What is the best source for an updated list of repetitive element sequences in the human and mouse genomes?
You can get this information from RepBase, the latest version is 18.01 and it was released on 1-30-13. You will have to create an account, but it is free if you are at an academic institution. I'm sure you can download these files from other sites but there everything is one place and you can select whatever format you need (e.g., you can download the repeatmasker libraries directly).
If consensus sequences fits your needs, Repbase has the fasta files. You can also use UCSC to retrieve BED files of genomic repeats (RepeatMasker track - you can grep out repeats of interest), then use BED tools (fastaFromBed) to pull out fastas from the genome giving you actual genomic instances of repeats rather than consensus sequences. It depends on what you are doing with them.
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