A method for sequencing a target double stranded polynucleotide molecule, comprising the steps of: a) providing a plurality of double-stranded polynucleotide molecules having a known length; b) attaching the plurality of double-stranded polynucleotide molecules to a surface, wherein a first portion on a first end of each of the polynucleotide molecules is attached to a first location of the surface and a second portion on a second end of each of the polynucleotide molecules is attached to a second location of the surface, wherein the first portion and second portion are located at the opposite ends of the polynucleotide molecules; c) separating the first portion and second portion of each of the plurality of double-stranded polynucleotide molecules on the surface; d) amplifying the first portion and second portion of each of the double-stranded polynucleotide molecules at the first location and second location, thereby producing a plurality of clusters on the surface; e) identifying the locations of the first portion and second portion of each of the plurality of double-stranded polynucleotide molecules on the surface using an imaging device, and determining the distance from one location to another location of first portion and second portion of each of the plurality of double-stranded polynucleotide molecules on the surface; f) determining the sequences of the first portion and the second portion of each of the double-stranded polynucleotide molecules in the plurality of double-stranded polynucleotide molecules; g) comparing the sequences and the locations of the first portion and second portion of each of the plurality of double-stranded polynucleotide molecules on the surface, wherein the distance from one said location to another location determines the probability of whether the sequence of the first portion and the sequence of the second portion are located on the same target polynucleotide molecule; and h) using sequences of the first and second portions to determine the sequence of the plurality of target polynucleotide molecules. a) providing a plurality of double-stranded polynucleotide molecules having a known length; b) attaching the plurality of double-stranded polynucleotide molecules to a surface, wherein a first portion on a first end of each of the polynucleotide molecules is attached to a first location of the surface and a second portion on a second end of each of the polynucleotide molecules is attached to a second location of the surface, wherein the first portion and second portion are located at the opposite ends of the polynucleotide molecules; c) separating the first portion and second portion of each of the plurality of double-stranded polynucleotide molecules on the surface; d) amplifying the first portion and second portion of each of the double-stranded polynucleotide molecules at the first location and second location, thereby producing a plurality of clusters on the surface; e) identifying the locations of the first portion and second portion of each of the plurality of double-stranded polynucleotide molecules on the surface using an imaging device, and determining the distance from one location to another location of first portion and second portion of each of the plurality of double-stranded polynucleotide molecules on the surface; f) determining the sequences of the first portion and the second portion of each of the double-stranded polynucleotide molecules in the plurality of double-stranded polynucleotide molecules; g) comparing the sequences and the locations of the first portion and second portion of each of the plurality of double-stranded polynucleotide molecules on the surface, wherein the distance from one said location to another location determines the probability of whether the sequence of the first portion and the sequence of the second portion are located on the same target polynucleotide molecule; and h) using sequences of the first and second portions to determine the sequence of the plurality of target polynucleotide molecules.