Eukaryotic DNAs exist in a highly compacted form known as chromatin. The nucleosome is the fundamental repeating subunit of chromatin, formed by wrapping a short stretch of DNA,147bp in length, around four pairs of  histone proteins. Nucleosome DNA obtained by experiments however varies in  length due to imperfect digestion. We develop a mixture model that characterizes the known dinucleotide periodicity probabilistically to improve the alignment of nucleosomal DNAs. To further investigate chromatin structure, we experimentally cloned and sequenced di-nucleosome sequences from yeast. Each dinucleosome sequence roughly cover two
nucleosomes (located toward the two ends) with a linker DNA in between. A HMM model is trained based on the nucleosome sequence alignment for prediction of nucleosome positioning. Results show that Eukaryotic cells do favor periodic linker length in chromatin forming on a roughly 10 bp basis.