AutoCloner

Multiple sequence alignment - TraesCS3A01G432000

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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	TraesCS3A01G432000	chr3A	100.000	2432	0	0	1	2432	672915146	672917577	0.000000e+00	4492.0
1	TraesCS3A01G432000	chr3A	96.883	1861	43	11	1	1851	692572996	692571141	0.000000e+00	3101.0
2	TraesCS3A01G432000	chr3A	97.556	450	10	1	1916	2365	672925048	672925496	0.000000e+00	769.0
3	TraesCS3A01G432000	chr5D	97.961	1864	24	8	1	1851	560879663	560877801	0.000000e+00	3219.0
4	TraesCS3A01G432000	chr5D	97.586	1864	25	10	1	1851	503213097	503211241	0.000000e+00	3175.0
5	TraesCS3A01G432000	chrUn	97.904	1861	26	7	1	1848	93417153	93419013	0.000000e+00	3208.0
6	TraesCS3A01G432000	chrUn	97.598	1457	22	7	1	1444	327660685	327662141	0.000000e+00	2484.0
7	TraesCS3A01G432000	chr3B	97.265	1865	34	10	1	1851	201521869	201520008	0.000000e+00	3145.0
8	TraesCS3A01G432000	chr3B	82.885	520	70	12	1919	2430	480459992	480460500	1.330000e-122	449.0
9	TraesCS3A01G432000	chr3B	98.400	125	2	0	1628	1752	624469931	624469807	1.130000e-53	220.0
10	TraesCS3A01G432000	chr6A	96.613	1860	52	7	1	1851	271184641	271182784	0.000000e+00	3075.0
11	TraesCS3A01G432000	chr6A	88.025	476	56	1	1916	2391	137588880	137589354	1.630000e-156	562.0
12	TraesCS3A01G432000	chr1A	96.121	1856	57	12	1	1848	168443429	168445277	0.000000e+00	3014.0
13	TraesCS3A01G432000	chr7A	92.988	1854	111	14	1	1848	352186886	352188726	0.000000e+00	2686.0
14	TraesCS3A01G432000	chr7A	94.545	55	3	0	1864	1918	579575183	579575129	4.310000e-13	86.1
15	TraesCS3A01G432000	chr2A	98.126	587	11	0	1186	1772	588085546	588084960	0.000000e+00	1024.0
16	TraesCS3A01G432000	chr2A	96.318	516	18	1	1918	2432	303389001	303388486	0.000000e+00	846.0
17	TraesCS3A01G432000	chr2A	96.117	515	19	1	1919	2432	303380970	303380456	0.000000e+00	839.0
18	TraesCS3A01G432000	chr2A	96.364	55	2	0	1864	1918	699934435	699934381	9.260000e-15	91.6
19	TraesCS3A01G432000	chr5A	96.712	517	17	0	1916	2432	577984730	577985246	0.000000e+00	861.0
20	TraesCS3A01G432000	chr5A	96.325	517	19	0	1916	2432	577992975	577993491	0.000000e+00	850.0
21	TraesCS3A01G432000	chr5A	96.304	514	19	0	1919	2432	495263426	495263939	0.000000e+00	845.0
22	TraesCS3A01G432000	chr5A	96.132	517	19	1	1916	2432	495271448	495271963	0.000000e+00	843.0
23	TraesCS3A01G432000	chr5A	89.177	462	48	2	1919	2380	604844109	604843650	2.100000e-160	575.0
24	TraesCS3A01G432000	chr2B	74.128	545	95	39	1918	2432	532069268	532068740	1.490000e-42	183.0
25	TraesCS3A01G432000	chr4A	96.364	55	2	0	1864	1918	22286515	22286569	9.260000e-15	91.6
26	TraesCS3A01G432000	chr7D	100.000	38	0	0	1881	1918	107730759	107730722	1.210000e-08	71.3
27	TraesCS3A01G432000	chr6B	97.500	40	1	0	1879	1918	31339706	31339745	4.340000e-08	69.4

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	TraesCS3A01G432000	chr3A	672915146	672917577	2431	False	4492	4492	100.000	1	2432	1	chr3A.!!$F1	2431
1	TraesCS3A01G432000	chr3A	692571141	692572996	1855	True	3101	3101	96.883	1	1851	1	chr3A.!!$R1	1850
2	TraesCS3A01G432000	chr5D	560877801	560879663	1862	True	3219	3219	97.961	1	1851	1	chr5D.!!$R2	1850
3	TraesCS3A01G432000	chr5D	503211241	503213097	1856	True	3175	3175	97.586	1	1851	1	chr5D.!!$R1	1850
4	TraesCS3A01G432000	chrUn	93417153	93419013	1860	False	3208	3208	97.904	1	1848	1	chrUn.!!$F1	1847
5	TraesCS3A01G432000	chrUn	327660685	327662141	1456	False	2484	2484	97.598	1	1444	1	chrUn.!!$F2	1443
6	TraesCS3A01G432000	chr3B	201520008	201521869	1861	True	3145	3145	97.265	1	1851	1	chr3B.!!$R1	1850
7	TraesCS3A01G432000	chr3B	480459992	480460500	508	False	449	449	82.885	1919	2430	1	chr3B.!!$F1	511
8	TraesCS3A01G432000	chr6A	271182784	271184641	1857	True	3075	3075	96.613	1	1851	1	chr6A.!!$R1	1850
9	TraesCS3A01G432000	chr1A	168443429	168445277	1848	False	3014	3014	96.121	1	1848	1	chr1A.!!$F1	1847
10	TraesCS3A01G432000	chr7A	352186886	352188726	1840	False	2686	2686	92.988	1	1848	1	chr7A.!!$F1	1847
11	TraesCS3A01G432000	chr2A	588084960	588085546	586	True	1024	1024	98.126	1186	1772	1	chr2A.!!$R3	586
12	TraesCS3A01G432000	chr2A	303388486	303389001	515	True	846	846	96.318	1918	2432	1	chr2A.!!$R2	514
13	TraesCS3A01G432000	chr2A	303380456	303380970	514	True	839	839	96.117	1919	2432	1	chr2A.!!$R1	513
14	TraesCS3A01G432000	chr5A	577984730	577985246	516	False	861	861	96.712	1916	2432	1	chr5A.!!$F3	516
15	TraesCS3A01G432000	chr5A	577992975	577993491	516	False	850	850	96.325	1916	2432	1	chr5A.!!$F4	516
16	TraesCS3A01G432000	chr5A	495263426	495263939	513	False	845	845	96.304	1919	2432	1	chr5A.!!$F1	513
17	TraesCS3A01G432000	chr5A	495271448	495271963	515	False	843	843	96.132	1916	2432	1	chr5A.!!$F2	516

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
449	455	4.040461	CGAATACTGATGTGGGATAGGGTT	59.96	45.833	0.0	0.0	0.0	4.11	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1912	1936	0.108329	ATCCGGGCGTCACACTTTAG	60.108	55.0	0.0	0.0	0.0	1.85	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
438	444	9.001542	GGTCTAGTTCTATACGAATACTGATGT	57.998	37.037	0.00	0.00	33.45	3.06
449	455	4.040461	CGAATACTGATGTGGGATAGGGTT	59.960	45.833	0.00	0.00	0.00	4.11
807	823	7.254932	GCTCTAATCCGAAGCATAAACAAAGAT	60.255	37.037	0.00	0.00	0.00	2.40
1042	1065	5.432885	AATTGGTTCACGTAAGAAAGTGG	57.567	39.130	0.00	0.00	43.62	4.00
1766	1790	7.495934	CAGGTATTGAAGAATCCGTACAAGAAT	59.504	37.037	0.00	0.00	0.00	2.40
1848	1872	2.817258	CCATTTGCGTCAAAGGTCCTAA	59.183	45.455	13.17	0.00	36.76	2.69
1851	1875	5.469479	CATTTGCGTCAAAGGTCCTAAATT	58.531	37.500	10.06	0.00	36.76	1.82
1852	1876	5.523438	TTTGCGTCAAAGGTCCTAAATTT	57.477	34.783	0.00	0.00	0.00	1.82
1853	1877	5.523438	TTGCGTCAAAGGTCCTAAATTTT	57.477	34.783	0.00	0.00	0.00	1.82
1854	1878	4.865776	TGCGTCAAAGGTCCTAAATTTTG	58.134	39.130	0.00	0.00	33.09	2.44
1855	1879	4.339814	TGCGTCAAAGGTCCTAAATTTTGT	59.660	37.500	0.00	0.00	33.46	2.83
1856	1880	4.679654	GCGTCAAAGGTCCTAAATTTTGTG	59.320	41.667	0.00	0.00	33.46	3.33
1857	1881	4.679654	CGTCAAAGGTCCTAAATTTTGTGC	59.320	41.667	0.00	0.00	33.46	4.57
1858	1882	5.596845	GTCAAAGGTCCTAAATTTTGTGCA	58.403	37.500	0.00	0.00	33.46	4.57
1859	1883	5.462068	GTCAAAGGTCCTAAATTTTGTGCAC	59.538	40.000	10.75	10.75	33.46	4.57
1860	1884	4.600692	AAGGTCCTAAATTTTGTGCACC	57.399	40.909	15.69	0.67	0.00	5.01
1861	1885	3.571590	AGGTCCTAAATTTTGTGCACCA	58.428	40.909	15.69	0.00	0.00	4.17
1862	1886	3.320826	AGGTCCTAAATTTTGTGCACCAC	59.679	43.478	15.69	0.00	34.56	4.16
1863	1887	3.305110	GTCCTAAATTTTGTGCACCACG	58.695	45.455	15.69	0.00	37.14	4.94
1864	1888	2.294791	TCCTAAATTTTGTGCACCACGG	59.705	45.455	15.69	3.73	37.14	4.94
1865	1889	2.609244	CCTAAATTTTGTGCACCACGGG	60.609	50.000	15.69	2.14	37.14	5.28
1866	1890	0.105778	AAATTTTGTGCACCACGGGG	59.894	50.000	15.69	0.00	37.14	5.73
1878	1902	4.954970	ACGGGGTGGCAGCACAAG	62.955	66.667	20.14	6.00	0.00	3.16
1885	1909	4.095590	GGCAGCACAAGGCCTTTA	57.904	55.556	17.61	0.00	46.74	1.85
1886	1910	1.885871	GGCAGCACAAGGCCTTTAG	59.114	57.895	17.61	12.58	46.74	1.85
1887	1911	0.895559	GGCAGCACAAGGCCTTTAGT	60.896	55.000	17.61	9.24	46.74	2.24
1888	1912	1.613255	GGCAGCACAAGGCCTTTAGTA	60.613	52.381	17.61	0.00	46.74	1.82
1889	1913	1.468914	GCAGCACAAGGCCTTTAGTAC	59.531	52.381	17.61	6.67	46.50	2.73
1890	1914	2.084546	CAGCACAAGGCCTTTAGTACC	58.915	52.381	17.61	6.49	46.50	3.34
1891	1915	1.702957	AGCACAAGGCCTTTAGTACCA	59.297	47.619	17.61	0.00	46.50	3.25
1892	1916	2.084546	GCACAAGGCCTTTAGTACCAG	58.915	52.381	17.61	4.24	36.11	4.00
1893	1917	2.552373	GCACAAGGCCTTTAGTACCAGT	60.552	50.000	17.61	4.99	36.11	4.00
1894	1918	3.751518	CACAAGGCCTTTAGTACCAGTT	58.248	45.455	17.61	0.00	0.00	3.16
1895	1919	3.502211	CACAAGGCCTTTAGTACCAGTTG	59.498	47.826	17.61	2.77	0.00	3.16
1896	1920	3.081804	CAAGGCCTTTAGTACCAGTTGG	58.918	50.000	17.61	0.00	42.17	3.77
1915	1939	2.460757	GTTGCTCCAACCGGTACTAA	57.539	50.000	8.00	0.00	38.30	2.24
1916	1940	2.769893	GTTGCTCCAACCGGTACTAAA	58.230	47.619	8.00	0.00	38.30	1.85
2276	2301	6.831868	GGGCTAATTTACAACCTCCATTTAGA	59.168	38.462	0.00	0.00	0.00	2.10

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
438	444	8.395605	ACTTACTTCAATTTTAACCCTATCCCA	58.604	33.333	0.00	0.00	0.00	4.37
625	638	9.436957	TCTCTTCGCTTGAATTTAAGAACTTAT	57.563	29.630	13.77	0.00	0.00	1.73
697	713	9.477484	GAACGGAAGCTCTTATTTTCATATCTA	57.523	33.333	0.00	0.00	0.00	1.98
699	715	8.142994	TGAACGGAAGCTCTTATTTTCATATC	57.857	34.615	0.00	0.00	0.00	1.63
807	823	7.455891	AGTTCTTTTTCGAAAGATTACCCCTA	58.544	34.615	10.98	0.00	41.60	3.53
1042	1065	4.877251	TGCATTCCTACGTAAACCAATACC	59.123	41.667	0.00	0.00	0.00	2.73
1264	1287	3.386486	CTCGTTGCAAACCTACTGTACA	58.614	45.455	0.00	0.00	46.28	2.90
1420	1444	8.211629	AGCGGGTTAATTCTTTTATAGACATCT	58.788	33.333	0.00	0.00	30.90	2.90
1423	1447	8.570068	AAAGCGGGTTAATTCTTTTATAGACA	57.430	30.769	0.00	0.00	30.90	3.41
1428	1452	7.892609	AGTTGAAAGCGGGTTAATTCTTTTAT	58.107	30.769	0.00	0.00	0.00	1.40
1848	1872	1.045911	ACCCCGTGGTGCACAAAATT	61.046	50.000	20.43	0.00	45.58	1.82
1861	1885	4.954970	CTTGTGCTGCCACCCCGT	62.955	66.667	0.00	0.00	41.35	5.28
1869	1893	1.468914	GTACTAAAGGCCTTGTGCTGC	59.531	52.381	21.33	4.61	40.92	5.25
1870	1894	2.084546	GGTACTAAAGGCCTTGTGCTG	58.915	52.381	21.33	10.07	40.92	4.41
1871	1895	1.702957	TGGTACTAAAGGCCTTGTGCT	59.297	47.619	21.33	5.57	40.92	4.40
1872	1896	2.084546	CTGGTACTAAAGGCCTTGTGC	58.915	52.381	21.33	16.64	40.16	4.57
1873	1897	3.418684	ACTGGTACTAAAGGCCTTGTG	57.581	47.619	21.33	17.07	0.00	3.33
1874	1898	3.497942	CCAACTGGTACTAAAGGCCTTGT	60.498	47.826	21.33	16.26	0.00	3.16
1875	1899	3.081804	CCAACTGGTACTAAAGGCCTTG	58.918	50.000	21.33	10.33	0.00	3.61
1876	1900	3.434940	CCAACTGGTACTAAAGGCCTT	57.565	47.619	13.78	13.78	0.00	4.35
1896	1920	2.460757	TTAGTACCGGTTGGAGCAAC	57.539	50.000	15.04	1.99	42.89	4.17
1897	1921	2.369532	ACTTTAGTACCGGTTGGAGCAA	59.630	45.455	15.04	0.00	39.21	3.91
1898	1922	1.972795	ACTTTAGTACCGGTTGGAGCA	59.027	47.619	15.04	0.00	39.21	4.26
1899	1923	2.289257	ACACTTTAGTACCGGTTGGAGC	60.289	50.000	15.04	0.00	39.21	4.70
1900	1924	3.006110	TCACACTTTAGTACCGGTTGGAG	59.994	47.826	15.04	7.01	39.21	3.86
1901	1925	2.964464	TCACACTTTAGTACCGGTTGGA	59.036	45.455	15.04	0.00	39.21	3.53
1902	1926	3.062042	GTCACACTTTAGTACCGGTTGG	58.938	50.000	15.04	0.00	42.84	3.77
1903	1927	2.727798	CGTCACACTTTAGTACCGGTTG	59.272	50.000	15.04	5.32	0.00	3.77
1904	1928	2.863704	GCGTCACACTTTAGTACCGGTT	60.864	50.000	15.04	0.00	0.00	4.44
1905	1929	1.336240	GCGTCACACTTTAGTACCGGT	60.336	52.381	13.98	13.98	0.00	5.28
1906	1930	1.343506	GCGTCACACTTTAGTACCGG	58.656	55.000	0.00	0.00	0.00	5.28
1907	1931	1.343506	GGCGTCACACTTTAGTACCG	58.656	55.000	0.00	0.00	0.00	4.02
1908	1932	1.718396	GGGCGTCACACTTTAGTACC	58.282	55.000	0.00	0.00	0.00	3.34
1909	1933	1.343506	CGGGCGTCACACTTTAGTAC	58.656	55.000	0.00	0.00	0.00	2.73
1910	1934	0.244450	CCGGGCGTCACACTTTAGTA	59.756	55.000	0.00	0.00	0.00	1.82
1911	1935	1.005394	CCGGGCGTCACACTTTAGT	60.005	57.895	0.00	0.00	0.00	2.24
1912	1936	0.108329	ATCCGGGCGTCACACTTTAG	60.108	55.000	0.00	0.00	0.00	1.85
1913	1937	1.184431	TATCCGGGCGTCACACTTTA	58.816	50.000	0.00	0.00	0.00	1.85
1914	1938	0.322322	TTATCCGGGCGTCACACTTT	59.678	50.000	0.00	0.00	0.00	2.66
1915	1939	0.539986	ATTATCCGGGCGTCACACTT	59.460	50.000	0.00	0.00	0.00	3.16
1916	1940	0.539986	AATTATCCGGGCGTCACACT	59.460	50.000	0.00	0.00	0.00	3.55

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.