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Old 10-07-2010, 03:50 AM   #3
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Location: Germany

Join Date: May 2010
Posts: 101

Blast is a local alignment tool, so it will only consider the aligned part, in you example the ATGC, which is the same in all 3 sequences. There are 4 perfect matches, giving the same score for all 3. The e value is calcuated from the length of the match and the score - also the same. At no point the length of the whole target sequence is taken into account. That means to get your "best alignment" for the same size, you have to filter the results by target sequence length, probably by writing a small script. I don't know of any Blast parameter that could be useful.
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