AutoCloner

Multiple sequence alignment - TraesCS4A01G306800

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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	TraesCS4A01G306800	chr4A	100.000	1991	0	0	1	1991	601177223	601179213	0.000000e+00	3677
1	TraesCS4A01G306800	chr4A	100.000	373	0	0	2291	2663	601179513	601179885	0.000000e+00	689
2	TraesCS4A01G306800	chr4A	77.928	666	109	21	1000	1661	601194762	601194131	5.380000e-102	381
3	TraesCS4A01G306800	chr4A	86.000	100	9	4	696	792	601156176	601156273	4.690000e-18	102
4	TraesCS4A01G306800	chrUn	94.600	1926	52	15	1	1888	60942354	60944265	0.000000e+00	2933
5	TraesCS4A01G306800	chrUn	81.015	906	154	8	970	1858	60930717	60931621	0.000000e+00	704
6	TraesCS4A01G306800	chrUn	95.203	271	10	2	2330	2599	60944509	60944777	2.450000e-115	425
7	TraesCS4A01G306800	chrUn	78.293	668	130	12	997	1664	60935688	60936340	1.470000e-112	416
8	TraesCS4A01G306800	chrUn	74.431	966	191	38	704	1657	60928430	60929351	5.420000e-97	364
9	TraesCS4A01G306800	chrUn	100.000	74	0	0	2590	2663	60946297	60946370	1.290000e-28	137
10	TraesCS4A01G306800	chr4B	92.221	1337	60	17	591	1893	5531589	5532915	0.000000e+00	1853
11	TraesCS4A01G306800	chr4B	90.532	602	32	10	1	592	5530480	5531066	0.000000e+00	773
12	TraesCS4A01G306800	chr5D	81.818	968	137	16	716	1666	412448535	412449480	0.000000e+00	776
13	TraesCS4A01G306800	chr5B	81.011	969	145	22	716	1666	496549454	496550401	0.000000e+00	734
14	TraesCS4A01G306800	chr5B	80.825	970	148	19	716	1666	496805754	496806704	0.000000e+00	726
15	TraesCS4A01G306800	chr5B	79.755	978	128	37	717	1666	496569154	496570089	0.000000e+00	645
16	TraesCS4A01G306800	chr5A	79.918	971	131	29	716	1666	524389009	524389935	0.000000e+00	654
17	TraesCS4A01G306800	chr5A	79.014	1034	135	42	656	1666	524309070	524310044	1.350000e-177	632

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	TraesCS4A01G306800	chr4A	601177223	601179885	2662	False	2183	3677	100.0000	1	2663	2	chr4A.!!$F2	2662
1	TraesCS4A01G306800	chr4A	601194131	601194762	631	True	381	381	77.9280	1000	1661	1	chr4A.!!$R1	661
2	TraesCS4A01G306800	chrUn	60942354	60946370	4016	False	1165	2933	96.6010	1	2663	3	chrUn.!!$F3	2662
3	TraesCS4A01G306800	chrUn	60928430	60931621	3191	False	534	704	77.7230	704	1858	2	chrUn.!!$F2	1154
4	TraesCS4A01G306800	chrUn	60935688	60936340	652	False	416	416	78.2930	997	1664	1	chrUn.!!$F1	667
5	TraesCS4A01G306800	chr4B	5530480	5532915	2435	False	1313	1853	91.3765	1	1893	2	chr4B.!!$F1	1892
6	TraesCS4A01G306800	chr5D	412448535	412449480	945	False	776	776	81.8180	716	1666	1	chr5D.!!$F1	950
7	TraesCS4A01G306800	chr5B	496549454	496550401	947	False	734	734	81.0110	716	1666	1	chr5B.!!$F1	950
8	TraesCS4A01G306800	chr5B	496805754	496806704	950	False	726	726	80.8250	716	1666	1	chr5B.!!$F3	950
9	TraesCS4A01G306800	chr5B	496569154	496570089	935	False	645	645	79.7550	717	1666	1	chr5B.!!$F2	949
10	TraesCS4A01G306800	chr5A	524389009	524389935	926	False	654	654	79.9180	716	1666	1	chr5A.!!$F2	950
11	TraesCS4A01G306800	chr5A	524309070	524310044	974	False	632	632	79.0140	656	1666	1	chr5A.!!$F1	1010

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
515	542	0.687757	TAGGGACACTGCTAGCTGGG	60.688	60.0	21.11	21.11	0.0	4.45	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2397	5183	0.17668	AGCGGAGGCAGAACATGTAG	59.823	55.0	0.0	0.0	43.41	2.74	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
119	120	4.660938	GGCTGGGTTGGCGGAGTT	62.661	66.667	0.00	0.00	0.00	3.01
155	156	1.602165	CGTGTAGGTGAAGAACGTGCT	60.602	52.381	0.00	0.00	31.40	4.40
267	268	3.665675	GACGGCGAGGGCAAGACAT	62.666	63.158	16.62	0.00	42.47	3.06
284	285	4.326826	AGACATGACGACACCATTTTCAT	58.673	39.130	0.00	0.00	0.00	2.57
306	310	7.149973	TCATGTAGTAGTAAGGTTGTGTGAAC	58.850	38.462	0.00	0.00	0.00	3.18
515	542	0.687757	TAGGGACACTGCTAGCTGGG	60.688	60.000	21.11	21.11	0.00	4.45
651	1202	5.970023	GCAGATCATATTTGTCAAGTTGAGC	59.030	40.000	5.62	2.31	0.00	4.26
833	1447	1.117150	AATGTTCATGCATGGCCCTC	58.883	50.000	25.97	12.30	0.00	4.30
929	1560	3.627395	TCTTCACCACAACTCACAACT	57.373	42.857	0.00	0.00	0.00	3.16
954	3615	2.154462	CGTTCACCAATCAGCCTCTTT	58.846	47.619	0.00	0.00	0.00	2.52
956	3617	2.887152	GTTCACCAATCAGCCTCTTTGT	59.113	45.455	0.00	0.00	0.00	2.83
957	3618	2.783135	TCACCAATCAGCCTCTTTGTC	58.217	47.619	0.00	0.00	0.00	3.18
958	3619	2.106338	TCACCAATCAGCCTCTTTGTCA	59.894	45.455	0.00	0.00	0.00	3.58
1200	3883	0.748450	CCATGAACATGACCATGCCC	59.252	55.000	19.41	3.24	42.39	5.36
1201	3884	1.476477	CATGAACATGACCATGCCCA	58.524	50.000	15.25	8.25	42.39	5.36
1202	3885	2.036387	CATGAACATGACCATGCCCAT	58.964	47.619	15.25	9.93	42.39	4.00
1203	3886	1.476477	TGAACATGACCATGCCCATG	58.524	50.000	18.25	18.25	44.12	3.66
1204	3887	0.103572	GAACATGACCATGCCCATGC	59.896	55.000	19.21	6.49	42.77	4.06
1205	3888	1.332144	AACATGACCATGCCCATGCC	61.332	55.000	19.21	0.00	42.77	4.40
1206	3889	2.520020	ATGACCATGCCCATGCCG	60.520	61.111	2.75	0.00	37.49	5.69
1207	3890	3.059326	ATGACCATGCCCATGCCGA	62.059	57.895	2.75	0.00	37.49	5.54
1208	3891	2.203394	GACCATGCCCATGCCGAT	60.203	61.111	2.75	0.00	37.49	4.18
1209	3892	2.520020	ACCATGCCCATGCCGATG	60.520	61.111	2.75	0.00	37.49	3.84
1210	3893	3.986006	CCATGCCCATGCCGATGC	61.986	66.667	2.75	0.00	37.49	3.91
1211	3894	3.986006	CATGCCCATGCCGATGCC	61.986	66.667	0.00	0.00	36.33	4.40
1485	4168	1.909302	CACTATCAGTCCAACCCAGGT	59.091	52.381	0.00	0.00	0.00	4.00
1667	4350	1.531883	GCCACCGAAGAAATGATTCGC	60.532	52.381	2.70	0.00	46.23	4.70
1683	4366	2.749839	GCCGGTGTATTGCTGCCA	60.750	61.111	1.90	0.00	0.00	4.92
1697	4380	3.348119	TGCTGCCACCGTGAATAATAAA	58.652	40.909	0.00	0.00	0.00	1.40
1703	4388	4.202111	GCCACCGTGAATAATAAAGCCATT	60.202	41.667	0.00	0.00	0.00	3.16
1862	4565	6.052360	TGTGTCTGTTATGCAACTCTGTTTA	58.948	36.000	0.00	0.00	35.56	2.01
1894	4597	9.975218	ATTTCCATGGTTACAAGTAAACTCTAT	57.025	29.630	12.58	0.00	34.02	1.98
1895	4598	9.444600	TTTCCATGGTTACAAGTAAACTCTATC	57.555	33.333	12.58	0.00	34.02	2.08
1897	4600	8.768397	TCCATGGTTACAAGTAAACTCTATCAT	58.232	33.333	12.58	0.00	34.02	2.45
1898	4601	8.830580	CCATGGTTACAAGTAAACTCTATCATG	58.169	37.037	2.57	3.92	34.02	3.07
1900	4603	9.959721	ATGGTTACAAGTAAACTCTATCATGTT	57.040	29.630	9.21	0.00	34.02	2.71
1951	4654	5.968528	TTTGCGGGAAAATGTTACATACT	57.031	34.783	0.00	0.00	0.00	2.12
1953	4656	7.633193	TTTGCGGGAAAATGTTACATACTAT	57.367	32.000	0.00	0.00	0.00	2.12
1954	4657	6.612247	TGCGGGAAAATGTTACATACTATG	57.388	37.500	0.00	0.00	0.00	2.23
1955	4658	6.116806	TGCGGGAAAATGTTACATACTATGT	58.883	36.000	6.90	6.90	46.92	2.29
1956	4659	6.600032	TGCGGGAAAATGTTACATACTATGTT	59.400	34.615	7.01	0.00	41.63	2.71
1957	4660	7.769507	TGCGGGAAAATGTTACATACTATGTTA	59.230	33.333	7.01	0.00	41.63	2.41
1984	4687	9.944376	ATCATTATTGTACAAGTGAGTAGTGTT	57.056	29.630	14.65	1.40	0.00	3.32
1985	4688	9.203421	TCATTATTGTACAAGTGAGTAGTGTTG	57.797	33.333	14.65	0.00	0.00	3.33
1986	4689	8.988934	CATTATTGTACAAGTGAGTAGTGTTGT	58.011	33.333	14.65	0.00	37.00	3.32
1987	4690	6.844696	ATTGTACAAGTGAGTAGTGTTGTG	57.155	37.500	14.65	0.00	34.92	3.33
1988	4691	4.116961	TGTACAAGTGAGTAGTGTTGTGC	58.883	43.478	0.00	0.00	36.43	4.57
1990	4693	3.873910	ACAAGTGAGTAGTGTTGTGCTT	58.126	40.909	0.00	0.00	31.94	3.91
2308	5011	3.314083	TGTGTGTGTGTGTGTGTGT	57.686	47.368	0.00	0.00	0.00	3.72
2310	5013	0.871722	GTGTGTGTGTGTGTGTGTGT	59.128	50.000	0.00	0.00	0.00	3.72
2312	5015	0.871722	GTGTGTGTGTGTGTGTGTGT	59.128	50.000	0.00	0.00	0.00	3.72
2330	5033	0.871722	GTGTGTGTGTGTGTGTGTGT	59.128	50.000	0.00	0.00	0.00	3.72
2331	5034	1.265635	GTGTGTGTGTGTGTGTGTGTT	59.734	47.619	0.00	0.00	0.00	3.32
2332	5035	1.265365	TGTGTGTGTGTGTGTGTGTTG	59.735	47.619	0.00	0.00	0.00	3.33
2333	5036	1.533299	GTGTGTGTGTGTGTGTGTTGA	59.467	47.619	0.00	0.00	0.00	3.18
2334	5037	1.533299	TGTGTGTGTGTGTGTGTTGAC	59.467	47.619	0.00	0.00	0.00	3.18
2335	5038	1.533299	GTGTGTGTGTGTGTGTTGACA	59.467	47.619	0.00	0.00	0.00	3.58
2336	5039	2.031595	GTGTGTGTGTGTGTGTTGACAA	60.032	45.455	0.00	0.00	32.49	3.18
2337	5040	2.225255	TGTGTGTGTGTGTGTTGACAAG	59.775	45.455	0.00	0.00	32.49	3.16
2397	5183	2.232941	TCAGTAGTGTCCATTCCGGTTC	59.767	50.000	0.00	0.00	35.57	3.62
2427	5213	1.376037	CCTCCGCTTTGACCACTCC	60.376	63.158	0.00	0.00	0.00	3.85
2437	5223	0.323816	TGACCACTCCTCGAGCTGAT	60.324	55.000	6.99	0.00	32.04	2.90
2444	5230	2.356382	ACTCCTCGAGCTGATTTAGACG	59.644	50.000	6.99	0.00	32.04	4.18
2445	5231	1.065701	TCCTCGAGCTGATTTAGACGC	59.934	52.381	6.99	0.00	0.00	5.19
2453	5239	2.932614	GCTGATTTAGACGCACTCACAT	59.067	45.455	0.00	0.00	0.00	3.21
2489	5275	6.543831	GGCTTCATCTTATCCAAACATACACT	59.456	38.462	0.00	0.00	0.00	3.55
2490	5276	7.067494	GGCTTCATCTTATCCAAACATACACTT	59.933	37.037	0.00	0.00	0.00	3.16

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
155	156	1.005037	AATGCGTCGCTCCTCAACA	60.005	52.632	19.50	0.00	0.00	3.33
267	268	4.637276	ACTACATGAAAATGGTGTCGTCA	58.363	39.130	0.00	0.00	0.00	4.35
284	285	5.507817	CCGTTCACACAACCTTACTACTACA	60.508	44.000	0.00	0.00	0.00	2.74
306	310	2.283966	ACCTCCAGTCCTCCACCG	60.284	66.667	0.00	0.00	0.00	4.94
445	462	7.902920	ACCATGAACTAGCAATGGAATTATT	57.097	32.000	20.26	0.68	32.46	1.40
450	467	4.406456	ACAACCATGAACTAGCAATGGAA	58.594	39.130	20.26	0.00	36.33	3.53
498	517	1.990060	TCCCAGCTAGCAGTGTCCC	60.990	63.158	18.83	0.00	0.00	4.46
499	518	1.219393	GTCCCAGCTAGCAGTGTCC	59.781	63.158	18.83	0.00	0.00	4.02
589	1140	7.388776	CCTGCAAGTATGTAATGTAGCACATAT	59.611	37.037	2.80	0.00	37.97	1.78
651	1202	6.149973	TCTCATTCTGATACAAACTTTGCAGG	59.850	38.462	1.14	0.00	0.00	4.85
833	1447	3.923461	GTGATGAAGAGTCTGAGAAACCG	59.077	47.826	0.00	0.00	0.00	4.44
929	1560	1.017177	GCTGATTGGTGAACGCGGTA	61.017	55.000	12.47	0.00	0.00	4.02
954	3615	4.558226	AGCTAATGATCTTGTGGTGACA	57.442	40.909	0.00	0.00	38.70	3.58
956	3617	6.299805	AGTAAGCTAATGATCTTGTGGTGA	57.700	37.500	0.00	0.00	0.00	4.02
957	3618	6.676456	GCAAGTAAGCTAATGATCTTGTGGTG	60.676	42.308	0.00	0.00	35.96	4.17
958	3619	5.355350	GCAAGTAAGCTAATGATCTTGTGGT	59.645	40.000	0.00	0.00	35.96	4.16
1210	3893	0.890996	GTGAAGTTCTGTGCCCCTGG	60.891	60.000	4.17	0.00	0.00	4.45
1211	3894	0.109342	AGTGAAGTTCTGTGCCCCTG	59.891	55.000	4.17	0.00	0.00	4.45
1485	4168	3.294493	GCAACTGCGGGGCTTTGA	61.294	61.111	0.00	0.00	0.00	2.69
1667	4350	2.406616	GGTGGCAGCAATACACCGG	61.407	63.158	12.58	0.00	44.41	5.28
1683	4366	5.221048	GCTCAATGGCTTTATTATTCACGGT	60.221	40.000	0.00	0.00	0.00	4.83
1697	4380	2.799017	TCATTCACAAGCTCAATGGCT	58.201	42.857	0.00	0.00	45.30	4.75
1703	4388	2.040145	TCCACCATCATTCACAAGCTCA	59.960	45.455	0.00	0.00	0.00	4.26
1709	4394	3.411446	GTTCACTCCACCATCATTCACA	58.589	45.455	0.00	0.00	0.00	3.58
1927	4630	6.750148	AGTATGTAACATTTTCCCGCAAAAA	58.250	32.000	0.00	0.00	37.52	1.94
1928	4631	6.334102	AGTATGTAACATTTTCCCGCAAAA	57.666	33.333	0.00	0.00	38.38	2.44
1957	4660	9.944376	ACACTACTCACTTGTACAATAATGATT	57.056	29.630	9.13	9.95	0.00	2.57
1960	4663	8.988934	ACAACACTACTCACTTGTACAATAATG	58.011	33.333	9.13	8.35	0.00	1.90
1961	4664	8.988934	CACAACACTACTCACTTGTACAATAAT	58.011	33.333	9.13	0.00	0.00	1.28
1962	4665	7.042321	GCACAACACTACTCACTTGTACAATAA	60.042	37.037	9.13	0.00	0.00	1.40
1963	4666	6.422701	GCACAACACTACTCACTTGTACAATA	59.577	38.462	9.13	0.00	0.00	1.90
1965	4668	4.569162	GCACAACACTACTCACTTGTACAA	59.431	41.667	8.28	8.28	0.00	2.41
1966	4669	4.116961	GCACAACACTACTCACTTGTACA	58.883	43.478	0.00	0.00	0.00	2.90
1967	4670	4.369182	AGCACAACACTACTCACTTGTAC	58.631	43.478	0.00	0.00	0.00	2.90
1969	4672	3.543680	AGCACAACACTACTCACTTGT	57.456	42.857	0.00	0.00	0.00	3.16
2298	5001	0.871057	CACACACACACACACACACA	59.129	50.000	0.00	0.00	0.00	3.72
2300	5003	0.871057	CACACACACACACACACACA	59.129	50.000	0.00	0.00	0.00	3.72
2302	5005	0.871057	CACACACACACACACACACA	59.129	50.000	0.00	0.00	0.00	3.72
2306	5009	0.871057	CACACACACACACACACACA	59.129	50.000	0.00	0.00	0.00	3.72
2308	5011	0.871057	CACACACACACACACACACA	59.129	50.000	0.00	0.00	0.00	3.72
2310	5013	0.871057	CACACACACACACACACACA	59.129	50.000	0.00	0.00	0.00	3.72
2312	5015	1.265365	CAACACACACACACACACACA	59.735	47.619	0.00	0.00	0.00	3.72
2330	5033	1.473258	AGTTGTGGCTTGCTTGTCAA	58.527	45.000	0.00	0.00	0.00	3.18
2331	5034	1.405105	GAAGTTGTGGCTTGCTTGTCA	59.595	47.619	0.00	0.00	0.00	3.58
2332	5035	1.678101	AGAAGTTGTGGCTTGCTTGTC	59.322	47.619	0.00	0.00	0.00	3.18
2333	5036	1.767759	AGAAGTTGTGGCTTGCTTGT	58.232	45.000	0.00	0.00	0.00	3.16
2334	5037	4.510038	AATAGAAGTTGTGGCTTGCTTG	57.490	40.909	0.00	0.00	0.00	4.01
2335	5038	5.183904	CCTTAATAGAAGTTGTGGCTTGCTT	59.816	40.000	0.00	0.00	0.00	3.91
2336	5039	4.702131	CCTTAATAGAAGTTGTGGCTTGCT	59.298	41.667	0.00	0.00	0.00	3.91
2337	5040	4.700213	TCCTTAATAGAAGTTGTGGCTTGC	59.300	41.667	0.00	0.00	0.00	4.01
2397	5183	0.176680	AGCGGAGGCAGAACATGTAG	59.823	55.000	0.00	0.00	43.41	2.74
2427	5213	1.849219	GTGCGTCTAAATCAGCTCGAG	59.151	52.381	8.45	8.45	0.00	4.04
2437	5223	4.461431	TCCTAGAATGTGAGTGCGTCTAAA	59.539	41.667	0.00	0.00	0.00	1.85
2444	5230	2.548875	CTGCTCCTAGAATGTGAGTGC	58.451	52.381	0.00	0.00	0.00	4.40
2445	5231	2.741228	GCCTGCTCCTAGAATGTGAGTG	60.741	54.545	0.00	0.00	0.00	3.51
2453	5239	2.756907	AGATGAAGCCTGCTCCTAGAA	58.243	47.619	0.00	0.00	0.00	2.10

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.