The region between promoter and terminator was compared by BLAST to the genomes of Salmonella typhi, S. paratyphi, and S. typhimurium.  Predicted sequences with statistically significant alignment scores (under 0.001)  were further evaluated if one of the following criteria was satisfied:
1) The conserved region covered more than 70% of the candidate sRNA.
2) the conserved region covered 50%-70% of the candidate sRNA and either the promoter or terminator was predicted with high values.
3) the conserved region covered only 30%-50% of the candidate sRNA, but both promoter and terminator were predicted with high values.
Sequences that passed this screening stage were also compared to genome sequences of Klebsiella pneumoniae and Yersinia pestis.  All predictions shown in Table I identified sequences that were at least conserved in Salmonella and Klebsiella pneumoniae.  Conservation in Yersinia pestis provided further support to the prediction.
After the final list of predictions was obtained, candidate sRNAs suspected as potential trailers of upstream genes were excluded.

A summery of the conservation results for the 24 candidate small RNAs that were found, can be seen here.