BlastAlign: a program that uses blast to align nucleotide sequences that have large indels (INsertions/DELetions) or are otherwise difficult to align
You need to have your sequences in the following format.
>name of the first sequence
>name of the second sequence
This web interface should cope with most variants of the above format, e.g. additional line breaks, upper case nucleotides, etc. For a full definition of FASTA format go to
Developed by Robert Belshaw and Aris Katzourakis
Web-interface developed by Aris Katzourakis, Robert Belshaw and Tulio de Oliveira.