how do I design a primer to target different loci of the gene?
For gDNA primers, you specify the exact genomic location in base pairs - ie. 2L:2,000,000
Is it possible to specify the exon or intergenic region when designing the primer?
for gDNA primers, yes, for cDNA primers, they will target exon-exon junctions
How can I check the primer's dimerisation probality if I have designed several primers?
Primer 3 will do this internally within AgamPrimer. If you want to see dimerisation results, you have to use the long AgamPrimer notebook, and look at the 'primer_dict' otherwise i recommend tools on IDT website
how can I specify the primers binding regions for example exon 1 to exon 4 with a single pair primer?
you cant but you can play around with the amplicon preferred size and target until it does so
In one of the exercises, SNPs were found only on the probe sequence, could this affect the efficiency of the qpcr?
It depends where in the probe and what kind of assay you are doing. you havent mentioned?
how do I design a primer to target different loci of the gene? For gDNA primers, you specify the exact genomic location in base pairs - ie. 2L:2,000,000 Is it possible to specify the exon or intergenic region when designing the primer? for gDNA primers, yes, for cDNA primers, they will target exon-exon junctions How can I check the primer's dimerisation probality if I have designed several primers? Primer 3 will do this internally within AgamPrimer. If you want to see dimerisation results, you have to use the long AgamPrimer notebook, and look at the 'primer_dict' otherwise i recommend tools on IDT website how can I specify the primers binding regions for example exon 1 to exon 4 with a single pair primer? you cant but you can play around with the amplicon preferred size and target until it does so In one of the exercises, SNPs were found only on the probe sequence, could this affect the efficiency of the qpcr? It depends where in the probe and what kind of assay you are doing. you havent mentioned?