You can use geneious software, it is not free, but you can download the trial. 

You can use ScanProsite:

http://prosite.expasy.org/scanprosite/

Select "Option 3 - Submit PROTEIN sequences and MOTIFS to scan them against each other."

https://www.expasy.org/proteomics

ScanProsite is the best tool for finding short motifs

http://prosite.expasy.org/scanprosite/

you can add signature of your own motif and search them

other options are

http://www.ebi.ac.uk/pdbe-site/pdbemotif/

https://www.genome.jp/tools/motif/

and MEME Tools

and for Nucleotide or genome sequence you can use: RSAT: http://www.rsat.eu/