Before revision:  Instead of off-the-shelf search and alignment algorithms, which failed to discover the orthologs, we used a special alignment scoring that does not penalize C/T and A/G mismatches  . RNA bases C and U both can bind to G;
After revision:  Instead of off-the-shelf search and alignment algorithms, which failed to discover the orthologs, we used a special alignment scoring that does not penalize C/T and A/G mismatches as much as the other mutations . RNA bases C and U both can bind to G;