AutoCloner

Multiple sequence alignment - TraesCS4A01G195100

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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	TraesCS4A01G195100	chr4A	100.000	2336	0	0	1	2336	477027606	477025271	0.000000e+00	4314
1	TraesCS4A01G195100	chr4A	87.163	1706	172	22	2	1677	163215684	163213996	0.000000e+00	1893
2	TraesCS4A01G195100	chr4A	90.525	1066	80	6	1	1046	89694045	89692981	0.000000e+00	1389
3	TraesCS4A01G195100	chr4A	88.804	652	56	11	1038	1678	89684265	89683620	0.000000e+00	784
4	TraesCS4A01G195100	chr4A	89.860	286	21	3	1400	1678	60355693	60355409	6.140000e-96	361
5	TraesCS4A01G195100	chr5A	95.492	1708	46	7	1	1681	621007990	621006287	0.000000e+00	2699
6	TraesCS4A01G195100	chr5A	88.837	1720	147	23	1	1683	648908939	648907228	0.000000e+00	2071
7	TraesCS4A01G195100	chr5A	84.687	1404	171	22	310	1682	35638352	35636962	0.000000e+00	1362
8	TraesCS4A01G195100	chr5A	82.575	901	148	9	1	898	700887878	700886984	0.000000e+00	785
9	TraesCS4A01G195100	chr5A	88.685	654	57	12	1038	1679	599774859	599774211	0.000000e+00	782
10	TraesCS4A01G195100	chr7A	94.959	1706	54	8	1	1679	149312265	149310565	0.000000e+00	2645
11	TraesCS4A01G195100	chr5D	86.620	1704	181	23	1	1675	311901567	311903252	0.000000e+00	1840
12	TraesCS4A01G195100	chr1D	86.114	1714	187	28	1	1679	408846493	408848190	0.000000e+00	1799
13	TraesCS4A01G195100	chr1D	90.231	563	36	4	1786	2336	207656181	207655626	0.000000e+00	717
14	TraesCS4A01G195100	chr4D	92.623	366	10	4	1782	2138	98938802	98939159	5.760000e-141	510
15	TraesCS4A01G195100	chr4D	95.872	218	6	1	2119	2336	98940290	98940504	1.330000e-92	350
16	TraesCS4A01G195100	chr4D	89.256	121	4	2	1679	1790	98938660	98938780	2.420000e-30	143
17	TraesCS4A01G195100	chr4B	95.633	229	8	2	2108	2336	140894886	140895112	1.320000e-97	366

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	TraesCS4A01G195100	chr4A	477025271	477027606	2335	True	4314.000000	4314	100.000000	1	2336	1	chr4A.!!$R5	2335
1	TraesCS4A01G195100	chr4A	163213996	163215684	1688	True	1893.000000	1893	87.163000	2	1677	1	chr4A.!!$R4	1675
2	TraesCS4A01G195100	chr4A	89692981	89694045	1064	True	1389.000000	1389	90.525000	1	1046	1	chr4A.!!$R3	1045
3	TraesCS4A01G195100	chr4A	89683620	89684265	645	True	784.000000	784	88.804000	1038	1678	1	chr4A.!!$R2	640
4	TraesCS4A01G195100	chr5A	621006287	621007990	1703	True	2699.000000	2699	95.492000	1	1681	1	chr5A.!!$R3	1680
5	TraesCS4A01G195100	chr5A	648907228	648908939	1711	True	2071.000000	2071	88.837000	1	1683	1	chr5A.!!$R4	1682
6	TraesCS4A01G195100	chr5A	35636962	35638352	1390	True	1362.000000	1362	84.687000	310	1682	1	chr5A.!!$R1	1372
7	TraesCS4A01G195100	chr5A	700886984	700887878	894	True	785.000000	785	82.575000	1	898	1	chr5A.!!$R5	897
8	TraesCS4A01G195100	chr5A	599774211	599774859	648	True	782.000000	782	88.685000	1038	1679	1	chr5A.!!$R2	641
9	TraesCS4A01G195100	chr7A	149310565	149312265	1700	True	2645.000000	2645	94.959000	1	1679	1	chr7A.!!$R1	1678
10	TraesCS4A01G195100	chr5D	311901567	311903252	1685	False	1840.000000	1840	86.620000	1	1675	1	chr5D.!!$F1	1674
11	TraesCS4A01G195100	chr1D	408846493	408848190	1697	False	1799.000000	1799	86.114000	1	1679	1	chr1D.!!$F1	1678
12	TraesCS4A01G195100	chr1D	207655626	207656181	555	True	717.000000	717	90.231000	1786	2336	1	chr1D.!!$R1	550
13	TraesCS4A01G195100	chr4D	98938660	98940504	1844	False	334.333333	510	92.583667	1679	2336	3	chr4D.!!$F1	657

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
364	365	0.322456	GGCTGTGGCAAGATGTGGTA	60.322	55.0	0.0	0.0	40.87	3.25	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1449	1491	0.029834	CCGCACCAAAGCATCATAGC	59.97	55.0	0.0	0.0	0.0	2.97	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
21	22	4.448537	CTGACTGGGAGTATATAGCAGC	57.551	50.000	0.00	0.00	0.00	5.25
205	206	1.814429	TTTTCTGGTGTGGAGGGAGA	58.186	50.000	0.00	0.00	0.00	3.71
274	275	1.230212	GAATAAGGGTGGGCTGGGG	59.770	63.158	0.00	0.00	0.00	4.96
340	341	3.773119	GGTGGTGGAAGTTAGATACAGGA	59.227	47.826	0.00	0.00	0.00	3.86
364	365	0.322456	GGCTGTGGCAAGATGTGGTA	60.322	55.000	0.00	0.00	40.87	3.25
644	648	5.073428	AGTGGAGATATATTCAGACGCAGA	58.927	41.667	0.00	0.00	0.00	4.26
926	952	1.843851	TCCCAGGTGTTCTTTCTGTGT	59.156	47.619	0.00	0.00	0.00	3.72
1068	1094	2.446435	TGGTGCTATGCTTTTCTTCCC	58.554	47.619	0.00	0.00	0.00	3.97
1162	1188	6.091305	GGCTACCTTTGAATTCAAGAAAATGC	59.909	38.462	19.64	18.43	37.15	3.56
1359	1385	1.661341	CTGCTGGGATGCTAAGTCAC	58.339	55.000	0.00	0.00	0.00	3.67
1380	1417	5.482175	TCACTTTTGGAAAACCTTTTGGAGA	59.518	36.000	0.00	0.00	44.07	3.71
1419	1459	4.292977	CAAGACTTTGGAGAGCGTTTTT	57.707	40.909	0.00	0.00	0.00	1.94
1449	1491	9.875675	GAGCTTTGTTTCTTATATTCTGCATAG	57.124	33.333	0.00	0.00	0.00	2.23
1470	1514	0.254462	TATGATGCTTTGGTGCGGGA	59.746	50.000	0.00	0.00	35.36	5.14
1484	1528	2.942376	GTGCGGGATTGTAATGTGATCA	59.058	45.455	0.00	0.00	0.00	2.92
1501	1545	8.918202	ATGTGATCAGAACTTTAGTTTGGTTA	57.082	30.769	0.00	0.00	38.56	2.85
1544	1595	1.670083	GCCTCGTAGTGGGCGTTTT	60.670	57.895	0.00	0.00	42.22	2.43
1722	1776	7.704472	TGTGAATAACTCAAATGGTTTGACAAC	59.296	33.333	1.24	0.00	44.21	3.32
1755	1818	0.740737	GGATGGCACCAAAGGAATCG	59.259	55.000	0.00	0.00	0.00	3.34
1760	1823	1.611491	GGCACCAAAGGAATCGTTTCA	59.389	47.619	8.41	0.00	33.23	2.69
1839	1931	4.441495	GCTTGACAAATGGTTATTAGCCCC	60.441	45.833	0.00	0.00	0.00	5.80
2074	2169	1.144057	CATCTAGGCGGGCGAACTT	59.856	57.895	0.00	0.00	0.00	2.66
2231	3485	1.816835	TCTAAACACTGATCGACGGCT	59.183	47.619	0.00	0.00	0.00	5.52
2248	3502	6.036735	TCGACGGCTATCTTAATTTGGAAAAG	59.963	38.462	0.00	0.00	0.00	2.27

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
190	191	0.041238	TACCTCTCCCTCCACACCAG	59.959	60.000	0.00	0.00	0.00	4.00
205	206	7.933215	AACCAGATAATAACGCTTTTTACCT	57.067	32.000	0.00	0.00	0.00	3.08
274	275	6.377327	TTCTGTTTGTGAAGATCTTTCACC	57.623	37.500	23.52	14.77	46.01	4.02
340	341	1.927527	ATCTTGCCACAGCCCCTCT	60.928	57.895	0.00	0.00	38.69	3.69
364	365	6.987403	TTGTTCTTAAGGTATTTTGCCCTT	57.013	33.333	1.85	0.00	43.41	3.95
644	648	0.982704	AGCTCAGGTCTGCATTCAGT	59.017	50.000	0.00	0.00	41.10	3.41
705	709	1.686325	TTATCTGGACCAGCCGAGGC	61.686	60.000	17.33	5.89	40.66	4.70
817	821	4.571951	AGGTAATCTAGCCCTCCAAATCT	58.428	43.478	0.00	0.00	0.00	2.40
926	952	7.665559	ACAGATGTAAATAGGTTTCTCTGCAAA	59.334	33.333	0.00	0.00	34.80	3.68
1068	1094	0.251742	TGAAGCACCATTCCCCTTGG	60.252	55.000	0.00	0.00	40.26	3.61
1359	1385	5.237127	GCATCTCCAAAAGGTTTTCCAAAAG	59.763	40.000	0.00	0.00	43.73	2.27
1380	1417	2.202932	GCGTCTCGACCCATGCAT	60.203	61.111	0.00	0.00	0.00	3.96
1419	1459	7.362056	GCAGAATATAAGAAACAAAGCTCCACA	60.362	37.037	0.00	0.00	0.00	4.17
1449	1491	0.029834	CCGCACCAAAGCATCATAGC	59.970	55.000	0.00	0.00	0.00	2.97
1484	1528	3.501062	GCCGCTAACCAAACTAAAGTTCT	59.499	43.478	0.00	0.00	37.25	3.01
1501	1545	3.049674	CACCATCAACACGCCGCT	61.050	61.111	0.00	0.00	0.00	5.52
1544	1595	2.048316	TGTGAGCGCTCGCAATCA	60.048	55.556	42.48	25.02	45.85	2.57
1654	1708	0.996583	TTTTGACCCGGGCTAATCCT	59.003	50.000	24.08	0.00	34.39	3.24
1755	1818	1.953559	TGTCTGTGCACTCCTGAAAC	58.046	50.000	19.41	6.18	0.00	2.78
1760	1823	0.464036	TTCGTTGTCTGTGCACTCCT	59.536	50.000	19.41	0.00	0.00	3.69
1817	1909	4.956075	AGGGGCTAATAACCATTTGTCAAG	59.044	41.667	0.00	0.00	0.00	3.02
1981	2076	4.799564	TCAGCCCGCTTTGATTTTTATT	57.200	36.364	0.00	0.00	0.00	1.40
1982	2077	5.343307	AATCAGCCCGCTTTGATTTTTAT	57.657	34.783	0.00	0.00	40.19	1.40
1983	2078	4.799564	AATCAGCCCGCTTTGATTTTTA	57.200	36.364	0.00	0.00	40.19	1.52
1984	2079	3.683365	AATCAGCCCGCTTTGATTTTT	57.317	38.095	0.00	0.00	40.19	1.94
1985	2080	5.505654	CGTATAATCAGCCCGCTTTGATTTT	60.506	40.000	8.82	5.22	42.37	1.82
1986	2081	4.024048	CGTATAATCAGCCCGCTTTGATTT	60.024	41.667	8.82	2.54	42.37	2.17
1987	2082	3.498397	CGTATAATCAGCCCGCTTTGATT	59.502	43.478	8.62	8.62	44.05	2.57
1988	2083	3.067106	CGTATAATCAGCCCGCTTTGAT	58.933	45.455	0.00	0.00	35.63	2.57
2074	2169	9.896645	AAGTTCAGCTTTTCTATGATCTTATCA	57.103	29.630	0.00	0.00	37.70	2.15
2115	2210	4.900635	AAAACAAGAAGCGTGAAGATGT	57.099	36.364	0.00	0.00	0.00	3.06
2116	2211	5.273170	TGAAAAACAAGAAGCGTGAAGATG	58.727	37.500	0.00	0.00	0.00	2.90
2117	2212	5.499139	TGAAAAACAAGAAGCGTGAAGAT	57.501	34.783	0.00	0.00	0.00	2.40
2119	2214	6.233500	GTTTTGAAAAACAAGAAGCGTGAAG	58.766	36.000	12.61	0.00	45.72	3.02
2120	2215	6.147038	GTTTTGAAAAACAAGAAGCGTGAA	57.853	33.333	12.61	0.00	45.72	3.18
2121	2216	5.755330	GTTTTGAAAAACAAGAAGCGTGA	57.245	34.783	12.61	0.00	45.72	4.35
2150	3404	5.987953	ACAGCTGTATTATCACATAGTGCAG	59.012	40.000	20.16	1.38	37.92	4.41
2248	3502	4.550422	GAGTGGTTTCAGAAAAATGCTCC	58.450	43.478	0.00	0.00	0.00	4.70
2282	3536	1.200519	TGGTGTTCGCTAGGGCTATT	58.799	50.000	1.02	0.00	36.09	1.73

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.