(A) Abscissa: Human SLC25A21 (490,793 nucleotides; the sequence from start to stop codons after removal of exons). Ordinate: the same sequence as in the Abscissa. Number of matches: 7704. Note the perfect alignment along the diagonal from the lower left corner to the upper right corner and the large number of matches outside the diagonal. (B) Abscissa: Human GHR (292,898 nucleotides; the sequence from start to stop codons after removal of exons). Ordinate: the same sequence as in the Abscissa. Number of matches: 1840. Note the perfect alignment along the diagonal from the lower left corner to the upper right corner and the large number of matches outside the diagonal. (C) Abscissa: Human SLC25A21 (490,793 nucleotides). Ordinate: Human SLC25A21 after removal of all the 130 SINE Alus (462,572 nucleotides). Number of matches: 3220 (compared with A). Note the seemingly perfect alignment along the diagonal from the lower left corner to the upper right corner. (D) A partial, magnified, view of panel (C), showing a 10 K per 10 K area from the lower left corner, magnified by 50×. The gaps correspond to the removed SINE Alus. (E) Abscissa: Human SLC25A21 (490,793 nucleotides). Ordinate: Human SLC25A21 after removal of all TEs (298,209 nucleotides). These additional TEs belong to different categories, and some of them are much larger than the SINE Alus. Number of matches: 505. Note that the gaps (due to TEs) along the diagonal from the lower left corner to the upper right corner are now more visible at low magnification.
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