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Among the six bacteria screened, a partial operon was found only in E. coli, where the first three coding sequences had strong homologues, but the fourth gene encoding for the outer membrane efflux protein exhibited a homologue at a more distant locus.
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Moreover, more distant loci would have a higher probability of homologous recombination, favoring the occurrence of large deletions.
LOD threshold for map calculation was set as 3.0 except for LG2, LG8 and LG4, in which the LOD scores of 2.0, 2.0 and as low as 0.1 were used respectively, in order to allow the inclusion of more distant loci.
Alternatively, even if similar selection goals might have driven to fixation the same variant in all the breeds compared, different SNP alleles might still be associated to it at more distant loci.
Indeed, transcripts connecting exons of nearby loci and more distant loci separated by other genes on both strands were commonly found [ 1- 3].
All recombination rates up to r = 0.4999 within a linkage group were taken into account to allow the inclusion of more distant loci that are not closely linked, therefore also the LOD threshold for map calculation was set to the minimum of 0.0001.
PNFs were previously found to have a strong concordance among NF1 MZ twins, yet while concordance was lower in more distant relatives, loci other than NF1 were thought to modulate this feature [ 9, 10].
However, these previous studies detected positive selection acting during the more distant evolutionary history of this locus to produce a diverse cluster of paralogous genes apparently established early in mammalian evolution [ 9, 10].
Note that locus order is ignored by the Dirichlet process: it does not incorporate the expectation that adjacent loci belong to the same cluster more often than distant loci.
A user may assign specific genetic relations for these pairs such as siblings (which share 50% of common genetic material IBD), second order of genetic relations (e.g., aunt/niece with 25% of common genetic material IBD), third order of relations (cousins with 12.5% of common IBD loci), or other more distant relatives with any user-defined percentage for common genetic loci.
The hCD2 loci were more distant in the hCD2+ than the hCD2- cells (comparisons of the distributions using Kolmogorov-Smirnov test, P < 0.001).
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com