Terminators and other stem-loop structures

This is a plot of the Bacillus subtilis UTP-glucose-1-phosphate uridylyltransferase gene against itself. The cursor is positioned at the location of a translation terminator, which in this case is a stem-loop in th RNA molecule. This means that the sequence is locally similar to its reversed complement, hence the appearance of small perpendiculars to the main diagonal. This is also clearly shown in the alignment window.

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