Escherichia coli - Tandem Repeat Analysis Protocol

Experimental procedure

1. The file e_coli.fasta corresponds to the frozen data (June 4, 2004 http://www.ncbi.nlm.nih.gov GB U00096) of Escherichia coli genome.
   
   
2. Genome sequence FASTA file Genome complexity - 4,639,675 bp
   
   
3. The file was submitted to Tandem Repeats Finder (TRF) (Benson, 1999) program using the following parameters:
   2 5 7 80 10 25 1000.
   
   
4. TRF output files were analyzed by the Tandem Repeat Analysis Program (TRAP) using the following parameters:
   • Minimum period size of repeats - 7
   • Maximum period size of repeats - 10
   • Minimum identity percentage - 90
   • Create HTML and CSV files - yes
   • Create TRF-like HTML files - yes
   • Sorting - according to the total number of bases
   • Create feature table files - yes
   • Create redundancy report file - yes
     

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