Charakterwise Diff-tool
This tool was developed while working on GAIA.
Since a comfortable tool to mark differences in two aligned strings was not available online, we implemented it. Case sensitivity can be enabled, if needed, whitespaces and newlines are ignored, which makes handling FASTA files easy.
Characterwise Diff-tool

There is a known issue with some versions of Safari freezing the content of textareas, if that is the case please try another browser.