Figure 3

Multi-alignments of 34 S. japonicum genome contigs representing duplicated loci to assign putative source locus. Graph shows the sequence similarity (A) and absolute complexity (B) of the DNA sequence of the 34 contigs in S. japonicum genome containing the duplicated loci. This multiple alignment was used to putatively assign the most prominent contig [GenBank:CABF01020060], the longest among the identified dataset (43.7 kb), which significantly covered the length of the other contigs as the putative duplication ‘source locus’. The curve shows the probable length of the duplicated locus, terminating with RTE-SJ at the 5` end (trimmed out in this figure) and Perere at the 3` end. ‘Similarity’ curve is a measure of the level of similarity of the aligned sequences. The y-axis on the ‘similarity’ curve will read ‘1’ when the sequences are 100 % similar in each position. The output shows the maximum score on the y-axis. Absolute complexity is a measure of the level of conservation or variability of nucleotides in the aligned sequences. It is a measure of the likelihood that the observed similarity did not occur by chance. The maximum positive score on the y-axis of the ‘absolute complexity’ curve is expected to be higher than the negative value to exclude any possibility that the observed similarity occurred by chance. The x-axes in both curves represent the nucleotide positions. The numbering of the nucleotides started at the 30000^th position in this figure because we trimmed output figure at the 5` end for ease of presentation.