Talk:20.109(S14):Diagnostic primer design (Day2): Difference between revisions

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|Is bp # for VC or EH? Which gene?
|Is bp # for VC or EH? Which gene?
|-
|-
| Grey (Platinum) :)
|  
| CAT GCT TGC CAA CAC AG<br>Agi: PT so unchanged
|  
| GAA TGG TCT GGT TGC TTC<br>Agi: PT so unchanged
|  
| bp 9
|  
| bp 251
|  
| E. Hellem: polar tube protein gene
|  
|-
|-
|Green
|
|AGG TTG ATT CTG CCT GAC<br>Agi: fine
|
|CGG AAC CAA ACC CTG AT<br>Agi: '''C''' CGG '''T'''AC '''A'''AA ACC CT'''A''' AT<br>new G/C = 44.4%, new Tm = 55.8<br>added 1 extra base to increase Tm    
|     
|bp 5
|
|bp 236
|
|VC: SSU rRNA
|
|-
|-
|Pink
|
|ttctgcctgacgtagatg<br>Agi: fine
|
|cctctccggaaccaaac<br>Agi: CCT CTC CGG '''T'''AC '''A'''AA AC <br>new G/C = 52.9%, new Tm = 55.6
|
|bp 12
|
|bp 226
|
|VC
|
|-
|-
|Yellow
}
|CTGACGTGGATGCTATTC<br>Agi: '''c''' ctg acg t'''a'''g atg cta '''g'''tc<br>new G/C = 50%, new Tm = 56.4 - oops, 55.1<br>added one more "c" at 5' for Tm = 57.7
|CCGTCAACCGTCACTGTC<br>Agi: fine
|bp 18
|bp 199
|VC small subunit ribosomal RNA gene
|-
|}


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Revision as of 12:16, 11 February 2014

Yellow team - selectivity! Blue team-selectivity Orange team - selectivity! Red Team - sensitivity Green Team - sensitivty

Sensitivity

}

Specificity

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?
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?
Purple 5' GCG ATG ATT TAG TCT GGC 3'
Agi: fine 		5’ CAA TTT CCA ACG ACC ATG C 3’
Agi: fine 		bp 93, F bp 879, R VC, SSU rRNA
Red GGT TGA TTC TGC CTG ACG TGG
Agi:fine 		CCT TCG TCC TTC ATC ACC ACA A
Agi: CCT TCG TCC TTG ATC ACC GAA T (yours doesn't match any known sequence in last 4 bp -- do I have right region?)
new G/C = 50%, new Tm = 63.5 		bp 6, F bp 588, R VC, SSU RNA
Orange 5'cgt agt cat aga agg gca aag ag3'
Agi: fine 		5' ctc tct ctc tac ctg cta ttg ta 3'
Agi: fine 		441 1005 V. corneae TV4/TV5 SSU rRNA
Blue CCGCAATCAGGGACGAA
Agi: fine 		GTCAACGTCACTGTCTTGG
Agi: GTC AAC C GTC ACT GTC TTG G (insertion)
new G/C = 55%, new Tm = 61.8 		60 195 V. corneae TV4/TV5 SSU rRNA


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