Additional file 2 of Circular DNA intermediates in the generation of large human segmental duplications

Additional file 2: Table S1. Genomic coordinates of duplicated SD clusters and blocks and identity percentage between duplicates. * Duplication 1 in SD clusters 15 and 16 is present twice because there are SD blocks with different sizes between duplication 2 and duplication. Table S2. Ratio of repetitive elements content size versus total size of cSDPs or corresponding chromosomes. Table S3. Repetitive elements overlapping the closing, opening and insertion breaking junctions during the formation and integration of the circular intermediates. Percentage of repetitive elements in 500 bp of sequence flanking each side of the respective junction are shown in parenthesis and in bold numbers. Table S4. NCBI RefSeq curated elements described in the cSDP regions. This table shows the different elements described in the RefSeq curated database that are included in the cSDP regions. In the column “Paralog genes” those genes that may have paralog genes are highlighted in bold. Anc: ancestral; der: derivative; dup: duplicon; BX: Block number X of the cSDP. *: UPK3c is not described in RefSeq, but corresponds to UPK3BL. EST DB249571 shows the expression on the derivative sequence of the first 3 exons of ancestral UPK3c. Table S5. Description of the 160 putative SD cluster pairs. This table shows the 160 hits of putative SD clusters pairs, highlighting in green colour those 34 which have a reliable homology plot and there is a breaking junction between the two SD cluster pairs. Dup1: Duplication cluster 1; Dup2: Duplication cluster 2; Alignment length: Length of the alignment between Dup1 and Dup2 in nucleotides; Aligned matches: Number of matching nucleotides in the alignment in nucleotides; Match fraction: Fraction of matching nucleotides; SD blocks: Number of blocks involved in the putative SD cluster pairs; AB: Values belonging to the A-B block described in the proposed mechanism; CD: Values belonging to the C-D block described in the proposed mechanism; Duplication color code: green - putative SD cluster pair with reliable homology plot and a breaking junction between the SD cluster pairs.