It is not possible to use simple plotting or charting programs to view the data and draw meaningful conclusions. A dedicated viewer that enables large data sets to be displayed correctly is one of the best options. It is open source with copyrights by Broad and U. California
If you are looking at genomics data and you need a easy way to view the data sets, integrative genomics viewer is a nice resource. It has access to amazing visualizations that will enable you to look at the data in different ways and forms. It has some tools like BLAT search and Motif finder but they are not very extensive.
Try it out here: http://software.broadinstitute.org/software/igv/home
And if you would like to learn more then click on the link below to go to the learning channel