Newly identified transcriptionally active regions of the genome. Mapping of cDNA reads to the A. marginale genome allowed us to detect regions without previous annotation that exhibited transcriptional activity. A shows the region of the St. Maries genome that spans from bp 336042 to 336685. Three different gene identification algorithms did not detect a CDS that would span the length of the transcript. The top panel shows the six reading frames containing forty-five stop codons, shown as black bars. The bottom panel shows some of the mapped cDNA reads in green and red (indicating direction of the read). The grey histogram under the reads represents depth (read height). This transcript was up-regulated in the St. Maries strain by a fold change of 23.7 at p < 1E-10. B shows the region of the St. Maries genome that spans from bp 1084944 to 1085520. The newly identified gene is found between genes polA (not shown) and AM1216. One ORF on the leading strand seems to span the length of this transcript and is shown as PUTATIVE_CDS in this figure. This new gene was found to be up-regulated in the transmissible St. Maries strain by a fold change of 6.9 at p < 1E-10.