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Most primer nucleotide sequences were obtained from the literature and validated by PRIMER3.
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Since most primer pairs used in qPCR span an average of 50 non-overlapping nucleotides, a significant proportion of SNPs (17% in humans) may be predicted to fall within primers based on chance alone.
The actin primer nucleotide sequences were 5'-ATGTCGGCGACGCTAC-3' as forward primer and 5'-GCTATACTGATACGGAC-3' as reverse primer.
The most upstream nucleotide of primer F7 is arbitrarily designed +1.
Primers used for amplification of exons 10 14, which are known to be repeated on several other chromosomes (Sodha et al, 2000), were designed so that both primers for each primer pair had a base mismatch in the most 3′ nucleotide, compared with sequences from nonfunctional copies of CHEK2.
Based on these data, nested PCR primers using the diagnostic T̄ or Ā as the most 3′ nucleotide were designed for each species.
Polymerase chain reaction with confronting two-pair primers (PCR-CTPP) is an inexpensive, time-saving genotyping method that is applicable for most single nucleotide polymorphisms.
Consequently, BLASTN "hits" for each primer were permitted to differ from its sequence by at most 10 nucleotides in alignment length and by at most 10% in sequence identity.
In order to prevent 5′-to-3′ DNA degradation in extract, primers were synthetized with phosphorothioate bonds connecting the twelve most 5′ nucleotides.
The output of maxAlike can also be used for designing degenerate primers, where two or more nucleotides are allowed at one position, by choosing the most likely occurring nucleotides for this site.
The PCR products were purified using a QIAGEN MinElute PCR Purification Kit to remove unincorporated primers and nucleotides.
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