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One specific primer, LbLMA1-rev, was designed by analysing similarities between the nucleotide sequence of the spacer between the 16S and 23S rRNA genes in a number of Lactobacillus strains.
Overall there was a good correlation between the nucleotide sequence and physico-chemical and geometrical DNA properties of the aligned σ promoters.
To further ascertain the degree to which nucleotide differences affect the accuracy of the exon intron structure predictions generated by interspecies mapping, we examined the relationship between the nucleotide sequence identity and the SP of all introns in our representative CDSs (Fig. 4).
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Moreover, homology also exists between the nucleotide sequences that separate one gene from another.
The relationship between the nucleotide sequences of genes and the amino-acid sequences of proteins is determined by the rules of translation, known collectively as the genetic code.
Evolutionary distances between the nucleotide sequences were calculated by Kimura's two parameter method [ 23].
The cost of a unit mutation is proportional to the Hamming/edit distance between the nucleotide sequences of the units.
The difference between two melting points is supposed to result from the difference between the nucleotide sequences of the respective two fragments.
An alignment of the 404-bp region flanked by primers Tox-8 and Tox-5 showed complete homology between the nucleotide sequences among the investigated strains.
The completion and regulation of splicing leans on the complicated biochemical reactions between the nucleotide sequences (cis-acting elements) and different proteins binding to them (trans-acting elements).
The identity between the nucleotide sequences was calculated by using the program MegAlign (DNAstar package version 5.03; Lasergene, DNAstar Inc., Madison, WI, USA).
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