melanogaster CCCATGCCTAGCCATAGAGAGCCAGTGAGATTCCCAGAGCTGAATACTCCAAACTGCGAT------ACTCCATTCACGTGGTAATTGCAGTCCGAGAGCTGAG-----------AGCGCT
simulans CCCATGCCGAGCTATAGAGAGCCAGTGAGATTCCCAGAGCTGGAT-------ACTGCGAT------ACTCCATTCACGTGGTAATTGCAGT-CGAGAGCTGAG-----------AGCGCT
sechellia CCCATGCCGAGCTATAGAGAGCCAGTGAGATTCCCAGAGCTGGATACTCCAAACTGCGAT------ACTCCATTCACGTGGTAATTGCAGT-CGAGAGCTGAG-----------AGCGCT
yakuba CCCATGCCGAGCCATAGAGAGCCAGAGAGATTCCCAGAGCTGGACTCGCC--TTT-------------TCCATTCACGTGGTAATTGCAGT-CGAGAGCTGAG-----------AGCGCT
erecta CCCATGCCGAGCTGCAGAGAGCCAGAGAGATTCCCAGAGCTGGACTCTCC--ACT-------------TCCATTCGCGTGGTAATGGCAGT-CGAGAGCTGTG-----------AGCGCT
ananassae ---------TACTGCTAAGAGCCAG---------------------------------------------------------AGTTACGG--CAAGATCTGAG-----------ATTG--
pseudoobscura CCCCTG---GGCCCCTGGGCCTCTG----ATTCCCA--------------------------------TTCACTTCCAGCATAATTGCAAG-CCCAAGTT-TG-----------AGCGCT
persimilis CCCCTG---GTCCCCTGGGCCTCTG----ATTCCCA--------------------------------TTCACTTCCAGCATAATTGCAAG-CCCAAGTT-TG-----------AGCGCT
virilis CCTTTTCAATGTTATACAAC--TAGCTACATTCCCAG-----------------------------------------------------------------------------------
mojavensis CCCTTGGAGTGTTATACAAC-TTGGTTTCATTCCCAG-------------------CGTTTAGCCAGCTCAGCTGTCCCATTCATTGCGTA-CAGGAACTAAGCTGAAGAGCCCAACACT
grimshawi ------------------------------------------------------------------------------------------------------------------------
Summary BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
melanogaster AAACGAAGTCGAAAATGCTTTATGACCCTGCCAATAGATG-------------------------------------------AGGGGTTTTGCAATCAGCCAGC------GAATGAATA
simulans AAACGAAGTCGAAAATGCTTTATGACCCTGCCAATAGATG-------------------------------------------AGGGGTTTTGCAATCAGCCAGC------GGATGAATA
sechellia AAACGAAGTCGAAAATGCTTTATGATCCTGCCAATAGATG-------------------------------------------AGGGGTTTCGAAATCAGCCAGC------GGATGAATA
yakuba AAACGAAGTCGAAAATGCTTTATGACCCTGCCAATAGATG-------------------------------------------AGGGGTTTTGCAATCAGCCAGC------GCATGAATA
erecta AAACGAAGTCG-AAATGCTTTATGACCCTGCCAATAGATG-------------------------------------------AGGTCTTTTGCAATCAGCCAGC------GGATGAATA
ananassae ----------------ACTTTTTG---CTG-----GAATG-------------------------------------------AGAGGCTTTGCAGCT------T------CGATGAATA
pseudoobscura AAACGAAGTCGAAAATGTTTTATGAGTGTGCCAATAGATGTACAGACATAGATACA----TATGTATCTTAAGGTGGCACCTAGAGGGTTTTGCAATCAGCTCGC------CAATGAATA
persimilis AAACGAAGTCGAAAATGTTTTATGAGTGTGCCAATAGATGTACAGACATAGATACATATGTATGTATCTTAAGGTGGCACCTAGAGGGTTTTGCAATCAGCTCGC------CAATGAATA
virilis ---------------------------------------------------------------------------------------------------------------GCATGAATA
mojavensis AGACAA---CAAAAATG----------------------------------------------------------------------------------GTCGTC------GCATGAATA
grimshawi ----------------------------------------------------------------------------------------TTTAGCTGTTG---GCCCAAAATGGATGAATA
Summary BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
melanogaster AACATCTTTGTAAAATGATGATGCC----AG--CACT-GAAATAATTTCACACGTTTCTC---GCACACACAGCATC------TA--TCTAGT--GTGTGTATG-CGTCATGAGGGGCAG
simulans AACATCTTTGTAAAATGATGATGCC----AG--CACT-GAAATAATTTCACACGTTTCTC---GCACACACAGCATC------TA--TCTAGT--GTGTGTATG-CGTCATGAGGGGCAG
sechellia AACATCTTTGTAAAATGATGATGCC----AG--CACT-GAAATAATTTCACACGTTTCTC---GCACACACAGCATC------TA--TCTA----GTGTGTATG-CGTCATGAGGGGCAG
yakuba AACATCTTTGTAAAATGATGATGCC----AG--CACT-GAAATAATTTCACACGTTTCTC---GCACACACAGCATC------TA----------GTGTGTATG-CGTCATG-AGGCCAC
erecta AACATCTTTGTAAAATGATGATGCC----AG--CACT-GAAATAATTTCACACGTTTCGC---GCACACACAGCACA------CACATCCAATGTGTGTGTATG-CGTCATG-GGCCCA-
ananassae AACATCTTTGTAAAATGATGATGCC----AG--CACT-GAAATAATTTCACACATTTCTC---GCACACACAGCTCC------CC--G-------AAATATATA-TGCCATG----CTAG
pseudoobscura AACATCTTTGTAAAATGATGATGCCAGCAAG--CATC-GGAATAATTTCACACGTTTCAG---GCACACACAGCCTC------AGAGAGTAGA--ACCCGTTTGTCGCCACAAATATGCG
persimilis AACATCTTTGTAAAATGATGATGCCAGCAAG--CATC-GGAATAATTTCACACGTTTCAG---GCACACACAGCCTC------AGAGAGTAGA--ACCCGTTTGTCGCCACAAATATGCG
virilis AACATCTTTGTAAAATGATAATGCC----GT--CGCA-CAAATAATTTCACACATTCAAC---GCATACACAGCGCCCAGTCA--------GC--GCGCGTATT-GGCTATG-CTGTCAT
mojavensis AACATCTTTGTAAAATGATAATGCC----GCTACGCA-CAAATAATTTCACACATTTAAC---GCATACACAGC----------------------------------------------
grimshawi AACATCTTTGTAAAATGATGATGCC----GG--CGCACCAAATAATTTCACACATTCAACACAGCATACACAGCACC-------------------------------------------
Summary BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBRRRRRRRRRRRBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
melanogaster AGATT------------------------------CGGTTTCGGACGCGGAATCG------AAAT---------------CGGATTCAGATACTTTATTGGCATGGT-ATTTGC-----C
simulans AGATT------------------------------CGGATTCGTAGTCGGAATCG------AAAT---------------CGGATTCAGATACTTTATAGGCATGGT-ATTTGC-----C
sechellia AGATT------------------------------CGGATTCGGAGTCGGAATCG------AAAT---------------CGGATTCAGATACTTTATATGCATGGT-ATTTGC-----C
yakuba AGATTCGCATTCAGACTCGGAGACTCGGAGACTCGGGGACTCGGAATCGAAATCG------AAAT---------------CGGATTCAGATACTTTATAGGCATGCT-ATTTGC-----C
erecta -----------------------------------GTGACTTGGATTCGGATTCG------GATT---------------CGGATCCAGATACTTTATTGGCATGGT-ATTTGC-----C
ananassae CTATT----------------------------------TTCGCAAT--GTATCT------ACAT---------------GTGTAGCCGATGTATCCATGGGATA-C-ATTGGC-----C
pseudoobscura AGACT------------------------------CTGACTCGACACAGATACTGTTGTACAAATGTATCTTCCGCTACACATGTACATATGTATTGTATCCATGGG-ATGTGCTGTGGC
persimilis AGACT------------------------------CTGACTCGACACAGATACTGTTGTACAAATGTATCTTCCGCTACACATGTACATATGTATTGTATCCATGGG-ATGTGCTGTGGC
virilis GGA--------------------------------GGGGTTTGGTGGAGGGGGTG------GAAGGGG------------GGTGTTC---TGCTGTTTTGGCA-----GTTGGC-----C
mojavensis -------------------------------------------------------------------------------------------------------TGGCATTTGGC-----C
grimshawi ----------------------------------------------------------------------------------------GCTCCTCAGTTGGCA-----GTTGGC-----C
Summary BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
melanogaster AATTTGCACGCTGTCCATTAACG-----------GACCATGCG-----C---CGTTTATCGGACTCGTA----T-----------GCGAGCCATTCTGCCAAT----CCATTTTCATGGA
simulans AATTTGCACGCTGCCCATTAACG-----------GACCATGCG-----C---CGTTTATCGGACTCGTA----T-----------TCGAGCCATTCTGCCAAT----CCATTTTCATGGA
sechellia AATTTGCACGCTGCCCATTAACG-----------GACCATGCG-----C---CGTTTATCGGACTCGTA----T-----------TCGAGCCATTCTGCCAAT----CCATTTTCACGGA
yakuba AATTTGCACGCTGTCCATTAACG-----------GACCATGCG-----C---CGTTTATCGGACTCGAA----T-----------TCGAGCCATTCTG---------CCATTTTCACGGA
erecta AATTTGCACGCTGTCCATTAACG-----------GACCATGCG-----C---CGTTTATCGGACTCGCA----T-----------TCGAGCCATTCTG---------CCATTTTCATGGG
ananassae AATTTGCACGCTGTCCATTAACG-----------GGCCATGCG-----C---CATTTATCGGA-TCGGA----TCGGCCGGCGGACAGACCGATTCCTCA-------TAATTTTCATGGA
pseudoobscura AATTTGCACGCTGTCCATTAACGGGGACCATGGAGACCATGGGCCATTC---CGTTTATCGGA-TCTCA----T-----------TGGATTCATTCTGCCAGCCTCATCATTTTCATGGA
persimilis AATTTGCACGCTGTCCATTAACGGGGACCATGGAGACCATGCGCCATTC---CGTTTATCGGA-TCTCA----T-----------TGGATTCATTCTGCCAGCCTCATCATTTTCATGGA
virilis AATTTGCACGCTGTCCATTAACA----------TGGCCATGCG-----C---CGCTTATCTAA-CGGCGGCTCC-----------AGGCATCATTCTGCTGGTCTCAACATTTTCATGGA
mojavensis AATTTTCATGCTGTCCATTAACG----------AGG-CAGGCG-----TCCACGCTTATCTG-----------T-----------GAGCATTTTTCTGTTGGTCTCATCATTTTCATGGA
grimshawi AATTTGCACGCTGTCCATTAACG----------GGACCATGCG-----C---CGCTTATCTGA-CTGCGTCC-G-----------CAGCATT-TTCTGTTGGTCTCATCATTTTCATGGA
Summary BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
melanogaster TATTAACGCACTGATAATCGC-GACAATCAAACT-----------------------------------------------CG-----TGTTTAGC---------CAACA----------
simulans TATTAACGCACTGATAATCGC-GACAATCAAACT-----------------------------------------------CG-----TGTTTAGC---------CAACA----------
sechellia TATTAACGCACTGATAATCGC-GACAATCAAACT-----------------------------------------------CG-----TATTTAGC---------CAACA----------
yakuba TATTAACGCACTGATAATCGC-GACAATCAAACT-----------------------------------------------CG-----TGTTTAGC---------CAACA----------
erecta TATTAACGCACTGATAATCGC-GACAATCAAACT-----------------------------------------------CG-----TGTTTAGCCAACACTCGCAACA----------
ananassae TATTAACAAACTGATAATCGC-GACAATCAAATG-----------------------------------------------AGGGCGATGTTGTGC---------CAACA----------
pseudoobscura TATTAACAAACTGATAATCGC-AACAATCAAATTACAAATGCGAGGACGGTTGACCGGGGGGGTGGAGACGGAGTGAATGCCT-----TGTTTAGC---------CAACA----------
persimilis TATTAACAAACTGATAATCGC-AACAATCAAATTACGAATGCGAGGACGGTTGACCGGGGGGGTGGAGACGGAGTGAATGCCT-----TGTTTAGC---------CAACA----------
virilis TATTAACA-TGCGATAATCGC-AACAATCGAAAC-----------------------------------------------GC-----GGCCAAAA---------CAACAAAACAAGGCA
mojavensis TATTAACA-ACTGATAATCGC-AACAATCAAA----------------------------------------------------------------------------------------
grimshawi TATTAACA-ACTGATAATCGCGAACCATCGAAAC-----------------------------------------------GG-----GGCCAAAA---------CAAAA----------
Summary BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
melanogaster -------------GTCGCAGCATTTCCAT---------ACCATGGGGGTGGT-------CTCTGCT----GGGTGTT------GCGAATGCGACGCCAATTGG-------TCAGGGTTCA
simulans -------------GTCGCAGCATTTCCAT---------ACTG-GGGGGTGGT-------CTCCGCT----GGGTGTT------GCGAATGCGTCGCCAATTGG-------TCAGGGTTCA
sechellia -------------GTCGCAGCATTTCCAT---------ACT--GGGGGTGGT-------CTCTGCT----GGGTGTT------GCGAATGCGTCGCCAATTGG-------TCAGGGTTCA
yakuba -------------GTCCCAACATCTCCAT---------ACT--GGGGGTGGT-------CTCCGCT----GGGTGTGAGTGTTGCGAATGCGTCGCCAATTGG-------TCAGGGTTCA
erecta -------------TTCCCAACATTTCCAT---------ACT--GGGGGTGGTCTGTGGCCTCTGCT----GTGTGTG------GCGAATGCGTCGCCAATTGG-------TCAGGGTTCA
ananassae -------------TTTCCATACCAGCCAT---------ACC--AGCCAAGAA-------CCATACCACAAGGGGGTG------GGTGAATCAATGGCAATTGGTCAGGCTTCAGGCTTCA
pseudoobscura -------------TTTCCA---TATCTATCAGGGGCGGAGC--GGGGGAGGG-------GGCGACA----GTAGGCC------GC--ATTCGACTGCAATTGG-------TCAGGGTTCA
persimilis -------------TTTCCA---TATCTATCAGGGGCGGAGC--AGGGGAGGG-------GGCGACA----GTAGGCC------GC--ATTCGACTGCAATTGG-------TCAGGGTTCA
virilis GTTATATAGAGGA-------------------------------GGGGCGG------------------------------------------ACGCAGACAA-------ACGAAATTGC
mojavensis -----------------------------------------------------------------------------------GCAATTGCCATGGCAAAAAC-------ACGAAAATTG
grimshawi ------------------------------------------------------------------------------------------------------------------------
Summary BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
melanogaster CTGTAAA--TGGCCCA-G-CC--------------------------AAATGGGAAGCGGCAGTTGAG-----GAGC-GCCCGAATCAATTG-CCCTGATGGATGCTGCGGCTGTCC--A
simulans CTGTAAA--TGGCCCA-G-CC--------------------------AAATGGGAAGCGGCAGTTGAG-----GAGG-GCCCGAATCAATTG-CCCTGATGGATGCTGCGGCTGTCC--A
sechellia CTGTAAA--TGGCCCA-GCCC--------------------------AAATGGGAAGCGGCAGTTGAG-----GAGG-GCCCGAATCAATTG-CCCTGATGGATGCTGCGGCTGTCC--A
yakuba CTGTAAA--TGG-CCG-C-CC--------------------------AAATGGGAAGCGGCAGTCGAG-----G----GCCCGAATCAATTG-CCCTGATGGATGCTGCGGCTGTCC--A
erecta CTGTAAA--CGGCCCA-G-CC--------------------------AAATGGGAAGCGGCAATCAAT-----GGGAAGCCCGAATCAATTG-CCCTGATGGATGCTGCGGCTGGCC--A
ananassae CTGTAAA--TGG-ACA-A-TA--------------------------AAAT------------------------------CGAATCAATTGCCCCTGATGGATGCTGCGGCTGTCC--G
pseudoobscura TGGTAAA--TGGTGAATG-CT--------------------------CAATGGAAATCGACAATAAAATGCCCGGGA-AATCAAATCAATTGCCCTTGATGGATGCTGCGGCTGTCCGAA
persimilis TGGTAAA--TGGTGAATG-CT--------------------------CAATGGAAATCGACAATAAAATGCCCGGGA-AATCAAATCAATTGCCCTTGATGGATGCTGCGGCTGTCCGAA
virilis CCTGAAAATCTGACCA-G-TC---------------------------GACGAGGGGCAACAATAAAG-----CGAA-ATAAAAATCAATTGCTGTTGATAGATGCTGTGGCTGTCCGAA
mojavensis CCATAAAATTTGACCA-G-TCAAAGTGGGAGAGGGAGAGGGAGAGGGAGAGGAAGGTTCACAATAAAG-----CGAA-AATAAAATCAATTGCTGTTGATAGATGCTGCGGCTGTCC--A
grimshawi -----------------------------------------------------------------------------------AATCAATTGCTGTTGATAGATGCTGCGGCTATTT--G
Summary BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
melanogaster AAG---TTGCAGC--TTTTCGGGTCACTC--------------CGCGCTGGGGC-TGGAG-----------------------GGCTATAAATCCGCAGGCCAGATAATGAAACTAGAAT
simulans AAG---TTGCAGC---TTTCGGGTCACTC--------------CGCGCTGGGGC-AGGAG-----------------------GGCTATAAATCCGCAGGCCAGATAATGAAACTAGAAT
sechellia AAG---TTGCAGC--TTTTCGGGTCACTC--------------CGCGCTGGGGC-AGGAG-----------------------GGCTATAAATCCGCAGGCCAGATAATGAAACTAGAAT
yakuba GAG---CTGCAGC--TTTTCGGGTCACTC--------------CGCGCTGGGGA-ATGAG-----------------------GGCTATAAATCCGCAGGCCAGATAATGAAACTAGAAT
erecta AAGCTACTGCAGC--TTTTCGGGCCACTC--------------GGCGCTGGGGGCAGGAG-----------------------GGCTATAAATCCGCTGGCCAGATAATGAAACTAGAAT
ananassae AGG------GAGA--TGGGCGGAGGA------------------GCTACGAGGG-GTCAG-----------------------GGCCATAAATCTGCTGGCCAGATAATGAAACTAGAAT
pseudoobscura AAG---TTGCAAGATTTTTAGGGTCAACCAAGGAGGGGGGACAGGGGCCAGGGA-GAGCGTCCTGTGGCAGCGTAGAAGGACAGGCCATAAATCTGCAGCTGAGATAATGAAACTAGAAT
persimilis AAG---TTGCAAGATTTTTAGGGTCAACCAAGGAGGGGGGACAGGGGCCAGGGA-GAGAGTCCTGTGGCAGCGTAGAAGGACAGGCCATAAATCTGCAGCTGAGATAATGAAACTAGAAT
virilis GAG--------------CTCGGGTCAAGCGTGG----------G----TGGGTG-GGCCC-----------------------AACAATAAATCTGCAGCTGAGCTAATGAAACTAGAAT
mojavensis GCG--------------CTTG----------------------------GGGTC-G--CC-----------------------GACAATAAATCTGCAGCTGAGATAATGAAACTAGAAT
grimshawi GAG--------------TTTGGGTCAGCAGTAG----------GAGTCGAGGAG-GGGAG-----------------------GGCTATAAATCTGCAGCTGAGATAATGAAACTAGAAT
Summary BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBMMMMMMMMMMMBBB
melanogaster GATTGAGGCAAT----CACTGGTGTGGC--CAGCAGT---------------CTGCT---GGCGGAGTTTCCTACGCTCTGCGCATGTCC-----TGGATACA-----------------
simulans GATTGAGGCAAT----CACTGGTGTGGC--CAGCAGC---------------CTGCT---GGCGGAGTGTCCTCCGCTCTGCGCATGTCC-----TGGATACA-----------------
sechellia GATTGAGGCAAT----CACTGGTGTGGC--CAGCAGC---------------CTGCT---GGCGGAGTGTCCTCCGCTCTGCGCATGTCC-----TGGATACA-----------------
yakuba GATTGAGGCAAT----CACTGGTGTGGC--CAGCAGC---------------CCGCT---GGCGGAGGCTCCTCCGCTCTGCGCATGTCC-----TGGGTACA-----------------
erecta GATTGAGGCAAT----CACTGGTGTGGC--CAGCAGC-------------------------CGGCGGGTCCTGCGCTCTGCGCATGTCC-----TGGGTACA-----------------
ananassae GATTGCGGCAAT----CACTGGTGTGGC--TGGGA-------------------------------------------CTGCGCATGTCC-----TGGATACATGT--------------
pseudoobscura GATTGCGGCAAT----CACTGGTGTGGC--TAAAAGG-AGTCCATGTCCATGCCGCCAGAGGTGGAGCATACACTGCTCTGCGCATGTCC-----CTGCCGCA-----------------
persimilis GATTGCGGCAAT----CACTGGTGTGGC--TAAAAGG-AGTCCATGTCCATGCCGCCAGAGGTGGAGCATATATTGCTCTGCGCATGTCC-----CTGCCGCA-----------------
virilis GATTGCGGCAATCACACACGGGTGTGGC------------------------GAG-----TGTAGA-----------CGTGTACGTGCCGGGCACTGGCTACGGCCAAGGAGGAGCAACG
mojavensis GATTGCAGCAAT----CACTGGTGTGGTGGAAGCTGGAAGCTGAGCATTAGAGAG-----TGTAGAATGTG------TGTGTGTGTGTTG-----TGGCTGCG-----------------
grimshawi GATTGCGGCAAT----CACTGGTGTGGC--GAGTAGCCAGCACAGCCACAGTCAGCTTGCTGTGGAACGTGC--CACAATGAGAGTCCTGGACT-GGGCTGTGGCTG-------------
Summary BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
melanogaster -----------------CAC--AGCTCGGCGCACATAGCGATAGATACAGATGCAGATACA-GATACAGAGGCAGATAGATACGTATGCGGATACA-T--------------------AG
simulans -----------------CAC--AGCTCGGCGCACATAGCGATAGATACAGATGCAGATACA-GATACAGATGCAGA--------------GATACA-T--------------------AG
sechellia -----------------CAC--AGCTCGGCGCACATAGCGATAGATACAGATGCAGATACA-GATATAGATGCAGA--------------GATACA-T--------------------AG
yakuba -----------------CAC--TGCTCAG-CCACATTGCGATAGATACAGATGTAGATGTA-GATGCAGATACAGATACA----------GATACG-TATGCGGATACGGATACATAGAG
erecta -----------------CAG--CGCTCGGCCCACATAGCGATAGATACAGATACAGATGCA-GTTGCAGATACAGATACA----------GATACA-T--------------------AG
ananassae -----------------CCT--AAAGCGGAGCACCTAGCTATAGATAC---------------CTACAG---------------------GATACA-T--------------------AG
pseudoobscura -------------------------------TACATAGTGATAGATACAG-----GATACAGGATACAGATACAGGACCATGGCC-----AGTACA-T--------------------AG
persimilis -------------------------------TACATAGTGATAGATACAG-----GATACAGGATACAGATACAGGACCATGGCC-----AGTACA-T--------------------AG
virilis GACACTGGGCTGTGGCTCTTGCCGGGCAATGCGCATGTCCTG-----CAATCAAATACATA-CACACATAT---------------TTTTTGTGCC-T--------------------TT
mojavensis -----------------CTT--CAGTCAATGCGCATGTC--------------------------------------------------GAGTGCCAT--------------------TT
grimshawi -----------------CTCG-CATGCAATGCGCATGACGAGAG-TCCAACCAAAAACACA-CACACACACACACAGAGATGGGGATGTAAGCATGGC--------------------TT
Summary BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
melanogaster --AGCACGTTACATTATGTG-----G---------CGAAGG-AC---------TGG-----------------------------------CGATTACCGATTC----------------
simulans --AGCACTTTACATTATGTG-----G---------CGAAGG-AC---------TGG-----------------------------------CGATTACCGATTC----------------
sechellia --AGCACTTTACATTATGTG-----G---------CGAAGG-AC---------TGG-----------------------------------CGATTACCGATTT----------------
yakuba --AGCACTTTACATTATGTG-----G---------CGAAGG-AC---------TGG-----------------------------------CGATTACCGATTC----------------
erecta --AGCAGGGTACATTATGTG-----G---------CGAAGG-AC---------TGG-----------------------------------CGATTACCGATGC----------------
ananassae CAGGGCCTGTACATTATGTGTTTTTG---------TGGAGACAC---------TCG-----------------------------------CATTTGCC--TTC----------------
pseudoobscura --AA-----TACATTATGTA-----G---------AGAAGG-ACCCTCTCTTTTGG----------TCTGTTCTGTTCTGTTCTGTTCTGCCGATTACCGATTC----------------
persimilis --AA-----TACATTATGTA-----G---------AGAAGG-ACCCTCTCTTTTGGTCTGTTCTGTTCTGTTCTGTTCTGTTCTGTTCTGCCGATTACCGATTC----------------
virilis --GGCA---TACATTATGTA-----C----------------AC---------G--------------------------------------------TCGTCT----------------
mojavensis --GGCA---TACATTATGTA-----C----------------AC---------GA------------------------------------------TTCGTCT----------------
grimshawi --GGCA---TACATTATGTA-----CTATATAGTACAAGTG-AC---------GAG---------GACTACTCTG----------------CAGCTCCTGGTCCAGGTTGAGGTCCAGGA
Summary BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
melanogaster ------C--------GCAG-TTCAGGACCTCTGGATTTGC--GATCCTGCGCAC----GAC-GTGTCAACTTTATTGCGGTTTGACTTTGCC----------GCGGCCCCTCGAA-----
simulans ------C--------GCAG-TTCAGGACCTCTGGATTTGC--GATCCTGCGCAC----GAC-GTGTCAACTTTATTGCGGTTTGACTTTGCC----------GCGGCCCCTCGAA-----
sechellia ------C--------GCAG-TTCAGGACCTCTGGATTTGC--GATCCTGCGCAC----GAC-GTGTCAACTTTATTGCGGTTTGACTTTGCC----------GCGGCCCCTCGAA-----
yakuba ------C--------GCAG-TTCAGGACCTCTAGATTTGC--GATCCTGCGCAC----GAC-GTGTCAACTTTATTGCGGTTTGACTTTGCC----------GCGGCCCCTCGCA-----
erecta ------C--------GCAG-CTCAGGACCTCTGGATTTGC--GATCCTGCGCAC----GAC-GTGTCAACTTTATTGCGGTTTGACTTTGCC----------GCGGCCCCTCGAA-----
ananassae ------CTGAAACTGGTGT-TTCGGTTTCGCAGTCTTTCA--GATCCTGCGCAC----GAT-GTGTCAACTTTATTGCGGTTTGACTTTCCA----------G-----CTCTGTA-----
pseudoobscura ------T--------AGAGTTTCAGGAC-------TTTCA--GATCCTGCGCAC----GACGGTGTCAACTTTATTGCGGTTTGACTTTGCC----------------CCTCGAG-----
persimilis ------T--------AGAGTTTCAGGAC-------TTTCA--GATCCTGCGCAC----GACGGTGTCAACTTTATTGCGGTTTGACTTTGCC----------------CCTCGAGGAGTC
virilis ----CAC--------TGGA-CCCATGCT-------CTTACCGGATCCTGCGCATTTG-AAC-GTGTCAATTTTATTGCGGTTTGACTTTGCCGCGGCCAGGAAAAGCCCTTCAAG-----
mojavensis ----GCT--------CCGG-CTCAGGTTCGC----CTGAACGGATCCTGCGCATTTGAAAC-GTGTCAATTTTATTGCGGTTTGACTTTGCC----------------------------
grimshawi CCAGGAC--------CAGG-TCCAGGTCCTG----TTTACC-GACCCTGCGCATTTG-AGC-GTGTCAATTTTATTGTGGTTTGACTTTGCT---GCTGCAAAAAG----TCAGA-----
Summary BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
melanogaster --------------A----CTCACAAACGTATCCTGGAACC--------CAGGATCCCTGGGC------------TCTGGG-------CTCTG-GACTATCC---------GCCGACCCT
simulans --------------A----CTCACAAACGTGTCCTGGAACC--------CAGGATCCCTGGGC------------TCTGGGCTGTGGACTCTG-GACTATCC---------GCCGACCCT
sechellia --------------A----CTCACAAACGTATCCTGGAACC--------CAGAATCCCTGGGC------------TCTGGGCTGTGGACTCTG-GACTATCC---------GCCGACCCT
yakuba --------------A----CTCACAAACGTGTCCTGGAACCCTAGAACCCAGGAACCCGGGGC------------TCCGGACTCCGGACTCTG-GACT--------------------CT
erecta --------------A----CTCACAAATGTATCCTGGAACCCAGGAACTCAGGAACCCGGGGC------------TCTGAACTCTGGACGCTG-GACTAT------------CCGACCCA
ananassae --------------G----CCCGAAGCTGTGTCCTGAATCC---------------CCTGGG--------------CAGTCCCCTGAGTCCTGCGACCATT-----------CCGATTC-
pseudoobscura -GAGTCAGAGCCAGA----GCCAGAGCCAGATACAAAAACC----------AGGACCATG----------------CAAGGTCCCAGGTTCTG---CT--------------TCGA----
persimilis AGAGTCAGAGCCAGA----GCCAGAGCCAGATACTAAAACC----------AGGACCATG----------------CAAGGTCCCAGGTTCTG---CT--------------TCGA----
virilis --------------GCGGTCGCTCTGCTCTGCT--------CAGC------GCAGCTCTG-----------------------CTCTGCTCTG-CTCTGTCTTTAGTTAAAGTCGACTTT
mojavensis -----------------------------------------AAGTCAAGGAAAAGCCCTGAGGCTGACTGCTTCTTCTTTTTCTTCTTCTTCT-CTCTGTTT--------------CTTT
grimshawi --------------G----CCCTCAACTTTATT--------CATCAACTGACATGTTTTG-------------CCTTCTGTTAGTTTGGTCGC-CTCTTTAT-----------------T
Summary BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
melanogaster CCAT-----AT-----CCATGATTTACAATTCTCG-TTTTTTTCGCGTTATTTTTTTA-GGGGC--TTTAATGACCGTCGTAAAG-----------------------------------
simulans CCAT-----AT-----CCATGATTTACAATTCTCG-TTTTTTTCGCGTTATTTTTTTA-GGGGC--TTTAATGACCGTCGTAAAG-----------------------------------
sechellia CCAT-----AT-----CCATGATTTACAATTCTCG-TTTTTTTCGCGTTATTTTTTTA-GGGGC--TTTAATGACCGTCGTAAAG-----------------------------------
yakuba CCAT-----TT-----CCATGATTTACAATTCTCG-TTTTTTTCGCGTTATTTTTTTA-GGGGC--TTTAATGACCGTCGTAAAG-----------------------------------
erecta CCAT-----TT-----TCATGATTTACAATTCTCG-TTTTTTTCGCGTTATTTTTTTA-GGGGC--TTTAATGACCGTCGTAAAG-----------------------------------
ananassae CCAT-----TTTTCGCCCATGATTTATAATTCTTGTTTTTTTTCGCGTTATTTTTTTACGGGGCCATTTAATGGCCATCGTCAGGACAGTCCACAGTACCTTCTCGGCATCCTGCTCTGG
pseudoobscura ----------------CCATGATTTACAATTCTCA-TTTTTTTCGCGTTATTTTTTTA-GGGGC--TTTAATGGCCATCGTAAAG-----------------------------------
persimilis ----------------CCATGATTTACAATTCTCA-TTTTTTTCGCGTTATTTTTTTA-GGGGC--TTTAATGGCCATCGTAAAG-----------------------------------
virilis TTGG-TTGACT-----TTATGATTTACAGCGCTCG-TTTTTTTCGCGTTATTTTTTTA-GGAGC--GTTAATGGCCATCGTAAAG-----------------------------------
mojavensis CTGGCTTGACT-----TTGTGATTTATTGCGCTCG-TTTTTTTCGCGTTATTTTTTTA-GG-GC--GTTAATGGCCATCGTAAAG-----------------------------------
grimshawi TTAT-TTGCCT-----TCATGATTTACAGCGCTCG-TTTTTTTCGCGTTATTTTTTTA-GG-GC--TTTAATGGCCATCGTAAAG-----------------------------------
Summary BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
melanogaster -------------CCGCAG-G------AGGACCAGGACC-----------------------AGGACTCT------------------------------------------GCTCA--C
simulans -------------CCGCAG-GAGGACTAGGACTAGGACC-----------------------AGGACTCT------------------------------------------GCTCA--C
sechellia -------------CCGCAG-GAGGACTAGGACTAGGACC-----------------------AGGACTCT------------------------------------------GCTCA--C
yakuba -------------CCGCAG-G------AGGACTAGGACC-----------------------AGCACTCT------------------------------------------GCTCA--C
erecta -------------CCGCAG-G------AGGACCAGGACC-----------------------AAAACTCT------------------------------------------GCTCA--C
ananassae TGTCTTTAAGCCTCCGCTG-G--TGCGACGGAGAGGGTC---------------------GGAGAGTCCT------------------------------------------GTTCA--C
pseudoobscura -------------CCGCAG-G--------ACCTGAGACC-----------------------TCTACTCT------------------------------------------GTTCC--C
persimilis -------------CCGCAG-G--------ACTCGAGACC-----------------------TCTACTCT------------------------------------------GTTCC--C
virilis -------------CCGCAGTG--------------GGCC--------------------------------ATGTCG----CAGTCGCAGTC--------------GCCGTCGTCGT--C
mojavensis -------------CCGCAGTG--------------GGCCTGCTTCCAGCTCGACTGCCAACACCAACACCAATACCAATACCAATACCAATCCAA-CTGCCAACTGCCCATTGCAGTTGC
grimshawi -------------CCGCAGTG--------------GGCC------------------CGATTTCGACTTCGACGTCC----AAGTCGAAGTCGAAGCTGATGTT--GCAGTTGCAGT--C
Summary BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
melanogaster ATTTCGCGCACTGATTCTAAAAAATGAAATCA-TTTTTTCTTGAA---------TTTCAC--------------------GGCG-CGCCT-CGAGCAGGACTCTTTG-------------
simulans ATTTCGCGCACTGATTCTAAAAAATGAAATCA-TTTTTTCTTGAA---------TTTCAC--------------------GGCG-CGCCT-CGAGCAGGACTCTTTG-------------
sechellia ATTTCGCGCACTGATTCTAAAAAATGAAATCA-TTTTTTCTTGAA---------TTTCAC--------------------GGCG-CGCCT-CGAGCAGGACTCTTTG-------------
yakuba ATTTCGCGCACTGATTCTAAAAAATGAAATCA-TTTTTTCTTGAA---------TTTCAC--------------------GGCG-CGCCT-CGAGCAGGACTCTTTG-------------
erecta ATTTCGCGCACTGATTCTAAAAAATGAAATCA-TTTTTTCTTGAA---------TTTCAC--------------------GGCG-CGTCT-CGAGCAGGACTCTTTG-------------
ananassae AATCCGCGCACTGATTCTAAAAAATGGAATAATTTTTTTCTCGAA---------TTTCTG--------------------GGCG-CGCCTGCGAGCAGGACTCTTTG-------------
pseudoobscura ATTTCGCGAACTGATTCTAAAAAATGAAATCA-TTTTTTCTCGAA---------TTTCGC--------------------AGAGACGACT-GTGTAAAGGCTCTTTG-------------
persimilis ATTTCGCGAACTGATTCTAAAAAATGAAATCA-TTTTTTCTCGAA---------TTTCGC--------------------AGAGACGACT-GTGTAAAGGCTCTTTG-------------
virilis GATTCGCGCACTGATTCTAAAAAATGAAAACA-GTTTTTATGAATT--------TCTCAC--------------------AACG-CGCCT-CGACT---GCGACTTG-------------
mojavensis AGTTCGCGCACTGATTCTAAAAAATGAAAACA-GTTTTTATGAATTCTCTGGTCTCTGAC---------------------TCG-GACTC-TGGCC---GCA--TTGTTC---AATGTGC
grimshawi GATTCGCGCACTGATTCTAAAAAATGAAATCA-GTTTTTATGAAAT--------TTTCACGTGGCGGCGGCTCGTTCAGCAACG-ATCCT-TGGTTCGAGCGTATTGTTTTTGAATGTGC
Summary BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
melanogaster TTCTCGGCCAGGCAATTGTCCTTTTTTG--CGCTCAGCT----CTCAGTTT-----TTTCGTCC--AG-----------CGGGCA---TTACC--------TACA-C------------G
simulans TTCTCGGCCAGGCATTTGTCCTTTTTTG--CGCTCGGCT----CTCAGTTT-----TTTCGGCC--AG-----------CGGGCA---TTACC--------TACA-T------------G
sechellia TTCTCGGCCAGGCAATTGTCCTTTTTTG--CGCTCGGCT----CTCAGTTT-----TTTCGGCC--AG-----------CGGGCA---TTACC--------TACA-T------------G
yakuba TTTTCGGCCGGGCAGTTGTCCTTTTTTG--CGCTCGGCT----CTCAGTTT-----TTTCGGCC--AG-----------CGGGCA---TTACC--------TACA-C------------G
erecta TTTTCGTTTGGGCAATTGTCCTTTTTTG--CGCTCGGCT----CTCAGTTTTTTCATTTCGGCC--AG-----------CGGGCA---TTACCTATGGGTATACA-C------------G
ananassae TTAGCCGAGCGTCCCTTGTCCTTTTTTG--CAATAGTCC----TT---TTT-----TGCCGTC----G-----------AGAGTG---TTACC--------TAGGCC------------G
pseudoobscura TCCTGGACCAG-TGCTCGTCCTTTTTTGCACACTCGGCA----TCGTTTCT-----TTTTCCCC--CG--CTT------CGAGTG---CTACC--------TAGG-C-------CTCCGG
persimilis TCCTGGACCAG-TGCTCGTCCTTTTTTGCACACTCGGCA----TCGTTTTT-----TTTCCCCC--CG--CTT------CGAGTG---CTACC--------TAGG-C-------CTCCGG
virilis GCCTGTTCCTGTGCGTTGTCCTTTTTCG--C---CGTTTTCTACTATTTTC-----TTGTTGTT--GTTTTTT------TTTGCCTTTTTACC--------TAGC-CGAGTCGAGCCTGG
mojavensis GCCTGATCCTGCGCGTTGTCCCTTTTCG--CATACATTT----CTATTTTT-----TGTCCGCTCGCCTCTTC------GCTGGATTTTTACC--------TAGC-C-------------
grimshawi GCCTTATCCTGGCCAATGTCCTTTTTCG--C---ATTTT----CTGTGTTT-----TTTCTTCT--TTTTTTTTTGTCGTTTGCCTTTTTACC--------TAGC---------------
Summary BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
melanogaster GCGTTTTATGGCGGA------------GATGATAT----------TCGCCTGGGAT--------CG------------GTTCCGTTTTTTAGGCCATAAAAATTAGGCGGCATAAAAAAA
simulans GCGTTTTATGGCGGA------------GATGATAT----------TCGCCTGGGAT--------CG------------GTTCCGTTTTTTAGGCCATAAAAATTAGGCGGCATAAAAAAA
sechellia TCGTTATATGGCGGA------------GATGATAT----------TCGCCTGGGAT--------CG------------GTTCCGTCTTTTAGGCCATATAAATGACGCGGCAT-ATATAA
yakuba GCGTTTTATGGCGGA------------GATGATAT----------TCGCCAGGGAT--------CG------------GTTCCGTTTTTTAGGCCATAAAAATTAGGCGGCATAAAAAAA
erecta GCGTTTTATGGCGGA------------GATGATAT----------TCGCCTGGGAT--------CG------------GTTCCGTTTTTTAGGCCATAAAAATTAGGCGGCATAAAAAAA
ananassae GTGGTTTATGGCCAA------------GATGATAC----------TTGGTC---------------------------GTTCCGTTTTTTAGGCCATAAAAATTAGGCAGCATAAAAAAA
pseudoobscura GGTTTTTATGACGGA------------GATGATATTCTGTGAGGCTCGGCTCGGCT--------CGGCTCTCGGTGCTGTTCCGTTTTTTAGGCCATAAAAATTAGGCGGCATAAAAAAA
persimilis GGTTTTTATGACGGA------------GATGATATTCTGTGAGGCTCGGCTAGGCT--------CGGCTCTCGGTGCTGTTCCGTTTTTTAGGCCATAAAAATTAGGCGGCATAAAAAAA
virilis CTCTTTTATGGGCAAACAAATGGCAGCGATTATAT----------TCGGTTTCGGTTTT-----TG------------GTTCTGTTTTTTAGGCCATAAAAATTAGGCGGCATAAAAAAA
mojavensis CTCTTTTATGGCCAAACAAATGGCAGCGATTATAT----------TCGGTTTCGGTTTC-----TG------------GCTCTGTTTTTTAGGCCATAAAAATTAGGCGGCATAAAAAAA
grimshawi GATTTTTATGGGCAAACAAATGGCAGCGATTATAT----------TCGGTTTCAGTTTCGGTTTCG------------GTTCTGTTTTTTAGGCCATAAAAATTAGGTGGCATAAAAAAA
Summary BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBRRRRRRRRRRRBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
melanogaster CTGCATTGGAATTCTAGTT-CTAGTTTCAAGTTTTT--------AGGTTTCCAG-GTTTCTGCCAGC------------CCGCCTAGA--TTCGCAT----TT-----------------
simulans CTGCATTGGAATTCTAGTT-CTAGTTTCAGGTTTTT--------AGGTTTCCAG-GTTTCTGCCAGC------------CCGCCTAGA--TTCGCAT----TT-----------------
sechellia CTGCATTGCAATTCTAGGTACTAGTCTCA-GTTCTG--------ATGTTTCCAG-GTTTCTGCCAGC------------CCGCCTAGA--TTCGCAT----TT-----------------
yakuba CTGCATTGGAATTCTAGTT-CTAGTTTCAGGTTTTT--------AGGTTTCCAG-GTTTCCGACAGC------------CCGGAAAGA--TTCGCAA----TT-----------------
erecta CTGCATTGGAATTCTAGTT-CTAGTTTCAGGTTTTTAGGTTTTCAGGTTTTCAG-GTTTCTGCCAGC------------CCGGATAGA--TTCGCAT----TT-----------------
ananassae CTGCATTGGAATTCTAGTT-CTAGTTTCAGATTTTT--------AGGTTTC------------CAGC------------CCGGCGAAAATTTCGCAT----TT-----------------
pseudoobscura CTGCATTGGAATTCTAGTT-CTAGTTTCAGATTTTT--------AGGTTTCCAGAGTTTTTCGGACT------------TTGGGCAGA--TTTTTATGAAATT-----------------
persimilis CTGCATTGGAATTCTAGTT-CTAGTTTCAGATTTTT--------AGGTTTCCAGAGTTTTTCGGACT------------TTGGGCAGA--TTTTTATGAAATT-----------------
virilis CTGCATTGGAATTCTAGTT-CTAGTTTCAGATTTTT--------AGGTTTTCAG-GCTT---CGCGTTGCTGTTTTCTATTTACAATT--TTTGTTT----TT------------TTTTT
mojavensis CTGCATTGGAATTCTAGTT-CTAGTTTCAGATTTTT--------AGATTTTTAG-GTTTTTGCACATTTCCTTTTCTAGTTTTCTATA--TTTGTGT----TTTTATTTTTTGTATTTTT
grimshawi CTGCATTGGAATTCTAGTT-CTAGTTTCAGATTTTT--------AGGTTTTCAG-ATTTT--CAGGT------------TTTGCAGTG--CAGATTT----TT------------TTCAT
Summary BBBBBBBBBBBBRRRRRRRRRRRBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
melanogaster ------------CGCGGAA-TTCGGAAGCGGAA--CAGAAT-GC---------CAGAATGGTCAGA----------ATCC---------TGGC----------------TGACCTTGCCT
simulans ------------CGCGGAA-TTCGGAAGCGGAA--CAGAAT-GC---------CAGAATGGACAGA----------ATCC---------TGGC----------------TGACCTTGCCT
sechellia ------------CGCGGAA-TTCGGAAGCGGAA--CAGAAT-GC---------CAGAATGGACAGA----------ATCC---------TGGC----------------TGACCTTGCCT
yakuba ------------CGCGGAA-TTCGGAAGCGGAA--CA---------------------------------------ATCC---------TGGC----------------CGACCTTGCCT
erecta ------------CGCGGAA-TTCGGAAGCGGAA--CAGAATGGC---------CAGAATGGCCAGAATGGACGGGCATCC---------TGGC----------------TGACCTTGCCT
ananassae ------------CGCGGAA-TTCGGAAGCGGAA--CAGATC-CC---------GATCCT-----------------GTCC---------TGACCGAAATAAAAAAGGCATGACCTTGCCC
pseudoobscura ------------CGCGGAA-TTCGGAAGCAAAATGCGGAAT-GCGGAACGGAACAGAATGGCAAAT----------ATCCGATATTCCGGGGC----------------TGACCTTGCCT
persimilis ------------CGCGGAA-TTCGGAAGCAAAATGCGGAAT-GCGGAACGGAACAGAATGGCAAAT----------ATCCGATATTCCGGGGC----------------TGACCTTGCCG
virilis TTTTTAAATTTTCGCGGAA-TTCGGAAGCGGAA--CA--AC-GA-----------------------------------C---------GGCC----------------CGACCTTGCCG
mojavensis TTTTTTAGAATTCGCAGAATTTCGGAAGCGGAA----------------------------------------------------------------------------CGACCTTGTCG
grimshawi ATTTT----TTTCGCCGAA-TTCGGAAGCGGAA--CA--AC-GA--------------------------------TCCT---------TGAC----------------TGACCTTGTCA
Summary BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
melanogaster TTT-------------GGCC-------AGGGGCCGTAAAAAAATTGACTCGCTGCGGTGCGCGGAA--TATTTTTT-AAATCTGACTTT------------------------CCAA---
simulans TTT-------------GGCC-------AGGGGCCGTAAAAAAATTGACTCGCTGCGGTGCGCGGAA--TATTTTTT-AAATCTGACTTT------------------------CCAA---
sechellia TTT-------------GGCC-------AGGGGCCGTAAAAAAATTGACTCGCTGCGGTGCGCGGAA--TATTTTTT-AAATCTGACTTT------------------------CCAA---
yakuba TTT-------------GGCC-------AGGGGCCGTAAAAAAATTGACTCGCTGCGGTGCGCGGAA--TATTTTTT-AAATCTGACTTT------------------------CCAA---
erecta TTT-------------GGCC------AAGGGGCCGTAAAAAAATTGACTCGCTGCGGTGCGCGGAA--TATTTTTTAAAATCTGACTTT------------------------CCAA---
ananassae TCT-------------GGCC------GGAGGGCCGTAAAAAAATTGACTCGCTGCGGTGCGCGGAATGTATTTTTT-AGAACTGACTCG------------------------GCGA---
pseudoobscura TCTTCTCCGCCTTCTTCTCT-------GAGGGCCGTAAAAAAATTGACTCGCTGCGGTGCGGTGGA--TATTTTTT-AGAAATGACTTTTTCTGC--------AGCCTCCTTGCCGATCG
persimilis TCTTCTCCGC------CTCT-------GAGGGCCGTAAAAAAATTGACTCGCTGCGGTGCGGTGGA--TATTTTTT-AGAAATGACTTTTTCTGCAGCCTCCTAGCCTCCTTGCCGATCC
virilis TCT-CTGAAG------AGCTATTCAAAGCGAAACATTTGGAAATTGACTCGCTGCGGTGCGCGAAA--TATTTTTT-AGAACTGACTTT--------------------CGAATCGT---
mojavensis C----------------GCT------------------------------GCAGCGGTGCGCGAAA--TATTTTTTAAGAACTGACTTT------------------------TCGT---
grimshawi AATAATAAAC------AACA-------------------AAAATTGACTCGCTGCGGTGCGCGAAA--TATTTTTT-AGAACTGACTT-------------------------TCGT---
Summary BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
melanogaster ------CAAT-CTC----TGATCTGGGTT------------CGAATCGT-AAAAAAAAAGCAGAACA---AA---AAGCGGGCATTT------TCGTCGGCAA-----ATGATCTGTTAA
simulans ------CAAT-C-C----TGATCTGGGTT------------TGAATCGTAAAAAAAAATGCAGAACA---AA---AAGCGGGCATTT------TCGACTGCAA-----ATGATCTGTTAA
sechellia ------CAAT-C-C----TGATCTGGGTT------------CGAATCGT-AAAAAAAATGCAGAACA---AA---AAGCGGGCATTT------TCGACAGCAA-----ATGATCTGTTAA
yakuba ------CAAT-C-C----TGATCTGGGTTCGAATCTCGGTCCGAATCGT-AAAAAA---GCAGAACA---AA---AAGCGGGCATTT------TCGCCTGCAA-----ATGATCTGTTAA
erecta ------CAATCC-C----TGATCTGGGTT------------CGAATCGT-AAAAAA---GCAGAACA---AAACCAAGCGGCCATTCGGGCAATCGGCTGCAA-----ATGAGCCGTTAA
ananassae -----------A-C----TGATCTG-------------------ATCGT-AAAAAA---GCAAAACG---AC-----------------------------AA-----ATGATATCTTTA
pseudoobscura CGATCCCGAT-T-C----TGATCCTGGCC------------TGAATCGT-AAAAAAA--GAAGAGCGTACAA---AGGCGGAAATGG------CACTCAACAAAAAATATGATCTTTTTA
persimilis CGATCCCGAC-T-C----TGATCCTGGCC------------TGAATCGT-AAAAAAA--GAAGAGCGTACAA---AGGCGGAAATGG------CACTCAACAAAAAATATGATCTTTTTA
virilis --ATGTCAAT-T-GTCTCTGATCTGAGCT--------------GATCAT-AAAAAA-----AAAGCA---GA---AAA---------------ACGATCGGGC-----ATGATTTTTTTA
mojavensis AAATGTCAAT-T-G----TGATCGCAGCT--------------CATCAT-AAAAAA-----AGATCA---AACCGAAA---------------GTCTCTAGAA-----ATGATTTTTTTA
grimshawi AAATGTCAAT-T-G----TGATCTGAGCT--------------CATCAT-AAAAAA-----AGATCA---AT---ATACC-------------GTTGCCAGAA-----ATGATTTTTTTA
Summary BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
melanogaster TGGGC------CGGGCTAAAAAACTAAGTCAC-------------------AAAGTCACA------AGGTTG------------TCCGGTAAATTGACC---------CGGTTAAGAATG
simulans TGGGC------CGGGCTAAAAAACT---------------------------AAGTCACA------AGGTTG------------TCCGGGAAACTGACC---------CGGTTAAGAATG
sechellia TGGGC------CGGGCTAAAAAACTAAGTCAC-------------------AAAGTCACA------AGGTTG------------TCCGGGAAATTGACC---------CGGTTAAGAATG
yakuba TGGCCCAAAAACGGGCTAAAAAACTAAGTCAC-------------------AAAGTCACA------AGGTTGCAAGGTT----GTCCGGCAAATCGACC---------GGGTTAAGGATG
erecta TGGGCCAAAAACGGGCTAAAAAACTAAGTCAC-------------------AAAGTCACA------AGGTTGT-----------CCGGGAAAACTGACC---------CGGTTAAGGA--
ananassae TGGTCCAA---AGGACCAAAAAACTAAGTCAC-------------------AAAGTCACA------AGGTTA------------TCCTGGAAATTGATCCCTGACTGACGTTAAAGGATG
pseudoobscura TGGGCCC----ATCGCTAAAAAAGTAAGTCAC-------------------AAAGTCGC------------------TTTCCCTTCTCTGTCACTGACT---------TCG--AAGGAAG
persimilis TGGGCCC----ATCGCTAAAAAAGTAAGTCAC-------------------AAAGTCGC-------------------------------------------------------------
virilis TTAT-------TGGCCTAAAAAACTAAGACGC----------------------------------------------------------------------------------------
mojavensis TTAT-------TGACCTAAAAAACTAAG------------------------AAGTCGAACAATGCGAACGG------------CCCAAAAAGTCAGCC---------AGGCCTAGAAGG
grimshawi TTAT-------TGGCCTAAAAAAGTAAAACGTTAAACAATGCAATGGCCAAAAAGTC--ACTACGAAGACGG------------CCTGGAAA----------------------------
Summary BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
melanogaster --------------------------------------------TCTGTCTG--TACCGAGAAGGATGCAGGACATT-------CAGCACTTCAAAGCTCCCACCGC--TCGAA--G---
simulans --------------------------------------------TCTGTCTG--TACCGAGAAGGACGCAGAACACT-------CAGCACTTCAAAGCTCCCACCGC--CCGAA--G---
sechellia --------------------------------------------TCTGTCTG--TACCGAGAAGGACGCAGGACACT-------CAGCACTTCAAAGCTCCCATCGC--CCGAA--G---
yakuba --------------------------------------------TGTGTGTG--TACCGAGAAGGACGCAGGACACT-------CAGCACTTCAAAGCTTCCAGCGC--CCGAA--G---
erecta --------------------------------------------TGTGCATG--TACCGAGAAGAGCGCAGGACACT-------CCGCACTTCAAAGCTCCCAGTGC--CCGAC--G---
ananassae C-----------------------------------GGCAGAGTTCTGATAG--TACGGCGAAATCCGCAGGACTCCATCTCCGTGGCAGTTCAAAGCTCCTGCCGC--CCAAATTG---
pseudoobscura CCGCTTCTCTCTCGCTCCCTCGCTGGCATCGGGAAGAGCAGAGATCTG------TACGGGGAAAGCCGCAGGACTCTA------TTCCACATCAAAGCTCTATGCGCCGCCGCA--GCTT
persimilis ------------------------------------------------------TACGGGGAAAGCCGCAGGACTCTA------TTCCACATCAAAGCTCTCTGCGCCGCCGCA--GCTT
virilis ------------------------------------------------------------------------------------------------------------------------
mojavensis --------------------------------------------CGAACGTTAA-----AGCAGAGTAAAGTGTGAT-------TTACACATTA---CTTACAAGGC--TAGCA--A---
grimshawi ------------------------------------------------------------------------------------------------------------------------
Summary BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
melanogaster --GATTCCCCCGAAGATTCACACGGCTGGCGGG-----GGGGATCAACGTTTGATCAG----AAACCGCCGGCGGCTGTTAACGGCCACAAAAAGCAAGTGACATGCAAATTAGGCAGAT
simulans --GATTCCCCCGAAGATTCACACGGCTGGCGGG-----GGGGATCACCGTTTGATCAG----AAACCGCCGTC----GTTAACGGCCACAAAAAGCAAGTGACATGCAAATTAGCCAGAT
sechellia --GATTCCCCCGAAGATTCACACGGCTGGCGGG-----GGGGATCACCGTTTGATCAG----AAACCGCCGTC----GTTAACGGCGACAAAAAGCAAGTGACATGCAAATTAGCCAGAT
yakuba --GATTCCCCCGAAAACTCACCCGGCTGGC--------GGGGATCCCCGTGTGATCAA----AAACCGCCGGC---TGCTAACGGCCACAAAAAGCAAGTGACATGCAAATTAGGCGGAT
erecta --GATTCCACCGAAGATTCACACGGCTGGC--------GGGGATGCCCGTTTGATCCA----AACCCGCCGCC---TGTTAATGGCCACAAAAAGCAAGTGACATGCAAATTATACGGAT
ananassae --GATTTTCTCCAAAACACGCACGCCCGTG--------GGAGATCCTCCTTTG---------AAGCCGACCGC----------------------CGGGTGACATGCAAATTAACTGCCC
pseudoobscura CAGCTTCCACGGAAGATTCACACGATTAGC--G-----GCATTTTCACGTTTG-------------------------------------AAACGGACATGCCATGCAAATTATCCGAAT
persimilis CAGCTTCCACGGAAGATTCACACGATTAGC--G-----GCATTTTCACGTTTG-------------------------------------AAACGGACATGCCATGCAAATTATCCGAAT
virilis ------------------------------------------------------------------------------------------------------------------------
mojavensis --------------AATCAATGTGGCTAACGGGGCAATGGGAATTAACTTCTGGCCGGGTCAACACTGAAGAC-----------------GAAAGAGAGTG------AAAATCGACAGTT
grimshawi ------------------------------------------------------------------------------------------------------------------------
Summary BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
melanogaster TACTGC----TGGCCAGCAA---GGTCAGGCCGCCCTTAATGGGCGTGACCGCTGGATCTACCTCCCTCCCCACCCCTGCCCTTCAACGGCAA-AGGAACCGA-----CAACGGCA-GCA
simulans TAATGG----TGGCCAGCAA---GGTCAGGCCGCCCTTAATGGGCGTGACCGCTGGATCTCCCTCCCTTCCCTCCCCACCCTCACAACGGCAA-AGGAACCGC-----CAACGGCA-GCA
sechellia TAATGG----TGGCCAGCAA---GGTCAGGCCGCCCTTAATGGGTGTGACCGCTGGATCTCCCTCCCTTCCCTCCCCTCCCTCTCAACGGCAA-AGGAACCGC-----CAACGGCA-GCA
yakuba TACCAGCAAGCGGGCAGCAA---GGTCAGGCCGCCCCTAATGGGCGTGACCGCTGGATCTCCCTCCCCTCCC-----------TAATCGGCAA-AGGTACCGC-----CAACGGCA-GCA
erecta TA--------TGGATAGCAA---GGTCAGGCCGAACTTAATGGGCGTGACCGCTGGATCTCCCTCCCCTCCT-----------TAATCGGCAA-AGGAACCGC-----CAACGGCA-GCA
ananassae TAA-------TTTGCGGCAA---GGTCTGACC-----TTGTGGCAGGATGCTCTGGCACCTTCCCCACCCCC-------------------------ATCCGC-----CAACGGCA-GCA
pseudoobscura TAATTC----CGGCCAGT-----GGTCATGCC--CATTAGGGAGT-------CGAGTCCCCCCTCCCCTCCG-------CCCACCAGCAGCAGCAGCAACCACTGCTGCAGCCACAGGCA
persimilis TAATTC----CGGCCAGT-----GGTCATGCC--CATTAGGGAGT-------CGAGTCCCCCCTCCCCTCCG-------CCCACCAGCAGCAGCAGCAACCACTGCTGCAGCCACAGGCA
virilis ------------------------------------------------------------------------------------------------------------------------
mojavensis TATGGC----AGAGTAAAGAAGCGGGGAGGTAAATATCTATATGTGCTTGAGCTGAGTCT------------------------------------------------------------
grimshawi ------------------------------------------------------------------------------------------------------------------------
Summary BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
melanogaster ATACGATCACCA--C------AACCACCGATCGATCGATCGAGTGACCTTCGACCTG------------CCGC-ATTGTTATCTGCGTGC-TGCGATTTTTTCTTCATTTTTCACAGGCC
simulans GTACCATCACCA--C------AACCACCGATCGATCGATCGAGTGACCTTCGACCTG------------CCGC-ATTGTTATCTGCGTGC-TGCGATTTTTTCTTCATTTTTCACAGGCC
sechellia GTACCATCACCA--C------AACCACCGATCGATCGATCGAGTGACCTTCGACCTG------------CCGC-ATTGTTATCTGCGTGC-TGCGATTTTTTCTTCATTTTTCACAGGCC
yakuba GTGCCACCACCA--C--------------AACCACCGATCGAGTGACCTTCGACCTG------------CCGC-ATTGTTATCTGCGCGC-AGCGATTTTTTCTTCTTTTTTCACAGGCC
erecta GCACCACCACCA--CCACCAGCACCACCAAACCACCGATCGAGTGACCTTCGACCTG------------CCGC-ATTGTTATCTGCGTGC-AGCGATTTTTTCTTCTTTTTTCACAGGCC
ananassae CCACCACAATCGGCC------TACTGCCATTCCG-AGGGCGAGTGACCTTCA--CTA------------CTCA-AT--------------------TTTTTCCATCTTTTTTCACAGGCT
pseudoobscura CTGCCACTGCCA--C------TGCCATCAGTCA--CTGCCGCATGACCTTCAGATCG------------T-----TTATTGTCCCTG---------ATTTTGCTTATTTTTTCACAGGCA
persimilis CTGCCACTGCCA--C------TGCCATCAGTCA--CTGCCGCATGACCTTCAGATCG------------T-----TTATTGTCCCTG---------ATTTTGCTTATTTTTTCACAGGCA
virilis ------------------------------------------GTGACCTTCGACCTTTTATAGTTGCTGTTGTTGCTGCTGCTGCTGCTACTCTTCTTTATGCACATTTTTTCACAGGCA
mojavensis ------------------------------------------GTGACCTTCAACCTT------------TTGTTGTTGTCGTTTCTGGTCGTCTTCTTTAG--ATATTTTTTCACAGGCC
grimshawi ------------------------------------------GTGACCTTCGACCTT------------TTATTGTCGTTGTTGCTT----------------GCATTTTTTCACAGGCA
Summary BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBRRRRRRRRRRRBBBB
melanogaster ATTT---GCGTGCGCTCCTGCTGT--------CCTTG-------------GTGTGT-CCTTTCAGCATGCGTGTCCTTTTT--A-------GCATGCTAAAAATCAAGCGATCAAGAATC
simulans ATTT---GCGCGCGCTCCTGCTGT--------CCTTG-------------GTGTGT-CCTTTTAGCATGCGTGTCCTTTTT--A-------GCATGCTAAAAATCAAGCGATCGACAATC
sechellia ATTT---GCGTGCGCTCCTGCTGT--------CCTTC-------------GTGTGT-CCTTTTAGCATGCGTGTCCTTTTT--A-------GCATGCTAAAAATCAAGCAATCGACAATC
yakuba ATTT---GCGAGCGCTCCTGCTGT--------CCTTG---------------GTGT-CCTTTTAGCATGCGTGTCCTTTTT--A-------GCATGCTAAAAATCAAGCGATCGAAAATC
erecta ATTT---GCGTGCGCTCCTGCTGT--------CCTTG---------------GTGT-CCTTTTAGCATGCGTGTCCTTTTT--A-------GCATGCTAAAAATCATGCGATCGAATATC
ananassae ATTG---CC--GCACTGCTGCTGT--------CCGTC-----------------GT-CCTGCCCGT-----TGTCCTTTTT--A-------GCATAGCAAAAA--------------ATC
pseudoobscura ATTT---GCGCCTGCTTCTGATGT--------CCCTC--TCGCTCTCCGTTTGTGTGCCTGTTGTCGGTCGTGTCCTTTTT--AGCATTTGGCATGCTAAAA---------------ATC
persimilis ATTT---GCGCCTGCTTCTGATGT--------CCCTC--TCGCTCTCCGTTTGTGTGCCTGTTGTCGGTCGTGTCCTTTTT--AGCATTTGGCATGCTAAAA---------------ATC
virilis ATTTCGGTCTGCCGTTGCGGCTGC--------CTGTC----------------CGG-CCTGTTCGCGCCTGTGTCCTTTTTTGA-------GGATGCTAAAAATC---------------
mojavensis ATTTCATGCCGCTGCTCCTGCTGCTGCTGCTGCTGCCGTTGTTGTTGTTGTTGCTG-CCTGTTCGTCGTGTCGTCCTTTTTTGA-------GCATGCTAAAAATC---------------
grimshawi ACTTTTGACTTCTGCTGCTGCTGTTGCTGGTGTTGCC--------------TGTTG-CCTGTTT-TGCGGCTGTCCTTTTT--A-------GGCTGCTAAAAATC---------------
Summary BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
melanogaster TGCGCGATCTTAGCCGGAATC------G----GGATTAG-TC--G-TTTATGGCC-------CACGC-----------CCTCAATC-------C--TCCATAAAACACTAAGCGCTTTCG
simulans TGCGCGATCTTAGCCGGAATC------G----GGATTAG-TC--G-TTTATGGCC-------CACGC-----------CCTCAATC-------C--TCCATAAAACACTAAGCGCTTTCG
sechellia TGCGCGATCTTAGCCGGAATC------G----GGATTAG-TC--G-TTTATGGCC-------CACGC-----------CCTCAATC-------C--TCCATAAAACACTAAGCGCTTTCG
yakuba TGCGCGATCTTAGCCGGAATT------G----GGATTAG-TC--G-TTTATGGCC-------CACGC-----------CTTCAATCCATAAAAC--TCCATAAAACACTAAGCGCTTT-G
erecta TGCGCGATCTTAGCCGGAATT------G----GGATTAG-TC--G-TTTATGGCC-------CACGC-----------CTTCAATC-------C--TCCATAAAACACTAAGCGCTTTCG
ananassae TTAGCGATCTTAGCCGGAATC------GAAGTGGATTAG-GCCAG-TTTATGGCC-------CACGC-----------CCTCAATC-------C--TCCATAAAACACTAAGCGCTTC-G
pseudoobscura TGCGCGATCTTAGCCGGAATCCG-AGTG----GGATTAGAGC--G-TTTATGGCCCTTAGAGCACGCCCTCGTCCCGGCCTCAATC-------C--TCCATAAAACACTAAGCGCTTTCC
persimilis TGCGCGATCTTAGCCGGAATCCG-AGTG----GGATTAGAGC--G-TTTATGGCCTTTAGAGCACGCCCTCGTCCCGGCCTCAATC-------C--TCCATAAAACACTAAGCGCTTTCC
virilis -GCGACATCTTAGCCAGAATTTTTGGCC----GGATTAA-GC--ATTTTATGG---------CCAGC--------------AAATG-------CTGTCAATAAAACGCTAAGCGCTTCCC
mojavensis -GCGACATTTTATCCAGAATTTCTGGCC----GGATTAA-GC--ATTTTATGA----------CGGC--------------AAATG-------CTGTCAATAAAACGCTAAGCGCTTTCC
grimshawi -GCAACATCTTAGCCAGAATTTCAGGCC----GGATTAG-GC--ATTTTATGGTATTCGCGCCGAGC-----------CCAAAATG-------CAGGCAATAAAACGCTAAGCGCTTTCC
Summary BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
melanogaster CCTA----ATGTA-T--GTATCT-CTTCATATCTGGAA-------ATCTCACTATGGGTGTGGGTG---------------TGGGTATCTGTATCTG--------TATCTATATCTGTTG
simulans CCTA----ATGTA-T--GTATCT-CCTGATATCTGGAA-------ATCTCACTATGGGTATGG---------------------------GTATCTG--------TATCTGTTTCTGTTG
sechellia CCTA----ATGTA-T--GTATCT-CCTGATATCTGGAA-------ATCTCACTATGGGTATGG---------------------------GTATCTG--------TATCTGTTTCTGTTG
yakuba CCTAATGTATGTA-T--GTATCT-CTTGATATCTGGAA-------ATCTCACTATCTCAATATGTGGCTAT----------TTGGTATCTGTATCTGT-------TA-CTGTTGCTGTTG
erecta CCCAATGTATGTA-T--GTATCT-CTTGATATCTCGAATATGTGGGTATCGGTATCTGTATCTGTATCTGTACC-------TCTGTATCTGTATCTGTATCGCTGTATCTGTTGCTG-TG
ananassae ACTA----ATGCACT--GCATTC-CAAAATGTATCTGT-------ATCTCTGCATCTGCGCTGTTGCGTGA-------------------GTATTGG--------TAAGTTTTTTTAATA
pseudoobscura CCTA----ATGCA-T--CTTTTA-GATGCTGTATCTG-----------------------------------------------------------------------------------
persimilis CCTA----ATGCA-T--CTTTTA-GATGCTGTATCTG-----------------------------------------------------------------------------------
virilis ACTA----ATCTC-C--AACCGT-AGACGTATCCTTAGCC-----ATATCTGTATCTGTATCTGTATCT---------------------GTATCTG--------TATCTCT--------
mojavensis GCTA----ATCCC-CCAAACTGTAAAATCTAGCTTCGTCT-----GTATCTGTATCTGTATCTGTATCT---------------------GTATCTG--------TATCTGT--------
grimshawi GCTA----ATCTC-C--AACTGT-AAATGTATCTTCAA-------ATTTCTATATCTGCATTTTTATTTAATGAACACCAAATTTCAGCAGCGTTTC--------TATCGAC--------
Summary BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
melanogaster CTGT--GATGAATAAAT-----------AACTTCTTA-ATGGGAT-----------------GCTGCTCAAAATGG------------CTCCCACTC------------AT-CCCCATTG
simulans CTGT--GATGAATAAAC-----------AACTTCTTA-ATGGGAT-----------------GCTGCTCAAAATGG------------CTCCCACTC------------AT-CCCCATTG
sechellia CTGT--GATGAATAAAC-----------AACTTCTTA-ATGGGAT-----------------GCTGCTCAAAATGG------------CTCCCACTC------------AT-CCCCATTG
yakuba CTGT--GATGAATAAAC-----------AACTTCTAA-ATGCGAT-----------------GCCGCTCAAAATGG------------AGCCCACTC------------ATCCCCCATTG
erecta CTGT--GATGGATAAAC-----------AACTTCTTA-ATGCGAT-----------------GCGGCTCAAAATGG------------CTCCCACTC------------AT-CCCCATTG
ananassae GAGT------------------------------------------------------------------------------------TTTCCATTC------------AT-CCCCATTG
pseudoobscura ------------TAAAC-----------AACTTTTTA-ATAGAGC-----------------ATTCCACAAGATGG------------CTCCCATCC---------------CCCCATTG
persimilis ------------TAAAC-----------AACTTTTTA-ATAGAGC-----------------ATTCCACAAGATGG------------CTCCCATCC---------------CCCTATTG
virilis ----TGGA--CATGTATCTGCCGCTTTAAATTTTGTATATTTGGTGTGTTTATTTTTTTTTTAATGCACCCAGCAGCC-TCCCCCCGCCCTCTCCCCCTCGACAGCCACGC-CGCAGCTG
mojavensis ------------------------------------------------------------------------------------------------------------------------
grimshawi ----AAAA--AATAAAT-----------AAATAAATAAATAAA-------------------AATCCGCCAAGCAGCTGGCATTTAAATGTCTGTTCCGGAACTGAGCAAC-CAAAAATA
Summary BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
melanogaster GCGGCTG--------GGAGAG----TCGTTG----GGCAT----CCGGAA---GCGGGGGCAGCCAAAAATAT--ACCCACATCCCATGG-A---TGCCATCAATTAGCATACAATTAAA
simulans GCGGCTG--------GGAGAG----TCGTTG----GGCAT----CCGGAA---GCGGGGGCAGCCAAAAATAT--ACCCACATCCCATGG-A---TGCCATCAATTAGCATACAATTAAA
sechellia GCGGCTG--------GGAGAG----TCGTTG----GGCAT----CCGGAA---GCGGGGGCAGCCAAAAATAT--ACCCACATCCCATGG-A---TGCCATCAATTAGCATACAATTAAA
yakuba GCAGCTA--------GGAGAC----TCGATG----GGCAT----CCGGAA---GCGGGGGAAGCCAAAAATAT--ACCCACATCCCATGG-A---GGCCATCAATTAGCATACAATTAAA
erecta GCAGCTATGGGCATTGGAGAC----TCGATG----GGCAT----CCGGAA---GC-GGGGAAGCCAAAAATATACACACACATCCCATGG-A---TGCCATCAATTAGCATACAATTAAA
ananassae GCAGCTG--------GGAAAG----TGGCAGCAACAGCAG----CCGGAA---CTGCTGCGCTCCAAAAATAT----------CCAATGG-A---TGCCATCAATTAGCATACAATTAAA
pseudoobscura GCAGTTG--------GCAG----------TT----GGCAG----CTGGGAAATGCATCCGGATCCAGAAATAT-----CCCATCCCATGG-AAGCAGCCATCAATTAGCATACAATTAAA
persimilis GCAGTTG--------GCAG----------TT----GGCAG----CTGGGAAATGCATCCGGATCCAGAAATAT-----CCCATCCCATGG-AAGCAGCCATCAATTAGCATACAATTAAA
virilis GCATTTG--------AAATGC----CATCAG----AATATGGTTCCGGAA---CTGTGCGC---CAAATATAG---TACAAGTATCTTTGAA---TGCAATCAATTAGCATACAATTAAA
mojavensis -------------------------------------------------------------------------------------------A---TGCAATCAATTAGCATACAATTAAA
grimshawi GTATCTG--------AGTAGCTGAGTAGCTG----AGTAT-CTTGTGGAT---GCGTTTGC---------TGC---CACTGCTGCCATTGAA---TGCAATCAATTAGCATACAATTAAA
Summary BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
melanogaster AAATGCTTAAACAGGGAAATCGTCTTGGGA-------TGCGAG--------------------------------------TGGTTCGG------CCGCAGAT------GCAGCCGCAGC
simulans AAATGCTTAAACAGGGAAATCGACTTGGGA-------TGCGAG--------------------------------------TGGTTCGG------CCGCAGAT------GCAGCCGCAGC
sechellia AAATGCTTAAACAGGGAAATCGACTTGGGA-------TGCGAG--------------------------------------TGGTTCGG------CCGCAGAT------GCAGCCGCAGA
yakuba AAATGCTTAAACAGGGAAATCGACTTGGGA-------TGCGAG--------------------------------------TGCTTAGG------CCACAGATGCAGCCGCAGCCGCAAC
erecta AAATGCTTAAACAGGGAAATCGACTTGGGA-------TGCGAG--------------------------------------TGGTTCGG------CCACAGAT------GCAGCCGCAAC
ananassae AACTGCTTAAATAG-------------------------------------------------------------------TGGTCTGG------CCGCAGAA------GCCGCCAGAGA
pseudoobscura GAATGCTTAAACAGGGAAATCAACTTGAAC-------TGCA----------------------------------------TGCGGCAG------ATACATAT------GTATCTGTATC
persimilis GAATGCTTAAACAGGGAAATCAACTTGAAC-------TGCA----------------------------------------TGCGGCAG------ATACATAT------GTATCTGTATC
virilis AAATGCTTAAACAAGGAAATCAACTCGAGC-------TGCAGACGCACA--------CACAGCCTTATTTGTATCTGTATCTAATGCGGGCGCAACTGTATCT------GTATCTGCATC
mojavensis AAATGCTTAAACAAGGAAATCAAC---AGC-------AGCAGATGCACA---------GCAGACTCA---GTCCATGTAGCTGATGTAGAGG---ATGTATCT------GTGGTAGTAGC
grimshawi AAATGCTTAAACAAGGAAATCAACTCGAGCGCCCGCAAACAGATGCACAGATACAGATACAGATACAGATGCAGATACA---GATACGGACAC--ACATTGCT------ATGGATGCAGA
Summary BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
melanogaster AGCATTTGTAT----------CTC--------------CAAGTGG--C---------------GGGCAGCAGATCAAAGCGA
simulans CGCATTTGTAT----------CTC--------------CAAGTGG--C---------------GGGCAGCAGATCAAAGCGA
sechellia CGCATTTGTAT----------CTC--------------CAAGTGG--C---------------GGGCAGCAGATCAAAGCGA
yakuba AGCATTTGTAT----------CTC--------------CAAGTGG--C---------------GGGCAGCAGATCAAAGCGA
erecta AGCATTTGTAT----------CTC--------------CAAGTGG--C---------------GGGCAGCAGATCAAAGCGA
ananassae CACAGATACAGATACAGGCCACAC--------------CAAGTGG--CTTCCACAAGAGCGG-GGGGGACAGATCAAAGCGA
pseudoobscura TGTATCTGGGA----------CTG--------------TAAGTGG--C--CAACGGCTGCGGCTGGGAGCAGATCAAAGCGA
persimilis TGTATCTGTGA----------CTG--------------TAAGTGG--C--CAACGGCTGCGGCTGGGATCAGATCAAAGCGA
virilis TGCAACTGTAT----------CTCTGTCTGTGTCTGTGCAGATGC--C--TTGTAAGT-----GGGCCGCAGATCAAAGCGA
mojavensis TGCATCTGTAT----------CTC------------TACAGATGC--G--TCGTAAGT------GGTCGCAGATCAAAGCGA
grimshawi TACAGTTAGAG----------ATT--------------CAGATGCATG--TTGTAAGT------GGCCGCAGATCAAAGCGA
Summary BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBMMMMMMMMMMMRRR
kni