For the purpose of molecular identification I have sequenced the ITS1, 5.8s rDNA and ITS2 regions of an endophytic fungi using ITS1 and ITS4 primers. And obtained a contiguous sequence out of these two sequences using CAP3 sequence assembly programme. The sequences individually and as contig. are giving the same hits. Now I want to annotate the sequence with features. I know it has complete sequence of ITS1, 5.8s and ITS2 with partial 23s sequences. But don't know the exact positions of these three regions. kindly help me with some software names to annotate the ITS sequence. (Note: I did not find any ITS sequence database for my fungus).