Sequence Motifs are a short recurring patterns in DNA that are presumed to have biological function. So to identify motifs the genes are turned ON/OFF by regulatory proteins and these proteins bind to upstream regulatory regions of genes to either attract or block RNA polymerase then regulatory proteins or Transcription Factors binds to short DNA sequence called motifs or Transcription factors binding sites so finding the same motif in multiple genes regulatory regions suggest regulatory relationship among those genes. Motifs profiles and consensus create by line up the alignment sequence patterns by their start indexes to construct matrix profile with frequencies of each nucleotide in columns to consensus nucleotide in each position that has the highest score in each column (Watch Related Video in #geneticteacher)
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