Molecule: S. avermitilis chromosome S. avermitilis plasmid SAP1 S. avermitilis plasmid SAP2 S. avermitilis SUKA4 chromosome S. avermitilis SUKA5 chromosome S. avermitilis SUKA11 chromosome S. avermitilis SUKA13 chromosome S. avermitilis SUKA17 chromosome S. avermitilis SUKA22 chromosome S. coelicolor A3(2) chromosome S. coelicolor A3(2) plasmid SCP1 S. coelicolor A3(2) plasmid SCP2 S. griseus IFO13350 chromosome S. ambofaciens ATCC 23877 chromosome S. scabies 87.22 chromosome S. parvulus 2297 chromosome S. kanamyceiticus ATCC 12853 chromosome S. bingchenggensis BCW-1 chromosome S. clavuligerus ATCC 27064 chromosome S. clavuligerus ATCC 27064 plasmid pSCL4 S. venezuelae ATCC 10712 chromosome S. lividans TK24 chromosome Kitasatospora setae KM-6054 chromosome Saccharopolyspora erythraea NRRL2338 chromosome S. lividans 1326 plasmid SLP2 S. parvulus 2297 plasmid pSPA1 S. violaceoruber plasmid pSV2 S. rochei plasmid pSLA2-L Bacteriophage phiC31 Bacteriophage phiBT1 Bacteriophage TG1 From 0 1 2 3 4 5 6 7 8 9 . 0 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 6 7 8 9 Mbp

Sequence from: to: Span: 1,000 bp 2,500 bp 5,000 bp 10,000 bp 25,000 bp 50,000 bp 75,000 bp 100,000 bp 200,000 bp 250,000 bp 500,000 bp 1,000,000 bp

Enzyme 1: AatII(GACGTC) AarI(CACCTGCnnnnnnnn) Acc36I(ACCTGCnnnnnnnn) AccII(CGCG) AflII(CTTAAG) AgeI(ACCGGT) AluI(AGCT) ApaI(GGGCCC) ApaLI(GTGCAC) ApoI(rAATTy) AscI(GGCGCGCC) AseI(ATTAAT) AvrII(CCTAGG) BamHI(GGATCC) BbsI(GAAGACnnnnnn) BbvCI(CCTCAGG) BciVI(GTATCCnnnnnn) BclI(TGATCA) BfaI(CTAG) BfiI(ACTGGGnnnnn) BglII(AGATCT) BmgBI(CACGTC) BseYI(CCCAGC) BsiWI(CGTACG) BspEI(TCCGGA) BspHI(TCATGA) BspLU11I(ACATGT) BsrBI(CCGCTC) BsrGI(TGTACA) BssHII(GCGCGC) BssSI(CACGAG) Bst1107I(GTATAC) BstBI(TTCGAA) BstYI(rGATCy) ClaI(ATCGAT) DraI(TTTAAA) EagI(CGGCCG) Eco47III(AGCGCT) EcoRI(GAATTC) EcoRV(GATATC) FseI(GGCCGGCC) FspI(TGCGCA) HaeIII(GGCC) HhaI(GCGC) HindIII(AAGCTT) HpaI(GTTAAC) HpaII(CCGG) IPpoI(CTCTCTTAAGGTAGC) KpnI(GGTACC) MboI(GATC) MfeI(CAATTG) MluI(ACGCGT) MscI(TGGCCA) MseI(TTAA) NarI(GGCGCC) NcoI(CCATGG) NdeI(CATATG) NgoMI(GCCGGC) NheI(GCTAGC) NlaIII(CATG) NotI(GCGGCCGC) NruI(TCGCGA) NsiI(ATGCAT) PacI(TTAATTAA) PmeI(GTTTAAAC) PmlI(CACGTG) PsiI(TTATAA) Psp1406I(AACGTT) PstI(CTGCAG) PvuI(CGATCG) PvuII(CAGCTG) RsaI(GTAC) SacI(GAGCTC) SacII(CCGCGG) SalI(GTCGAC) SapI(GCTCTTCnnnn) ScaI(AGTACT) SgfI(GCGATCGC) SmaI(CCCGGG) SnaBI(TACGTA) SpeI(ACTAGT) SphI(GCATGC) SrfI(GCCCGGGC) Sse8387I(CCTGCAGG) SspI(AATATT) StuI(AGGCCT) SwaI(ATTTAAAT) TaqI(TCGA) Tsp509I(AATT) TthHB8I(TCGA) XbaI(TCTAGA) XhoI(CTCGAG) ZraI(GACGTC) CTAG-family GATC-family Enzyme 2: nothing AatII(GACGTC) AarI(CACCTGCnnnnnnnn) Acc36I(ACCTGCnnnnnnnn) AccII(CGCG) AflII(CTTAAG) AgeI(ACCGGT) AluI(AGCT) ApaI(GGGCCC) ApaLI(GTGCAC) ApoI(rAATTy) AscI(GGCGCGCC) AseI(ATTAAT) AvrII(CCTAGG) BamHI(GGATCC) BbsI(GAAGACnnnnnn) BbvCI(CCTCAGG) BciVI(GTATCCnnnnnn) BclI(TGATCA) BfaI(CTAG) BfiI(ACTGGGnnnnn) BglII(AGATCT) BmgBI(CACGTC) BseYI(CCCAGC) BsiWI(CGTACG) BspEI(TCCGGA) BspHI(TCATGA) BspLU11I(ACATGT) BsrBI(CCGCTC) BsrGI(TGTACA) BssHII(GCGCGC) BssSI(CACGAG) Bst1107I(GTATAC) BstBI(TTCGAA) BstYI(rGATCy) ClaI(ATCGAT) DraI(TTTAAA) EagI(CGGCCG) Eco47III(AGCGCT) EcoRI(GAATTC) EcoRV(GATATC) FseI(GGCCGGCC) FspI(TGCGCA) HaeIII(GGCC) HhaI(GCGC) HindIII(AAGCTT) HpaI(GTTAAC) HpaII(CCGG) IPpoI(CTCTCTTAAGGTAGC) KpnI(GGTACC) MboI(GATC) MfeI(CAATTG) MluI(ACGCGT) MscI(TGGCCA) MseI(TTAA) NarI(GGCGCC) NcoI(CCATGG) NdeI(CATATG) NgoMI(GCCGGC) NheI(GCTAGC) NlaIII(CATG) NotI(GCGGCCGC) NruI(TCGCGA) NsiI(ATGCAT) PacI(TTAATTAA) PmeI(GTTTAAAC) PmlI(CACGTG) PsiI(TTATAA) Psp1406I(AACGTT) PstI(CTGCAG) PvuI(CGATCG) PvuII(CAGCTG) RsaI(GTAC) SacI(GAGCTC) SacII(CCGCGG) SalI(GTCGAC) SapI(GCTCTTCnnnn) ScaI(AGTACT) SgfI(GCGATCGC) SmaI(CCCGGG) SnaBI(TACGTA) SpeI(ACTAGT) SphI(GCATGC) SrfI(GCCCGGGC) Sse8387I(CCTGCAGG) SspI(AATATT) StuI(AGGCCT) SwaI(ATTTAAAT) TaqI(TCGA) Tsp509I(AATT) TthHB8I(TCGA) XbaI(TCTAGA) XhoI(CTCGAG) ZraI(GACGTC) Enzyme 3: nothing AatII(GACGTC) AarI(CACCTGCnnnnnnnn) Acc36I(ACCTGCnnnnnnnn) AccII(CGCG) AflII(CTTAAG) AgeI(ACCGGT) AluI(AGCT) ApaI(GGGCCC) ApaLI(GTGCAC) ApoI(rAATTy) AscI(GGCGCGCC) AseI(ATTAAT) AvrII(CCTAGG) BamHI(GGATCC) BbsI(GAAGACnnnnnn) BbvCI(CCTCAGG) BciVI(GTATCCnnnnnn) BclI(TGATCA) BfaI(CTAG) BfiI(ACTGGGnnnnn) BglII(AGATCT) BmgBI(CACGTC) BseYI(CCCAGC) BsiWI(CGTACG) BspEI(TCCGGA) BspHI(TCATGA) BspLU11I(ACATGT) BsrBI(CCGCTC) BsrGI(TGTACA) BssHII(GCGCGC) BssSI(CACGAG) Bst1107I(GTATAC) BstBI(TTCGAA) BstYI(rGATCy) ClaI(ATCGAT) DraI(TTTAAA) EagI(CGGCCG) Eco47III(AGCGCT) EcoRI(GAATTC) EcoRV(GATATC) FseI(GGCCGGCC) FspI(TGCGCA) HaeIII(GGCC) HhaI(GCGC) HindIII(AAGCTT) HpaI(GTTAAC) HpaII(CCGG) IPpoI(CTCTCTTAAGGTAGC) KpnI(GGTACC) MboI(GATC) MfeI(CAATTG) MluI(ACGCGT) MscI(TGGCCA) MseI(TTAA) NarI(GGCGCC) NcoI(CCATGG) NdeI(CATATG) NgoMI(GCCGGC) NheI(GCTAGC) NlaIII(CATG) NotI(GCGGCCGC) NruI(TCGCGA) NsiI(ATGCAT) PacI(TTAATTAA) PmeI(GTTTAAAC) PmlI(CACGTG) PsiI(TTATAA) Psp1406I(AACGTT) PstI(CTGCAG) PvuI(CGATCG) PvuII(CAGCTG) RsaI(GTAC) SacI(GAGCTC) SacII(CCGCGG) SalI(GTCGAC) SapI(GCTCTTCnnnn) ScaI(AGTACT) SgfI(GCGATCGC) SmaI(CCCGGG) SnaBI(TACGTA) SpeI(ACTAGT) SphI(GCATGC) SrfI(GCCCGGGC) Sse8387I(CCTGCAGG) SspI(AATATT) StuI(AGGCCT) SwaI(ATTTAAAT) TaqI(TCGA) Tsp509I(AATT) TthHB8I(TCGA) XbaI(TCTAGA) XhoI(CTCGAG) ZraI(GACGTC)