Screen_seq is currently set to be able to process a maximum of 10,000 readings and 5000 screening sequences in a single run. The maximum length of any screening sequence is 100,000 although this can be overridden by use of the -m parameter (set it to 5000000 for E. coli). At present the sequences to screen against must be stored in simple text files containing individual sequences, with no entry names, and <100 characters per line.