AutoCloner

Multiple sequence alignment - TraesCS6A01G075900

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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	TraesCS6A01G075900	chr6A	100.000	2387	0	0	1	2387	46561589	46559203	0.000000e+00	4409
1	TraesCS6A01G075900	chr6A	86.578	1736	211	20	1	1722	121740943	121739216	0.000000e+00	1895
2	TraesCS6A01G075900	chr6A	83.004	506	60	13	1738	2233	46672968	46673457	3.640000e-118	435
3	TraesCS6A01G075900	chr7D	89.936	1729	164	8	1	1722	88140700	88142425	0.000000e+00	2220
4	TraesCS6A01G075900	chr4D	89.815	1728	169	6	1	1722	22994030	22992304	0.000000e+00	2209
5	TraesCS6A01G075900	chr3D	89.352	1728	175	8	1	1722	93036556	93034832	0.000000e+00	2163
6	TraesCS6A01G075900	chr5A	88.249	1736	186	16	1	1725	468358816	468360544	0.000000e+00	2060
7	TraesCS6A01G075900	chr7A	86.774	1739	203	23	1	1722	644729573	644727845	0.000000e+00	1912
8	TraesCS6A01G075900	chr7A	85.731	1738	224	22	1	1722	690429610	690431339	0.000000e+00	1814
9	TraesCS6A01G075900	chr7B	85.599	1729	240	9	1	1722	581409196	581407470	0.000000e+00	1805
10	TraesCS6A01G075900	chr4B	84.923	1678	241	11	1	1670	448811665	448813338	0.000000e+00	1687
11	TraesCS6A01G075900	chr4B	87.368	95	11	1	1719	1813	82172237	82172330	9.020000e-20	108
12	TraesCS6A01G075900	chrUn	89.766	684	33	11	1725	2387	27608388	27607721	0.000000e+00	841
13	TraesCS6A01G075900	chrUn	83.665	502	55	12	1769	2261	27598469	27598952	4.680000e-122	448
14	TraesCS6A01G075900	chrUn	85.163	337	31	11	1722	2053	27555029	27554707	6.360000e-86	327
15	TraesCS6A01G075900	chr6B	83.716	522	60	13	1722	2233	80005060	80004554	9.990000e-129	470
16	TraesCS6A01G075900	chr6B	81.548	168	23	3	1722	1881	79951268	79951101	5.350000e-27	132

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	TraesCS6A01G075900	chr6A	46559203	46561589	2386	True	4409	4409	100.000	1	2387	1	chr6A.!!$R1	2386
1	TraesCS6A01G075900	chr6A	121739216	121740943	1727	True	1895	1895	86.578	1	1722	1	chr6A.!!$R2	1721
2	TraesCS6A01G075900	chr7D	88140700	88142425	1725	False	2220	2220	89.936	1	1722	1	chr7D.!!$F1	1721
3	TraesCS6A01G075900	chr4D	22992304	22994030	1726	True	2209	2209	89.815	1	1722	1	chr4D.!!$R1	1721
4	TraesCS6A01G075900	chr3D	93034832	93036556	1724	True	2163	2163	89.352	1	1722	1	chr3D.!!$R1	1721
5	TraesCS6A01G075900	chr5A	468358816	468360544	1728	False	2060	2060	88.249	1	1725	1	chr5A.!!$F1	1724
6	TraesCS6A01G075900	chr7A	644727845	644729573	1728	True	1912	1912	86.774	1	1722	1	chr7A.!!$R1	1721
7	TraesCS6A01G075900	chr7A	690429610	690431339	1729	False	1814	1814	85.731	1	1722	1	chr7A.!!$F1	1721
8	TraesCS6A01G075900	chr7B	581407470	581409196	1726	True	1805	1805	85.599	1	1722	1	chr7B.!!$R1	1721
9	TraesCS6A01G075900	chr4B	448811665	448813338	1673	False	1687	1687	84.923	1	1670	1	chr4B.!!$F2	1669
10	TraesCS6A01G075900	chrUn	27607721	27608388	667	True	841	841	89.766	1725	2387	1	chrUn.!!$R2	662
11	TraesCS6A01G075900	chr6B	80004554	80005060	506	True	470	470	83.716	1722	2233	1	chr6B.!!$R2	511

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
685	688	0.172352	CAGACGAAGGCTCACTCCTC	59.828	60.0	0.0	0.0	34.82	3.71	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2341	2390	0.317479	ACGACCAGGGTTTTCTCGAG	59.683	55.0	5.93	5.93	0.0	4.04	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
23	24	4.036380	GCATGCTTGTTAGTTATACCACCC	59.964	45.833	11.37	0.00	0.00	4.61
25	26	5.093849	TGCTTGTTAGTTATACCACCCTC	57.906	43.478	0.00	0.00	0.00	4.30
348	350	9.520515	AAACAGAACATTAGTCTGATGGTAAAT	57.479	29.630	9.25	0.00	35.62	1.40
368	370	0.181587	TGGTGGTGGAAGCTCGAAAA	59.818	50.000	0.00	0.00	33.76	2.29
374	376	3.193691	TGGTGGAAGCTCGAAAAACAAAA	59.806	39.130	0.00	0.00	33.76	2.44
398	400	1.956477	GGTGTGGCAAGACATTGTTCT	59.044	47.619	0.00	0.00	38.76	3.01
422	424	3.777478	CTCGTTACTTGCGGAATAGGAA	58.223	45.455	0.00	0.00	0.00	3.36
438	440	5.700402	ATAGGAAAGTAGCTGATGTTGGT	57.300	39.130	0.00	0.00	0.00	3.67
476	478	1.667722	CTTGTTGGAAAGCCCTGCC	59.332	57.895	0.00	0.00	35.38	4.85
564	566	3.386726	TGTGGAGTGATCCTATTAACGGG	59.613	47.826	0.00	0.00	0.00	5.28
592	595	3.118408	TCCGTTCAAGGATCAATACCCTG	60.118	47.826	0.00	0.00	34.92	4.45
597	600	5.779241	TCAAGGATCAATACCCTGAACTT	57.221	39.130	0.00	0.00	32.12	2.66
652	655	9.398170	CTATCAAACAAGTGTTTAATGTGGAAG	57.602	33.333	9.01	0.00	45.54	3.46
654	657	4.223320	ACAAGTGTTTAATGTGGAAGCG	57.777	40.909	0.00	0.00	0.00	4.68
685	688	0.172352	CAGACGAAGGCTCACTCCTC	59.828	60.000	0.00	0.00	34.82	3.71
692	695	3.383185	CGAAGGCTCACTCCTCTTCTATT	59.617	47.826	0.00	0.00	34.82	1.73
767	770	4.351874	AAGAGAATCGAGTGGTTTGGAA	57.648	40.909	0.00	0.00	42.67	3.53
814	817	6.245408	AGCACCAAATCTGTTTATAAGTGGA	58.755	36.000	0.00	0.00	0.00	4.02
815	818	6.375455	AGCACCAAATCTGTTTATAAGTGGAG	59.625	38.462	0.00	0.00	0.00	3.86
989	992	8.689251	TGTTCATTCTGTAACGAAATAGAGAG	57.311	34.615	0.00	0.00	0.00	3.20
1000	1003	4.218635	ACGAAATAGAGAGTTCTCAGCACA	59.781	41.667	11.44	0.00	45.21	4.57
1113	1117	3.758554	TCTTTGCTTGGTGCTATTCCTTC	59.241	43.478	0.00	0.00	43.37	3.46
1178	1182	3.842923	CTGGGCGATCTGGCTCGT	61.843	66.667	10.05	0.00	44.11	4.18
1194	1198	2.810650	CTCGTTCGCAATAAGGCTACT	58.189	47.619	0.00	0.00	0.00	2.57
1246	1251	6.441093	TTGAAATCATGTTCTCTATGTGCC	57.559	37.500	0.00	0.00	0.00	5.01
1253	1258	3.686016	TGTTCTCTATGTGCCCTTTTCC	58.314	45.455	0.00	0.00	0.00	3.13
1257	1262	5.772393	TCTCTATGTGCCCTTTTCCTTTA	57.228	39.130	0.00	0.00	0.00	1.85
1270	1275	6.194967	CCTTTTCCTTTATATTGGACAGGGT	58.805	40.000	9.22	0.00	32.89	4.34
1292	1297	1.202268	GCAGAAAGGTGATGATGCTGC	60.202	52.381	0.00	0.00	40.15	5.25
1324	1329	0.397675	AGGTGCCGAGATGATCAGGA	60.398	55.000	10.49	0.00	0.00	3.86
1399	1405	1.940613	GAGCTTGAAGAACGTTGTGGT	59.059	47.619	5.00	0.00	0.00	4.16
1451	1462	3.414193	CTGCTGGGAGGGCCATCA	61.414	66.667	20.75	0.00	35.15	3.07
1454	1465	2.459086	GCTGGGAGGGCCATCATCT	61.459	63.158	20.75	0.00	35.15	2.90
1496	1512	4.794169	ACGTTTATGATCTTTTGGTGTGC	58.206	39.130	0.00	0.00	0.00	4.57
1522	1538	4.392940	CATGTTTCTCTCTCTGGGTTTGT	58.607	43.478	0.00	0.00	0.00	2.83
1535	1551	2.158385	TGGGTTTGTTGGAGCTTGGTAT	60.158	45.455	0.00	0.00	0.00	2.73
1542	1559	4.922206	TGTTGGAGCTTGGTATTCTTGAT	58.078	39.130	0.00	0.00	0.00	2.57
1647	1665	0.178301	CGCCTTACCTCTTTCCCTCC	59.822	60.000	0.00	0.00	0.00	4.30
1772	1792	8.352942	GTTTGGAGTATGTTGAATGGATATTCC	58.647	37.037	0.00	0.00	41.62	3.01
1799	1822	2.143925	GTGCTTCACAAGGTACTGGTC	58.856	52.381	0.00	0.00	39.17	4.02
1844	1872	6.534475	AAAATTATGACATGATGTGTGGCT	57.466	33.333	1.23	0.00	42.36	4.75
1854	1882	0.036483	ATGTGTGGCTGTACGATGCA	60.036	50.000	0.00	0.00	0.00	3.96
1863	1891	2.848302	GCTGTACGATGCAAAATTCTGC	59.152	45.455	0.00	0.00	42.95	4.26
1912	1941	1.153958	GCGCTCAAATGAACCCTGC	60.154	57.895	0.00	0.00	0.00	4.85
1920	1949	6.572519	GCTCAAATGAACCCTGCAAATAATA	58.427	36.000	0.00	0.00	0.00	0.98
1921	1950	6.698766	GCTCAAATGAACCCTGCAAATAATAG	59.301	38.462	0.00	0.00	0.00	1.73
1922	1951	6.572519	TCAAATGAACCCTGCAAATAATAGC	58.427	36.000	0.00	0.00	0.00	2.97
1923	1952	6.154192	TCAAATGAACCCTGCAAATAATAGCA	59.846	34.615	0.00	0.00	39.25	3.49
1924	1953	6.736110	AATGAACCCTGCAAATAATAGCAT	57.264	33.333	0.00	0.00	40.42	3.79
1925	1954	5.518848	TGAACCCTGCAAATAATAGCATG	57.481	39.130	0.00	0.00	40.42	4.06
1926	1955	5.199723	TGAACCCTGCAAATAATAGCATGA	58.800	37.500	0.00	0.00	40.42	3.07
1927	1956	5.300034	TGAACCCTGCAAATAATAGCATGAG	59.700	40.000	0.00	0.00	40.42	2.90
1928	1957	4.796606	ACCCTGCAAATAATAGCATGAGT	58.203	39.130	0.00	0.00	40.42	3.41
1929	1958	4.823989	ACCCTGCAAATAATAGCATGAGTC	59.176	41.667	0.00	0.00	40.42	3.36
1930	1959	5.068636	CCCTGCAAATAATAGCATGAGTCT	58.931	41.667	0.00	0.00	40.42	3.24
1978	2007	5.160607	TCCGACTTGTGATTTCCACTTAT	57.839	39.130	0.00	0.00	45.86	1.73
2031	2060	7.283329	AGTTCACCCCTTGATTATATCAGTTC	58.717	38.462	0.00	0.00	40.94	3.01
2080	2109	3.396560	CATCCACATGCACTATCACGAT	58.603	45.455	0.00	0.00	0.00	3.73
2111	2140	2.479566	AGTCGCACCATGTCTGATTT	57.520	45.000	0.00	0.00	0.00	2.17
2190	2219	3.220222	TGCGCTACCTAGCTGCAT	58.780	55.556	9.73	0.00	45.95	3.96
2252	2281	0.178891	AGGTGGTGGGTGTGAGAGAT	60.179	55.000	0.00	0.00	0.00	2.75
2289	2338	6.939622	ACCATATATCTGATCGAATGAGCAA	58.060	36.000	0.00	0.00	40.57	3.91
2296	2345	3.864686	CGAATGAGCAACCCCGCG	61.865	66.667	0.00	0.00	36.85	6.46
2300	2349	3.958147	ATGAGCAACCCCGCGTGAG	62.958	63.158	4.92	0.00	36.85	3.51
2321	2370	4.899239	GAGCGCGGGGATGGTCAG	62.899	72.222	8.83	0.00	33.00	3.51
2331	2380	2.607750	ATGGTCAGGACACCGCCT	60.608	61.111	1.41	0.00	39.62	5.52
2341	2390	3.989787	CACCGCCTGCAAAACCCC	61.990	66.667	0.00	0.00	0.00	4.95
2342	2391	4.218686	ACCGCCTGCAAAACCCCT	62.219	61.111	0.00	0.00	0.00	4.79
2343	2392	3.373565	CCGCCTGCAAAACCCCTC	61.374	66.667	0.00	0.00	0.00	4.30
2344	2393	3.737172	CGCCTGCAAAACCCCTCG	61.737	66.667	0.00	0.00	0.00	4.63
2372	2421	4.807039	GGTCGTACGGCCGCATGT	62.807	66.667	28.58	8.43	0.00	3.21

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
6	7	6.938698	TTCTGAGGGTGGTATAACTAACAA	57.061	37.500	0.00	0.00	0.00	2.83
38	39	1.522668	TTGCAGACAATGAACTCCCG	58.477	50.000	0.00	0.00	0.00	5.14
112	113	5.715070	ACAACAGAGTCTAATAGAGTGTGC	58.285	41.667	18.62	0.00	41.22	4.57
257	258	4.730657	CAGATTCTGCTCCATTTCACAAC	58.269	43.478	0.00	0.00	0.00	3.32
317	319	4.211164	TCAGACTAATGTTCTGTTTGTGCG	59.789	41.667	0.00	0.00	33.57	5.34
348	350	0.181587	TTTCGAGCTTCCACCACCAA	59.818	50.000	0.00	0.00	0.00	3.67
368	370	1.140652	CTTGCCACACCCCATTTTGTT	59.859	47.619	0.00	0.00	0.00	2.83
374	376	0.114954	AATGTCTTGCCACACCCCAT	59.885	50.000	0.00	0.00	0.00	4.00
398	400	1.803334	ATTCCGCAAGTAACGAGCAA	58.197	45.000	0.00	0.00	0.00	3.91
422	424	3.560025	CCTTGGACCAACATCAGCTACTT	60.560	47.826	1.69	0.00	0.00	2.24
438	440	3.318313	AGGAGAGTCAGAAAACCTTGGA	58.682	45.455	0.00	0.00	0.00	3.53
476	478	7.645340	CAGCCATATAAATTTCCTTGACTTTCG	59.355	37.037	0.00	0.00	0.00	3.46
514	516	4.999950	AGCAATGTTCCCAGATTCGATATC	59.000	41.667	0.00	0.00	0.00	1.63
564	566	0.729690	GATCCTTGAACGGAAGCAGC	59.270	55.000	0.00	0.00	36.49	5.25
592	595	6.073276	GGGGTATTGCAAATGTCAAAAAGTTC	60.073	38.462	1.71	0.00	0.00	3.01
597	600	4.590647	TCAGGGGTATTGCAAATGTCAAAA	59.409	37.500	1.71	0.00	0.00	2.44
652	655	0.237498	CGTCTGAAAAAGGAACCCGC	59.763	55.000	0.00	0.00	0.00	6.13
654	657	2.552743	CCTTCGTCTGAAAAAGGAACCC	59.447	50.000	11.92	0.00	41.78	4.11
833	836	7.941238	CCTTCCAGATCCATTTATAATGACACT	59.059	37.037	1.11	0.00	0.00	3.55
900	903	1.159713	TCAGCACCGTGTCTTGCAAG	61.160	55.000	20.81	20.81	41.48	4.01
902	905	1.887242	GTCAGCACCGTGTCTTGCA	60.887	57.895	0.00	0.00	41.48	4.08
963	966	9.307121	CTCTCTATTTCGTTACAGAATGAACAT	57.693	33.333	0.00	0.00	39.72	2.71
989	992	4.757149	AGGTAAAGAACATGTGCTGAGAAC	59.243	41.667	7.24	3.52	0.00	3.01
1178	1182	5.242434	TCTCAAAAGTAGCCTTATTGCGAA	58.758	37.500	0.00	0.00	36.02	4.70
1194	1198	9.313118	GGAGACTTAATTTGCTTTTTCTCAAAA	57.687	29.630	0.00	0.00	36.02	2.44
1246	1251	6.194967	ACCCTGTCCAATATAAAGGAAAAGG	58.805	40.000	14.24	14.24	38.70	3.11
1253	1258	5.192927	TCTGCAACCCTGTCCAATATAAAG	58.807	41.667	0.00	0.00	0.00	1.85
1257	1262	3.737559	TTCTGCAACCCTGTCCAATAT	57.262	42.857	0.00	0.00	0.00	1.28
1270	1275	2.490509	CAGCATCATCACCTTTCTGCAA	59.509	45.455	0.00	0.00	32.18	4.08
1451	1462	8.258708	ACGTAAAGGAAAAGCTACTATGAAGAT	58.741	33.333	0.00	0.00	0.00	2.40
1454	1465	8.611654	AAACGTAAAGGAAAAGCTACTATGAA	57.388	30.769	0.00	0.00	0.00	2.57
1474	1486	4.518970	AGCACACCAAAAGATCATAAACGT	59.481	37.500	0.00	0.00	0.00	3.99
1496	1512	2.630158	CCAGAGAGAGAAACATGCCAG	58.370	52.381	0.00	0.00	0.00	4.85
1522	1538	5.188434	CAGATCAAGAATACCAAGCTCCAA	58.812	41.667	0.00	0.00	0.00	3.53
1535	1551	6.440647	ACCTGATAACACCTACAGATCAAGAA	59.559	38.462	0.00	0.00	32.90	2.52
1542	1559	5.475719	CGAAAACCTGATAACACCTACAGA	58.524	41.667	0.00	0.00	32.90	3.41
1598	1616	1.145571	TTACCAGGAAACCCACTGCT	58.854	50.000	0.00	0.00	33.43	4.24
1647	1665	4.927978	ATTCCGAATACAGAGTCAGGAG	57.072	45.455	0.00	0.00	0.00	3.69
1772	1792	1.283793	CTTGTGAAGCACCTTGCCG	59.716	57.895	0.00	0.00	46.52	5.69
1863	1891	6.486993	GCCCTCCCTTTTTATCAGTAGTATTG	59.513	42.308	0.00	0.00	0.00	1.90
1882	1910	2.821810	GAGCGCTTTGAGCCCTCC	60.822	66.667	13.26	0.00	39.57	4.30
1901	1930	6.324512	TCATGCTATTATTTGCAGGGTTCATT	59.675	34.615	6.01	0.00	42.74	2.57
1927	1956	6.016610	GGATGGTAAGTGAGAGTCTCATAGAC	60.017	46.154	25.17	20.24	45.38	2.59
1928	1957	6.065374	GGATGGTAAGTGAGAGTCTCATAGA	58.935	44.000	25.17	10.86	42.73	1.98
1929	1958	5.242838	GGGATGGTAAGTGAGAGTCTCATAG	59.757	48.000	25.17	0.00	42.73	2.23
1930	1959	5.141182	GGGATGGTAAGTGAGAGTCTCATA	58.859	45.833	25.17	12.25	42.73	2.15
2001	2030	2.044793	ATCAAGGGGTGAACTCAGGA	57.955	50.000	0.00	0.00	40.50	3.86
2031	2060	4.588899	TCATCTAAACCCACATTGTCCAG	58.411	43.478	0.00	0.00	0.00	3.86
2080	2109	4.861883	GCGACTAGCTGTTCACGA	57.138	55.556	0.00	0.00	44.04	4.35
2119	2148	6.922957	GTCACTGCCAAGATAAACAAAATGAA	59.077	34.615	0.00	0.00	0.00	2.57
2120	2149	6.265196	AGTCACTGCCAAGATAAACAAAATGA	59.735	34.615	0.00	0.00	0.00	2.57
2122	2151	6.655078	AGTCACTGCCAAGATAAACAAAAT	57.345	33.333	0.00	0.00	0.00	1.82
2216	2245	3.561097	CCACCTTCTCACTCTCTCTCTCA	60.561	52.174	0.00	0.00	0.00	3.27
2252	2281	5.713389	CAGATATATGGTAGTAACGGGTCCA	59.287	44.000	0.00	0.00	0.00	4.02
2321	2370	2.335011	GTTTTGCAGGCGGTGTCC	59.665	61.111	0.00	0.00	0.00	4.02
2331	2380	1.679153	GTTTTCTCGAGGGGTTTTGCA	59.321	47.619	13.56	0.00	0.00	4.08
2334	2383	1.497716	AGGGTTTTCTCGAGGGGTTTT	59.502	47.619	13.56	0.00	0.00	2.43
2341	2390	0.317479	ACGACCAGGGTTTTCTCGAG	59.683	55.000	5.93	5.93	0.00	4.04
2342	2391	1.270550	GTACGACCAGGGTTTTCTCGA	59.729	52.381	2.08	0.00	0.00	4.04
2343	2392	1.706443	GTACGACCAGGGTTTTCTCG	58.294	55.000	0.00	0.00	0.00	4.04
2344	2393	1.670967	CCGTACGACCAGGGTTTTCTC	60.671	57.143	18.76	0.00	0.00	2.87

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.