Solution For The Exercises on The Alignment of Two Sequences

1.

 

4.

       1.The big square spot is a low-complexity region, as it happens a serine-rich
          region.
       2.It is a mature mRNA plotted against the corresponding gene. The
          interruptions in the diagonal are introns.
       3.It's a lab artifact: during the reverse transcription of an mRNA (an EST, in
          that case), the reverse transcriptase did a U-turn, so that the end of the
          cDNA is the reverse complement of its start (this is why you see a second
          diagonal). This is an example of why you should be careful with EST data.
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5.

        1-This sequence contains nine repeats, all homologous to one another, hence the stripes observed on the plot.
 
        2-Lalign produces by default the 10 best non-overlapping alignments. None of them gives you the coordinates of the repeats, but by extrapolation it is possible to find a near exact solution of: [BACK]