Classification of 454 contigs. Contig classification is based on a model of a minimal transcription unit. RBS, ribosomal binding site. Five classes were defined: (a) trans-encoded sRNAs are located at least 60 nt upstream and 20 nt downstream from the translation start and stop codons, respectively. Type 1 is located antisense to both adjacent genes, type 2 sRNAs are flanked by at least one adjacent gene in the same orientation. (b) Cis-encoded antisense sRNA in the opposite direction of the minimal transcription unit grouped into type 1-3 depending on the relative location to the associated gene. Type 1, 2 and 3 are located antisense to the 5'-UTR, to the coding region and to the 3'-UTR, respectively. (c) mRNA leader sequences either overlap the 40 nucleotides upstream of the minimal transcription unit or starting between position -40 and +1. The 3'-end of each contig is located inside the open reading frame (dashed line). (d) A sense sRNA is located in the same direction as the minimal transcription unit and assigned to one of four subclasses: type 1, 2, 3 and 4 overlaps the 5'-UTR, is located inside the ORF, overlaps the 3'-UTR, and starts inside the 3'-UTR, respectively. (e) Open reading frame: A contig that overlaps the whole ORF. The boxes highlighted in grey indicate classes used for classification of candidates derived from the microarray- and Affymetrix Symbiosis Chip-based screenings.