Identification of presence of genes by aligning the illumina reads to reference genome with Geneious

Question

[rthapa]

Hi, I am trying to find if the particular gene is present in the illumina reads. I have gene sequence for this particular gene. I tried using Geneious software for aligning the illumina reads to the gene sequence but the Geneious sent a message that there is no contig. I wonder if that is because there is no alignment. Does anyone have any idea? Do you have suggestion on any other way that could be used for finding the presence of gene in any organism based on illumina sequence reads? Thanks