                         SEQUENCE LISTING

<110>  Zymergen Inc.
 
<120>  RAPID REMOVAL OF A SELF-REPLICATING FUNGAL PLASMID FOR EFFICIENT 
       MARKER CYCLING

<130>  ZYMR-074/01WO 327574-2407

<150>  US 63/053,069
<151>  2020-07-17

<160>  8     

<170>  PatentIn version 3.5

<210>  1
<211>  5749
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  AMA1 element

<400>  1
ccgggcccag tatatgttcc gcagatgact ggagctctgc catacgtgcc ctctcaagca       60

ccatttgttc catctacaga gactagtcac caactagtct atcaagactc acagggtaca      120

ttgctgagac caactgacca gaggcagggt agcggattga cggctccatc tccttcactt      180

acaaggtcta ttgaaagccc tttagcatca ccaagcggag aatagattgt taagcttatt      240

ttttgtatac tgttttgtga tagcacgaag tttttccacg gtatcttgta aaaatatata      300

tttgtggcgg gcttacctac atcaaattaa taagagacta attataaact aaacacacaa      360

gcaagctact ttagggtaaa agtttataaa tgcttttgac gtataaacgt tgcttgtatt      420

tattattaca attaaaggtg gatagaaaac ctagagacta gttagaaact aatctcaggt      480

ttgcgttaaa ctaaatcaga gcccgagagg ttaacagaac ctagaagggg actagatatc      540

cgggtaggga aacaaaaaaa aaaaacaaga cagccacata ttagggagac tagttagaag      600

ctagttccag gactaggaaa ataaaagaca atgataccac agtctagttg acaactagat      660

agattctaga ttgaggccaa agtctctgag atccaggtta gttgcaacta atactagtta      720

gtatctagtc tcctataact ctgaagctag aataacttac tactattatc ctcaccactg      780

ttcagctgcg caaacggagt gattgcaagg tgttcagaga ctagttattg actagtcagt      840

gactagcaat aactaacaag gtattaacct accatgtctg ccatcaccct gcacttcctc      900

gggctcagca gccttttcct cctcattttc atgctcattt tccttgttta agactgtgac      960

tagtcaaaga ctagtccaga accacaaagg agaaatgtct taccactttc ttcattgctt     1020

gtctcttttg cattatccat gtctgcaact agttagagtc tagttagtga ctagtccgac     1080

gaggacttgc ttgtctccgg attgttggag gaactctcca gggcctcaag atccacaaca     1140

gagccttcta gaagactggt caataactag ttggtctttg tctgagtctg acttacgagg     1200

ttgcatactc gctccctttg cctcgtcaat cgatgagaaa aagcgccaaa actcgcaata     1260

tggctttgaa ccacacggtg ctgagactag ttagaatcta gtcccaaact agcttggata     1320

gcttaccttt gccctttgcg ttgcgacagg tcttgcaggg tatggttcct ttctcaccag     1380

ctgatttagc tgccttgcta ccctcacggc ggatctgcca taaagagtgg ctagaggtta     1440

taaattagca ctgatcctag gtacggggct gaatgtaact tgcctttcct ttctcatcgc     1500

gcggcaagac aggcttgctc aaattcctac cagtcacagg ggtatgcacg gcgtacggac     1560

cacttgaact agtcacagat tagttagcaa ctagtctgca ttgaatggct gtacttacgg     1620

gccctcgcca ttgtcctgat catttccagc ttcaccctcg ttgctgcaaa gtagttagtg     1680

actagtcaag gactagttga aatgggagaa gaaactcacg aattctcgac tcccttagta     1740

ttgtggtcct tggacttggt gctgctatat attagctaat acactagtta gactcacaga     1800

aacttacgca gctcgcttgc gcttcttggt aggagtcggg gttgggagaa cagtgccttc     1860

aaacaagcct tcataccatg ctacttgact agtcagggac tagtcaccaa gtaatctaga     1920

taggacttgc ctttggcctc catcagttcc ttcatagtgg gaggaccatt gtgcaatgta     1980

aactccatgc cgtgggagtt cttgtccttc aagtgcttga ccaatatgtt tctgttggca     2040

gagggaacct gtcaactagt taataactag tcagaaacta tgatagcagt agactcactg     2100

tacgcttgag gcatcccttc actcggcagt agacttcata tggatggata tcaggcacgc     2160

cattgtcgtc ctgtggacta gtcagtaact aggcttaaag ctagtcgggt cggcttacta     2220

tcttgaaatc cggcagcgta agctccccgt ccttaactgc ctcgagatag tgacagtact     2280

ctggggactt tcggagatcg ttatcgttat cgcgaatgct cggcatacta actgttgact     2340

agtcttggac tagtcccgag caaaaaggat tggaggagga ggaggaaggt gagagtgaga     2400

caaagagcga aataagagct tcaaaggcta tctctaagca gtatgaaggt taagtatcta     2460

gttcttgact agatttaaag agatttcgac tagttatgta cctggagttt ggatatagga     2520

atgtgttgtg gtaacgaaat gtaaggggga ggaaagaaaa agtcgtcaag aggtaactct     2580

aagtcggcca ttcctttttg ggaggcgcta accataaacg gcatggtcga cttagagtta     2640

gctcagggaa tttagggagt tatctgcgac caccgaggaa cggcggaatg ccaaagaatc     2700

ccgatggagc tctagctggc ggttgacaac cccacctttt ggcgtttctg cggcgttgca     2760

ggcgggactg gatacttcgt agaaccagaa aggcaaggca gaacgcgctc agcaagagtg     2820

ttggaagtga tagcatgatg tgccttgtta actaggtacc aatctgcagt atgcttgatg     2880

ttatccaaag tgtgagagag gaaggtccaa acatacacga ttgggagagg gcctaggtat     2940

aagagttttt gagtagaacg catgtgagcc cagccatctc gaggagatta aacacgggcc     3000

ggcatttgat ggctatgtta gtaccccaat ggaaacggtg agagtccagt ggtcgcagat     3060

aactccctaa attccctgag ctaactctaa gtcgaccatg ccgtttatgg ttagcgcctc     3120

ccaaaaagga atggccgact tagagttacc tcttgacgac tttttctttc ctccccctta     3180

catttcgtta ccacaacaca ttcctatatc caaactccag gtacataact agtcgaaatc     3240

tctttaaatc tagtcaagaa ctagatactt aaccttcata ctgcttagag atagcctttg     3300

aagctcttat ttcgctcttt gtctcactct caccttcctc ctcctcctcc aatccttttt     3360

gctcgggact agtccaagac tagtcaacag ttagtatgcc gagcattcgc gataacgata     3420

acgatctccg aaagtcccca gagtactgtc actatctcga ggcagttaag gacggggagc     3480

ttacgctgcc ggatttcaag atagtaagcc gacccgacta gctttaagcc tagttactga     3540

ctagtccaca ggacgacaat ggcgtgcctg atatccatcc atatgaagtc tactgccgag     3600

tgaagggatg cctcaagcgt acagtgagtc tactgctatc atagtttctg actagttatt     3660

aactagttga caggttccct ctgccaacag aaacatattg gtcaagcact tgaaggacaa     3720

gaactcccac ggcatggagt ttacattgca caatggtcct cccactatga aggaactgat     3780

ggaggccaaa ggcaagtcct atctagatta cttggtgact agtccctgac tagtcaagta     3840

gcatggtatg aaggcttgtt tgaaggcact gttctcccaa ccccgactcc taccaagaag     3900

cgcaagcgag ctgcgtaagt ttctgtgagt ctaactagtg tattagctaa tatatagcag     3960

caccaagtcc aaggaccaca atactaaggg agtcgagaat tcgtgagttt cttctcccat     4020

ttcaactagt ccttgactag tcactaacta ctttgcagca acgagggtga agctggaaat     4080

gatcaggaca atggcgaggg cccgtaagta cagccattca atgcagacta gttgctaact     4140

aatctgtgac tagttcaagt ggtccgtacg ccgtgcatac ccctgtgact ggtaggaatt     4200

tgagcaagcc tgtcttgccg cgcgatgaga aaggaaaggc aagttacatt cagccccgta     4260

cctaggatca gtgctaattt ataacctcta gccactcttt atggcagatc cgccgtgagg     4320

gtagcaaggc agctaaatca gctggtgaga aaggaaccat accctgcaag acctgtcgca     4380

acgcaaaggg caaaggtaag ctatccaagc tagtttggga ctagattcta actagtctca     4440

gcaccgtgtg gttcaaagcc atattgcgag ttttggcgct ttttctcatc gattgacgag     4500

gcaaagggag cgagtatgca acctcgtaag tcagactcag acaaagacca actagttatt     4560

gaccagtctt ctagaaggct ctgttgtgga tcttgaggcc ctggagagtt cctccaacaa     4620

tccggagaca agcaagtcct cgtcggacta gtcactaact agactctaac tagttgcaga     4680

catggataat gcaaaagaga caagcaatga agaaagtggt aagacatttc tcctttgtgg     4740

ttctggacta gtctttgact agtcacagtc ttaaacaagg aaaatgagca tgaaaatgag     4800

gaggaaaagg ctgctgagcc cgaggaagtg cagggtgatg gcagacatgg taggttaata     4860

ccttgttagt tattgctagt cactgactag tcaataacta gtctctgaac accttgcaat     4920

cactccgttt gcgcagctga acagtggtga ggataatagt agtaagttat tctagcttca     4980

gagttatagg agactagata ctaactagta ttagttgcaa ctaacctgga tctcagagac     5040

tttggcctca atctagaatc tatctagttg tcaactagac tgtggtatca ttgtctttta     5100

ttttcctagt cctggaacta gcttctaact agtctcccta atatgtggct gtcttgtttt     5160

ttttttttgt ttccctaccc ggatatctag tccccttcta ggttctgtta acctctcggg     5220

ctctgattta gtttaacgca aacctgagat tagtttctaa ctagtctcta ggttttctat     5280

ccacctttaa ttgtaataat aaatacaagc aacgtttata cgtcaaaagc atttataaac     5340

ttttacccta aagtagcttg cttgtgtgtt tagtttataa ttagtctctt attaatttga     5400

tgtaggtaag cccgccacaa atatatattt ttacaagata ccgtggaaaa acttcgtgct     5460

atcacaaaac agtatacaaa aaataagctt aacaatctat tctccgcttg gtgatgctaa     5520

agggctttca atagaccttg taagtgaagg agatggagcc gtcaatccgc taccctgcct     5580

ctggtcagtt ggtctcagca atgtaccctg tgagtcttga tagactagtt ggtgactagt     5640

ctctgtagat ggaacaaatg gtgcttgaga gggcacgtat ggcagagctc cagtcatctg     5700

cggaacatat actgggcccg ggaagatctc atggtcatag ctgtttccg                 5749


<210>  2
<211>  3048
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  half AMA1 element

<400>  2
ccgggcccag tatatgttcc gcagatgact ggagctctgc catacgtgcc ctctcaagca       60

ccatttgttc catctacaga gactagtcac caactagtct atcaagactc acagggtaca      120

ttgctgagac caactgacca gaggcagggt agcggattga cggctccatc tccttcactt      180

acaaggtcta ttgaaagccc tttagcatca ccaagcggag aatagattgt taagcttatt      240

ttttgtatac tgttttgtga tagcacgaag tttttccacg gtatcttgta aaaatatata      300

tttgtggcgg gcttacctac atcaaattaa taagagacta attataaact aaacacacaa      360

gcaagctact ttagggtaaa agtttataaa tgcttttgac gtataaacgt tgcttgtatt      420

tattattaca attaaaggtg gatagaaaac ctagagacta gttagaaact aatctcaggt      480

ttgcgttaaa ctaaatcaga gcccgagagg ttaacagaac ctagaagggg actagatatc      540

cgggtaggga aacaaaaaaa aaaaacaaga cagccacata ttagggagac tagttagaag      600

ctagttccag gactaggaaa ataaaagaca atgataccac agtctagttg acaactagat      660

agattctaga ttgaggccaa agtctctgag atccaggtta gttgcaacta atactagtta      720

gtatctagtc tcctataact ctgaagctag aataacttac tactattatc ctcaccactg      780

ttcagctgcg caaacggagt gattgcaagg tgttcagaga ctagttattg actagtcagt      840

gactagcaat aactaacaag gtattaacct accatgtctg ccatcaccct gcacttcctc      900

gggctcagca gccttttcct cctcattttc atgctcattt tccttgttta agactgtgac      960

tagtcaaaga ctagtccaga accacaaagg agaaatgtct taccactttc ttcattgctt     1020

gtctcttttg cattatccat gtctgcaact agttagagtc tagttagtga ctagtccgac     1080

gaggacttgc ttgtctccgg attgttggag gaactctcca gggcctcaag atccacaaca     1140

gagccttcta gaagactggt caataactag ttggtctttg tctgagtctg acttacgagg     1200

ttgcatactc gctccctttg cctcgtcaat cgatgagaaa aagcgccaaa actcgcaata     1260

tggctttgaa ccacacggtg ctgagactag ttagaatcta gtcccaaact agcttggata     1320

gcttaccttt gccctttgcg ttgcgacagg tcttgcaggg tatggttcct ttctcaccag     1380

ctgatttagc tgccttgcta ccctcacggc ggatctgcca taaagagtgg ctagaggtta     1440

taaattagca ctgatcctag gtacggggct gaatgtaact tgcctttcct ttctcatcgc     1500

gcggcaagac aggcttgctc aaattcctac cagtcacagg ggtatgcacg gcgtacggac     1560

cacttgaact agtcacagat tagttagcaa ctagtctgca ttgaatggct gtacttacgg     1620

gccctcgcca ttgtcctgat catttccagc ttcaccctcg ttgctgcaaa gtagttagtg     1680

actagtcaag gactagttga aatgggagaa gaaactcacg aattctcgac tcccttagta     1740

ttgtggtcct tggacttggt gctgctatat attagctaat acactagtta gactcacaga     1800

aacttacgca gctcgcttgc gcttcttggt aggagtcggg gttgggagaa cagtgccttc     1860

aaacaagcct tcataccatg ctacttgact agtcagggac tagtcaccaa gtaatctaga     1920

taggacttgc ctttggcctc catcagttcc ttcatagtgg gaggaccatt gtgcaatgta     1980

aactccatgc cgtgggagtt cttgtccttc aagtgcttga ccaatatgtt tctgttggca     2040

gagggaacct gtcaactagt taataactag tcagaaacta tgatagcagt agactcactg     2100

tacgcttgag gcatcccttc actcggcagt agacttcata tggatggata tcaggcacgc     2160

cattgtcgtc ctgtggacta gtcagtaact aggcttaaag ctagtcgggt cggcttacta     2220

tcttgaaatc cggcagcgta agctccccgt ccttaactgc ctcgagatag tgacagtact     2280

ctggggactt tcggagatcg ttatcgttat cgcgaatgct cggcatacta actgttgact     2340

agtcttggac tagtcccgag caaaaaggat tggaggagga ggaggaaggt gagagtgaga     2400

caaagagcga aataagagct tcaaaggcta tctctaagca gtatgaaggt taagtatcta     2460

gttcttgact agatttaaag agatttcgac tagttatgta cctggagttt ggatatagga     2520

atgtgttgtg gtaacgaaat gtaaggggga ggaaagaaaa agtcgtcaag aggtaactct     2580

aagtcggcca ttcctttttg ggaggcgcta accataaacg gcatggtcga cttagagtta     2640

gctcagggaa tttagggagt tatctgcgac caccgaggaa cggcggaatg ccaaagaatc     2700

ccgatggagc tctagctggc ggttgacaac cccacctttt ggcgtttctg cggcgttgca     2760

ggcgggactg gatacttcgt agaaccagaa aggcaaggca gaacgcgctc agcaagagtg     2820

ttggaagtga tagcatgatg tgccttgtta actaggtacc aatctgcagt atgcttgatg     2880

ttatccaaag tgtgagagag gaaggtccaa acatacacga ttgggagagg gcctaggtat     2940

aagagttttt gagtagaacg catgtgagcc cagccatctc gaggagatta aacacgggcc     3000

ggcatttgat ggctatgtta gtaccccaat ggaaacggtg agagtcca                  3048


<210>  3
<211>  5
<212>  DNA
<213>  Staphylococcus aureus


<220>
<221>  misc_feature
<222>  (1)..(1)
<223>  n is any nucleotide

<400>  3
ngrrt                                                                    5


<210>  4
<211>  5
<212>  DNA
<213>  Staphylococcus aureus


<220>
<221>  misc_feature
<222>  (1)..(1)
<223>  n is any nucleotide

<220>
<221>  misc_feature
<222>  (5)..(5)
<223>  n is any nucleotide

<400>  4
ngrrn                                                                    5


<210>  5
<211>  8
<212>  DNA
<213>  Neisseria meningitidis


<220>
<221>  misc_feature
<222>  (1)..(4)
<223>  n is any nucleotide

<400>  5
nnnngatt                                                                 8


<210>  6
<211>  8
<212>  DNA
<213>  Campylobacter jejuni


<220>
<221>  misc_feature
<222>  (1)..(4)
<223>  n is any nucleotide

<400>  6
nnnnryac                                                                 8


<210>  7
<211>  7
<212>  DNA
<213>  Streptococcus thermophiles


<220>
<221>  misc_feature
<222>  (1)..(2)
<223>  n is any nucleotide

<400>  7
nnagaaw                                                                  7


<210>  8
<211>  4
<212>  DNA
<213>  Unknown

<220>
<223>  Lachnospiraceae bacterium or Acidaminococcus sp.

<400>  8
tttv                                                                     4


