Figure 4

Output of the program pipeline. Hits of a search with the TTX-3 consensus binding site is shown. num: number in list. mis: Number of base mismatches between first C. elegans and first C. briggsae hits. segtype: Type of non-exonic region (see Figure 3). str1/2: negative (N) or positive (P), strand on which the first/second of the two genes that flank the identified target site are located; offset1/2: distance of the target site to the flanking gene(s) (in relation to the start codon if the target site is 5' or located in an intron; in relation to the stop codon if the site is 3' to the gene; in the latter two cases, the number has a positive value); ID: cosmid name of the flanking genes, name: flanking gene names (if available). Gene IDs/names are linked to the WormBase gene model at http://www.wormbase.org, which contains further information about the gene. In case there are multiple target sites located in a defined inter/intragenic region, there is an option to report the n highest scoring hits for each ortholog. If this option is used, the top-scoring C. elegans or C. briggsae hit in each hit-pair will be highlighted, and the next n-1 hits will be gray. Color coding: Orthologous C. elegans/C. briggsae genes ("hit-pairs") are color coded in blue (Y39A3B.5 and CBG15122 are orthologs) and green (M01E10.2 and CBG15118 are orthologs).