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Transposable elements were identified with the program RepeatMasker (http://www.repeatmasker.org).org
TagSNPs were identified with the program Tagger [ 19].
Open reading frames (ORFs) were identified with the program Getorf from the EMBOSS-package [ 96].
Genes were identified with the program getorf from the EMBOSS package (http://emboss.sourceforge.net/) [72].
Surface pockets were identified with the program DoGSiteScorer (Volkamer et al., 2012).
These loci were identified with the program Tandem Repeat Finder (11 ).
Differentially expressed genes were identified with the program Significance Analysis of Microarrays (SAM) [ 63].
Potential hydrogen bonds were identified with the program CONTACT in CCP4 (Winn et al., 2011) and manually inspected.
Repetitive sequences were identified with the program SATFIND, which was developed in order to determine the position of long tandem repeats (satellites).
Novel repetitive regions were identified with the program RepeatScout (Price et al. 2005), the output of which was combined with fungal repeats downloaded from RepBase version 17.1 (Jurka et al. 2005) to create a custom library of repetitive elements for the genome.
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