Answer / guest

Yes, but this is not very useful because PatternHunter will
find that the whole sequence matches itself and will find
every repeat twice. To compare a DNA sequence to itself,
you should omit the -j argument, which forces PatternHunter
to ignore the trivial match and the duplicate matches.

Answer / rakesh

We can use bl2seq program to (Compare)align 2 sequence

This bl2seq program will avaialbe in Stand alon Blast.

We can write the perl script for this.

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