Please note: 
T. muris genome assembly version 2.1 (file "Tmuris_genome_v2.1.fa") is the version that corresponds to the gene models (file "Tmuris_genes_v2.3.gff").

Genome assembly version 2.2 submitted under BioProject PRJEB126 to ENA/NCBI (http://www.ebi.ac.uk/ena/data/view/PRJEB126, http://www.ncbi.nlm.nih.gov/bioproject/PRJEB126) is essentially the same as assembly version 2.1, but with different gap sizes.