I tried to to align the tyr gene region for zebrafish and xenopus genomes from UCSC (the genomic region that is annotated as 'tyr' in the genomes for both the taxa). I imported the genomic region and aligned them using geneious. But the alignment gives me both sequences lined up end to end. Could anyone tell me where I am going wrong ?
It is not clear what you mean and the reason that you consider what you see to be "wrong". Perhaps it is not what you wanted but does not make it wrong. It all depends on what you need to do.
I suspect that you are most likely performing a global alignment