Matrix Details

The Matrix block provides the nucleotide frequencies observed in aligned binding sites of the corresponding transcription factor (or, more general, in aligned sites of the described function); an additional column depicts the IUPAC string consensus derived from the matrix according to the following rules, adapted from Cavener, 1987:

  1. A single nucleotide (A, C, G, T) is shown if its frequency is at least 50% and at least twice as high as the second most frequent nucleotide.

  2. A double-degenerate code indicates that the corresponding two nucleotides occur in at least 75% of the underlying sequences and rule 1 does not apply. (W = A or T), (S = C or G), (R = A or G), (Y = C or T), (K = G or T), (M = A or C).

  3. Usage of triple-degenerate codes is restricted to those positions where one of the nucleotides did not show up at all in the sequence set and none of the afore mentioned rules applies. (B = C, G or T), (D = A, G or T), (H = A, C or T), (V = A, C or G).

  4. All other frequency distributions are represented by the letter "N" (= A, C, G or T).

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