Overview of the reconstruction of the MAL2 locus in S. cerevisiae CEN.PK113-7D. A) Depth of coverage analysis of MAL loci. Sequencing reads from the CEN.PK113-7D and S288C have been mapped onto the S288C genome sequence. Log2-ratio's of the average sequencing depth in 414-bp windows of CEN.PK113-7D over S288C have been plotted versus genomic position. Log2-ratio's were capped at -4. B) Schematic representation of the paired-end linkage analysis that showed anomalous read pairs (red arrows) on the end of chromosome III that mapped to BIO2 on CHRVII. C) Southern blots and karyotypes, denoted with 'b' and 'k', respectively, of S288C and CEN.PK113-7D, denoted with 'S' anc 'C', respectively. Probes for IMA1, BIO2 and MAL32 were amplified with the primers listed in Additional file 5: Table S8. Square boxes indicate hybridized chromosomes. Chromosomes marked with an asterisk (*) depicts cross-hybridization of the IMA1 probe to paralogs of IMA1 (see text). D) Schematic organization of the MAL loci in CEN.PK113-7D. Loci marked with (#) were individually amplified, sequenced and assembled.