Non-Coding Regions of Chloroplast Genomes Exhibit a Structuredness of Five Types Michael Sadovsky 1,2(B ) , Maria Senashova 1 , Inna Gorban 2 , and Vladimir Gustov 2 1 Institute of Computational Modelling of SB RAS, Akademgorodok 660036, Krasnoyarsk, Russia {msad,msen}@icm.krasn.ru 2 Institute of Fundamental Biology and Biotechnology, Siberian Federal University, Svobodny prosp., 79, 660049 Krasnoyarsk, Russia inn.gorban@gmail.com, v.gustows@mail.ru http://icm.krasn.ru Abstract. We studied the statistical properties of non-coding regions of chloroplast genomes of 391 plants. To do that, each non-coding region has been tiled with a set of overlapping fragments of the same length, and those fragments were transformed into triplet frequency dictionaries. The dictionaries were clustered in 64-dimensional Euclidean space. Five types of the distributions were identified: ball, ball with tail, ball with two tails, lens with tail, and lens with two tails. Besides, the multi- genome distribution has been studied: there are ten species performing an isolated and distant cluster; surprisingly, there is no immediate and simple relation in taxonomy composition of these clusters. Keywords: Order · Probability · Triplet · Symmetry · Projection · Clustering 1 Introduction Non-coding regions in DNA sequences have been supposed to be a kind of an evolutionary junk; currently, it is a well knows fact that such regions play essen- tial role in gene regulation, and in the genetic information processing, in general [1–6]. The role of non-coding regions is not absolutely clear yet, and a lot could be found behind them. The non-coding regions are found elsewhere, in a genome of any taxonomy level, including organelle genomes. Here we studied the non- coding regions of chloroplast genomes, following the way present in [7–12]. Previously, a seven-cluster pattern claiming to be a universal one in bacterial genomes has been reported and very elegant theory explaining the observed pat- terns was proposed [7, 8, 11]. Later, we have expanded the approach for chloro- plast genomes [12, 13]. Here se present some preliminary results of a study of c  Springer Nature Switzerland AG 2019 I. Rojas et al. (Eds.): IWBBIO 2019, LNBI 11465, pp. 346–355, 2019. https://doi.org/10.1007/978-3-030-17938-0_31