Exons and introns

The horizontal sequence is the Emericella (Aspergillus) nidulans calmodulin gene, translated into the three forward frames; and the vertical sequence is the gene product.
We have chosen a very stringent matrix, since we expect an exact match in the correct frames, and a very small window, since exon-intron boundaries are as sharp as can be. We clearly see four introns, actually there is one more but it is very small, and it can be seen only if we lower the window size (but this also heightens the nackground noise - try it out for yourself.).
We have positioned the cursor at the beginning of an exon, and the alignment window shows a perfect match starting from this position, in the second reading frame.

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