You are talking about a more general question than genes comparison. This is a question for all alignments that can be done between 2 sequences.
To guide you in your question, you have to figured out that, parameters and threshold in order to decide "these two sequences are different" is an open one. It means, the percentage of identity, coverage, number of gap, scores, bit-score, e-value, etc... are lot's of descriptors that can help you but thresholds have to be smartly selected depending on what are you comparing.
So, if you want to know how much two sequences are similar, you can use descriptors as cited above.