One of the inputs is a file of 16384 strings given in below example format:

Given a string of 7 fasta characters, you can form 4^7= 16384 unique strings from T, A, G, C. So, his algorithm is checking every possible 7 char fasta string against the mutifasta file (number of lines in the multifasta file is 61913917).

In reply to Re^3: counting the number of 16384 pattern matches in a large DNA sequence by Cristoforo
in thread counting the number of 16384 pattern matches in a large DNA sequence by anonym

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