AutoCloner

Multiple sequence alignment - TraesCS2A01G169200

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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	TraesCS2A01G169200	chr2A	100.000	2461	0	0	1	2461	123740559	123738099	0.000000e+00	4545.0
1	TraesCS2A01G169200	chr2A	90.537	391	25	3	1797	2186	123706293	123705914	7.850000e-140	507.0
2	TraesCS2A01G169200	chr2A	84.932	219	27	6	2246	2461	445805625	445805410	1.480000e-52	217.0
3	TraesCS2A01G169200	chr2A	82.906	117	16	3	1923	2037	124795457	124795571	4.330000e-18	102.0
4	TraesCS2A01G169200	chr2A	80.556	144	14	12	1982	2116	535884740	535884878	5.600000e-17	99.0
5	TraesCS2A01G169200	chr2A	81.513	119	14	6	1923	2037	124770692	124770806	9.370000e-15	91.6
6	TraesCS2A01G169200	chr7A	97.752	1023	21	2	1	1023	641404512	641403492	0.000000e+00	1760.0
7	TraesCS2A01G169200	chr7A	97.051	780	18	3	1020	1797	641403430	641402654	0.000000e+00	1308.0
8	TraesCS2A01G169200	chr7A	95.062	243	10	2	771	1011	194561773	194562015	4.970000e-102	381.0
9	TraesCS2A01G169200	chr7A	89.302	215	18	5	2250	2461	323919741	323919529	5.220000e-67	265.0
10	TraesCS2A01G169200	chr7A	79.817	218	32	11	2249	2461	550524090	550523880	5.480000e-32	148.0
11	TraesCS2A01G169200	chr7A	83.230	161	25	2	1797	1956	353465214	353465373	1.970000e-31	147.0
12	TraesCS2A01G169200	chr3A	97.654	1023	23	1	1	1023	170229597	170228576	0.000000e+00	1755.0
13	TraesCS2A01G169200	chr3A	95.387	737	26	5	1020	1753	170228513	170227782	0.000000e+00	1166.0
14	TraesCS2A01G169200	chr3A	87.317	205	18	8	2262	2461	308551823	308552024	6.850000e-56	228.0
15	TraesCS2A01G169200	chr3A	88.235	187	18	3	2276	2461	328485365	328485182	1.150000e-53	220.0
16	TraesCS2A01G169200	chr3A	86.735	196	20	6	2269	2461	328495264	328495072	1.920000e-51	213.0
17	TraesCS2A01G169200	chr3A	90.196	153	15	0	1804	1956	584724072	584723920	1.490000e-47	200.0
18	TraesCS2A01G169200	chr3A	88.750	160	17	1	1797	1956	584734282	584734124	6.940000e-46	195.0
19	TraesCS2A01G169200	chr3A	76.393	305	50	13	1797	2088	150574281	150574576	7.090000e-31	145.0
20	TraesCS2A01G169200	chr4D	97.559	1024	23	2	1	1023	379508835	379507813	0.000000e+00	1751.0
21	TraesCS2A01G169200	chr4D	95.134	781	30	3	1020	1798	379507750	379506976	0.000000e+00	1225.0
22	TraesCS2A01G169200	chr1A	96.961	1020	30	1	1	1020	520787031	520788049	0.000000e+00	1711.0
23	TraesCS2A01G169200	chr1A	95.897	780	26	4	1020	1797	520788115	520788890	0.000000e+00	1258.0
24	TraesCS2A01G169200	chr1A	82.774	685	78	28	1797	2461	138915068	138914404	2.120000e-160	575.0
25	TraesCS2A01G169200	chr1A	82.587	201	25	8	1797	1991	171328838	171329034	4.210000e-38	169.0
26	TraesCS2A01G169200	chr4B	95.317	1025	45	3	1	1023	575618929	575617906	0.000000e+00	1624.0
27	TraesCS2A01G169200	chr4B	93.077	780	52	2	1020	1797	575617843	575617064	0.000000e+00	1140.0
28	TraesCS2A01G169200	chr3B	93.854	1025	59	4	1	1023	62531658	62530636	0.000000e+00	1541.0
29	TraesCS2A01G169200	chr3B	91.677	781	63	2	1020	1798	62530573	62529793	0.000000e+00	1081.0
30	TraesCS2A01G169200	chr3B	91.035	792	64	6	1022	1809	612314369	612315157	0.000000e+00	1062.0
31	TraesCS2A01G169200	chr3B	84.646	508	68	9	1	503	629796970	629797472	4.730000e-137	497.0
32	TraesCS2A01G169200	chr5B	93.990	1015	56	5	1	1012	395331226	395332238	0.000000e+00	1531.0
33	TraesCS2A01G169200	chr5B	92.159	778	59	2	1022	1797	695846380	695845603	0.000000e+00	1098.0
34	TraesCS2A01G169200	chr5B	93.725	255	14	2	771	1023	39517332	39517078	4.970000e-102	381.0
35	TraesCS2A01G169200	chr1D	92.337	796	59	2	1020	1813	467475746	467474951	0.000000e+00	1131.0
36	TraesCS2A01G169200	chr2D	85.490	510	62	11	1	503	344565438	344565942	2.800000e-144	521.0
37	TraesCS2A01G169200	chr4A	80.617	681	95	26	1797	2461	214887678	214887019	2.200000e-135	492.0
38	TraesCS2A01G169200	chr4A	83.432	169	24	4	1797	1962	436222399	436222566	1.180000e-33	154.0
39	TraesCS2A01G169200	chr4A	84.049	163	21	4	1797	1956	296208775	296208615	4.240000e-33	152.0
40	TraesCS2A01G169200	chr4A	83.432	169	23	5	1797	1962	436240506	436240672	4.240000e-33	152.0
41	TraesCS2A01G169200	chr4A	82.812	128	18	4	1983	2109	186592026	186591902	7.190000e-21	111.0
42	TraesCS2A01G169200	chr4A	81.343	134	19	6	1979	2109	186584288	186584158	1.200000e-18	104.0
43	TraesCS2A01G169200	chr6A	88.406	207	19	5	2258	2461	233618602	233618398	6.800000e-61	244.0
44	TraesCS2A01G169200	chr6A	77.273	440	64	20	1797	2222	366191127	366190710	2.460000e-55	226.0
45	TraesCS2A01G169200	chr5A	89.119	193	21	0	1797	1989	385504908	385504716	8.790000e-60	241.0
46	TraesCS2A01G169200	chr5A	75.394	317	45	21	1799	2095	92787347	92787044	3.320000e-24	122.0
47	TraesCS2A01G169200	chr5A	91.954	87	7	0	1975	2061	92805749	92805663	3.320000e-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	TraesCS2A01G169200	chr2A	123738099	123740559	2460	True	4545.0	4545	100.0000	1	2461	1	chr2A.!!$R2	2460
1	TraesCS2A01G169200	chr7A	641402654	641404512	1858	True	1534.0	1760	97.4015	1	1797	2	chr7A.!!$R3	1796
2	TraesCS2A01G169200	chr3A	170227782	170229597	1815	True	1460.5	1755	96.5205	1	1753	2	chr3A.!!$R5	1752
3	TraesCS2A01G169200	chr4D	379506976	379508835	1859	True	1488.0	1751	96.3465	1	1798	2	chr4D.!!$R1	1797
4	TraesCS2A01G169200	chr1A	520787031	520788890	1859	False	1484.5	1711	96.4290	1	1797	2	chr1A.!!$F2	1796
5	TraesCS2A01G169200	chr1A	138914404	138915068	664	True	575.0	575	82.7740	1797	2461	1	chr1A.!!$R1	664
6	TraesCS2A01G169200	chr4B	575617064	575618929	1865	True	1382.0	1624	94.1970	1	1797	2	chr4B.!!$R1	1796
7	TraesCS2A01G169200	chr3B	62529793	62531658	1865	True	1311.0	1541	92.7655	1	1798	2	chr3B.!!$R1	1797
8	TraesCS2A01G169200	chr3B	612314369	612315157	788	False	1062.0	1062	91.0350	1022	1809	1	chr3B.!!$F1	787
9	TraesCS2A01G169200	chr3B	629796970	629797472	502	False	497.0	497	84.6460	1	503	1	chr3B.!!$F2	502
10	TraesCS2A01G169200	chr5B	395331226	395332238	1012	False	1531.0	1531	93.9900	1	1012	1	chr5B.!!$F1	1011
11	TraesCS2A01G169200	chr5B	695845603	695846380	777	True	1098.0	1098	92.1590	1022	1797	1	chr5B.!!$R2	775
12	TraesCS2A01G169200	chr1D	467474951	467475746	795	True	1131.0	1131	92.3370	1020	1813	1	chr1D.!!$R1	793
13	TraesCS2A01G169200	chr2D	344565438	344565942	504	False	521.0	521	85.4900	1	503	1	chr2D.!!$F1	502
14	TraesCS2A01G169200	chr4A	214887019	214887678	659	True	492.0	492	80.6170	1797	2461	1	chr4A.!!$R3	664

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
523	529	0.933796	GCATCGTCTTCTGCTAAGGC	59.066	55.0	0.44	0.0	35.49	4.35	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1945	2036	0.033228	CGTCCAGATCCAGATCCAGC	59.967	60.0	4.01	0.0	38.58	4.85	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
225	227	6.127366	CCTTCATAACTGCATTTAATGGTGGT	60.127	38.462	7.08	0.00	0.00	4.16
265	267	4.787551	TCAAAGAAAGGTTGTCTAGCCAA	58.212	39.130	0.00	0.00	0.00	4.52
313	315	3.947834	CTGACACCAAATCAGTAATCCCC	59.052	47.826	0.00	0.00	39.04	4.81
483	489	4.868171	TCATGCTAATGTAGTTTGACGGAC	59.132	41.667	0.00	0.00	35.15	4.79
523	529	0.933796	GCATCGTCTTCTGCTAAGGC	59.066	55.000	0.44	0.00	35.49	4.35
1015	1022	3.134985	TGATTTTATGGCTGGGTACGCTA	59.865	43.478	11.59	0.00	0.00	4.26
1058	1131	1.078918	CTCCAGCATGACCGCTTCA	60.079	57.895	0.00	0.00	41.38	3.02
1431	1507	2.688446	CTGCACTACAACGGGAGATCTA	59.312	50.000	0.00	0.00	0.00	1.98
1434	1510	3.288964	CACTACAACGGGAGATCTAGGT	58.711	50.000	0.00	0.00	0.00	3.08
1606	1684	7.703058	ATAGTACAACTTAAAGCCTTGCATT	57.297	32.000	0.00	0.00	0.00	3.56
1847	1929	5.591643	AACAATTCGATATATCACACGCC	57.408	39.130	13.11	0.00	0.00	5.68
1862	1944	0.679960	ACGCCCAAAATGGAGCTACC	60.680	55.000	0.00	0.00	40.96	3.18
1903	1985	6.262944	TGCGATGAACATGGCTAGAAAATATT	59.737	34.615	18.94	0.00	42.10	1.28
1904	1986	7.443879	TGCGATGAACATGGCTAGAAAATATTA	59.556	33.333	18.94	0.00	42.10	0.98
1909	1991	7.719633	TGAACATGGCTAGAAAATATTAGGGAC	59.280	37.037	0.00	0.00	0.00	4.46
1910	1992	7.394144	ACATGGCTAGAAAATATTAGGGACT	57.606	36.000	0.00	0.00	46.37	3.85
1911	1993	7.816411	ACATGGCTAGAAAATATTAGGGACTT	58.184	34.615	0.00	0.00	41.75	3.01
1912	1994	8.282256	ACATGGCTAGAAAATATTAGGGACTTT	58.718	33.333	0.00	0.00	41.75	2.66
1914	1996	7.060421	TGGCTAGAAAATATTAGGGACTTTGG	58.940	38.462	0.00	0.00	41.75	3.28
1915	1997	7.092174	TGGCTAGAAAATATTAGGGACTTTGGA	60.092	37.037	0.00	0.00	41.75	3.53
1939	2030	4.961438	AAACGAGTCAACCTAGGGTTTA	57.039	40.909	14.81	0.00	44.33	2.01
1940	2031	3.949842	ACGAGTCAACCTAGGGTTTAC	57.050	47.619	14.81	7.37	44.33	2.01
1943	2034	3.257624	CGAGTCAACCTAGGGTTTACTGT	59.742	47.826	15.00	0.00	46.23	3.55
1945	2036	5.392811	CGAGTCAACCTAGGGTTTACTGTAG	60.393	48.000	15.00	4.49	46.23	2.74
1955	2046	3.432326	GGGTTTACTGTAGCTGGATCTGG	60.432	52.174	0.00	0.00	0.00	3.86
1956	2047	3.451178	GGTTTACTGTAGCTGGATCTGGA	59.549	47.826	0.00	0.00	0.00	3.86
1957	2048	4.101741	GGTTTACTGTAGCTGGATCTGGAT	59.898	45.833	0.00	0.00	0.00	3.41
1958	2049	5.293560	GTTTACTGTAGCTGGATCTGGATC	58.706	45.833	0.00	2.24	37.11	3.36
1959	2050	3.326946	ACTGTAGCTGGATCTGGATCT	57.673	47.619	9.96	0.00	37.92	2.75
1961	2052	2.299582	CTGTAGCTGGATCTGGATCTGG	59.700	54.545	9.96	5.22	37.92	3.86
1962	2053	2.091111	TGTAGCTGGATCTGGATCTGGA	60.091	50.000	9.96	0.00	37.92	3.86
1963	2054	1.422531	AGCTGGATCTGGATCTGGAC	58.577	55.000	9.96	0.00	37.92	4.02
1964	2055	0.033228	GCTGGATCTGGATCTGGACG	59.967	60.000	9.96	0.00	37.92	4.79
1968	2059	0.683973	GATCTGGATCTGGACGGCAT	59.316	55.000	0.00	0.00	35.04	4.40
1971	2062	2.969238	GGATCTGGACGGCATGCG	60.969	66.667	12.44	9.76	0.00	4.73
1980	2071	2.279451	CGGCATGCGAATCGAGGA	60.279	61.111	12.44	0.00	0.00	3.71
1981	2072	1.665916	CGGCATGCGAATCGAGGAT	60.666	57.895	12.44	0.00	0.00	3.24
1982	2073	1.621301	CGGCATGCGAATCGAGGATC	61.621	60.000	12.44	0.00	0.00	3.36
1996	2099	0.397675	AGGATCGCTGGAGATGGACA	60.398	55.000	0.00	0.00	0.00	4.02
2328	2433	2.885644	CGTGTGATTCGGCGGAGG	60.886	66.667	7.21	0.00	0.00	4.30
2330	2435	3.781307	TGTGATTCGGCGGAGGGG	61.781	66.667	7.21	0.00	0.00	4.79

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
10	11	6.679327	AAAAACTCACAGAAACTCCACTAC	57.321	37.500	0.00	0.00	0.00	2.73
60	61	4.082300	CACCCACATTATAGCAGCAACAAA	60.082	41.667	0.00	0.00	0.00	2.83
225	227	5.299028	TCTTTGAGCAAAGTGAGCATAACAA	59.701	36.000	19.15	0.00	45.88	2.83
265	267	8.678199	GCCTATTTCTTAAATCACAAAGTAGCT	58.322	33.333	0.00	0.00	32.38	3.32
313	315	0.040067	GGCCAACAAAGCAGAAGTCG	60.040	55.000	0.00	0.00	0.00	4.18
424	430	4.717233	TCACGCATTCAAAAATATGGCT	57.283	36.364	0.00	0.00	0.00	4.75
483	489	4.156922	TGCCTATCCATTGGTTTTACAACG	59.843	41.667	1.86	0.00	33.13	4.10
523	529	5.004448	GGTTCTAAAGAAGGGTGAAAGGAG	58.996	45.833	0.00	0.00	34.27	3.69
819	826	8.882736	CACTGATTAATGTTATAGCACACAAGA	58.117	33.333	0.00	0.00	0.00	3.02
890	897	8.506083	AGAGGGGTTAGATTATGTTCAAATGAT	58.494	33.333	0.00	0.00	0.00	2.45
1015	1022	5.621197	TTACGCTATGCACAGATGTTTTT	57.379	34.783	0.00	0.00	0.00	1.94
1058	1131	2.182791	CGACTCGAGGCAGCACAT	59.817	61.111	20.47	0.00	0.00	3.21
1431	1507	1.683385	GAAGCCACAAAGAAGCAACCT	59.317	47.619	0.00	0.00	0.00	3.50
1434	1510	1.774110	TGGAAGCCACAAAGAAGCAA	58.226	45.000	0.00	0.00	0.00	3.91
1832	1914	4.378356	CCATTTTGGGCGTGTGATATATCG	60.378	45.833	8.19	0.00	32.67	2.92
1838	1920	1.176527	CTCCATTTTGGGCGTGTGAT	58.823	50.000	0.00	0.00	38.32	3.06
1862	1944	4.986659	TCATCGCATCATAACTCTGTCATG	59.013	41.667	0.00	0.00	0.00	3.07
1931	2022	4.649674	CAGATCCAGCTACAGTAAACCCTA	59.350	45.833	0.00	0.00	0.00	3.53
1932	2023	3.452627	CAGATCCAGCTACAGTAAACCCT	59.547	47.826	0.00	0.00	0.00	4.34
1933	2024	3.432326	CCAGATCCAGCTACAGTAAACCC	60.432	52.174	0.00	0.00	0.00	4.11
1935	2026	4.737855	TCCAGATCCAGCTACAGTAAAC	57.262	45.455	0.00	0.00	0.00	2.01
1937	2028	4.586421	CAGATCCAGATCCAGCTACAGTAA	59.414	45.833	4.01	0.00	38.58	2.24
1939	2030	2.964464	CAGATCCAGATCCAGCTACAGT	59.036	50.000	4.01	0.00	38.58	3.55
1940	2031	2.299582	CCAGATCCAGATCCAGCTACAG	59.700	54.545	4.01	0.00	38.58	2.74
1943	2034	2.603021	GTCCAGATCCAGATCCAGCTA	58.397	52.381	4.01	0.00	38.58	3.32
1945	2036	0.033228	CGTCCAGATCCAGATCCAGC	59.967	60.000	4.01	0.00	38.58	4.85
1955	2046	0.882042	ATTCGCATGCCGTCCAGATC	60.882	55.000	13.15	0.00	38.35	2.75
1956	2047	0.882042	GATTCGCATGCCGTCCAGAT	60.882	55.000	13.15	0.00	38.35	2.90
1957	2048	1.521457	GATTCGCATGCCGTCCAGA	60.521	57.895	13.15	0.00	38.35	3.86
1958	2049	2.874694	CGATTCGCATGCCGTCCAG	61.875	63.158	13.15	0.00	38.35	3.86
1959	2050	2.889988	CGATTCGCATGCCGTCCA	60.890	61.111	13.15	0.00	38.35	4.02
1961	2052	2.589492	CCTCGATTCGCATGCCGTC	61.589	63.158	13.15	6.82	38.35	4.79
1962	2053	2.369257	ATCCTCGATTCGCATGCCGT	62.369	55.000	13.15	0.00	38.35	5.68
1963	2054	1.621301	GATCCTCGATTCGCATGCCG	61.621	60.000	13.15	10.03	38.61	5.69
1964	2055	1.621301	CGATCCTCGATTCGCATGCC	61.621	60.000	13.15	0.00	43.74	4.40
1971	2062	0.955178	TCTCCAGCGATCCTCGATTC	59.045	55.000	0.00	0.00	43.74	2.52
1980	2071	0.467384	CCTTGTCCATCTCCAGCGAT	59.533	55.000	0.00	0.00	0.00	4.58
1981	2072	0.614697	TCCTTGTCCATCTCCAGCGA	60.615	55.000	0.00	0.00	0.00	4.93
1982	2073	0.460987	GTCCTTGTCCATCTCCAGCG	60.461	60.000	0.00	0.00	0.00	5.18
1985	2088	1.899437	GCCGTCCTTGTCCATCTCCA	61.899	60.000	0.00	0.00	0.00	3.86
2047	2150	3.083349	CACCTCCGGCCAGATCCA	61.083	66.667	2.24	0.00	0.00	3.41
2059	2162	2.726351	CGCCTTCCTCCTCCACCTC	61.726	68.421	0.00	0.00	0.00	3.85
2155	2258	4.451150	ATCGCGCCACCATCACGT	62.451	61.111	0.00	0.00	0.00	4.49
2156	2259	3.928769	CATCGCGCCACCATCACG	61.929	66.667	0.00	0.00	0.00	4.35
2312	2417	2.511600	CCCTCCGCCGAATCACAC	60.512	66.667	0.00	0.00	0.00	3.82
2324	2429	2.225791	GAAAATTGCACCGCCCCTCC	62.226	60.000	0.00	0.00	0.00	4.30
2326	2431	2.635443	CGAAAATTGCACCGCCCCT	61.635	57.895	0.00	0.00	0.00	4.79
2328	2433	1.443702	GACGAAAATTGCACCGCCC	60.444	57.895	0.00	0.00	0.00	6.13
2330	2435	1.795962	CGGACGAAAATTGCACCGC	60.796	57.895	0.00	0.00	34.36	5.68
2331	2436	1.154301	CCGGACGAAAATTGCACCG	60.154	57.895	0.00	0.00	40.03	4.94
2333	2438	1.001745	GCACCGGACGAAAATTGCAC	61.002	55.000	9.46	0.00	0.00	4.57
2334	2439	1.284408	GCACCGGACGAAAATTGCA	59.716	52.632	9.46	0.00	0.00	4.08
2373	2478	1.536418	CCTAGATCCATCCCCGCCA	60.536	63.158	0.00	0.00	0.00	5.69

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.