Each motif instance is given as a triple "seq#, position, substring",
one per line and comma-separated.  An example would be
  2,-649,TGGACGA

    * "seq#" is the input sequence number in which the instance is
      found.
    * "position" is the position of the first nucleotide in
      "substring", measured from the 3' end of the input string. For the
      example given above, the T occurs at position -649, where the
      last character of the input sequence is numbered -1.
    * "substring" is given on the strand of the input string,
      independent of the strand your program predicts to contain the
      instance. That is, "substring" must be a substring of our
      supplied sequence "seq#" beginning at "position".