Sequence analysis of intermediate size PCR products from the pRK1Δ att 340/184neo rescue assay. DNA was prepared from colonies arising from the second round of the pRK1Δatt340/184neo provirus rescue assay and analysed by PCR as described in Methods. PCR products that were intermediate in size to the SIN LTR and the repaired LTR were sequenced and showed partial repair of the U3 sequence, with the sequence truncated at the 5' end. Four of these clones also contained partial duplications of the R/SV40 polyadenylation sequence from the 3' LTR. Δatt 3' LTR, structure of the 3' LTR from pRK1Δatt340/184neo; Δatt 5' LTR, structure of the 5' LTR from pRK1Δatt340/184neo; predicted post-RT 5' LTR, structure of the pRK1Δatt340/184neo proviral 5' LTR after reverse transcription and integration; 5' LTR variant 1 and 2, structure of sequenced PCR products for which the PCR product did not correspond to the size predicted for the SIN or the repaired LTR. Of the 5 PCR products sequenced, 4 corresponded to variant 2.