When characters are homologous with conserverd function, they are orthologous. When characters are homologous with divergent function, they are paralogous. Homology is therefore NOT synonomous with similarity. Homology is a judgement, similarity is a measurement. Similarity between two sequences can be detected as a diagonal on an identitiy matrix.
Humans are remarkable in their ability to recognize patterns by 'just looking at it'.
At the same time, humans are poor at highly repetitive tasks with large quantities of data. Graphic similarity comparisons use the power of the computer to present relationships between sequences in such a graphic form that enables the human researcher to discern patterns in the data. If we wish to determine whether two sequences are similar, we must compare all parts of one sequence with all parts of the other. This could be accomplished by sliding one sequence along the other and noting the number of identities at each alignment. The alignment with the greatest number of identities would be the optimal alignment.