The program is invoked by giving it a series of optional command line
parameters, then a list of one or more sequence files written in the
FASTA format (see appendix A for example of FASTA format):
tRNAscan-SE [-options] FASTA_file(s)
By default, the header credits and selected command-line options are printed to the screen via standard error, followed by the final results of the tRNA search written to standard output in a tabular format (see below). By default, tRNAscan-SE searches for eukaryotic cytoplasmic tRNAs. To search for prokaryotic, archaeal, or organellar tRNAs, use search mode options -P, -A, -O, repectively. If the sequences are from more than one phylogenetic domain, the general tRNA model (option -G) may be used with minimal loss of sensitivity and selectivity (the publication describing tRNAscan-SE used the general tRNA model exclusively, ref. 4).
Sequence tRNA Bounds tRNA Anti Intron Bounds Cove Name tRNA # Begin End Type Codon Begin End Score -------- ------ ----- --- ---- ----- ----- ----- ----- CELF22B7 1 12619 12738 Leu CAA 12657 12692 60.01 CELF22B7 2 19480 19561 Ser AGA 0 0 80.44 CELF22B7 3 26367 26439 Phe GAA 0 0 80.32 CELF22B7 4 26992 26920 Phe GAA 0 0 80.32 CELF22B7 5 23765 23694 Pro CGG 0 0 75.76
Each new tRNA in a sequence is consecutively numbered in the 'tRNA #' column. 'tRNA Bounds' specify the starting (5') and ending (3') nucleotide bounds for the tRNA. tRNAs found on the reverse (lower) strand are indicated by having the Begin (5') bound greater than the End (3') bound (see tRNAs #4 & #5 in output above).
The 'tRNA Type' is the predicted amino acid charged to the tRNA
molecule based on the predicted 'Anticodon' (written 5' 
3') displayed in the next column. tRNAs that fit criteria for
potential pseudogenes (poor primary or secondary structure, discussed
in Methods), will be marked with ``Pseudo'' in the 'tRNA Type' column.
If there is a predicted intron in the tRNA, the next two columns
indicate the nucleotide bounds. If there is no predicted intron, both
of these columns contain zero. The final column is the Cove score for
the tRNA in bits. Note that this score will vary somewhat depending
on the particular tRNA covariance model used in the analysis (the
search mode selects which tRNA covariance model will be used:
eukaryote-specific, prokaryote-specific, archae-specific, or general).
tRNAscan-SE counts any sequence that attains a score of 
20.0
bits as a tRNA (based on empirical studies conducted by Eddy & Durbin
in ref #2).