1. A method for barcoding a polynucleotide, comprising the steps of: a) immobilizing on a solid phase and stretching an isolated, individual polynucleotide comprising nucleotide targets; b) labeling each of the targets using a corresponding target-specific hybridization probe; and c) directly optically detecting a single, individual fluorescent label of each unamplified probe at each of the targets, and determining label order to form a barcode representation of the polynucleotide wherein the targets and their relative positions are represented, wherein in the labeling step, discontinuous padlock probes are hybridized to the targets, and gap-filled with fluorescent nucleotides.