Although tRNAscan-SE was designed with non-organellar tRNA detection in mind, we also tested it on a complete mitochondrial genome, that of Podospora anserina (Genbank ID PANMTPACGA). tRNAscan-SE detected 22 of the 27 annotated tRNAs (81.5 %), tRNAscan 1.3 detected 18 of 27 (66.7%), and covariance model analysis detected all 27 tRNAs (Table 2.3). Since organellar genomes are usually small, the computational demand of covariance model analysis alone (without the use of fast first-pass scanners) is not prohibitive. For this reason, tRNAscan-SE can be run in covariance model analysis-only mode (-C option) for maximum sensitivity, bypassing dependence on tRNAscan 1.4 and EufindtRNA. This mode gives the same results as would be obtained by running the covariance model search program alone, but in addition, produces annotated tRNA output identical in format to that found in the default tRNAscan-SE search mode.