Technical Abstract: Previous work has established a genomic signature, based on relative counts of the 16 possible dinucleotides. This signature has been used as a means of detecting genes that have undergone recent horizontal transfer events, as additional evidence supporting or contradicting evolutionary relationship, and even as a tool to suggest that double stranded DNA is of opposite rather than similar polarity. Until now it has been generally accepted that the dinucleotide signature is characteristic of a genome and is relatively homogeneous across a genome. However, we found some local regions of the soybean genome with a signature differing widely from that of the rest of the genome. Those regions were mostly centromeric and pericentromeric, and repetitive. We found that DNA binding energy also presented large-scale patterns across soybean chromosomes. These gradients were helpful during assembly and quality control of soybean whole genome shotgun scaffold sequences into pseudomolecule chromosome sequences.