[Genome] (no subject)

[JONATHAN COOPER]

Hi.
   
  I am required for an Msc project to compare 1400 human RE1(repressor element 1) sites (each 21bp) against chimp, rat, & mouse genomes for sequence homology. Although i could  do this manually, it'd take me quite a while, & wouldn't be much fun. Could you please tell me - are there any scripts you know of that can do this for me? Failing that, can you suggest the most appropriate data to download to write a script for. At the moment i am considering using the "axtNet" genome alignments - but am not sure if it is the best format to use. All i really need is for a file to contain the most similar match to the sequences i give it (and possibly a blast score)
   
  Thanks for your time,
  best regards,
  Jon.