I have not checked the rest of your code, but:

> for line in seqalign:
>     for i in len(finalmotif_seqs):      # for item in finalmotif_seqs:
>         for i in len(finalmotif_annot):     # for item in finalmotif_annot:

I see two problems here:
1. You are using the same loop variable in both loops here. That's
likely to cause problems
2. You let the loops go over len(finalmotif_seqs).
len(finalmotif_seqs) is a number, and you can't loop over a number.
You should use the form as you write after the #.

-- 
André Engels, andreeng...@gmail.com
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