Talk:20.109(S14):Diagnostic primer design (Day2)

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(Specificity)
(Sensitivity)
Line 11: Line 11:
|Is bp # for VC or EH? Which gene?
|Is bp # for VC or EH? Which gene?
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|-
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|Red
+
|Red (Final)
| CAC CAG GTT GAT ACT GCC TGA C
| CAC CAG GTT GAT ACT GCC TGA C
| CCT ATC CCG AAC CAA ACC CTG
| CCT ATC CCG AAC CAA ACC CTG

Revision as of 17:12, 17 February 2014

Contents

T/R Section

Sensitivity

Team color Forward (F) primer Reverse (R) primer Target site (e.g. bp 60), F Target side (e.g., bp 300), R Is bp # for VC or EH? Which gene?
Red (Final) CAC CAG GTT GAT ACT GCC TGA C CCT ATC CCG AAC CAA ACC CTG bp 1 bp 260 EH, SSU rRNA
Green ACC AGG TTG ATT CTG CCT GAC TGC CAT CCT TGG ACG TAG TAG bp 2/bp 1 bp 295/bp 257 EH/VC SSU rRNA
Pink ACC AGG TTG ATT CTG CCT GAC TCT CTC ACG CTC CCT CTC C bp1/bp2 bp252/bp290 EH/VC SSU rRna


Specificity

Team Color Forward primer Reverse primer Target site (e.g. bp 60), F Target side (e.g., bp 300), R Is bp # for VC or EH? Which gene?
Yellow CCAGGTTGATTCTGCCTGACG CCGGAGAGGGAGCCTGAG bp 2 (VC) / bp 3 (EH) bp 250 (VC) / bp 288 (EH) VC/EH, SSU rRNA
Blue (FINAL) GATTCTGCCTGACGTAGATGC CTGCTGGCACCAAACTTGC 10 bp 408 bp E. hellem (AF118143)
Orange CACCAGGTTGATTCTGCCTGAC GCAAGTCGGGTGCCAGCAGC 1bp(EH)/1bp(VC) 427bp(EH)/386bp(VC) EH/VC SSU rRNA


W/F Section

Sensitivity

Team color Forward (F) primer Reverse (R) primer Target site (e.g. bp 60), F Target site (e.g., bp 300), R Is bp # for VC or EH? Which gene?
Pink ACC AGG TTG ATT CTG CTG ACG TTGCGAGCATACTATCCCCAG bp 1/2 bp 741/768 VC/EH SSU rRNA
Red ACC AGG TTG ATT CTG CCT GAC ATA TTA CCG CGG CTG CTG bp 1/2 bp 380/421 VC/EH small subunit rRNA
Orange CCA GGT TGA CTC TGC CTC ACG TCG CCT CTC CGG GAC CAA ACC CTG BP 2/3 BP222 VC/EH SSU rRNA
Yellow (FINAL) ACC AGG TTG ATT CTG CCT GAC CGT TGA GTC AAA TTA AGC CGC AC 2 859 EH (SSU rRNA Gene)


Specificity

Team color Forward (F) primer Reverse (R) primer Target site (e.g. bp 60), F Target site (e.g., bp 300), R Is bp # for VC or EH? Which gene?
White CAC CAG GTT GAT TCT GCC TGA C CGC TAC TAA ATC AGA CCG ACA CAT C 1 92 VC; SSU rRNA
Blue (final) CAC CAG GTT GAT TCT GCC TGA C CTG CTG GCA CCA GAC TTG C 1 426 for EH; 386 for VC Both. SSU rRNA
Silver CAC CAG GTT GAT TCT GCC TGA C TTC ACC ATA GAC ACT ACT GGA GC 1 441 EH
Purple GTCTGGCTGTGTAGATAACTACG CACTGTGAGACCTCGCATC 102 465 VC
Green agattgctcccacgtccaag caacgaccatgcaccactc 251 872 VC



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