Talk:20.109(S14):Diagnostic primer design (Day2): Difference between revisions
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|Orange FINAL | |Orange FINAL | ||
| | | GTT GAT TCT GCC TGA CGT GG | ||
| CCT CTC CGG | | CCT CTC CGG AAC AAA ACC CTG | ||
| BP | | BP 7/8 | ||
| BP222 | | BP222 | ||
| VC/EH SSU rRNA | | VC/EH SSU rRNA | ||
Latest revision as of 11:58, 21 February 2014
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 (Final) | 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 (final) | 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 (FINAL) | CCAGGTTGATTCTGCCTGACG | CGGAGAGGGAGCCTGAG | 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 (Final) | CACCAGGTTGATTCTGCCTGAC | GCA AGT CTG TTG CCA GCA (FINAL) | 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 (Final) | ACC AGG TTG ATT CTG CCT GAC G | TTGCGAGCATACTATCCCCAG | bp 1/2 | bp 741/768 | VC/EH SSU rRNA |
| Red (Final) | 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 FINAL | GTT GAT TCT GCC TGA CGT GG | CCT CTC CGG AAC AAA ACC CTG | BP 7/8 | 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 (final) | CAC CAG GTT GAT TCT GCC TGA C | CTA CAC AGC CAG ACT AAA TCA TCG 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 (Final) | CAC CAG GTT GAT TCT GCC TGA C | TTC ACC ATA GAC ACT ACT GGA GC | 1 | 441 | EH |
| Purple (Final) | GTCTGGCTGTGTAGATAACTACG | CACTGTGAGACCTCGCATC | 102 | 465 | VC |
| Green (Final) | GAG AGA TGC GAG GTC TCA CAG | CCA CTG TGT CCA ATG AGC ATG | 461 | 685 (Ends) | VC |
