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Unformatted text preview: TGTTTA? MA0040 (or FoxQ1). Visually, this sequence logo matches the motif best. To assess it quantitatively, we could plug in the motif and position weight matrix into the pwm.xls form. 3. atatatataggctgg 10.95 ctatatatatgctgg 10.55 ctataaataggccgg 14.99 best TATA box 4. The sequence shown is the reverse complement of the best match in Q3. Therefore, the TATA box is on the other strand (and the gene points the other way). C: Do and write out answers to Discovery Questions 2-12 and 2-13. Q 2-12 Testcode values 1: 0.549 2: 0.468 3: 0.961 best value The third sequence has the ORF. Q 2-13 -- Scrambling obviously randomizes the amino acid sequence, leaving it unlikely that a large ORF could be formed. This part of the exercise is merely meant to illustrate that the discovery of a good ORF most likely indicates a real gene as opposed to just a chance arrangement of amino acids with no stop codon....
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- Spring '09