Motif Discovery

Find a motif NOBODY TYPED: given a set of sequences (multi-record FASTA), report the short pattern they share, as a consensus, a position-weight matrix and one site per sequence. This is the opposite question from motif_finder, which searches for a pattern you already have. Gibbs site sampler (Lawrence et al., Science 1993), one occurrence per sequence, both strands by default. ⚠️ READ found BEFORE THE CONSENSUS: a Gibbs sampler returns a motif from ANY input, including pure noise, because its objective has a maximum whether or not anything is there — so every run is scored against shuffled copies of the same sequences, which hold the same length and base composition and no arrangement. found is true only when the real alignment beats every shuffle outright AND clears the control mean by the margin in control.zScore; when it is false the consensus and sites are still returned, so you can see what was rejected. Measured: 0 of 20 pure-noise sets were reported as found, and a 10-mer planted in all 12 sequences was recovered exactly on 5 of 5 seeds. The sampler is deterministic — the same input gives the same answer, so a saved or shared result reproduces; pass a different seed to see whether the motif survives a different starting point, because one that does not is weak.