I would like to ask how I can interpret objectively multiple alignment results. I have used JALVIEW and TCOFFEE. I would like to ask if consistency score plays any role in the interpretation? Moreover, I would like to ask for a region of a protein to be considered conserved, all the amino acids should have similar properties? So even if only one protein has a different amino acid (among the proteins that are included in the multiple alignment), then there is no conservation? for example, in this picture, I am curious why there is no dot beneath some columns with almost identical amino acids (expect one sequence for example).

Thank you a lot!