AutoCloner

Multiple sequence alignment - TraesCS6B01G076600

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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	TraesCS6B01G076600	chr6B	100.000	3155	0	0	1	3155	52569242	52566088	0.000000e+00	5827.0
1	TraesCS6B01G076600	chr6B	94.155	1728	95	4	981	2708	16428988	16430709	0.000000e+00	2627.0
2	TraesCS6B01G076600	chr6B	93.552	1008	56	5	1700	2706	52987888	52986889	0.000000e+00	1493.0
3	TraesCS6B01G076600	chr6B	91.816	1063	86	1	1095	2157	15225632	15224571	0.000000e+00	1480.0
4	TraesCS6B01G076600	chr6B	94.725	455	22	2	2702	3155	52986839	52986386	0.000000e+00	706.0
5	TraesCS6B01G076600	chr6B	96.667	330	9	2	2827	3155	16431101	16431429	5.950000e-152	547.0
6	TraesCS6B01G076600	chr6B	98.571	140	2	0	2702	2841	16430762	16430901	6.760000e-62	248.0
7	TraesCS6B01G076600	chr6B	87.324	71	4	2	2773	2843	15749300	15749235	3.370000e-10	76.8
8	TraesCS6B01G076600	chr6D	92.217	2724	169	28	6	2708	8398155	8395454	0.000000e+00	3816.0
9	TraesCS6B01G076600	chr6D	91.279	2557	141	29	1	2540	8898540	8901031	0.000000e+00	3411.0
10	TraesCS6B01G076600	chr6D	83.235	1181	194	3	979	2157	8894035	8895213	0.000000e+00	1081.0
11	TraesCS6B01G076600	chr6D	96.035	454	18	0	2702	3155	8901316	8901769	0.000000e+00	739.0
12	TraesCS6B01G076600	chr6D	92.747	455	26	2	2702	3155	8395401	8394953	0.000000e+00	651.0
13	TraesCS6B01G076600	chr6D	95.302	149	6	1	2535	2683	8901109	8901256	5.260000e-58	235.0
14	TraesCS6B01G076600	chr6D	91.667	48	4	0	2758	2805	8918524	8918571	2.030000e-07	67.6
15	TraesCS6B01G076600	chr6A	87.609	1267	128	12	1364	2625	8804185	8802943	0.000000e+00	1443.0
16	TraesCS6B01G076600	chr1B	84.915	1180	168	8	984	2157	630644732	630645907	0.000000e+00	1184.0
17	TraesCS6B01G076600	chr3A	84.302	1204	181	6	959	2156	45938015	45936814	0.000000e+00	1170.0
18	TraesCS6B01G076600	chr3D	83.333	1206	190	7	959	2155	33330537	33329334	0.000000e+00	1103.0
19	TraesCS6B01G076600	chr2B	80.805	1193	220	7	970	2156	709426202	709425013	0.000000e+00	926.0
20	TraesCS6B01G076600	chr2B	84.259	108	10	4	2758	2865	373066914	373066814	7.200000e-17	99.0
21	TraesCS6B01G076600	chr1D	92.941	85	5	1	2754	2838	416354728	416354645	4.270000e-24	122.0

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	TraesCS6B01G076600	chr6B	52566088	52569242	3154	True	5827.000000	5827	100.000000	1	3155	1	chr6B.!!$R3	3154
1	TraesCS6B01G076600	chr6B	15224571	15225632	1061	True	1480.000000	1480	91.816000	1095	2157	1	chr6B.!!$R1	1062
2	TraesCS6B01G076600	chr6B	16428988	16431429	2441	False	1140.666667	2627	96.464333	981	3155	3	chr6B.!!$F1	2174
3	TraesCS6B01G076600	chr6B	52986386	52987888	1502	True	1099.500000	1493	94.138500	1700	3155	2	chr6B.!!$R4	1455
4	TraesCS6B01G076600	chr6D	8394953	8398155	3202	True	2233.500000	3816	92.482000	6	3155	2	chr6D.!!$R1	3149
5	TraesCS6B01G076600	chr6D	8894035	8901769	7734	False	1366.500000	3411	91.462750	1	3155	4	chr6D.!!$F2	3154
6	TraesCS6B01G076600	chr6A	8802943	8804185	1242	True	1443.000000	1443	87.609000	1364	2625	1	chr6A.!!$R1	1261
7	TraesCS6B01G076600	chr1B	630644732	630645907	1175	False	1184.000000	1184	84.915000	984	2157	1	chr1B.!!$F1	1173
8	TraesCS6B01G076600	chr3A	45936814	45938015	1201	True	1170.000000	1170	84.302000	959	2156	1	chr3A.!!$R1	1197
9	TraesCS6B01G076600	chr3D	33329334	33330537	1203	True	1103.000000	1103	83.333000	959	2155	1	chr3D.!!$R1	1196
10	TraesCS6B01G076600	chr2B	709425013	709426202	1189	True	926.000000	926	80.805000	970	2156	1	chr2B.!!$R2	1186

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
954	5462	0.179032	TCACACCCACGCAAATCACT	60.179	50.0	0.0	0.0	0.0	3.41	F
955	5463	0.238289	CACACCCACGCAAATCACTC	59.762	55.0	0.0	0.0	0.0	3.51	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1875	6418	1.482365	GGTTCAAACCCCACCTTGGAT	60.482	52.381	0.10	0.0	43.43	3.41	R
2533	7105	4.216472	TGTGTCAGAGAGTGCTTAGTACTG	59.784	45.833	7.87	0.0	0.00	2.74	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
30	4536	3.636764	GGGGTCAAACACTTGTTGAGATT	59.363	43.478	0.00	0.00	38.44	2.40
45	4551	7.206981	TGTTGAGATTTGTCAAGAATTCCTC	57.793	36.000	0.65	0.00	37.12	3.71
103	4610	7.503566	TCAGAAAAGAGGATGAAACACTTTGAT	59.496	33.333	0.00	0.00	32.36	2.57
117	4624	6.976934	ACACTTTGATGGGTTTATGAGTTT	57.023	33.333	0.00	0.00	0.00	2.66
152	4659	8.740123	TGAAGAATAAGTGTTCAACAAACCTA	57.260	30.769	0.00	0.00	37.03	3.08
157	4664	9.836076	GAATAAGTGTTCAACAAACCTATAACC	57.164	33.333	0.00	0.00	37.03	2.85
188	4695	4.998671	TGATGTTGTGAGGCTTCAAAAA	57.001	36.364	2.50	0.00	32.42	1.94
283	4790	1.981495	CCCTCCTTCTCCACAGACTTT	59.019	52.381	0.00	0.00	0.00	2.66
308	4815	3.285484	ACCAAAGCAGATAAGGCATCAG	58.715	45.455	0.00	0.00	35.96	2.90
313	4820	1.336125	GCAGATAAGGCATCAGCAACC	59.664	52.381	0.00	0.00	43.67	3.77
362	4869	0.396811	ACCTTGACGAAGACCCCTTG	59.603	55.000	0.00	0.00	31.62	3.61
431	4938	2.654749	TACAGATCTCACACAAGCCG	57.345	50.000	0.00	0.00	0.00	5.52
506	5013	1.849097	AAAGTCTCAACCGACACGAC	58.151	50.000	0.00	0.00	36.38	4.34
545	5052	9.584008	AGAGATCCAATTTATATGCACAAAGAT	57.416	29.630	0.00	0.00	0.00	2.40
579	5086	4.262079	CCGTCCCTCCTACTATCATGTTTC	60.262	50.000	0.00	0.00	0.00	2.78
786	5293	8.655935	ACATTCTCCAACTTATTTTTCCTCAT	57.344	30.769	0.00	0.00	0.00	2.90
787	5294	9.093458	ACATTCTCCAACTTATTTTTCCTCATT	57.907	29.630	0.00	0.00	0.00	2.57
788	5295	9.578439	CATTCTCCAACTTATTTTTCCTCATTC	57.422	33.333	0.00	0.00	0.00	2.67
793	5300	8.796475	TCCAACTTATTTTTCCTCATTCTTCTG	58.204	33.333	0.00	0.00	0.00	3.02
880	5387	5.423931	AGCCCACCTGTTTTTCTTTTCTTTA	59.576	36.000	0.00	0.00	0.00	1.85
881	5388	6.070481	AGCCCACCTGTTTTTCTTTTCTTTAA	60.070	34.615	0.00	0.00	0.00	1.52
907	5414	1.867363	GAGGGAAAGGAGCTCACCTA	58.133	55.000	17.19	0.00	39.62	3.08
925	5432	1.831736	CTAGGTTGGGTCGAACCAGAT	59.168	52.381	23.72	14.80	46.94	2.90
926	5433	0.613777	AGGTTGGGTCGAACCAGATC	59.386	55.000	23.72	16.39	46.94	2.75
930	5437	1.639722	TGGGTCGAACCAGATCAGAA	58.360	50.000	20.95	0.00	41.02	3.02
938	5445	3.862267	CGAACCAGATCAGAACAGATCAC	59.138	47.826	9.22	0.00	45.39	3.06
954	5462	0.179032	TCACACCCACGCAAATCACT	60.179	50.000	0.00	0.00	0.00	3.41
955	5463	0.238289	CACACCCACGCAAATCACTC	59.762	55.000	0.00	0.00	0.00	3.51
956	5464	0.889186	ACACCCACGCAAATCACTCC	60.889	55.000	0.00	0.00	0.00	3.85
957	5465	0.888736	CACCCACGCAAATCACTCCA	60.889	55.000	0.00	0.00	0.00	3.86
958	5466	0.889186	ACCCACGCAAATCACTCCAC	60.889	55.000	0.00	0.00	0.00	4.02
959	5467	1.586154	CCCACGCAAATCACTCCACC	61.586	60.000	0.00	0.00	0.00	4.61
960	5468	1.497278	CACGCAAATCACTCCACCG	59.503	57.895	0.00	0.00	0.00	4.94
961	5469	2.325082	ACGCAAATCACTCCACCGC	61.325	57.895	0.00	0.00	0.00	5.68
962	5470	2.480555	GCAAATCACTCCACCGCG	59.519	61.111	0.00	0.00	0.00	6.46
963	5471	2.480555	CAAATCACTCCACCGCGC	59.519	61.111	0.00	0.00	0.00	6.86
1041	5578	1.305633	CCTCACCCAGCTCCTCTCA	60.306	63.158	0.00	0.00	0.00	3.27
1825	6368	3.876589	TTGTCCACGCTTCCGCCTC	62.877	63.158	0.00	0.00	38.22	4.70
1875	6418	5.361285	GGAGAGCAAGTCAGAGTTCCTAATA	59.639	44.000	0.00	0.00	0.00	0.98
2183	6726	4.261280	GGTAACACTACGGCACAACAATTT	60.261	41.667	0.00	0.00	0.00	1.82
2312	6858	4.962362	TGATTTGATGGTGCTAGTCTAGGA	59.038	41.667	8.97	2.76	0.00	2.94
2313	6859	5.604231	TGATTTGATGGTGCTAGTCTAGGAT	59.396	40.000	8.97	0.00	0.00	3.24
2314	6860	5.537300	TTTGATGGTGCTAGTCTAGGATC	57.463	43.478	8.97	6.85	0.00	3.36
2412	6959	2.938956	AGCTTGTGCACTCTAAGGTT	57.061	45.000	19.41	0.00	42.74	3.50
2533	7105	1.586422	TGTCAGAGAAAGCACTGCAC	58.414	50.000	3.30	0.00	33.41	4.57
2913	7842	7.392393	TGCACTACTCAGTAGTTTGTATCAGTA	59.608	37.037	15.30	0.00	45.68	2.74
3102	8032	5.051816	CAGAGGCAAATTTCTGAAAAGCAA	58.948	37.500	19.79	0.00	42.67	3.91

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	6.493189	ACAAGTGTTTGACCCCAAATATTT	57.507	33.333	0.00	0.00	43.37	1.40
1	2	6.098982	TCAACAAGTGTTTGACCCCAAATATT	59.901	34.615	0.00	0.00	43.37	1.28
2	3	5.600484	TCAACAAGTGTTTGACCCCAAATAT	59.400	36.000	0.00	0.00	43.37	1.28
3	4	4.956700	TCAACAAGTGTTTGACCCCAAATA	59.043	37.500	0.00	0.00	43.37	1.40
30	4536	4.307432	GACGTGAGAGGAATTCTTGACAA	58.693	43.478	5.23	0.00	35.87	3.18
45	4551	2.657237	GGTGGTGGAGGACGTGAG	59.343	66.667	0.00	0.00	0.00	3.51
103	4610	3.558321	CGACAGGGAAACTCATAAACCCA	60.558	47.826	0.00	0.00	42.62	4.51
117	4624	4.466370	ACACTTATTCTTCATCGACAGGGA	59.534	41.667	0.00	0.00	0.00	4.20
283	4790	4.640201	GATGCCTTATCTGCTTTGGTACAA	59.360	41.667	0.00	0.00	36.73	2.41
308	4815	6.377146	TCACCTTTCTTATTCCTATTGGTTGC	59.623	38.462	0.00	0.00	34.23	4.17
313	4820	7.067494	CCCTTGTCACCTTTCTTATTCCTATTG	59.933	40.741	0.00	0.00	0.00	1.90
349	4856	2.610438	TACCTACAAGGGGTCTTCGT	57.390	50.000	0.00	0.00	40.58	3.85
431	4938	3.120304	GCACGGTGGATTTCTCTTGTTAC	60.120	47.826	10.60	0.00	0.00	2.50
506	5013	2.564504	TGGATCTCTCGAATGCCTATGG	59.435	50.000	0.00	0.00	0.00	2.74
545	5052	3.948719	GGGACGGGCCTTGTCACA	61.949	66.667	23.85	0.00	39.58	3.58
579	5086	4.361451	AATTATTTCCAGCAACAGCGAG	57.639	40.909	0.00	0.00	0.00	5.03
645	5152	4.253685	CGGATACTGACACATTCACCTTT	58.746	43.478	0.00	0.00	0.00	3.11
646	5153	3.260884	ACGGATACTGACACATTCACCTT	59.739	43.478	0.00	0.00	0.00	3.50
762	5269	9.578439	GAATGAGGAAAAATAAGTTGGAGAATG	57.422	33.333	0.00	0.00	0.00	2.67
763	5270	9.539194	AGAATGAGGAAAAATAAGTTGGAGAAT	57.461	29.630	0.00	0.00	0.00	2.40
793	5300	5.923665	TCTTTCTTTTTATCGCTTCGTTCC	58.076	37.500	0.00	0.00	0.00	3.62
880	5387	3.759086	GAGCTCCTTTCCCTCGAAAAATT	59.241	43.478	0.87	0.00	37.53	1.82
881	5388	3.244911	TGAGCTCCTTTCCCTCGAAAAAT	60.245	43.478	12.15	0.00	37.53	1.82
907	5414	0.613777	GATCTGGTTCGACCCAACCT	59.386	55.000	2.35	0.00	45.54	3.50
925	5432	1.000843	CGTGGGTGTGATCTGTTCTGA	59.999	52.381	0.00	0.00	0.00	3.27
926	5433	1.432514	CGTGGGTGTGATCTGTTCTG	58.567	55.000	0.00	0.00	0.00	3.02
930	5437	0.179032	TTTGCGTGGGTGTGATCTGT	60.179	50.000	0.00	0.00	0.00	3.41
938	5445	0.888736	TGGAGTGATTTGCGTGGGTG	60.889	55.000	0.00	0.00	0.00	4.61
956	5464	3.051392	GAATGGGGAAAGCGCGGTG	62.051	63.158	13.41	0.00	0.00	4.94
957	5465	2.750237	GAATGGGGAAAGCGCGGT	60.750	61.111	4.23	4.23	0.00	5.68
958	5466	3.518068	GGAATGGGGAAAGCGCGG	61.518	66.667	8.83	0.00	0.00	6.46
959	5467	3.518068	GGGAATGGGGAAAGCGCG	61.518	66.667	0.00	0.00	0.00	6.86
960	5468	2.043953	AGGGAATGGGGAAAGCGC	60.044	61.111	0.00	0.00	0.00	5.92
961	5469	1.819632	CGAGGGAATGGGGAAAGCG	60.820	63.158	0.00	0.00	0.00	4.68
962	5470	2.121538	GCGAGGGAATGGGGAAAGC	61.122	63.158	0.00	0.00	0.00	3.51
963	5471	1.453928	GGCGAGGGAATGGGGAAAG	60.454	63.158	0.00	0.00	0.00	2.62
1041	5578	2.519780	GGAGACGCGGAGGGAGAT	60.520	66.667	12.47	0.00	46.37	2.75
1790	6333	1.965930	AAAGCAATGCGCACCTCGA	60.966	52.632	14.90	0.00	46.13	4.04
1825	6368	3.834489	ATGGTTAGACCTCATCAGCAG	57.166	47.619	0.00	0.00	39.58	4.24
1875	6418	1.482365	GGTTCAAACCCCACCTTGGAT	60.482	52.381	0.10	0.00	43.43	3.41
2312	6858	8.568676	TCAAATCAAATTGCCAATTTCATGAT	57.431	26.923	12.34	10.50	38.97	2.45
2313	6859	7.878644	TCTCAAATCAAATTGCCAATTTCATGA	59.121	29.630	12.34	8.69	38.97	3.07
2314	6860	8.035165	TCTCAAATCAAATTGCCAATTTCATG	57.965	30.769	12.34	9.17	38.97	3.07
2412	6959	8.288913	CGTAAATCCAATATGTATGTCAATGCA	58.711	33.333	0.00	0.00	32.58	3.96
2533	7105	4.216472	TGTGTCAGAGAGTGCTTAGTACTG	59.784	45.833	7.87	0.00	0.00	2.74
3047	7977	0.612732	CAGGGCCTCCAAAATGCTCA	60.613	55.000	0.95	0.00	34.83	4.26
3049	7979	1.305549	CCAGGGCCTCCAAAATGCT	60.306	57.895	0.95	0.00	34.83	3.79
3102	8032	7.961326	AAGTTCTGTTATATGAAATGCCCTT	57.039	32.000	0.00	0.00	0.00	3.95

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.