Programs similar to a Genome browser, but specialized on plotting alignments over smaller sequences.

Question

[grokaine]

Looking for a program that searches a given sequence for a list of sub-sequences and provides a nice colored output. My application for it would be to delineate flankers, spacers and direct repeats in given CRISPR sequences. Exact match and multiple alignment friendly.

I can make a python script, in fact I am doing it right now, but I would really need a nice program with visualizations and analysis options.

[GenoMax]

Take a look at SequenceServer. It is free for organizations and may provide what you need (search and display). It is meant for Query/Subject type displays so it is NOT a genome browser substitute (if that is strictly what you are looking for).