Final answer:
A sequence being found in multiple locations via BLASTN does not signify an exact genome-wide match but suggests similar regions are present. The significance of a match is gauged by the E-value, with lower values indicating more significant alignments. It's important to consider whether global or local alignment is used, as this affects the interpretation of the BLAST results.
Step-by-step explanation:
When using BLASTN to compare a DNA sequence against the known sequences in the human genome, finding that a sequence occurs at over a hundred places does not indicate an exact match to the entire DNA sequence. The occurrence of the sequence in multiple locations suggests that there are regions within the genome that are similar to the query sequence, but this does not confirm an identical match throughout. To determine the quality of the alignment, one should look at the E-value which represents the significance threshold of the alignment; the closer the E-value is to zero, the more significant the match is. Additionally, gaps may be introduced in the alignment to achieve a better overall match. The presence of gaps indicates that the match is not exact and that some differences exist between the query sequence and the matching sequences found within the genome.
BLAST searches can involve either global alignment, which aligns the entire query sequence to sequences in the database, or local alignment, which focuses on regions of high similarity. Local alignment is often more practical for identifying functionally important and conserved regions across different sequences. The results of a BLAST search are useful for various applications such as phylogenetic analysis, discovery of functional regions, and comparative genomics.