Look for 'profile alignment' mode in your MSA tool of choice. Muscle and Clustal have this feature for sure, as does t-coffee.

HTH.

Hi,

I know I'm too late so this is just for future reference:

You could try the new version of Clustal (Clustal Omega), which automatically turns already aligned sequences into a HMM which is then used to guide the following alignment process. This is especially useful if you want to align more than one sequence to your profile (i.e. your pre-aligned sequence set) but might be overkill if you just have one sequence.

Andreas

One option is to use PAGAN, which will take your large mitochondrial alignment and, if you have one, its associated tree, as references where you will add new sequences. If you have multiple overlapping short sequences in your dataset, you can also build contigs from the clusters of sequences (reads) that fall into the same place in the reference alignment:

Basic reads alignment options:
  --ref-seqfile arg     reference alignment file (FASTA)
  --ref-treefile arg    reference tree file (NH/NHX)
  --readsfile arg       reads file (FASTA/FASTQ)
  --pair-end            connect paired reads
  --454                 correct homopolymer error
  --use-consensus       use consensus for read ancestors
  --build-contigs       build contigs of read clusters
  --test-every-node     test every node for each read
  --fast-placement      use Exonerate to quickly assign reads to nodes

You could easily do this using HMMER. Simply use hmmbuild to construct a Hidden Markov Model from your pre-made alignment. You can then use hmmalign to align each of your short sequences against the HMM.

ClustalW lets you do this too. The is an option for adding sequences to an already calculated alignment.