Table 1. Secondary structure and conservation analysis for C. jejuni ncRNA candidates.

ID, unique identifier containing genomic location; maxRnazP, the maximal RNAz probability on the forward or reverse strand – values greater than 0.5 were classified as putative ncRNA genes; minAlifoldZ, the lowest (best) Z-score from the RNAalifoldZ predictions on the forward or reverse strand; numSeqs, no. of homologous sequences used in the Rfam seed alignment; aveLen, average length of the sequences in the Rfam seed alignment; GC content, average G+C content for all the sequences in the Rfam seed alignment; GC enrichment, enrichment of G+C nucleotides relative to the genomic background [computed as log₂(GC-content/0.3055)]. One homologue was identified in the C. jejuni genome (EMBL ACC:AL111168.1) for each ncRNA candidate.

ID no.	MaxRnazP		MinAlifoldZ		numSeqs	aveLen	aveID	GC
	Forward	Reverse	Forward	Reverse				Content	Enrichment
Intergenic_671549–671895	0.957647	0.796566	−5.9	−5.1	8	342.9	74	0.285	−0.1001
Intergenic_722652–722740	0.995352	0.995194	−4.6	−4.4	5	89.4	89	0.295	−0.0504
Intergenic_906748–907066	0.932765	0.89473	−1.1	−6.6	5	311	89	0.232	−0.397
Intergenic_1127982–1128192	0.999921	0.559228	−8.6	−2.4	5	206.8	78	0.281	−0.1205
Intergenic_1575021–1575288	0.999869	0.999657	−7.7	−8.2	5	262.6	88	0.221	−0.4671