STREME Position Distribution Alignment

[Ariana Treat]

Hello,

I'm running sequences on STREME with motifs that I know are not occuring in symmetric positions. But the position distribution is symmetric and looks identical (except for the range of the x-axis) when I align center, right, and left. I have used STREME on sequences from three different phylogenetic orders, and I'm getting the same unexpected symmetry. Has anyone else had this problem?

[cegrant]

Are all your sequences the same length? That would explain why changing the alignment option wouldn't affect the position distribution plot.  I'm not sure I understand you issue about symmetry. Could you forward us your input files and the command line you used? That would help us understand the problem.