Click here for an example of text output from Meme. This example uses a set of nucleotide sequences. If you're comparing protein sequences, your output will look a bit different.

Comments on the output:

• Under Training Set you'll find a list of all the sequences you put in and their lengths
• Scroll down to Motif 1, the best that Meme found in this run. You'll see the width (the number of nucleotides in the motif) and how many sites were found in your sequences.
• Below this is a crude graphical representation of the information content at each position of the motif. High bars indicate high information content (e.g. homogeneity). Low bars indicate low information content (randomness).
• Under "Posible examples of motif 1..." is a listing of the instances of motif 1 in the sequence set, plus 10 nucleotides on either side of the motif.
• You probably have no need for the letter-probability matrix, but it is the frequency at each position of the motif of each of the available letters. The four columns are A, C, G, and T. Each row is a different position, left-to-right, of the motif.
• The format is repeated for each motif found

Contact me
  Jeff Elhai
  Life Sciences Building, Room 335
  828-0794
  ElhaiJ@VCU.Edu