This type of program is expecting a raw sequence file. However, if you used as input an email message containing a sequence, all the A's, G's, C's 'T's or U's in the message woudl be read in, along with the actual sequence. One good check is to note how long your sequence should be. If the program tells you it is the correct length, it has probably been read correctly.
Most programs allow either upper- or lowercase letters for nucleic acids.
Also, the most programs automatically convert U's to T's as sequences are read in. B. Amino acids Typically, programs only allow 1-letter symbols input. Also, most programs will only recognize uppercase symbols as amino acids. Although some errors in input file format will be caught, others may result in the interpretation of legal nucleotide or amino acid characters as being incorrectly added to the sequence. For example, if the user attempted to read in a GenBank file as a free format file, any legal nucleotide characters in the sequence name would be added to the sequence.