A method for identifying a nucleotide in a single stranded nucleic acid template bound to a support comprising: (a) hybridizing a sequencing primer to the single stranded nucleic acid template at a sequencing primer hybridization site, (b) hybridizing an oligonucleotide probe comprising a template-hybridizing nucleic acid sequence and a template-nonhybridizing nucleic acid structure to the single stranded nucleic acid template at a site adjacent to the sequencing primer hybridizing site and ligating the hybridized oligonucleotide probe to the sequencing primer to form an extended hybridized sequence, wherein a nucleotide at a specific position within the template-hybridizing nucleic acid sequence of the oligonucleotide probe is known, wherein the template-nonhybridizing nucleic acid structure is cleavably attached to the template-hybridizing nucleic acid sequence of the oligonucleotide probe, and wherein the template-nonhybridizing nucleic acid structure inhibits multiple ligations in a single ligation cycle and comprises a detectable label corresponding to the known nucleotide at the specific position within the template-hybridizing nucleic acid sequence of the oligonucleotide probe and a cleavable nucleotide immediately attached to a terminal hybridized nucleotide of the oligonucleotide probe, (c) identifying the known nucleotide at the specific position within the template-hybridizing nucleic acid sequence in the oligonucleotide probe by detecting the corresponding label, and identifying a nucleotide that is complementary to the known nucleotide detected by the corresponding label in the single stranded nucleic acid template, and (d) optionally removing the template-nonhybridizing nucleic acid structure by cleavage of the cleavable nucleotide and generating an extendable terminus on the extended hybridized sequence. (a) hybridizing a sequencing primer to the single stranded nucleic acid template at a sequencing primer hybridization site, (b) hybridizing an oligonucleotide probe comprising a template-hybridizing nucleic acid sequence and a template-nonhybridizing nucleic acid structure to the single stranded nucleic acid template at a site adjacent to the sequencing primer hybridizing site and ligating the hybridized oligonucleotide probe to the sequencing primer to form an extended hybridized sequence, wherein a nucleotide at a specific position within the template-hybridizing nucleic acid sequence of the oligonucleotide probe is known, wherein the template-nonhybridizing nucleic acid structure is cleavably attached to the template-hybridizing nucleic acid sequence of the oligonucleotide probe, and wherein the template-nonhybridizing nucleic acid structure inhibits multiple ligations in a single ligation cycle and comprises a detectable label corresponding to the known nucleotide at the specific position within the template-hybridizing nucleic acid sequence of the oligonucleotide probe and a cleavable nucleotide immediately attached to a terminal hybridized nucleotide of the oligonucleotide probe, (c) identifying the known nucleotide at the specific position within the template-hybridizing nucleic acid sequence in the oligonucleotide probe by detecting the corresponding label, and identifying a nucleotide that is complementary to the known nucleotide detected by the corresponding label in the single stranded nucleic acid template, and (d) optionally removing the template-nonhybridizing nucleic acid structure by cleavage of the cleavable nucleotide and generating an extendable terminus on the extended hybridized sequence.