Final answer:
Sequence alignment quality is primarily affected by the introduction and extension of gaps, random sequence similarity, and nucleotide mismatches. The E-value and careful analysis of amino acid conservation are crucial for accurate interpretation of alignments.
Step-by-step explanation:
Factors that can have the most detrimental effect on the quality of sequence alignment include gaps and random similarity between sequences. Introducing gaps in sequence alignment is sometimes necessary for an optimal alignment, but it comes at a cost to the score. Each gap opens with a penalty of -3, and every extension of an existing gap incurs an additional -1 penalty. More significantly, due to the random nature of nucleotide sequences, some similarities may occur by chance rather than actual biological significance. To mitigate this, the Expected value (E-value) is used as a measure of random matches, where a lower E-value indicates a more reliable alignment. Furthermore, alignment programs like BLAST optimize the process by breaking down sequences into shorter segments or 'words' and scoring matches and mismatches to efficiently compare large genomic databases.
Issues like nucleotide mismatches and non-homologous regions can mislead the assessment of sequence conservation. Thus, percentages of sequence conservation should be interpreted with caution. When examining amino acid conservation, it is also important to consider the trends in the types of amino acids that are conserved, as the conservation of apolar, polar, and charged amino acids could reflect functional or structural constraints in the proteins.