Final answer:
The purple and green bars are not red because the sequence alignment tool uses a different color coding, with specific colors typically indicating various levels of sequence conservation or features within a sequence.
Step-by-step explanation:
The purple and green bars in the human homolog alignment are not red as in the BLASTp graphic output because the sequence alignment tool uses different color coding. Different software tools and analyses use specific color schemes to signify various levels of sequence conservation or other features within a molecular sequence.
In sequence alignments like those used for tRNA molecules or other genetic data, color coding is typically used to represent differing degrees of sequence conservation such as 100% conservation (often red), high level of conservation (often blue), or no significant conservation (often black). Similar to how BLAST uses color intensities to indicate sequence conservation, the human homolog alignment uses different colors to indicate specific features or areas of conservation within the sequence.
The color scheme used in a particular alignment output is often predefined by the software displaying the results or in some cases can be user-defined, but it generally aims to provide visual aid for interpreting the alignment data. The difference in colors, such as the use of purple and green bars instead of red, signifies that a different color representation is being used, likely specific to the analysis purpose or the software's default settings.