Base-wise conservation scores (PhyloP score calculated with PHAST), based on the multiple alignment of placental mammal genomes, were downloaded from the UCSC Genome Browser. The 50 bp window in each lincRNA transcript with the highest average PhyloP score was identified. The process was repeated for RefSeq NM genes and a set of size-matched (to lincRNAs) repetitive elements from RepeatMasker (UCSC Genome Browser). PhyloP scores for the maximally conserved 50 bp windows of each lincRNA are listed in Table S4.
