use meme to find motifs
./meme ../../markfilter/shrtincor.fa -protein -mod zoops -nmotifs 20 -minsites 2 -maxsites 5 -minw 3 -maxw 50 -evt 10000 -time 7200 -maxsize 60000 -nostatus -maxiter 25 > output.html

use meta-meme to make hmm
./mhmm -meme ../../../meme.3.0.4/bin/output.html > test.mhmm

test sequences using that hmm
./mhmmscan -hmm test.mhmm -seq ../../../markfilter/shrtcor.fa 2>/dev/null | more