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.
The results are organized into tables where all the genes in one table belong to the same directon. In the example below genes 1, 3, 4, 5, and 6 belong to the same directon (a set of consecutive genes on the same DNA strand):
|gene 1||gene 3||confidence=80 n=5|
|gene 4||gene 5||confidence=100 n=23|
|gene 4||gene 6||confidence=99 n=20|
|gene 5||gene 6||confidence=99 n=21|
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.