In Queer contexts, alignment generally refers to whether two or more parts of an identity are in cohesion or not; whether they ‘match’ or are ‘different’.
In gender identity, one such example is the alignment of birth sex and gender. Typically, a transgender individual is transgender because their birth sex and perceived gender do not align; for example, a Trans man may be assigned female at birth, but identify as a woman – therefore, their assigned sex at birth and gender identity do not align. They may therefore take steps to align their sex and gender, by undergoing gender reassignment surgery, hormone therapy, and/or going through the various steps needed to officially recognise their gender.
A cisgender person generally has their sex and gender aligned; their sex assigned at birth and gender identity are the same.
In sexual identity, this may refer to the alignment between one’s sexual attractions and one’s romantic attractions. This is particularly pertinent with people on the asexual spectrum: their sexual identity (asexual) may not be aligned with their romantic identity (for example, homoromantic). Similarly, an aromantic person may be homosexual (e.g. homosexual-aromantic). An asexual with their sexual and romantic identities aligned may be aromantic as well.
In allosexual people, an example would be somebody who is bisexual but homoromantic. That is, somebody who is sexually attracted to their own and other genders, but only romantically attracted to their own.
In gender identities, being aligned may also refer to experiences nonbinary individuals have: for example, a nonbinary individual may describe themselves as male-aligned, because of the experiences they have with being male.