Table 1.

Description of COOP parameters.

Step	Parameter	Description	Range	Example
Search for pattern occurrences	q	Quorum (minimum number out of N input sequences in which a given pattern must be represented)	1 - N	≥ 20 out of 100 sequences
Clustering	d	Physical distance between 5'-ends of occurrences of patterns of length p	0 - |p|	≤ 2 nucleotides
	o	Ratio between observed overlapping occurrences of two patterns and their average number of occurrences	0 – 1	≥ 0.8
Consensus building	i	Ratio between the number of nucleotides per alignment position and the total number of lines in the alignment. The maximal number of adjacent positions exceeding the threshold i (m) is further analysed for determining the consensus sequence of the motif	0 – 1	≥ 0.5
	l	Nucleotide length of the lateral region of the motif	0 - m/2	3 bp (out of 10)
	f l	Frequency of a single nucleotide in each position of the lateral region to be considered specified	0 – 1	≥ 0.6
	f c	Frequency of a single nucleotide in each position of the core region to be considered specified	0 – 1	≥ 0.8