Scores of proto-splice sites. The distributions of splice site scores are shown separately for donor, acceptor, and the sum of donor and acceptor sites, displaying different sets of sites: (RS) 16766 reference splice sites of D. melanogaster, (TD) the 18 proto-splice sites from 7 apomorphic NIP introns potentially arised by tandem duplications, (ON) the 236 proto-splice sites from all other NIP introns, (RP) 16506 potential proto-splice sites corresponding to the reference introns, and (IS) 52626 exonic AGGY motif surroundings which are located more than 31 nt apart from exon boundaries. (A-C) Results that refer to complete splice consensus sites. TD proto-splice sites are potentially functional splice sites as (1) they are within the range of functional splice site scores of the reference set (RS), and (2) they reside within the top range of proto-splice site scores of the intron reference set (RP). (D-F) Scores determined as in (A-C) that refer to a partial splice consensus excluding the motif AG/GY. (G) Identical nts between the donor and acceptor sites of each intron excluding the motif AG/GY. 15 nts (-13 to -3 and +3 to +6 in relation to start and end of each intron, respectively) were compared between both sites. Given no similarity between both sites, 3.75 identical nt positions would be expected at random.