1. A method for amplifying a plurality of target sequences from a nucleic acid sample and analyzing the amplified target sequences, the method comprising:(a) mixing the nucleic acid sample with (a1) an array of probes arranged in features and (a2) a plurality of oligonucleotides,
wherein the nucleic acid sample comprises target fragments comprising target sequences,
each feature comprises multiple copies of a target specific array probe having (i) a first probe region that is complementary to a first target region, (ii) a second probe region that is complementary to a second target region, and (iii) a central probe region that is complementary to one of the oligonucleotides, said central probe region being between the first and second probe regions,
the target fragments hybridize to complementary target specific array probes to form probe:target fragment complexes, and
in the probe:target fragment complexes, the first target region hybridizes to the first probe region, the second target region hybridizes to the second probe region, and the oligonucleotide hybridizes to the central probe region;
(b) joining the first target region, the oligonucleotide, and the second target region that hybridize to the same array probe to form a target circle;
(c) extending the array probe using the target circle as a template, thereby obtaining an extended array probe comprising a plurality of copies of the complement of the target sequences; and
(d) analyzing the copies.