Good afternoon, apologies if this question appears too basic.
I am attempting to find TFBSs in a 10kb DNA sequence. To do this, I've tried using TomTom. I followed the instructions by converting my 10kb seq fasta file into a .meme file using
iupac2meme -dna my_file.fasta >my_meme_file.meme. However, looking at the .meme file, I'm confused at what the matrix represents. Based on the documentation, I understand the rows are positions in a motif and the columns are for each nucleotide (A,T,G,C). But since my sequence was 10kb long, what exactly happened to the rest of the information? Are the rows just for a single, short motif that was most common in my 10kb sequence?
Secondly, are there any other recommended tools to search for TFBSs that are free and stringent? Appreciate any advice, as I'm fairly new to this. Thank you!