first you may try to sequence D1 and D2 domine and ITS regions of the gens it give better results..single 18s rRNA sequence not give effective results

Dear Stefanos,

You can find a variability map of 18S in Eukaryota through this link:

http://bioinformatics.psb.ugent.be/webtools/rRNA/

However, you have to upload the site, but you will find what you want I think!

Or upload via this link:

http://onlinelibrary.wiley.com/doi/10.1111/j.1755-0998.2009.02795.x/suppinfo

the file entilted:

MEN_2795_sm_FigS1.tif

You will have an idea about what you will find ont the ancient European ribosomal database site.

You can also search publications from Van de Peer that works on 18S variability.

V-Xtractor will indicate the D regions in fungal 18S sequences:

https://www.researchgate.net/publication/46094759_V-Xtractor_an_open-source_high-throughput_software_tool_to_identify_and_extract_hypervariable_regions_of_small_subunit_%2816S18S%29_ribosomal_RNA_gene_sequences?ev=srch_pub

Article V-Xtractor: An open-source, high-throughput software tool to...