I have a set of sequences in the form of a multiple sequence alignment. I have generated a Sequence logo image to look for any potential motifs within these set of sequences. I have identified several areas that appear to be relevant. I would like to generate a weighted position matrix of these specific motifs (based on the specific range of bases I have identified) and use this matrix to generate a file that can be used with FIMO to search a database of sequences for that motif.

I know I can use MEME to find the motifs and use that file as my input, however it doesn't seem to find the same motifs as I do because it is not aligning the sequences in the same manner. I have found this post but it doesnt seem to generate them in the correct format.

What is the best way to generate a position matrix for my identified region that is compatible with the MEME suite?

EDIT: Another process that I would be OK with is the following: Use MEME to discover motifs but be able to manually adjust the multiple sequence alignment that it performs before it looks for the motifs. I know based on my own multiple sequence alignment that my sequences do not align on there own as they should.

Thanks in advance