Unlike the traditional nucleotide BLAST and contiguous megablast, discontiguous megablast uses a discontiguous word template to find the initial alignment seeds, considering only certain positions for matches while ignoring the matching status for the rest. The table below depicts the type and length of templates, selectable through the 'TEMPLATE_TYPE' and 'TEMPLATE_LENGTH' options in discontiguous MEGABLAST. The '1's represent required matches. When either the '-N 2' or the 'TEMPLATE_TYPE=2' options are used, both type of word matches will be evaluated.
| Table 6.12 Word Size, Template Length, and Template Template Type | |||
| Word Size | Template Length | Template | Template Type |
|---|---|---|---|
| W = 11 | t = 16 | 1101101101101101 | coding (-N 0) |
| W = 11 | t = 16 | 1110010110110111 | non-coding (-N 1) |
| W = 12 | t = 16 | 1111101101101101 | coding (-N 0) |
| W = 12 | t = 16 | 1110110110110111 | non-coding (-N 1) |
| W = 11 | t = 18 | 101101100101101101 | coding (-N 0) |
| W = 11 | t = 18 | 111010010110010111 | non-coding (-N 1) |
| W = 12 | t = 18 | 101101101101101101 | coding (-N 0) |
| W = 12 | t = 18 | 111010110010110111 | non-coding (-N 1) |
| W = 11 | t = 21 | 100101100101100101101 | coding (-N 0) |
| W = 11 | t = 21 | 111010010100010010111 | non-coding (-N 1) |
| W = 12 | t = 21 | 100101101101100101101 | coding (-N 0) |
| W = 12 | t = 21 | 111010010110010010111 | non-coding (-N 1) |