AutoCloner

Multiple sequence alignment - TraesCS1B01G095100

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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	TraesCS1B01G095100	chr1B	100.000	2992	0	0	1	2992	98448455	98445464	0.000000e+00	5526.0
1	TraesCS1B01G095100	chr1D	94.102	1492	59	10	850	2324	61944332	61942853	0.000000e+00	2241.0
2	TraesCS1B01G095100	chr1D	91.696	578	45	2	2392	2968	112796207	112795632	0.000000e+00	798.0
3	TraesCS1B01G095100	chr1A	95.332	1371	49	8	851	2218	59842478	59841120	0.000000e+00	2163.0
4	TraesCS1B01G095100	chr1A	89.752	644	41	10	2324	2944	444170243	444170884	0.000000e+00	800.0
5	TraesCS1B01G095100	chr1A	89.557	632	47	10	2324	2944	575546733	575547356	0.000000e+00	784.0
6	TraesCS1B01G095100	chr3B	96.134	595	19	2	247	837	811058344	811058938	0.000000e+00	968.0
7	TraesCS1B01G095100	chr3B	95.294	595	18	4	247	837	581119670	581120258	0.000000e+00	935.0
8	TraesCS1B01G095100	chr3B	98.206	223	4	0	1	223	811057970	811058192	1.010000e-104	390.0
9	TraesCS1B01G095100	chr3B	97.758	223	5	0	1	223	581119295	581119517	4.680000e-103	385.0
10	TraesCS1B01G095100	chr2B	95.798	595	21	2	247	837	793968442	793969036	0.000000e+00	957.0
11	TraesCS1B01G095100	chr2B	95.126	595	24	3	247	837	632888947	632889540	0.000000e+00	933.0
12	TraesCS1B01G095100	chr2B	98.206	223	4	0	1	223	769033231	769033453	1.010000e-104	390.0
13	TraesCS1B01G095100	chr2B	97.758	223	5	0	1	223	247622837	247623059	4.680000e-103	385.0
14	TraesCS1B01G095100	chr2B	100.000	29	0	0	1351	1379	76081288	76081316	1.000000e-03	54.7
15	TraesCS1B01G095100	chr5B	95.439	592	23	2	250	837	246146293	246145702	0.000000e+00	941.0
16	TraesCS1B01G095100	chr5B	99.103	223	2	0	1	223	246146670	246146448	4.650000e-108	401.0
17	TraesCS1B01G095100	chr5B	98.206	223	4	0	1	223	645921188	645920966	1.010000e-104	390.0
18	TraesCS1B01G095100	chr7A	95.126	595	25	2	247	837	268855228	268855822	0.000000e+00	935.0
19	TraesCS1B01G095100	chr7A	94.932	592	26	2	250	837	236702	236111	0.000000e+00	924.0
20	TraesCS1B01G095100	chr7A	94.932	592	26	2	250	837	546590506	546589915	0.000000e+00	924.0
21	TraesCS1B01G095100	chr7A	97.758	223	5	0	1	223	237080	236858	4.680000e-103	385.0
22	TraesCS1B01G095100	chr4B	95.101	592	25	2	250	837	25808473	25807882	0.000000e+00	929.0
23	TraesCS1B01G095100	chr4B	97.309	223	6	0	1	223	25808850	25808628	2.180000e-101	379.0
24	TraesCS1B01G095100	chr4A	88.774	677	53	8	2312	2968	654185934	654185261	0.000000e+00	808.0
25	TraesCS1B01G095100	chr4A	88.183	677	58	7	2311	2968	654156504	654155831	0.000000e+00	787.0
26	TraesCS1B01G095100	chr4A	82.515	652	59	16	2323	2943	665440832	665441459	3.420000e-144	521.0
27	TraesCS1B01G095100	chr6B	89.291	635	51	5	2341	2962	123476373	123477003	0.000000e+00	780.0
28	TraesCS1B01G095100	chr6B	82.504	663	57	20	2324	2953	181100312	181100948	7.350000e-146	527.0
29	TraesCS1B01G095100	chr6B	100.000	33	0	0	2960	2992	123477019	123477051	8.960000e-06	62.1
30	TraesCS1B01G095100	chr4D	92.058	554	41	3	2416	2968	417350045	417349494	0.000000e+00	776.0
31	TraesCS1B01G095100	chr6A	90.674	579	53	1	2391	2968	291419105	291418527	0.000000e+00	769.0
32	TraesCS1B01G095100	chr7B	87.743	669	61	6	2313	2962	609147116	609147782	0.000000e+00	761.0
33	TraesCS1B01G095100	chr3A	97.309	223	6	0	1	223	695535840	695536062	2.180000e-101	379.0

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	TraesCS1B01G095100	chr1B	98445464	98448455	2991	True	5526.00	5526	100.0000	1	2992	1	chr1B.!!$R1	2991
1	TraesCS1B01G095100	chr1D	61942853	61944332	1479	True	2241.00	2241	94.1020	850	2324	1	chr1D.!!$R1	1474
2	TraesCS1B01G095100	chr1D	112795632	112796207	575	True	798.00	798	91.6960	2392	2968	1	chr1D.!!$R2	576
3	TraesCS1B01G095100	chr1A	59841120	59842478	1358	True	2163.00	2163	95.3320	851	2218	1	chr1A.!!$R1	1367
4	TraesCS1B01G095100	chr1A	444170243	444170884	641	False	800.00	800	89.7520	2324	2944	1	chr1A.!!$F1	620
5	TraesCS1B01G095100	chr1A	575546733	575547356	623	False	784.00	784	89.5570	2324	2944	1	chr1A.!!$F2	620
6	TraesCS1B01G095100	chr3B	811057970	811058938	968	False	679.00	968	97.1700	1	837	2	chr3B.!!$F2	836
7	TraesCS1B01G095100	chr3B	581119295	581120258	963	False	660.00	935	96.5260	1	837	2	chr3B.!!$F1	836
8	TraesCS1B01G095100	chr2B	793968442	793969036	594	False	957.00	957	95.7980	247	837	1	chr2B.!!$F5	590
9	TraesCS1B01G095100	chr2B	632888947	632889540	593	False	933.00	933	95.1260	247	837	1	chr2B.!!$F3	590
10	TraesCS1B01G095100	chr5B	246145702	246146670	968	True	671.00	941	97.2710	1	837	2	chr5B.!!$R2	836
11	TraesCS1B01G095100	chr7A	268855228	268855822	594	False	935.00	935	95.1260	247	837	1	chr7A.!!$F1	590
12	TraesCS1B01G095100	chr7A	546589915	546590506	591	True	924.00	924	94.9320	250	837	1	chr7A.!!$R1	587
13	TraesCS1B01G095100	chr7A	236111	237080	969	True	654.50	924	96.3450	1	837	2	chr7A.!!$R2	836
14	TraesCS1B01G095100	chr4B	25807882	25808850	968	True	654.00	929	96.2050	1	837	2	chr4B.!!$R1	836
15	TraesCS1B01G095100	chr4A	654185261	654185934	673	True	808.00	808	88.7740	2312	2968	1	chr4A.!!$R2	656
16	TraesCS1B01G095100	chr4A	654155831	654156504	673	True	787.00	787	88.1830	2311	2968	1	chr4A.!!$R1	657
17	TraesCS1B01G095100	chr4A	665440832	665441459	627	False	521.00	521	82.5150	2323	2943	1	chr4A.!!$F1	620
18	TraesCS1B01G095100	chr6B	181100312	181100948	636	False	527.00	527	82.5040	2324	2953	1	chr6B.!!$F1	629
19	TraesCS1B01G095100	chr6B	123476373	123477051	678	False	421.05	780	94.6455	2341	2992	2	chr6B.!!$F2	651
20	TraesCS1B01G095100	chr4D	417349494	417350045	551	True	776.00	776	92.0580	2416	2968	1	chr4D.!!$R1	552
21	TraesCS1B01G095100	chr6A	291418527	291419105	578	True	769.00	769	90.6740	2391	2968	1	chr6A.!!$R1	577
22	TraesCS1B01G095100	chr7B	609147116	609147782	666	False	761.00	761	87.7430	2313	2962	1	chr7B.!!$F1	649

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
964	1102	0.43883	CGAAACGCTGGAGCAAGTAC	59.561	55.0	0.0	0.0	42.21	2.73	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2266	2421	0.468226	AGCTGAGGAAACAACGGTCA	59.532	50.0	0.0	0.0	0.0	4.02	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
185	186	6.255020	GCGTTCTCCGAAAACTAATATTGAGA	59.745	38.462	0.00	0.00	39.56	3.27
223	224	1.070134	AGTTGCAACGTAGGCTTCTCA	59.930	47.619	23.21	0.00	0.00	3.27
224	225	2.076863	GTTGCAACGTAGGCTTCTCAT	58.923	47.619	14.90	0.00	0.00	2.90
225	226	2.472695	TGCAACGTAGGCTTCTCATT	57.527	45.000	12.59	0.00	0.00	2.57
226	227	2.778299	TGCAACGTAGGCTTCTCATTT	58.222	42.857	12.59	0.00	0.00	2.32
229	230	3.426292	GCAACGTAGGCTTCTCATTTTCC	60.426	47.826	0.00	0.00	0.00	3.13
230	231	3.983044	ACGTAGGCTTCTCATTTTCCT	57.017	42.857	0.00	0.00	0.00	3.36
231	232	3.600388	ACGTAGGCTTCTCATTTTCCTG	58.400	45.455	0.00	0.00	0.00	3.86
232	233	3.260884	ACGTAGGCTTCTCATTTTCCTGA	59.739	43.478	0.00	0.00	0.00	3.86
233	234	3.868077	CGTAGGCTTCTCATTTTCCTGAG	59.132	47.826	0.00	0.00	43.33	3.35
234	235	2.720915	AGGCTTCTCATTTTCCTGAGC	58.279	47.619	0.00	0.00	42.00	4.26
235	236	1.747924	GGCTTCTCATTTTCCTGAGCC	59.252	52.381	0.00	0.00	42.00	4.70
236	237	2.440409	GCTTCTCATTTTCCTGAGCCA	58.560	47.619	0.00	0.00	42.00	4.75
237	238	2.821969	GCTTCTCATTTTCCTGAGCCAA	59.178	45.455	0.00	0.00	42.00	4.52
238	239	3.119566	GCTTCTCATTTTCCTGAGCCAAG	60.120	47.826	0.00	0.00	42.00	3.61
240	241	2.644299	TCTCATTTTCCTGAGCCAAGGA	59.356	45.455	0.77	0.77	44.88	3.36
241	242	3.267812	TCTCATTTTCCTGAGCCAAGGAT	59.732	43.478	5.84	0.00	45.84	3.24
242	243	4.021916	CTCATTTTCCTGAGCCAAGGATT	58.978	43.478	5.84	0.00	45.84	3.01
243	244	4.419282	TCATTTTCCTGAGCCAAGGATTT	58.581	39.130	5.84	0.00	45.84	2.17
245	246	5.653769	TCATTTTCCTGAGCCAAGGATTTAG	59.346	40.000	5.84	0.00	45.84	1.85
248	379	2.511218	TCCTGAGCCAAGGATTTAGCAT	59.489	45.455	0.77	0.00	41.60	3.79
263	394	2.969628	AGCATAAAGGTGAGTCGGAG	57.030	50.000	0.00	0.00	0.00	4.63
544	675	2.361771	GACTCCCACCGGGACCTA	59.638	66.667	6.32	0.00	46.17	3.08
623	754	1.676529	CGTCCTCCGTATGACATGAGT	59.323	52.381	0.00	0.00	0.00	3.41
661	792	4.978580	GCTCAGTTTCTTTTCAAAGCGATT	59.021	37.500	0.00	0.00	35.99	3.34
713	844	5.121298	CAGCTTACGATGATGAATGGGTATG	59.879	44.000	0.00	0.00	0.00	2.39
724	855	5.702065	TGAATGGGTATGCCTAAGTACAA	57.298	39.130	0.00	0.00	34.45	2.41
777	912	6.549433	TTGTTTATACGTATCCTGGTCCTT	57.451	37.500	12.24	0.00	0.00	3.36
788	923	2.443255	TCCTGGTCCTTCTTTGCTCTTT	59.557	45.455	0.00	0.00	0.00	2.52
837	972	6.603201	TGGAAGTTAATTTTGAGGCCAGATAG	59.397	38.462	5.01	0.00	0.00	2.08
838	973	6.603599	GGAAGTTAATTTTGAGGCCAGATAGT	59.396	38.462	5.01	0.00	0.00	2.12
839	974	7.773690	GGAAGTTAATTTTGAGGCCAGATAGTA	59.226	37.037	5.01	0.00	0.00	1.82
840	975	9.174166	GAAGTTAATTTTGAGGCCAGATAGTAA	57.826	33.333	5.01	0.00	0.00	2.24
841	976	8.507524	AGTTAATTTTGAGGCCAGATAGTAAC	57.492	34.615	5.01	6.35	0.00	2.50
842	977	8.329502	AGTTAATTTTGAGGCCAGATAGTAACT	58.670	33.333	5.01	8.53	0.00	2.24
843	978	8.613482	GTTAATTTTGAGGCCAGATAGTAACTC	58.387	37.037	5.01	0.00	0.00	3.01
844	979	6.567602	ATTTTGAGGCCAGATAGTAACTCT	57.432	37.500	5.01	0.00	0.00	3.24
845	980	5.344743	TTTGAGGCCAGATAGTAACTCTG	57.655	43.478	5.01	0.00	39.88	3.35
871	1006	6.317140	GTGATATCCAGCTGTTCAAAGAATCA	59.683	38.462	13.81	9.96	0.00	2.57
930	1068	6.014840	ACCTACAAAATAGTCAACTTCGGAGA	60.015	38.462	0.00	0.00	0.00	3.71
931	1069	6.531948	CCTACAAAATAGTCAACTTCGGAGAG	59.468	42.308	0.00	0.00	38.43	3.20
933	1071	5.011738	ACAAAATAGTCAACTTCGGAGAGGA	59.988	40.000	0.00	0.00	38.43	3.71
934	1072	5.941555	AAATAGTCAACTTCGGAGAGGAT	57.058	39.130	0.00	0.00	38.43	3.24
935	1073	7.093465	ACAAAATAGTCAACTTCGGAGAGGATA	60.093	37.037	0.00	0.00	38.43	2.59
937	1075	4.993029	AGTCAACTTCGGAGAGGATAAG	57.007	45.455	0.00	0.00	38.43	1.73
939	1077	3.700038	GTCAACTTCGGAGAGGATAAGGA	59.300	47.826	0.00	0.00	38.43	3.36
940	1078	4.159879	GTCAACTTCGGAGAGGATAAGGAA	59.840	45.833	0.00	0.00	38.43	3.36
941	1079	4.775780	TCAACTTCGGAGAGGATAAGGAAA	59.224	41.667	0.00	0.00	38.43	3.13
942	1080	4.739587	ACTTCGGAGAGGATAAGGAAAC	57.260	45.455	0.00	0.00	38.43	2.78
943	1081	3.130693	ACTTCGGAGAGGATAAGGAAACG	59.869	47.826	0.00	0.00	38.43	3.60
944	1082	2.029623	TCGGAGAGGATAAGGAAACGG	58.970	52.381	0.00	0.00	0.00	4.44
945	1083	1.538419	CGGAGAGGATAAGGAAACGGC	60.538	57.143	0.00	0.00	0.00	5.68
963	1101	2.822306	CGAAACGCTGGAGCAAGTA	58.178	52.632	0.00	0.00	42.21	2.24
964	1102	0.438830	CGAAACGCTGGAGCAAGTAC	59.561	55.000	0.00	0.00	42.21	2.73
965	1103	1.797025	GAAACGCTGGAGCAAGTACT	58.203	50.000	0.00	0.00	42.21	2.73
966	1104	2.670229	CGAAACGCTGGAGCAAGTACTA	60.670	50.000	0.00	0.00	42.21	1.82
967	1105	3.522553	GAAACGCTGGAGCAAGTACTAT	58.477	45.455	0.00	0.00	42.21	2.12
984	1122	8.775527	CAAGTACTATAGTTGAGATCGAAGCTA	58.224	37.037	11.40	0.00	40.68	3.32
995	1133	6.382608	TGAGATCGAAGCTAATTAATCGAGG	58.617	40.000	17.32	0.00	46.09	4.63
1004	1142	4.083271	GCTAATTAATCGAGGGAACATGGC	60.083	45.833	0.00	0.00	0.00	4.40
1030	1168	0.318275	GCTTAGAGGGCTCGTGATCG	60.318	60.000	0.00	0.00	38.55	3.69
1200	1338	0.250338	GCTTCTTCAACCGGACCACT	60.250	55.000	9.46	0.00	0.00	4.00
1241	1379	3.489229	CGCCTCTACATCGACTTCATTGA	60.489	47.826	0.00	0.00	0.00	2.57
1262	1400	0.179078	ACGTACCTTGCGTCCAAACA	60.179	50.000	0.00	0.00	38.23	2.83
1292	1430	3.423539	TTAGTTCCATGCAAGCAGAGT	57.576	42.857	0.00	0.00	0.00	3.24
1308	1446	2.049063	GTTCAGCTCCGACGTGCT	60.049	61.111	0.00	6.75	39.39	4.40
1322	1460	0.863799	CGTGCTATCGATTGCATGCT	59.136	50.000	31.14	0.00	40.36	3.79
2237	2375	6.594788	TTTTGGTCGAGGTGTAAGTACTAT	57.405	37.500	0.00	0.00	0.00	2.12
2238	2376	7.701539	TTTTGGTCGAGGTGTAAGTACTATA	57.298	36.000	0.00	0.00	0.00	1.31
2241	2379	6.653020	TGGTCGAGGTGTAAGTACTATAAGA	58.347	40.000	0.00	0.00	0.00	2.10
2242	2380	7.285566	TGGTCGAGGTGTAAGTACTATAAGAT	58.714	38.462	0.00	0.00	0.00	2.40
2243	2381	7.443575	TGGTCGAGGTGTAAGTACTATAAGATC	59.556	40.741	0.00	0.00	0.00	2.75
2266	2421	4.724279	AAAACTGGATCAGGTACACCTT	57.276	40.909	0.00	0.00	46.09	3.50
2307	2462	2.288273	ACTAATAAGATCCGCTCCACGC	60.288	50.000	0.00	0.00	41.76	5.34
2560	2761	8.472007	TTGACCACAAAGACAATAATAAGGTT	57.528	30.769	0.00	0.00	32.73	3.50
2593	2794	3.727726	TGCAGTATCATACACGAATGGG	58.272	45.455	0.00	0.00	0.00	4.00
2638	2839	0.179032	TCAGAGCAACGCCAAAAGGA	60.179	50.000	0.00	0.00	0.00	3.36
2751	2953	3.596066	TTCAGGCGCTGCTCTGACC	62.596	63.158	17.78	3.89	36.29	4.02
2758	2960	1.078637	GCTGCTCTGACCTCATGCA	60.079	57.895	0.00	0.00	35.25	3.96
2801	3003	5.159209	GTCACTTCTTCAATGCTTGGATTG	58.841	41.667	8.28	8.28	35.05	2.67
2802	3004	3.924686	CACTTCTTCAATGCTTGGATTGC	59.075	43.478	9.50	0.00	33.95	3.56
2880	3083	5.532557	AGATTAGCAAGTTTCCAGCAAAAC	58.467	37.500	2.24	2.24	39.03	2.43

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
185	186	4.804261	GCAACTGTTCTACAATCCACTCCT	60.804	45.833	0.00	0.00	0.00	3.69
223	224	4.403752	GCTAAATCCTTGGCTCAGGAAAAT	59.596	41.667	9.68	3.16	46.50	1.82
224	225	3.763897	GCTAAATCCTTGGCTCAGGAAAA	59.236	43.478	9.68	0.00	46.50	2.29
225	226	3.245229	TGCTAAATCCTTGGCTCAGGAAA	60.245	43.478	9.68	0.00	46.50	3.13
226	227	2.308570	TGCTAAATCCTTGGCTCAGGAA	59.691	45.455	9.68	0.00	46.50	3.36
229	230	5.009410	CCTTTATGCTAAATCCTTGGCTCAG	59.991	44.000	0.00	0.00	39.64	3.35
230	231	4.889409	CCTTTATGCTAAATCCTTGGCTCA	59.111	41.667	0.00	0.00	39.64	4.26
231	232	4.889995	ACCTTTATGCTAAATCCTTGGCTC	59.110	41.667	0.00	0.00	39.64	4.70
232	233	4.646492	CACCTTTATGCTAAATCCTTGGCT	59.354	41.667	0.00	0.00	39.64	4.75
233	234	4.644685	TCACCTTTATGCTAAATCCTTGGC	59.355	41.667	0.00	0.00	39.38	4.52
234	235	5.888161	ACTCACCTTTATGCTAAATCCTTGG	59.112	40.000	0.00	0.00	0.00	3.61
235	236	6.238211	CGACTCACCTTTATGCTAAATCCTTG	60.238	42.308	0.00	0.00	0.00	3.61
236	237	5.817816	CGACTCACCTTTATGCTAAATCCTT	59.182	40.000	0.00	0.00	0.00	3.36
237	238	5.360591	CGACTCACCTTTATGCTAAATCCT	58.639	41.667	0.00	0.00	0.00	3.24
238	239	4.511826	CCGACTCACCTTTATGCTAAATCC	59.488	45.833	0.00	0.00	0.00	3.01
240	241	5.353394	TCCGACTCACCTTTATGCTAAAT	57.647	39.130	0.00	0.00	0.00	1.40
241	242	4.382685	CCTCCGACTCACCTTTATGCTAAA	60.383	45.833	0.00	0.00	0.00	1.85
242	243	3.132289	CCTCCGACTCACCTTTATGCTAA	59.868	47.826	0.00	0.00	0.00	3.09
243	244	2.693591	CCTCCGACTCACCTTTATGCTA	59.306	50.000	0.00	0.00	0.00	3.49
245	246	1.473434	CCCTCCGACTCACCTTTATGC	60.473	57.143	0.00	0.00	0.00	3.14
248	379	1.262640	GGCCCTCCGACTCACCTTTA	61.263	60.000	0.00	0.00	0.00	1.85
263	394	2.019156	GCTCAGGTAAATGTGAGGCCC	61.019	57.143	0.00	0.00	40.57	5.80
560	691	5.306160	GGTCCTTACCAGTATGCCTATGTTA	59.694	44.000	0.00	0.00	45.98	2.41
623	754	3.631250	ACTGAGCTGTTGGAAAGGAAAA	58.369	40.909	0.00	0.00	0.00	2.29
661	792	3.264947	CTTGAGTGGAAATGCATCGAGA	58.735	45.455	0.00	0.00	0.00	4.04
713	844	3.431905	GGCTCCTTACCTTGTACTTAGGC	60.432	52.174	12.74	0.00	36.17	3.93
724	855	1.992557	TGTGAATTGGGCTCCTTACCT	59.007	47.619	0.00	0.00	0.00	3.08
788	923	6.690957	CACAAGAGCGAATTGTTTTACTTTGA	59.309	34.615	2.07	0.00	38.80	2.69
794	929	5.298276	ACTTCCACAAGAGCGAATTGTTTTA	59.702	36.000	2.07	0.00	38.80	1.52
844	979	3.998913	TTGAACAGCTGGATATCACCA	57.001	42.857	19.93	0.54	38.33	4.17
845	980	4.517285	TCTTTGAACAGCTGGATATCACC	58.483	43.478	19.93	0.00	0.00	4.02
846	981	6.317140	TGATTCTTTGAACAGCTGGATATCAC	59.683	38.462	19.93	4.80	0.00	3.06
847	982	6.417258	TGATTCTTTGAACAGCTGGATATCA	58.583	36.000	19.93	13.47	0.00	2.15
848	983	6.541641	ACTGATTCTTTGAACAGCTGGATATC	59.458	38.462	19.93	11.00	34.25	1.63
891	1026	0.526662	GTAGGTGTCTGGGTCGACTG	59.473	60.000	16.46	6.47	35.00	3.51
930	1068	2.353323	GTTTCGCCGTTTCCTTATCCT	58.647	47.619	0.00	0.00	0.00	3.24
931	1069	1.061566	CGTTTCGCCGTTTCCTTATCC	59.938	52.381	0.00	0.00	0.00	2.59
945	1083	0.438830	GTACTTGCTCCAGCGTTTCG	59.561	55.000	0.00	0.00	45.83	3.46
966	1104	9.347934	CGATTAATTAGCTTCGATCTCAACTAT	57.652	33.333	0.00	0.00	33.59	2.12
967	1105	8.565416	TCGATTAATTAGCTTCGATCTCAACTA	58.435	33.333	1.91	0.00	35.85	2.24
984	1122	3.897239	TGCCATGTTCCCTCGATTAATT	58.103	40.909	0.00	0.00	0.00	1.40
1004	1142	2.208431	CGAGCCCTCTAAGCATTCTTG	58.792	52.381	0.00	0.00	33.85	3.02
1015	1153	2.473760	CGACGATCACGAGCCCTCT	61.474	63.158	3.67	0.00	42.66	3.69
1050	1188	1.301558	GAGCTCACAGCACTGCAGT	60.302	57.895	15.25	15.25	45.56	4.40
1241	1379	2.288948	TGTTTGGACGCAAGGTACGTAT	60.289	45.455	0.00	0.00	45.24	3.06
1262	1400	2.351726	GCATGGAACTAAACGAGCGATT	59.648	45.455	0.00	0.00	0.00	3.34
1292	1430	0.100682	GATAGCACGTCGGAGCTGAA	59.899	55.000	20.39	5.95	40.45	3.02
1308	1446	2.761392	GCACAAGCATGCAATCGATA	57.239	45.000	21.98	0.00	45.39	2.92
1322	1460	3.630013	AGGCTCTCGGCTGCACAA	61.630	61.111	0.50	0.00	45.42	3.33
1663	1801	3.788766	CTTCGACCTTTGCGGCGG	61.789	66.667	9.78	0.00	35.61	6.13
1670	1808	1.292541	GACGGCCTCTTCGACCTTT	59.707	57.895	0.00	0.00	0.00	3.11
1712	1850	0.753867	TGTACACCCAGAACTTGCGA	59.246	50.000	0.00	0.00	0.00	5.10
1878	2016	3.437795	CCCGCAGTACTCGTCCGT	61.438	66.667	11.85	0.00	0.00	4.69
2005	2143	2.180017	CGTAGTTGTACGGCGGCT	59.820	61.111	13.24	3.68	46.93	5.52
2202	2340	3.283751	TCGACCAAAATCACAAGTGGTT	58.716	40.909	0.00	0.00	44.42	3.67
2213	2351	5.479124	AGTACTTACACCTCGACCAAAAT	57.521	39.130	0.00	0.00	0.00	1.82
2237	2375	7.606456	GTGTACCTGATCCAGTTTTTGATCTTA	59.394	37.037	0.00	0.00	38.53	2.10
2238	2376	6.431234	GTGTACCTGATCCAGTTTTTGATCTT	59.569	38.462	0.00	0.00	38.53	2.40
2241	2379	5.010282	GGTGTACCTGATCCAGTTTTTGAT	58.990	41.667	0.00	0.00	0.00	2.57
2242	2380	4.104102	AGGTGTACCTGATCCAGTTTTTGA	59.896	41.667	2.06	0.00	46.55	2.69
2243	2381	4.398319	AGGTGTACCTGATCCAGTTTTTG	58.602	43.478	2.06	0.00	46.55	2.44
2266	2421	0.468226	AGCTGAGGAAACAACGGTCA	59.532	50.000	0.00	0.00	0.00	4.02
2307	2462	8.027771	AGTCATCTAGTTCCAGTAAAAACTACG	58.972	37.037	0.00	0.00	37.02	3.51
2355	2515	4.768968	ACTCATTCAATACTTGGCTTGCTT	59.231	37.500	0.00	0.00	0.00	3.91
2560	2761	9.093970	GTGTATGATACTGCATGTACACTTTAA	57.906	33.333	0.00	0.00	35.97	1.52
2593	2794	9.883142	AGCAAGATATGTATAGCCTTTAGATTC	57.117	33.333	0.00	0.00	0.00	2.52
2638	2839	8.588472	TCATATCAATCGATCCAGTATCTTTGT	58.412	33.333	0.00	0.00	31.91	2.83
2751	2953	5.928839	AGAGGTTACGCTATATTTGCATGAG	59.071	40.000	0.00	0.00	0.00	2.90
2758	2960	4.202080	TGACGCAGAGGTTACGCTATATTT	60.202	41.667	0.00	0.00	0.00	1.40
2880	3083	6.867293	ACAGATATGTGATTCTCATGTGATCG	59.133	38.462	6.90	6.13	0.00	3.69
2910	3113	9.300681	TGTTGGATTTCTGTTTCTCTTCATATT	57.699	29.630	0.00	0.00	0.00	1.28
2962	3165	5.125097	CCTATGCAATCAAGCTTCTGTTCTT	59.875	40.000	0.00	0.00	34.99	2.52
2964	3167	4.201990	CCCTATGCAATCAAGCTTCTGTTC	60.202	45.833	0.00	0.00	34.99	3.18

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.