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This was not simply because the same loci were being identified for both species, as only 20% of the total number of searched contigs shared sufficient identity (BLASTN; E<10-80 or E<10-20 E<10-20potontial homologues.
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This interpretation is complicated by the need to generate percentage methylation statistics per cytosine residue because the same locus can have different methylation levels across cells.
The Ty1 pattern is characterized by a low level of polymorphism between individuals because almost all the same loci are occupied in many strains.
Capturing transcript diversity is important because probes may be derived from the same loci, but match different transcript sequences due to alternative splicing.
Because different libraries did not exactly contain the same loci and some of the loci did not pass the coverage threshold, we obtained ∼25% missing data.
The application of a Bonferroni correction would be too conservative because SNPs within the same locus are highly correlated.
Because we expect alleles at the same locus to anti-correlate, and because it is unknown which DBLα alleles share a common locus, we only analyze positive correlations.
Second, the phenotypes of different lines carrying a series of transgenes (e.g., encoding variants of a protein of interest) can be directly compared because all are inserted at the same locus and subjected to identical positional effects.
These complex repeats suggest the presence of an additional restriction site within the repeat array for the enzyme used to digest the flanking regions or the presence of a homologous or duplicated repeat array elsewhere in the genome but probably on the same locus because the two fragments were always co-segregating when inherited by the offspring.
After aligning all 277 isotigs of the isogroup 00007, we found that all of them were derived from the same locus, because only one sequence variant (contig) corresponded to each exon of the homologous Arabidopsis gene, At1g27980, coding for sphingoid long-chain base 1-phosphate lyase (LCB-1-P lyase) (Additional file 3).
We correct this number to 48 hh-related genes here, because C. briggsae wrt-8 is the same locus as wrt-4.
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