Talk:20.109(S15):Diagnostic primer design (Day2): Difference between revisions

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Enter your primer sequences here:
Enter your primer sequences here:
The 'bp' column refers to where your primers start and end in the ClustalW alignment file. We need this information so we can double check the sequences before ordering. We don't want a typo to keep your experiment from working!


<center>
<center>
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! Forward primer name
! Forward primer name
! Forward primer sequence (5'-->3')
! Forward primer sequence (5'-->3')
! Bp
! Reverse primer name
! Reverse primer name
! Reverse primer sequence (5'-->3')
! Reverse primer sequence (5'-->3')
! Bp
|-
|-
| Red  
| Red  
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|
|
|
|
|
|
|-
| Orange FINAL
|Orange Avian Influenza A Matrix Forward
|CAGCGATTCAAGTGATCCTCTCG
|
|Orange Avian Influenza A Matrix Reverse
|GGTACTCTTCCCTCATAGACTCAGG
|[http://openwetware.org/wiki/Image:Primerlocations.png BP]
|-
|-
| Orange
| Yellow Final
|Yellow Avian Influenza Detection Primer Forward
|5’- GTTCTCTCTATCRTYCCRTCAGGC-3’
|
|Yellow Avian Influenza Detection Primer Reverse
|5’- CYTTAGTCAGAGGTGACARGATTGGT-3’
|[http://openwetware.org/images/9/9f/S14_M1D4_Yellow-AIV-detection-primers.png Primer Positions]
|-
| Green
|Green Team AIV Forward Primer
|GCAGCGATTCAAGTGATCCTC
|
|Green Team AIV Reverse Primer
|GRTACTCYTCCCTCATAGACTCAGG
|[[Image:Green team.jpg]]
|-
| Blue FINAL
|Superior Team Blue Influenza A Forward Primer
|GGATCAAGYGARCAGGCAGC
|
|Superior Team Blue Influenza A Reverse Primer
|GAATCGCTGCATCTGCACTCC
|[[Image: TeamBluePrimers.jpg]]
|-
| Pink
|
|
|
|
|
|
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|
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|-
|-
| Yellow
| Purple FINAL
|  
|Purple Infuenza diagnostic primer forward
|  
|GGT RCA GGC AAT GAG RAC AAT TGG
|  
|
|Purple influenza diagnostic reverse
|CTG CAT YTG CAC TCC CAT TCG
|http://openwetware.org/wiki/Image:MIT_20.109%28S15%29_purple_diag_primer_bind_locations.docx
|-
| White
|
|
|
|
|
|
|-
|-
|}
|}
</center>
</center>


<center>
{| border="1"
! Team (W/F)
! Team (W/F)
! Forward primer name
! Forward primer name
! Forward primer sequence (5'-->3')
! Forward primer sequence (5'-->3')
! Bp
! Reverse primer name
! Reverse primer name
! Reverse primer sequence (5'-->3')
! Reverse primer sequence (5'-->3')
! Bp
|-
| Red
| Red AIV Matrix Forward Primer
| GAACGGTGACTACRGARGTRG
| 21
| Red AIV Matrix Reverse Primer
| GCACCATTCTGTTYTCATGYCTG
| 23
|
|-
| Orange FINAL
| Or_20.109sp15_WF_AIV_Matrix_Fwd
| TACAAYAGRATGGGAACRGTGAC
| [http://openwetware.org/wiki/Image:Orange_primers.png 23]
| Or_20.109sp15_WF_AIV_Matrix_Rev
| TRTTTCRTGYCTGATTARTGGRTTGG
| [http://openwetware.org/wiki/Image:Orangeprimers2.png 26]
|-
| Yellow FINAL
|Yellow AIV Matrix Primer Forward
|GCAGCGATTCAAGTGATCCTC
|[http://openwetware.org/wiki/Image:Forward_Reverse_Primer_Spots.jpg 21]
|Yellow AIV Matrix Primer Reverse
|ACTCYTCCCTCATAGACTCAGG
|[http://openwetware.org/wiki/Image:Forward_Reverse_Primer_Spots.jpg 22]
|-
| Green FINAL
|CDLA_FP(Flu Detection)
|AGTGCARATGCAGCGATTCAAG
|
|CDLA_RP(Flu Detection)
|TACTCYTCCCTCATAGACTCAGGYAC
|
|-
| Blue
|Blue AIV Matrix Forward Primer
|5’-GGCTAAAGACAAGACCAATCCTG-3’
|23
|Blue AIV Matrix Reverse Primer
|5’—CCATTTAGGGCATTCTGGACAAAGC-3’
|[http://openwetware.org/wiki/Image:FinalPrimerDesignABRK.png 25 Image]
|-
| Pink
| Pink Avian Influenza A Matrix Forward Primer
| AAGCTAGACAGATGGTGCAG
|20
| Pink Avian Influenza A Matrix Reverse Primer
| AGGATCACTTGAATCGCTGC
| 20
|-
| Purple FINAL
| Purple AIV Forward
| CGTTCTCTCTATCRTYCCRTCAG
|[[http://openwetware.org/wiki/Image:S15_M1D2_WF_PM_Purple-ForwardPrimer.jpg  L=23, 3' @ 77]]
| Purple AIV Reverse
| TYCCYTTAGTCAGAGGTGACARG
|[[http://openwetware.org/wiki/Image:S15_M1D2_WF_PM_Purple-ReversePrimer.jpg  L=23, 3' @ 178]]
|-
| Platinum
|Pt Forward Primer
|AGTGCARATGCAGCGATTCAAG
|22
|Pt Reverse Primer
|TCATAGACTCAGGCACYCCTTC
|22
|-
|}
</center>

Latest revision as of 14:48, 20 February 2015

Enter your primer sequences here: The 'bp' column refers to where your primers start and end in the ClustalW alignment file. We need this information so we can double check the sequences before ordering. We don't want a typo to keep your experiment from working!

Team (T/R) Forward primer name Forward primer sequence (5'-->3') Bp Reverse primer name Reverse primer sequence (5'-->3') Bp
Red
Orange FINAL Orange Avian Influenza A Matrix Forward CAGCGATTCAAGTGATCCTCTCG Orange Avian Influenza A Matrix Reverse GGTACTCTTCCCTCATAGACTCAGG BP
Yellow Final Yellow Avian Influenza Detection Primer Forward 5’- GTTCTCTCTATCRTYCCRTCAGGC-3’ Yellow Avian Influenza Detection Primer Reverse 5’- CYTTAGTCAGAGGTGACARGATTGGT-3’ Primer Positions
Green Green Team AIV Forward Primer GCAGCGATTCAAGTGATCCTC Green Team AIV Reverse Primer GRTACTCYTCCCTCATAGACTCAGG
Blue FINAL Superior Team Blue Influenza A Forward Primer GGATCAAGYGARCAGGCAGC Superior Team Blue Influenza A Reverse Primer GAATCGCTGCATCTGCACTCC
Pink
Purple FINAL Purple Infuenza diagnostic primer forward GGT RCA GGC AAT GAG RAC AAT TGG Purple influenza diagnostic reverse CTG CAT YTG CAC TCC CAT TCG http://openwetware.org/wiki/Image:MIT_20.109%28S15%29_purple_diag_primer_bind_locations.docx
White



Team (W/F) Forward primer name Forward primer sequence (5'-->3') Bp Reverse primer name Reverse primer sequence (5'-->3') Bp
Red Red AIV Matrix Forward Primer GAACGGTGACTACRGARGTRG 21 Red AIV Matrix Reverse Primer GCACCATTCTGTTYTCATGYCTG 23
Orange FINAL Or_20.109sp15_WF_AIV_Matrix_Fwd TACAAYAGRATGGGAACRGTGAC 23 Or_20.109sp15_WF_AIV_Matrix_Rev TRTTTCRTGYCTGATTARTGGRTTGG 26
Yellow FINAL Yellow AIV Matrix Primer Forward GCAGCGATTCAAGTGATCCTC 21 Yellow AIV Matrix Primer Reverse ACTCYTCCCTCATAGACTCAGG 22
Green FINAL CDLA_FP(Flu Detection) AGTGCARATGCAGCGATTCAAG CDLA_RP(Flu Detection) TACTCYTCCCTCATAGACTCAGGYAC
Blue Blue AIV Matrix Forward Primer 5’-GGCTAAAGACAAGACCAATCCTG-3’ 23 Blue AIV Matrix Reverse Primer 5’—CCATTTAGGGCATTCTGGACAAAGC-3’ 25 Image
Pink Pink Avian Influenza A Matrix Forward Primer AAGCTAGACAGATGGTGCAG 20 Pink Avian Influenza A Matrix Reverse Primer AGGATCACTTGAATCGCTGC 20
Purple FINAL Purple AIV Forward CGTTCTCTCTATCRTYCCRTCAG [L=23, 3' @ 77] Purple AIV Reverse TYCCYTTAGTCAGAGGTGACARG [L=23, 3' @ 178]
Platinum Pt Forward Primer AGTGCARATGCAGCGATTCAAG 22 Pt Reverse Primer TCATAGACTCAGGCACYCCTTC 22
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