A method for sequencing nucleic acid templates, comprising (a) providing an array comprising a plurality of sites, wherein each site comprises a first nucleic acid template and a second nucleic acid template, wherein the first nucleic acid template has a sequence that is different from the sequence of the second nucleic acid template, wherein a first primer is bound to the first nucleic acid template, a reversible blocking moiety being attached to the first primer, wherein a second primer is bound to the second nucleic acid template, a reversible blocking moiety being attached to the second primer, and wherein the reversible blocking moiety that is attached to the first primer is different from the reversible blocking moiety that is attached to the second primer; (b) selectively removing the reversible blocking moiety that is attached to the first primer while retaining the reversible blocking moiety that is attached to the second primer; (c) extending the first primer by addition of a first nucleotide analog comprising a reversible blocking moiety; (d) selectively removing the reversible blocking moiety that is attached to the second primer while retaining the reversible blocking moiety that is attached to the nucleotide analog that is added to the first primer; (e) extending the second primer by addition of a second nucleotide analog comprising a reversible blocking moiety, wherein the reversible blocking moiety of the first nucleotide analog is different from the reversible blocking moiety of the second nucleotide analog; and (f) detecting the nucleotide analog that is added to the first primer and the nucleotide analog that is added to the second primer, at each of the sites, thereby determining the different sequences of the first template and the second template at each of the sites in an orthogonal manner by using a selective deblocking of nucleotides. (a) providing an array comprising a plurality of sites, wherein each site comprises a first nucleic acid template and a second nucleic acid template, wherein the first nucleic acid template has a sequence that is different from the sequence of the second nucleic acid template, wherein a first primer is bound to the first nucleic acid template, a reversible blocking moiety being attached to the first primer, wherein a second primer is bound to the second nucleic acid template, a reversible blocking moiety being attached to the second primer, and wherein the reversible blocking moiety that is attached to the first primer is different from the reversible blocking moiety that is attached to the second primer; (b) selectively removing the reversible blocking moiety that is attached to the first primer while retaining the reversible blocking moiety that is attached to the second primer; (c) extending the first primer by addition of a first nucleotide analog comprising a reversible blocking moiety; (d) selectively removing the reversible blocking moiety that is attached to the second primer while retaining the reversible blocking moiety that is attached to the nucleotide analog that is added to the first primer; (e) extending the second primer by addition of a second nucleotide analog comprising a reversible blocking moiety, wherein the reversible blocking moiety of the first nucleotide analog is different from the reversible blocking moiety of the second nucleotide analog; and (f) detecting the nucleotide analog that is added to the first primer and the nucleotide analog that is added to the second primer, at each of the sites, thereby determining the different sequences of the first template and the second template at each of the sites in an orthogonal manner by using a selective deblocking of nucleotides.