Rapid identification and mapping of insertion sequences in Escherichia coli genomes using vectorette PCR

Zhong, Shaobin; Dean, Antony M

doi:10.1186/1471-2180-4-26

BMC Microbiology

Table 1 IS elements in closely related E. coli strains MG1655, CGSC6300, TD2 and TD10

From: Rapid identification and mapping of insertion sequences in Escherichia coli genomes using vectorette PCR

					A-side	B-side	Strain
Element	start (bp)	end (bp)	Flanking Genes	Direction	fragment size^a	fragment size^a	MG1655	CGSC6300	TD2	TD10
Known Elements
IS1-1	19811	20508	b0020-b0023	-	272	199*	P^b	P	P	P
IS1-2	278402	279099	b0263-b0266	-	174	191*	P	P	P	P
IS1-3	289873	290570	b0273-b0276	-	171*	577	P	P	P	P
IS1-4	1049056	1049753	b0987-b0989	+	281*	139	P	P	P	P
IS1-5	1976542	1977239	b1892-b1895	-	452	226	P	P
IS1-6	3581114	3581811	b3443-b3446	+	712	1020	P	P	P	P
IS1-7	4516095	4516370	b4293-b4295	+	1354	575*	P	P	P	P
IS2-1	380530	381803	b0359-b0362	+	308	841	P	P	P	P
IS2-2	1465945	1467218	b1401-b1405	-	194	203*	P	P	P	P
b1579 transposase	1649536	1650732	b1578-b1580	+		778	P	P	P	P
IS2-3	2066974	2068247	b1995-b1998	-	287*	444	P	P	P	P
IS2-4	2994394	2995622	b2859-b2862	-	589	219	P	P	P	P
IS2-5	3184203	3185431	b3043-b3046	+	410	672	P	P	P	P
IS2-6	4495795	4497068	b4271-b4274	+	204*	163	P	P	P	P
IS3-1	390963	391829	b0371-b0373	-	489*	142	P	P	P	P
IS3-2	566361	567227	b0540-b0542	+	787	346	P	P	P	P
IS3-3	1093498	1094364	b1025-b1027	-	1009	772	P	P	P	P
IS3-4	2168554	2169420	b2088-b2090	+	502	842	P	P	P	P
IS3-5	314811	315677	b0298-b0300	+	863	158*	P	P	P	P
IS4	4499671	4500999	b4277-b4279	-	629	450	P	P	P	P
IS5-1	273325	274341	b0258-b0260	-	489*	497	P	P	P	P
IS5-2	573960	574976	b0551-b0553	-	590	1605	P	P	P	P
IS5-3	687220	688236	b0655-b0657	-	348	420*	P	P	P	P
IS5-4	1394100	1395116	b1330-b1332	+	569*	471*	(P)^c	(P)	(P)	(P)
IS5-5	1425770	1426750	b1369-b1371	-	491	1543	P	P	P	P
IS5-6	2064327	2065343	b1993-b1995	-	747	1210	P	P	P	P
IS5-7	2099917	2100933	b2029-b2031	-	306	303	P	P	P	P
IS5-8	2287085	2288101	b2191-b2193	-	314*	411	P	P	P	P
IS5-9	3128193	3129209	b2981-b2983	+	1085	672	P	P	P	P
IS5-10	3363337	3364353	b3217-b3219	-	207*	1126	P	P	P	P
IS5-11	3649812	3650828	b3504-b3506	-	734*	1335	P	P	P	P
IS30-1	269827	270978	b0255-b0257	+	720	314	P	P	P	P
IS30-2	1467382	1468533	b1401-b1405	+	305	297	P	P	P	P
IS30-3	4505034	4506185	b4283-b4285	-	405	766	P	P	P	P
IS 150	3718309	3719678	b3556-b3559	+	195	176	P	P	P	P
IS186-1	15445	16557	b0015-b0017	+	503	1501	P	P	P	P
IS186-2	607288	608400	b0581-b0583	+	2204	417	P	P	P	P
IS186-3	2512345	2513463	b2393-b2395	+	764	667	P	P	P	P
Additional Elements
IS1-a	257908		b0240	-	1488	738		P
IS1-b	335460		b0319-b0326	-	609	309				P
IS1-c	1871063		b1786	-	1211	484		P
IS1-d	2037484		b1970-b1971	+	617*	1066			P	P
IS1-e	2623548		b2502	+	282*	368			P	P
IS1-f	2768501		b2635	+	1608	544*		P	P	P
IS1-g	3275070		b3130	+	529	2117			P	P
IS1-h	4539642		b4313	-	175*	1119			P	P
IS2-a	1588558		b1506	+	765	717			P	P
IS2-b	2927499		b2796	+	138	368			P	P
IS3-a	331175		b0314-b0315	+	1002*	563				P
IS3-b	838769		b0805	+	450	870*		P	P	P
IS3-c	2460317		b2351	+	489*	1642			P	P
IS3-d	3427623		b3280	-	953	646			P	P
IS3-e	3776882		b3604	-	1435	935*		P	P	P
IS3-f	4466303		b4242	-	640	935*		P	P	P
IS5-a	1102866		b1040-b1041	+	365	400			P	P
IS30-a	4115565		b3927	-	692	186			P	P
IS30-b	2246187		b2156	-	303*	445		P	P	P
IS186-a	4541184		b4314	-	606	534			P	P

^a * indicates a fragment not recovered. ^b P, present. ^c Neither IS5-4 fragment is detected. Conventional PCR of gDNA confirms IS5-4 is present.

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