                         SEQUENCE LISTING

<110>  AMYRIS, INC.
       Platt, Darren M.
       Bissell, Michael W.
       Chandran, Sunil S.
       Hawthorne, Brian L.
       Dean, Jedediah Erik
       Dolan, Christopher
 
<120>  Systems and Methods for Engineering Nucleic Acid Constructs Using
        Scoring Techniques

<130>  060261-5004-WO

<140>  Herewith
<141>  2012-11-16

<150>  US  13/442,625
<151>  2012-04-09

<150>  US 61/561,241
<151>  2011-11-17

<160>  18    

<170>  PatentIn version 3.5

<210>  1
<211>  28
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Upstream primer

<400>  1
gacggcacgg ccacgcgttt aaaccgcc                                          28


<210>  2
<211>  23
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Upstream primer

<400>  2
gggtatctcg aagcacacga aac                                               23


<210>  3
<211>  24
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Downstream primer

<400>  3
aggtccgccg gcgttggacg agcg                                              24


<210>  4
<211>  21
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Downstream primer

<400>  4
atttgctcgg catgccggta g                                                 21


<210>  5
<211>  1511
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Downstream primer

<400>  5
gggtatctcg aagcacacga aactttttcc ttccttcatt cacgcacact actctctaat       60

gagcaacggt atacggcctt ccttccagtt acttgaattt gaaataaaaa aaagtttgct      120

gtcttgctat caagtataaa tagacctgca attattaatc ttttgtttcc tcgtcattgt      180

tctcgttccc tttcttcctt gtttcttttt ctgcacaata tttcaagcta taccaagcat      240

acaatcaact atctcatata caatgtctat cccagaaact caaaaaggtg ttatcttcta      300

cgaatcccac ggtaagttgg aatacaaaga tattccagtt ccaaagccaa aggccaacga      360

attgttgatc aacgttaaat actctggtgt ctgtcacact gacttgcacg cttggcacgg      420

tgactggcca ttgccagtta agctaccatt agtcggtggt cacgaaggtg ccggtgtcgt      480

tgtcggcatg ggtgaaaacg ttaagggctg gaagatcggt gactacgccg gtatcaaatg      540

gttgaacggt tcttgtatgg cctgtgaata ctgtgaattg ggtaacgaat ccaactgtcc      600

tcacgctgac ttgtctggtt acacccacga cggttctttc caacaatacg ctaccgctga      660

cgctgttcaa gcggcccata tcccccaggg cacggatctc gagcaagtcg cccccatctt      720

gtgtgctggt atcaccgtct acaaggcttt gaagtctgct aacttgatgg ccggtcactg      780

ggttgctatc tccggtgctg ctggtggtct aggttctttg gctgttcaat acgccaaggc      840

tatgggttac agagtcttgg gtattgacgg tggtgaaggt aaggaagaat tattcagatc      900

catcggtggt gaagtcttca ttgacttcac taaggaaaag gacattgtcg gtgctgttct      960

aaaggccact gacggtggtg ctcacggtgt catcaacgtt tccgtttccg aagccgctat     1020

tgaagcttct accagatacg ttagagctaa cggtaccacc gttttggtcg gtatgccagc     1080

tggtgccaag tgttgttctg atgtcttcaa ccaagtcgtc aagtccatct ctattgttgg     1140

ttcttacgtc ggtaacagag ctgacaccag agaagctttg gacttcttcg ccagaggttt     1200

ggtcaagtct ccaatcaagg ttgtcggctt gtctaccttg ccagaaattt acgaaaagat     1260

ggaaaagggt caaatcgttg gtagatacgt tgttgacact tctaaataag cgaatttctt     1320

atgatttatg atttttatta ttaaataagt tataaaaaaa ataagtgtat acaaatttta     1380

aagtgactct taggttttaa aacgaaaatt cttattcttg agtaactctt tcctgtaggt     1440

caggttgctt tctcaggtat agcatgaggt cgctcttatt gaccacacct ctaccggcat     1500

gccgagcaaa t                                                          1511


<210>  6
<211>  33
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Forward primer

<400>  6
gcggcccata tcccccaggg cacggatctc gag                                    33


<210>  7
<211>  20
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Forward primer

<400>  7
caagtcgccc ccatcttgtg                                                   20


<210>  8
<211>  33
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Reverse primer

<400>  8
ctcgagatcc gtgccctggg ggatatgggc cgc                                    33


<210>  9
<211>  20
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Reverse primer

<400>  9
ttgaacagcg tcagcggtag                                                   20


<210>  10
<211>  31
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Upstream primer

<400>  10
tcctgtatct atgcaattgc aatccaacta c                                      31


<210>  11
<211>  24
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Downstream primer

<400>  11
aggtccgccg gcgttggacg agcg                                              24


<210>  12
<211>  36
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Downstream primer

<400>  12
gcgaatttct tatgatttat gatttttatt attaaa                                 36


<210>  13
<211>  800
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Downstrream primer

<400>  13
gcgaatttct tatgatttat gatttttatt attaaataag ttataaaaaa aataagtgta       60

tacaaatttt aaagtgactc ttaggtttta aaacgaaaat tcttattctt gagtaactct      120

ttcctgtagg tcaggttgct ttctcaggta tagcatgagg tcgctcttat tgaccacacc      180

tctaccggca tgccgagcaa atgcctgcaa atcgctcccc atttcaccca attgtagata      240

tgctaactcc agcaatgagt tgatgaatct cggtgtgtat tttatgtcct cagaggacaa      300

cacctgttgt aatcgttctt ccacacggat ccacagccta gccttcagtt gggctctatc      360

ttcatcgtca ttcattgcat ctactagccc cttacctgag cttcaagacg ttatatcgct      420

tttatgtatc atgatcttat cttgagatat gaatacataa atatatttac tcaagtgtat      480

acgtgcatgc tttttttacg gcagcatttt tttttcaact ctgatcgccc ctttactgct      540

ccctccgccc aaattccatt gcagttcaaa tgtatactga aaaaaacccc attgctattg      600

ttaaacagtg aactctcttt ttgcccaata ataacattat aacaagtaac taccagcacc      660

ataacaccgt gtcctatcct ggtattaatt actacttgaa gaacgactac atcgcttttt      720

gcaactacaa ttagaacgct ccgccccttc cttttgacgt cgtataagtg tagttggatt      780

gcaattgcat agatacagga                                                  800


<210>  14
<211>  39
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synethetic

<400>  14
tatgcgggca taaagtggct caatggcagc tgcatggag                              39


<210>  15
<211>  4042
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic


<220>
<221>  misc_feature
<222>  (1)..(28)
<223>  Linker

<220>
<221>  misc_feature
<222>  (29)..(678)
<223>  gADH1

<220>
<221>  misc_feature
<222>  (679)..(717)
<223>  Linker

<220>
<221>  misc_feature
<222>  (718)..(1666)
<223>  gADH1

<220>
<221>  misc_feature
<222>  (1667)..(1690)
<223>  Linker_2

<220>
<221>  misc_feature
<222>  (1691)..(3190)
<223>  URA3

<220>
<221>  misc_feature
<222>  (3191)..(3214)
<223>  Linker_2

<220>
<221>  misc_feature
<222>  (3215)..(4014)
<223>  gADH1

<220>
<221>  misc_feature
<222>  (4015)..(4042)
<223>  Linker_0

<400>  15
gacggcacgg ccacgcgttt aaaccgcctc ttttctctct cccccgttgt tgtctcacca       60

tatccgcaat gacaaaaaaa tgatggaaga cactaaagga aaaaattaac gacaaagaca      120

gcaccaacag atgtcgttgt tccagagctg atgaggggta tctcgaagca cacgaaactt      180

tttccttcct tcattcacgc acactactct ctaatgagca acggtatacg gccttccttc      240

cagttacttg aatttgaaat aaaaaaaagt ttgctgtctt gctatcaagt ataaatagac      300

ctgcaattat taatcttttg tttcctcgtc attgttctcg ttccctttct tccttgtttc      360

tttttctgca caatatttca agctatacca agcatacaat caactatctc atatacaatg      420

tctatcccag aaactcaaaa aggtgttatc ttctacgaat cccacggtaa gttggaatac      480

aaagatattc cagttccaaa gccaaaggcc aacgaattgt tgatcaacgt taaatactct      540

ggtgtctgtc acactgactt gcacgcttgg cacggtgact ggccattgcc agttaagcta      600

ccattagtcg gtggtcacga aggtgccggt gtcgttgtcg gcatgggtga aaacgttaag      660

ggctggaaga tcggtgacta tgcgggcata aagtggctca atggcagctg catggagtgt      720

gaatactgtg aattgggtaa cgaatccaac tgtcctcacg ctgacttgtc tggttacacc      780

cacgacggtt ctttccaaca atacgctacc gctgacgctg ttcaagccgc tcacattcct      840

caaggtaccg acttggccca agtcgccccc atcttgtgtg ctggtatcac cgtctacaag      900

gctttgaagt ctgctaactt gatggccggt cactgggttg ctatctccgg tgctgctggt      960

ggtctaggtt ctttggctgt tcaatacgcc aaggctatgg gttacagagt cttgggtatt     1020

gacggtggtg aaggtaagga agaattattc agatccatcg gtggtgaagt cttcattgac     1080

ttcactaagg aaaaggacat tgtcggtgct gttctaaagg ccactgacgg tggtgctcac     1140

ggtgtcatca acgtttccgt ttccgaagcc gctattgaag cttctaccag atacgttaga     1200

gctaacggta ccaccgtttt ggtcggtatg ccagctggtg ccaagtgttg ttctgatgtc     1260

ttcaaccaag tcgtcaagtc catctctatt gttggttctt acgtcggtaa cagagctgac     1320

accagagaag ctttggactt cttcgccaga ggtttggtca agtctccaat caaggttgtc     1380

ggcttgtcta ccttgccaga aatttacgaa aagatggaaa agggtcaaat cgttggtaga     1440

tacgttgttg acacttctaa ataagcgaat ttcttatgat ttatgatttt tattattaaa     1500

taagttataa aaaaaataag tgtatacaaa ttttaaagtg actcttaggt tttaaaacga     1560

aaattcttat tcttgagtaa ctctttcctg taggtcaggt tgctttctca ggtatagcat     1620

gaggtcgctc ttattgacca cacctctacc ggcatgccga gcaaatcgct cgtccaacgc     1680

cggcggacct gttcatcatc tcatggatct gcacatgaac aaacaccaga gtcaaacgac     1740

gttgaaattg aggctactgc gccaattgat gacaatacag acgatgataa caaaccgaag     1800

ttatctgatg tagaaaagga ttaaagatgc taagagatag tgatgatatt tcataaataa     1860

tgtaattcta tatatgttaa ttaccttttt tgcgaggcat atttatggtg aaggataagt     1920

tttgaccatc aaagaaggtt aatgtggctg tggtttcagg gtccataaag cttttcaatt     1980

catctttttt ttttttgttc ttttttttga ttccggtttc tttgaaattt ttttgattcg     2040

gtaatctccg agcagaagga agaacgaagg aaggagcaca gacttagatt ggtatatata     2100

cgcatatgtg gtgttgaaga aacatgaaat tgcccagtat tcttaaccca actgcacaga     2160

acaaaaacct gcaggaaacg aagataaatc atgtcgaaag ctacatataa ggaacgtgct     2220

gctactcatc ctagtcctgt tgctgccaag ctatttaata tcatgcacga aaagcaaaca     2280

aacttgtgtg cttcattgga tgttcgtacc accaaggaat tactggagtt agttgaagca     2340

ttaggtccca aaatttgttt actaaaaaca catgtggata tcttgactga tttttccatg     2400

gagggcacag ttaagccgct aaaggcatta tccgccaagt acaatttttt actcttcgaa     2460

gacagaaaat ttgctgacat tggtaataca gtcaaattgc agtactctgc gggtgtatac     2520

agaatagcag aatgggcaga cattacgaat gcacacggtg tggtgggccc aggtattgtt     2580

agcggtttga agcaggcggc ggaagaagta acaaaggaac ctagaggcct tttgatgtta     2640

gcagaattgt catgcaaggg ctccctagct actggagaat atactaaggg tactgttgac     2700

attgcgaaga gcgacaaaga ttttgttatc ggctttattg ctcaaagaga catgggtgga     2760

agagatgaag gttacgattg gttgattatg acacccggtg tgggtttaga tgacaaggga     2820

gacgcattgg gtcaacagta tagaaccgtg gatgatgtgg tctctacagg atctgacatt     2880

attattgttg gaagaggact atttgcaaag ggaagggatg ctaaggtaga gggtgaacgt     2940

tacagaaaag caggctggga agcatatttg agaagatgcg gccagcaaaa ctaaaaaact     3000

gtattataag taaatgcatg tatactaaac tcacaaatta gagcttcaat ttaattatat     3060

cagttattac ccgggaatct cggtcgtaat gatttctata atgacgaaaa aaaaaaaatt     3120

ggaaagaaaa agcttcatgg cctttataaa aaggaactat ccaatacctc gccagaacca     3180

agtaacagta aggtccgccg gcgttggacg agcggcgaat ttcttatgat ttatgatttt     3240

tattattaaa taagttataa aaaaaataag tgtatacaaa ttttaaagtg actcttaggt     3300

tttaaaacga aaattcttat tcttgagtaa ctctttcctg taggtcaggt tgctttctca     3360

ggtatagcat gaggtcgctc ttattgacca cacctctacc ggcatgccga gcaaatgcct     3420

gcaaatcgct ccccatttca cccaattgta gatatgctaa ctccagcaat gagttgatga     3480

atctcggtgt gtattttatg tcctcagagg acaacacctg ttgtaatcgt tcttccacac     3540

ggatccacag cctagccttc agttgggctc tatcttcatc gtcattcatt gcatctacta     3600

gccccttacc tgagcttcaa gacgttatat cgcttttatg tatcatgatc ttatcttgag     3660

atatgaatac ataaatatat ttactcaagt gtatacgtgc atgctttttt tacggcagca     3720

tttttttttc aactctgatc gcccctttac tgctccctcc gcccaaattc cattgcagtt     3780

caaatgtata ctgaaaaaaa ccccattgct attgttaaac agtgaactct ctttttgccc     3840

aataataaca ttataacaag taactaccag caccataaca ccgtgtccta tcctggtatt     3900

aattactact tgaagaacga ctacatcgct ttttgcaact acaattagaa cgctccgccc     3960

cttccttttg acgtcgtata agtgtagttg gattgcaatt gcatagatac aggaggcggt     4020

ttaaacgcgt ggccgtgccg tc                                              4042


<210>  16
<211>  102
<212>  PRT
<213>  Saccharomyces cerevisiae

<400>  16

Met Pro Pro Lys Lys Phe Lys Asp Leu Asn Ser Phe Leu Asp Asp Gln 
1               5                   10                  15      


Pro Lys Asp Pro Asn Ile Val Ala Ser Pro Phe Gly Gly Tyr Phe Phe 
            20                  25                  30          


Lys Asn Pro Ala Ala Asp Ala Gly Ser Asn Asn Ala Ser Lys Lys Ser 
        35                  40                  45              


Ser Tyr Gln Gln Gln Arg Asn Trp Lys Gln Gln Gly Gly Asn Tyr Gln 
    50                  55                  60                  


Gln Gly Gly Tyr Gln Ser Tyr Asn Ser Asn Tyr Asn Asn Tyr Asn Asn 
65                  70                  75                  80  


Tyr Asn Asn Tyr Asn Asn Tyr Asn Asn Tyr Asn Asn Tyr Asn Lys Phe 
                85                  90                  95      


His Gly Gln Gly Tyr Gln 
            100         


<210>  17
<211>  300
<212>  DNA
<213>  Homo sapiens

<400>  17
atgcctccaa agaagtttaa ggatctaaac tcttccttga cgaccaacca aaggacccaa       60

atctagtcgc ttctcccttc cggtggttat tttaaaaacc ctgctgctga tgccggtagt      120

aataacgctt ccaaaaaaag tagctaccaa caacagcgta attggaaaca ggggggcaac      180

taccaacaag gtggttacca atcgtataac agtaattaca acaattacaa caactacaac      240

aactacaaca attataacaa ctacaataac tataataaat acaatggcca gggctatcaa      300


<210>  18
<211>  300
<212>  DNA
<213>  Homo sapiens

<400>  18
atgcctccaa agaagtttaa ggatctaaac tctttccttg acgaccaacc aaaggaccca       60

aatctagtcg cttctccctt cggtggttat tttaaaaacc ctgctgctga tgccggtagt      120

aataacgctt ccaaaaaaag tagctaccaa caacagcgta attggaaaca ggggggcaac      180

taccaacaag gtggttacca atcgtataac agtaattaca acaattacaa caactacaac      240

aactacaaca attataacaa ctacaataac tataataaat acaatggcca gggctatcaa      300


