A method for amplifying nucleic acids, comprising (a) providing an amplification reagent comprising (i) an array of amplification sites, wherein the amplification sites comprise two populations of capture nucleic acids, each population comprising a capture sequence, wherein a first population comprises a first capture sequence and a second population comprises a second capture sequence, and (ii) a solution comprising a plurality of different modified double-stranded target nucleic acids, wherein the different modified target nucleic acids comprise at the 3' end a first universal capture binding sequence having less affinity for the first capture sequence than a first universal capture binding sequence having 100% complementarity with the first capture sequence; and (b) reacting the amplification reagent to produce a plurality of amplification sites that each comprise a clonal population of amplicons from an individual target nucleic acid from the solution, optionally wherein the reacting comprises (i) producing a first amplicon from an individual target nucleic acid that transports to each of the amplification sites, and (ii) producing subsequent amplicons from the individual target nucleic acid that transports to each of the amplification sites or from the first amplicon, wherein the average rate at which the subsequent amplicons are generated at the amplification sites is less than the average rate at which the first amplicon is generated at the amplification sites. (a) providing an amplification reagent comprising (i) an array of amplification sites, wherein the amplification sites comprise two populations of capture nucleic acids, each population comprising a capture sequence, wherein a first population comprises a first capture sequence and a second population comprises a second capture sequence, and (ii) a solution comprising a plurality of different modified double-stranded target nucleic acids, wherein the different modified target nucleic acids comprise at the 3' end a first universal capture binding sequence having less affinity for the first capture sequence than a first universal capture binding sequence having 100% complementarity with the first capture sequence; and (i) an array of amplification sites, wherein the amplification sites comprise two populations of capture nucleic acids, each population comprising a capture sequence, wherein a first population comprises a first capture sequence and a second population comprises a second capture sequence, and wherein the amplification sites comprise two populations of capture nucleic acids, each population comprising a capture sequence, wherein a first population comprises a first capture sequence and a second population comprises a second capture sequence, and (ii) a solution comprising a plurality of different modified double-stranded target nucleic acids, wherein the different modified target nucleic acids comprise at the 3' end a first universal capture binding sequence having less affinity for the first capture sequence than a first universal capture binding sequence having 100% complementarity with the first capture sequence; and (b) reacting the amplification reagent to produce a plurality of amplification sites that each comprise a clonal population of amplicons from an individual target nucleic acid from the solution, optionally wherein the reacting comprises (i) producing a first amplicon from an individual target nucleic acid that transports to each of the amplification sites, and (ii) producing subsequent amplicons from the individual target nucleic acid that transports to each of the amplification sites or from the first amplicon, wherein the average rate at which the subsequent amplicons are generated at the amplification sites is less than the average rate at which the first amplicon is generated at the amplification sites. (i) producing a first amplicon from an individual target nucleic acid that transports to each of the amplification sites, and (ii) producing subsequent amplicons from the individual target nucleic acid that transports to each of the amplification sites or from the first amplicon,