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To address whether or not the mapped ORC1/CDC6 binding sites correspond with replication origins, we employed marker frequency analysis (MFA).
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Moreover, 48 of the 732 genes associated with Dsx binding sites correspond to genes identified in the dimorphism microarray experiments (Additional file 2).
To examine whether DNA regions with significantly enriched motif binding sites correspond to regulatory sequences, we focused on regions that have binding sites significantly more than average (Z score ≥ 3.09, P ≤ 10−3).
Consensus binding sites corresponded to sequences at positions –295 (CAACaG), -799 (-CAACgG), -1454 (CAACaG), and –2251 (TAACtG).
One binding site corresponds to the consensus CGCGCg identified as the integration site, and a second binding site with a different sequence is located in close proximity.
The nucleotide sequence of the miR-548j binding site corresponded to the PRTRSC oligopeptide.
These transcriptional modules contained evolutionary-conserved clusters of putative transcription factor binding sites that correspond to a "molecular signature" associated with robust gene expression in the heart.
miRNA binding sites may correspond to 3 open reading frames.
High quality sequence alignment revealed that the size variant alleles showing step-wise distribution contained the expected microsatellite repeat sequences with conserved primer binding sites, but corresponded exactly to the step-wise multiples of the number of repeat units.
A large positive wi indicates a binding site that is strongly associated with the enhancers, whereas negative weights correspond to the binding sites associated with the control set.
The identification of 12 positively selected sites that correspond with putative peptide binding sites, along with strong support for an adaptive evolution model among the class II sequences, lends weight to the suggestion that many of the class II sequences represent functional, classical loci.
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