Table 2.
Procedure for building a consensus sequence starting from a matrix of nucleotide counts, according to selected parameters. Rows from two to five represent the matrix of nucleotide counts in different positions of an alignment associated to a cluster of pattern occurrences. The sixth row contains, for each alignment position, the ratio between number of sequences in the position and the total number of lines in the alignment. Out of 11 positions of the matrix, positions from one to ten (shaded in grey) fulfil the minimum i (0.5) and are considered for building the consensus. If the lateral region length is set to 3 nucleotides, a 3-4-3 motif is obtained. The fl (0.6) threshold is applied to the positions in the lateral regions, whereas the fc (0.8) is applied to positions in the core region. Cells containing values fulfilling the condition reported on the left are in bold. In the last row, the derived consensus sequence is shown.
| 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | |
| A | 0 | 0 | 0 | 4 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| C | 0 | 0 | 5 | 0 | 5 | 2 | 0 | 0 | 0 | 0 | 2 |
| G | 0 | 4 | 0 | 0 | 0 | 3 | 5 | 5 | 0 | 4 | 0 |
| T | 3 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 5 | 0 | 0 |
| i (0.5) | 0.6 | 0.8 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 0.8 | 0.4 |
| fl (0.6) | 1 | 1 | 1 | 1 | 1 | 1 | |||||
| fc(0.8) | 0.8 | 1 | 0.6 | 1 | |||||||
| Consensus sequence | T | G | C | A | C | N | G | G | T | G | - |