44way conservation levels are available as a set of WIG/BIGWIG files at the UCSC. For example, see: ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/phastCons46way/primates/
you can query and convert those wig/bigwig files using wigtobigwig and bigWigToBedGraph in http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/
================================================================ ======== bigWigToBedGraph ==================================== ================================================================ bigWigToBedGraph - Convert from bigWig to bedGraph format. usage: bigWigToBedGraph in.bigWig out.bedGraph options: -chrom=chr1 - if set restrict output to given chromosome -start=N - if set, restrict output to only that over start -end=N - if set, restict output to only that under end -udcDir=/dir/to/cache - place to put cache for remote bigBed/bigWigs
In the title you ask how to calculate the conservation score, and in the description just how to extract conservation score from multiple regions.
For extracting you might want to take a look at biopieces. It includes a program for exactly that purpose: http://code.google.com/p/biopieces/wiki/get_genome_phastcons
Of course, the genome and conservation scores have to be downloaded from UCSC and set up for biopieces first.