BMC Genomics 2006, 7:73 Additional material Additional File 1 RH017.fasta.all.cr – Multiple FASTA file. Multiple FASTA file contain- ing output from the sequencing reactions generated by the M13 Reverse primer. Click here for file [http://www.biomedcentral.com/content/supplementary/1471- 2164-7-73-S1.cr] Additional File 2 RH017.fasta.all.c21 – Multiple FASTA file. Multiple FASTA file con- taining output from the sequencing reactions generated by the M13 For- ward primer. Click here for file [http://www.biomedcentral.com/content/supplementary/1471- 2164-7-73-S2.c21] Additional File 3 pair_count4.pl – Perl script to extract spacer sequences from sequence reads. This file is a Perl script that detected successful recombinants from the sequencing reads. Spacer sequence was extracted and immediately deposited into a MySQL database. Click here for file [http://www.biomedcentral.com/content/supplementary/1471- 2164-7-73-S3.pl] Additional File 4 Table S1 – Table_S1_mismatch_analysis.xls – Sequence of spacers participating in recombination. This file is an Excel spreadsheet all of the loxP spacers that successfully recombined. Contains pre- and post- recombination sequence as inferred from the location of the scissile bonds and reaction mechanism (see Figure 3 for details). This is the effective output of the pair_count4.pl script. All data analysis was performed on the inferred spacer sequences as they were considered the input oligonucle- otides into the reaction. Click here for file [http://www.biomedcentral.com/content/supplementary/1471- 2164-7-73-S4.xls] Additional File 5 Analysis_scripts.zip – zip file containing all analysis scripts. All SQL, Perl and shell scripts used in this analysis. Detailed explanation of their functionality given in the README.txt file. 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