DNA replication requires an ori, the origin of replication, and is performed by DNA Polymerase. Finding the ori is similar to finding a hidden message in a string. The ori can be identified by looking for a kmer appearing frequently in the DNA sequence.
Motifs are biologically significant nucleotide sequences in the DNA or protein. Regulatory motifs act as binding sites for transcription factors or master regulatory proteins which control the expression of specific genes. Motif finding requires identifying similar kmers in a DNA sequence by having a consensus string as reference.