If two nucleotides have the same score, Consensus picks one to add to the consensus arbitrarily. This may be somewhat misleading. The sequences follow with one sequence per line. Every sequence is the same length. The maximum size for the sequences is 130 bases.
Consensus assumes optimal alignment of the sequences.
All parameters for this program may be put on the command line. Use the option -CHEck to see the summary below and to have a chance to add things to the command line before the program executes. In the summary below, the capitalized letters in the qualifier names are the letters that you must type in order to use the parameter.