Team:Cambridge/Oligos

From 2010.igem.org

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(Notes on alterations to the SLOCK pHK724 clone)
 
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>BBa_G00101 Part-only sequence (20 bp)
>BBa_G00101 Part-only sequence (20 bp)
attaccgcctttgagtgagc
attaccgcctttgagtgagc
 +
 +
===The Vibrio Lux operon===
 +
[http://www.ncbi.nlm.nih.gov/nuccore/5726577 AF170104-1]
 +
 +
===The Phosphoreum Lux operon===
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[http://www.ncbi.nlm.nih.gov/nuccore/166797857 DQ988873]
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 +
[http://partsregistry.org/cgi/partsdb/dna.cgi?part_name=BBa%20I0500 Pbad Promoter Part]
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[http://www.fasebj.org/cgi/reprint/7/11/1016 Phosphoreum LuxL gene upstream of LuxC]
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[[Team:Cambridge/PhosphoreumOligos | The phosphoreum oligos we ordered]]
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 +
===Notes on alterations to the SLOCK pHK724 clone===
 +
*The sequence which SLOCK sent us is just the sequence which is found on [http://www.ncbi.nlm.nih.gov/nuccore/AF170104.1 NCBI] (found by sequence alignment of the two sequences)
 +
*We do not know exactly what is in the plasmid, maybe some information can be found in the references [[Team:Cambridge/References/ProjectBioluminescence/Luciferase#Plasmid_experiment | here]]
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*From the annotated start of the lux ICDABEG operon from NCBI there are no restriction sites in conflict with the BioBrick standards.
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*Editing ideas:
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**Remove I and G regions from the operon (are these useful?)
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**Attach suffices and prefixes
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**Is this sufficient to then put into a BioBrick? what Chassis should we use?
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*A good [http://www.bio.cmu.edu/courses/03441/TermPapers/97TermPapers/lux/operon.html summary] of the lux operon with quality references
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*How to design a [http://partsregistry.org/Ribosome_Binding_Sites/Design RBS]
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[[Team:Cambridge/OligoOrderVibrio13.08.10 | Oligo Order for Vibrio Fischeri on 13.08.10]]
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[[Team:Cambridge/OligoOrderVibrio17.08.10 | Oligo Order for Vibrio Fischeri on 17.08.12]]
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===Firefly Oligos to be ordered===
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*[[Team:Cambridge/mutagenesisprimers17.08.10 | Mutagenesis Oligos to be ordered before DNA 2.0 comes through]]
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*[[Team:Cambridge/biobrickingoligosfirefly | Oligos to biobrick our DNA 2.0 order]]
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===Our first attempts at oligo design (a little excessive)===
 +
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[[Team:Cambridge/Biobrickingluxoperon | Oligos to BioBrick the whole lux operon]] (never ordered as too expensive)
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[[Team:Cambridge/luxICDABEoperon | luxICDABE operon sequence]] from NCBI
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[[Team:Cambridge/LuxR | LuxR sequence]] from NCBI
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==Thioesterase==
 +
 +
ygcB gene from E. Coli K12 to over-express thioesterase:
 +
GTGAATACAACGCTGTTTCGATGGCCGGTTCGCGTCTACTATGAAGATACCGATGCCGGTGGTGTGGTGTACCACGCCAGTTACGTCGCTTTTTATGAAA
 +
GAGCACGCACAGAGATGCTGCGTCATCATCACTTCAGTCAGCAGGCGCTGATGGCTGAACGCGTTGCCTTTGTGGTACGTAAAATGACGGTGGAATATTA
 +
CGCACCTGCGCGGCTCGACGATATGCTCGAAATACAGACTGAAATAACATCAATGCGTGGCACCTCTTTGGTTTTCACGCAACGTATTGTCAACGCCGAG
 +
AATACTTTGCTGAATGAAGCAGAGGTTCTGGTTGTTTGCGTTGACCCACTCAAAATGAAGCCTCGTGCGCTTCCCAAGTCTATTGTCGCGGAGTTTAAGC
 +
AGTGA
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 +
Forward Primer:
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 +
gaattcgcggccgcttctagaGTGAATACAACGCTGTTTC
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 +
Complement (for Gibson):
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 +
GAAACAGCGTTGTATTCACtctagaagcggccgcgaattc
 +
 +
Bacward primer:
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 +
ctgcagcggccgctactagtaTCACTGCTTAAACTCCG
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Complement:
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CGGAGTTTAAGCAGTGAtactagtagcggccgctgcag
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-
===luxICDABE operon===
 
-
gtcgaccttcctggttcagagcctcatatccatattacgaccacttcaat
 
-
gggcgatcaaaaagtacattacatgattttttgcccaacagaaaaagcct
 
-
ctcatttagagcagcttattcgtcaagatttcatggaaatgtatgagatc
 
-
aattttccacaaaaaacagagtaacaaagagaaaaacctataggtataaa
 
-
gctttacttacgtacttaatttttaaagtatgggcaatcaattgctcctg
 
-
ttaaaattgctttagaaatactttggcagcggtttgttgtattgagtttc
 
-
atttgcgcattggttaaatggaaagtgacagtacgctcactgcagcctaa
 
-
tatttttgaaatatcccaagagctttttccttcgcatgcccacgctaaac
 
-
attctttttctcttttggttaaatcgttgtttgatttattatttgctata
 
-
tttatttttcgataattatcaactagagaaggaacaattaatggtatgtt
 
-
catacacgcatgtaaaaataaactatctatatagttgtctttttctgaat
 
-
gtgcaaaactaagcattccgaagccattgttagccgtatgaatagggaaa
 
-
ctaaacccagtgataagacctgatgttttcgcttctttaattacatttgg
 
-
agattttttatttacagcattgttttcaaatatattccaattaattggtg
 
-
aatgattggagttagaataatctactataggatcatattttattaaatta
 
-
gcgtcatcataatattgcctccattttttagggtaattatctagaattga
 
-
aatatcagatttaaccatagaatgaggataaatgatcgcgagtaaataat
 
-
attcacaatgtaccattttagtcatatcagataagcattgattaatatca
 
-
ttattgcttctacaagctttaattttattaattattctgtatgtgtcgtc
 
-
ggcatttatgtttttcatacccatctctttatccttacctattgtttgtc
 
-
gcaagttttgcgtgttatatatcattaaaacggtaatggattgacatttg
 
-
attctaataaattggatttttgtcacactattgtatcgctgggaatacaa
 
-
ttacttaacataagcacctgtaggatcgtacaggtttacgcaagaaaatg
 
-
gtttgttatagtcgaataaacgcaagggaggttggtatgactataatgat
 
-
aaaaaaatcggattttttggcaattccatcggaggagtataaaggtattc
 
-
taagtcttcgttatcaagtgtttaagcaaagacttgagtgggacttagtt
 
-
gtagaaaataaccttgaatcagatgagtatgataactcaaatgcagaata
 
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tatttatgcttgtgatgatactgaaaatgtaagtggatgctggcgtttat
 
-
tacctacaacaggtgattatatgctgaaaagtgtttttcctgaattgctt
 
-
ggtcaacagagtgctcccaaagatcctaatatagtcgaattaagtcgttt
 
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tgctgtaggtaaaaatagctcaaagataaataactctgctagtgaaatta
 
-
caatgaaactatttgaagctatatataaacacgctgttagtcaaggtatt
 
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acagaatatgtaacagtaacatcaacagcaatagagcgatttttaaagcg
 
-
tattaaagttccttgtcatcgtattggagacaaagaaattcatgtattag
 
-
gtgatactaaatcggttgtattgtctatgcctattaatgaacagtttaaa
 
-
aaagcagtcttaaattaatgttgttaaatcattaatttattttaaatact
 
-
aagtatattatagggaaaataatgaataaatgtattccaatgataattaa
 
-
tggaatgattcaagattttgataattatgcatataaagaagttaaactaa
 
-
ataatgataatagagtaaaattatctgtcattactgaaagttcagtttca
 
-
aaaacattaaatatcaaagatagaattaatctaaatttaaatcagattgt
 
-
gaattttttatataccgttggtcaacgatggaaaagtgaagaatataatc
 
-
ggcgacgaacctatatccgtgagttaaaaacatatcttggttattctgat
 
-
gaaatggcaagattagaagcgaattggattgcaatgttattgtgctctaa
 
-
aagtgctttgtatgacattgttaattatgatttgggctctatacacgtat
 
-
tagatgaatggcttccacgtggtgattgctatgttaaagcacaaccgaaa
 
-
ggtgtttctgttcacttgttagctggtaatgttccattatcaggagtgac
 
-
atctattttgcgtgctattttaacaaaaaatgagtgcattattaaaactt
 
-
cgtcttcagatccttttactgcaaacgctttagtttccagttttattgat
 
-
gttaatgcagaccatccaataaccaaatcaatgtctgttatgtattggcc
 
-
gcatgatgaagatatgactctatctcaaagaataatgaatcatgccgacg
 
-
tggttattgcttggggtggagacgaggcgattaaatgggcggtaaaatat
 
-
tcaccaccgcatgtcgatattctgaaatttggaccaaagaaaagcttaag
 
-
tattattgaagctcctaaagatatagaagccgcagcaatgggggttgctc
 
-
atgatatttgtttctatgaccagcaagcctgcttctctactcaagacgtt
 
-
tattatataggagataatttacctttatttttaaatgaacttgaaaaaca
 
-
gctagatcgatacgcgaaaattttaccaaaaggttcaaatagttttgatg
 
-
aaaaagcggcgtttactcttactgaaaaagaaagtctatttgctggatat
 
-
gaagtgagaaagggagataagcaagcttggttaatagtcgtatcacctac
 
-
aaatagctttggaaatcaaccgctatcacgaagtgtgtatgttcatcaag
 
-
tatctgatattaaagagataattccttttgttaataaaaatagaacacaa
 
-
actgtttctatttatccttgggaagcgtcattaaaatatcgagataaatt
 
-
agcaagaagtggagttgaaagaattgttgaatcaggcatgaataatattt
 
-
tcagagttggaggggctcatgattcattatctcctctccagtacctagtt
 
-
aggtttgtatcgcatgagagaccatttaattatacgacaaaagatgttgc
 
-
ggttgaaatcgaacaaacacgttacttagaggaagataagtttttagttt
 
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ttgtcccatagttaaaggaaattatatgaaagatgaaagtgcttttttta
 
-
cgattgatcacatcatcaagcttgataatggtcagtctatccgagtttgg
 
-
gaaacactccctaaaaagaacgtaccagagaaaaaacatacaatacttat
 
-
tgcttcgggttttgctagaagaatggatcattttgcaggtcttgctgagt
 
-
atttatctactaacggttttcatgtcattcgctacgattctttgcatcat
 
-
gttggattaagcagtggatgtataaatgaatttacgatgtcgattggaaa
 
-
aaatagcctgcttacagtcgtagattggcttacagatcatggtgtcgaac
 
-
gaatagggctgattgctgctagtttgtcagcgagaatcgcctatgaggta
 
-
gtaaataaaattaaattatcatttttaattacggccgtaggtgtcgttaa
 
-
tcttagagatacattagaaaaagcattggagtatgactatttgcaattac
 
-
ctatttcagagttaccagaagatcttgactttgaaggtcataatttagga
 
-
tcggaggtctttgttacagattgctttaaacataattgggacacgttaga
 
-
ctcgacacttaatagtgttaaaggattagcgattccatttattgctttta
 
-
ctgcaaacgatgatagttgggtaaagcaaagtgaagttatagagctcatt
 
-
gatagcattgaatctagtaattgtaagctctattcgctaattggaagttc
 
-
acatgatcttggggaaaatttggttgtattaagaaatttttatcaatcag
 
-
tgacgaaggcagccttagcattagatgatggtttattggatttagagata
 
-
gacattattgaacctcgatttgaggacgttacaagtattactgttaagga
 
-
gcgtagattaaaaaatgaaattgaaaatgaattattagaattggcttaaa
 
-
taaacagaatcaccaaaaaggaatagagtatgaagtttggaaatatttgt
 
-
ttttcgtatcaaccaccaggtgaaactcataagcaagtaatggatcgctt
 
-
tgttcggcttggtatcgcctcagaagaggtagggtttgatacatattgga
 
-
ccttagaacatcattttacagagtttggtcttacgggaaatttatttgtt
 
-
gctgcggctaacctgttaggaagaactaaaacattaaatgttggcactat
 
-
gggggttgttattccgacagcacacccagttcgacagttagaagacgttt
 
-
tattattagatcaaatgtcgaaaggtcgttttaattttggaaccgttcga
 
-
gggctataccataaagattttcgagtatttggtgttgatatggaagagtc
 
-
tcgagcaattactcaaaatttctaccagatgataatggaaagcttacaga
 
-
caggaaccattagctctgatagtgattacattcaatttcctaaggttgat
 
-
gtatatcccaaagtgtactcaaaaaatgtaccaacctgtatgactgctga
 
-
gtccgcaagtacgacagaatggctagcaatacaagggctaccaatggttc
 
-
ttagttggattattggtactaatgaaaaaaaagcacagatggaactctat
 
-
aatgaaattgcgacagaatatggtcatgatatatctaaaatagatcattg
 
-
tatgacttatatttgttctgttgatgatgatgcacaaaaggcgcaagatg
 
-
tttgtcgggagtttctgaaaaattggtatgactcatatgtaaatgcgacc
 
-
aatatctttaatgatagcaatcaaactcgtggttatgattatcataaagg
 
-
tcaatggcgtgattttgttttacaaggacatacaaacaccaatcgacgtg
 
-
ttgattatagcaatggtattaaccctgtaggcactcctgagcagtgtatt
 
-
gaaatcattcaacgtgatattgatgcaacgggtattacaaacattacatg
 
-
cggatttgaagctaatggaactgaagatgaaataattgcttccatgcgac
 
-
gctttatgacacaagtcgctcctttcttaaaagaacctaaataaattact
 
-
tatttgatactagagataataaggaacaagttatgaaatttggattattt
 
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tttctaaactttcagaaagatggaataacatctgaagaaacgttggataa
 
-
tatggtaaagactgtcacgttaattgattcaactaaatatcattttaata
 
-
ctgcctttgttaatgaacatcacttttcaaaaaatggtattgttggagca
 
-
cctattaccgcagctggttttttattagggttaacaaataaattacatat
 
-
tggttcattaaatcaagtaattaccacccatcaccctgtacgtgtagcag
 
-
aagaagccagtttattagatcaaatgtcagagggacgcttcattcttggt
 
-
tttagtgactgcgaaagtgatttcgaaatggaattttttagacgtcatat
 
-
ctcatcaaggcaacaacaatttgaagcatgctatgaaataattaatgacg
 
-
cattaactacaggttattgtcatccccaaaacgacttttatgattttcca
 
-
aaggtttcaattaatccacactgttacagtgagaatggacctaagcaata
 
-
tgtatccgctacatcaaaagaagtcgtcatgtgggcagcgaaaaaggcac
 
-
tgcctttaacatttaagtgggaggataatttagaaaccaaagaacgctat
 
-
gcaattctatataataaaacagcacaacaatatggtattgatatttcgga
 
-
tgttgatcatcaattaactgtaattgcgaacttaaatgctgatagaagta
 
-
cggctcaagaagaagtgagagaatacttaaaagactatatcactgaaact
 
-
taccctcaaatggacagagatgaaaaaattaactgcattattgaagagaa
 
-
tgcagttgggtctcatgatgactattatgaatcgacaaaattagcagtgg
 
-
aaaaaacagggtctaaaaatattttattatcctttgaatcaatgtccgat
 
-
attaaagatgtaaaagatattattgatatgttgaaccaaaaaatcgaaat
 
-
gaatttaccataataaaattaaaggcaatttctatattagattgcctttt
 
-
taaatttctgttgatattaggtattactggagagggtatgactgtccata
 
-
ctgaatataaaagaaatcaaatcattgctagttcagaaattgatgatctt
 
-
atctttatgacgaaaccacaagagtggtcatttgaagagcaaaaagaaat
 
-
acgggataaattagttcgtgaggctttttattttcactacaatagaaatg
 
-
aagaatatagaaattattgtatcaatcagcatgtgagtgataatttacac
 
-
actattgatgaaatacccgtgtttccaacatctgtttttaaatataagaa
 
-
attacatactgtcacagccgaggacattgaaaattggtatacaagtagtg
 
-
gaactcgtggagtaaaaagtcatattgcacgtgatcgtcttagcattgaa
 
-
cgcttgcttggttctgtcaacttcggaatgaaatacgttggagattggtt
 
-
tgagcatcaaatggaattgataaatttaggaccagatagattcaatacaa
 
-
ataatatttggtttaaatatgtcatgagtttggtcgagttactttatccg
 
-
actgaatttacagttgataatgacaaaatagattttgaaaaaacagtaaa
 
-
acatctatttagaattaagaatagtaaaaaagacatttgcttaattgggc
 
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caccattttttgtgtatcttttgtgccaatatatgaaagaaaacaatatt
 
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gaatttaaaggaggagatagagtacatattattactggtggaggatggaa
 
-
atctaatcagaatgactctttagatcgtgctgattttaatcaattattaa
 
-
tggatactttccaactcgacaagattaatcaaattagagatacctttaat
 
-
caagttgagcttaatacttgtttttttgaagatgaatttcaaagaaaaca
 
-
tgttccaccgtgggtatatgctcgggctcttgatcctgaaaccttgaaac
 
-
ccgtagcagatggtgagatcgggttgttaagttatatggacgcctcatca
 
-
actgcttaccctgcttttattgttactgatgatatcggtattgtaaaaga
 
-
aattagagaaccagatccttacccaggggtaactgttgagattgttcggc
 
-
gcttaaatacacgtgcgcaaaaaggatgcgcgctctctatggctaatgtc
 
-
atacaaaagaatatcaaggattaagttatgattgttgatggtagagtttc
 
-
aaaaatagtattagcgtcaataagaaataatatatataaggtatttatta
 
-
ctgtaaattcaccaataaagttcatcgctggacaatttgtaatggtcacg
 
-
attaatgggaaaaaatgccctttttcaattgcgaattgcccgacaaaaaa
 
-
ttacgaaatagaattgcatattggtagttcgaatagagactgctcattgg
 
-
atattatcgaatattttgtcgatgctcttgttgaggaagtcgcaattgag
 
-
ttagatgctccccatggaaacgcttggttacggtctgaaagtaataaccc
 
-
attgctattaattgcgggaggtacaggtttatcatatataaatagcattc
 
-
taacaaattgcttaaataggaatatacctcaagatatttatctttactgg
 
-
ggagtaaaagacagttctcttttgtatgaagatgaagagttactaaactt
 
-
atcactaaacaacaaaaactttcattatattcctgttattgaagataaaa
 
-
gtgaagaatggatagggagaaaaggcactgttcttgatgctgtcatggaa
 
-
gattttactgatcttacttattttgatatttatgtttgtggacccttcat
 
-
gatggctaaaacagcaaaagaaaaattaattgaagagaaaaaagcaaagt
 
-
cagaacagatgtttgccgatgcttttgcatacgtataaagagaatataaa
 
-
aagccagattattaatccggcttttttattatttcaatgtgtccaagggt
 
-
aaccaagttacttcaactcccgcctgagagaacatatcttggctcacttg
 
-
aattttttcaccccaacgagataagaagtcttcagtttgttcagggcaat
 
-
atacttttgatattcctgtttggatgatttttgctgcgcagtttggacaa
 
-
gggaagtgagtaacccaaatatcgcaaccttctaaatcacgcttggcaaa
 
-
taaaatggcattttcttcagcatgaagtgtttttaaatatttaatttcac
 
-
gttcatctgtatctgcactgtctgatacaccatgtgggtagccattaaat
 
-
ccaacagaaacaatacggttatgcttggtgattactgcaccaacttgagt
 
-
cgac
 
-
===luxR===
 
-
ATGAAAAACATAAATGCCGACGACACATACAGAATAATTAATAAAATTAAAGCTTGTAGAAGCAATAATGATATAATCAATGCTTATCTGATATGACTAAAATGGTACATTGTGAATATTATTTATTCGCGATCATTTATCCTCATTCTATGGTTAAATCTGATATTTCAATCTAGATAATTACCCTAAAAAATGGAGGCAATATTATGATGACGCTAATTTAATAAAATATGATCCTATAGTAGATTATTCTAACTCCAATCATTCACCAATTAATTGGAATATATTTGAAAACAATGCTGTAAATAAAAAATCTCCAAATGTAATTAAGAAGCGAAAACATCAGGTCTTATCACTGGGTTTAGTTTCCCTATTCATACGGCTAACAATGCCTTCGGAATGCTTAGTTTTGCACATTCAGAAAAAGACAACTATATAGATAGTTTATTTTTACATGCGTGTATGAACATACCATTAATTGTTCCTTCTCTAGTGTATAATTATCGAAAAATAAATATAGCAAATAATAAATCAAACAACGATTTAACCAAAAGAGAAAAAGAATGTTTAGCGTGGGCATGCGAAGGAAAAGGCTCTTGGGATATTTCAAAAATATTAGGCTGCAGTGAGCGTACTGTCACTTTCCATTTAACCAATGCGCAAATGAAACTCAATACACCAAACCGCTGCCAAAGTATTTCTAAAGCAATTTTAACAGGAGCAATTGATTGCCCATACTTTAAAAATTAA
 
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Latest revision as of 10:27, 18 August 2010