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Concurrent variation within loci is extensive in the immune system, greatly reduced in both gene-based biological evolution and SCC evolution, and reduced even further in operant learning.
Bootstrapping was performed by resampling loci and sites within loci as described earlier.
Of these, 487 resided within loci of high-amplitude CNA (Table 4).
For each individual, candidate RAD loci were identified and candidate RAD alleles called within loci as follows.
However, not all of these loci (or genes within loci) are functional, as some HMR loci appear to be affected by either a frameshift mutation (e.g. the merA gene of CMGI-1 and the nccB gene of CMGI-30b) or by partial deletion (e.g. hmzA of CMGI-4 and merP of CMGI-30a ).
However the largest predicted function categories associated with the anti-macrophage loci were either toxin/enzyme related (hemolysins, proteases, phospholipases) with 44 associated CDSs within loci, or proteins involved in transport/secretion (ABC transporters, efflux transporters, and proteins involved in type III and VI secretion) with 84 related CDSs within positive loci.
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Recently, a multilocus sequence analysis approach was proposed to reconstruct phylogenetic histories of bacterial clonal complexes by using concatenated sequences of housekeeping genes when within-loci and between-loci recombinations are infrequent (5 ).
Such within-locus rearrangements may increase the spacer effectiveness whereas the immunity range remains unchanged.
All tr loci normally rearrange in cis, or in other words, strictly within locus.
The genomic region specifying EBER1 occurs within locus 12 (Additional file 1).
Phylogenetic comparison indicated that the four FhaB homologs within locus I were most closely related to each other as were the six FhaB homologs within locus IV (data not shown).
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