Table 2. Example of alignment.
| True | Maximal | clustal w |
|---|---|---|
| TTATAT-G-ACTTG-CC-GG | T-TATA-TGACTTGCCGG | TTATAT--GAC-TTGC-CGG |
| CT-TCG-G-ACGTG-GC-TC | C-T-TC-GGACGTGGCTC | CT-T-C-GGACGTGGCTC-- |
| CCAAAC-GGACGTTAC--GC | CCAAAC-GGACGTTACGC | CCAAAC-GGACGTTACGC |
| -AAAACAG-GACTTAT-A-C | A-AAACAGGAC-TTATAC | -AAAACAGGAC-TTATAC-- |
Four sequences and their true alignment that generated the sequences, the maximal alignment obtained from the Viterbi algorithm, and the alignment obtained from the CLUSTAL W program (www.ebi.ac.uk/clustalw).