1) View this sequencing chromatogram. First, look at the overall sequence and dont bother trying to read the letters. Can you tell which end is the 5 end?
2) Beginning at base 80, read 50 bases of the sequence and write down both strands of this portion of the DNA, with the top strand being the one on the chromatogram.
3) Go to BLAST <http://www.ncbi.nlm.nih.gov:80/BLAST/> and do a BLASTn search with this sequence but only use 30 bases of your 50. What was your best match? Look to the right at the E value. Is it a small number or something closer to 1.0?
4) Now submit all 50 bases and compare your results from the search with only 30 bases. Which submitted sequence gives you the better search result?
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