What is the acceptable range when checking the primers using Primer-BLAST
Hello, the maximum theoretical self complementarity score (globally or only at 3' end) is the length of the primer itself. The 3'-self complementarity is useful to predicting primer-dimers, while the self-complementarity score is useful to predict possible secondary structures between the primer itself or even primer pairs. As described by PRIMER3 manual, there is an option to specify the maximum tolerated self complemntarity score: PRIMER_MAX_SELF_ANY. The default value is 8.00.
The scores are output from PRIMER3 algorithm (which powers the NCBI's PrimerBLAST website as well) and is described in great detail at
http://primer3.sourceforge.net/primer3_manual.htm#PRIMER_MAX_SELF_ANY
Hope this info will help you.
Good luck!
Hello, the maximum theoretical self complementarity score (globally or only at 3' end) is the length of the primer itself. The 3'-self complementarity is useful to predicting primer-dimers, while the self-complementarity score is useful to predict possible secondary structures between the primer itself or even primer pairs. As described by PRIMER3 manual, there is an option to specify the maximum tolerated self complemntarity score: PRIMER_MAX_SELF_ANY. The default value is 8.00.
The scores are output from PRIMER3 algorithm (which powers the NCBI's PrimerBLAST website as well) and is described in great detail at
http://primer3.sourceforge.net/primer3_manual.htm#PRIMER_MAX_SELF_ANY
Hope this info will help you.
Good luck!
Thank you very much! I have a question. Regarding to your explanation, higher scores for self-complementarity shows less possibility of primer-dimer formation?
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