basically i am doing some alignment analysis on promoters between two species, this means i will have to analysis quite a lot of gene sequence data (thousands files), i have worked out how meme with the tomtom can give me the ranked motif anlysis result. However, is there anyway that can show the ranked motif on both aligned sequences? ( mene showed the rough position and tomtom only tells the ranked motif). I have written some code in R to show the alignment for the two sequences, but the meme result can hardly be applied in R. I know geneious can show the alignment quite easily and beautifully, is there anyway to combine the geneious and meme analysis together and visuallizing a lot of aligned sequences with highlighted motifs from meme and tomtom results??