Help!

I am looking for a software (such as Ssrtool or Tandem Repeats Finder) to help me spot motifs in my multiple (thousands) proteins, e.g.:

>seq1
nnnnnnindcndnnindcndnnindcndnnindcndnninycndnnindcndnnindcnd
nnindcndnninycndnnindcndnninycndnnindcndnnindcndnninycndnnnn
yyyyyncn

I tried searching for existing methods of analyzing such data, but I failed. K-mer analysis method would not be a particularly good one because my data is highly repetitive. I also tried to use UGENE and its built-in Smith-Waterman Search plugin, but either it did not work with just one set of data and comparing it to itself, or I did something horribly wrong.

Would you happen to be able to help me find a method or software that would work with such data format? I am happy to answer any follow-up questions.