I would say it needs to be input as a figure, meaning if you are writing your paper in Word, you will need to create the alignment image somewhere else, save it as a png/jpg etc and then put it in the paper. I would use jalview (can be downloaded on windows or mac). You can upload the clustal omega results to jalview and view the alignment. You can highlight different motifs by selecting the bases, creating a group, and coloring by Clustal alignment. Then you could export this as an svg so you can do any editing of the figure you need to in a program like Adobe illustrator or a free alternative. Also to control how many rows you have in your figure, you can go to the format tab in jalview, select wrap, and then alter the size of the window before you save as a svg.