Figure 5
From: Fast local fragment chaining using sum-of-pair gap costs
Alignment of Human H/ACA snoRNA 42 and homologous H/ACA snoRNA candidates in mouse retrieved by BLAST and clasp with sum-of-pair gap costs. Alignment of the Human H/ACA snoRNA 42 (SNORA42 in the snoRNABase) and 7 H/ACA snoRNA candidates in mouse retrieved by combined use of BLAST (with options -W 8 -e 1e+20 -F F) and clasp (sum-of-pair gap costs with 
, 
, fragment scores according to the length of the BLAST hit, and a minimal required chain score of 30). Sequence alignment and consensus secondary structure were computed using ClustalW and RNAalifold with constraints, i.e. demanding single-stranded regions at the H-box (blue rectangle) and ACA-motif (green rectangle).