGTCGT-------CGTTCGGTTT-GGT--------TGGAT---CATCGGATGCTTGAG------T--TGCCGTTGCT-GTGGAGCTCCCC-AAGT-----ATCTGCTCCTCCTGCA
      sechellia  TGATTGTCGT-------CGTTCGGTTT-GGT--------TGGAT---CATCGGATGCTTGAG------T--TGCCGTTGCT-GTTGAGCTCCCC-AAGT-----ATCTGCTCCTCCTGCA
         yakuba  TGATTGTCGT-------CGTTCGGTTT-GCT--------TGGAA---GATCGGATGCTTCAG------T--TGCCGGTGCG-CGTGAGCTCCCC-AAGT-----TTCTGCTCCTCCTGCA
         erecta  TGATTGTCGT-------CGTTCGGTTT-GGT--------CGGAT---GATCGGATGCCTGAG------T--TGCCGGCGCG-GTTGAGCTCCCC-AAGT-----TTCTGCTCCTCCTGCA
      ananassae  TGATTGTCGT--CGTTCCGTTCGGTTC-GGT--------TGGAT---GATCGGATGCTCCAA------TGGTGCGGTTGCCAGTTGAGTTCCTTGGAGTCTCCAGTCTACTCCTCCAGCA
  pseudoobscura  CGATTGTCGT-------TGTCGGCTGCGGGT--------TCGATTCCCTTCGATTCTTTGAG------G--TGCCTTTGCA-CGCGATTGCCTC-TA-------CTCTTCTCCTCGTTCT
     persimilis  CGATTGTCGT-------TGTCGGCTGCGGGT--------TCGATTCCCTTCGATTCTTTGAG------G--TGCCTTTGCA-CGCGATTGCCTC-TA-------CTCTTCTCCTCGTTCT
        virilis  TCGTTGAAGC---------TTCCTTTG-CAC--------GCGAT---TCCCGTGTTGCTCACGATACCC--TGCAATACAG-TTGAAGTACTTC-ACTTGGCT-CTTGAGTTATGTTGCT
     mojavensis  TGATCGATGCCACAGTGGATTTCTTCG-GCCTGACTGGGGCGAT---TGTCG----------------C--TGCATCA-----------GCTTC----------------TCCTTTTGCA
      grimshawi  TCGTTGCAGC----------TTCTTTG-CAC--------GCGAT---ACTCTTGTAGTTAATAATACTC--TACAAGTCGT-TTGGATGGGCTC-AGCTGAAT-GTTGAAG---------
        Summary  BBBBBBBBMMMMMMMMMBBBBBBBBBBBMMMMMMMMMBBBBBBBBBBBBBBBBBBBBBBBRRRRRRRRRBBBBBBBBBBBBBBBBBBBBBBBBBBBRRRRRRRRRBBBBBBBBBBBBBBB

                 
   melanogaster  CGC---GATTAC-----------------CTTGTA---------------------GGGGGCAGGATGTA--------------------------------------------------
       simulans  CGC---GATTAC-----------------CTTGTA---------------------GGGGGCAGGATGTA--------------------------------------------------
      sechellia  CGC---GATTAC-----------------CTTGTA---------------GGG---GGGGGCAGGATGTA--------------------------------------------------
         yakuba  CGC---GATTAC-----------------CTTGTA---------------------GGGGGCAGGATGTG--------------------------------------------------
         erecta  CGC---GATTAC-----------------CTTGTA---------------------GGGGGCAGGATGTA--------------------------------------------------
      ananassae  CGC---GATTGC-----------------CTTGTA---------------------GAAGATTGCA------------------------------------------------------
  pseudoobscura  TAT---AATTGG-----------------GGTATATTTGAAGATGTTGGTGGGTTTGGGGATAATATATAAGAGAGAAAAGCGTGGAGAGGCCCAGGCGCAGGCTGAAAAAGAGCACAGA
     persimilis  TAT---AATTGG-----------------GGTATATTTGAAGATGTTGGTGAGTTTGGGGATGGTATATAGGAGAGAAAAGCGTGGAGAGGCCCAGGCGCAGGCTGAAAAAGAGAAAATA
        virilis  CGCATGGATTATATATATCAATTAGTCAACTTCTT---------------------G-TGAGTAGGTGGC--------------------------------------------------
     mojavensis  CGC---GATTCC-----------------CTTGTC---------------------G---------------------------------------------------------------
      grimshawi  ----------------------------------------------------------TGAGGAAATATT--------------------------------------------------
        Summary  BBBBBBBRRRRRRRRRMMMMMMMMMBBBBBBBBMMMMMMMMMMMMMMMMMMBBBBBBBBBBBBBBRRRRRRRRRRRRRRRRRRMMMMMMMMMRRRRRRRRRRRRRRRRRRRRRRRRRRRM

                 
   melanogaster  ----CACTTC---------TATCAGCAG----GGTCATT--------GAGTTGACGCAA------------------TTGTTTTGAATGCT--ATAAAAGGGAACTAATTC---------
       simulans  ----CCCTTC---------TATCAGCAG----GGTCATT--------CAGTAGAAGGAA------------------TTGTTTTGAATGGTAGAAAAAAGGAAACAAACTC---------
      sechellia  ----CCCTTC---------CATCAGCAG----GGTCATT--------CAGTAGAAGGAA------------------TTGTTGTGAATTGT--AAAAAAGGGAACTAATTT---------
         yakuba  ----CACTTC---------TTTCAGCAG----ATACATGCTACCTTACAGTATGAAGTA------------------TTGTTTTAAATTGAA-AAAAATGCTAACTAATTC---------
         erecta  ----CTCTTC---------CTTCAGCAG----ATACATG--------CGGCAGAGAGGA------------------TTATTTTGAATTGAC-AAAAAAAGGAA----------------
      ananassae  -----ACTTG---------CAACACGAA----AGTTTGG--------GAATATAAAACAAGGGTGAAAGCCGAGGGTTAATCTTGAAATTAT-ATAAAAGAGA-----------------
  pseudoobscura  CACGAATTGC---------AAGCGCAGC----ATACATG--------TCGTGTGCATGA------------------CTCGACTCTATTTTC-ACTGATTTAAGCAGATTTAAGCATAT-
     persimilis  CACGAATTGC---------CAGCGCAGC----ATACATG--------TCGTGTGCATGA------------------CTCGACTCTATTTAC-GCTAATGTAAGCAGATTTAAATATAT-
        virilis  ----CAGTTC---------AAATCCCAGATTTGATCCTT--------ATCCTTAA--TA------------------TTGTGCTTTATGTGC-AAAAAAATTGTATCTTTT---------
     mojavensis  ------------------------------------------------------------------------------------------------------------------------
      grimshawi  ----CATTTTTGGAGAGAATATTTCTAG----------T--------AACCATAATTTA------------------TTTTGATAGATAGGT-AATACTATAACAACTTCTAATTATGCC
        Summary  MMMMMMMMMMMMMMMMMBBBBBBBBMMMMMMMMMBMMMMMMMMMRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRBBBBBMMMMMMMMMBBBBBMMMMMMMMMMMMMMMMMMRRR

                 
   melanogaster  ----CCTTTTTGATTGCTTAAATACCAA----------GA---------------TTATTA-----AGAA-----------TTACTAAGGATAGATCATGCGATCTTCAAGA-------T
       simulans  ----CCTTTTTGATTGCTTAAATACCAA----------GG---------------TTATTA-----AGCA----TCTAAACTTACTAAGGATAGACCATGCGATCTTTAAGA-------T
      sechellia  ----TCTTTTCGATTGCTTAAATACCAA----------GG---------------TTATTA-----AGAA----TCTAAACTTACTAAGGATAGATTATGCGATCTTTAAGA-------T
         yakuba  ----CCTTTATGATGGCTTTGTTACTAA----------GC---------------TT-------------------TGAACTAACTGCGAATAGATCATGCTATCTTCAAGA-------T
         erecta  ---------ATTATGGCTTTGATACCAA----------GC---------------TTATGG-----AGAC----ACTGAACTTGCTAAGAATAGAGCATGCGATCGTCAAGA-------C
      ananassae  --------TATAATAAACTTGATGTCTA----------GG---------------GCTTCA-----AA--------TAAACTTAC-------AACTCATAC------TAAGG-------C
  pseudoobscura  ---AACAATATAATATATTTATTTTTAAAGTGTTTTATAT---------------TTATTATTATTAAAATACTTTTAAATTTAA----ATCAAAGTGAATTTTCTCTGGGAATACGAGT
     persimilis  ---AACAATATAATATATATTTTTGTAA----------GT---------------TTATTATTATTAAAATACTTTTAAATTTGC----ATCAAAGTGAATTTTCTCTGGGAATACGAGT
        virilis  ---TTCAAATCCAT--ATTTATTTCGAT----------TT-------------------TA-----AGATCAAGCTCAAGCTCAT----GGTGGTAAGGACTTTGGTGAGGA-------C
     mojavensis  ------------------------------------------------------------------------------------------------------------------------
      grimshawi  AACATCAACCTCATTGATTTCTTATGAG----------TTTACTTTTGTTGTATATTAATA-----ATATCAGATTTGATTTCCC----ACTCAATCCACATCTCATAATAA-------T
        Summary  RRRRRRBBBBBBBBBBBBBBBBBRRRRRRRRRMMMMMMMMMRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRBBBBBBBBBBBBBBBBBBBBBBRRRRRRRRRBBB

                 
   melanogaster  ACTTTCTATC----------CCAGG-----------C---------AAGGGTATTTTTAGTT--CGTGTCGATCTGTC-------------------------ATTTCGTGGA------C
       simulans  ACTTTCTATC----------CCAGG-----------C---------AAGGGTATTTTTAGTT--C--GTCCATCTGTC-------------------------ATTTCTTGGG------C
      sechellia  ACTTTCTATC----------CCAGG-----------C---------AAGGGTATTTTTAGTT--C--GTCCATCTGTC-------------------------ATTTCTTGGG------C
         yakuba  ACATTCCAAC----------CCAGG-----------C---------AAGGGTATTTTTAGTT--C--GCCAATCTGCCT------------------------TTTTCCTGGG------C
         erecta  GCATTCCATC----------CCAAG-----------C---------AAGGGTATTTTTAGTT--C--GCCGATCGGCC-------------------------ATTTCCTGGG------C
      ananassae  AAGCTTTATT----------TTAAAGTTCAATGTCTT---------AAGAGTATTCCACATT--C--GTA---TTGTA-------------------------TTTTTATAAATTTAATT
  pseudoobscura  ACTCTTCAGC----------CCAGA-------------------------GTATCTCCCATT--C--GTGTTTCGTTT-------------------------GTGCCTTGAC-TGTTTT
     persimilis  ACTCTTAATC----------CCAGA-------------------------GTATCTCCCATT--C--GTGTTTCGTTT-------------------------GTGCCTTGAC-TGTTTT
        virilis  ATTACCGATTCGTAAATACCCTAAC-----------T---TTCTTCAACTTAACTGTTGATT--T--TTTGTTGTTCTTGTTGATG-----------------CTTTTTTTTT------G
     mojavensis  ------------------------------------------------------------------------------------------------------------------------
      grimshawi  -CCAACAACTTCTAGTTACGCCAGT-----------CGAACTCCAGAAGGATATTGCCGATTCGT--GTAGTTTCTCCAATTGTTGCAATTTTAGCTTTAGATCTTTTTTTTG------C
        Summary  BBBBBBBBBMMMMMMMMMBBBBRRRRRRRRRMMMMMMMMMRRRRRRRRRBBBBBBBBBBBBBBBBBBBBBBBBBRRRRRRRRRMMMMMMMMMMMMMMMMMMBBBBBBBBBBBBBMMMMMM

                 
   melanogaster  CA--GCA---CTGATAGAGCATCGACACCTTCAATTG-GG---GCTGCTGGTGGGAG---AGCTTTTCGGGA-----AACCTGGGATCTG------GCATCT--------TGAGTCTGGG
       simulans  CA--GCA---CTGATAGAGCATCGACACCTTCAACTG-GG---GCTGCTGGTGGGAG---AGCTTTTCGGGA-----AACCTGGGATATG------GCATCT--------TGAGTCTGGG
      sechellia  CA--GCA---CTGATAGAGCATCGACACCTTCAACTG-GG---GCTGCTGGTGGGAG---AGCTTTTCGGGA-----AACCTGGGATCTG------GCATCT--------TGAGTCTGGG
         yakuba  CG--CCA---CTGATAGAGCATCGACACCTTCCACTG-GGACTGCTGCTGGTGGGAG---AGAGTTTCGGA------AACCTGGGATCTG------GGATCT--------TGAGTCTGGT
         erecta  CATTCCAATTCCGATAGAGCATCGACACCTTCCACTT-GG---GCCGCTGGTGGGAG---AGCTTTTCGGG------AACCTGGGATCTG------GGATCT--------TGAGTCTGCT
      ananassae  TG--CTT---CTGATAGAGGCTCGACACCTTCCATTC-CG----------GTGGGAGA-CAGCCTTTCGG-------AGCCTGGGATCTG------GAATC---------TGACGATGGT
  pseudoobscura  CA--GTGTTTCTTCTAGACCTTCGACACCTTCCTTTT-CGATGGTTTTTGTCAGGAGC-------------------AGAGCTGTCTTTG------GGGCCT---CTGTCTGGGTGCTCT
     persimilis  CA--GTGTTTCTTCTAGACCTTCGACACCTTCCTTTT-CGATGGTTTTTGTCAGGAGCAGAGCTTTTGGGTAGGAGAAGAGCTGTCTTTG------CGGCCT---CTGTCTGGGTGCTCT
        virilis  CA--TCA----TTTTATATGCTCAACACCTTCTGTCT-AC---GCCA-------------AGACTCTTGG--------ACATGGGGTCTG-GCCCTGGGTCT---GACTCGCAGTCGGAG
     mojavensis  -----------------------------------------------------------------------------------GGATCTGTGTCTCGAGTCTCGAGTCTTCCAGTCAGAG
      grimshawi  CA--ACA----TTTTATATGCTCAACACCTTCTGTCTGAC---GCTG-------------AAGCTCTTGGC------ACCATGGACTCTGGTCCCAGAGTCT---GGATCTGTGTCTGCG
        Summary  MMMBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBRRRRRRRRRBBBRRRRRRRRRBBBBBBBBBBBBBBBBBBBBBBBBBBMMMMMMMMMBBBBBBBBB

                 
   melanogaster  GCGG---ATGGTGTTGTATGCGGCCATGTCTGGGTCTGGTCACGATTTGTTGGGACTCGTAAAACATTTTTAGCACCTCAACGACGACTAAGACG---------ACTGACGATC-----A
       simulans  GCGG---ATGGTGTTGTATGCGGCCATGTCTGGGTCTGGTCACGATTTGTTGGGACTCGTAAAACATTTTTAGCACCTCAACGACGACCAAGACG---------ACTGACGATC-----A
      sechellia  GCGG---ATGGTGTTGTATGCGGCCATGTCTGGGTCTGGTCACGATTTGTTGGGACTCGTAAAACATTTTTAGCACCTCAACGACGACCAAGACG---------ACTGACGATC-----A
         yakuba  GCGGATGGCGGTGTTGTATGCGGCCATGTCTGGGTCTGGTCACGATTTGTTGGGACTCGTAAAACATTTTTAGCACCTCGACGACGACCACGAGA---------ACTGACGATC-----A
         erecta  GCTGC--ATGGTGTTGGATGCGGCCATGTCTGGGTCTGGTCACGATTTGTTGGGACTCGTAAAACATTTTTAGCACCTCGACGACGACCAAGTCG---------ACTGACGATC-----A
      ananassae  G------ATGGTGCT-----------TGTCTGGGTCTGGTCACGATTTGTTGAGACTCGTAAAACATTTTTAGCACCTCAACGACGATCCAGACG---------ACTGACGACCAGGCGA
  pseudoobscura  GTGG---ATGG--------------------GGCTCTGGTCACGATTTGTTGAGACTCGTAAAACATTTTTAGCACCTCAACGACCAGGCAGACGTTTGCCCGAAACGGCGACG-----A
     persimilis  GTGG---ATGG--------------------GGCTCTGGTCACGATTTGTTGAGACTCGTAAAACATTTTTAGCACCTCAACGACCAGGCAGACGTTTGCCCGAAACGGCGACG-----A
        virilis  TCGGA--ATCG---AAGACGCAGCCA-----AAGTCTGGTCACGATTTGTGAAGACTCGTAAAACATTTTTAGCACCTCAACG------------------------------------A
     mojavensis  TCTG-----------------AGTCA-----AAGTCTGGTCACGATTTGTGAAGACTCGTAAAACATTTTTAGCACCTCAACG------------------------------------A
      grimshawi  ACGG-----------------AGTCG-----GAGTCTGGTCACGATTTGTTGAGACTCGTAAAACATTTTTAGCACCTCAACG------------------------------------A
        Summary  BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBRRRRRRRRRBBBBBBBBBMMMMMMMMMB

                 
   melanogaster  TCTAT-----AC--ACAT-------------CGAT--------CCGCG--------T---GCACTTCTGCTGT-----TCGGCACTCG--------ATTGCCTTTGTTCTCGCTG--AGT
       simulans  TCTAT-----AC--ACAT-------------CGAT--------CCGCG--------T---GCACTTCTGCAGT-----TCGGCACTCG--------ATTGCCTTTGTTCTCGCTG--AGT
      sechellia  TCTAT-----AC--ACAT-------------CGAT--------CCGCG--------T---GCACTTCTGCAGT-----TCGGCACTCG--------ATTGCCTTTGTTCGCGCTG--AGT
         yakuba  TCCAT-----AC--ACAT-------------CGAT--------CCGCGTGCAATACT---GCACTTCAGCAGT-----TCGACACTCG--------ATTGCCTTTGTTCTCGCTG--AGT
         erecta  TCCAT-----AC--AGAT-------------CGAT--------CCGCG--------T---GCACTTCTGCAGC-----TCGGCACTCG--------ATTGCCTTTGTTCTCGCTG--AGT
      ananassae  TCTAT-----AT--ACATGCAGCACATACCCCGTA--------CAGCA--------T---ATACCTCATCGAT-----CCGATCCACGTACATGGTGGGGCTTTTGTTCTC-CTG--TCT
  pseudoobscura  TCTATATACAAT--ACAT-------------CGAT----------GCA--------TTCAGTATTCCCTCTATATGTATCTCTCCTTA--------TTTTTTTTTTTTGTTGCTG--TTG
     persimilis  TCTATATACAAT--ACAT-------------CGATGCTGCATTCAGCA--------TTCAGTATTCCCCCTATATGTATCTCTCCTTA----------TATTTTTGTTGTTGCTG--TTG
        virilis  TCTAT-----ATACACGT-------------ACAT----------GAG--------T---GCA---GCACAGT-----TT--------------------------TTGTTGTTG--TTC
     mojavensis  TCTAT-----AT--ACGT-------------ACAT----------GAA--------T---GCA---CCACAAT-----TTCATC-------------------TGGTTGTTGTTGGTTTC
      grimshawi  TCTAT-----AT--ACGT-------------ACAT----------GA---------------A---GCACATT-----TCTGTAGTTG---TTGTTGTTGTTGTTGTTGTTGTTG--TTT
        Summary  BBMMMMMMMMMBBRRRRRRRRRRRRRRRRRRBMMMMMMMMMBBBRRRRRRRRRBBBBBBBBBBBBBBBBBMMMMMMMMMBBBBBBRRRRRRRRRBBBBBBBBBBBBBBBBBBBBBBBBBB

                 
   melanogaster  TCGCCAGCC-CGTTTTAATGGCATTTTTGCATTTTTGTGTTTC--------------------TGTTCCAGCTACC-AAGCAGAACGCCCACTCG-------------------GTGGGA
       simulans  TCGCCAGCC-CGTTTTAATGGCATTTTTGCATTTTTGTGTTTC--------------------TGTTCCAGCTACC-AAGCAGAACGCCCACTCG-------------------GTGGGA
      sechellia  TCGCCAGCC-CGTTTTAATGGCATTTTTGCATTTTTGTGTTTC--------------------TGTTCCAGCTACC-AAGCAGAACGCCCACTCG-------------------CTGGGA
         yakuba  TCGCCAGCC-CGTTTTAATGGCATTTTTGCATTTTTGTGTTTC--------------------TGTTCCAGCTACC-AAGCAGAACGCCCACTCG-------------------GTGGGA
         erecta  TCGCCAGCC-CGTTTTAATGGCATTTTTGCATTTTTGTGTTTC--------------------TGTTCCAGCTACC-AAGCAGAACGCCCACTCG-------------------GTGGGA
      ananassae  CTGGCTCCC-CGTTTTAATGGCATTTTTGCATTTTTTTTCTTCATCGCAGCTCTGAGATGCAGCTTCCCAGCTACC-AAGCAGAACGCCCACTCA-------------------GTTGCA
  pseudoobscura  T-----------TTTTAATGGCATTTTTGCATTTTG---------------------------TGTTCCAGCTACC-AAGGAGAACGCCCACTCGCAGGCGGCTGCAGTTTGCTGTGGGA
     persimilis  T-----------TTTTAATGGCATTTTTGCATTTTG---------------------------TGTTCCAGCTACC-AAGGAGAACGCCCACTCGCAGGCGGCTGCAGTTTGCTGTGGGA
        virilis  TTCTTCGTTTTTTTTTAATGGCA-TTTTGCATTTT----------------------------TGCTCTGGCTACC-AAACACGACGCCCACTCGAGCGCG---TTGGC--T--GTGGGA
     mojavensis  TCTTTATACTTTTTTTAATGGCATTTTTGCATTTT----------------------------TGCTGTGGCTACCAAAACACGACGCCCACTCGAACGCGTTCTTGGCTGT--GTGGGA
      grimshawi  CTTATACTTTTTTTTTAATGGCA-GTTTGCATTTT----------------------------TGCTC-GGCTACC-AAACACGACGCCCACTC--------------------------
        Summary  BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBMMMMMMMMMRRRRRRRRRRRRRRRRRRBBBBBBBBBBBBBBBBBBBBBBBBBBBRRRRRRRRRMMMMMMMMMBBBBBBBBBB

                 
   melanogaster  ACTCAATT-TTTATCTTATTTTTTTTTTTTTTTTGTA---TT--------------------------------TTAGCAC-TGCTGCCAAACACATCCTGTCATTAGGG-AAATATTTA
       simulans  ACTCAATT-T--------TTTGGATTTTTTTTTTGTA---TT--------------------------------TTAGCAC-TGCTGCCAAACACATCCTGTCATTAGGG-AAATATTTA
      sechellia  ACTCAATTGT--------TTTGTTTTTTTTTTTTGTA---TT--------------------------------TTAGCAC-TGCTGCCAAACACATCCTGTCATTAGGG-AAATATTTA
         yakuba  ACTCGATT-T----------------TTTTT---------TT--------------------------------TCGTTAC-TGCTGCCAAACACATCCTGTCATTAGGG-AAATATTTA
         erecta  ACTCTTTT-C----------------TTTTTTTTGTATTCTT--------------------------------TTGCCAC-TGCTGCCAAACACATCCTGTCATTAGGG-AAATATTTA
      ananassae  TCGCCATG-G------GAACTGTTTCTTATTTTTAAG---TT--------------------------------TGAGTGCATATCGTCCGGCACATCCTGTCATTAGGG-AAATATTTA
  pseudoobscura  ACTGTTTT-T--------TATTCTGTTTTTTTTTCTG---TTGGTTGGAATGCATGGAAGCTCTTCTCGATCGATCAGCA--GATCAGCAAACACATCCTGTCATTAGGG-AAATATTTA
     persimilis  ACTGTTTT-T--------TTTTCTG-TTTTTTTTCTG---TTGGTTGGAATGCATGGAAGCTCTTCTCGATCGATCAGCA--GATCAGCAAACACATCCTGTCATTAGGG-AAATATTTA
        virilis  AA-------------------------CTCTGTCGAA---CT--------------------------------CTCGCCC-TGG---CTAAGACATCCTGTCATTAGGC-AAATATTTA
     mojavensis  AA---------------------------------------------------------------------------------------AAAAACATCCTGTCATTAGGCAAAATATTTA
      grimshawi  ----------------------------------------------------------------------------------------CGAAGACATCCTGTCATTAGGC-AAATATTTA
        Summary  BBBBMMMMMMMMMMMMMMMMMMBBBBBBBBRRRRRRRRRMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB

                 
   melanogaster  TGTAGATATCGGCTG--------------------GGATCGAAGTGTT---CG--G-----------GAGGAGCAGCTGCC---------------------------------------
       simulans  TGTAGATATCGGCTG--------------------GGATCGAAGTGGT---GG--G-----------GAGGAGCAGCTGCC---------------------------------------
      sechellia  TGTAGATATCGGCTG--------------------GGATCGAAGTGAT---GG--G-----------CAGGAGCAGCTGCC---------------------------------------
         yakuba  TGTAGATATCGGATCGTTTTGAATCTGATTGAAGAGGAGAGGAGAGGA---GA--GGCGAGAGAAAAGAGGAGCATCTGCC---------------------------------------
         erecta  TGTAGATATCGGATC--------------------GGATGGGATAGAA---GC--G----GAGAAGAGGGGAGCAGCTGCC---------------------------------------
      ananassae  TGTAGATATAGCACC--------------------GATTTGGGGAATC---TGCCG-----------AAAAGGCAGCTGCC---------------------------------------
  pseudoobscura  TGTAGATCTCAA-----------------------GGGTAGCCGCAGC---TG--C-----------TGCTGTCAGCCGCA---------------------------------------
     persimilis  TGTAGATCTCAA-----------------------GGGTAGCCGCAGC---TG--C-----------TGCTGTCAGCCGCA---------------------------------------
        virilis  TGTAGATT-------------------AT------GGCCAGGCAGACG-GT-------------------CGCCAGCTGCT---------------------------------------
     mojavensis  TGTAGATT-------------------AA------CGAAACGCAGACGAAT-------------------CGCCAGCTGCG---------------------------------------
      grimshawi  TGTAGATT-------------------ATCAACG-GGGCAGGCAGACG-AT-------------------CGTCAGCTGCTGCTGCTGTTGCAACTACCGCCACTGCTGCTGCTGCTGCT
        Summary  BBBBBBBBBBBBRRRRRRRRRMMMMMMMMMBRRRRRRRRRBRRRRRRRRRRRRRRRRRRMMMMMMMMMBBBBBBBBBBBMMMMMMMMMRRRRRRRRRRRRRRRRRRMMMMMMMMMMMMMM

                 
   melanogaster  ---T-CCTAACGGTGCCCCCAATCAGGGGCAGTCAAATTAGTCCCCACATAATTAACTCAACAAG-----TTTTTGGG-ACCAGACGATTTTA--TTTGGGCATT-----A---GGCG--
       simulans  ---T-CCTAACGGTGCCCCCAATCACTGGCAGTCAAATTAGTCTCCACATAATTAACTCAACAAG-----TTTTTGGG-ACCAGACGATTTTA--TTTGGGCATT-----A---GGCG--
      sechellia  ---T-CCTAACGGTGCCCCCAATCAGAGGCAGTCAAATTAGTCTCCACATAATTAACTCAACAAG-----TTTTTGGG-ACCAGACGATTTTA--TTTGGGCATT-----A---GGCG--
         yakuba  ---T-CCTAACGGTGCCCCCAATCAGAGGCAGTCAAATTAGTCCCCACATAATTAACTCAACAAG-----TTTTTGGGCCCCAGACGATTTTA--TTTGGGCATTAGAGGA---GGCG--
         erecta  ---T-CCTAACGGTGCCCCCAATCAGAGGCAGTCAAATTAGTCCCCGCATAATTAACTCAACAAG-----TTTTTGGG-CCCAGACGATTTTA--TTTGGGCATT-----A---GGCG--
      ananassae  ---T-CCTAACGGTG---------------AGGCCAATTAGTCGCCGCATAATTAACTCAACAAC-----TTT---GG-ATCAGACTGGTTTCGTTTTTGGCATT-----AGTTGGCG--
  pseudoobscura  ---T--CTAACGGTG---------------------------CTCCACGAAATGA----GGCAAG-----TCCTCGCT-GCGGCAGAAATTAG--CTCCGAAATT-----A---GGCG--
     persimilis  ---T--CTAACGGTG---------------------------CTCCACGAAATGA----GGCAAG-----TCCTCGCT-GCGGCAGAAATTAG--CTCAGAAATT-----A---GGCG--
        virilis  ---GATCTAACGGTGCCAA------------GCAAAAATTAGACCCG--AAATTAGCTCAGCAAAATGGTTTTTGGGG-----------------GCGCAAAATT-----G---GTCGGT
     mojavensis  ---CATCTAACGGTGC-----------------------------------ATTTGCT--ACAAA-----TTTTCGAC-----------------TCCCTCAATT--AGGA---GTCGAA
      grimshawi  GCCGATCTAACGGTAC---------------TTGAGACATGCGCTCGC-AAATTAAATTGGCCAA---GTTTTTGGGT-----------------ATATAAAATT-----A---GTCG--
        Summary  MMMMBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBRRRRRRRRRBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBRRRRRRRRRBBBBBBBBB

                 
   melanogaster  GCTG-CTTTGAGCTCCCTTTTATAAGCTATCTTCTCTT-TTATTTTTTCCTCA-G---------CGGCGATTA-GC-CAAATTTATGCAGAGCGCCCTCT----------GGCG------
       simulans  GCTG-CTTTGAGCTACCTTTTATAAGCTATCTTCGCTT-TTATTTTTTCCTCG-G---------CGGCGATTA-GC-CAAATTTATGCAGAGCGCCCTCT----------GGCG------
      sechellia  GCTG-CTTTGAGCTACCTTTTATAAGCTATCTTCGCTT-TTATTTTTTCCTCG-G---------CGGCGATTA-GC-CAAATTTATGCAGAGCGCCCTCT----------GGCG------
         yakuba  GCTG-CTTTGAGTTCTCTTTTATAA--TATTATAGCTTCTCCTTTTTGCCTTG-G---------CGGCGATTA-GC-CAAATTTATGCAGAGCGCCCTCT----------GGCG------
         erecta  GCTG-CTTTGAGCCCTC-----------------GTTTCTCCTTTTTTGCTTG-G---------CGGCGATTA-GC-CAAATTTATGCAGAGCGCCCTCT----------GGCG------
      ananassae  GCTG-CTTTGAGCCATCTCGTTT-----------CCTCCTGGTTTTTTTTTTG-GCTAAAAGGCCAGCGATTAGGC-AAAATTTATGCAGAGCGCCCTCT----------GGCG------
  pseudoobscura  GCTG-CTTTGAG------------------------------------GCTCT-C---------CACCGATTA-GT-GAAATTTATGAAGAGCGCCCTCTGTGGCTGGCCGGCGGCATAT
     persimilis  GCTG-CTTTGAGGCTCT---------------------------------------------------------------------GCAGAGCGCCCTCTGTGGCTGGCCGGCGGCATAT
        virilis  GCGGCCTTTGAGTTGGC-----------------------------------CCA---------AAGCGATTA-GA-GAAATTTATGCGCAGCGCCCTCT----------GGCG------
     mojavensis  GCGAACCCCAA-------------------------------------------A---------GAGCGATTA-AA-AATTTGTATGCGCAGCGCCCTCT----------GGCG------
      grimshawi  GTTGCCTTTGAGGATGC-----------------------------------G-A---------AAGCGATTA-GATGAAATTTATGCACAGCGCCCTCT----------GGCG------
        Summary  BBBBBBBBBBBBBRRRRRRRRRRRRRRRRRRMMMMMMMMMBBBBBBBBBRRRRRRRRRRRRRRRRRRBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBMMMMMMMMMBBBBBBMMMMMM

                 
   melanogaster  -TTGGC------------------------------------------GAAATGATATTCCCGGAAATTGGCAAGGATTCG-TAATCGGC-------CGAAAGA-------GGAGAGGGA
       simulans  -TTGGC------------------------------------------GAAATGATATTCCCGGAAATTGGCAAGGATTCG-TAATCGGC-------CGAAAGA-------GGAGAGGGA
      sechellia  -TTGGC------------------------------------------GAAATGATATTCCCGGAAATTGGCAAGGATTCG-TAATCGGC-------CGAAAGA-------GGAGAGGGA
         yakuba  -TTGGC------------------------------------------GAAATGATATTCCCGGAAATTGGCAAGGATTCG-TAATCGGT-------TGAAAGA-------GGAGAGGGA
         erecta  -TTGGC------------------------------------------GAAATGATATTCCCGGAAATTGGCAAGGATTCG-TAATCGGC-------CGAAAGA-------GGAGAGGGA
      ananassae  -TTGGT------------------------------------------GAAATGATATTCCCGGAAATTGGCAAGGATTCG-TAATCGGC-------GGGAAGGAGGAGGTAGGGAGGGA
  pseudoobscura  TTTGGC------------------------------------------CAAATGTGATTCCCGGAAATTGGCAAGGATTCGTTAATCAGCGACGAGGCGAAAGG--GCGACGGAGAGGAA
     persimilis  TTTGGC------------------------------------------CAAATGTGATTCCCGGAAATTGGCAAGGATTCGTTAATCAGCGACGAGGCGAAAG--------GGAGAGGAA
        virilis  -CTGGCTGGCGGCATTTTCTCTCTCTGTGTGTGTGTGTGTTGGCCACGCAAATAATATTCCCGGAAATTGGCAAGGATTCG----------------AGAG------------------T
     mojavensis  -TTTGTTAGCGG----------CTGTGCAAAAGCATGCATGAACCACGCAAATAATATTCCCGGAAATTGGCAAGGATTTG----------------AAAGAGA------CGAGTTGTTG
      grimshawi  -CTGGCTGGCGGCACTCGCAG-CTGAGGGAAATAATTTGCTAGCCACGCAAATAATATTCCCGGAAATTGGCAAGGATTCA----------------A----------------------
        Summary  MMMBBBMMMMMMMMMRRRRRRRRRRRRRRRRRRMMMMMMMMMBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBMMMMMMMMMBBBRRRRRRRRRBBBBBBBBBBB

                 
   melanogaster  A----TGAGTTGC--CTGGGTGC--GTGGCG----------------TGGTGGCATGGCGTGTCGTAAAAACTC-TTTGCGAATCA---GGCAGC---------------------GGCA
       simulans  A----TGAGTTGC--CTGGGTGC--GTGGCGTG--------GTGGCATGGTGGCATGGCGTGTCGTAAAAACTC-TTTGCGAATCA---GGCAGC---------------------GGCA
      sechellia  A----TGAGTTTC--CTGGGTGC--GTGGCGTG--------GTGGCATGGTGGCATGGCGTGTCGTAAAAACTC-TTTGCGAATCA---GGCAGC---------------------GGCA
         yakuba  A----TGAGTTGC--CTGGGTGC--GTGGCATGGTGGCTCAGTGGCTCAGTGGCATGGCGTGTCGTAAAAACTC-TTTGCGAATCA---GGCAGC---------------------GGCA
         erecta  A----TGAGTTGC--CTGGGTGC--GTGGCATG----------------GTGGCATAGCGTGTCGTAAAAACTC-TTTGCGAATCA---GGCAGC---------------------GGCA
      ananassae  AGAGGTGAGTCGC--C-GGCGGC--ATCGCAGG-------------------GCCTGGCCTGCCGTAAAAACTC-TTTGCGAATCG---GGCAGC---------------------A---
  pseudoobscura  A-------GCGACAAGAGGGCAA--GAGGTAAG-------------ACTGCTGCGTGTCGCATCATAAAAACTCTTTTGCGAATCATCGGACATC--------------------AGGCA
     persimilis  A-------GCGAC--GAGGGCAA--GAGGTAAG-------------ACTGCTGCGTGTCGCATCATAAAAACTCTTTTGCGAATCATCGGACATC--------------------AGGCA
        virilis  C----TGTGCCTG--CTTGGCCA--GTTGTGTG-----------------------TGCGTGTCGTAAAAACTC-TTTGCGAATCG---GACGGCAGCGATTGAGACAGCGACTGAGGCA
     mojavensis  T----TGCGGTTG--TTGTGTTGTTGTTGTTGT-----------------------TGCGTGTCGTAAAAACTC-TTTGCGAATCG---GACAGCAGCAGCAGAGGCAGAGGCAGAGGCA
      grimshawi  -----TGCTGTCG--CTGAGCTG---------------------------------TGCGTGTCGTAAAAACTC-TTTGCGAATCG---GACGGT-------------------------
        Summary  BBBBBBBBBBBBBBBBBBBBBBBBBBBRRRRRRRRRRRRRRRRRRBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBMMMMMMMMMRRRRRRRRRBBBBBBBB

                 
   melanogaster  GCGGGT--------------------TCGCATCGGCGGTATTAGCCATCAAGGCCATGAAAGACATTAG-----CTTGGTGGATCGTAAAATCCCTGAA-C---AAC--GGACA----CA
       simulans  GCGGGT--------------------TCGCATCGGCGGTATTAGCCATCAAGGCCATGAAAGACATTAG-----CTTGGTGGATCGTAAAACCCCTGAA-C---AAC--GGACA----CA
      sechellia  GCGGGT--------------------TCGCATCGGCGGTATTAGCCATCAAGGCCATGAAAGACATTAG-----CTTGGTGGATCGTAAAACCCCTGAA-C---AAC--GGACG----CA
         yakuba  GCGGGT--------------------TTGCATCGGCGGTATTAGCCATCAAGGCCATGAAAGACATTAG-----CTTGGTGGATCGTAAAACCCCTGAA-C---AACAGAGACA----GA
         erecta  GCGGCT--------------------T--CGGCAGCGGTATTAGCCATCAAGGCCACGAAGGACATTAG-----CTTGGTGGATCGTAAAACCCCTGAA-C---AAC--GGACA----GA
      ananassae  --------------------------TCGCTTCA-----AGCAGCCTTCAAGGCTGTGAGGGACATTAGTGGACTTTGGATGACCATAAAACCCATATA-C---CAT--CGGCC------
  pseudoobscura  ACAGG---------------------------CAGC--------CCATCAAGGACACTCTGGACATTAGT----TTTGGGCGATCATAAAACCCGAAAACC---AAA--AGACAACACCA
     persimilis  ACAGG---------------------------CAGC--------CCATCAAGGACACTCTGGACATTAGT----TTTGGGCGATCATAAAACCCGAAAACC---AAA--AGACAACACCA
        virilis  GCGACT----------------------GCGACAGCGAC-----TCATCAAGGACATGCGGCACATTAG-----CGTGAC-GCTCATAAAGCCAAAACC-C-------------------
     mojavensis  GAGACTCTCAGCAGCAGCGGCAGCAGCAGCAGCAGCTAT-----GCATCAAGGACATGCGGCACATTAG-----CGAGCC-GCTCATAAAGCCAAAACC-CCGATAG--AGACA--GCCA
      grimshawi  --GGCT--------------------------CAGTCTC-----TCATCAAGGACATGCGGCACATTAG-----CGTGAC-GCTCATAAAACCAAACTC-C---GAT--AGCCA--GCCG
        Summary  BBBRRRRRRRRRRRRRRRRRRRRRRRRRRRBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBRRRRRRRRRBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBMMMMMMM

                 
   melanogaster  GAG-------GTCTAATCCGTGGAAACTCTAAACTCTAT---------CCCAGA---GA-GAACCTCTTTCGGCGCGAGACTACTCAGTTAGTTGGC--TAGGTAAAAGCCGTAGAACTC
       simulans  GAG-------GGCTAATCCGTGGAAACTCTAAACTCTAT---------CCCAGA---GA-GAACCTCTTTCGGCGCGAGACTACTC----AGTTGGC--TAGGTAAAAGCCGTAGAACTC
      sechellia  GAG-------GGCTAATCCGTGGAAACTCTAAACTCTAT---------CCCAGA---GA-GAACCTCTTTCGGCGCGAGACTACTC----AGTTGGC--TAGGTAAAAGCCGTAGAACTC
         yakuba  GAG-------GGCTAATCCGTGGAAACTCTAAACTCTAT---------CCCAGA---GA-GAACCTCTTTCGGCGCGAGACTACGC----CGTCGGC--TAGGTAAAAGCCGTAGAACTC
         erecta  GAG-------GGCTAATCCGTGGAAACTCTAAACTCTAT---------CCCAGA---GA-GAACCTCTTTCGGCGCGAGACTACTC----AGTTGGC--TAGGTAAAAGCGGCAGAACTC
      ananassae  ----------AGCTAATCCGTGGAAACTCTAAACTCTAT---------CCCAAA---GAGGAACCTCTTTCGGCGCGAGTCGCAAC----------------------------------
  pseudoobscura  AAG--GACTCGTCTAATCCGTGGAAACTCT-ATCGCAAC---------AGAAGA---AG-GATACTCTTTCGGCGCGAGTCGCCTC---------------------------GTCACTC
     persimilis  AAG--GACTCGTCTAATCCGTGGAAACTCT-ATCGAAAC---------AGAAGA---AG-GATACTCTTTCGGCGCGAGTCGCCTC---------------------------GTCACTC
        virilis  -----GCC--AGCTAATCCGTGGAAACCCTAAACTCTAC---------CCTATGCC-AG-CAACCTCTTTCGGCGCGAGTCTAATG----------C--TAGGT--A------AGAACTC
     mojavensis  AAGCAGTC--AGCTAATCCGTGGAAACCCTAAACTCTAC---------CCTATGCCGAA-AAACCTCTTTCGGCGCGAGTCTAACG----------CG-TAGGTAAA------AGAACTC
      grimshawi  AAA--GCC--AGCTAATCCGTGGAAACTCTAAACTCTACGATGCCAAACCGATACC--A-AAACCTCTTTCGGCGCGAGTCTTATG----------CGCTAGGT--A------AAAACTC
        Summary  MMBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBRRRRRRRRRBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBRRRRRRRRRBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB

                 
   melanogaster  TTTC-------------CACTCTTT------C------------------CCGA----------------------TTCC-CCGATC------------------------GCCG-----
       simulans  TTTC-------------CACTCTTT------C------------------CCGA----------------------TTCC-CCGATC------------------------GCCG-----
      sechellia  TTTC-------------CACTCTTT------C------------------CCGA----------------------TTCC-CCGATC------------------------GCCG-----
         yakuba  TTTC-------------CACTCCTT------CCACTCTTTCGACTCTTTGCCGA----------------------TTCC-CCGATC-----------------------ACCGG-----
         erecta  TTTC-------------CACTCTTT------C------------------CCGG----------------------TTCC-CCGATC-----------------------TGCCG-----
      ananassae  --CC-------------TACTTTTA------C------------------CC-A----------------------TCCC-GCAACC-----------------------CATCG-----
  pseudoobscura  TTTC-------------CACTCTTTACATGCC------------------CC------------------------TGCC-CCTGCCATG---------------CCC-CTGCCG-----
     persimilis  TTTC-------------CACTCTTTACATGCC------------------CCTGCCCCTGCCCCTGCCTCTGCCCTTGCC-CCTGCCATG---------------CCC-CTGCCGCCTCT
        virilis  TTTCGCCTGCGGCTGTTTACTCCTT------C---------------------G----------------------TGCC-ACAGGTAAAGGTAAACAGCCGTGGCAC-AAGCTG-----
     mojavensis  TTTCCT------CCGTTTACTCCTT------C---------------------G----------------------TGCCGGCAGGTAGAGCCAGACAGAGCCAGCACTATGCTG-----
      grimshawi  TTTCGCCTCGGGTTGTTTACTCCTT------C---------------------G----------------------TGCC-GCAGGTAAA------------CAGTAC-AGATGG-----
        Summary  BBRRRRRRRRRBMMMMMMMMMBBRRRRRRRRRRRRRRRRRRMMMMMMMMMBMMMMMMMMMRRRRRRRRRRRRRRRRRRBBBBBBBBBRRRRRRRRRRRRRRRRRRRRRRRRRRRMMMMMM

                 
   melanogaster  ----AGC-------CGTAC---------------------------CTGT--CC---------------------TGCG----------------T-GT---------TTGACGTTTGTC
       simulans  ----AGC-------CCTAC---------------------------CTGT--CC---------------------TGCG----------------A-GT---------TTGACGTTTGTC
      sechellia  ----AGC-------CCTAC---------------------------CTGT--CC---------------------TGCG----------------A-GT---------TTGACGTTTGTC
         yakuba  ----AGTCCAACTACCTAC---------------------------CTGT--CC---------------------ACCG----------------A-GT---------TTGACGTTTGCC
         erecta  ----AGT-------CCTAC---------------------------CTGT--CC---------------------GCCG----------------A-GT---------TTGACGTTTGCC
      ananassae  ----CGT--------TTAC---------------------------CTGT--CCGCCGTAAAAAGGATATGCGTTTGCG----------------G-GTCCTGACGAGTTGACGTTTGCA
  pseudoobscura  ----CCA-------CTCAC---------------------------CTCTTACC---------------------TGTG----------------G-GTCTTGACGAGTTGACGTTTGTC
     persimilis  CTCACCT-------CTCAC---------------------------CTCTTACC---------------------TGTG----------------G-GTCTTGACGAGTTGACGTTTGTC
        virilis  ----TGC-------GCG--------AGGAAGGGAGAGGCAG-----GAGC--TA---------------------GTTG----------------G-TC--TGACGAGTTGACGTTTGCA
     mojavensis  ----AGT-------GAGAG--CGGTAGACAGAGAGAGGGAGACCGAGAGC--TA---------------------GAGGCAGAACCAGCGAGAGCG-GG--TGAGGAGTTGACGTTTGCA
      grimshawi  ----AGA-------AAGGGACAGATAGATAGGGAGAGAGGG--AGAGTGT--TG---------------------GTTA----------------GCAC--TGACGAGTTGACGTTTGCA
        Summary  MMMMMMMMMMMMBBBBBRRRRRRRRRMMMMMMMMMRRRRRRRRRBBBBBRRRRRRRRRRRRRRRRRRMMMMMMMMMBMMMMMMMMMMMMMMMMMMRRRRRRRRRBBBBBBBBBBBBBBBB

                 
   melanogaster  CGCCAATTGATTTGACATTGAAGG-----------------------------------------------------CTCTC-TACCGTC------------AAATAACCCTAAATAAAA
       simulans  CGCCAATTGATTTGACATTGAAGG-----------------------------------------------------CTCTC-TACCGTC------------AAATAACCCTAAATAAAA
      sechellia  CGCCAATTGATTTGACATTGAAGG-----------------------------------------------------CTCTC-TACCGTC------------AAATAACCCTAAATAAAA
         yakuba  CGCCAATTGATTTGACATTGAAGG-----------------------------------------------------CTCTC-TACCGTC------------AAATAACCCTAAATAAAA
         erecta  CGCCAATTGATTTGACATTGAAGG-----------------------------------------------------CTCTC-TACCGTC------------AAATAACCCTAAATAAAA
      ananassae  CGCCAATCGATTTGACATTGAAGGGATAAGGATAGGGATATATGGCATGCAGCATGAAGGGATGAGGAAGATGCGGATGCGC-GACTG-C------------AAATAACCCTAAATAAAA
  pseudoobscura  CGCCAATTGATTTGACATTGAAGGGAGACCCCGAGGACCA-------------------------------------CTCGC-TCTCGTCCTACTCGGCTGTAAATAACCCTAAATAAAA
     persimilis  CGCCAATTGATTTGACATTGAAGGGAGACCCCGAGGACCA-------------------------------------CTCGC-TCTCGTCCTACTCGGCTGTAAATAACCCTAAATAAAA
        virilis  CGCCAATTGATTTGGCATTGAGGAGG---------------------------------------------------CGAACACACCGT-------------AAATAACCCTAAATAAAA
     mojavensis  CGCCAATTGATTTGGCATTGAGGCGT---------------------------------------------------AGAG-----CGT-------------AAATAACCCTAAATAAAA
      grimshawi  CGCCAATTGATTTGGCATTGAGG------------------------------------------------------CGAGCGTAGCGT-------------AAATAACCCTAAATAAAA
        Summary  BBBBBBBBBBBBBBBBBBBBBBBRRRRRRRRRRRRRRRRRRMMMMMMMMMMMMMMMMMMMMMMMMMMMRRRRRRRRRBBBBBBBBBBBRRRRRRRRRBBBBBBBBBBBBBBBBBBBBBBB

                 
   melanogaster  CCATAAAATCCTTCTGCATGCTGCG-------------------AACCCATCCATCGAAAGATCCTCACCTTGA--G-----CCACC------------------CGCC--------ATC
       simulans  CCATAAAATCCTTCTGCATGCTGCG-------------------AACCCATCCATCGAGAGATCCTCACCTTGA--G-----CCACC------------------CGCC--------ATC
      sechellia  CCATAAAATCCTTCTGCATGCTGCG-------------------AACCCATCCATCGAAAGATCCTCACCTTGA--G-----CCACC------------------CGCC--------ATC
         yakuba  CCATAAAATCCTTCTGCATGCTGCG-------------------AACCCATCCATCGAAAGATCCTCACCTTGA--G-----CCACC------------------CGCC--------ATC
         erecta  CCATAAAATCCTTCTGCATGCTGCG-------------------AACCCATCCATCGAAAGATCCTCACCTTGA--G-----CCACC------------------CGCC--------ATC
      ananassae  CCATAAAATCCTTCTGCATGCTGAG-------------------AACCCATCCATCCATCGATCCTCACCTTGA--GTCGCCTCACC------------------CGCG--------ATC
  pseudoobscura  CCATAAAATCCTTCTGCATGCTGCGC---------GACAC-GGACACCCATCCATCCTCTCG-CCTCACCTTGA--G-----CCACC------------------AATC-------GATC
     persimilis  CCATAAAATCCTTCTGCATGCTGCGC---------GACAC-GGACACCCATCCATCCTCTCG-CCTCACCTTGA--G-----CCACC------------------AATC-------GATC
        virilis  CCATAAAATCCTTCTGCATGTTGCGCTTTTGTGCGCGGGC-TCAAACCCA------------TCCTCACCTTGA--G-----AGCCCAGCCATGGGTTAAGTTGTTTCCCATTTTATTTT
     mojavensis  CCATAAAATCCTTCTGCATGTTGCGCTTTTGTGTTGGCCCATCAAACCCA------------TCCTCACCTTGAGTG-----TGCCTAGGCTCGGATCGGATCTTTGCC------ATTTT
      grimshawi  CCATAAAATCCTTCTGCATGTTGCGCTTTTGTTTGTGCC--TCAAACCCAAC----------CCCTCACCTTGAGGG-----TTCCC--------GCGAGACTCTCAGC------CCATT
        Summary  BBBBBBBBBBBBBBBBBBBBBBBBMMMMMMMMMBMMMMMMMMMBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBRRRRRRRRRBBBBBBMMMMMMMMMBBBBBBBBBRRRRRRRRRBBBBB

                 
   melanogaster  TAAGGTTTG----TTTTT-------------TT---------T-TCTTCACTTTTTTG----ACGCGTTTTTTAGCCGAACTCG------TAAATGTG-----AGGAAATCA-TTTTTTA
       simulans  TAAGGTTTG------TTT-------------TT---------T-TCCTCACATTTTTG----ACGCGTTTTTTAGCCGAACTCG------TAAATGTG-----AGGAAATCA-TTTTTTA
      sechellia  TAAGGTTTG------TTT-------------TT---------T-TCCTCACTTTTTTG----ACGCGTTTTTTAGCCGAACTCG------TAAATGTG-----AGGAAATCA-TTTTTTA
         yakuba  TAAGGTTTG------TTT-------------TT---------TCTTTCCACTTTTTTTTTTCACGCGCTTTTTAGCCGAACTCG------TAAATGTG-----AGGAAATCA-TTTTTTA
         erecta  TAAGGTTTG------TTT-------------TT-----------TTTCCACTTTTTTG----ACGCGTTTTTTAGCCGAACTCG------TAAATGCG-----AGGAAAGCA-TTTTTTA
      ananassae  TAAGGACTT------TTT-------------TGGCTGGCGTGT-TTTTTATTTATTT-----ACTTTTTTTTTAGCCGAACTCG------TAAATGTG-----AGG-AGTCA-TTTTTTA
  pseudoobscura  TAAGGTTTGCGTTTATTT-------------TT---------C-TTCTTG----TTTT---------TTTTTTAGCCGAAATCG------TAAAGGAG------GCAAGGCG-TTTTTTA
     persimilis  TAAGGTTTGCGTTTATTT-------------TT---------C-TTCTTGTTTTTTTT---------TTTTTTAGCCGAAATCG------TAAAGGAG------GCAAGGCG-TTTTTTA
        virilis  TTTTACATT------TCATTTGCAATTTCGCTT---------T-CTCTTCTCTTTTTT----TTTTTTTTTTTAG-CGAACTCG------TAAATGCTGTTAGTGCACATCAGTTTTTTA
     mojavensis  TTAGATACG------TCG-------------AT---------T-TTCTTTTTCTTTTC----TCTTTTTTTTTAG-CGAACTCG------TAAATGCAGT---TGCA------TTTTTTA
      grimshawi  TCAGATATT------TTT-------------TC---------T-CTTGTTTTCTTTTT----TTTTTTTTTTTAG-CGAACTCGTAATCATAAATGCTGTAAGTGAACATCA-TTTTTTA
        Summary  BBBBBMMMMMMMMMMMMMMMMMMRRRRRRRRRRRRRRRRRRBBBBBBBBBBBBBRRRRRRRRRBBBBBBBBBBBBBBBBBBRRRRRRRRRBBBBBMMMMMMMMMBBBBBBBBBBBBBBBB

                 
   melanogaster  TGCAATTCGTTGTCAACGACTTTTG-AGAATTC-AG---------------------------------GGAACTGTT--GCGTTCGTTTTTTACGCAATGCCATGTAACG---------
       simulans  TGCAATTCGTTGTCAACGACTTTTG-AGAATTC-AG---------------------------------GGAAC---T--GCGTTCGTTTTTTACGCAATGCCATGTAACG---------
      sechellia  TGCAATTCGTTGT---CGACTTTTG-AGAATTC-AG---------------------------------GGAAC---T--GCGTTCGTTTTTTACGCAATGCCATGTAACG---------
         yakuba  TGCAATTCGTTGTCAACGACTTCTGAAAAATTC-AG---------------------------------GGAAC---T--GCGTTCGTTTTTTACGCAATGCCATGTAACG---------
         erecta  TGCAATTCGTTGTCAACGACTTCTG-AAAATTC-AG---------------------------------GGAAC---T--GCGTTCGTTTTTTACGCAATGCCATGTAACG---------
      ananassae  TGCAATTTGTTGTCAACAGTTTCGA-GCATTTC-AC---------------------------------GGAAG---T--GCGTTCGTTTTTTACGCAATGCGATGTAACT---------
  pseudoobscura  TGCAATTTTTTTGTGAGGCTTCCAC-GTTTTTCAAA---------------------------------GGAAC---TGCGCGTTCGTTTTTTACGCAATACCATGTAATA---------
     persimilis  TGCAATTTTTTTGTGAGGATTCCAC-GTTTTTCAAA---------------------------------GGAAC---TGCGCGTTCGTTTTTTACGCAATGCCATGTAATA---------
        virilis  TGCAATTTGTTGTCAACGAA------GAGATTT-GCCAACAGAAATTTTCGATC----CTTGTTTAGTTGGAAT---T--GCGTGCGTTTTTTACGCAACGCCACGCAACAG--------
     mojavensis  TGCAATTTGTCGTCAACAAAATTTT-GAAATTC-GC--AAGAGAATTTGCGAACGGCGACTTTTTACTCGGAAG---T--GCGTTCGTTTTTTACGCAACTAGACGCAACGGCAGTTAAA
      grimshawi  TGCAATTTGTTGTCAACAAG------GCGATTT-AC-------------------------------GTGGAAC---T--GCGTTCGTTTTTTACGCAACTCCACGCAACG---------
        Summary  BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBRRRRRRRRRMMMMMMMMMRRRRRRRRRMMMMMMMMMBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBMMMMMMMMMM

                 
   melanogaster  -------TCTGCTGGT---------------------TTGTTGTTTT--------TTCTTTATGGGAGGCGAGTTGACTTTTTTAGAGAAAA------------------------TTAT
       simulans  -------TCTGTTGGT---------------------TTGTTGTTTT--------TTCTTTATGGGAGGCGAGTTGACTTTTTTAGAGAAAA------------------------TTAT
      sechellia  -------TCTGCTGGT---------------------TTGTTGTTTT--------TTCTTTATGGGAGGCGAGTTGACTTTTTTAGAGAAAA------------------------TTAT
         yakuba  -------TCTGTTGGA---------------------TTGTTGTTCT--------TTCTTTATGGATGGCGAGTTGACTTTTTTAGAGAAAA------------------------TTAT
         erecta  -------TCTG-TGGA---------------------TTGTTGTTTC--------TTCTTTATGGGCGGCGAGTTGACTTTTTTAGAGAAAA------------------------TTAT
      ananassae  -------TCTGCTGCC---------------------TTGTTGTTTC--------TTTTTTATGG-AGGCGAGTTGACTTTTTTAGAGAAAA----------------------------
  pseudoobscura  -------CTCG-TAAC---------------------ATGTTTTTTTCGGCG---TTTTTTTTTACCCGGTACTCGAAGAATTTAAGGGACATATTAGTTGGTTTTTGTCTGTTTTTTAT
     persimilis  -------CTCG-TAAC---------------------ATGTTTTTTTCAGCGTTTTTTTTTTTTACCCGGTACTCGAAGAATTTAGGGGACATATTAGTTTGTTTTTGTCTGTTTTTTAT
        virilis  -------AACG-CAGC---------ATTTTTTCGT--CGGTTTGTTG--------TTTTTTATGAGCC-AAAGTTGACTTTTTTAGTGAAAA------------------------TGAT
     mojavensis  AAAAAAAAACG--------------------------------ATGA--------TTTTTTATGAGCCGAAAGTTGACTTTTTTAGTGGAAA------------------------TGAT
      grimshawi  -------AACG-TGTCTATGATTGGTTTTTTAAGTTGTGTTTTTGTG--------TCTTTTATGAGCACAAAGTTGACTTTTTTAGTGAATT------------------------TGAT
        Summary  MMMMMMMMBBBMMMMMMMMMMMMMMMMMMMMMMMMMMMBBBBBBRRRRRRRRRBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBMMMMMMMMMMMMMMMMMMMMMMMMMMMBBB

                 
   melanogaster  GAGGGAGGAGCG-------------GGC--ATTAAAAA--AGGGAGT--------CAAG----GAAAAGGGAAAACT---GCCAA-TACCAGGAAATCCTAAAGTAAAAA---AAAAAAA
       simulans  GAGGGAGGAGCG-------------GGC--ATTAAAAA--AGGGAGT--------CAAG----GAAAAGGGAAAACT---GCCAG-TACCAGGAAACCCTAAACT--------AAAAAAA
      sechellia  GAGGGAGGAGCG-------------GGC--ATTAAAAA--AGGGAGT--------CAAG----GAAAAGGGAAAACT---GCCAG-TACCAGGAAACCCTAAACT----A---AAAAAAA
         yakuba  GAGGGAGGAGCG-------------GGC--ATTAAAAA--AGGGAGT--------CAAG----GAAAAGGGAAAACGTGCTGCAG-TACCAGGAAACTCTAAAGT----GAAAAAAAAAA
         erecta  GAGGGAGGAGCG-------------GGC--ATTAAAAA--AGGGAGT--------CAAG----GAAAAGGGAAAACG---TCCAG-TACCAGGAAACGCTAAAGT----G---TAAAAAA
      ananassae  -AATGATGAGCC-------------GGC-----AAGAA--GAGGAGT--------CAGG----AC---------------TCGAA-TACCAGGAAGTGTTG--------A---CAAAAAA
  pseudoobscura  GA-TTAGAAGTT-------------GACTTTTTTAGTG--AAGAAGT--------CG---------CAGGAGTACCA---GGAAG-TGGCAGGGAAGACAAA------------------
     persimilis  GA-TTAGAAGTT-------------GACTTTTTTAGTG--AAGAAGT--------CG---------CAGGAGTACCA---GGAAG-TGGCAGGGAA-------------------ACAAA
        virilis  GATAGAAGGCTG-------------GAC-----AAGTACCAGGAAGTCCTACGTCCAACAATGTGAGAGGGGAAGAG---AGGAG------GAGAGAGTGA--------------GAGAA
     mojavensis  GAGGCGAGATTG-------------TGC------GGCAGCAAAAAA---------CAAC------AGAGGAAAGGAA---ACAAGCTCTTAGAAGGCGAAG--------------GAGAA
      grimshawi  GAGAGAAGATTGCCTGAAGAAAAACCGC-----CAGTACTGAGAAGT--------CAAC-GTGCAAACGATAGATAG---GGAAG-ATATAGGGAGAAAGA--------------GAGAT
        Summary  BBBBBBBBRRRRRRRRRBBBBBBBBBBBBBBBBBBBBBBBBBBBRRRRRRRRRBBBRRRRRRRRRBBBBBBBBRRRRRRRRRBBBBBBBBBBBBBBBBMMMMMMMMMMMMMMMMMMBBBB

                 
   melanogaster  CGGAAAAGTATTCGTATGTACTTGGCCAAAAGAGCCGTTCGCATCGCTC--TCTTTGCTAAAATC-------CTCTCCAGAAC----------------TCAAGT-------TTCAACGG
       simulans  CGTAGAAGTATTCGTATGTATTTGGCCAAAAGAGCCGTACGCATCGATC--TC-TCGCTGAAATC-------CTCTCCAGAAC----------------TCAAGT-------TTCAACGG
      sechellia  CGTAGAAGTATTCGTATGCATTTGACCAAAAGAGCCGTACGCATCGATC--TC-TCGCTGAAATC-------CTCTCCAAAAC----------------TCAAGT-------TTCAACGG
         yakuba  CAGAGAAGTATTCCTGTGTACTTGGCTTAACTAGCCGTTCGCTTCGATC--GC-TTGCTGAAATC-------TTCGCCAGCAC----------------TCAAGT-------TTCAACGG
         erecta  CAGAA----ATTCGTATGTACTTGGCTAAAATAGCCGAACGCTTAGATC--TC-TTGCTGAAATC-------CTCTCCAGAAC----------------TCCAGC-------TTCAACGG
      ananassae  CGGCTAACTATTTCGTCAAACTAGAC--AGCTAGATGTATCTCTAACTCTGTC-CTACCGAAGTCTGGACGGTTCTCCTAG-------------------CCATT-------TCAAAGGG
  pseudoobscura  --------------------------------------------------------TGTGAAGGG-------CTCTCCCTCTC---------------GTCTGCT-------TTGAACGG
     persimilis  TCTCTCTCTCTCTCTCTCTATCTC-------------------TCTCTC--TC-TCTGTGAAGGG-------CTCTCCCTCTC---------------GTCTGCT-------TTCAACGG
        virilis  CGGCAGAAGTCGCTGCT-----------AGATCATGGGATGCA----------------TGGGCC-------A----GAGCAC----------------------------GGCCAACGG
     mojavensis  TGAGTGAAGCCGAGTCTCT-CTCACTAGAGAACATTAGA-GTA----------------GAGCTC-------A----TAGCACTCACTCATAGGAAACTTCTAGCTCTCTGGCTCAACGG
      grimshawi  CGGGAG---------------TTGGTAGAGGGAGCAGAATATA----------------GAGATC-------ACTGCTAGCAT-----------------------------TTCAAGGG
        Summary  BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBRRRRRRRRRBBBBBBBBBMMMMMMMMMMMMMMMMMMBBBBRRRRRRRRRBBBBBBBBB

                 
   melanogaster  GTTAAC-TT--------GGTCCAGTGGCGTGTGAGCTACGTCTAACCCTATGTATATAGATATAGATATAGATATAGATAGATATAG----------ATAGATAGACAGGGA-TAGAGGT
       simulans  GTTAAC-TT--------GGTCCAGCGGCGTGTGAGCTACGTCTAACCCTATGCATATAGAT----------------ATAGATATAG----------ATAGATAGACAGGGA-TAGAGGT
      sechellia  GTTAAC-TT--------GGTCCAGCGGCGTGAGAGCTACGTATAATCCTATGC------AT----------------ATAGATATAG----------ATAGATAGACAGGGA-TAGAGGT
         yakuba  GTTAAC-TT--------GGTGCAGAGGCGTG-------------------TGGATATAGAC----------------ATAGATATAGATATATAGATATAGATAGAGAGGGA-TAGAGGT
         erecta  GTTAAC-TT--------GGTCCAGCGGCGTGTGAGCTAAGCATGAACCTATGGATATAGAT----------------ATAAATATAG--ATAAAGATATAGATAGACAGGGA-TGGAGGT
      ananassae  GTTAAC-TT--------GGCCGAAAGGCGTGCGAG------------------------AT----------------GTCCTGGTAA-------------------------------CC
  pseudoobscura  GTTAACTTT--------GGCCCAAAGGC-------------------------------AT-----------------------------------------------------------
     persimilis  GTTAACTTT--------GGCCCAAAGGC-------------------------------AT-----------------------------------------------------------
        virilis  GTTAAG-AGCAAAG-----CAAAGGGGCGTGCGGT--TCGTCTAACCCTACG--------------------------------------------------------GCAGTCCGAAGC
     mojavensis  GTTAAG-G------------AAAGGGGCGTGC-GT--TTGTCTAACCCTACA--------------------------------------------------------------------
      grimshawi  GTTAAC-TGCTGCGACTGCTTCTAGGGCGTGCGGTCGTCGTCTAACCCT--------------------------------------------------------ACAGCAG-CAGAAGC
        Summary  BBBBBBRRRRRRRRRBBBBBBBBBBBBBBBBBBBBMMMMMMMMMBBBMMMMMMMMMRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRBRRRRRRRRRBBBBBBBBBBBBBBBBBB

                 
   melanogaster  ATACCTGCACC--CACCACGCCCATAATCCTTTTATGGCAAATAAACAAACAACGTCACGGCGACT-----------CAGTCGCGA-------------------AGGAT-------TGC
       simulans  ATACCTGCACC--CACCACGCCCATAATCCTTTTATGGCAAATAAACAAACAACGTCACGGCGACT-----------CAGTCGCGA-------------------AGGAT-------TGC
      sechellia  ATACCTGCACC--CACCACGCCCATAATCCTTTTATGGCAAATAAACAAACAACGTCACGGCGACT-----------CAGTCGCGA-------------------AGGAT-------TGC
         yakuba  ATACCTGCACC--CACCACGCCCATAATCCTTTTATGGCAAATAAACAAACAACGTCACGGCGACT-----------CAGTCGCGA-------------------AGGAT-------TGC
         erecta  ATACCTGCACC--CACCACGCCCATAATCCTTTTATGGCAAATAAACAAACAACGTCACGGCGACT-----------CAGTCGCGA-------------------AGGAT-------TGC
      ananassae  CTACCTGCGCCCGCACCACGCCCATAATCCTTTTATGGCAAACAAACAAACACTGTCACGGATA--------------------GA-------------------AGGATAGAACGATGT
  pseudoobscura  ------GCACC--CACCACGCCCATAATCCTTTTATGGCAAATAAACAAACAACGTCACGGCGC-------------------------------------------GAT-------CGC
     persimilis  ------GCACC--CACCACGCCCATAATCCTTTTATGGCAAATAAACAAACAACGTCACGGCGC-------------------------------------------GAT-------CGC
        virilis  CTACCTGCCC-------ACGCCCATAATCCTTTTATGGCAAATAAACAAACA-TGTCACGGCTCGGCTCGGTACGGTCCGGCACGGCACGGCAGCCCAGTGCAGTGGGAA-------TCC
     mojavensis  -TACCTGTTCG-----GACGTTCATAATCCTTTTATGGCAAATAAACAAACACCGTCACGGCTCTGGCCGAGAC---CGAGACCGAGACCGAGACCGAGTGA---GAGAA-------TCC
      grimshawi  CTACCTGCCC-------ACGCCCATAATCCTTTTATGGCAAATAAACAAACACGGTCACGG------GCAGAAC---CAAGTGCAA----------TAGTCC---GTGCA-------TCC
        Summary  BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBMMMMMMMMMBBBBBBBBBBBRRRRRRRRRRRRRRRRRRBBBBMMMMMMMMMBBBB

                 
   melanogaster  C----------------------ATG--------GC--TAGGT--AAAAAGTGCCA--------------AAAGGGTGCAATAAACCGGGTTGAGATGGCCAAAGGGTATGGCCA---CG
       simulans  C----------------------ATG--------GC--TAGGT--AAAAAGTGCCA--------------AAAGGGTGCAATAAACCGGGTTGAGATGACCAAAGGGTATGGCCA---CG
      sechellia  C----------------------ATG--------GC--TAGGT--AAAAAGTGCCA--------------AAAGGGTGCAATAAACCGGGTTGAGATGGCCAAAGGGTATGGCCA---CG
         yakuba  C----------------------GTG--------GC--TAGGT--AAAAAGTGCCA--------------AAAGGGTGCAATAAACCGGGTTGAGATGGCCAAAG--------------G
         erecta  C----------------------GTG--------GC--TAGGT--AAAAAGTGCCA--------------AAAGGGTGCAATAAACCGGGTTGAGATGGCCAAAAGGGTAGGGCA---CG
      ananassae  C--------TA-----------TATG--------GC--TAGGTAAAAAAAGTGTTG--------------AAAGGGTGCAATAAAGCGGGTTGAGA---CCGAACG-------------G
  pseudoobscura  C----------------------GGA--------TCCGTAGGT--AAAAAGAACCGAAATGCGGGCCTC-AAAGGGTGCAATAAAGTTGGCAAAGG-----AAAGGGTATAG-------G
     persimilis  C----------------------GGA--------TCCGTAGGT--AAAAAGAACCGAAATGCGGGCCTC-AAAGGGTGCAATAAAGTTGGCAAAGG-----AAAGGGTATAG-------G
        virilis  TTAGCCGTATCGGGCCTAAACCTTTG--------GC--TAGGT--AAAAAGCAGCT--------CGCGCAAAAGGGTGCAATAAAC-------AGA-----AGAGTTGATGGCCT-----
     mojavensis  T--------TTGGCCAAAAACCCTTG--------AC--TAGGT--AAAAAGCAGCT--------CGCTC-AAAGGGTGCAATAAAC-------AGA-----AGAGTTG-TTCCTT-----
      grimshawi  T--------TT-GCCTGCATTCTTTGCCAGCCATGC--TAGGT--AAAAAGCAGCT--------CGCGT-AAAGGGTGCAATAAAC-------AGA-----AGAGTTGCTGGTCGAGTTG
        Summary  BMMMMMMMMMBRRRRRRRRRRRRRRRRRRMMMMMMMMMBBBBBBBBBBBBBBBMMMMMMMMMBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBMMMMMMMMMBBBB

                 
   melanogaster  GTATGGCATGGTTATAGA--------------------TAT------GGAAGG--------ATAGGGA----AGAGTT---------GTTGCACACGCGCG--GTGGC-ATTGTTGCACA
       simulans  GCATGGCATGGTTATAGA--------------------TAT------GGAAGG--------ATAGGGA----AGAGTT---------GTTGCACACGCGCA--GTGGC-ATTGTTGCACA
      sechellia  GTATGGCATGGTTATAGA--------------------TAT------GGAAGG--------ATAGGGA----AGAGTT---------GTTGCACACGCGCA--GTGGC-ATTGTTGCACA
         yakuba  GTATG----GGTTATCGA--------------------TAT------GGAAGG--------ATGGGCA----AGAGTT---------GTTGCACACGCGCA--GTGGC-ATTGTTGCACA
         erecta  GTATGGCATGGTTATAGA--------------------TAT------GGAAGG--------ATAGAGA----AGAGTT---------GTTGCACACGCGCA--GTGGC-ATTGTTGCACA
      ananassae  GTA------GGCCAAAAG--------------------GGT------AGGAGG--------AAATCGA----AGAGTT---------GTTGCACACGCGCA--GTGGC-ATTGTTGCACG
  pseudoobscura  GTATG----GGTTATAGGCTATAGGGTATAGGGTAGATGGT------AGATGGTATGGGTTATAGGGA----AGAGTT---------GTTGCACACGCGCT--TTGGCTTTTGTTGCACG
     persimilis  GTATG----GGTTATAGGGTATAG--------------GGT------AGATGGTATGGGTTATAGGGA----AGAGTT---------GTTGCACACGCGCT--TTGGCTTTTGTTGCACG
        virilis  -GATGAACGGGCTGTGGT--------------------GGTTAGCCGGTTAGA--------GTCCTGCGTTCTGGGTCCTGCGAC---TTGTACACGCGT---TTGCC-ATTGTTGCACG
     mojavensis  -GATGAACTGGCTGCGGC--------------------TGT------GGTGGA-------------------CGGGTTGTGCGGCCT-TTGCACACGCGTTCCTTCCC-ATTGTTGCACG
      grimshawi  AGATGAACGGGCTGTGA---------------------------------AGA--------GTCCTG-----TGTGTCCTGC--------GTACACGCGT---TTGCC-ATTGTTGCACG
        Summary  BBBBBBBBBBBBBBBMMMMMMMMMMMMMMMMMMBRRRRRRRRRBBBBBBRRRRRRRRRBBBBBBBBBBBBBBBBBMMMMMMMMMBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB

                 
   melanogaster  CTCGGTTTTATGGGTGTGTGGTTTTAGCCCTTTGATGGGCATGATCATC--CTGTTAATAGAAAGCGTGGAA---ACCCG------------------TTGCAACTTGTAACC-----C-
       simulans  CTCGGTTTTATGGGTGTGTGGTTTTAGCCCTTTGATGGGCATGATCATC--CTGTTAATAGAAAGCGTGGAA---ACCCG------------------TTGCAACTTGTAACC-----C-
      sechellia  CTCGGTTTTATGGGTGTGTGGTTTTAGCCCTTTGATGGGCATGATCATC--CTGTTAATAGAAAGCGTGGAA---ACCCG------------------TTGCAACTTGTAACC-----C-
         yakuba  CTCGGTTTTATGGGTGTGTGGTTTTAGCCCTTTGATGGGCATGATCATC--CTGTTAATAGAAAGCGTGGAA---ACCCGC-----------------TTGCAACTTGTAACC-----C-
         erecta  CTCGGTTTTATGGGTGTGTGGTTTTAGCCCTTTGATGGGCATGATCATC--CTGTTAATAGAAAGCGTGGAA---ACCCG------------------TTACCACTTGTAACC-----C-
      ananassae  GTCGGTTTTATGGGTGTGTGGTTTTAGCCCTTTGATGGGCATGATCATC--CTGTTAATAGAAAGCGTGGAA---GCCCG--------------------------CATATCC-----CA
  pseudoobscura  TTCAGTTTTATGGGTGTGTGGTTTTAGCCCTTTGATGGGCATGATCATC--CTGTTAATAGAAACCGTGCAAAGGACCTGTAC---------------CTGTATCTCTAATCCTTTCGC-
     persimilis  TTCAGTTTTATGGGTGTGTGGTTTTAGCCCTTTGATGGGCATGATCATC--CTGTTAATAGAAACCGTGCAAGGGACCTGTACCTGTACCCTGTCTATCTGTATCTCTAATCCTTTCGC-
        virilis  GCCAGTTTTATGGGTGTGTGGTTTTAGCCCTTTGATGTGCATGATCATC--CTGTTAATAGAAACC-----------------------------------------GTAACG-----C-
     mojavensis  TTCAGTTTTATGGGTGTGTGGTTTTAGCCCTTTGATGTGCATGATCATC--CTGTTAATAGAAACCCAAGGT---ACCTG--------------------------TGTACCA-----C-
      grimshawi  GTCAGTTTTATGGGTGTGTGGTTTTAGCCCTTTGATGTGCATGATCATCCTCTGTTAATAGAAAACCCGCTT---ACCTG-----------------------------ACCG-----C-
        Summary  BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBRRRRRRRRRRRRRRRRRRBBBBBBBBBBBBMMMMMMMMMBBM

                 
   melanogaster  -TAC--------CTG--CACGCCCA--ACCAATCTCTAATCCTTTCCGCGGC---GATC----CTGAACCCTTTTCGGTCCAG-CTCGTTT------GGAGGGGG----CGAGCGTGTCT
       simulans  -TAC--------CTG--CACGCCCA--ACCAATCTCTAATCCTTTCCGCGGC---GATC----CTGAACCCTTTTCGGTCCAG-CTCGTTT------GGAGGGGG----CGAGCGTGTCT
      sechellia  -TAC--------CTG--CACGCCCA--ACCAATCTCTAATCCTTTCCGCGGC---GATC----CTGAACCCTTTTCGGTCCAG-ATCGTTT------GGAGGAGG----CGAGCGTGTCT
         yakuba  -TAC--------CTG--ACTCTA--------------AATCCTTTCCGCGGC---GATT----CTGAACCCTTTTTGGGCCAGAATCATTGCGAGGAGGCGGAGG----CGAGCGTGTCT
         erecta  -TAC--------CTG--GCCGCAT---ACCAATCTCTAATCCTTTCCGCGGC---GATC----CTGAACCCTTTTCGGCCCAG-ATCGGTGCGCTT-GGAGGGGG----CGAGCGTGTCT
      ananassae  GTAC--------CTG--TACCGGC-----------CTAATCCTTTCCAGAACTCTAGCA----CCGAACCCTTTTCCGACTCT-ACCCATG------ATTGCCGGCCACCGAGCGTGTCC
  pseudoobscura  -TAC--------CAG--CA----------TCCTCTCCTCTCCCCTGCTCTGCTCTGCTCTCCTCTGAACCCTTTTGCTGCTGG-CCCATGA------TTGCACGG----CGAGCGTGTCT
     persimilis  -TAC--------CAG--CACCCTC-----TCCTCTCCTCTCCTCTCCCCTGCCCTGCTCTCCTCTGAACCCTTTTGCTGCTGG-CCCATGA------TTGCACGG----CGAGCGTGTCT
        virilis  -TAC--------CTGGTCCACTGTG---CGC---CCTAATCCTTTC---------G--------GAAACCCTTTTGGCC-----ATCATTGCGG---CCATCTCG----CGAGCGTGTCC
     mojavensis  -TGCCACTGTCACTG--CCACTGTGCCACGCACACTTAATCCTTTC---------G-------CCAAACCCTTTCGTCC---G-ATCATCA-------------------GAGCGTGTCC
      grimshawi  -CAC--------CGG--CGTTTTTG--------GCTTAATCCTTTC---------G--------CAAACCCTTTCGCC------ATCA----------------------GAGCGTGTCC
        Summary  MMMMMMMMBBBBBBBBBMMMMMMMMMBBBBBBBBBBBBBBBBBBBBBBBBBBMMMMMMMMMBBBBBBBBBBBBBBBBBBBBBBBBBBRRRRRRRRRBBBBBBBBBBBBBBBBBBBBBBBB

                 
   melanogaster  AAGGCGATTTAATTAACGCGG---TCGCAACTAAGCCACCGA-----------------------AT------------------ACCAG--------GACATGGCTTA--AATC-----
       simulans  AAGGCGATTTAATTAACGCGG---TCGCAACTAAGCCACCGA-----------------------AT------------------ACCAG--------GACATGGCTTA--AATC-----
      sechellia  AAGGCGATTTAATTAACGCGG---TCGCAACTAAGCCACCGA-----------------------AT------------------ACCAG--------GACATGGCTTA--AATC-----
         yakuba  AAGGCGATTTAATTAACGCGG---TCGCAACTAAGCCACCGA-----------------------AT------------------ACCAG--------GACATGGCTTA--AATC-----
         erecta  AAGGCGATTTAATTAACGCGG---TCGCAACTAAGCCACCGA-----------------------GT------------------ACCAG--------GACATGGCTTA--AATC-----
      ananassae  AAAGCGATTTAATTAACGCGG---TCGCAACTAAGCCACCGA-----------------------TTCGGGAATCTCTCTCGCTAACCAG--------GACATGGATTACGAATCTGTGG
  pseudoobscura  AAGGCGATTTAATTAACGCGG---TTGCAACTAAGCCACCGATACGGGGACCAGCGGCAGATCCTGT------------------ATCAG--------GACACGGCTTA--AAAC-----
     persimilis  AAGGCGATTTAATTAACGCGG---TTGCAACTAAGCCACCGATACGGGGACCAGCGGCAGATCCTGT------------------ATCAG--------GACACGGCTTA--AAAC-----
        virilis  AAAGCGATTTAATTAACGCGG---TCGCATCTAAGCTCACG------------------------GC------------------ACCAG-GAGCAGTAGCTGCGCCTA--AATC-----
     mojavensis  AAACTGATTTAATTAACGCGGTTTTCGAAACTAAGCTCC--------------------------GT------------------ATCA-----TCGTAGCTTCGCCTA--AAT------
      grimshawi  AAAGCGATTTAATTAACGCGG---TCGCAACTAATCCCA--------------------------GT------------------CACAGTTACCAAGAGCAGCGCCTA--AATC-----
        Summary  BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBMMMMMMMMMRRRRRRRRRMMMMMMMMMRRRRRRRRRRRRRRRRRRBBBRRRRRRRRRBBBBBBBBBBBMMMMMMMMMMMM

                 
   melanogaster  -GGAACCCTTTCGCTC----------GGCCAG--GAGGAGGTGG-----CCCTGCTAAAAGCCATCCGGCTACTGTTCCGAGG----ACGGGTTAAGGATGCATGGA--TGCAGTAGC-T
       simulans  -GGAACCCTTTC-CTC----------GGCCGG--GAGGAGGTGG-----CCCTGCTAAAAGCCATCCGGCTACTGTTCCGAGG----ACGGGTTAAGGATGCATGGA--TGCAGTAGC-A
      sechellia  -GGAACCCTTTC-CTC----------GGCCGG--GAGGAGGTGG-----CCCTGCTAAAAGCCATCCGGCTACTGTTCCGAGG----ACGGTTT-AGGAGGCATGGA--TGCAGTAGC-A
         yakuba  -GGAACCCTTTC-CTC------CGGAGGACAG--GAGGAGGTGG-----CCCTGCTAAAAGCCATCCGGCTACTGTTCCGAGG----ACGGGTTAAGGATGCATCGA--TGCAGTAGCAA
         erecta  -GGAACCCTTTC-CTC----------GGACAG--GAGGAGGTGG-----CCCTGCTAAAAGCCATCCGGCTACTGTTCCGAGG----ACGGGTTAAGGATGCATGGA--TGCAGTAGC-A
      ananassae  AAGAACCCTTTC-CTTTAAC--CAGTGGACAGTTGTGGGCGTGGA----CCCTGCTAAAAGCCATCCGGCTACTGTTCCGAGG----ACGGGTTA---------------GCAGTAGC--
  pseudoobscura  -----CCTTTCC-CGCTAGTCGCGCGGAACGG--AAGAAGGGCGGTGTCCCGTGCTAAAAGCCAAGCAGCTACTGTTCCAAGGAGTTACAGTTCCAGTTTTCAGGGAGTTCCAGTAGC-A
     persimilis  -----CCTTTCC-CGCTAGTCGCGCGGAACGG--AAGAAGGGCGGTGTCCCGTGCTAAAAGCCAAGCAGCTACTGTTCCAAGG------AGTTCCAGTTTTCAGGGAGTTCCAGTAGC-A
        virilis  -------CTTTC-GC----------TGGCCGA--GGGGCGTACT-----GGCTGCTTAACGCCCAACGGCTA------------------------------------------------
     mojavensis  ----------------------------CCGA--AG----------------TCCTCAACGCCCATCAGCTACTGTTCCA----------------------------------------
      grimshawi  -------CTTTC-GCC------ACATAGCCAG--TAGGCGTATC-----TGCTGCTAAAGGCCCAGGAGCTACTGTTCCG----------------------------------------
        Summary  MMMMMMBBBBBBRRRRRRRRRBBBBBBBBBBBBBBBBBBBBBBBMMMMMMMMMBBBBBBBBBBBBBBBBBBBBBBBBBBRRRRRRRRRBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB

                 
   melanogaster  ACGTGGGCGTCATCGG-------AAAAGTCAGACA---GGG-----AGCGGGTGGGCGGAAGGATT-------TGACTTCCAGCGAAAGG-ATTGC-CGGA-CTTAA-------------
       simulans  ACGTGGGCGTCATCGG-------AAAAGTCAGACA---GGG-----AGCGGGTGGGCGGATGGATT-------TGACTTCCAGCGAAAGG-ATTGC-CGGA-CTTAA-------------
      sechellia  ACGTGGGCGTCATCGG-------AAAAGTCAGACA---GGG-----AGCGGGTGGGCGGAGGGATT-------TGACTTCCAGCGAAAGG-ATTGG-CGGA-CTTAA-------------
         yakuba  TTGTGGGCGTTATCGA-------AAAAGTCAGACA---GGG-----AGC-GGTGGGCGTATGGATT-------TGACTTCCAGCGAAAGG-ATTGC-CGGA-CTTAA-------------
         erecta  TCGTGGGCGTTGTTGG-------AAAAGTCAGACGCTCGCT-----GGC-GGTGGGCGGATGGATT-------TGACTTCCAGCGAAAGG-ATTGC-CGGA-CTTAA-------------
      ananassae  TAGGGGGCGGTATCCG-------AAAGT----------GGG-----AGGAGGCGGA-GGTGGGACT-------TGACTTCCAGGGAAAGG-ATTGC-TGGGTCTTAA-------------
  pseudoobscura  ATG----------CCA-------AAAAG----------GAGTCACCAGTAGGGGAGTGGATGGACT-------TGACTTCCAGCGAAAGG-ATTGCAAGGA-CTTAA-------------
     persimilis  ATG----------CCA-------AAAAG----------GAGTCACCAGTAGGGGAGTGGATGGACT-------TGACTTCCAGCGAAAGG-ATTGCAAGGA-CTTAA-------------
        virilis  -------------CCG-------AACGG-AACCCA---TTGGC---AAAGGGTTGGCCCAGGAGCTGTTCTGC-CACTTCCAGCGAAAGG-ATT---TAAC-TCTTAACTTGCCGTTCGC
     mojavensis  ------------GCCA-------AGCTG-AGCCTT---CCG-----AACATCCTAGCCAAAGGGTTGGACTGA-CTTTTCCAGCGAAAGG-ATT---TGCA-TATGA-------------
      grimshawi  ------------TCCGCCTGGTAAGCGG-AACACA---GCG-----AA-----------AGGGGTT--------CGTTTCCAGCGAAAGGAATT---TGCA-TTTGGAAA----------
        Summary  BBBBBBBBBBRRRRRRRRRBBBBBBBBBBBBBBBMMMMMMMMMBBBBBBBBBBBBBBBBBBBBMMMMMMMMMBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBRRRRRRRRRRRRRRRRR

                 
   melanogaster  ---CTTTCGGAAAAA----CTCCAATATTTACCAAATA---CCAAAGGGCCACC-AAGTGCACTTTGTTCAGCACTTGGC--------CA------------------GC--AGTCGAAA
       simulans  ---CTTTCGGAAAAA----CTCCAATATTTACCAAATA---CCAAAGGGCCACC-AAGTGCACTTTGTTCAGCACTTGGC--------CA------------------GC--AGTCGAAA
      sechellia  ---CTTTCGGAAAAA----CTCCAATATTTACCAAATA---CCAAAGGGCCACC-AAGTGCACTCTGTTGAGCACTTGGC--------CA------------------GC--AGTCGAAA
         yakuba  ---CTTTCGGAAAAA----CTCCAATATTTACCAAATA---CCAAAGGGCCACA-CAGTGCACTTTGTTCAGCACTTGGC--------CA------------------GC--AGTCGAAA
         erecta  ---CTTTCGGAAAAA----CTCCAATATTTACCAA--A---CCAGAGGGCCACA-AAGTGCACTTTGTGCAGCACTTGGC--------CG------------------GC--AGTCGAAA
      ananassae  ---CTTTTGGAAAAA----CTCCAATATTTACCAAATA---CCCA-------------TGCACTTGGTCCAG----------------------------------------AGTCGAGA
  pseudoobscura  ---CTTTTGGGAAAA---TCTCCAATATTTACCAAATA---CA---------------------------AGGACCTG----------CA------------------GCAGAGTCGAAA
     persimilis  ---CTTTTGGGAAAA---TCTCCAATATTTACCAAATA---CAATAGGGATAGG-GAG------------AGGACCTG----------CA------------------GCAGAGTCGAAA
        virilis  TATTTTGCCCGGAAA-TTTCACGAATATTTACCAAACA---GC-------CAAGACAGTTGACTTTAT--AAGACCTGAC--------TATGATGTCGACT-------AA--AGTCGAAA
     mojavensis  ---CTTGCATGGAAATTTTCTTGAATATTTACCAAACA---TC-------CAAG-CAGTTGACTTTAT--AAGACCTGACT-------TTTGATGCCGAATCGAGCGAAA--AGTCGAAA
      grimshawi  ---CTTGC--------CTTTTGCTATATTTACCAAATACTCGC-------CAAA-CAGTTGACTTTAT--AAGAATTGACTTTCTTGCTTTGTTGCAAAATGCAGAC-AG--AGTCGAAA
        Summary  RBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBRRRRRRRRRMMMMMMMMMMMMMMMMMMRRRRRRRRRBBBBBBBB

                 
   melanogaster  AGTCAAGTC------T-GGTTTT-GGGATTTCAACAGCAAATT-AACCGGCTGAGCCGGCAAAGC----GAGGATCC------ACA---------------------------AGGCATT
       simulans  AGTCAAGTC------A-GG-TTT-GGGATTTCAACAGCAAATT-AACCGGCTGAGCCGGCAAAGC----GAGGATCC------ACA---------------------------AGGCATT
      sechellia  AGTCAAGTC------A-GGTTTT-GGGATTTCAACAGCAAATT-AACCGGCTGAGCCGGCAAAGC----GAGGATCC------ACA---------------------------AGGCATT
         yakuba  AGTCAAGTC------T-GGTTTT-GGGATTTCAACAGCAAATT-ATCCGGCTGAGCCGGCAAAAC----GAGGATCC------ACA---------------------------AGGCATT
         erecta  AGTCAAGTC------T-GGTTTT-GGGATTTCAACAGCAAATT-AACCGGCTGAGCCGGCAAAGC----GAGGATCC------ACA---------------------------AGGCATT
      ananassae  AGTCAAGTC------G-GGTTTTCGGGGTTTCAGCTGCAATTT-GAGCAGCTCAGCCGGTTTAGTG---GAGGAGCC------TTT---------------------------AGGCTCT
  pseudoobscura  AGTCAAGTC------TCGGTTTT-GG----------CCAAATTGAAGCGGCTGAGCCGGCCAAACGAGTGAGGATCCCAACAAACA---------------------------GGGCTCA
     persimilis  AGTCAAGTC------TCGGTTTT-GG----------CCAAATTGAAGCGGCTGAGCCGGCCAAACGAGTGAGGATCCCAACAAACA---------------------------GGGCTCA
        virilis  AGTCAAGCCAACCAAA-AACTAT-------------ACAAAAT-GGTCGACTGAGCT-GCAAAATGA--GAGGATCC------CAG---------------------------ACGGA-T
     mojavensis  AGTCAAGCTACACTTA-GACTAT-------------ACAAAAT-GGTAGACTGAGCT-GCTATATGA--GGGGATCC------TTA---------------------------AAGGAT-
      grimshawi  AGTCAAGCC------A-GACAAT-------------GTGGAA-----AGACTTAGCT-GCAAAATGA--GGGGATCC------GTGCAGGATGATAGACTCAGATTACAATGGCAGTCA-
        Summary  BBBBBRRRRRRRRRBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBRRRRRRRRRRRRRRRRRRRRRRRRRRRMMMMMMMMMBBBBBBB

                 
   melanogaster  GAGAAATACCCATATCTGAGGGATTAGAAAACATTGTAGCTCC-------------------CTTTG
       simulans  GAAATATACCCATATCTGAGGGATTAGGAAACATTGTAGCTCC-------------------CTTTG
      sechellia  GAGATATACCCATATCTGAGGGATTAGGAAACATTGTAGCTCC-------------------CTTTG
         yakuba  GAGGTATGCCCATTTCTAGGGGATTAGGAAACACGGCAGCTCC-------------------CTTTG
         erecta  GAGGTATACCCATATCTATGGGATTAGGAAACATTGTAGCTCC-------------------CTTTG
      ananassae  AGGGGAT---TATGTGTATGGCAT------ACACTGTA--TGC-------------------CTCTG
  pseudoobscura  AAGGGA-------ATCACGAGGATTAG----CAT-------CC-------------------CCCCC
     persimilis  AAGGGA-------ATCACGAGGATTAG----CATCCCCCCCCC-------------------CCCCC
        virilis  GATGTATAGAGATTACAGATAAGCTCGGGAATCGGCTGGACCCTTTTTAA------------CTCTA
     mojavensis  -------------------------------------------------------------------
      grimshawi  --------------TCAGAGAAATCCAAAAGATGTCTTAATCAGTACTAAATGCGACTCATTCTTTA
        Summary  BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBMMMMMMMMMRRRRRRRRRBBBBBB