What is the meaning of the output of meme on each discovered motif

[Malik Yousef]

Hello

What is the meaning of the output of meme on each discovered motif?

For example i see this information and i want to understan it

motif=1

SEED WIDTHS: 8 11 15 21 29 41 50

em: w=  50, psites=1236, iter=  40

Best

[CharlesEGrant]

These messages are logging the progress of MEME's search for motifs. The SEED WIDTHS lists the width of the initial guesses MEME will make for the motif candidates. The lines that start with "em:" show the progress of the Expectation Maximization (EM) algorithm in refining the initial guesses for a motif. "w" indicates the width of the initial guess, "psites" lists the number of sites that seem to be instances of the motif, and "iter" is the number of iterations of the EM algorithm that were needed to refine the initial guess. 

Note that each of "em:" message overwrites the previous message on the screen, so all you've copied here is the last message displayed before EM halts, and MEME begins looking for the next motif.

These messages are primarily intended for the MEME developers so we can see that the algorithm is not getting stuck in its search for motifs.