AutoCloner

Multiple sequence alignment - TraesCS3A01G162100

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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	TraesCS3A01G162100	chr3A	100.000	2297	0	0	1	2297	164418576	164420872	0.000000e+00	4242
1	TraesCS3A01G162100	chr3A	96.482	2075	38	6	1	2068	143679310	143681356	0.000000e+00	3395
2	TraesCS3A01G162100	chr3A	89.860	641	61	4	1	641	106243697	106243061	0.000000e+00	821
3	TraesCS3A01G162100	chr3A	97.143	210	5	1	2089	2297	143682287	143682496	1.010000e-93	353
4	TraesCS3A01G162100	chr6B	90.952	641	58	0	1	641	521527036	521527676	0.000000e+00	863
5	TraesCS3A01G162100	chr6B	90.031	642	63	1	1	641	259458561	259459202	0.000000e+00	830
6	TraesCS3A01G162100	chr3D	90.796	641	57	2	1	641	89379519	89378881	0.000000e+00	856
7	TraesCS3A01G162100	chr3D	90.566	636	59	1	1	636	347670429	347671063	0.000000e+00	841
8	TraesCS3A01G162100	chr3D	90.328	641	62	0	1	641	432483133	432482493	0.000000e+00	841
9	TraesCS3A01G162100	chr2D	90.528	644	57	2	1	641	452409524	452410166	0.000000e+00	848
10	TraesCS3A01G162100	chr2B	89.548	641	67	0	1	641	335633575	335632935	0.000000e+00	813

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	TraesCS3A01G162100	chr3A	164418576	164420872	2296	False	4242	4242	100.0000	1	2297	1	chr3A.!!$F1	2296
1	TraesCS3A01G162100	chr3A	143679310	143682496	3186	False	1874	3395	96.8125	1	2297	2	chr3A.!!$F2	2296
2	TraesCS3A01G162100	chr3A	106243061	106243697	636	True	821	821	89.8600	1	641	1	chr3A.!!$R1	640
3	TraesCS3A01G162100	chr6B	521527036	521527676	640	False	863	863	90.9520	1	641	1	chr6B.!!$F2	640
4	TraesCS3A01G162100	chr6B	259458561	259459202	641	False	830	830	90.0310	1	641	1	chr6B.!!$F1	640
5	TraesCS3A01G162100	chr3D	89378881	89379519	638	True	856	856	90.7960	1	641	1	chr3D.!!$R1	640
6	TraesCS3A01G162100	chr3D	347670429	347671063	634	False	841	841	90.5660	1	636	1	chr3D.!!$F1	635
7	TraesCS3A01G162100	chr3D	432482493	432483133	640	True	841	841	90.3280	1	641	1	chr3D.!!$R2	640
8	TraesCS3A01G162100	chr2D	452409524	452410166	642	False	848	848	90.5280	1	641	1	chr2D.!!$F1	640
9	TraesCS3A01G162100	chr2B	335632935	335633575	640	True	813	813	89.5480	1	641	1	chr2B.!!$R1	640

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
755	765	0.953727	TTTGTGAGCACATGACCTGC	59.046	50.0	0.0	0.0	41.52	4.85	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1894	1907	0.322277	CTCCATGCACAAGAGGCACT	60.322	55.0	0.0	0.0	45.23	4.4	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
487	497	8.929827	TGCATGTGATGTTTATCTTTTTATGG	57.070	30.769	0.00	0.00	34.31	2.74
544	554	7.020827	TGAGATGATCCCTTCACTTAGTTTT	57.979	36.000	0.00	0.00	37.11	2.43
573	583	5.856126	TTGTGTTCTTTCTAAGTATGCGG	57.144	39.130	0.00	0.00	0.00	5.69
649	659	6.151985	AGACTCTACGTTCTCATTGTTCTCAT	59.848	38.462	0.00	0.00	0.00	2.90
714	724	2.500098	ACGCCTAGGCATACTCTGAAAA	59.500	45.455	32.47	0.00	42.06	2.29
755	765	0.953727	TTTGTGAGCACATGACCTGC	59.046	50.000	0.00	0.00	41.52	4.85
791	801	3.226347	GCGTTAGTTCATTTGTGAGCAC	58.774	45.455	0.00	0.00	0.00	4.40
938	948	5.242838	GTGTTGGAAAAGAGAGAGAGAGAGA	59.757	44.000	0.00	0.00	0.00	3.10
939	949	5.476599	TGTTGGAAAAGAGAGAGAGAGAGAG	59.523	44.000	0.00	0.00	0.00	3.20
1020	1030	0.038166	TGGAAGACAATGGAGGTGCC	59.962	55.000	0.00	0.00	37.10	5.01
1043	1053	0.036858	AAGCGGAAGGAGAAGCTGAC	60.037	55.000	0.00	0.00	40.17	3.51
1091	1101	2.152016	GTTTAGTGCCCTCTTGTCACC	58.848	52.381	0.00	0.00	0.00	4.02
1155	1165	7.230309	CAGAAGAAAGAAAAGAAGGAACAGGAT	59.770	37.037	0.00	0.00	0.00	3.24
1282	1292	1.663173	GCGGCAAGCCTAAAACCAA	59.337	52.632	9.73	0.00	40.81	3.67
1428	1438	2.898729	ACCACCGATGAGCAAGATAG	57.101	50.000	0.00	0.00	0.00	2.08
1437	1447	7.064609	CACCGATGAGCAAGATAGTTTTTAGAA	59.935	37.037	0.00	0.00	0.00	2.10
1754	1764	1.677217	GGAGGTCCATGTTGTGAGCTC	60.677	57.143	16.15	16.15	40.30	4.09
1878	1891	2.202298	CGACGGGCGAAAACATGC	60.202	61.111	0.00	0.00	44.57	4.06
1879	1892	2.950673	GACGGGCGAAAACATGCA	59.049	55.556	0.00	0.00	0.00	3.96
1880	1893	1.506262	GACGGGCGAAAACATGCAT	59.494	52.632	0.00	0.00	0.00	3.96
1881	1894	0.109319	GACGGGCGAAAACATGCATT	60.109	50.000	0.00	0.00	0.00	3.56
1882	1895	0.109319	ACGGGCGAAAACATGCATTC	60.109	50.000	0.00	0.00	0.00	2.67
1888	1901	2.833497	CGAAAACATGCATTCGTTCGA	58.167	42.857	22.01	0.00	42.47	3.71
1889	1902	2.583801	CGAAAACATGCATTCGTTCGAC	59.416	45.455	22.01	8.98	42.47	4.20
1890	1903	2.226262	AAACATGCATTCGTTCGACG	57.774	45.000	0.00	0.00	44.19	5.12
1891	1904	0.442310	AACATGCATTCGTTCGACGG	59.558	50.000	0.00	0.00	42.81	4.79
1892	1905	1.348250	CATGCATTCGTTCGACGGG	59.652	57.895	0.00	0.92	42.81	5.28
1893	1906	2.461110	ATGCATTCGTTCGACGGGC	61.461	57.895	0.00	9.02	42.81	6.13
1894	1907	3.115892	GCATTCGTTCGACGGGCA	61.116	61.111	0.00	0.00	42.81	5.36
2087	2100	3.371063	GTCGCAGGGACGAGGTCA	61.371	66.667	1.18	0.00	43.89	4.02
2088	2101	3.371063	TCGCAGGGACGAGGTCAC	61.371	66.667	0.00	0.00	37.09	3.67
2089	2102	3.680786	CGCAGGGACGAGGTCACA	61.681	66.667	0.36	0.00	38.63	3.58
2090	2103	2.262915	GCAGGGACGAGGTCACAG	59.737	66.667	0.36	0.00	38.63	3.66
2134	3058	6.257423	TCTTGTCATGCATGCGTTTAATTAG	58.743	36.000	22.25	8.28	0.00	1.73
2202	3126	4.273480	AGCATCATGGTGACGTAATTAAGC	59.727	41.667	11.02	0.00	0.00	3.09
2275	3199	5.108141	GGAAAAAGGTTTTAAATCGCGTCAC	60.108	40.000	5.77	0.00	0.00	3.67

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
96	100	4.263435	ACAAAAACAAGTTAGACGTCCCA	58.737	39.130	13.01	0.00	0.00	4.37
487	497	5.050972	CCGTCGTCCTAAGCAAAATAAGATC	60.051	44.000	0.00	0.00	0.00	2.75
561	571	2.323968	TGCAATGCCGCATACTTAGA	57.676	45.000	6.22	0.00	36.86	2.10
573	583	3.857923	AACGACAAACATTTGCAATGC	57.142	38.095	0.00	0.00	41.79	3.56
583	593	4.477780	GAGGTGTTTTGAAACGACAAACA	58.522	39.130	0.00	0.00	41.74	2.83
694	704	2.890808	TTTCAGAGTATGCCTAGGCG	57.109	50.000	28.28	12.50	45.51	5.52
714	724	2.165998	GAACTGATGCCAGCTCCTTTT	58.834	47.619	0.00	0.00	44.16	2.27
791	801	2.829003	CCAGCAGGCCAGCTCATG	60.829	66.667	21.40	10.34	44.54	3.07
938	948	5.158889	CCTACCCCTCCATTTTATCTCTCT	58.841	45.833	0.00	0.00	0.00	3.10
939	949	4.287326	CCCTACCCCTCCATTTTATCTCTC	59.713	50.000	0.00	0.00	0.00	3.20
1020	1030	1.153549	CTTCTCCTTCCGCTTCCCG	60.154	63.158	0.00	0.00	0.00	5.14
1091	1101	8.574196	AATAAAAAGGAATTGTGTCAAAGTCG	57.426	30.769	0.00	0.00	0.00	4.18
1155	1165	7.884877	ACTGAAAATGTGATGTTATTCTGGAGA	59.115	33.333	0.00	0.00	0.00	3.71
1282	1292	6.987403	AACTGACTCTTACTTCTCTTTCCT	57.013	37.500	0.00	0.00	0.00	3.36
1869	1882	2.583801	CGTCGAACGAATGCATGTTTTC	59.416	45.455	0.00	2.13	46.05	2.29
1870	1883	2.570169	CGTCGAACGAATGCATGTTTT	58.430	42.857	0.00	0.00	46.05	2.43
1871	1884	1.136085	CCGTCGAACGAATGCATGTTT	60.136	47.619	0.00	0.00	46.05	2.83
1872	1885	0.442310	CCGTCGAACGAATGCATGTT	59.558	50.000	0.00	0.00	46.05	2.71
1873	1886	1.358725	CCCGTCGAACGAATGCATGT	61.359	55.000	0.00	0.00	46.05	3.21
1874	1887	1.348250	CCCGTCGAACGAATGCATG	59.652	57.895	0.00	0.00	46.05	4.06
1875	1888	2.461110	GCCCGTCGAACGAATGCAT	61.461	57.895	8.63	0.00	46.05	3.96
1876	1889	3.115892	GCCCGTCGAACGAATGCA	61.116	61.111	8.63	0.00	46.05	3.96
1877	1890	3.083600	CTGCCCGTCGAACGAATGC	62.084	63.158	8.63	3.11	46.05	3.56
1878	1891	1.736645	ACTGCCCGTCGAACGAATG	60.737	57.895	8.63	0.00	46.05	2.67
1879	1892	1.736645	CACTGCCCGTCGAACGAAT	60.737	57.895	8.63	0.00	46.05	3.34
1880	1893	2.355363	CACTGCCCGTCGAACGAA	60.355	61.111	8.63	0.00	46.05	3.85
1892	1905	1.211969	CATGCACAAGAGGCACTGC	59.788	57.895	0.00	0.00	45.23	4.40
1893	1906	0.607217	TCCATGCACAAGAGGCACTG	60.607	55.000	0.00	0.00	45.23	3.66
1894	1907	0.322277	CTCCATGCACAAGAGGCACT	60.322	55.000	0.00	0.00	45.23	4.40
2073	2086	2.262915	CTGTGACCTCGTCCCTGC	59.737	66.667	0.00	0.00	0.00	4.85
2074	2087	2.262915	GCTGTGACCTCGTCCCTG	59.737	66.667	0.00	0.00	0.00	4.45
2075	2088	3.374402	CGCTGTGACCTCGTCCCT	61.374	66.667	0.00	0.00	0.00	4.20
2076	2089	4.436998	CCGCTGTGACCTCGTCCC	62.437	72.222	0.00	0.00	0.00	4.46
2077	2090	3.681835	ACCGCTGTGACCTCGTCC	61.682	66.667	0.00	0.00	0.00	4.79
2079	2092	3.208884	GACACCGCTGTGACCTCGT	62.209	63.158	15.72	0.00	45.76	4.18
2080	2093	2.430921	GACACCGCTGTGACCTCG	60.431	66.667	15.72	0.00	45.76	4.63
2081	2094	1.373497	CAGACACCGCTGTGACCTC	60.373	63.158	15.72	2.33	45.76	3.85
2082	2095	2.134287	ACAGACACCGCTGTGACCT	61.134	57.895	15.72	8.46	46.72	3.85
2083	2096	2.421739	ACAGACACCGCTGTGACC	59.578	61.111	15.72	6.32	46.72	4.02
2088	2101	0.597637	AGAACGAACAGACACCGCTG	60.598	55.000	0.00	0.00	41.63	5.18
2089	2102	0.956633	TAGAACGAACAGACACCGCT	59.043	50.000	0.00	0.00	0.00	5.52
2090	2103	1.774639	TTAGAACGAACAGACACCGC	58.225	50.000	0.00	0.00	0.00	5.68
2202	3126	1.524355	CGTGAGACTGACACAAAGCTG	59.476	52.381	0.00	0.00	38.04	4.24
2238	3162	6.496338	AACCTTTTTCCAGTAGAAATAGCG	57.504	37.500	0.00	0.00	43.93	4.26
2246	3170	6.304683	CGCGATTTAAAACCTTTTTCCAGTAG	59.695	38.462	0.00	0.00	0.00	2.57

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.