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Additionally, studies of species that are substantially diverged have more sequence differences and other possible sources of variation (alternative splicing, repetitive elements, duplications, etc).
Higher ERs lead to more sequence differences between taxa (and hence more variability), but also to greater averaging of rates within taxa (and hence less variability).
The average number of pHaps in a family was calculated to be 9. Potential gene and paralog sequences (pHaps) within a gene family are differentiated by one or more sequence differences termed locus defining sequence differences (LDSDs).
Moreover, SNP variation and divergence do not differ significantly between miRNAs occurring in introns versus intergenic locations, or, it is the intergenic miRNAs that show more sequence differences (supplementary fig. S7, Supplementary Material online).
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More specifically, sequence differences can result in differing affinities for associated signalling factors or even an association with isoform-specific factors, a possibility we explore in the following section on receptor interactions.
According to theoretical consideration regarding the mutation rate of influenza A viruses (14 ) and to practical experiences during outbreaks (4 ), if HPAIV had gone through a transmission chain consisting of several hosts, more extensive sequence differences would likely have resulted.
Evidence of relatively minor variation was small insertion/deletion events involving up to four CDSs, plus more scattered sequence differences, mostly single nucleotide polymorphisms (data not shown), presumably indicative of genetic drift.
To determine more comprehensively sequence differences and similarities in Rhizobiales (alpha proteobacteria) and Enterobacteriales (gamma proteobacteria), we selected five organisms from each: S. meliloti, A. tumefaciens, M. loti, B. melitensis and R. palustris for the first and E. coli, S. typhimurium, S. flexneri, Buchnera sp. and E. carotovora for the last.
Group A strains differed by no more than five sequence positions (one nonsynonymous substitution) in their rbcL genes, and the psbA/ rbcL spacer regions aligned well over their entire lengths, with no more than 11 sequence differences.
Genes coding for some secreted proteins (especially mucins) and proteases contribute more to the sequence differences than others, suggesting they are under selection and therefore may serve as good targets for the development of diagnostic tools and intervention measures.
Accordingly, we have undertaken the construction of a Hawaiian reference genome sequence that more completely reflects the sequence differences between the two isolates.
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