TABLE 2.

Integration sites analyzed and their similarities to known sequences

Sequence namea	Length (bp)b	Dup seqc	Identified similaritiesd	Identified similarities truncated to 50 bpe
MolH 1	106	ATGTC	*f	*
MolH 2	60	CAAGC	*	*
SupH 1	156	TCTTC	LINE-1 [2–153, SW = 508]	*
SupH 2	132	GCTAC	*	*
SupH 3	91	GGAAA	*	*
SupH 4	139	GTGGT	*	*
SupH 5	140	TATAT	*	*
SupH 6	114	ATCCC	*	*
SupH 7	230	GCATG	*	*
SupH 9	82	CTATA	*	*
SupH 10	212	TACAC	LINE-1 [2–107, SW = 251]	*
SupH 11	166	CATGC	Alu [15–110, SW = 716]	Alu [SW = 304]
SupH 12	89	GTTGG	*	*
SupH 13	63	CTCAC	Transcription unit (cDNA) [5–62, P = 1.6 × 10−16]	Transcription unit (cDNA) [P = 1.9 × 10−12]
SupH 14	111	GTCAC	*	*
SupH 15	164	TATGG	LINE-1 [2–107, SW = 400]	*
SupH 16	66	AACAG	*	*
SupH 17	54	CTCAC	*	*
SupH 18	159	GTTGT	*	*
SupH 20	342	GTTTC	Alu [3–125, SW = 956]	Alu [SW = 373]
SupH 21	173	CATAT	*	*
SupH 22	38	CACAC	*	Excluded
SupH 23	258	CATTC	*	*
SupH 24	110	GTAAT	*	*
SupH 25	37	CTTTT	*	Excluded
SupH 27	160	CCATT	*	*
SupH 28	93	AATAC	Transcription unit (cDNA) [1–93, P = 3.7 × 10−33]	Transcription unit (cDNA) [P = 1.5 × 10−13]
SupH 29	143	GCCCA	*	*
SupH 31	188	ATATT	*	*
SupH 32	157	GTTGA	Transcription unit (cDNA) [59–157, P = 5.9 × 10−34]	*
SupH 33	50	CTTCA	Transcription unit (VACH1 gene) [1–50, P = 6 × 10−13]	Transcription unit (VACH1 gene) [P = 6 × 10−13]
SupH 34	50	AGTTG	*	*
SupH 35	420	TTAAC	Transcription unit (cDNA) [52–143, P = 2.8 × 10−25]; LINE-2 [223–274, SW = 252]	*
SupH 36	237	CTTGT	*	*
SupH 37	69	CACAC	Alu [1–69, SW = 471]	Alu [SW = 371]
SupH 38	68	GTTAT	*	*
SupH 39	89	CAAAA	*	*
SupH 41	41	ATGGC	*	Excluded
SupH 42	437	AAAAC	LINE-1 [1–437, SW = 2684]	LINE-1 [SW = 264]
SupH 43	179	ATAGT	Transcription unit (cDNA) [1–179, P = 9.4 × 10−65]; other repeat (LTR element) [98–152, SW = 198]	Transcription unit (cDNA) [P = 3.8 × 10−13]
SupH 44	337	GAAAC	Other repeat (MIR, SINE) [191–315, SW = 493]	*
SupH 46	81	GGGAG	Transcription unit (cDNA) [1–33, P = 3.9 × 10−6]	Transcription unit (cDNA) [P = 4.6 × 10−6]
SupH 47	111	AAAAC	Transcription unit (cDNA) [1–57, P = 2.1 × 10−13]	Transcription unit (cDNA) [P = 2.2 × 10−9]
SupH 48	125	CTGTG	Other repeat (MIR, SINE) [1–123, SW = 474]	Other repeat (MIR, SINE) [SW = 245]
SupH 49	260	TTTTG	Alu [1–128, SW = 698]	Alu [SW = 300]
SupS 1	176	GCAGG	Transcription unit (CD27 gene) [1–176, P = 2.7 × 1062]	Transcription unit (cDNA) [P = 5.4 × 10−13]
SupS 2	113	GTTCT	*	*
SupS 3	125	ATACC	Alu [4–115, SW = 540]	Alu [SW = 195]
SupS 4	215	CCCTC	Other repeat (MER74, LTR element) [1–213, SW = 599]	Other repeat (MER74, LTR element) [SW = 277]
SupS 5	147	CAGCA	*	*
SupS 7	171	GAGTC	*	*
SupS 8	85	TGAGT	Transcription unit (cDNA) [1–81, 3.2 × 10−26]	Transcription unit (cDNA) [P = 3.6 × 10−13]
SupS 9	86	GTACC	*	*
SupS 10	52	AAAGC	Alu [2–59, SW = 356]	Alu [SW = 310]
SupS 11	147	CTAAC	*	*
SupS 12	131	GTTTC	*	*
SupS 13	94	ATGTG	Transcription unit (cDNA) [1–94, P = 5.1 × 10−28]	Transcription unit (cDNA) [P = 3.4 × 10−12]
SupS 14	184	GAGAC	*	*
SupS 15	120	AAATG	*	*
SupS 16	161	CTCTG	*	*
SupS 17	215	GTATG	*	*
Total bp	8,809			2,900
Avg	144			50

^aLaboratory designation for each DNA clone. 

^bNumber of human DNA base pairs sequenced adjacent to the HIV cDNA terminus. 

^cNucleotide sequence of the 5 bp of human DNA at the junction with viral DNA expected to be duplicated upon integration. 

^dSequence similarities found by comparison to sequence databases (the first designation is the sequence class given in Table 3, the name in parentheses is a more detailed designation, and the numbers in brackets represent the location of the sequence match [e.g., 1 = the first cDNA-proximal base pair in host DNA] and the degree of similarity). 

^eSimilarities identified in the 50-bp sequence data set. For explanation of bracketed data, see footnote d. 

^f*, anonymous.