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Your lab works on an organism isolated from radioactive waste. However, you show that 3 very similar, but not quite identical, ssu-rRNA sequences can be amplified from the culture even though it is supposed to be pure. how could a pure culture be represented by more than one ssu rRNA sequence?

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Is this a homework question? – leonardo Nov 8 '12 at 3:28
We'll need some more information. The easiest answer is that the culture is not pure. Are you comparing the entire rRNA sequence? How are you sequencing? Can we see some alignments? – terdon Nov 8 '12 at 15:07

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