There are compressed multiple alignments of 59 assemblies to the mouse genome (mm10/GRCm38, Dec. 2011)
Readme and directory:
http://hgdownload-test.sdsc.edu/goldenPath/mm10/multiz60way/
MAF files:
http://hgdownload-test.sdsc.edu/goldenPath/mm10/multiz60way/maf/

We have thousands of mouse transcripts in bed format (file name: mouse.bed).
How can we get the alignments in FASTA format for all the mouse transcripts as follows (we only need the specified five species, not all the 60 species):

>mm10|chr6(+):2345-7890
ATCGAAAATTGCCCAAA...
>oryCun2
AT-GAAAAT-GCCCAAA...
>speTri2
--CGAAAATTGCCCAAA...
>hg19
ATCGAAAATTGC-----...
>otoGar3
ATCGAAA----CCCAAA...

Thanks a lot, in advance.

Aimin Li