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Assume a read aligner (such as e.g. BWA) is fed with a pattern P = GACT. Now, the text that BWA has preprocssed is NNNAGTCNNN. The aligner would not find the pattern, and then would fall back to reverse-complementing it to AGTC and searching again. The question is, what it would report in the SAM-file? For POS = 3 and the FLAG with a bit 0x10 set?

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closed as off topic by leonardo, jonsca, Konrad Rudolph, Michael Kuhn, Daniel Standage May 17 '12 at 0:45

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I think this question is better suited to Biostars.org where they focus on bioinformatics and software questions. While your question is perfectly valid, it does not have a biological focus and therefore is not a good fit to be addressed by our community. –  leonardo May 10 '12 at 22:22
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