Potential misannotation of the S. pneumoniae ATCC 700669 genome. RNA-seq data is displayed as described in Figure 6. In addition to the published annotation of S. pneumoniae ATCC 700669, dashed boxes indicate alternative open reading frames encoded by BOX elements. a) i) The locus around SPN23F05060, encoded by a BOX element. The CDS is annotated on the bottom strand, but the RNA-seq results indicate it is co-transcribed with the operon on the top strand. ii) This BOX element appears to be cotranscribed with the upstream SPN23F17620 CDS at a low level, rather than encoding the 603 bp putative CDS SPN23F17630. iii) The BOX element encompassing putative CDS SPN23F21390 appears to transcribed on the reverse strand, along with the neighbouring CDSs. b) For each of the three loci displayed in a), two experiments were performed, each as described in Figure 6. One, using PL (left primer) and PR (right primer) tested for expression of the BOX element itself. The second used PL or PR and PS (stop codon primer), which tested whether the full length open reading frame on the transcribed strand was expressed. At all three loci, both reactions were positive using a cDNA sample as template.