Talk:20.109(S14):Diagnostic primer design (Day2): Difference between revisions
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| Line 11: | Line 11: | ||
|Is bp # for VC or EH? Which gene? | |Is bp # for VC or EH? Which gene? | ||
|- | |- | ||
|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 | ||
| Line 18: | Line 18: | ||
| EH, SSU rRNA | | EH, SSU rRNA | ||
|- | |- | ||
|Green | |Green (Final) | ||
| ACC AGG TTG ATT CTG CCT GAC | | ACC AGG TTG ATT CTG CCT GAC | ||
| TGC CAT CCT TGG ACG TAG TAG | | TGC CAT CCT TGG ACG TAG TAG | ||
| | | bp 2/bp 1 | ||
| bp | | bp 295/bp 257 | ||
| | | EH/VC SSU rRNA | ||
|- | |- | ||
|Pink | |Pink (final) | ||
|ACC AGG TTG ATT CTG CCT GAC | |ACC AGG TTG ATT CTG CCT GAC | ||
|TCT CTC ACG CTC CCT CTC C | |TCT CTC ACG CTC CCT CTC C | ||
| Line 46: | Line 46: | ||
|Is bp # for VC or EH? Which gene? | |Is bp # for VC or EH? Which gene? | ||
|- | |- | ||
| Yellow | | Yellow (FINAL) | ||
|CCAGGTTGATTCTGCCTGACG | |CCAGGTTGATTCTGCCTGACG | ||
| | |CGGAGAGGGAGCCTGAG | ||
|bp 2 (VC) / bp 3 (EH) | |bp 2 (VC) / bp 3 (EH) | ||
|bp 250 (VC) / bp 288 (EH) | |bp 250 (VC) / bp 288 (EH) | ||
|VC/EH, SSU rRNA | |VC/EH, SSU rRNA | ||
|- | |- | ||
|Blue | |Blue (FINAL) | ||
|GATTCTGCCTGACGTAGATGC | |GATTCTGCCTGACGTAGATGC | ||
|CTGCTGGCACCAAACTTGC | |CTGCTGGCACCAAACTTGC | ||
| Line 60: | Line 60: | ||
|E. hellem (AF118143) | |E. hellem (AF118143) | ||
|- | |- | ||
|Orange | |Orange (Final) | ||
| | |CACCAGGTTGATTCTGCCTGAC | ||
| | |GCA AGT CTG TTG CCA GCA (FINAL) | ||
| | |1bp(EH)/1bp(VC) | ||
| | |427bp(EH)/386bp(VC) | ||
| | |EH/VC SSU rRNA | ||
|- | |- | ||
|} | |} | ||
| Line 83: | Line 83: | ||
|Is bp # for VC or EH? Which gene? | |Is bp # for VC or EH? Which gene? | ||
|- | |- | ||
|Pink | |Pink (Final) | ||
|ACC AGG TTG ATT CTG | |ACC AGG TTG ATT CTG CCT GAC G | ||
|TTGCGAGCATACTATCCCCAG | |TTGCGAGCATACTATCCCCAG | ||
|bp 1/2 | |bp 1/2 | ||
| Line 90: | Line 90: | ||
|VC/EH SSU rRNA | |VC/EH SSU rRNA | ||
|- | |- | ||
|Red | |Red (Final) | ||
|ACC AGG TTG ATT CTG CCT GAC | |ACC AGG TTG ATT CTG CCT GAC | ||
|ATA TTA CCG CGG CTG CTG | |ATA TTA CCG CGG CTG CTG | ||
| Line 97: | Line 97: | ||
|VC/EH small subunit rRNA | |VC/EH small subunit rRNA | ||
|- | |- | ||
|Orange | |Orange FINAL | ||
| | | GTT GAT TCT GCC TGA CGT GG | ||
| | | CCT CTC CGG AAC AAA ACC CTG | ||
| BP | | BP 7/8 | ||
| | | BP222 | ||
| VC/EH SSU rRNA | | VC/EH SSU rRNA | ||
|- | |- | ||
|Yellow | |Yellow (FINAL) | ||
| | |ACC AGG TTG ATT CTG CCT GAC | ||
| | |CGT TGA GTC AAA TTA AGC CGC AC | ||
| | |2 | ||
| | |859 | ||
|EH | |EH (SSU rRNA Gene) | ||
|- | |- | ||
| | | | ||
| Line 132: | Line 132: | ||
|Is bp # for VC or EH? Which gene? | |Is bp # for VC or EH? Which gene? | ||
|- | |- | ||
|White | |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 | |Blue (final) | ||
| CAC CAG GTT GAT TCT GCC TGA C | | CAC CAG GTT GAT TCT GCC TGA C | ||
| CTG CTG GCA CCA GAC TTG C | | CTG CTG GCA CCA GAC TTG C | ||
| Line 146: | Line 147: | ||
|Both. SSU rRNA | |Both. SSU rRNA | ||
|- | |- | ||
|Silver | |Silver (Final) | ||
| CAC CAG GTT GAT TCT GCC TGA C | | CAC CAG GTT GAT TCT GCC TGA C | ||
| TTC ACC ATA GAC ACT ACT GGA GC | | TTC ACC ATA GAC ACT ACT GGA GC | ||
| Line 153: | Line 154: | ||
|EH | |EH | ||
|- | |- | ||
|Purple | |Purple (Final) | ||
|GTCTGGCTGTGTAGATAACTACG | |GTCTGGCTGTGTAGATAACTACG | ||
|CACTGTGAGACCTCGCATC | |CACTGTGAGACCTCGCATC | ||
| Line 160: | Line 161: | ||
| VC | | VC | ||
|- | |- | ||
|Green | |Green (Final) | ||
| | |GAG AGA TGC GAG GTC TCA CAG | ||
| | |CCA CTG TGT CCA ATG AGC ATG | ||
| | |461 | ||
| | |685 (Ends) | ||
|VC | |VC | ||
|- | |- | ||
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 |
