Table 1 The statistics of conserved sequence between pairs of species for a range of parameters that maximized the correlation between the experimental binding sites and the conserved sequence. Two alignment programs were used along with two measures of intersection: (a) site counted only if entirely within a conserved block, (b) number of conserved bases belonging to site. Columns indicate the fraction of the total sequence aligned in conserved blocks (the percent identity of the conserved blocks), the fraction of sites in blocks, the fraction when sites are placed randomly. (see Methods), and the statistical significance. The percentage intervals in the three columns correspond.
From: Conservation of regulatory elements between two species of Drosophila
D. melanogaster versus D. pseudoobscura | ||||
|---|---|---|---|---|
method | conserved seq. (%) | sites in conserved seq. (%) | random sites in conserved seq. (%) | Z score |
SMASH (a) | 41–51 (82–92%) | 51–71 | 37–54 | 5.0 |
SMASH (b) | 33–51 (82–92%) | 48–74 | 42–57 | 5.0 |
LAGAN (a) | 33–71 (82–92%) | 36–53 | 25–39 | 5.0 |
LAGAN (b) | 31–54 (82–92%) | 50–80 | 41–58 | 6.0–8.0 |
D. melanogaster versus D. virilis | ||||
method | conserved seq. (%) (PID) | sites in conserved seq. (%) | random sites in conserved seq. (%) | Z score |
SMASH (a) | 25–31 (83–92%) | 18–32 | 13–25 | 2.0 |
SMASH (b) | 25–26 (83–92%) | 36–41 | 27 | 4.5 |
LAGAN (a) | 29–56 (81–92%) | 23–36 | 18–32 | 2.25 |
LAGAN (b) | 30–48 (81–92%) | 45–61 | 30–50 | 5.0 |