Confidence is an estimation of the lower boundary of the probability that the two corresponding genes are located in the same operon, n is a number of other genomes that have the same pair of genes located in the same directon (a set of consecutive genes on the same DNA strand). Clicking on n or confidence shows all homologies gene pairs in other genomes, clicking on gene locus shows information on the gene.
This table indicates that genes 1 and 3 co-occur in the same directon in 5 other genomes. Althouth this gives some evidence that genes 1 and 3 may belong to the same operon, the evidence is not strong enough and confidence is only 80%. There is also a gene 2 in the same directon (it is located between 1 and 3), but it is not shown because it never occurs in the same directon with genes 1, 3, 4, 5, or 6 in genomes other than the given genome. Genes 4, 5, and 6 are often co-occur together, and, based on confidence value, they are very likely to belong to the same operon.
The program only analyses co-occrence of genes that are located within the same directon and are separated by 4 or less genes. Calculation of confidence is based on rates of co-occurence of genes that belong to different operons (rate of false positives). Each pair of genes is analyzed separately.