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

Table 1 Counts for selected HCNE sets

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

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.

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