I am identifying yeast species based on the sequencing of the its1-5.8s-its2 region in ribosomal DNA. For all yeast species identified sequencing reads have turned to be very good except for two species of the same genus. In fact except for some sequences belonging to these two species while other sequences were contamination free. Cutures of the corresponding microorganisms were purified several times, DNA extracted again each time, PCR repeated and products sequenced. And results always turned out to be the same : a contamination of the sequences always beginning from the same length spot (ex 200pb) and on, but not from the beginning of the sequences. Sequences corresponding to other species but run in the same PCRs were contamination free as well as the negative controls.
Any suggestions about what this contamination might be ? Thank you