AutoCloner

Multiple sequence alignment - TraesCS2A01G093400

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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	TraesCS2A01G093400	chr2A	100.000	2875	0	0	1	2875	47693471	47690597	0.000000e+00	5310.0
1	TraesCS2A01G093400	chr2A	94.777	1857	79	7	971	2821	676712142	676713986	0.000000e+00	2876.0
2	TraesCS2A01G093400	chr2A	97.533	973	20	1	4	972	47701163	47700191	0.000000e+00	1661.0
3	TraesCS2A01G093400	chr1D	95.842	1852	69	4	971	2819	447755308	447753462	0.000000e+00	2987.0
4	TraesCS2A01G093400	chr5D	95.622	1850	73	3	971	2819	363006567	363008409	0.000000e+00	2961.0
5	TraesCS2A01G093400	chr5D	95.647	1815	76	2	971	2784	320661702	320663514	0.000000e+00	2911.0
6	TraesCS2A01G093400	chr2D	95.455	1848	70	6	971	2815	82210199	82208363	0.000000e+00	2935.0
7	TraesCS2A01G093400	chr2D	96.552	58	2	0	2818	2875	43966941	43966884	2.360000e-16	97.1
8	TraesCS2A01G093400	chr3D	95.032	1852	84	7	971	2818	252332948	252331101	0.000000e+00	2904.0
9	TraesCS2A01G093400	chr5A	94.672	1858	84	6	971	2822	673389850	673388002	0.000000e+00	2868.0
10	TraesCS2A01G093400	chr5A	94.346	1857	92	6	971	2820	573661472	573659622	0.000000e+00	2835.0
11	TraesCS2A01G093400	chr5A	97.322	971	24	2	1	971	708709320	708708352	0.000000e+00	1648.0
12	TraesCS2A01G093400	chr7D	94.394	1855	97	5	971	2821	550636989	550638840	0.000000e+00	2843.0
13	TraesCS2A01G093400	chr3A	97.947	974	17	3	1	974	743164509	743165479	0.000000e+00	1685.0
14	TraesCS2A01G093400	chr3A	97.636	973	18	2	1	973	719805758	719804791	0.000000e+00	1664.0
15	TraesCS2A01G093400	chr1A	97.634	972	22	1	1	972	577459726	577460696	0.000000e+00	1666.0
16	TraesCS2A01G093400	chr7A	97.431	973	23	2	1	972	697031515	697030544	0.000000e+00	1657.0
17	TraesCS2A01G093400	chr7A	97.333	975	22	2	1	972	7750001	7749028	0.000000e+00	1653.0
18	TraesCS2A01G093400	chr7A	97.222	972	25	2	1	971	7739994	7739024	0.000000e+00	1644.0
19	TraesCS2A01G093400	chr7A	97.219	971	26	1	1	971	697024674	697023705	0.000000e+00	1642.0
20	TraesCS2A01G093400	chr2B	97.059	34	1	0	2819	2852	68758039	68758006	1.110000e-04	58.4

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	TraesCS2A01G093400	chr2A	47690597	47693471	2874	True	5310	5310	100.000	1	2875	1	chr2A.!!$R1	2874
1	TraesCS2A01G093400	chr2A	676712142	676713986	1844	False	2876	2876	94.777	971	2821	1	chr2A.!!$F1	1850
2	TraesCS2A01G093400	chr2A	47700191	47701163	972	True	1661	1661	97.533	4	972	1	chr2A.!!$R2	968
3	TraesCS2A01G093400	chr1D	447753462	447755308	1846	True	2987	2987	95.842	971	2819	1	chr1D.!!$R1	1848
4	TraesCS2A01G093400	chr5D	363006567	363008409	1842	False	2961	2961	95.622	971	2819	1	chr5D.!!$F2	1848
5	TraesCS2A01G093400	chr5D	320661702	320663514	1812	False	2911	2911	95.647	971	2784	1	chr5D.!!$F1	1813
6	TraesCS2A01G093400	chr2D	82208363	82210199	1836	True	2935	2935	95.455	971	2815	1	chr2D.!!$R2	1844
7	TraesCS2A01G093400	chr3D	252331101	252332948	1847	True	2904	2904	95.032	971	2818	1	chr3D.!!$R1	1847
8	TraesCS2A01G093400	chr5A	673388002	673389850	1848	True	2868	2868	94.672	971	2822	1	chr5A.!!$R2	1851
9	TraesCS2A01G093400	chr5A	573659622	573661472	1850	True	2835	2835	94.346	971	2820	1	chr5A.!!$R1	1849
10	TraesCS2A01G093400	chr5A	708708352	708709320	968	True	1648	1648	97.322	1	971	1	chr5A.!!$R3	970
11	TraesCS2A01G093400	chr7D	550636989	550638840	1851	False	2843	2843	94.394	971	2821	1	chr7D.!!$F1	1850
12	TraesCS2A01G093400	chr3A	743164509	743165479	970	False	1685	1685	97.947	1	974	1	chr3A.!!$F1	973
13	TraesCS2A01G093400	chr3A	719804791	719805758	967	True	1664	1664	97.636	1	973	1	chr3A.!!$R1	972
14	TraesCS2A01G093400	chr1A	577459726	577460696	970	False	1666	1666	97.634	1	972	1	chr1A.!!$F1	971
15	TraesCS2A01G093400	chr7A	697030544	697031515	971	True	1657	1657	97.431	1	972	1	chr7A.!!$R4	971
16	TraesCS2A01G093400	chr7A	7749028	7750001	973	True	1653	1653	97.333	1	972	1	chr7A.!!$R2	971
17	TraesCS2A01G093400	chr7A	7739024	7739994	970	True	1644	1644	97.222	1	971	1	chr7A.!!$R1	970
18	TraesCS2A01G093400	chr7A	697023705	697024674	969	True	1642	1642	97.219	1	971	1	chr7A.!!$R3	970

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
991	1002	2.158813	AGGTCGAACAACATGAAGTGGT	60.159	45.455	1.87	0.0	35.29	4.16	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2830	2858	0.03467	GGCAAGCTCCTCCAAGTCAT	60.035	55.0	0.0	0.0	0.0	3.06	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
34	35	4.495422	GTGTCTCGGTCATGTCTACATTT	58.505	43.478	0.00	0.00	33.61	2.32
44	45	6.369065	GGTCATGTCTACATTTTTCTCGAACT	59.631	38.462	0.00	0.00	33.61	3.01
682	693	4.325472	CCTACGACGGTTAAACATCAAGAC	59.675	45.833	0.00	0.00	0.00	3.01
991	1002	2.158813	AGGTCGAACAACATGAAGTGGT	60.159	45.455	1.87	0.00	35.29	4.16
1058	1069	4.237976	TCTCTAGTGGAGTTAGGACTGG	57.762	50.000	3.16	0.00	42.40	4.00
1070	1081	1.000396	GGACTGGCAAGGGCTTCAT	60.000	57.895	0.00	0.00	40.87	2.57
1082	1093	1.028868	GGCTTCATGGAGGTGCACTC	61.029	60.000	17.98	11.88	45.84	3.51
1115	1126	3.299340	GAAGCAGGTGTTCGAGTTCTA	57.701	47.619	0.00	0.00	0.00	2.10
1212	1223	1.587613	GAGAGACCTTAGCAGCGCG	60.588	63.158	0.00	0.00	0.00	6.86
1232	1243	3.678806	GCGTCATGGGATGAGAACACTTA	60.679	47.826	0.00	0.00	40.53	2.24
1262	1273	0.244994	CTTGAGGCAGAGCACTACGT	59.755	55.000	0.00	0.00	0.00	3.57
1415	1427	2.714250	ACCCATCCAGAACTACAACCAA	59.286	45.455	0.00	0.00	0.00	3.67
1506	1518	0.044092	TCCCATGCCTGACTTCCCTA	59.956	55.000	0.00	0.00	0.00	3.53
1526	1538	3.122250	GACCCCGGACGTCGAGATG	62.122	68.421	9.92	3.60	42.43	2.90
1761	1778	0.813821	CAGTGACGAGGCTCTCATGA	59.186	55.000	13.50	0.00	0.00	3.07
1813	1830	2.193786	GGGTGTTGGGTCCGTTGT	59.806	61.111	0.00	0.00	0.00	3.32
1948	1965	0.656259	ACGACGACGATGACGATGAT	59.344	50.000	15.32	0.00	42.66	2.45
1952	1969	1.400494	ACGACGATGACGATGATGACA	59.600	47.619	0.00	0.00	42.66	3.58
1967	1984	7.549134	ACGATGATGACATACATTTTGTGTAGT	59.451	33.333	0.00	0.00	45.94	2.73
2009	2026	8.821686	TTTGATGGTCTGTATATTTTGGTGAT	57.178	30.769	0.00	0.00	0.00	3.06
2046	2064	4.028131	ACCCTCACGGTATGATGAACTTA	58.972	43.478	0.00	0.00	45.97	2.24
2076	2094	2.552373	GGACGACACCCTCTTTTGGATT	60.552	50.000	0.00	0.00	0.00	3.01
2122	2140	5.017294	AGTGCTAGGAAGAACTTGCTATC	57.983	43.478	14.20	11.48	38.62	2.08
2124	2142	4.033709	TGCTAGGAAGAACTTGCTATCCT	58.966	43.478	14.20	6.72	41.52	3.24
2201	2227	0.519077	GCTTGCTACTTGTGCTCCAC	59.481	55.000	0.00	0.00	34.56	4.02
2345	2371	7.283807	TCGTATAGCAACAACAACTATAGAGGA	59.716	37.037	6.78	0.00	31.31	3.71
2421	2447	0.250467	AGGCAGCAGTGTCGACAATT	60.250	50.000	21.95	9.04	31.53	2.32
2614	2640	1.948104	ACATGTACGCCGTATGCAAT	58.052	45.000	0.00	0.00	41.33	3.56
2699	2727	6.377429	CGTATTATCTAATGCAGGGACTAGGA	59.623	42.308	0.00	0.00	36.02	2.94
2800	2828	3.684305	CGATGCAGGAACTATTGACAACA	59.316	43.478	0.00	0.00	36.02	3.33
2815	2843	0.457509	CAACAGCAACCAAACACGCA	60.458	50.000	0.00	0.00	0.00	5.24
2822	2850	1.263217	CAACCAAACACGCACCTAGTC	59.737	52.381	0.00	0.00	0.00	2.59
2823	2851	0.756903	ACCAAACACGCACCTAGTCT	59.243	50.000	0.00	0.00	0.00	3.24
2824	2852	1.140252	ACCAAACACGCACCTAGTCTT	59.860	47.619	0.00	0.00	0.00	3.01
2825	2853	2.218603	CCAAACACGCACCTAGTCTTT	58.781	47.619	0.00	0.00	0.00	2.52
2826	2854	2.616842	CCAAACACGCACCTAGTCTTTT	59.383	45.455	0.00	0.00	0.00	2.27
2827	2855	3.810941	CCAAACACGCACCTAGTCTTTTA	59.189	43.478	0.00	0.00	0.00	1.52
2828	2856	4.084013	CCAAACACGCACCTAGTCTTTTAG	60.084	45.833	0.00	0.00	0.00	1.85
2829	2857	2.685100	ACACGCACCTAGTCTTTTAGC	58.315	47.619	0.00	0.00	0.00	3.09
2830	2858	2.036733	ACACGCACCTAGTCTTTTAGCA	59.963	45.455	0.00	0.00	0.00	3.49
2831	2859	3.262420	CACGCACCTAGTCTTTTAGCAT	58.738	45.455	0.00	0.00	0.00	3.79
2832	2860	3.062639	CACGCACCTAGTCTTTTAGCATG	59.937	47.826	0.00	0.00	0.00	4.06
2833	2861	3.056107	ACGCACCTAGTCTTTTAGCATGA	60.056	43.478	0.00	0.00	0.00	3.07
2834	2862	3.307242	CGCACCTAGTCTTTTAGCATGAC	59.693	47.826	0.00	0.00	0.00	3.06
2835	2863	4.508662	GCACCTAGTCTTTTAGCATGACT	58.491	43.478	0.00	0.00	41.61	3.41
2836	2864	4.938226	GCACCTAGTCTTTTAGCATGACTT	59.062	41.667	0.00	0.00	39.86	3.01
2837	2865	5.163814	GCACCTAGTCTTTTAGCATGACTTG	60.164	44.000	0.00	0.00	39.86	3.16
2839	2867	5.248477	ACCTAGTCTTTTAGCATGACTTGGA	59.752	40.000	22.31	0.00	46.70	3.53
2840	2868	5.814705	CCTAGTCTTTTAGCATGACTTGGAG	59.185	44.000	14.39	1.73	46.70	3.86
2841	2869	4.583871	AGTCTTTTAGCATGACTTGGAGG	58.416	43.478	0.00	0.00	36.68	4.30
2842	2870	4.287067	AGTCTTTTAGCATGACTTGGAGGA	59.713	41.667	0.00	0.00	36.68	3.71
2843	2871	4.633565	GTCTTTTAGCATGACTTGGAGGAG	59.366	45.833	0.00	0.00	0.00	3.69
2844	2872	2.698855	TTAGCATGACTTGGAGGAGC	57.301	50.000	0.00	0.00	0.00	4.70
2845	2873	1.871418	TAGCATGACTTGGAGGAGCT	58.129	50.000	0.00	0.00	34.84	4.09
2846	2874	0.990374	AGCATGACTTGGAGGAGCTT	59.010	50.000	0.00	0.00	0.00	3.74
2847	2875	1.093159	GCATGACTTGGAGGAGCTTG	58.907	55.000	0.00	0.00	0.00	4.01
2848	2876	1.093159	CATGACTTGGAGGAGCTTGC	58.907	55.000	0.00	0.00	0.00	4.01
2849	2877	0.034670	ATGACTTGGAGGAGCTTGCC	60.035	55.000	0.00	0.00	0.00	4.52
2850	2878	1.377856	GACTTGGAGGAGCTTGCCC	60.378	63.158	0.00	0.00	0.00	5.36
2851	2879	2.044551	CTTGGAGGAGCTTGCCCC	60.045	66.667	0.00	0.00	0.00	5.80
2852	2880	2.858476	TTGGAGGAGCTTGCCCCA	60.858	61.111	0.00	0.00	0.00	4.96
2853	2881	2.220786	CTTGGAGGAGCTTGCCCCAT	62.221	60.000	0.00	0.00	31.27	4.00
2854	2882	2.123982	GGAGGAGCTTGCCCCATG	60.124	66.667	0.00	0.00	0.00	3.66
2855	2883	2.832201	GAGGAGCTTGCCCCATGC	60.832	66.667	0.00	0.00	41.77	4.06
2856	2884	4.809496	AGGAGCTTGCCCCATGCG	62.809	66.667	0.00	0.00	45.60	4.73

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
34	35	1.542915	CGGACCCTACAGTTCGAGAAA	59.457	52.381	0.00	0.00	41.48	2.52
44	45	1.534336	TTAAGCGTGCGGACCCTACA	61.534	55.000	0.00	0.00	0.00	2.74
121	122	2.163509	CGTGATCATATCCGGGACTCT	58.836	52.381	0.00	0.00	0.00	3.24
171	172	9.378551	GCCGTCCAATATATCAATCTTTATGTA	57.621	33.333	0.00	0.00	0.00	2.29
662	673	3.062042	GGTCTTGATGTTTAACCGTCGT	58.938	45.455	0.00	0.00	0.00	4.34
752	763	0.040692	TGACACACGTACAGCTCGAC	60.041	55.000	0.00	0.00	0.00	4.20
860	871	0.035152	TACCCTCGTAGACCGAAGCA	60.035	55.000	0.00	0.00	46.75	3.91
991	1002	0.319083	AACGTGGACATGAACGGCTA	59.681	50.000	19.10	0.00	43.96	3.93
1058	1069	1.000396	ACCTCCATGAAGCCCTTGC	60.000	57.895	0.00	0.00	37.95	4.01
1070	1081	1.069090	GTGTTCGAGTGCACCTCCA	59.931	57.895	14.63	0.43	36.82	3.86
1082	1093	2.127758	GCTTCGCAACGGTGTTCG	60.128	61.111	0.66	0.00	45.88	3.95
1115	1126	1.001641	GCAGACACCTCTTGCCCAT	60.002	57.895	0.00	0.00	0.00	4.00
1212	1223	5.091261	AGTAAGTGTTCTCATCCCATGAC	57.909	43.478	0.00	0.00	35.06	3.06
1232	1243	3.445008	TCTGCCTCAAGAACTATGGAGT	58.555	45.455	0.00	0.00	37.59	3.85
1262	1273	3.709880	CTAACCGCGACATGGCCGA	62.710	63.158	8.23	0.00	0.00	5.54
1392	1404	2.084546	GTTGTAGTTCTGGATGGGTGC	58.915	52.381	0.00	0.00	0.00	5.01
1415	1427	2.803030	AGGAGAAGATGTGCTGCATT	57.197	45.000	5.27	0.00	38.06	3.56
1526	1538	2.187073	CTTGTCAGGGCCATCAAGC	58.813	57.895	17.46	0.00	32.54	4.01
1560	1574	1.273327	GGGGTCAAATGGCTTGTTGAG	59.727	52.381	0.00	0.00	34.52	3.02
1563	1577	0.469144	ACGGGGTCAAATGGCTTGTT	60.469	50.000	0.00	0.00	36.34	2.83
1761	1778	3.067091	CAGGTGGCTGAGAGCTGT	58.933	61.111	0.00	0.00	41.99	4.40
1813	1830	3.647649	CTGTGAGCGTCGGCCATGA	62.648	63.158	2.24	0.00	41.24	3.07
1856	1873	3.698289	ACTCTAGTAGTAGTGCTTGCCA	58.302	45.455	4.51	0.00	36.36	4.92
1882	1899	2.045634	ATGCACGCTCACAGGCAT	60.046	55.556	0.00	0.00	41.81	4.40
1948	1965	6.373216	GCCCTAACTACACAAAATGTATGTCA	59.627	38.462	0.00	0.00	43.01	3.58
1952	1969	6.717289	TGAGCCCTAACTACACAAAATGTAT	58.283	36.000	0.00	0.00	43.01	2.29
1967	1984	6.723977	ACCATCAAATAGTTTTTGAGCCCTAA	59.276	34.615	13.15	0.00	41.13	2.69
2009	2026	6.395426	CGTGAGGGTTTAGTATATACCACA	57.605	41.667	9.32	0.00	43.46	4.17
2038	2056	2.165030	CGTCCTACCACCGTAAGTTCAT	59.835	50.000	0.00	0.00	0.00	2.57
2046	2064	2.270986	GGTGTCGTCCTACCACCGT	61.271	63.158	0.00	0.00	39.29	4.83
2122	2140	4.848562	AAAGCATGCATGATCATACAGG	57.151	40.909	30.64	14.83	0.00	4.00
2124	2142	6.769341	AGAAGTAAAGCATGCATGATCATACA	59.231	34.615	30.64	11.03	0.00	2.29
2201	2227	4.227538	CAAGAGTTGAAGCAGCAAATCAG	58.772	43.478	17.24	8.55	43.21	2.90
2345	2371	2.290514	TGCTGCCTGCTTAGTCTTGAAT	60.291	45.455	0.00	0.00	43.37	2.57
2397	2423	2.970639	GACACTGCTGCCTCCGTA	59.029	61.111	0.00	0.00	0.00	4.02
2614	2640	0.306228	CACATGAACACGGCGTTTGA	59.694	50.000	11.19	2.99	38.19	2.69
2699	2727	1.972795	ACTTGATTGGTTGCCTGCATT	59.027	42.857	0.00	0.00	0.00	3.56
2800	2828	0.464735	TAGGTGCGTGTTTGGTTGCT	60.465	50.000	0.00	0.00	0.00	3.91
2815	2843	5.248477	TCCAAGTCATGCTAAAAGACTAGGT	59.752	40.000	0.00	0.00	41.45	3.08
2822	2850	3.376546	GCTCCTCCAAGTCATGCTAAAAG	59.623	47.826	0.00	0.00	0.00	2.27
2823	2851	3.009473	AGCTCCTCCAAGTCATGCTAAAA	59.991	43.478	0.00	0.00	0.00	1.52
2824	2852	2.573462	AGCTCCTCCAAGTCATGCTAAA	59.427	45.455	0.00	0.00	0.00	1.85
2825	2853	2.191400	AGCTCCTCCAAGTCATGCTAA	58.809	47.619	0.00	0.00	0.00	3.09
2826	2854	1.871418	AGCTCCTCCAAGTCATGCTA	58.129	50.000	0.00	0.00	0.00	3.49
2827	2855	0.990374	AAGCTCCTCCAAGTCATGCT	59.010	50.000	0.00	0.00	0.00	3.79
2828	2856	1.093159	CAAGCTCCTCCAAGTCATGC	58.907	55.000	0.00	0.00	0.00	4.06
2829	2857	1.093159	GCAAGCTCCTCCAAGTCATG	58.907	55.000	0.00	0.00	0.00	3.07
2830	2858	0.034670	GGCAAGCTCCTCCAAGTCAT	60.035	55.000	0.00	0.00	0.00	3.06
2831	2859	1.376466	GGCAAGCTCCTCCAAGTCA	59.624	57.895	0.00	0.00	0.00	3.41
2832	2860	1.377856	GGGCAAGCTCCTCCAAGTC	60.378	63.158	0.00	0.00	0.00	3.01
2833	2861	2.759795	GGGCAAGCTCCTCCAAGT	59.240	61.111	0.00	0.00	0.00	3.16
2834	2862	2.044551	GGGGCAAGCTCCTCCAAG	60.045	66.667	3.07	0.00	32.70	3.61
2835	2863	2.240918	ATGGGGCAAGCTCCTCCAA	61.241	57.895	12.92	0.00	37.51	3.53
2836	2864	2.614969	ATGGGGCAAGCTCCTCCA	60.615	61.111	12.92	8.27	37.51	3.86
2837	2865	2.123982	CATGGGGCAAGCTCCTCC	60.124	66.667	12.92	0.00	37.51	4.30
2838	2866	2.832201	GCATGGGGCAAGCTCCTC	60.832	66.667	12.92	0.00	43.97	3.71
2839	2867	4.809496	CGCATGGGGCAAGCTCCT	62.809	66.667	12.92	0.00	45.17	3.69

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.