For a small set of sequences, such as yours, you could also use Meme, Weeder or others online without installing them locally. Finally, the Regulatory Sequence Analysis Tools (RSAT) ( http://rsat.ulb.ac.be/rsat/ or http://rsat.ccb.sickkids.ca/) are a great place to start for pattern matching and discovery.
In case it is of any use I have put up a short presentation about DNA motif finding from a course I gave earlier this year. You can find it here.
Some time ago I used SOMBRERO (http://bioinf.nuigalway.ie/sombrero/download.html) with a good degree of success on finding motifs in a very diverse set of sequences. They have a Mac version for download as well as parallel versions for Irix and Linux.
The first step when looking for conservation of single bases or motives is often a multiple sequence alignment that will align the sequences in a way such that conserved regions are best visible. This can be a first step before using explicit motif finders like MEME. A good way of visualizing multiple alignments is the sequence-logo that will give a graphical representation of base conservation.
Here is the wikipedia list of mult.-sequence alignment tools.
I recommend to start with the EBI web-server of ClustalW though, if that is not enough you can also try MAFFT or T-Coffee.
Weblogo can generate sequence-logo graphics from the output and also from fasta input directly.
Advantage of these tools is that you don't need to install them, so good for a first attempt irrespective of using a Mac.
Meme has been the first program to be published for doing that. As an alternative you can find one of the EMBOSS tools; if you are scared by a terminal and want to do it from a web-based interface, you can use the EMBOSS tools from galaxy
You may check out these pages:
These are ca 2 years old (links may not work etc.) but as a starting point should be OK. Also in unlikely case you did not found it yet: in yeast there has been an extensive motif search study done by Kellis with insane number of citations:
- Nature. 2003 May 15;423(6937):241-54.
- Kellis M, Patterson N, Endrizzi M, Birren B, Lander ES. Sequencing and comparison of yeast species to identify genes and regulatory elements
ACGGGCCCGACGATGCGTCGTA ACGTACGTCGAACCGTCGTCGT ACGTGCGTCGAAACGTCAGTCG ACGGGTTCGATCGTCGTCGTCG
may be in Python I will break down the first sequence of required motif length into a sliding window and will search for those list of motifs in the rest of sequences using regular expression in python using