AutoCloner

Multiple sequence alignment - TraesCS7B01G186600

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Download Multiple Sequence Alignment: (Fasta) (Clustal)

BLAST Results

Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

	qseqid	sseqid	percentage.identical	alignment.length	no.mismatch	no.gap.openings	qstart	qend	sstart	send	evalue	bitscore
0	TraesCS7B01G186600	chr7B	100.000	4244	0	0	1	4244	311512572	311508329	0.000000e+00	7838
1	TraesCS7B01G186600	chr7B	93.411	683	37	3	3567	4244	311492158	311491479	0.000000e+00	1005
2	TraesCS7B01G186600	chr7B	82.540	567	84	12	4	557	645134912	645134348	6.380000e-133	484
3	TraesCS7B01G186600	chr7B	82.540	567	84	11	4	557	645341919	645342483	6.380000e-133	484
4	TraesCS7B01G186600	chr7D	96.056	2840	93	9	746	3566	335455409	335458248	0.000000e+00	4606
5	TraesCS7B01G186600	chr7D	87.141	661	82	3	86	746	335450035	335450692	0.000000e+00	747
6	TraesCS7B01G186600	chr7A	94.535	2946	125	13	455	3399	377637966	377635056	0.000000e+00	4516
7	TraesCS7B01G186600	chr7A	82.657	542	78	11	7	536	522504585	522504048	2.310000e-127	466
8	TraesCS7B01G186600	chr7A	91.608	143	12	0	3424	3566	377634989	377634847	9.310000e-47	198
9	TraesCS7B01G186600	chr3B	92.308	689	40	4	3567	4244	355116236	355116922	0.000000e+00	966
10	TraesCS7B01G186600	chr3B	90.857	700	38	4	3568	4244	355108332	355109028	0.000000e+00	915
11	TraesCS7B01G186600	chr3B	93.434	594	32	6	3567	4154	398377076	398376484	0.000000e+00	874
12	TraesCS7B01G186600	chr3B	90.878	592	40	9	3566	4154	364137849	364137269	0.000000e+00	782
13	TraesCS7B01G186600	chr6B	92.140	598	41	5	3649	4244	285086170	285085577	0.000000e+00	839
14	TraesCS7B01G186600	chr6B	92.193	538	36	5	3642	4177	285094233	285093700	0.000000e+00	756
15	TraesCS7B01G186600	chr6B	91.406	512	31	4	3567	4073	328376530	328377033	0.000000e+00	689
16	TraesCS7B01G186600	chr4B	91.993	562	35	7	3566	4126	520499143	520498591	0.000000e+00	780
17	TraesCS7B01G186600	chr4A	83.303	551	76	11	20	557	383589411	383588864	1.060000e-135	494
18	TraesCS7B01G186600	chr4D	82.832	565	77	11	4	549	208149947	208149384	4.930000e-134	488
19	TraesCS7B01G186600	chr1D	84.449	508	64	13	42	536	116697579	116698084	1.770000e-133	486
20	TraesCS7B01G186600	chr5A	81.690	568	88	11	4	557	176926461	176925896	3.870000e-125	459
21	TraesCS7B01G186600	chr5A	77.932	648	109	28	3615	4244	349257836	349257205	1.440000e-99	374
22	TraesCS7B01G186600	chr5A	77.689	623	101	34	3649	4244	113701296	113700685	3.140000e-91	346
23	TraesCS7B01G186600	chr5A	75.944	715	112	48	3567	4244	351091611	351090920	3.190000e-81	313
24	TraesCS7B01G186600	chr5A	75.070	710	127	45	3566	4244	351128955	351128265	6.950000e-73	285
25	TraesCS7B01G186600	chr6A	82.033	551	81	14	1	536	65432012	65432559	1.800000e-123	453
26	TraesCS7B01G186600	chr3A	74.126	572	104	37	3612	4160	262187497	262186947	3.350000e-46	196
27	TraesCS7B01G186600	chr2A	92.793	111	8	0	4027	4137	303359973	303360083	1.220000e-35	161
28	TraesCS7B01G186600	chr2A	72.973	333	77	10	3565	3889	288106185	288105858	2.090000e-18	104
29	TraesCS7B01G186600	chr2B	72.432	584	127	34	3567	4129	611537129	611536559	5.680000e-34	156

These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

	query	scaffold	start	end	length	rev.comp	avg.bitscore	max.bitscore	avg.percent.identical	query.start	query.end	num_hsp	groupid	homo_length
0	TraesCS7B01G186600	chr7B	311508329	311512572	4243	True	7838	7838	100.0000	1	4244	1	chr7B.!!$R2	4243
1	TraesCS7B01G186600	chr7B	311491479	311492158	679	True	1005	1005	93.4110	3567	4244	1	chr7B.!!$R1	677
2	TraesCS7B01G186600	chr7B	645134348	645134912	564	True	484	484	82.5400	4	557	1	chr7B.!!$R3	553
3	TraesCS7B01G186600	chr7B	645341919	645342483	564	False	484	484	82.5400	4	557	1	chr7B.!!$F1	553
4	TraesCS7B01G186600	chr7D	335455409	335458248	2839	False	4606	4606	96.0560	746	3566	1	chr7D.!!$F2	2820
5	TraesCS7B01G186600	chr7D	335450035	335450692	657	False	747	747	87.1410	86	746	1	chr7D.!!$F1	660
6	TraesCS7B01G186600	chr7A	377634847	377637966	3119	True	2357	4516	93.0715	455	3566	2	chr7A.!!$R2	3111
7	TraesCS7B01G186600	chr7A	522504048	522504585	537	True	466	466	82.6570	7	536	1	chr7A.!!$R1	529
8	TraesCS7B01G186600	chr3B	355116236	355116922	686	False	966	966	92.3080	3567	4244	1	chr3B.!!$F2	677
9	TraesCS7B01G186600	chr3B	355108332	355109028	696	False	915	915	90.8570	3568	4244	1	chr3B.!!$F1	676
10	TraesCS7B01G186600	chr3B	398376484	398377076	592	True	874	874	93.4340	3567	4154	1	chr3B.!!$R2	587
11	TraesCS7B01G186600	chr3B	364137269	364137849	580	True	782	782	90.8780	3566	4154	1	chr3B.!!$R1	588
12	TraesCS7B01G186600	chr6B	285085577	285086170	593	True	839	839	92.1400	3649	4244	1	chr6B.!!$R1	595
13	TraesCS7B01G186600	chr6B	285093700	285094233	533	True	756	756	92.1930	3642	4177	1	chr6B.!!$R2	535
14	TraesCS7B01G186600	chr6B	328376530	328377033	503	False	689	689	91.4060	3567	4073	1	chr6B.!!$F1	506
15	TraesCS7B01G186600	chr4B	520498591	520499143	552	True	780	780	91.9930	3566	4126	1	chr4B.!!$R1	560
16	TraesCS7B01G186600	chr4A	383588864	383589411	547	True	494	494	83.3030	20	557	1	chr4A.!!$R1	537
17	TraesCS7B01G186600	chr4D	208149384	208149947	563	True	488	488	82.8320	4	549	1	chr4D.!!$R1	545
18	TraesCS7B01G186600	chr1D	116697579	116698084	505	False	486	486	84.4490	42	536	1	chr1D.!!$F1	494
19	TraesCS7B01G186600	chr5A	176925896	176926461	565	True	459	459	81.6900	4	557	1	chr5A.!!$R2	553
20	TraesCS7B01G186600	chr5A	349257205	349257836	631	True	374	374	77.9320	3615	4244	1	chr5A.!!$R3	629
21	TraesCS7B01G186600	chr5A	113700685	113701296	611	True	346	346	77.6890	3649	4244	1	chr5A.!!$R1	595
22	TraesCS7B01G186600	chr5A	351090920	351091611	691	True	313	313	75.9440	3567	4244	1	chr5A.!!$R4	677
23	TraesCS7B01G186600	chr5A	351128265	351128955	690	True	285	285	75.0700	3566	4244	1	chr5A.!!$R5	678
24	TraesCS7B01G186600	chr6A	65432012	65432559	547	False	453	453	82.0330	1	536	1	chr6A.!!$F1	535

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
938	969	0.179073	GCCTTTCATGCTCTCGCCTA	60.179	55.0	0.00	0.0	34.43	3.93	F
2057	2089	0.179100	CGGATCCTGTCATTGTCGCT	60.179	55.0	10.75	0.0	0.00	4.93	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2562	2594	0.397941	CCTGCACCTTCTTGTCTGGA	59.602	55.0	0.0	0.0	0.0	3.86	R
3647	3722	0.400213	TGCGAGGGTTTGAACATCCT	59.600	50.0	0.0	0.0	0.0	3.24	R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
28	29	4.737855	ACTAGTTCATGTCCGTTATGCT	57.262	40.909	0.00	0.00	0.00	3.79
30	31	4.870426	ACTAGTTCATGTCCGTTATGCTTG	59.130	41.667	0.00	0.00	0.00	4.01
83	88	4.785301	AGCCATCATACAATGCTTAGTGT	58.215	39.130	0.00	0.00	0.00	3.55
88	94	4.968626	TCATACAATGCTTAGTGTTTGCG	58.031	39.130	0.00	0.00	29.85	4.85
106	112	1.821216	CGGCAACCTCACCACTTAAT	58.179	50.000	0.00	0.00	0.00	1.40
107	113	2.937873	GCGGCAACCTCACCACTTAATA	60.938	50.000	0.00	0.00	0.00	0.98
138	144	6.290294	ACCCATTAAACTTCGCTAGTCTTA	57.710	37.500	0.00	0.00	35.54	2.10
139	145	6.338937	ACCCATTAAACTTCGCTAGTCTTAG	58.661	40.000	0.00	0.00	35.54	2.18
153	159	6.239232	CGCTAGTCTTAGTACCCATGGTAATT	60.239	42.308	11.73	0.00	40.12	1.40
154	160	7.040201	CGCTAGTCTTAGTACCCATGGTAATTA	60.040	40.741	11.73	0.00	40.12	1.40
156	162	7.613551	AGTCTTAGTACCCATGGTAATTAGG	57.386	40.000	11.73	0.35	40.12	2.69
159	165	7.930325	GTCTTAGTACCCATGGTAATTAGGTTC	59.070	40.741	11.73	0.00	40.12	3.62
190	196	6.150641	TCCTCGTGGCTCACATATTACTATAC	59.849	42.308	0.00	0.00	33.40	1.47
234	241	1.887198	ACGAGGATTTGACGTGAGAGT	59.113	47.619	0.00	0.00	38.79	3.24
317	333	2.072298	GATTAGCAGGATGGATGTCGC	58.928	52.381	0.00	0.00	35.86	5.19
322	338	1.745141	GCAGGATGGATGTCGCTCTTT	60.745	52.381	0.00	0.00	35.86	2.52
324	340	3.797039	CAGGATGGATGTCGCTCTTTTA	58.203	45.455	0.00	0.00	0.00	1.52
352	368	5.628134	GTTTGATTTCATCCGTAGTTGGAC	58.372	41.667	0.00	0.00	41.85	4.02
429	456	4.945246	TGGCGAGTGTAATCCTTTATCTC	58.055	43.478	0.00	0.00	0.00	2.75
437	464	9.400638	GAGTGTAATCCTTTATCTCGTATTCTG	57.599	37.037	0.00	0.00	0.00	3.02
476	503	7.142995	TGGTATGTTGTAATGATATCCACCA	57.857	36.000	0.00	0.00	0.00	4.17
477	504	6.995686	TGGTATGTTGTAATGATATCCACCAC	59.004	38.462	0.00	0.00	0.00	4.16
482	509	2.727123	AATGATATCCACCACGCCAA	57.273	45.000	0.00	0.00	0.00	4.52
557	584	3.924686	ACCTTTACATCTTGAACGCTACG	59.075	43.478	0.00	0.00	0.00	3.51
582	609	3.368190	CTGGGTCCTCGAGCTGCTG	62.368	68.421	7.01	0.00	0.00	4.41
594	621	2.827423	CTGCTGGATCCGATGGCT	59.173	61.111	7.39	0.00	0.00	4.75
600	627	2.579873	CTGGATCCGATGGCTCAAATT	58.420	47.619	7.39	0.00	0.00	1.82
616	643	6.075280	GCTCAAATTGCATCAAACAAATGAC	58.925	36.000	0.00	0.00	30.82	3.06
653	680	5.183969	TCTTCCAAATTGCTGAGAGAGATG	58.816	41.667	0.00	0.00	0.00	2.90
709	736	5.309323	TCAGTGTGTTCTGGTTCAAAAAG	57.691	39.130	0.00	0.00	36.25	2.27
742	770	5.586155	TGGGTGTCTAATTTTGTAGGGAA	57.414	39.130	0.00	0.00	0.00	3.97
743	771	5.566469	TGGGTGTCTAATTTTGTAGGGAAG	58.434	41.667	0.00	0.00	0.00	3.46
744	772	5.073965	TGGGTGTCTAATTTTGTAGGGAAGT	59.926	40.000	0.00	0.00	0.00	3.01
747	775	7.336176	GGGTGTCTAATTTTGTAGGGAAGTAAG	59.664	40.741	0.00	0.00	0.00	2.34
764	792	6.762187	GGAAGTAAGAAACAAGCCCTATAGAC	59.238	42.308	0.00	0.00	0.00	2.59
766	794	5.724854	AGTAAGAAACAAGCCCTATAGACCA	59.275	40.000	0.00	0.00	0.00	4.02
779	809	4.634004	CCTATAGACCAGACGCTAGATCTG	59.366	50.000	5.18	14.57	42.79	2.90
806	836	3.238108	ACTGCATGCACTCTGTAGTAC	57.762	47.619	18.46	0.00	37.72	2.73
826	857	7.253905	AGTACTCTCCATTTTAAGGCTTGTA	57.746	36.000	10.69	0.00	0.00	2.41
938	969	0.179073	GCCTTTCATGCTCTCGCCTA	60.179	55.000	0.00	0.00	34.43	3.93
1058	1089	4.770362	TGACCCCGAGCCATCCGA	62.770	66.667	0.00	0.00	0.00	4.55
1083	1114	1.700042	GGGCAAGGGAGATGGACGAT	61.700	60.000	0.00	0.00	0.00	3.73
1182	1213	1.488705	AATGCCACAACCTCCTCCGA	61.489	55.000	0.00	0.00	0.00	4.55
1209	1240	1.045350	AGCTCATCCTTCCGCTGCTA	61.045	55.000	0.00	0.00	0.00	3.49
1341	1372	2.288395	CGGCAGCAAAATCTTTCTGGTT	60.288	45.455	0.00	0.00	0.00	3.67
1384	1415	1.499007	TGTCTTTCTCCTTGCCCCTTT	59.501	47.619	0.00	0.00	0.00	3.11
1417	1448	3.645212	TGGCCTTGACCAATTGATTTGAA	59.355	39.130	7.12	0.00	36.55	2.69
1574	1605	6.548622	AGGTAAATGCATCATCAGTAATGCTT	59.451	34.615	0.00	0.13	46.64	3.91
1630	1662	9.631257	AATCACACATATGATCCTGTTGATTAA	57.369	29.630	10.38	0.00	38.40	1.40
1755	1787	1.667154	CGAGGAGAGGAATGCGGACA	61.667	60.000	0.00	0.00	0.00	4.02
1769	1801	0.251916	CGGACAGGGCAATACTGGAA	59.748	55.000	0.00	0.00	40.23	3.53
1823	1855	1.758514	GGATCTGAGGGCGGAGACA	60.759	63.158	0.00	0.00	37.00	3.41
1852	1884	2.462456	AAGAAGCTGATCAACGAGCA	57.538	45.000	7.34	0.00	37.70	4.26
1912	1944	1.202818	GCTCCTCCACAAGTTCAAGGT	60.203	52.381	0.00	0.00	0.00	3.50
1989	2021	4.373116	TCGACAAGTGCCCCTCGC	62.373	66.667	0.00	0.00	38.31	5.03
2057	2089	0.179100	CGGATCCTGTCATTGTCGCT	60.179	55.000	10.75	0.00	0.00	4.93
2325	2357	2.877300	GCTCAAGAACCTGATCCTGCAA	60.877	50.000	0.00	0.00	0.00	4.08
2409	2441	1.995626	CCACCCGAGGGAGGACATT	60.996	63.158	18.32	0.00	46.98	2.71
2416	2448	2.017559	GAGGGAGGACATTCCGTCGG	62.018	65.000	4.39	4.39	46.42	4.79
2775	2807	3.081409	ACGATCGGGACCCTTGGG	61.081	66.667	20.98	3.77	0.00	4.12
2994	3026	2.027073	GCTGTCGTCGCATCCAACA	61.027	57.895	0.00	0.00	0.00	3.33
3081	3113	1.165907	CCAAGAACAAGGAGTGCGCA	61.166	55.000	5.66	5.66	0.00	6.09
3084	3116	0.679505	AGAACAAGGAGTGCGCACTA	59.320	50.000	40.77	1.20	42.66	2.74
3162	3194	4.021925	GGCCTCCACGAGCACCTT	62.022	66.667	0.00	0.00	0.00	3.50
3266	3298	3.146066	TGTGAGAACCATTTGTACCTGC	58.854	45.455	0.00	0.00	0.00	4.85
3279	3311	4.150897	TGTACCTGCCTGTAATTCATCC	57.849	45.455	0.00	0.00	0.00	3.51
3341	3373	2.737376	GGAACCTGTCGCGTGGTC	60.737	66.667	17.90	8.84	35.17	4.02
3454	3528	4.382320	TTGGTGACCGCTACCGCC	62.382	66.667	0.00	0.00	41.18	6.13
3502	3576	1.115467	GCTCCCGAGAGAGATCCAAA	58.885	55.000	0.00	0.00	43.39	3.28
3539	3613	1.761449	TATACGACTTGGGCCGTACA	58.239	50.000	0.00	0.00	42.89	2.90
3563	3637	3.316573	CTGTGAGACCCGCTTCCCC	62.317	68.421	0.00	0.00	0.00	4.81
3592	3667	1.449353	CCCTAGCTCAGCCCATGTC	59.551	63.158	0.00	0.00	0.00	3.06
3663	3739	2.762535	TCGAGGATGTTCAAACCCTC	57.237	50.000	0.00	0.00	41.25	4.30
3755	3835	6.096001	AGTTCATGATTTCTGATTAAGGTGGC	59.904	38.462	0.00	0.00	0.00	5.01
3906	3990	5.456921	AATGTGGGTCACTGGAATAATCT	57.543	39.130	0.00	0.00	35.11	2.40
3929	4013	9.829507	ATCTAGAGAGAGTCCACAAATTATTTG	57.170	33.333	15.25	15.25	39.81	2.32
4167	4310	1.183676	ACCTCCTACTTCGCCGTGTT	61.184	55.000	0.00	0.00	0.00	3.32

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
2	3	6.073765	GCATAACGGACATGAACTAGTAATGG	60.074	42.308	18.05	7.25	0.00	3.16
14	15	3.848272	AAACCAAGCATAACGGACATG	57.152	42.857	0.00	0.00	0.00	3.21
15	16	4.585879	AGTAAACCAAGCATAACGGACAT	58.414	39.130	0.00	0.00	0.00	3.06
18	19	6.394025	AAAAAGTAAACCAAGCATAACGGA	57.606	33.333	0.00	0.00	0.00	4.69
51	54	6.073276	GCATTGTATGATGGCTAACATACGAA	60.073	38.462	19.69	16.06	46.53	3.85
57	60	6.260714	CACTAAGCATTGTATGATGGCTAACA	59.739	38.462	0.00	0.00	0.00	2.41
83	88	2.124109	TGGTGAGGTTGCCGCAAA	60.124	55.556	7.54	0.00	34.65	3.68
88	94	5.163550	GGAAATATTAAGTGGTGAGGTTGCC	60.164	44.000	0.00	0.00	0.00	4.52
106	112	7.057894	AGCGAAGTTTAATGGGTATGGAAATA	58.942	34.615	0.00	0.00	0.00	1.40
107	113	5.891551	AGCGAAGTTTAATGGGTATGGAAAT	59.108	36.000	0.00	0.00	0.00	2.17
124	130	3.960571	TGGGTACTAAGACTAGCGAAGT	58.039	45.455	0.00	0.00	42.80	3.01
138	144	5.294473	AGGAACCTAATTACCATGGGTACT	58.706	41.667	18.09	0.00	37.97	2.73
139	145	5.641789	AGGAACCTAATTACCATGGGTAC	57.358	43.478	18.09	0.00	37.97	3.34
153	159	2.731572	CCACGAGGACTTAGGAACCTA	58.268	52.381	0.00	0.00	36.89	3.08
154	160	1.558233	CCACGAGGACTTAGGAACCT	58.442	55.000	0.00	0.00	36.89	3.50
156	162	0.896226	AGCCACGAGGACTTAGGAAC	59.104	55.000	1.86	0.00	36.89	3.62
159	165	0.173708	GTGAGCCACGAGGACTTAGG	59.826	60.000	1.86	0.00	36.89	2.69
206	212	3.507233	ACGTCAAATCCTCGTGTTACCTA	59.493	43.478	0.00	0.00	36.46	3.08
234	241	5.302568	AGAACTCCAAACAAATCAAGCATCA	59.697	36.000	0.00	0.00	0.00	3.07
352	368	8.888579	AATAATCGTCATACAAAAGAGTAGGG	57.111	34.615	0.00	0.00	0.00	3.53
393	420	4.341235	ACACTCGCCATAAGCTACAAGATA	59.659	41.667	0.00	0.00	40.39	1.98
396	423	2.893637	ACACTCGCCATAAGCTACAAG	58.106	47.619	0.00	0.00	40.39	3.16
406	433	5.542779	GAGATAAAGGATTACACTCGCCAT	58.457	41.667	0.00	0.00	0.00	4.40
500	527	5.451659	CGTGATGAATTTATGATTGGGGCAA	60.452	40.000	0.00	0.00	0.00	4.52
536	563	3.306166	CCGTAGCGTTCAAGATGTAAAGG	59.694	47.826	0.00	0.00	0.00	3.11
537	564	4.031426	GTCCGTAGCGTTCAAGATGTAAAG	59.969	45.833	0.00	0.00	0.00	1.85
538	565	3.922240	GTCCGTAGCGTTCAAGATGTAAA	59.078	43.478	0.00	0.00	0.00	2.01
582	609	1.000938	GCAATTTGAGCCATCGGATCC	60.001	52.381	0.00	0.00	37.30	3.36
594	621	7.308049	CCATGTCATTTGTTTGATGCAATTTGA	60.308	33.333	0.00	0.00	0.00	2.69
600	627	4.558178	GTCCATGTCATTTGTTTGATGCA	58.442	39.130	0.00	0.00	0.00	3.96
616	643	3.819564	TGGAAGATCTAACCGTCCATG	57.180	47.619	8.71	0.00	37.29	3.66
663	690	5.825593	TCCATCTAGAAACAAGAACCACT	57.174	39.130	0.00	0.00	0.00	4.00
742	770	5.724854	TGGTCTATAGGGCTTGTTTCTTACT	59.275	40.000	0.00	0.00	0.00	2.24
743	771	5.985911	TGGTCTATAGGGCTTGTTTCTTAC	58.014	41.667	0.00	0.00	0.00	2.34
744	772	5.962031	TCTGGTCTATAGGGCTTGTTTCTTA	59.038	40.000	0.00	0.00	0.00	2.10
747	775	4.443621	GTCTGGTCTATAGGGCTTGTTTC	58.556	47.826	0.00	0.00	0.00	2.78
764	792	1.339291	TGCATCAGATCTAGCGTCTGG	59.661	52.381	18.86	9.49	42.58	3.86
766	794	3.131933	AGTTTGCATCAGATCTAGCGTCT	59.868	43.478	0.00	0.00	0.00	4.18
806	836	6.038714	GTCCATACAAGCCTTAAAATGGAGAG	59.961	42.308	12.43	0.00	42.54	3.20
826	857	0.737715	GCGCTTCTTCTGTCGTCCAT	60.738	55.000	0.00	0.00	0.00	3.41
938	969	3.688330	CGCGCGTGAGTGAAACGT	61.688	61.111	24.19	0.00	45.86	3.99
962	993	0.525668	CGAGCTGCGTACGGAGAAAT	60.526	55.000	36.59	22.31	35.50	2.17
1058	1089	3.642741	ATCTCCCTTGCCCGGGTCT	62.643	63.158	24.63	0.00	44.95	3.85
1128	1159	1.365699	GGCGAAATTCCGAGTAAGCA	58.634	50.000	0.00	0.00	0.00	3.91
1152	1183	0.537143	TGTGGCATTCCTTTCGCTGT	60.537	50.000	0.00	0.00	0.00	4.40
1236	1267	1.065928	GTAGGCATCGTCGGTGAGG	59.934	63.158	10.33	0.00	0.00	3.86
1341	1372	4.785767	GCATGGCCATCTGATCGA	57.214	55.556	17.61	0.00	0.00	3.59
1417	1448	0.734889	CGCCTGAAAATCGATTGGCT	59.265	50.000	25.84	10.48	38.33	4.75
1574	1605	2.413796	CGTACGTAAATGGCTTTGCAGA	59.586	45.455	7.22	0.00	0.00	4.26
1630	1662	1.078848	GCGTTCATCAGCTCCACCT	60.079	57.895	0.00	0.00	0.00	4.00
1655	1687	3.937706	CCGTTCTCTTCTTGCATCTCATT	59.062	43.478	0.00	0.00	0.00	2.57
1755	1787	1.002857	AGCCTTTCCAGTATTGCCCT	58.997	50.000	0.00	0.00	0.00	5.19
1793	1825	3.766644	CAGATCCGGCAACATCTGA	57.233	52.632	20.88	0.00	45.41	3.27
1800	1832	4.161295	CGCCCTCAGATCCGGCAA	62.161	66.667	0.00	0.00	43.17	4.52
1823	1855	3.054139	TGATCAGCTTCTTTATGGCCACT	60.054	43.478	8.16	0.00	0.00	4.00
1912	1944	2.889988	CGTCAATGCCGGCGATCA	60.890	61.111	23.90	3.74	0.00	2.92
1989	2021	0.747255	AAGTCGTCCGGGATCATCAG	59.253	55.000	0.00	0.00	0.00	2.90
2057	2089	4.735132	GCGCGTGCCTGTCCACTA	62.735	66.667	10.56	0.00	33.60	2.74
2075	2107	3.274288	AGAGGAATCAAGATTCGGCAAC	58.726	45.455	14.63	3.19	46.11	4.17
2175	2207	7.653311	GTCTGCATATTTCAAACCAACTTCTTT	59.347	33.333	0.00	0.00	0.00	2.52
2400	2432	1.153628	CACCGACGGAATGTCCTCC	60.154	63.158	23.38	0.00	45.23	4.30
2409	2441	3.998672	GCTTCCACCACCGACGGA	61.999	66.667	23.38	0.00	0.00	4.69
2416	2448	3.414700	CGACAGCGCTTCCACCAC	61.415	66.667	7.50	0.00	0.00	4.16
2539	2571	3.790437	CAGCAGGCCGATCAGGGT	61.790	66.667	0.00	0.00	41.48	4.34
2562	2594	0.397941	CCTGCACCTTCTTGTCTGGA	59.602	55.000	0.00	0.00	0.00	3.86
2565	2597	1.722034	TCTCCTGCACCTTCTTGTCT	58.278	50.000	0.00	0.00	0.00	3.41
2703	2735	4.117661	GTCGCCGCCGAGTTCTCT	62.118	66.667	0.00	0.00	45.38	3.10
2850	2882	2.237143	CTGCTGGTTGAGGATGAGGTTA	59.763	50.000	0.00	0.00	0.00	2.85
2925	2957	1.118965	TTCCAAGGCTCCTGTCGTCA	61.119	55.000	0.00	0.00	0.00	4.35
2994	3026	2.035632	GTCCCGATCTCTCCAAGACAT	58.964	52.381	0.00	0.00	36.65	3.06
3081	3113	1.395826	GCTCCAGCAGGACGGATAGT	61.396	60.000	0.00	0.00	39.61	2.12
3084	3116	2.364842	AGCTCCAGCAGGACGGAT	60.365	61.111	0.48	0.00	45.16	4.18
3162	3194	1.338105	CCAGTCTTGGCGATCTGTGAA	60.338	52.381	0.00	0.00	37.73	3.18
3266	3298	5.637006	TCAAAAACGGGATGAATTACAGG	57.363	39.130	0.00	0.00	0.00	4.00
3341	3373	1.825474	AGAGGTGTGGGTAGTGAATCG	59.175	52.381	0.00	0.00	0.00	3.34
3422	3496	4.390909	GGTCACCAAGAAATTGTACTACCG	59.609	45.833	0.00	0.00	0.00	4.02
3436	3510	2.813908	GCGGTAGCGGTCACCAAG	60.814	66.667	17.08	0.00	35.67	3.61
3454	3528	2.352960	GCAGGAAAGAGGTAGAAATGCG	59.647	50.000	0.00	0.00	0.00	4.73
3539	3613	2.923035	CGGGTCTCACAGTGGGGT	60.923	66.667	0.00	0.00	0.00	4.95
3544	3618	2.584391	GGGAAGCGGGTCTCACAGT	61.584	63.158	0.00	0.00	0.00	3.55
3545	3619	2.266055	GGGAAGCGGGTCTCACAG	59.734	66.667	0.00	0.00	0.00	3.66
3546	3620	3.319198	GGGGAAGCGGGTCTCACA	61.319	66.667	0.00	0.00	0.00	3.58
3592	3667	4.093850	TGACATGATGATCAAGCAAAGACG	59.906	41.667	0.00	0.00	0.00	4.18
3647	3722	0.400213	TGCGAGGGTTTGAACATCCT	59.600	50.000	0.00	0.00	0.00	3.24
3663	3739	5.354234	ACCCTAGTTGAGTTGATTTAATGCG	59.646	40.000	0.00	0.00	0.00	4.73
3755	3835	4.524316	TCATCATTTTTGGCAGAGGTTG	57.476	40.909	0.00	0.00	0.00	3.77
3929	4013	8.803397	ATACTAACCCATTTTGTAAACTCCTC	57.197	34.615	0.00	0.00	30.58	3.71
4143	4285	2.656069	GCGAAGTAGGAGGTGGCCA	61.656	63.158	0.00	0.00	0.00	5.36
4167	4310	2.683933	GGGAGGAAGGAGGCGTCA	60.684	66.667	8.91	0.00	0.00	4.35

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.