aafreq.txt	amino acid frequency
aaseq.fa	amino acid sequence
ntfreq.txt	nucleotide frequency
ntseq.fa	nucleotide sequence
tm_scores.txt	list of the scores for each ORF
tm_segs.txt	list of transmembrane segments
tm_segs_best.txt	list of best transmembrane segments with sumscore of 4
structure_matches.txt	nonredundant set of matches with SCOP domains
old/pdb_matches.txt	all the non-duplicate fasta matches plus non-duplicate psiblast matches for fold classes other than small protein
old/pdb_matches_all.txt	all the non-duplicate matches for each fold class
old/small_pdb_matches.txt	all the non-duplicate matches for small proteins
old/pdb_matches_fasta.txt	all the non-duplicate fasta matches for each fold class
old/zip/pdb_matches_psiblast.txt.gz	all the non-duplicate matches for each fold class with psiblast premade matrices
old/zip/pdb_matches_selfpsi.txt.gz	all the non-duplicate matches for each fold class with psiblast, generated on the fly
old/zip/pdb_matches_with_dup.txt.gz	all the duplicate matches for each fold class, with all three methods