AutoCloner

Multiple sequence alignment - TraesCS5D01G150700

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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	TraesCS5D01G150700	chr5D	100.000	4068	0	0	1	4068	239939217	239943284	0.000000e+00	7513
1	TraesCS5D01G150700	chr5B	97.560	1844	44	1	53	1896	263547788	263545946	0.000000e+00	3155
2	TraesCS5D01G150700	chr5B	96.392	776	18	8	1914	2680	263545961	263545187	0.000000e+00	1269
3	TraesCS5D01G150700	chr5B	91.558	616	36	6	2728	3342	263545192	263544592	0.000000e+00	835
4	TraesCS5D01G150700	chr5B	88.030	401	24	11	3412	3805	263544568	263544185	1.720000e-123	453
5	TraesCS5D01G150700	chr5B	89.879	247	20	4	3800	4045	263544105	263543863	3.050000e-81	313
6	TraesCS5D01G150700	chr5A	95.833	1896	56	6	1	1896	313907614	313905742	0.000000e+00	3042
7	TraesCS5D01G150700	chr5A	93.698	1444	64	17	1914	3342	313905757	313904326	0.000000e+00	2137
8	TraesCS5D01G150700	chr5A	93.167	600	16	8	3476	4066	313904271	313903688	0.000000e+00	857
9	TraesCS5D01G150700	chr1A	83.117	154	16	4	86	230	281893471	281893623	9.170000e-27	132

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	TraesCS5D01G150700	chr5D	239939217	239943284	4067	False	7513	7513	100.000000	1	4068	1	chr5D.!!$F1	4067
1	TraesCS5D01G150700	chr5B	263543863	263547788	3925	True	1205	3155	92.683800	53	4045	5	chr5B.!!$R1	3992
2	TraesCS5D01G150700	chr5A	313903688	313907614	3926	True	2012	3042	94.232667	1	4066	3	chr5A.!!$R1	4065

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
427	428	0.798776	AGTTATTCGTGCAGCACAGC	59.201	50.000	25.19	7.78	33.4	4.40	F
1437	1438	1.066929	CAAAGGGCTGGCATTGTTACC	60.067	52.381	0.82	0.00	0.0	2.85	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1953	1954	0.253044	GCTAACTGGACCATGCTCCA	59.747	55.0	9.43	9.43	38.05	3.86	R
3422	3440	0.034896	TTCCCACCGAAAGACTCTGC	59.965	55.0	0.00	0.00	0.00	4.26	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)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
88	89	6.518516	TTTTCTTTAACTTACCCCTCCTGA	57.481	37.500	0.00	0.00	0.00	3.86
101	102	5.024118	ACCCCTCCTGATAATAATCTACCG	58.976	45.833	0.00	0.00	32.93	4.02
125	126	6.089551	CGAATGTTAGTCCAGTACTCAGTTTG	59.910	42.308	0.00	0.00	39.80	2.93
138	139	2.051345	GTTTGTGACTTGGGCGCG	60.051	61.111	0.00	0.00	0.00	6.86
248	249	4.637534	ACTCATGTGTACATTCCATGAAGC	59.362	41.667	21.35	0.00	43.03	3.86
373	374	1.702182	TTGGCTTGCTGACCATTTGA	58.298	45.000	0.00	0.00	35.42	2.69
374	375	1.250328	TGGCTTGCTGACCATTTGAG	58.750	50.000	0.00	0.00	0.00	3.02
427	428	0.798776	AGTTATTCGTGCAGCACAGC	59.201	50.000	25.19	7.78	33.40	4.40
489	490	4.037208	CCTCACTGGTGCCATATGAATTTC	59.963	45.833	3.65	0.00	0.00	2.17
587	588	5.507637	TGTACCTTTCCTGTTGTTTGGTTA	58.492	37.500	0.00	0.00	0.00	2.85
631	632	1.282157	GGGTCAGGATAAGGTTGCACT	59.718	52.381	0.00	0.00	0.00	4.40
884	885	4.336433	GCAGTAAGATTGCCTGCTTGAATA	59.664	41.667	3.75	0.00	46.23	1.75
976	977	6.974932	ACAACTGATCATCAATAGTGTCAC	57.025	37.500	0.00	0.00	0.00	3.67
1227	1228	1.457346	CTGGGAATTCAGGCAGTCAC	58.543	55.000	7.93	0.00	0.00	3.67
1284	1285	2.114670	CATTACTGTGCCCCTGCCG	61.115	63.158	0.00	0.00	36.33	5.69
1318	1319	5.634118	AGACAGTGGATGAAATTTGGAGAA	58.366	37.500	0.00	0.00	0.00	2.87
1350	1351	4.338118	CAGGAAGAGGAGAGTAGTGATGAC	59.662	50.000	0.00	0.00	0.00	3.06
1437	1438	1.066929	CAAAGGGCTGGCATTGTTACC	60.067	52.381	0.82	0.00	0.00	2.85
1569	1570	4.619437	TGCGTATATTGTACGTCAGTCA	57.381	40.909	13.41	1.56	42.35	3.41
1682	1683	6.918067	TTCTGATCTTCAAAGTCCTAGTCA	57.082	37.500	0.00	0.00	0.00	3.41
1798	1799	8.360390	CAAGAGCTAGGAAACAGGTTTATTTTT	58.640	33.333	0.00	0.00	32.11	1.94
1851	1852	9.152595	ACTATAGAACTTGTTTAGCACTTTAGC	57.847	33.333	6.78	0.00	0.00	3.09
1901	1902	6.651975	AGAAACATACTAATAGAGACCCCG	57.348	41.667	0.00	0.00	0.00	5.73
1902	1903	4.868314	AACATACTAATAGAGACCCCGC	57.132	45.455	0.00	0.00	0.00	6.13
1903	1904	3.840991	ACATACTAATAGAGACCCCGCA	58.159	45.455	0.00	0.00	0.00	5.69

Showing 1 to 25 of 91 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
101	102	6.929606	ACAAACTGAGTACTGGACTAACATTC	59.070	38.462	0.00	0.00	39.06	2.67
248	249	3.318839	TCTCCCAAAAACTGTTGCTCATG	59.681	43.478	0.00	0.00	0.00	3.07
373	374	6.575244	TCATGGGATTAAAGTATGGACACT	57.425	37.500	0.00	0.00	0.00	3.55
374	375	7.227156	AGATCATGGGATTAAAGTATGGACAC	58.773	38.462	0.00	0.00	32.67	3.67
427	428	4.139786	CAGGTGGGACCATTCTTCATATG	58.860	47.826	0.00	0.00	41.95	1.78
489	490	3.054361	ACTGCAAATACACTTCCTAGGGG	60.054	47.826	9.46	5.02	0.00	4.79
631	632	2.305927	TGAAACCAAACCCAAAAGGCAA	59.694	40.909	0.00	0.00	40.58	4.52
745	746	8.076178	GCACTATCATATGTATTTTGTCCAACC	58.924	37.037	1.90	0.00	0.00	3.77
884	885	8.177013	GTGCAAAAACTGTTCAGATTTTGATTT	58.823	29.630	32.15	11.92	41.18	2.17
901	902	6.670077	TTTTGGTAATCCTTGTGCAAAAAC	57.330	33.333	0.00	0.00	34.23	2.43
976	977	4.582701	TGCCTGTTTTATGTTTGACCAG	57.417	40.909	0.00	0.00	0.00	4.00
1227	1228	0.381801	AACCAAAAGCTGACGTGCTG	59.618	50.000	0.57	0.00	43.24	4.41
1284	1285	2.838736	TCCACTGTCTTCTTGCTCAAC	58.161	47.619	0.00	0.00	0.00	3.18
1318	1319	1.558756	CTCCTCTTCCTGCTGGATGTT	59.441	52.381	20.44	0.00	42.81	2.71
1350	1351	3.248602	CACAACCTGAACTCCTTTTCTCG	59.751	47.826	0.00	0.00	0.00	4.04
1437	1438	1.875576	GCATCCTTCTGATACTGCCCG	60.876	57.143	0.00	0.00	30.56	6.13
1682	1683	5.669447	ACATCCTGGGAAGACATTCTCTTAT	59.331	40.000	0.00	0.00	39.53	1.73
1798	1799	8.777413	CATGACTTGAATTGTAAAGAGTCAGAA	58.223	33.333	9.47	0.00	44.41	3.02
1880	1881	4.652421	TGCGGGGTCTCTATTAGTATGTTT	59.348	41.667	0.00	0.00	0.00	2.83
1881	1882	4.220724	TGCGGGGTCTCTATTAGTATGTT	58.779	43.478	0.00	0.00	0.00	2.71
1882	1883	3.840991	TGCGGGGTCTCTATTAGTATGT	58.159	45.455	0.00	0.00	0.00	2.29
1883	1884	4.866508	TTGCGGGGTCTCTATTAGTATG	57.133	45.455	0.00	0.00	0.00	2.39
1884	1885	5.881923	TTTTGCGGGGTCTCTATTAGTAT	57.118	39.130	0.00	0.00	0.00	2.12
1885	1886	5.680594	TTTTTGCGGGGTCTCTATTAGTA	57.319	39.130	0.00	0.00	0.00	1.82
1886	1887	4.563140	TTTTTGCGGGGTCTCTATTAGT	57.437	40.909	0.00	0.00	0.00	2.24

Showing 1 to 25 of 81 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.