motiph
motiph -oc motiph_example_output_files --seed 0 --bg 2 --pseudocount 0.01 spiked.aln yeast.tree MCM1.meme.html
MCM1.meme.html
clustal-w alignment
0.0001
TTTCCTAAATGGG
6.15e-15
TAACCTCTTTGGG
9.37e-06
GAGCCCGTTTAGG
0.00172
CGACCGAATCAGG
0.00278
TTTGCCAATTTAG
0.00435
TTCCTAAATGGGT
0.00435
TTGCCAATTTAGC
0.00729
TAATCAAAAAAGG
0.00729
TTTGCTCTTAATG
0.00729
yes
CCCGTTTAGGAAA
5.98e-12
CCTAAATGGGTAA
1.09e-08
CCTCTTTGGGGAA
1.55e-07
CTCTTTGGGGAAA
2.5e-07
CCGAATCAGGAAA
9.47e-07
CTCTTAATGGAAA
0.000407
CCTCGAGGAAATA
0.00209
CCTCAAGAAGTAA
0.00209
CCAAATGCGGGTA
0.00359
CTAAATGGGTAAA
0.00399
TCCTAAATGGGTA
0.00433
yes