A newbie question pertaining a mitochondrial cytochrome c oxidase subunit I gene (COI) blast result. I performed blastx against the non-redundant database. The alignment picture is shown below.
Then I took a look at the first homologous gene shown below.
1. Does the result mean that my retrieved COI sequence got some errors so couldn't be translated into a complete protein without stop codon(s)? (I did choose the invertebrate mitochondrial code table) However, I sequenced several different individuals (of the same species) and had consistent results.
2. What are the gray lines in the figure? A gap or intron? Could this be the reason of different frames (+1, +2 and +3) in the comparison result? In addition, what are the short vertical lines in the figure (i.e., the two at about 50 and 745bp)?
3. I'm always curious about the lower case letters in the alignment result. Are they representing known motifs or what?
Thank you very much!