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. 2020 Jul 13;12(10):1765–1781. doi: 10.1093/gbe/evaa146

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© The Author(s) 2020. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

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Fig. 6. — Comparison of core gene similarity of the Pf (pro)phages (n = 108) from the lineage I (outer rings) and the lineage II (inner ring). Genes from the Pf4 prophage (the outermost black circle) were used as references. The red, blue, orange, purple, and green circles represent Pf-tRNA-Gly, Pf-tRNA-Met, Pf-tRNA-Sec, Pf-tmRNA, and Pf-DR prophages, respectively. The comparison was performed using BRIG software with BLASTn algorithm (e-value 0.1, word size 7 options). Identical Pf prophages, occupying the same branch of the tree presented in figure 4, were excluded for the clarity. The position of reference Pf prophages, Pf1, Pf6, Pf5, Pf7, and Pf-LESB58, are indicated by colored triangles (yellow, black, green, red, and dark blue) at the PA0721 gene position. The list of Pf prophages was included in supplementary figure S4, Supplementary Material online.