Table 1 Overview of the total number of sites of all alignments per alignment method and the number of derived splids with length \(\ge\) 2 bp for the ENCODE data set containing only alignments with sequence information for all taxa

ClustalW

Dialign-TX

Mafft

Mafft L-INS-i

Mafft G-INS-i

Muscle

ProbConsRNA

Prank

T-Coffee

TBA/Multiz