Skip to main content

Table 1 Counts for selected HCNE sets

From: Ancora: a web resource for exploring highly conserved noncoding elements and their association with developmental regulatory genes

Criteria for HCNE detection Number of HCNEs detected in indicated comparison
Minimum identity Minimum size (bp) Human vs mouse Human vs chicken Human vs zebrafish Zebrafish vs Tetraodon
80% over 30 columns 30 NC 125,174 19,596 57,681
90% over 30 columns 30 NC 78,831 8,260 26,157
96% over 30 columns 30 305,015 50,478 3,656 10,205
100% 30 150,487 35,338 1,721 4,737
70% over 50 columns 50 NC 93,162 16,725 45,828
80% over 50 columns 50 NC 63,304 7,169 25,997
90% over 50 columns 50 265,537 36,794 3,127 8,610
95% over 50 columns 50 107,860 22,530 1,228 3,078
98% over 50 columns 50 68,600 17,579 763 1,782
100% 50 34,785 11,934 330 754
90% over 50 columns 100 81,065 15,339 733 1,695
95% over 50 columns 100 25,801 7,901 188 450
100% 100 4,919 2,475 20 61
100% 200 494 365 0 2
  1. Counts indicate the number of HCNEs obtained by collapsing HCNEs onto the assembled chromosomes of selected reference genomes. HCNEs were counted in this way to reduce redundancy and thereby make counts more comparable between data sets. The underlying Ancora data sets are not biased by selecting either genome as a reference. Note that HCNEs are generally larger than the window size (30 or 50) used to identify them because the procedure that detects HCNEs merges overlapping conserved elements. NC, not calculated.