Using MULTIZalign, available in UCSC Genome Browser, I obtained multiple alignment of the 5k bp sequence across 100 species, which is stored in .MAF file. Now I am looking for a convinient way to visualize this file. I would like to obtain something that resembles subfig b) of this: http://cancerres.aacrjournals.org/content/71/1/277.long

I would like depict/highlight few fragments of this 5k sequence containg putative binding sites of some TF. Is there any way hove to do that, please. I will strongly appreciate any kind of help.